Hoxa5 (homeo box A5) - Rat Genome Database

Name: Hoxa5
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Hoxa5 (homeo box A5) Rattus norvegicus

Analyze

Symbol:

Hoxa5

Name:

homeo box A5

RGD ID:

620609

Description:

Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including negative regulation of angiogenesis; regulation of gene expression; and regulation of myeloid cell differentiation. Predicted to act upstream of or within several processes, including animal organ development; intestinal epithelial cell maturation; and respiratory system process. Predicted to be active in nucleus. Orthologous to human HOXA5 (homeobox A5); INTERACTS WITH all-trans-retinoic acid; ammonium chloride; diethylstilbestrol.

Type:

protein-coding

RefSeq Status:

VALIDATED

Also known as:

homeobox protein Hox-1.3; homeobox protein Hox-A5; homeobox protein Hox-A5-like; hox-1.3; LOC100909641; LOC100911546; LOC103689922

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	HOXA5 (homeobox A5)	HGNC	HomoloGene, Panther
Mus musculus (house mouse):	Hoxa5 (homeobox A5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Hoxa5 (homeobox A5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	HOXA5 (homeobox A5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	HOXA5 (homeobox A5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Hoxa5 (homeobox A5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	HOXA5 (homeobox A5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	HOXA5 (homeobox A5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Hoxa5 (homeobox A5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	HOXA5 (homeobox A5)	Alliance	DIOPT (HGNC\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Mus musculus (house mouse):	Hoxa5 (homeobox A5)	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Danio rerio (zebrafish):	hoxa5a (homeobox A5a)	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	Scr	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	4	81,302,341 - 81,306,234 (-)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	4	81,302,353 - 81,306,234 (-)	Ensembl
Rnor_6.0	4	82,170,383 - 82,174,788 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	4	82,170,387 - 82,173,207 (-)	NCBI	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	4	146,837,214 - 146,841,619 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	4	80,501,675 - 80,504,626 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	4	80,779,823 - 80,781,740 (-)	NCBI
Celera	4	76,192,532 - 76,196,931 (-)	NCBI		Celera
Cytogenetic Map	4	q24	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Diaphragmatic Hernia (ISO)

head and neck squamous cell carcinoma (ISO)

Mouth Neoplasms (ISO)

pleomorphic xanthoastrocytoma (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

17beta-estradiol (ISO)

2,3,7,8-tetrachlorodibenzodioxine (ISO)

2-butoxyethanol (ISO)

2-hydroxypropanoic acid (ISO)

4,4'-sulfonyldiphenol (ISO)

5-aza-2'-deoxycytidine (ISO)

all-trans-retinoic acid (EXP,ISO)

ammonium chloride (EXP)

antirheumatic drug (ISO)

arsenous acid (ISO)

benzo[a]pyrene (ISO)

bis(2-chloroethyl) sulfide (ISO)

bisphenol A (ISO)

bisphenol F (ISO)

calcitriol (ISO)

cisplatin (ISO)

clobetasol (ISO)

cyclosporin A (ISO)

cytarabine (ISO)

diarsenic trioxide (ISO)

diethylstilbestrol (EXP)

diuron (EXP)

etoposide (ISO)

flavonoids (EXP)

folic acid (ISO)

genistein (ISO)

gentamycin (EXP)

geraniol (ISO)

lipopolysaccharide (EXP)

mitoxantrone (ISO)

N1'-[2-[[5-[(dimethylamino)methyl]-2-furanyl]methylthio]ethyl]-N1-methyl-2-nitroethene-1,1-diamine (EXP)

nickel atom (ISO)

nitrofen (ISO)

oxaliplatin (EXP)

paracetamol (EXP,ISO)

perfluorodecanoic acid (ISO)

perfluorononanoic acid (ISO)

perfluorooctanoic acid (ISO)

phosgene (ISO)

pirinixic acid (ISO)

quercetin (ISO)

rac-lactic acid (ISO)

ranitidine (EXP)

S-(1,2-dichlorovinyl)-L-cysteine (ISO)

sodium arsenite (ISO)

stigmasterol (ISO)

temozolomide (ISO)

testosterone (ISO)

titanium dioxide (ISO)

topotecan (EXP)

trichloroethene (EXP)

trichostatin A (ISO)

urethane (ISO)

valproic acid (ISO)

vinclozolin (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

anterior/posterior pattern specification (IBA,ISO)

bronchiole development (ISO)

cartilage morphogenesis (ISO)

cell migration (ISO)

cell-cell signaling involved in mammary gland development (ISO)

embryonic skeletal system development (ISO)

embryonic skeletal system morphogenesis (ISO)

epithelial tube branching involved in lung morphogenesis (ISO)

intestinal epithelial cell maturation (ISO)

lobar bronchus epithelium development (ISO)

lung alveolus development (ISO)

lung development (ISO)

lung goblet cell differentiation (ISO)

lung-associated mesenchyme development (ISO)

mammary gland alveolus development (ISO)

mammary gland epithelial cell differentiation (ISO)

mesenchymal-epithelial cell signaling (ISO)

morphogenesis of an epithelium (ISO)

multicellular organism growth (ISO)

negative regulation of angiogenesis (IEA,ISO)

negative regulation of erythrocyte differentiation (IEA,ISO)

pattern specification process (ISO,TAS)

positive regulation of apoptotic process (IEA,ISO)

positive regulation of gene expression (IEA,ISO)

positive regulation of myeloid cell differentiation (IEA,ISO)

positive regulation of transcription by RNA polymerase II (IEA,ISO)

regulation of mammary gland epithelial cell proliferation (ISO)

regulation of transcription by RNA polymerase II (IBA,IEA)

respiratory gaseous exchange by respiratory system (ISO)

respiratory system process (ISO)

skeletal system development (ISO)

thyroid gland development (ISO)

trachea cartilage morphogenesis (ISO)

trachea morphogenesis (ISO)

Cellular Component

cellular_component (ND)

nucleus (IBA,IEA,ISO)

Molecular Function

DNA binding (IEA,ISO)

DNA-binding transcription activator activity, RNA polymerase II-specific (IEA,ISO)

DNA-binding transcription factor activity (ISO)

DNA-binding transcription factor activity, RNA polymerase II-specific (IBA,IEA)

molecular_function (ND)

protein binding (ISO)

RNA polymerase II cis-regulatory region sequence-specific DNA binding (IBA,IEA,ISO)

sequence-specific double-stranded DNA binding (ISO)

References

References - curated


1.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	GOA data from the GO Consortium
3.	Gorski DH, etal., Biotechniques 1994 May;16(5):856-8, 860-2, 865.
4.	MGD data from the GO Consortium
5.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
6.	RGD automated data pipeline
7.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8.	RGD automated import pipeline for gene-chemical interactions
9.	RGD comprehensive gene curation

Additional References at PubMed

PMID:2890554	PMID:7901120	PMID:7911971	PMID:8635464	PMID:8657138	PMID:9441679	PMID:9603431	PMID:10397719	PMID:10564089	PMID:10875927	PMID:10879542	PMID:11900462
PMID:12815622	PMID:15295088	PMID:15545268	PMID:16607641	PMID:16756717	PMID:17003488	PMID:17417799	PMID:17626057	PMID:17957028	PMID:23136161	PMID:29070584

Genomics

Comparative Map Data

Hoxa5
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	4	81,302,341 - 81,306,234 (-)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	4	81,302,353 - 81,306,234 (-)	Ensembl
Rnor_6.0	4	82,170,383 - 82,174,788 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	4	82,170,387 - 82,173,207 (-)	NCBI	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	4	146,837,214 - 146,841,619 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	4	80,501,675 - 80,504,626 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	4	80,779,823 - 80,781,740 (-)	NCBI
Celera	4	76,192,532 - 76,196,931 (-)	NCBI		Celera
Cytogenetic Map	4	q24	NCBI

HOXA5
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	7	27,141,052 - 27,143,681 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	7	27,141,052 - 27,143,681 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	7	27,180,671 - 27,183,300 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	7	27,147,521 - 27,149,812 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	7	26,954,235 - 26,956,527	NCBI
Celera	7	27,169,928 - 27,172,220 (-)	NCBI
Cytogenetic Map	7	p15.2	NCBI
HuRef	7	27,061,238 - 27,063,851 (-)	NCBI		HuRef
CHM1_1	7	27,180,379 - 27,182,993 (-)	NCBI		CHM1_1
CRA_TCAGchr7v2	7	27,231,823 - 27,234,436 (-)	NCBI

Hoxa5
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	6	52,178,734 - 52,181,567 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	6	52,178,734 - 52,181,567 (-)	Ensembl
GRCm38	6	52,201,754 - 52,204,587 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	6	52,201,754 - 52,204,587 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	6	52,151,753 - 52,154,586 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	6	52,131,337 - 52,134,170 (-)	NCBI			mm8
Celera	6	52,723,406 - 52,726,239 (-)	NCBI		Celera
Cytogenetic Map	6	B3	NCBI
cM Map	6	25.4	NCBI

Hoxa5
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955410	28,834,127 - 28,838,244 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955410	28,835,795 - 28,838,244 (-)	NCBI	ChiLan1.0	ChiLan1.0

HOXA5
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	7	27,385,175 - 27,388,990 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	7	27,385,175 - 27,388,990 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	7	27,786,040 - 27,789,339 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

HOXA5
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	14	40,315,409 - 40,319,001 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	14	40,315,639 - 40,317,768 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	14	39,746,469 - 39,750,543 (-)	NCBI
ROS_Cfam_1.0	14	40,253,687 - 40,258,302 (-)	NCBI
ROS_Cfam_1.0 Ensembl	14	40,254,476 - 40,256,603 (-)	Ensembl
UMICH_Zoey_3.1	14	40,368,242 - 40,372,352 (-)	NCBI
UNSW_CanFamBas_1.0	14	40,053,309 - 40,057,416 (-)	NCBI
UU_Cfam_GSD_1.0	14	40,411,943 - 40,416,018 (-)	NCBI

Hoxa5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024405118	84,557,026 - 84,560,322 (-)	NCBI
SpeTri2.0	NW_004936478	3,768,757 - 3,771,850 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

HOXA5
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	18	45,421,663 - 45,432,885 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	18	45,429,691 - 45,432,723 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	18	50,062,880 - 50,065,910 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

HOXA5
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	21	31,224,017 - 31,227,819 (+)	NCBI	ChlSab1.1		chlSab2
ChlSab1.1 Ensembl	21	31,224,977 - 31,227,994 (+)	Ensembl	ChlSab1.1		chlSab2
Vero_WHO_p1.0	NW_023666042	73,506,435 - 73,509,813 (-)	NCBI	Vero_WHO_p1.0

Hoxa5
(Heterocephalus glaber - naked mole-rat)

Naked Mole-rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624739	3,461,779 - 3,464,543 (+)	NCBI	HetGla_female_1.0		hetGla2

Position Markers

Hoxa5

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	81,302,662 - 81,302,813 (+)	MAPPER	mRatBN7.2
Rnor_6.0	4	82,257,017 - 82,257,167	NCBI	Rnor6.0
Rnor_6.0	4	82,171,223 - 82,171,373	NCBI	Rnor6.0
Rnor_5.0	4	146,923,848 - 146,923,998	UniSTS	Rnor5.0
Rnor_5.0	4	146,838,054 - 146,838,204	UniSTS	Rnor5.0
RGSC_v3.4	4	80,502,545 - 80,502,695	UniSTS	RGSC3.4
Celera	4	76,193,372 - 76,193,522	UniSTS
Cytogenetic Map	4	q24	UniSTS

stSG609349

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	81,302,015 - 81,302,234 (+)	MAPPER	mRatBN7.2
Rnor_6.0	4	82,170,575 - 82,170,793	NCBI	Rnor6.0
Rnor_6.0	4	82,256,369 - 82,256,587	NCBI	Rnor6.0
Rnor_5.0	4	146,923,200 - 146,923,418	UniSTS	Rnor5.0
Rnor_5.0	4	146,837,406 - 146,837,624	UniSTS	Rnor5.0
RGSC_v3.4	4	80,501,897 - 80,502,115	UniSTS	RGSC3.4
Celera	4	76,192,724 - 76,192,942	UniSTS
Cytogenetic Map	4	q24	UniSTS

MARC_6217-6218:992007117:1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	81,302,049 - 81,302,284 (+)	MAPPER	mRatBN7.2
Rnor_6.0	4	82,170,609 - 82,170,843	NCBI	Rnor6.0
Rnor_6.0	4	82,256,403 - 82,256,637	NCBI	Rnor6.0
Rnor_5.0	4	146,923,234 - 146,923,468	UniSTS	Rnor5.0
Rnor_5.0	4	146,837,440 - 146,837,674	UniSTS	Rnor5.0
RGSC_v3.4	4	80,501,931 - 80,502,165	UniSTS	RGSC3.4
Celera	4	76,192,758 - 76,192,992	UniSTS
Cytogenetic Map	4	q24	UniSTS

UniSTS:57649

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	81,302,195 - 81,302,539 (+)	MAPPER	mRatBN7.2
Rnor_6.0	4	82,170,755 - 82,171,099	NCBI	Rnor6.0
Rnor_6.0	4	82,256,549 - 82,256,893	NCBI	Rnor6.0
Rnor_5.0	4	146,923,380 - 146,923,724	UniSTS	Rnor5.0
Rnor_5.0	4	146,837,586 - 146,837,930	UniSTS	Rnor5.0
RGSC_v3.4	4	80,502,077 - 80,502,421	UniSTS	RGSC3.4
Celera	4	76,192,904 - 76,193,248	UniSTS
Cytogenetic Map	4	q24	UniSTS

REN100511

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	81,301,937 - 81,302,212 (+)	MAPPER	mRatBN7.2
Rnor_6.0	4	82,170,497 - 82,170,771	NCBI	Rnor6.0
Rnor_6.0	4	82,256,291 - 82,256,565	NCBI	Rnor6.0
Rnor_5.0	4	146,923,122 - 146,923,396	UniSTS	Rnor5.0
Rnor_5.0	4	146,837,328 - 146,837,602	UniSTS	Rnor5.0
RGSC_v3.4	4	80,501,819 - 80,502,093	UniSTS	RGSC3.4
Celera	4	76,192,646 - 76,192,920	UniSTS
Cytogenetic Map	4	q24	UniSTS

REN100512

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	81,302,197 - 81,302,454 (+)	MAPPER	mRatBN7.2
Rnor_6.0	4	82,170,757 - 82,171,014	NCBI	Rnor6.0
Rnor_6.0	4	82,256,551 - 82,256,808	NCBI	Rnor6.0
Rnor_5.0	4	146,923,382 - 146,923,639	UniSTS	Rnor5.0
Rnor_5.0	4	146,837,588 - 146,837,845	UniSTS	Rnor5.0
RGSC_v3.4	4	80,502,079 - 80,502,336	UniSTS	RGSC3.4
Celera	4	76,192,906 - 76,193,163	UniSTS
Cytogenetic Map	4	q24	UniSTS

REN100522

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	81,304,317 - 81,304,564 (+)	MAPPER	mRatBN7.2
Rnor_6.0	4	82,172,878 - 82,173,124	NCBI	Rnor6.0
Rnor_6.0	4	82,258,673 - 82,258,919	NCBI	Rnor6.0
Rnor_5.0	4	146,925,504 - 146,925,750	UniSTS	Rnor5.0
Rnor_5.0	4	146,839,709 - 146,839,955	UniSTS	Rnor5.0
RGSC_v3.4	4	80,504,201 - 80,504,447	UniSTS	RGSC3.4
Celera	4	76,195,021 - 76,195,267	UniSTS
Cytogenetic Map	4	q24	UniSTS

Hoxa5

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	81,301,920 - 81,302,068 (+)	MAPPER	mRatBN7.2
Rnor_6.0	4	82,256,274 - 82,256,421	NCBI	Rnor6.0
Rnor_6.0	4	82,170,480 - 82,170,627	NCBI	Rnor6.0
Rnor_5.0	4	146,923,105 - 146,923,252	UniSTS	Rnor5.0
Rnor_5.0	4	146,837,311 - 146,837,458	UniSTS	Rnor5.0
RGSC_v3.4	4	80,501,802 - 80,501,949	UniSTS	RGSC3.4
Celera	4	76,192,629 - 76,192,776	UniSTS
Cytogenetic Map	4	q24	UniSTS

Hoxa5

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	81,301,925 - 81,302,107 (+)	MAPPER	mRatBN7.2
Rnor_6.0	4	82,256,279 - 82,256,460	NCBI	Rnor6.0
Rnor_6.0	4	82,170,485 - 82,170,666	NCBI	Rnor6.0
Rnor_5.0	4	146,923,110 - 146,923,291	UniSTS	Rnor5.0
Rnor_5.0	4	146,837,316 - 146,837,497	UniSTS	Rnor5.0
RGSC_v3.4	4	80,501,807 - 80,501,988	UniSTS	RGSC3.4
Celera	4	76,192,634 - 76,192,815	UniSTS
Cytogenetic Map	4	q24	UniSTS

Hoxa5

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	81,304,245 - 81,304,330 (+)	MAPPER	mRatBN7.2
Rnor_6.0	4	82,172,806 - 82,172,890	NCBI	Rnor6.0
Rnor_6.0	4	82,258,601 - 82,258,685	NCBI	Rnor6.0
Rnor_5.0	4	146,839,637 - 146,839,721	UniSTS	Rnor5.0
Rnor_5.0	4	146,925,432 - 146,925,516	UniSTS	Rnor5.0
Celera	4	76,194,949 - 76,195,033	UniSTS
Cytogenetic Map	4	q24	UniSTS

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
2303168	Bp330	Blood pressure QTL 330	4.25	0.017	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	4	5214602	146446691	Rat
631261	Tcas3	Tongue tumor susceptibility QTL 3	6.88		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	4	10814170	91360527	Rat
2316958	Gluco58	Glucose level QTL 58	10		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	4	11320076	180699135	Rat
12798520	Anxrr55	Anxiety related response QTL 55	4.45	0.01	locomotor behavior trait (VT:0001392)	number of rearing movements with lid-pushing in an experimental apparatus (CMO:0002715)	4	32583980	114627242	Rat
8552782	Vie1	Viral induced encephalitis QTL 1	26.4		brain integrity trait (VT:0010579)	encephalitis incidence/prevalence measurement (CMO:0002361)	4	34430484	82490359	Rat
8552801	Bw143	Body weight QTL 143	7.3		body mass (VT:0001259)	change in body weight to body weight ratio (CMO:0002216)	4	34430484	82490359	Rat
8552809	Vie5	Viral induced encephalitis QTL 5	25.3		brain integrity trait (VT:0010579)	encephalitis incidence/prevalence measurement (CMO:0002361)	4	34430484	82490359	Rat
8655961	Kidm43	Kidney mass QTL 43	18		kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	4	36303261	103194984	Rat
1358352	Srcrt3	Stress Responsive Cort QTL 3	2.29		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	4	38465774	146803430	Rat
1300139	Hrtrt6	Heart rate QTL 6	2.85		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	4	39524264	116179656	Rat
61445	Strs3	Sensitivity to stroke QTL 3	3		cerebrum integrity trait (VT:0010549)	post-insult time to onset of cerebrovascular lesion (CMO:0002343)	4	40433388	85433388	Rat
8694439	Bw168	Body weight QTL 168	9.57	0.001	retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight to body weight ratio (CMO:0000635)	4	40433414	85433414	Rat
6893678	Bw108	Body weight QTL 108	2.6	0.006	body mass (VT:0001259)	body weight (CMO:0000012)	4	43457976	88457976	Rat
1576305	Emca6	Estrogen-induced mammary cancer QTL 6	5.8		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	4	44463720	155883716	Rat
1354612	Foco1	Food consumption QTL 1	8.87		eating behavior trait (VT:0001431)	food intake rate (CMO:0000427)	4	44463908	148090542	Rat
1354660	Salc1	Saline consumption QTL 1	11.26		drinking behavior trait (VT:0001422)	saline drink intake rate (CMO:0001627)	4	44463908	148090542	Rat
2312567	Glom19	Glomerulus QTL 19	1.9	0.006	kidney glomerulus morphology trait (VT:0005325)	index of glomerular damage (CMO:0001135)	4	45456990	146803430	Rat
1298082	Stresp4	Stress response QTL 4			blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	4	50119848	146803430	Rat
70200	Alc18	Alcohol consumption QTL 18	9.2		drinking behavior trait (VT:0001422)	ethanol intake volume to total fluid intake volume ratio (CMO:0001591)	4	56647873	149491524	Rat
1641833	Alc21	Alcohol consumption QTL 21	8.6	0.0001	drinking behavior trait (VT:0001422)	ethanol drink intake rate (CMO:0001407)	4	56698790	126192555	Rat
631546	Bp86	Blood pressure QTL 86	3.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	57114432	91360801	Rat
634311	Sach7	Saccharin preference QTL 7			taste sensitivity trait (VT:0001986)	saccharin intake volume to total fluid intake volume ratio (CMO:0001601)	4	57114432	102114432	Rat
1358363	Sradr3	Stress Responsive Adrenal Weight QTL 3	6.19		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	4	57486946	102486946	Rat
1558651	Swd3	Spike wave discharge measurement QTL 3	4.62	0.000024	brain electrophysiology trait (VT:0010557)	brain spike-and-wave discharge frequency (CMO:0001742)	4	58432133	92991462	Rat
738009	Sach4	Saccharine consumption QTL 4	4.9	0.000016	consumption behavior trait (VT:0002069)	saccharin intake volume to total fluid intake volume ratio (CMO:0001601)	4	59948935	154902892	Rat
738016	Alc16	Alcohol consumption QTL 16	3.6	0.00015	consumption behavior trait (VT:0002069)	ethanol drink intake rate to body weight ratio (CMO:0001616)	4	59948935	154902892	Rat
738031	Alc14	Alcohol consumption QTL 14	7.6	0.00003	consumption behavior trait (VT:0002069)	ethanol drink intake rate to body weight ratio (CMO:0001616)	4	59948935	154902892	Rat
1578657	Bss12	Bone structure and strength QTL 12	8.9		femur morphology trait (VT:0000559)	femoral neck cross-sectional area (CMO:0001697)	4	60220938	105220938	Rat
1578658	Bss13	Bone structure and strength QTL 13	8		femur strength trait (VT:0010010)	femoral neck polar moment of inertia (CMO:0001670)	4	60220938	105220938	Rat
2300179	Bmd50	Bone mineral density QTL 50	5.9	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	4	60928534	105928534	Rat
1549843	Bw53	Body weight QTL 53		0.0001	body mass (VT:0001259)	body weight gain (CMO:0000420)	4	61697658	103194791	Rat
1549839	Bw52	Body weight QTL 52		0.0001	body mass (VT:0001259)	body weight gain (CMO:0000420)	4	61697658	115089733	Rat
61418	Pia5	Pristane induced arthritis QTL 5	4.5		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	62277855	128289560	Rat
6478743	Anxrr40	Anxiety related response QTL 40		0.83076	defecation behavior trait (VT:0010462)	defecation rate (CMO:0000998)	4	62753847	107753847	Rat
6478772	Anxrr49	Anxiety related response QTL 49		0.15488	defecation behavior trait (VT:0010462)	defecation rate (CMO:0000998)	4	62753847	107753847	Rat
6478684	Anxrr30	Anxiety related response QTL 30		0.00087	defecation behavior trait (VT:0010462)	defecation rate (CMO:0000998)	4	62753847	107753847	Rat
631651	Bp124	Blood pressure QTL 124	3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	62879517	107879517	Rat
7394826	Bw126	Body weight QTL 126		0.002	body mass (VT:0001259)	body weight gain (CMO:0000420)	4	62933269	87483707	Rat
8552807	Vie4	Viral induced encephalitis QTL 4	7.3		brain integrity trait (VT:0010579)	encephalitis incidence/prevalence measurement (CMO:0002361)	4	62933508	82490359	Rat
70192	BpQTLcluster5	Blood pressure QTL cluster 5	4.183		arterial blood pressure trait (VT:2000000)	absolute change in mean arterial blood pressure (CMO:0000533)	4	62933508	114921294	Rat
70192	BpQTLcluster5	Blood pressure QTL cluster 5	4.183		arterial blood pressure trait (VT:2000000)	absolute change in pulse pressure (CMO:0001882)	4	62933508	114921294	Rat
70192	BpQTLcluster5	Blood pressure QTL cluster 5	4.183		arterial blood pressure trait (VT:2000000)	percent change in systolic blood pressure (CMO:0000747)	4	62933508	114921294	Rat
70192	BpQTLcluster5	Blood pressure QTL cluster 5	4.183		arterial blood pressure trait (VT:2000000)	percent change in mean arterial blood pressure (CMO:0002035)	4	62933508	114921294	Rat
70192	BpQTLcluster5	Blood pressure QTL cluster 5	4.183		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	4	62933508	114921294	Rat
70192	BpQTLcluster5	Blood pressure QTL cluster 5	4.183		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	62933508	114921294	Rat
70192	BpQTLcluster5	Blood pressure QTL cluster 5	4.183		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	4	62933508	114921294	Rat
631674	Iddm14	Insulin dependent diabetes mellitus QTL 14			blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	4	64528739	157573521	Rat
2312569	Pur19	Proteinuria QTL 19	3.4	0.001	total urine protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	4	65882107	96130297	Rat
61330	Eau1	Experimental allergic uveoretinitis QTL 1		0.0003	uvea integrity trait (VT:0010551)	experimental autoimmune uveitis score (CMO:0001504)	4	70362013	132642728	Rat
634344	Hcar7	Hepatocarcinoma resistance QTL 7	7.8		liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	4	70808386	115808386	Rat
634344	Hcar7	Hepatocarcinoma resistance QTL 7	7.8		liver integrity trait (VT:0010547)	liver tumorous lesion area to total liver area ratio (CMO:0001075)	4	70808386	115808386	Rat
631646	Stl4	Serum triglyceride level QTL 4	6.5	0.0001	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	4	73169846	132642728	Rat
724522	Bp146	Blood pressure QTL 146	2.2	0.0021	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	73630210	118630210	Rat
2302051	Pia28	Pristane induced arthritis QTL 28	5.3	0.001	blood autoantibody amount (VT:0003725)	serum immunoglobulin G-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002112)	4	73630210	118630210	Rat
70167	Bw22	Body weight QTL 22	3.1		body mass (VT:0001259)	body weight (CMO:0000012)	4	76647384	117676292	Rat
1357342	Bw40	Body weight QTL 40		0.001	body mass (VT:0001259)	body weight (CMO:0000012)	4	76647384	117676292	Rat
631662	Hcar2	Hepatocarcinoma resistance QTL 2	3.1	0.0003	liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	4	78878504	123878504	Rat
631556	Bp135	Blood pressure QTL 135		0.017	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	4	78881294	117676292	Rat
2317586	Eae25	Experimental allergic encephalomyelitis QTL 25	9.300000190734863		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis duration (CMO:0001424)	4	78882817	83007655	Rat
2317586	Eae25	Experimental allergic encephalomyelitis QTL 25	9.300000190734863		nervous system integrity trait (VT:0010566)	post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)	4	78882817	83007655	Rat
2317586	Eae25	Experimental allergic encephalomyelitis QTL 25	9.300000190734863		nervous system integrity trait (VT:0010566)	percentage of study population developing experimental autoimmune encephalomyelitis during a period of time (CMO:0001047)	4	78882817	83007655	Rat
2317586	Eae25	Experimental allergic encephalomyelitis QTL 25	9.300000190734863		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis severity score (CMO:0001419)	4	78882817	83007655	Rat
61364	Iddm2	Insulin dependent diabetes mellitus QTL 2			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	4	78885890	102684881	Rat
738015	Pia9	Pristane induced arthritis QTL 9	4.5	0.048	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	80694870	125694870	Rat
2306899	Bp338	Blood pressure QTL 338		0.071	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	81006124	120102625	Rat
1641919	Alc22	Alcohol consumption QTL 22		0.0005	drinking behavior trait (VT:0001422)	ethanol drink intake rate (CMO:0001407)	4	81192555	126192555	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	31
Count of miRNA genes:	31
Interacting mature miRNAs:	31
Transcripts:	ENSRNOT00000008523
Prediction methods:	Miranda, Rnahybrid
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

Expression

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_024389	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_001059031	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_001064984	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_003753897	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC122669	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000142	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	L03556	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000074167 ⟹ ENSRNOP00000064639

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	4	81,302,353 - 81,306,234 (-)	Ensembl
Rnor_6.0 Ensembl	4	82,170,387 - 82,173,207 (-)	Ensembl

RefSeq Acc Id:

NM_024389 ⟹ NP_077365

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	4	81,302,341 - 81,306,234 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_077365	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAA67844	(Get FASTA)	NCBI Sequence Viewer
	P52949	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_077365 ⟸ NM_024389

RefSeq Acc Id:

ENSRNOP00000064639 ⟸ ENSRNOT00000074167

Protein Domains

Homeobox

Transcriptome

eQTL		View at Phenogen
WGCNA		View at Phenogen
Tissue/Strain Expression		View at Phenogen

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

ACI/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

ACI/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

ACI/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

ACI/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

BBDP/Wor (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

BN-Lx/CubMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/NHsdMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/NHsdMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/SsN (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/SsN (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

BUF/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BXH2/CubMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BXH3/CubMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

Buf/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

COP/CrCrl (MCW & UW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob) University of Wisconsin (Dr. James Shull)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Charles River Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)

DA/OlaHsd (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Envigo
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/DuCrl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/NCrl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

F344/NRrrc (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

F344/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FHH/EurMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FHH/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHH/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

FHL/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHL/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

FXLE16/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FXLE18/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

GH/OmrMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

GK/FarMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

GK/Ox (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

HXB10/IpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB2/IpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB20/IpcvMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB31/IpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB4/IpcvMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LE/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LE/Stm (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/Crl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEW/Crl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/NCrlBR (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEXF10A/StmMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF11/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF1A/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF1C/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF2B/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF3/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF4/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LH/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LH/MavRrrcAek (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LL/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LL/MavRrrcAek (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LN/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LN/MavRrrcAek (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

M520/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

M520/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

M520/NRrrcMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

MHS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MNS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MR/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

MR/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

MWF/Hsd (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

PVG/Seac (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SBH/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBH/Ygl sequenced by MCW

SBH/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SBN/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBN/Ygl sequenced by MCW

SBN/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHR/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHR/OlalpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SHRSP/A3NCrl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SHRSP/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SR/JrHsd (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Envigo
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SR/JrHsd (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Harlan Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SR/JrHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/Jr (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/JrHsdMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SS/JrHsdMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SS/JrHsdMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WAG/Rij (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WAG/RijCrl (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WKY/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WKY/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

WKY/NCrl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WKY/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WN/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WN/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:620609	AgrOrtholog
Ensembl Genes	ENSRNOG00000006466	UniProtKB/TrEMBL
	ENSRNOG00000047951	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
	ENSRNOG00000052804	UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000008523	UniProtKB/TrEMBL
	ENSRNOP00000064639	ENTREZGENE, UniProtKB/TrEMBL
	ENSRNOP00000073150	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000008523	UniProtKB/TrEMBL
	ENSRNOT00000074167	ENTREZGENE, UniProtKB/TrEMBL
	ENSRNOT00000086112	UniProtKB/TrEMBL
InterPro	Homeobox-like_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Homeobox_antennapedia	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Homeobox_Antennapedia_CS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Homeobox_CS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Homeobox_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Homeobox_metazoa	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene	79241	ENTREZGENE
Pfam	Homeodomain	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Hoxa5	PhenoGen
PRINTS	ANTENNAPEDIA	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	HOMEOBOX	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE	ANTENNAPEDIA	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	HOMEOBOX_1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	HOMEOBOX_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART	HOX	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF46689	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	G3V6T2_RAT	UniProtKB/TrEMBL
	HXA5_RAT	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2021-03-09	Hoxa5	homeo box A5	LOC103689922	homeobox protein Hox-A5	Data Merged	737654	PROVISIONAL
2015-07-29	Hoxa5	homeo box A5	LOC100911546	homeobox protein Hox-A5-like	Data Merged	737654	PROVISIONAL
2015-07-29	Hoxa5	homeo box A5	LOC100909641	homeobox protein Hox-A5-like	Data Merged	737654	PROVISIONAL
2014-08-25	LOC103689922	homeobox protein Hox-A5			Symbol and Name status set to provisional	70820	PROVISIONAL
2012-07-05	LOC100911546	homeobox protein Hox-A5-like			Symbol and Name status set to provisional	70820	PROVISIONAL
2012-07-05	LOC100909641	homeobox protein Hox-A5-like			Symbol and Name status set to provisional	70820	PROVISIONAL
2004-09-10	Hoxa5	homeo box A5			Symbol and Name status set to approved	1299863	APPROVED
2002-08-07	Hoxa5	homeo box A5			Symbol and Name status set to provisional	70820	PROVISIONAL

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

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Imported Disease Annotations - ClinVar

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD