Hoxb1 (homeobox B1) - Rat Genome Database

Name: Hoxb1
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Hoxb1 (homeobox B1) Chinchilla lanigera

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Symbol:

Hoxb1

Name:

homeobox B1

RGD ID:

9049578

Description:

ENCODES a protein that exhibits DNA binding (ortholog); DNA-binding transcription activator activity, RNA polymerase II-specific (ortholog); protein domain specific binding (ortholog); INVOLVED IN anatomical structure formation involved in morphogenesis (ortholog); anatomical structure morphogenesis (ortholog); anterior/posterior pattern specification (ortholog); ASSOCIATED WITH Craniofacial Abnormalities (ortholog); genetic disease (ortholog); hereditary breast ovarian cancer syndrome (ortholog); FOUND IN nucleoplasm (ortholog)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

homeobox protein Hox-B1

RGD Orthologs

Alliance Orthologs

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):	HOXB1 (homeobox B1)	NCBI	Ortholog
Mus musculus (house mouse):	Hoxb1 (homeobox B1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus norvegicus (Norway rat):	Hoxb1 (homeo box B1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	HOXB1 (homeobox B1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	HOXB1 (homeobox B1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Hoxb1 (homeobox B1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	HOXB1 (homeobox B1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	HOXB1 (homeobox B1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Hoxb1 (homeobox B1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline

Latest Assembly:

ChiLan1.0 - Chinchilla ChiLan1.0 Assembly

Position:

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955451	12,707,462 - 12,709,899 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955451	12,707,560 - 12,708,950 (+)	NCBI	ChiLan1.0	ChiLan1.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Craniofacial Abnormalities (ISO)

genetic disease (ISO)

hereditary breast ovarian cancer syndrome (ISO)

Hereditary Congenital Facial Paresis (ISO)

Hereditary Congenital Facial Paresis 3 (ISO)

Nervous System Malformations (ISO)

Ventricular Outflow Obstruction (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

anatomical structure formation involved in morphogenesis (ISO)

anatomical structure morphogenesis (ISO)

anterior/posterior pattern specification (ISO)

embryonic skeletal system morphogenesis (ISO)

facial nerve structural organization (ISO)

facial nucleus development (ISO)

positive regulation of transcription by RNA polymerase II (ISO)

rhombomere 4 development (ISO)

rhombomere 5 development (ISO)

rhombomere development (ISO)

Cellular Component

nucleoplasm (ISO)

Molecular Function

DNA binding (ISO)

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

protein binding (ISO)

protein domain specific binding (ISO)

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

RNA polymerase II transcription regulatory region sequence-specific DNA binding (ISO)

sequence-specific DNA binding (ISO)

sequence-specific double-stranded DNA binding (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Transitive Annotation Pipeline	Automated assignment of GO, PW and RDO ISO annotations across species
2.	OMIM Disease Annotation Pipeline	OMIM Disease Annotation Pipeline

Additional References at PubMed

PMID:22301074	PMID:30032202

Genomics

Comparative Map Data

Hoxb1
(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_004955451	12,707,462 - 12,709,899 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955451	12,707,560 - 12,708,950 (+)	NCBI	ChiLan1.0	ChiLan1.0

HOXB1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	17	48,528,526 - 48,531,011 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	17	48,528,526 - 48,531,011 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	17	46,605,888 - 46,608,373 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	17	43,961,806 - 43,963,271 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	17	43,961,812 - 43,963,271	NCBI
Celera	17	43,060,953 - 43,062,427 (-)	NCBI		Celera
Cytogenetic Map	17	q21.32	NCBI
HuRef	17	41,976,125 - 41,977,599 (-)	NCBI		HuRef
CHM1_1	17	46,672,595 - 46,674,060 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	17	49,391,954 - 49,394,439 (-)	NCBI		T2T-CHM13v2.0

Hoxb1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	11	96,256,547 - 96,259,082 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	11	96,256,578 - 96,259,082 (+)	Ensembl		GRCm39 Ensembl
GRCm38	11	96,365,746 - 96,368,254 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	11	96,365,752 - 96,368,256 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	11	96,227,072 - 96,229,567 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	11	96,181,848 - 96,183,766 (+)	NCBI		MGSCv36	mm8
Celera	11	106,016,588 - 106,019,083 (+)	NCBI		Celera
Cytogenetic Map	11	D	NCBI
cM Map	11	59.86	NCBI

Hoxb1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	10	81,827,915 - 81,830,404 (+)	NCBI		GRCr8
mRatBN7.2	10	81,331,507 - 81,332,928 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	10	81,331,507 - 81,332,836 (+)	Ensembl		mRatBN7.2 Ensembl
Rnor_6.0	10	84,214,358 - 84,215,812 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	10	84,214,358 - 84,215,687 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	10	84,017,011 - 84,018,433 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	85,098,903 - 85,100,308 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	10	85,102,648 - 85,114,602 (+)	NCBI
Celera	10	80,097,554 - 80,099,008 (+)	NCBI		Celera
Cytogenetic Map	10	q26	NCBI

HOXB1
(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	19	16,571,773 - 16,573,681 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	17	18,537,363 - 18,539,898 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	17	9,005,745 - 9,008,230 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	17	9,190,137 - 9,191,696 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	17	9,190,137 - 9,191,696 (+)	Ensembl	panpan1.1		panPan2

HOXB1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	9	24,791,848 - 24,795,443 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	9	24,792,889 - 24,794,302 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	9	24,256,127 - 24,259,664 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	9	25,586,553 - 25,590,090 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	9	25,587,585 - 25,588,998 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	9	24,354,782 - 24,358,319 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	9	24,615,222 - 24,618,759 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	9	24,743,539 - 24,747,076 (-)	NCBI		UU_Cfam_GSD_1.0

Hoxb1
(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_024405602	24,218,714 - 24,222,497 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936490	12,853,983 - 12,855,428 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936490	12,853,983 - 12,855,428 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

HOXB1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	12	24,784,594 - 24,786,576 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	12	24,784,953 - 24,786,377 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	12	24,742,328 - 24,743,755 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

HOXB1
(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	16	68,940,726 - 68,945,153 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	16	68,941,746 - 68,943,111 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666077	39,995,445 - 39,997,937 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Hoxb1
(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_004624795	5,032,495 - 5,033,789 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624795	5,032,495 - 5,033,789 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_005394243	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AGCD01043422	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSCLAT00000019237 ⟹ ENSCLAP00000019052

Type:

CODING

Position:

Chinchilla Assembly	Chr	Position (strand)	Source
ChiLan1.0 Ensembl	NW_004955451	12,707,462 - 12,709,899 (+)	Ensembl

RefSeq Acc Id:

XM_005394243 ⟹ XP_005394300

Type:

CODING

Position:

Chinchilla Assembly	Chr	Position (strand)	Source
ChiLan1.0	NW_004955451	12,707,560 - 12,708,950 (+)	NCBI

Sequence:

show sequence

ATGGACTATAATAGGATGAACTCCTTCTTAGAGTACCCACTCTGTAACCGGGGACCCAGCGCCT
ACGGTGCCCATAGCGCCCCAACTTCCTTGCCCCCCAGCTCCAGCCAGGCGGTTGACAGCTACGC
AGGCGAGGGTCGCTATGGTGGGGGGCTGCCCAGCCAGGCCCTCCAGCAGAACTCGGGGTACCCC
AGCCAGCAGCTGCCTTCAGCGCTGGGGGTGCCCTTCCCCAGCTCCGCGCCCTCGGGGTACGCCC
CAGCCGCCTGCAGCCCCAGCTTTGGGCCTGCTCAGTACTACCCTCTGGGGGCATCGGAAGGAGA
TGGAGGCTACTTTCACCCCTCAAGCTACGGGGCCCAGCTGGCGGGCTTGCCCGACGGCTACGGA
GCCGGCGCGGCGGGCCAGGGGCCCTACCCTGGGCCGCAGCCCCCGTACGCCAGCGAGCAGGCAG
CCAGCTTCGCACCGGCCTACGCGGAGCTCCTCTCCGAGGACAAGGACGCGCCCTGCCCGTCGGA
ACCCAGCACCCCCACGGCCCGCACCTTCGACTGGATGAAGGTGAAGAGGAACCCGCCCAAGACA
GCCAAGGTGTCCGAGCTGGGCCCGGGCGCCCCCGGCGGGGTCCGAACCAACTTCAGCACGCGGC
AGCTGACCGAGCTGGAGAAGGAGTTCCACTTCAACAAGTACCTGAGCCGCGCGCGGAGGGTGGA
GATCGCCGCCACCCTGGAGCTCAACGAGACGCAGGTCAAGATTTGGTTCCAGAACCGGCGCATG
AAGCAGAAGAAGCGCGAGCGCCAGGGAGGCGGCGTGGCGCCCGTCCCCGCAGGCTGCCCCAAGG
AGGCGGCTGGAGACGCCTCGGACCAGTCCGCGTGCACCTCCCCGGAAGCCTCGCCCAGCTCCGT
CACCTCCTGAACCCCAACCCCAGCGCGGGAGCCCTCTCCTGGGCACCCCAGCCTCACTGCCCTG
GGGACCCCGGCCAAGGATGGGGC

hide sequence

Protein Sequences


Protein RefSeqs	XP_005394300	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSCLAP00000019052
	ENSCLAP00000019052.1

RefSeq Acc Id:

XP_005394300 ⟸ XM_005394243

- UniProtKB:

A0A8C2VXS8 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MDYNRMNSFLEYPLCNRGPSAYGAHSAPTSLPPSSSQAVDSYAGEGRYGGGLPSQALQQNSGYP
SQQLPSALGVPFPSSAPSGYAPAACSPSFGPAQYYPLGASEGDGGYFHPSSYGAQLAGLPDGYG
AGAAGQGPYPGPQPPYASEQAASFAPAYAELLSEDKDAPCPSEPSTPTARTFDWMKVKRNPPKT
AKVSELGPGAPGGVRTNFSTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRM
KQKKRERQGGGVAPVPAGCPKEAAGDASDQSACTSPEASPSSVTS

hide sequence

Ensembl Acc Id:

ENSCLAP00000019052 ⟸ ENSCLAT00000019237

Protein Domains

Homeobox

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSCLAG00000013047	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSCLAT00000019237	ENTREZGENE
	ENSCLAT00000019237.1	UniProtKB/TrEMBL
Gene3D-CATH	Homeodomain-like	UniProtKB/TrEMBL
InterPro	Homeobox-like_sf	UniProtKB/TrEMBL
	Homeobox_CS	UniProtKB/TrEMBL
	Homeobox_dom	UniProtKB/TrEMBL
	Homeobox_metazoa	UniProtKB/TrEMBL
	HXA1/B1/D1	UniProtKB/TrEMBL
NCBI Gene	Hoxb1	ENTREZGENE
PANTHER	HOMEOBOX PROTEIN HOX-B1	UniProtKB/TrEMBL
	PTHR45946	UniProtKB/TrEMBL
Pfam	Homeodomain	UniProtKB/TrEMBL
PRINTS	HOMEOBOX	UniProtKB/TrEMBL
PROSITE	HOMEOBOX_1	UniProtKB/TrEMBL
	HOMEOBOX_2	UniProtKB/TrEMBL
SMART	HOX	UniProtKB/TrEMBL
Superfamily-SCOP	SSF46689	UniProtKB/TrEMBL
UniProt	A0A8C2VXS8	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)

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