HOXB9 (homeobox B9) - Rat Genome Database
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Gene: HOXB9 (homeobox B9) Homo sapiens
Analyze
Symbol: HOXB9
Name: homeobox B9
RGD ID: 1314613
Description: Exhibits sequence-specific double-stranded DNA binding activity. Predicted to contribute to RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in cell chemotaxis. Localizes to mitochondrion and nucleoplasm.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: homeo box 2E; homeo box B9; homeobox protein Hox-2.5; homeobox protein Hox-2E; homeobox protein Hox-B9; HOX-2.5; HOX2; HOX2E
Orthologs:
Mus musculus (house mouse) : Hoxb9 (homeobox B9)  MGI  Alliance
Rattus norvegicus (Norway rat) : Hoxb9 (homeo box B9)  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Hoxb9 (homeobox B9)
Pan paniscus (bonobo/pygmy chimpanzee) : HOXB9 (homeobox B9)
Canis lupus familiaris (dog) : HOXB9 (homeobox B9)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Hoxb9 (homeobox B9)
Chlorocebus sabaeus (African green monkey) : HOXB9 (homeobox B9)
Heterocephalus glaber (naked mole-rat) : Hoxb9 (homeobox B9)
more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1748,621,156 - 48,626,358 (-)EnsemblGRCh38hg38GRCh38
GRCh381748,621,156 - 48,626,358 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371746,698,518 - 46,703,835 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361744,053,517 - 44,058,834 (-)NCBINCBI36hg18NCBI36
Build 341744,053,516 - 44,058,716NCBI
Celera1743,152,681 - 43,157,998 (-)NCBI
Cytogenetic Map17q21.32NCBI
HuRef1742,067,396 - 42,072,713 (-)NCBIHuRef
CHM1_11746,764,512 - 46,769,829 (-)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References

References - curated
1. GOA_HUMAN data from the GO Consortium
2. RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:1358459   PMID:1712647   PMID:1973146   PMID:1981366   PMID:2570724   PMID:2574852   PMID:2576652   PMID:8646877   PMID:9922051   PMID:10617598   PMID:11070089   PMID:11485933  
PMID:11585930   PMID:11857506   PMID:12477932   PMID:14702039   PMID:15489334   PMID:15839736   PMID:16189514   PMID:16344560   PMID:17148583   PMID:18029348   PMID:19060904   PMID:19274049  
PMID:19341834   PMID:19576624   PMID:20080567   PMID:20211142   PMID:21428455   PMID:21516116   PMID:21873635   PMID:21930940   PMID:21988832   PMID:22225776   PMID:22396001   PMID:22863320  
PMID:22990118   PMID:23332081   PMID:23350386   PMID:24462859   PMID:24582746   PMID:24600698   PMID:24999842   PMID:25025961   PMID:25081022   PMID:25136922   PMID:25281560   PMID:25324169  
PMID:25416956   PMID:25609649   PMID:25724625   PMID:25860510   PMID:26186194   PMID:26536658   PMID:26544896   PMID:26926958   PMID:26972000   PMID:26991799   PMID:27279480   PMID:27613418  
PMID:27684187   PMID:28298545   PMID:28473536   PMID:28514442   PMID:28656236   PMID:28808656   PMID:29408459   PMID:29654889   PMID:29724991   PMID:30404004   PMID:31310747   PMID:31372881  
PMID:32098919   PMID:32296183  


Genomics

Comparative Map Data
HOXB9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1748,621,156 - 48,626,358 (-)EnsemblGRCh38hg38GRCh38
GRCh381748,621,156 - 48,626,358 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371746,698,518 - 46,703,835 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361744,053,517 - 44,058,834 (-)NCBINCBI36hg18NCBI36
Build 341744,053,516 - 44,058,716NCBI
Celera1743,152,681 - 43,157,998 (-)NCBI
Cytogenetic Map17q21.32NCBI
HuRef1742,067,396 - 42,072,713 (-)NCBIHuRef
CHM1_11746,764,512 - 46,769,829 (-)NCBICHM1_1
Hoxb9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391196,162,156 - 96,167,421 (+)NCBI
GRCm381196,271,330 - 96,276,595 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1196,271,457 - 96,276,595 (+)EnsemblGRCm38mm10GRCm38
MGSCv371196,132,644 - 96,137,909 (+)NCBIGRCm37mm9NCBIm37
MGSCv361196,087,599 - 96,091,975 (+)NCBImm8
Celera11105,922,380 - 105,927,645 (+)NCBICelera
Cytogenetic Map11DNCBI
cM Map1159.81NCBI
Hoxb9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01084,119,772 - 84,124,963 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1084,119,884 - 84,123,390 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01083,922,929 - 83,926,435 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41085,002,254 - 85,005,760 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11085,016,590 - 85,020,992 (+)NCBI
Celera1080,003,380 - 80,054,023 (+)NCBICelera
Cytogenetic Map10q26NCBI
Hoxb9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495545112,616,465 - 12,616,926 (+)NCBIChiLan1.0ChiLan1.0
HOXB9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1179,095,438 - 9,100,755 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl179,095,438 - 9,100,747 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0178,910,421 - 8,916,128 (+)NCBIMhudiblu_PPA_v0panPan3
HOXB9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl924,872,950 - 24,889,376 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1924,884,101 - 24,889,904 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Hoxb9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493649012,761,668 - 12,765,658 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HOXB9
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl1669,035,701 - 69,039,069 (-)Ensembl
ChlSab1.11669,027,926 - 69,047,020 (-)NCBI
Hoxb9
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247955,118,483 - 5,123,294 (-)NCBI

Position Markers
RH104186  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371746,698,635 - 46,698,761UniSTSGRCh37
Build 361744,053,634 - 44,053,760RGDNCBI36
Celera1743,152,798 - 43,152,924RGD
Cytogenetic Map17q21.3UniSTS
HuRef1742,067,513 - 42,067,639UniSTS
GeneMap99-GB4 RH Map17338.99UniSTS
HOXB9_997  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371746,698,499 - 46,699,355UniSTSGRCh37
Build 361744,053,498 - 44,054,354RGDNCBI36
Celera1743,152,662 - 43,153,518RGD
HuRef1742,067,377 - 42,068,233UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1889
Count of miRNA genes:739
Interacting mature miRNAs:868
Transcripts:ENST00000311177, ENST00000550387
Prediction methods:Microtar, Miranda, Pita, Rnahybrid, Targetscan
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


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system adipose tissue appendage entire extraembryonic component
High
Medium 592 26 15 175 17 63 23 38 233 158 119 5 1
Low 376 46 210 30 456 32 718 35 440 146 867 147 4 618 350 1
Below cutoff 974 2005 895 252 927 150 3249 1435 1637 38 379 907 102 583 2231

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_024017 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC103702 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AH010085 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK026084 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK056123 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK056414 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK315480 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC015565 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BF305592 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX114117 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CA426693 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471109 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DA696753 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DA712230 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KT585248 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  LC466645 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X16172 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000311177   ⟹   ENSP00000309439
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1748,621,156 - 48,626,358 (-)Ensembl
RefSeq Acc Id: NM_024017   ⟹   NP_076922
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381748,621,156 - 48,626,358 (-)NCBI
GRCh371746,698,518 - 46,703,835 (-)ENTREZGENE
Build 361744,053,517 - 44,058,834 (-)NCBI Archive
HuRef1742,067,396 - 42,072,713 (-)ENTREZGENE
CHM1_11746,764,512 - 46,769,829 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_076922   ⟸   NM_024017
- UniProtKB: P17482 (UniProtKB/Swiss-Prot),   B3KPJ1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000309439   ⟸   ENST00000311177
Protein Domains
Hox9_act

Promoters
RGD ID:6811200
Promoter ID:HG_ACW:35113
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:K562
Transcripts:HOXB9.BAPR07-UNSPLICED
Position:
Human AssemblyChrPosition (strand)Source
Build 361744,055,861 - 44,056,361 (-)MPROMDB
RGD ID:6794213
Promoter ID:HG_KWN:26502
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   HeLa_S3,   K562,   Lymphoblastoid,   NB4
Transcripts:NM_024017
Position:
Human AssemblyChrPosition (strand)Source
Build 361744,058,356 - 44,059,112 (-)MPROMDB
RGD ID:7235519
Promoter ID:EPDNEW_H23505
Type:initiation region
Name:HOXB9_2
Description:homeobox B9
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H23506  EPDNEW_H23507  EPDNEW_H23509  EPDNEW_H23508  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381748,625,863 - 48,625,923EPDNEW
RGD ID:7235521
Promoter ID:EPDNEW_H23506
Type:initiation region
Name:HOXB9_1
Description:homeobox B9
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H23505  EPDNEW_H23507  EPDNEW_H23509  EPDNEW_H23508  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381748,626,340 - 48,626,400EPDNEW
RGD ID:7235523
Promoter ID:EPDNEW_H23507
Type:initiation region
Name:HOXB9_5
Description:homeobox B9
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H23505  EPDNEW_H23506  EPDNEW_H23509  EPDNEW_H23508  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381748,631,227 - 48,631,287EPDNEW
RGD ID:7235529
Promoter ID:EPDNEW_H23508
Type:initiation region
Name:HOXB9_4
Description:homeobox B9
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H23505  EPDNEW_H23506  EPDNEW_H23507  EPDNEW_H23509  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381748,633,581 - 48,633,641EPDNEW

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 17q21.33-24.2(chr17:36449220-68170214)x3 copy number gain See cases [RCV000050957] Chr17:36449220..68170214 [GRCh38]
Chr17:48563237..65936105 [GRCh37]
Chr17:45918236..63677950 [NCBI36]
Chr17:17q21.33-24.2
pathogenic
GRCh38/hg38 17q23.2-25.3(chr17:36449220-83086677)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052483]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052483]|See cases [RCV000052483] Chr17:36449220..83086677 [GRCh38]
Chr17:58617905..81044553 [GRCh37]
Chr17:55972687..78637842 [NCBI36]
Chr17:17q23.2-25.3
pathogenic
GRCh38/hg38 17q21.31-21.33(chr17:44955325-49381173)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052480]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052480]|See cases [RCV000052480] Chr17:44955325..49381173 [GRCh38]
Chr17:43032693..47458535 [GRCh37]
Chr17:40388219..44813534 [NCBI36]
Chr17:17q21.31-21.33
pathogenic
GRCh38/hg38 17q21.32-21.33(chr17:48520885-49511208)x1 copy number loss See cases [RCV000053431] Chr17:48520885..49511208 [GRCh38]
Chr17:46598247..47588570 [GRCh37]
Chr17:43953246..44943569 [NCBI36]
Chr17:17q21.32-21.33
pathogenic
GRCh38/hg38 17q21.32-21.33(chr17:47986886-49329397)x1 copy number loss See cases [RCV000142900] Chr17:47986886..49329397 [GRCh38]
Chr17:46064252..47406759 [GRCh37]
Chr17:43419251..44761758 [NCBI36]
Chr17:17q21.32-21.33
pathogenic
GRCh38/hg38 17q21.32-21.33(chr17:48450628-49552921)x3 copy number gain See cases [RCV000143451] Chr17:48450628..49552921 [GRCh38]
Chr17:46527990..47630283 [GRCh37]
Chr17:43882989..44985282 [NCBI36]
Chr17:17q21.32-21.33
uncertain significance
GRCh38/hg38 17q23.1-25.1(chr17:36449220-75053130)x3 copy number gain See cases [RCV000137437] Chr17:36449220..75053130 [GRCh38]
Chr17:57595736..73049225 [GRCh37]
Chr17:54950518..70560820 [NCBI36]
Chr17:17q23.1-25.1
pathogenic
GRCh37/hg19 17q21.31-25.3(chr17:42580684-81085615)x3 copy number gain See cases [RCV000447823] Chr17:42580684..81085615 [GRCh37]
Chr17:17q21.31-25.3
pathogenic
GRCh37/hg19 17p13.3-q25.3(chr17:526-81041938) copy number gain See cases [RCV000511439] Chr17:526..81041938 [GRCh37]
Chr17:17p13.3-q25.3
pathogenic
GRCh37/hg19 17q21.32-22(chr17:46481089-51396368)x1 copy number loss not provided [RCV000513510] Chr17:46481089..51396368 [GRCh37]
Chr17:17q21.32-22
likely pathogenic
GRCh37/hg19 17p13.3-q25.3(chr17:526-81041938)x3 copy number gain See cases [RCV000512441] Chr17:526..81041938 [GRCh37]
Chr17:17p13.3-q25.3
pathogenic
GRCh37/hg19 17p13.3-q25.3(chr17:8547-81060040)x3 copy number gain not provided [RCV000739324] Chr17:8547..81060040 [GRCh37]
Chr17:17p13.3-q25.3
pathogenic
GRCh37/hg19 17p13.3-q25.3(chr17:7214-81058310)x3 copy number gain not provided [RCV000739320] Chr17:7214..81058310 [GRCh37]
Chr17:17p13.3-q25.3
pathogenic
GRCh37/hg19 17p13.3-q25.3(chr17:12344-81057996)x3 copy number gain not provided [RCV000739325] Chr17:12344..81057996 [GRCh37]
Chr17:17p13.3-q25.3
pathogenic
NM_024017.5(HOXB9):c.466G>A (p.Gly156Arg) single nucleotide variant not provided [RCV000904522] Chr17:48625804 [GRCh38]
Chr17:46703166 [GRCh37]
Chr17:17q21.32
likely benign
NM_024017.5(HOXB9):c.232T>C (p.Tyr78His) single nucleotide variant not provided [RCV000967876] Chr17:48626038 [GRCh38]
Chr17:46703400 [GRCh37]
Chr17:17q21.32
benign
NM_024017.5(HOXB9):c.663C>T (p.Leu221=) single nucleotide variant not provided [RCV000967778] Chr17:48622990 [GRCh38]
Chr17:46700352 [GRCh37]
Chr17:17q21.32
benign

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:5120 AgrOrtholog
COSMIC HOXB9 COSMIC
Ensembl Genes ENSG00000170689 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSP00000309439 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000311177 ENTREZGENE, UniProtKB/Swiss-Prot
GTEx ENSG00000170689 GTEx
HGNC ID HGNC:5120 ENTREZGENE
Human Proteome Map HOXB9 Human Proteome Map
InterPro Homeobox-like_sf UniProtKB/Swiss-Prot
  Homeobox_CS UniProtKB/Swiss-Prot
  Homeobox_dom UniProtKB/Swiss-Prot
  Homeobox_metazoa UniProtKB/Swiss-Prot
  Hox9_activation_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HXA9/HXB9/HXC9 UniProtKB/Swiss-Prot
KEGG Report hsa:3219 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 3219 ENTREZGENE
OMIM 142964 OMIM
Pfam Homeodomain UniProtKB/Swiss-Prot
  Hox9_act UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA29396 PharmGKB
PIRSF Homeobox_Hox9 UniProtKB/Swiss-Prot
PRINTS HOMEOBOX UniProtKB/Swiss-Prot
PROSITE HOMEOBOX_1 UniProtKB/Swiss-Prot
  HOMEOBOX_2 UniProtKB/Swiss-Prot
SMART HOX UniProtKB/Swiss-Prot
Superfamily-SCOP SSF46689 UniProtKB/Swiss-Prot
UniGene Hs.463350 ENTREZGENE
UniProt B3KPJ1 ENTREZGENE, UniProtKB/TrEMBL
  HXB9_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary B2RDB7 UniProtKB/Swiss-Prot
  Q9H1I1 UniProtKB/Swiss-Prot