HOXA4 (homeobox A4) - Rat Genome Database

Name: HOXA4
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: HOXA4 (homeobox A4) Chlorocebus sabaeus

Analyze

Symbol:

HOXA4

Name:

homeobox A4

RGD ID:

18436719

Description:

ENCODES a protein that exhibits DNA binding (inferred); DNA-binding transcription factor activity, RNA polymerase II-specific (inferred); RNA polymerase II cis-regulatory region sequence-specific DNA binding (inferred); INVOLVED IN anterior/posterior pattern specification (ortholog); embryonic skeletal system morphogenesis (ortholog); ASSOCIATED WITH genetic disease (ortholog); pleomorphic xanthoastrocytoma (ortholog); FOUND IN nuclear body (inferred); nucleoplasm (inferred); nucleus (inferred)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

homeobox protein Hox-A4

RGD Orthologs

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):	HOXA4 (homeobox A4)	NCBI	Ortholog
Mus musculus (house mouse):	Hoxa4 (homeobox A4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus norvegicus (Norway rat):	Hoxa4 (homeo box A4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Hoxa4 (homeobox A4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	HOXA4 (homeobox A4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	HOXA4 (homeobox A4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Hoxa4 (homeobox A4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	HOXA4 (homeobox A4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Hoxa4 (homeobox A4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline

Latest Assembly:

ChlSab1.1 - Green Monkey 1.1 Assembly

Position:

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	21	31,238,087 - 31,240,406 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	21	31,238,182 - 31,240,384 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666042	73,481,035 - 73,495,699 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

genetic disease (ISO)

pleomorphic xanthoastrocytoma (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

anterior/posterior pattern specification (IEA,ISO)

embryonic skeletal system morphogenesis (IEA,ISO)

positive regulation of transcription by RNA polymerase II (IEA)

regulation of DNA-templated transcription (IEA)

Cellular Component

nuclear body (IEA)

nucleoplasm (IEA)

nucleus (IEA)

Molecular Function

DNA binding (IEA)

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

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

sequence-specific double-stranded DNA binding (IEA)

References

Additional References at PubMed

PMID:22301074	PMID:30032202

Genomics

Comparative Map Data

HOXA4
(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	31,238,087 - 31,240,406 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	21	31,238,182 - 31,240,384 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666042	73,481,035 - 73,495,699 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

HOXA4
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	7	27,128,525 - 27,130,757 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	7	27,128,507 - 27,130,780 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	7	27,168,144 - 27,170,376 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	7	27,134,651 - 27,136,924 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	7	26,941,249 - 26,943,639	NCBI
Celera	7	27,157,064 - 27,159,337 (-)	NCBI		Celera
Cytogenetic Map	7	p15.2	NCBI
HuRef	7	27,048,696 - 27,050,969 (-)	NCBI		HuRef
CHM1_1	7	27,167,837 - 27,170,110 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	7	27,264,506 - 27,266,738 (-)	NCBI		T2T-CHM13v2.0
CRA_TCAGchr7v2	7	27,219,281 - 27,221,554 (-)	NCBI

Hoxa4
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	6	52,166,662 - 52,168,683 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	6	52,166,651 - 52,168,733 (-)	Ensembl		GRCm39 Ensembl
GRCm38	6	52,189,682 - 52,191,703 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	6	52,189,671 - 52,191,753 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	6	52,139,686 - 52,141,702 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	6	52,119,270 - 52,121,286 (-)	NCBI		MGSCv36	mm8
Celera	6	52,711,346 - 52,713,362 (-)	NCBI		Celera
Cytogenetic Map	6	B3	NCBI
cM Map	6	25.4	NCBI

Hoxa4
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	4	82,620,294 - 82,622,302 (-)	NCBI		GRCr8
mRatBN7.2	4	81,289,677 - 81,291,685 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	4	81,289,682 - 81,291,685 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	4	86,511,488 - 86,513,496 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	4	82,286,880 - 82,288,888 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	4	80,714,011 - 80,716,019 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	4	82,158,234 - 82,160,317 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	4	82,158,892 - 82,160,240 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	4	146,825,065 - 146,827,156 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	4	80,489,558 - 80,491,562 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
Cytogenetic Map	4	q24	NCBI

Hoxa4
(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	28,823,500 - 28,825,020 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955410	28,822,814 - 28,827,294 (-)	NCBI	ChiLan1.0	ChiLan1.0

HOXA4
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	6	31,957,687 - 31,959,927 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	7	80,282,420 - 80,284,653 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	7	27,773,001 - 27,775,284 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	7	27,372,664 - 27,374,961 (-)	NCBI	panpan1.1	PanPan1.1	panPan2

HOXA4
(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	40,302,106 - 40,304,437 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	14	40,302,816 - 40,304,321 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	14	39,733,161 - 39,735,443 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	14	40,240,879 - 40,243,161 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	14	40,241,589 - 40,243,094 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	14	40,354,968 - 40,357,250 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	14	40,040,052 - 40,042,332 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	14	40,398,629 - 40,400,911 (-)	NCBI		UU_Cfam_GSD_1.0

Hoxa4
(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	84,544,554 - 84,546,285 (-)	NCBI		HiC_Itri_2
SpeTri2.0	NW_004936478	3,756,289 - 3,758,020 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

HOXA4
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1	18	45,443,268 - 45,445,662 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	18	50,076,492 - 50,080,299 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

Hoxa4
(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_female_1.0 Ensembl	NW_004624739	3,474,990 - 3,476,486 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624739	3,474,868 - 3,477,190 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	endocrine system	hemolymphoid system	nervous system
High
Medium
Low	20	11	4
Below cutoff		7

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_007981812	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JACDXN010000010	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSCSAT00000012371 ⟹ ENSCSAP00000010408

Type:

CODING

Position:

Green Monkey Assembly	Chr	Position (strand)	Source
ChlSab1.1 Ensembl	21	31,238,182 - 31,240,384 (+)	Ensembl

RefSeq Acc Id:

XM_007981812 ⟹ XP_007980003

Type:

CODING

Position:

Green Monkey Assembly	Chr	Position (strand)	Source
ChlSab1.1	21	31,238,087 - 31,240,406 (+)	NCBI
Vero_WHO_p1.0	NW_023666042	73,481,035 - 73,495,699 (-)	NCBI

Sequence:

show sequence

GGGATGGGAAGCGAGGCAGGAGGGGGAGGGGCCTCGGCGAGCCCAGAAAAAACGACAACGCGAG
AAAAATTAGTATTTTTGCACTTCACAAATTAATGACCATGAGCTCGTTTTTGATAAACTCCAAC
TACATCGAGCCCAAGTTCCCTCCCTTTGAGGAGTACGCGCAGCACAGCGGCCCGGGCGGCGAAG
ACGGCGGCCCGGGCGGGGGCCCCGGCTACCAGCAGCCCCTGGCGCCCCCGACCCAGCACCTGCC
GCCGCAGCAGCCCCAGCTCCCTCACGCGGGCGGCGGCCGAGAGCCCCCTGCCTCCTACTACGCG
CCGCGGACCGCCCGCGAGCCCGTCTACCCTGCCGCCGCGCTGTACCCCTCGCAAGGGGCCGCGG
ACACCGCCTACCCCTATGGCTACCGTGGCGGCGCGAGCCCCGGGCGGCCNCCCCAGCCTGAGCA
GCCCCTGGCGCACGCCAAGGGCCCGGCGCACGGCCTGCATGCGAGCCACGTCCTGCAGCCCCAG
CCGCCGCCGCCCCTGCAGCCTCGCGCTGTGCCCCCAGCGGCCCCGCGGCGCTGCGAGGCGGCCC
CCGCCACCCCTGGCGTCCCGGCAGGGGGCAGCGCCCCCGCGTGCCCGCTGCTCTTGGCCGACAA
GAGCCCGCTGGGCCTGAAGGGCAAGGAGCCCGTAGTGTACCCCTGGATGAAGAAGATCCATGTC
AGCGCCGTCAACCCCAGTTATAACGGAGGGGAGCCTAAGCGCTCTCGAACCGCCTACACCCGGC
AGCAGGTTTTGGAGCTGGAGAAGGAGTTCCACTTCAATCGCTACCTGACCCGGCGGCGCCGCAT
CGAGATCGCCCACACGCTCTGCTTGTCCGAGCGCCAGGTCAAGATCTGGTTTCAGAACCGGAGG
ATGAAGTGGAAGAAAGACCACAAACTGCCCAACACCAAGATGCGATCCTCCAATTCAGCCTCGG
CCTCTGCCGGCCCACCAGGGAAAGCACAAACTGAGAGCCCTCACCTCCATCCCCACCCCCACCC
GAGTACCTCCACACAGGTTCCCTCCTCCATATAATCTTCTAGAGACCTTGACCAGTTTCTATCC
CTTACTTGCTTTTCTCTTCTCTTCTCTTGCTCCTTTCCTCATCCACCCCTCCCCATCCGGACCA
TAATACACACCAAAACAAACCCAAATTGGTGAAAAGGATAACCAAAAAGAAGACATTATCCGGG
TAAGAGTGTGTGCTGGTTGCCACCCAAGAGAGGACAGTTGTCCAGGATGCTGGTTGGTGGAACA
ACCTGCTGGCCTGAAACAAGGCTGCCAGGTGTGGATACCTGAGAAGGACTGCTTGGTATCAAAT
ACTTTTGAGATGGCTACAGTCAGCTAGCTGGACAGCCCATGCTGACTGGGGATGTATACTTGCA
TCTTTGTTGAAAGCAGAAGAAAACAGACTCTTTCCCCACCTTCCTTACCTCCTCCTCCCCCATT
AAGGCAGCTCATCCAAGCTTGTATTGAACTGAATAAATGAGTAGACACTGTGGACCTCACAAGA
TTATTTAATTCTTAAGATGTGTAGACCTTGATGGTAGGTGTGACATGTTAGTTTTCCTTACTTG
CATTTATTTAAGATACTGTTACAGAGATACTGTTGTCCCCTTCTGGGACAGTCTTTGGGGAGAG
GGGAGTGCATTTAGACTTATGTGGAACTGTACAAATTGTGATGTGGCTATATAGAAAGCCATGT
GCTAAGAATAAACTCCATTTAAAAAACATTAAAAATCTAAGATTCA

hide sequence

Protein Sequences


Protein RefSeqs	XP_007980003	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSCSAP00000010408
	ENSCSAP00000010408.1

RefSeq Acc Id:	XP_007980003 ⟸ XM_007981812
- UniProtKB:	A0A0D9RP69 (UniProtKB/TrEMBL)

RefSeq Acc Id:

ENSCSAP00000010408 ⟸ ENSCSAT00000012371

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSCSAG00000014273	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSCSAT00000012371.1	UniProtKB/TrEMBL
Gene3D-CATH	Homeodomain-like	UniProtKB/TrEMBL
InterPro	Homeobox-like_sf	UniProtKB/TrEMBL
	Homeobox_antennapedia	UniProtKB/TrEMBL
	Homeobox_Antennapedia_CS	UniProtKB/TrEMBL
	Homeobox_CS	UniProtKB/TrEMBL
	Homeobox_dom	UniProtKB/TrEMBL
	Homeobox_metazoa	UniProtKB/TrEMBL
KEGG Report	csab:103226323	UniProtKB/TrEMBL
NCBI Gene	HOXA4	ENTREZGENE
PANTHER	HOMEOBOX PROTEIN HOX-A4	UniProtKB/TrEMBL
	HOMEOTIC PROTEIN DEFORMED	UniProtKB/TrEMBL
Pfam	Homeodomain	UniProtKB/TrEMBL
PRINTS	ANTENNAPEDIA	UniProtKB/TrEMBL
	HOMEOBOX	UniProtKB/TrEMBL
PROSITE	ANTENNAPEDIA	UniProtKB/TrEMBL
	HOMEOBOX_1	UniProtKB/TrEMBL
	HOMEOBOX_2	UniProtKB/TrEMBL
SMART	HOX	UniProtKB/TrEMBL
Superfamily-SCOP	SSF46689	UniProtKB/TrEMBL
UniProt	A0A0D9RP69	ENTREZGENE, UniProtKB/TrEMBL

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)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Send us a Message

Imported Disease Annotations - ClinVar