HOXA1 (homeobox A1) - Rat Genome Database

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Gene: HOXA1 (homeobox A1) Homo sapiens
Analyze
Symbol: HOXA1
Name: homeobox A1
RGD ID: 737614
HGNC Page HGNC
Description: Enables DNA-binding transcription activator activity, RNA polymerase II-specific; identical protein binding activity; and sequence-specific double-stranded DNA binding activity. Involved in several processes, including abducens nerve formation; embryonic organ morphogenesis; and optokinetic behavior. Predicted to be part of chromatin. Predicted to be active in nucleus. Implicated in Athabaskan brainstem dysgenesis syndrome and autistic disorder.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: BSAS; homeo box A1; homeobox 1F; homeobox protein Hox-1F; homeobox protein Hox-A1; Hox 1.6-like protein; HOX A1 homeodomain protein; HOX1; HOX1F; lab-like protein; MGC45232
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl727,092,993 - 27,096,000 (-)EnsemblGRCh38hg38GRCh38
GRCh38727,092,993 - 27,096,000 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37727,132,612 - 27,135,619 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36727,099,137 - 27,102,150 (-)NCBINCBI36hg18NCBI36
Build 34726,905,855 - 26,908,834NCBI
Celera727,121,549 - 27,124,562 (-)NCBI
Cytogenetic Map7p15.2NCBI
HuRef727,013,203 - 27,016,216 (-)NCBIHuRef
CHM1_1727,132,309 - 27,135,322 (-)NCBICHM1_1
CRA_TCAGchr7v2727,183,765 - 27,186,778 (-)NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-anisomycin  (ISO)
(-)-demecolcine  (EXP)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-amino-2-deoxy-D-glucopyranose  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-nonylphenol  (ISO)
5-azacytidine  (EXP)
5-fluorouracil  (EXP)
6-bromoindirubin-3'-oxime  (ISO)
aflatoxin B1  (EXP)
aldehydo-D-glucosamine  (ISO)
alendronic acid  (ISO)
all-trans-retinoic acid  (EXP,ISO)
all-trans-retinol  (ISO)
ammonium chloride  (ISO)
aristolochic acid  (EXP)
benzo[a]pyrene  (EXP)
beta-D-glucosamine  (ISO)
beta-naphthoflavone  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bucladesine  (EXP)
butylated hydroxyanisole  (ISO)
cadmium dichloride  (EXP)
camptothecin  (EXP,ISO)
carbamazepine  (EXP)
carbon nanotube  (ISO)
chloroprene  (ISO)
citral  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
cyclophosphamide  (EXP)
D-gluconic acid  (ISO)
decabromodiphenyl ether  (ISO)
deoxycholic acid  (ISO)
dibutyl phthalate  (ISO)
diethylstilbestrol  (ISO)
dimethylarsinic acid  (ISO)
dioxygen  (ISO)
dipentyl phthalate  (ISO)
disulfiram  (ISO)
dorsomorphin  (EXP)
endosulfan  (ISO)
entinostat  (EXP)
ethanol  (ISO)
flusilazole  (ISO)
folic acid  (ISO)
formaldehyde  (EXP)
genistein  (ISO)
geranial  (ISO)
hexaconazole  (ISO)
hydrogen peroxide  (EXP)
LY294002  (ISO)
medroxyprogesterone acetate  (EXP)
methylisothiazolinone  (EXP)
N-nitrosodiethylamine  (ISO)
nickel sulfate  (EXP)
niclosamide  (ISO)
nitrofen  (ISO)
panobinostat  (EXP)
paracetamol  (EXP)
paraquat  (ISO)
pirinixic acid  (ISO)
raloxifene  (ISO)
resveratrol  (EXP)
SB 431542  (EXP)
silicon dioxide  (ISO)
testosterone  (ISO)
titanium dioxide  (ISO)
triadimefon  (ISO)
triclosan  (EXP)
triptonide  (ISO)
valproic acid  (EXP,ISO)
WIN 18446  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
chromatin  (ISA)
nucleus  (IBA,IEA)

References

Additional References at PubMed
PMID:1973146   PMID:7488013   PMID:7622051   PMID:8646877   PMID:9463349   PMID:9582372   PMID:10529419   PMID:11070089   PMID:11091361   PMID:11840501   PMID:11857506   PMID:12210285  
PMID:12349873   PMID:12477932   PMID:12482855   PMID:12690205   PMID:12853948   PMID:12908836   PMID:15489334   PMID:15665309   PMID:16155570   PMID:16168961   PMID:16189514   PMID:16344560  
PMID:16373333   PMID:16528738   PMID:16597639   PMID:17131398   PMID:17167333   PMID:17171652   PMID:17213808   PMID:17967182   PMID:18276758   PMID:18482256   PMID:19018235   PMID:19018953  
PMID:19086053   PMID:19274049   PMID:19336002   PMID:19598235   PMID:20227628   PMID:20678259   PMID:21106538   PMID:21516116   PMID:21653829   PMID:21873635   PMID:21957483   PMID:21980499  
PMID:21988832   PMID:22020899   PMID:22407312   PMID:22498108   PMID:22864671   PMID:22950449   PMID:23088713   PMID:23321646   PMID:23332764   PMID:23435427   PMID:23455924   PMID:24312487  
PMID:24559685   PMID:24789793   PMID:24878468   PMID:25069511   PMID:25148682   PMID:25416956   PMID:25472883   PMID:25691658   PMID:25910212   PMID:26135141   PMID:26186194   PMID:26417931  
PMID:26496426   PMID:26707824   PMID:26791264   PMID:26812882   PMID:27382069   PMID:27992364   PMID:28473536   PMID:28514442   PMID:28540746   PMID:28657121   PMID:29137689   PMID:29164581  
PMID:29180619   PMID:29465778   PMID:29658571   PMID:29662483   PMID:29693150   PMID:29698677   PMID:29892012   PMID:30376874   PMID:30628697   PMID:30886144   PMID:31114990   PMID:31138758  
PMID:31210292   PMID:31325426   PMID:31391242   PMID:31515488   PMID:32013856   PMID:32296183   PMID:32497022   PMID:32814053   PMID:33048872   PMID:33328510  


Genomics

Comparative Map Data
HOXA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl727,092,993 - 27,096,000 (-)EnsemblGRCh38hg38GRCh38
GRCh38727,092,993 - 27,096,000 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37727,132,612 - 27,135,619 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36727,099,137 - 27,102,150 (-)NCBINCBI36hg18NCBI36
Build 34726,905,855 - 26,908,834NCBI
Celera727,121,549 - 27,124,562 (-)NCBI
Cytogenetic Map7p15.2NCBI
HuRef727,013,203 - 27,016,216 (-)NCBIHuRef
CHM1_1727,132,309 - 27,135,322 (-)NCBICHM1_1
CRA_TCAGchr7v2727,183,765 - 27,186,778 (-)NCBI
Hoxa1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39652,132,347 - 52,135,297 (-)NCBIGRCm39mm39
GRCm39 Ensembl652,132,570 - 52,135,297 (-)Ensembl
GRCm38652,155,367 - 52,160,007 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl652,155,590 - 52,158,317 (-)EnsemblGRCm38mm10GRCm38
MGSCv37652,105,366 - 52,108,316 (-)NCBIGRCm37mm9NCBIm37
MGSCv36652,084,950 - 52,087,900 (-)NCBImm8
Celera652,677,008 - 52,679,958 (-)NCBICelera
Cytogenetic Map6B3NCBI
cM Map625.4NCBI
Hoxa1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2481,255,814 - 81,258,504 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl481,255,883 - 81,258,504 (-)Ensembl
Rnor_6.0482,124,358 - 82,127,182 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl482,125,406 - 82,127,066 (-)EnsemblRnor6.0rn6Rnor6.0
Celera476,147,124 - 76,149,948 (-)NCBICelera
Cytogenetic Map4q24NCBI
Hoxa1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541028,787,817 - 28,790,962 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541028,788,245 - 28,790,971 (-)NCBIChiLan1.0ChiLan1.0
HOXA1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1727,336,737 - 27,339,747 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl727,335,710 - 27,339,747 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0727,737,432 - 27,740,442 (-)NCBIMhudiblu_PPA_v0panPan3
HOXA1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11440,267,033 - 40,272,212 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1440,267,528 - 40,269,681 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1439,698,088 - 39,703,711 (-)NCBI
ROS_Cfam_1.01440,205,795 - 40,211,418 (-)NCBI
UMICH_Zoey_3.11440,319,907 - 40,325,530 (-)NCBI
UNSW_CanFamBas_1.01440,004,976 - 40,010,599 (-)NCBI
UU_Cfam_GSD_1.01440,363,561 - 40,369,177 (-)NCBI
Hoxa1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511884,509,768 - 84,512,994 (-)NCBI
SpeTri2.0NW_0049364783,721,662 - 3,724,471 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HOXA1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1845,477,548 - 45,480,413 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11845,477,561 - 45,480,306 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21850,110,695 - 50,113,440 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HOXA1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12131,272,410 - 31,275,503 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2131,272,889 - 31,275,551 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604273,458,340 - 73,461,050 (-)NCBIVero_WHO_p1.0
Hoxa1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247393,509,020 - 3,511,890 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
SHGC-35668  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,134,637 - 27,134,837UniSTSGRCh37
Build 36727,101,162 - 27,101,362RGDNCBI36
Celera727,123,574 - 27,123,774RGD
Cytogenetic Map7p15.3UniSTS
Cytogenetic Map7p15.2UniSTS
HuRef727,015,228 - 27,015,428UniSTS
CRA_TCAGchr7v2727,185,790 - 27,185,990UniSTS
TNG Radiation Hybrid Map712769.0UniSTS
Stanford-G3 RH Map71122.0UniSTS
GeneMap99-GB4 RH Map7117.57UniSTS
Whitehead-RH Map775.6UniSTS
NCBI RH Map7448.7UniSTS
GeneMap99-G3 RH Map71122.0UniSTS
HOXA1__1199  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,132,709 - 27,133,558UniSTSGRCh37
Build 36727,099,234 - 27,100,083RGDNCBI36
Celera727,121,646 - 27,122,495RGD
HuRef727,013,300 - 27,014,149UniSTS
CRA_TCAGchr7v2727,183,862 - 27,184,711UniSTS
ECD00702  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,133,467 - 27,134,360UniSTSGRCh37
Build 36727,099,992 - 27,100,885RGDNCBI36
Celera727,122,404 - 27,123,297RGD
Cytogenetic Map7p15.3UniSTS
HuRef727,014,058 - 27,014,951UniSTS
CRA_TCAGchr7v2727,184,620 - 27,185,513UniSTS
ECD00936  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,134,388 - 27,135,272UniSTSGRCh37
Build 36727,100,913 - 27,101,797RGDNCBI36
Celera727,123,325 - 27,124,209RGD
Cytogenetic Map7p15.2UniSTS
Cytogenetic Map7p15.3UniSTS
HuRef727,014,979 - 27,015,863UniSTS
CRA_TCAGchr7v2727,185,541 - 27,186,425UniSTS
ECD02348  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,132,575 - 27,133,408UniSTSGRCh37
Build 36727,099,100 - 27,099,933RGDNCBI36
Celera727,121,512 - 27,122,345RGD
Cytogenetic Map7p15.3UniSTS
HuRef727,013,166 - 27,013,999UniSTS
CRA_TCAGchr7v2727,183,728 - 27,184,561UniSTS
ECD02529  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,136,247 - 27,137,074UniSTSGRCh37
Build 36727,102,772 - 27,103,599RGDNCBI36
Celera727,125,184 - 27,126,011RGD
Cytogenetic Map7p15.2UniSTS
Cytogenetic Map7p15.3UniSTS
HuRef727,016,838 - 27,017,665UniSTS
CRA_TCAGchr7v2727,187,400 - 27,188,227UniSTS
ECD03147  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,135,411 - 27,136,215UniSTSGRCh37
Build 36727,101,936 - 27,102,740RGDNCBI36
Celera727,124,348 - 27,125,152RGD
Cytogenetic Map7p15.2UniSTS
Cytogenetic Map7p15.3UniSTS
HuRef727,016,002 - 27,016,806UniSTS
CRA_TCAGchr7v2727,186,564 - 27,187,368UniSTS
REN100295  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,132,336 - 27,132,590UniSTSGRCh37
Build 36727,098,861 - 27,099,115RGDNCBI36
Celera727,121,273 - 27,121,527RGD
Cytogenetic Map7p15.3UniSTS
HuRef727,012,927 - 27,013,181UniSTS
CRA_TCAGchr7v2727,183,489 - 27,183,743UniSTS
REN100296  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,132,578 - 27,132,828UniSTSGRCh37
Build 36727,099,103 - 27,099,353RGDNCBI36
Celera727,121,515 - 27,121,765RGD
Cytogenetic Map7p15.3UniSTS
HuRef727,013,169 - 27,013,419UniSTS
CRA_TCAGchr7v2727,183,731 - 27,183,981UniSTS
REN100297  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,132,827 - 27,133,090UniSTSGRCh37
Build 36727,099,352 - 27,099,615RGDNCBI36
Celera727,121,764 - 27,122,027RGD
Cytogenetic Map7p15.3UniSTS
HuRef727,013,418 - 27,013,681UniSTS
CRA_TCAGchr7v2727,183,980 - 27,184,243UniSTS
REN100298  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,133,079 - 27,133,329UniSTSGRCh37
Build 36727,099,604 - 27,099,854RGDNCBI36
Celera727,122,016 - 27,122,266RGD
Cytogenetic Map7p15.3UniSTS
HuRef727,013,670 - 27,013,920UniSTS
CRA_TCAGchr7v2727,184,232 - 27,184,482UniSTS
REN100299  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,133,306 - 27,133,567UniSTSGRCh37
Build 36727,099,831 - 27,100,092RGDNCBI36
Celera727,122,243 - 27,122,504RGD
Cytogenetic Map7p15.3UniSTS
HuRef727,013,897 - 27,014,158UniSTS
CRA_TCAGchr7v2727,184,459 - 27,184,720UniSTS
REN100300  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,133,552 - 27,133,823UniSTSGRCh37
Build 36727,100,077 - 27,100,348RGDNCBI36
Celera727,122,489 - 27,122,760RGD
Cytogenetic Map7p15.3UniSTS
HuRef727,014,143 - 27,014,414UniSTS
CRA_TCAGchr7v2727,184,705 - 27,184,976UniSTS
REN100301  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,133,819 - 27,134,082UniSTSGRCh37
Build 36727,100,344 - 27,100,607RGDNCBI36
Celera727,122,756 - 27,123,019RGD
Cytogenetic Map7p15.3UniSTS
HuRef727,014,410 - 27,014,673UniSTS
CRA_TCAGchr7v2727,184,972 - 27,185,235UniSTS
REN100302  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,134,064 - 27,134,335UniSTSGRCh37
Build 36727,100,589 - 27,100,860RGDNCBI36
Celera727,123,001 - 27,123,272RGD
Cytogenetic Map7p15.2UniSTS
Cytogenetic Map7p15.3UniSTS
HuRef727,014,655 - 27,014,926UniSTS
CRA_TCAGchr7v2727,185,217 - 27,185,488UniSTS
REN100303  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,134,316 - 27,134,570UniSTSGRCh37
Build 36727,100,841 - 27,101,095RGDNCBI36
Celera727,123,253 - 27,123,507RGD
Cytogenetic Map7p15.2UniSTS
Cytogenetic Map7p15.3UniSTS
HuRef727,014,907 - 27,015,161UniSTS
CRA_TCAGchr7v2727,185,469 - 27,185,723UniSTS
REN100304  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,134,555 - 27,134,782UniSTSGRCh37
Build 36727,101,080 - 27,101,307RGDNCBI36
Celera727,123,492 - 27,123,719RGD
Cytogenetic Map7p15.2UniSTS
Cytogenetic Map7p15.3UniSTS
HuRef727,015,146 - 27,015,373UniSTS
CRA_TCAGchr7v2727,185,708 - 27,185,935UniSTS
REN100305  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,134,744 - 27,135,004UniSTSGRCh37
Build 36727,101,269 - 27,101,529RGDNCBI36
Celera727,123,681 - 27,123,941RGD
Cytogenetic Map7p15.2UniSTS
Cytogenetic Map7p15.3UniSTS
HuRef727,015,335 - 27,015,595UniSTS
CRA_TCAGchr7v2727,185,897 - 27,186,157UniSTS
REN100306  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,134,981 - 27,135,242UniSTSGRCh37
Build 36727,101,506 - 27,101,767RGDNCBI36
Celera727,123,918 - 27,124,179RGD
Cytogenetic Map7p15.2UniSTS
Cytogenetic Map7p15.3UniSTS
HuRef727,015,572 - 27,015,833UniSTS
CRA_TCAGchr7v2727,186,134 - 27,186,395UniSTS
REN100307  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,135,235 - 27,135,466UniSTSGRCh37
Build 36727,101,760 - 27,101,991RGDNCBI36
Celera727,124,172 - 27,124,403RGD
Cytogenetic Map7p15.2UniSTS
Cytogenetic Map7p15.3UniSTS
HuRef727,015,826 - 27,016,057UniSTS
CRA_TCAGchr7v2727,186,388 - 27,186,619UniSTS
REN100308  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,135,412 - 27,135,638UniSTSGRCh37
Build 36727,101,937 - 27,102,163RGDNCBI36
Celera727,124,349 - 27,124,575RGD
Cytogenetic Map7p15.2UniSTS
Cytogenetic Map7p15.3UniSTS
HuRef727,016,003 - 27,016,229UniSTS
CRA_TCAGchr7v2727,186,565 - 27,186,791UniSTS
REN100309  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,135,621 - 27,135,891UniSTSGRCh37
Build 36727,102,146 - 27,102,416RGDNCBI36
Celera727,124,558 - 27,124,828RGD
Cytogenetic Map7p15.2UniSTS
Cytogenetic Map7p15.3UniSTS
HuRef727,016,212 - 27,016,482UniSTS
CRA_TCAGchr7v2727,186,774 - 27,187,044UniSTS
REN100310  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,135,839 - 27,136,065UniSTSGRCh37
Build 36727,102,364 - 27,102,590RGDNCBI36
Celera727,124,776 - 27,125,002RGD
Cytogenetic Map7p15.2UniSTS
Cytogenetic Map7p15.3UniSTS
HuRef727,016,430 - 27,016,656UniSTS
CRA_TCAGchr7v2727,186,992 - 27,187,218UniSTS
REN100311  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,136,044 - 27,136,268UniSTSGRCh37
Build 36727,102,569 - 27,102,793RGDNCBI36
Celera727,124,981 - 27,125,205RGD
Cytogenetic Map7p15.2UniSTS
Cytogenetic Map7p15.3UniSTS
HuRef727,016,635 - 27,016,859UniSTS
CRA_TCAGchr7v2727,187,197 - 27,187,421UniSTS
REN100312  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,136,247 - 27,136,510UniSTSGRCh37
Build 36727,102,772 - 27,103,035RGDNCBI36
Celera727,125,184 - 27,125,447RGD
Cytogenetic Map7p15.2UniSTS
Cytogenetic Map7p15.3UniSTS
HuRef727,016,838 - 27,017,101UniSTS
CRA_TCAGchr7v2727,187,400 - 27,187,663UniSTS
REN100313  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,136,393 - 27,136,636UniSTSGRCh37
Build 36727,102,918 - 27,103,161RGDNCBI36
Celera727,125,330 - 27,125,573RGD
Cytogenetic Map7p15.2UniSTS
Cytogenetic Map7p15.3UniSTS
HuRef727,016,984 - 27,017,227UniSTS
CRA_TCAGchr7v2727,187,546 - 27,187,789UniSTS
REN100314  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,136,580 - 27,136,810UniSTSGRCh37
Build 36727,103,105 - 27,103,335RGDNCBI36
Celera727,125,517 - 27,125,747RGD
Cytogenetic Map7p15.2UniSTS
Cytogenetic Map7p15.3UniSTS
HuRef727,017,171 - 27,017,401UniSTS
CRA_TCAGchr7v2727,187,733 - 27,187,963UniSTS
REN100315  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,136,785 - 27,137,019UniSTSGRCh37
Build 36727,103,310 - 27,103,544RGDNCBI36
Celera727,125,722 - 27,125,956RGD
Cytogenetic Map7p15.2UniSTS
Cytogenetic Map7p15.3UniSTS
HuRef727,017,376 - 27,017,610UniSTS
CRA_TCAGchr7v2727,187,938 - 27,188,172UniSTS
REN100316  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,136,996 - 27,137,261UniSTSGRCh37
Build 36727,103,521 - 27,103,786RGDNCBI36
Celera727,125,933 - 27,126,198RGD
HuRef727,017,587 - 27,017,852UniSTS
CRA_TCAGchr7v2727,188,149 - 27,188,414UniSTS
REN100317  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,137,248 - 27,137,505UniSTSGRCh37
Build 36727,103,773 - 27,104,030RGDNCBI36
Celera727,126,185 - 27,126,442RGD
Cytogenetic Map7p15.2UniSTS
Cytogenetic Map7p15.3UniSTS
HuRef727,017,839 - 27,018,096UniSTS
CRA_TCAGchr7v2727,188,401 - 27,188,658UniSTS
STS-U10421  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,134,121 - 27,134,398UniSTSGRCh37
Build 36727,100,646 - 27,100,923RGDNCBI36
Celera727,123,058 - 27,123,335RGD
Cytogenetic Map7p15.2UniSTS
Cytogenetic Map7p15.3UniSTS
HuRef727,014,712 - 27,014,989UniSTS
CRA_TCAGchr7v2727,185,274 - 27,185,551UniSTS
GeneMap99-GB4 RH Map7117.36UniSTS
stSG609305  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,132,672 - 27,133,749UniSTSGRCh37
Build 36727,099,197 - 27,100,274RGDNCBI36
Celera727,121,609 - 27,122,686RGD
Cytogenetic Map7p15.3UniSTS
HuRef727,013,263 - 27,014,340UniSTS
CRA_TCAGchr7v2727,183,825 - 27,184,902UniSTS
stSG609307  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,135,111 - 27,136,177UniSTSGRCh37
Build 36727,101,636 - 27,102,702RGDNCBI36
Celera727,124,048 - 27,125,114RGD
HuRef727,015,702 - 27,016,768UniSTS
CRA_TCAGchr7v2727,186,264 - 27,187,330UniSTS
stSG609308  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,136,161 - 27,136,369UniSTSGRCh37
Build 36727,102,686 - 27,102,894RGDNCBI36
Celera727,125,098 - 27,125,306RGD
HuRef727,016,752 - 27,016,960UniSTS
CRA_TCAGchr7v2727,187,314 - 27,187,522UniSTS
stSG609309  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37727,136,385 - 27,137,560UniSTSGRCh37
Build 36727,102,910 - 27,104,085RGDNCBI36
Celera727,125,322 - 27,126,497RGD
HuRef727,016,976 - 27,018,151UniSTS
CRA_TCAGchr7v2727,187,538 - 27,188,713UniSTS
ha2793  
Human AssemblyChrPosition (strand)SourceJBrowse
HuRef3121,201,186 - 121,201,340UniSTS

miRNA Target Status

Confirmed Target Of
miRNA GeneMature miRNAMethod NameResult TypeData TypeSupport TypePMID
MIR10Ahsa-miR-10a-5pMirtarbaseexternal_infoLuciferase reporter assay//qRT-PCR//Western blot//Functional MTI16549775
MIR10Ahsa-miR-10a-5pTarbaseexternal_infoReporter GenePOSITIVE
MIR10Ahsa-miR-10a-5pMirecordsexternal_info{changed}NA16549775

Predicted Target Of
Summary Value
Count of predictions:1462
Count of miRNA genes:601
Interacting mature miRNAs:672
Transcripts:ENST00000343060, ENST00000355633
Prediction methods:Miranda, 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 22 7 4 49 5 44 9 3 43 56 58 6 1
Low 1689 886 255 46 988 49 3091 564 807 301 954 595 3 1033 1794 2
Below cutoff 721 1812 1312 482 822 353 1114 1430 1202 69 435 919 130 171 972 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NG_011813 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NG_033087 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_005522 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_153620 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC004079 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK308067 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK313514 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC032547 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH236948 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471073 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DB246535 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FB571437 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FB571439 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KT584012 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  S79869 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  S79871 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  S79910 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U10421 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U37431 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000355633   ⟹   ENSP00000347851
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl727,093,313 - 27,095,996 (-)Ensembl
RefSeq Acc Id: ENST00000643460   ⟹   ENSP00000494260
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl727,092,993 - 27,096,000 (-)Ensembl
RefSeq Acc Id: NM_005522   ⟹   NP_005513
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38727,092,993 - 27,096,000 (-)NCBI
GRCh37727,132,612 - 27,135,625 (-)ENTREZGENE
Build 36727,099,137 - 27,102,150 (-)NCBI Archive
HuRef727,013,203 - 27,016,216 (-)ENTREZGENE
CHM1_1727,132,309 - 27,135,322 (-)NCBI
CRA_TCAGchr7v2727,183,765 - 27,186,778 (-)ENTREZGENE
Sequence:
RefSeq Acc Id: NM_153620   ⟹   NP_705873
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38727,092,993 - 27,096,000 (-)NCBI
GRCh37727,132,612 - 27,135,625 (-)ENTREZGENE
Build 36727,099,137 - 27,102,150 (-)NCBI Archive
HuRef727,013,203 - 27,016,216 (-)ENTREZGENE
CHM1_1727,132,309 - 27,135,322 (-)NCBI
CRA_TCAGchr7v2727,183,765 - 27,186,778 (-)ENTREZGENE
Sequence:
Reference Sequences
RefSeq Acc Id: NP_705873   ⟸   NM_153620
- Peptide Label: isoform b
- Sequence:
RefSeq Acc Id: NP_005513   ⟸   NM_005522
- Peptide Label: isoform a
- Sequence:
RefSeq Acc Id: ENSP00000494260   ⟸   ENST00000643460
RefSeq Acc Id: ENSP00000347851   ⟸   ENST00000355633
Protein Domains
Homeobox

Promoters
RGD ID:7210155
Promoter ID:EPDNEW_H10824
Type:initiation region
Name:HOXA1_1
Description:homeobox A1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H10829  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38727,095,988 - 27,096,048EPDNEW
RGD ID:6805787
Promoter ID:HG_KWN:56662
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   HeLa_S3,   K562,   Lymphoblastoid,   NB4
Transcripts:NM_153620,   OTTHUMT00000059528,   OTTHUMT00000137960,   OTTHUMT00000139958,   OTTHUMT00000206845
Position:
Human AssemblyChrPosition (strand)Source
Build 36727,102,246 - 27,103,032 (-)MPROMDB

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_005522.4(HOXA1):c.175dup (p.Val59fs) duplication Bosley-Salih-Alorainy syndrome [RCV000016027]|Human HOXA1 syndromes [RCV000984930]|not provided [RCV001008325] Chr7:27095737..27095738 [GRCh38]
Chr7:27135356..27135357 [GRCh37]
Chr7:7p15.2
pathogenic
NM_005522.4(HOXA1):c.84C>G (p.Tyr28Ter) single nucleotide variant Bosley-Salih-Alorainy syndrome [RCV000016028] Chr7:27095829 [GRCh38]
Chr7:27135448 [GRCh37]
Chr7:7p15.2
pathogenic
NM_005522.4(HOXA1):c.76C>T (p.Arg26Ter) single nucleotide variant Human HOXA1 syndromes [RCV000016029] Chr7:27095837 [GRCh38]
Chr7:27135456 [GRCh37]
Chr7:7p15.2
pathogenic
NM_005522.4(HOXA1):c.185del (p.Gly62fs) deletion Bosley-Salih-Alorainy syndrome [RCV000016030] Chr7:27095728 [GRCh38]
Chr7:27135347 [GRCh37]
Chr7:7p15.2
pathogenic
NM_005522.4(HOXA1):c.*1354C>A single nucleotide variant Lung cancer [RCV000105978] Chr7:27093086 [GRCh38]
Chr7:27132705 [GRCh37]
Chr7:7p15.2
uncertain significance
GRCh38/hg38 7p22.3-14.1(chr7:54185-41875885)x3 copy number gain See cases [RCV000051159] Chr7:54185..41875885 [GRCh38]
Chr7:54185..41915483 [GRCh37]
Chr7:149268..41882008 [NCBI36]
Chr7:7p22.3-14.1
pathogenic
GRCh38/hg38 7p22.3-q36.3(chr7:53985-159282531)x1 copy number loss See cases [RCV000052250] Chr7:53985..159282531 [GRCh38]
Chr7:53985..159075220 [GRCh37]
Chr7:149068..158767981 [NCBI36]
Chr7:7p22.3-q36.3
pathogenic
GRCh38/hg38 7p15.2-14.3(chr7:25511691-30421133)x1 copy number loss See cases [RCV000052310] Chr7:25511691..30421133 [GRCh38]
Chr7:25551310..30460749 [GRCh37]
Chr7:25517835..30427274 [NCBI36]
Chr7:7p15.2-14.3
pathogenic
GRCh38/hg38 7p22.3-14.2(chr7:54185-37089712)x3 copy number gain See cases [RCV000053530] Chr7:54185..37089712 [GRCh38]
Chr7:54185..37129317 [GRCh37]
Chr7:149268..37095842 [NCBI36]
Chr7:7p22.3-14.2
pathogenic
GRCh38/hg38 7p21.1-15.2(chr7:20210912-27849400)x1 copy number loss See cases [RCV000134333] Chr7:20210912..27849400 [GRCh38]
Chr7:20250535..27889019 [GRCh37]
Chr7:20217060..27855544 [NCBI36]
Chr7:7p21.1-15.2
pathogenic
GRCh38/hg38 7p22.3-q36.3(chr7:54185-159282390)x1 copy number loss See cases [RCV000135401] Chr7:54185..159282390 [GRCh38]
Chr7:54185..159075079 [GRCh37]
Chr7:149268..158767840 [NCBI36]
Chr7:7p22.3-q36.3
pathogenic
GRCh38/hg38 7p21.1-14.3(chr7:20561456-32005143)x1 copy number loss See cases [RCV000136775] Chr7:20561456..32005143 [GRCh38]
Chr7:20601079..32044755 [GRCh37]
Chr7:20567604..32011280 [NCBI36]
Chr7:7p21.1-14.3
pathogenic
GRCh38/hg38 7p22.1-15.2(chr7:5682209-27230311)x3 copy number gain See cases [RCV000136649] Chr7:5682209..27230311 [GRCh38]
Chr7:5721840..27269930 [GRCh37]
Chr7:5688366..27236455 [NCBI36]
Chr7:7p22.1-15.2
pathogenic
GRCh38/hg38 7p22.3-15.2(chr7:1698124-27207295)x3 copy number gain See cases [RCV000143060] Chr7:1698124..27207295 [GRCh38]
Chr7:1737760..27246914 [GRCh37]
Chr7:1704286..27213439 [NCBI36]
Chr7:7p22.3-15.2
pathogenic
GRCh38/hg38 7p22.3-15.2(chr7:43360-27196404)x3 copy number gain See cases [RCV000143586] Chr7:43360..27196404 [GRCh38]
Chr7:43360..27236023 [GRCh37]
Chr7:138443..27202548 [NCBI36]
Chr7:7p22.3-15.2
pathogenic
GRCh37/hg19 7p15.3-14.3(chr7:22935369-32621975)x1 copy number loss See cases [RCV000240125] Chr7:22935369..32621975 [GRCh37]
Chr7:7p15.3-14.3
pathogenic
NM_005522.4(HOXA1):c.*1387C>G single nucleotide variant Bosley-Salih-Alorainy syndrome [RCV000355207] Chr7:27093053 [GRCh38]
Chr7:27132672 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.4(HOXA1):c.215A>C (p.His72Pro) single nucleotide variant not provided [RCV000190288] Chr7:27095698 [GRCh38]
Chr7:27135317 [GRCh37]
Chr7:7p15.2
not provided
NM_005522.4(HOXA1):c.566A>C (p.Glu189Ala) single nucleotide variant Bosley-Salih-Alorainy syndrome [RCV000375444]|History of neurodevelopmental disorder [RCV000715563]|Intellectual disability [RCV001252526]|not provided [RCV000876173] Chr7:27095347 [GRCh38]
Chr7:27134966 [GRCh37]
Chr7:7p15.2
benign|likely benign|uncertain significance
NM_005522.4(HOXA1):c.653-12A>G single nucleotide variant Bosley-Salih-Alorainy syndrome [RCV000337108] Chr7:27094807 [GRCh38]
Chr7:27134426 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.4(HOXA1):c.207C>T (p.His69=) single nucleotide variant Bosley-Salih-Alorainy syndrome [RCV000330584]|History of neurodevelopmental disorder [RCV000719768] Chr7:27095706 [GRCh38]
Chr7:27135325 [GRCh37]
Chr7:7p15.2
benign|uncertain significance
NM_005522.4(HOXA1):c.194A>C (p.His65Pro) single nucleotide variant Bosley-Salih-Alorainy syndrome [RCV000395378] Chr7:27095719 [GRCh38]
Chr7:27135338 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.4(HOXA1):c.*1345T>C single nucleotide variant Bosley-Salih-Alorainy syndrome [RCV000315730] Chr7:27093095 [GRCh38]
Chr7:27132714 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.4(HOXA1):c.691G>A (p.Ala231Thr) single nucleotide variant Bosley-Salih-Alorainy syndrome [RCV000376412] Chr7:27094757 [GRCh38]
Chr7:27134376 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.4(HOXA1):c.*470T>A single nucleotide variant Bosley-Salih-Alorainy syndrome [RCV000393282] Chr7:27093970 [GRCh38]
Chr7:27133589 [GRCh37]
Chr7:7p15.2
likely benign
NM_005522.4(HOXA1):c.*181G>A single nucleotide variant Bosley-Salih-Alorainy syndrome [RCV000370526] Chr7:27094259 [GRCh38]
Chr7:27133878 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.4(HOXA1):c.*563G>C single nucleotide variant Bosley-Salih-Alorainy syndrome [RCV000345394] Chr7:27093877 [GRCh38]
Chr7:27133496 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.4(HOXA1):c.435C>T (p.His145=) single nucleotide variant Bosley-Salih-Alorainy syndrome [RCV000358903] Chr7:27095478 [GRCh38]
Chr7:27135097 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.4(HOXA1):c.*953G>A single nucleotide variant Bosley-Salih-Alorainy syndrome [RCV000294392] Chr7:27093487 [GRCh38]
Chr7:27133106 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.4(HOXA1):c.*183G>A single nucleotide variant Bosley-Salih-Alorainy syndrome [RCV000313446]|Human HOXA1 syndromes [RCV000399978] Chr7:27094257 [GRCh38]
Chr7:27133876 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.4(HOXA1):c.552C>A (p.His184Gln) single nucleotide variant Bosley-Salih-Alorainy syndrome [RCV000397766] Chr7:27095361 [GRCh38]
Chr7:27134980 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.4(HOXA1):c.196C>T (p.His66Tyr) single nucleotide variant Bosley-Salih-Alorainy syndrome [RCV000295370] Chr7:27095717 [GRCh38]
Chr7:27135336 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.4(HOXA1):c.*907A>G single nucleotide variant Bosley-Salih-Alorainy syndrome [RCV000385130] Chr7:27093533 [GRCh38]
Chr7:27133152 [GRCh37]
Chr7:7p15.2
likely benign
NM_005522.4(HOXA1):c.549C>A (p.Leu183=) single nucleotide variant Bosley-Salih-Alorainy syndrome [RCV000315076] Chr7:27095364 [GRCh38]
Chr7:27134983 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.4(HOXA1):c.*56C>A single nucleotide variant Bosley-Salih-Alorainy syndrome [RCV000312312] Chr7:27094384 [GRCh38]
Chr7:27134003 [GRCh37]
Chr7:7p15.2
likely benign
NM_005522.4(HOXA1):c.741G>A (p.Glu247=) single nucleotide variant Bosley-Salih-Alorainy syndrome [RCV000381953]|History of neurodevelopmental disorder [RCV000716259]|not provided [RCV000945714] Chr7:27094707 [GRCh38]
Chr7:27134326 [GRCh37]
Chr7:7p15.2
likely benign|uncertain significance
NM_005522.4(HOXA1):c.216T>C (p.His72=) single nucleotide variant Bosley-Salih-Alorainy syndrome [RCV000378582]|Human HOXA1 syndromes [RCV000260377] Chr7:27095697 [GRCh38]
Chr7:27135316 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.4(HOXA1):c.825C>T (p.Ile275=) single nucleotide variant Bosley-Salih-Alorainy syndrome [RCV000324988] Chr7:27094623 [GRCh38]
Chr7:27134242 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.4(HOXA1):c.684A>G (p.Gln228=) single nucleotide variant not provided [RCV000277241] Chr7:27094764 [GRCh38]
Chr7:27134383 [GRCh37]
Chr7:7p15.2
conflicting interpretations of pathogenicity|uncertain significance
NM_005522.4(HOXA1):c.255C>G (p.Asn85Lys) single nucleotide variant Bosley-Salih-Alorainy syndrome [RCV000264065] Chr7:27095658 [GRCh38]
Chr7:27135277 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.4(HOXA1):c.*1150C>T single nucleotide variant Bosley-Salih-Alorainy syndrome [RCV000276648] Chr7:27093290 [GRCh38]
Chr7:27132909 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.4(HOXA1):c.71C>T (p.Ser24Leu) single nucleotide variant Bosley-Salih-Alorainy syndrome [RCV000302146] Chr7:27095842 [GRCh38]
Chr7:27135461 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.4(HOXA1):c.213C>T (p.His71=) single nucleotide variant Bosley-Salih-Alorainy syndrome [RCV000315648]|History of neurodevelopmental disorder [RCV000715468]|Human HOXA1 syndromes [RCV000374937]|Microtia, hearing impairment, and cleft palate [RCV000309605] Chr7:27095700 [GRCh38]
Chr7:27135319 [GRCh37]
Chr7:7p15.2
benign|likely benign
NM_005522.4(HOXA1):c.165G>A (p.Val55=) single nucleotide variant Bosley-Salih-Alorainy syndrome [RCV000347061] Chr7:27095748 [GRCh38]
Chr7:27135367 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_006735.4(HOXA2):c.*108C>T single nucleotide variant Bosley-Salih-Alorainy syndrome [RCV000366672]|Human HOXA1 syndromes [RCV000403488]|Microtia, hearing impairment, and cleft palate [RCV000318797] Chr7:27100618 [GRCh38]
Chr7:27140237 [GRCh37]
Chr7:7p15.2
likely benign
NM_005522.4(HOXA1):c.216_218del (p.His74del) deletion Microtia, hearing impairment, and cleft palate [RCV000339913] Chr7:27095695..27095697 [GRCh38]
Chr7:27135314..27135316 [GRCh37]
Chr7:7p15.2
likely benign
NM_005522.4(HOXA1):c.546T>C (p.Pro182=) single nucleotide variant Bosley-Salih-Alorainy syndrome [RCV000399852] Chr7:27095367 [GRCh38]
Chr7:27134986 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.4(HOXA1):c.218= (p.His73=) single nucleotide variant Microtia, hearing impairment, and cleft palate [RCV000391664] Chr7:27095695 [GRCh38]
Chr7:27135314 [GRCh37]
Chr7:7p15.2
benign
NM_005522.4(HOXA1):c.436C>A (p.His146Asn) single nucleotide variant Bosley-Salih-Alorainy syndrome [RCV000362467]|History of neurodevelopmental disorder [RCV000715552]|Human HOXA1 syndromes [RCV000272482]|Microtia, hearing impairment, and cleft palate [RCV000287158] Chr7:27095477 [GRCh38]
Chr7:27135096 [GRCh37]
Chr7:7p15.2
benign|likely benign
NM_005522.4(HOXA1):c.*331C>A single nucleotide variant Bosley-Salih-Alorainy syndrome [RCV000393307] Chr7:27094109 [GRCh38]
Chr7:27133728 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.4(HOXA1):c.*250G>C single nucleotide variant Bosley-Salih-Alorainy syndrome [RCV000338685] Chr7:27094190 [GRCh38]
Chr7:27133809 [GRCh37]
Chr7:7p15.2
uncertain significance
TMEM106B-BRAF fusion deletion Pleomorphic xanthoastrocytoma [RCV000454357] Chr7:12258147..140494267 [GRCh37]
Chr7:7p21.3-q34
pathogenic
GRCh37/hg19 7p21.3-14.2(chr7:11562624-36395416)x3 copy number gain See cases [RCV000446478] Chr7:11562624..36395416 [GRCh37]
Chr7:7p21.3-14.2
pathogenic
GRCh37/hg19 7p22.3-q36.3(chr7:43360-159119707)x1 copy number loss See cases [RCV000446044] Chr7:43360..159119707 [GRCh37]
Chr7:7p22.3-q36.3
pathogenic
GRCh37/hg19 7p15.3-15.2(chr7:25448425-27578387)x3 copy number gain See cases [RCV000447735] Chr7:25448425..27578387 [GRCh37]
Chr7:7p15.3-15.2
likely pathogenic
GRCh37/hg19 7p21.3-12.1(chr7:11048840-52863626)x3 copy number gain See cases [RCV000512091] Chr7:11048840..52863626 [GRCh37]
Chr7:7p21.3-12.1
pathogenic
GRCh37/hg19 7p22.3-q36.3(chr7:43361-159119707) copy number gain See cases [RCV000510686] Chr7:43361..159119707 [GRCh37]
Chr7:7p22.3-q36.3
pathogenic
GRCh37/hg19 7p22.3-14.3(chr7:704573-29257946)x3 copy number gain See cases [RCV000510275] Chr7:704573..29257946 [GRCh37]
Chr7:7p22.3-14.3
pathogenic
GRCh37/hg19 7p15.3-14.3(chr7:24344104-28879357)x1 copy number loss See cases [RCV000510695] Chr7:24344104..28879357 [GRCh37]
Chr7:7p15.3-14.3
pathogenic
GRCh37/hg19 7p22.3-q36.3(chr7:43361-159119707)x3 copy number gain See cases [RCV000511549] Chr7:43361..159119707 [GRCh37]
Chr7:7p22.3-q36.3
pathogenic
NM_005522.5(HOXA1):c.192CCA[6] (p.His71_His72del) microsatellite History of neurodevelopmental disorder [RCV000717359] Chr7:27095698..27095703 [GRCh38]
Chr7:27135317..27135322 [GRCh37]
Chr7:7p15.2
likely benign
NM_005522.4(HOXA1):c.174G>C (p.Gly58=) single nucleotide variant History of neurodevelopmental disorder [RCV000715567]|Human HOXA1 syndromes [RCV001159079]|not provided [RCV000870852] Chr7:27095739 [GRCh38]
Chr7:27135358 [GRCh37]
Chr7:7p15.2
benign|likely benign
NM_005522.5(HOXA1):c.192CCA[11] (p.His70_His72dup) microsatellite History of neurodevelopmental disorder [RCV000715826] Chr7:27095697..27095698 [GRCh38]
Chr7:27135316..27135317 [GRCh37]
Chr7:7p15.2
likely benign
NM_005522.5(HOXA1):c.192CCA[7] (p.His72del) microsatellite History of neurodevelopmental disorder [RCV000716476]|not provided [RCV000841513] Chr7:27095698..27095700 [GRCh38]
Chr7:27135317..27135319 [GRCh37]
Chr7:7p15.2
likely benign
NM_005522.4(HOXA1):c.778G>A (p.Val260Met) single nucleotide variant History of neurodevelopmental disorder [RCV000717820] Chr7:27094670 [GRCh38]
Chr7:27134289 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.5(HOXA1):c.192CCA[5] (p.His70_His72del) microsatellite History of neurodevelopmental disorder [RCV000715785]|not provided [RCV000865447] Chr7:27095698..27095706 [GRCh38]
Chr7:27135317..27135325 [GRCh37]
Chr7:7p15.2
benign
NM_005522.5(HOXA1):c.192CCA[9] (p.His72dup) microsatellite History of neurodevelopmental disorder [RCV000715604]|not provided [RCV000870966] Chr7:27095697..27095698 [GRCh38]
Chr7:27135316..27135317 [GRCh37]
Chr7:7p15.2
benign|likely benign
NM_005522.5(HOXA1):c.192CCA[10] (p.His71_His72dup) microsatellite History of neurodevelopmental disorder [RCV000717901] Chr7:27095697..27095698 [GRCh38]
Chr7:27135316..27135317 [GRCh37]
Chr7:7p15.2
likely benign
NM_005522.4(HOXA1):c.714C>G (p.Thr238=) single nucleotide variant History of neurodevelopmental disorder [RCV000719198]|not provided [RCV000950342] Chr7:27094734 [GRCh38]
Chr7:27134353 [GRCh37]
Chr7:7p15.2
likely benign
NM_005522.4(HOXA1):c.248C>G (p.Ser83Cys) single nucleotide variant History of neurodevelopmental disorder [RCV000719680] Chr7:27095665 [GRCh38]
Chr7:27135284 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.4(HOXA1):c.957C>T (p.Cys319=) single nucleotide variant History of neurodevelopmental disorder [RCV000719797] Chr7:27094491 [GRCh38]
Chr7:27134110 [GRCh37]
Chr7:7p15.2
likely benign
NC_000007.13:g.(20954043_21001537)_(114528369_114556605)inv inversion Speech-language disorder 1 [RCV000234948] Chr7:21001537..114528369 [GRCh37]
Chr7:7p15.3-q31.1
pathogenic
GRCh37/hg19 7p22.3-q36.3(chr7:44935-159126310)x3 copy number gain not provided [RCV000746280] Chr7:44935..159126310 [GRCh37]
Chr7:7p22.3-q36.3
pathogenic
GRCh37/hg19 7p22.3-q36.3(chr7:10704-159122532)x3 copy number gain not provided [RCV000746278] Chr7:10704..159122532 [GRCh37]
Chr7:7p22.3-q36.3
pathogenic
GRCh37/hg19 7p15.2(chr7:27026872-27322106)x3 copy number gain not provided [RCV000746569] Chr7:27026872..27322106 [GRCh37]
Chr7:7p15.2
benign
GRCh37/hg19 7p15.2(chr7:27065705-27286796)x1 copy number loss not provided [RCV000746570] Chr7:27065705..27286796 [GRCh37]
Chr7:7p15.2
benign
GRCh37/hg19 7p15.2(chr7:27089764-27322106)x3 copy number gain not provided [RCV000746571] Chr7:27089764..27322106 [GRCh37]
Chr7:7p15.2
benign
GRCh37/hg19 7p15.2(chr7:27118974-27264337)x3 copy number gain not provided [RCV000746572] Chr7:27118974..27264337 [GRCh37]
Chr7:7p15.2
benign
GRCh37/hg19 7p15.2(chr7:27118974-27286796)x3 copy number gain not provided [RCV000746573] Chr7:27118974..27286796 [GRCh37]
Chr7:7p15.2
benign
GRCh37/hg19 7p15.2(chr7:27123880-27286796)x1 copy number loss not provided [RCV000746574] Chr7:27123880..27286796 [GRCh37]
Chr7:7p15.2
benign
GRCh37/hg19 7p15.2(chr7:27130276-27286796)x3 copy number gain not provided [RCV000746575] Chr7:27130276..27286796 [GRCh37]
Chr7:7p15.2
benign
GRCh37/hg19 7p15.2(chr7:27135314-27264337)x3 copy number gain not provided [RCV000746576] Chr7:27135314..27264337 [GRCh37]
Chr7:7p15.2
benign
GRCh37/hg19 7p15.2(chr7:27135314-27286796)x3 copy number gain not provided [RCV000746577] Chr7:27135314..27286796 [GRCh37]
Chr7:7p15.2
benign
NM_005522.5(HOXA1):c.676C>T (p.Leu226=) single nucleotide variant not provided [RCV000904550] Chr7:27094772 [GRCh38]
Chr7:27134391 [GRCh37]
Chr7:7p15.2
likely benign
GRCh37/hg19 7p22.3-q36.3(chr7:10365-159119707)x3 copy number gain not provided [RCV000848126] Chr7:10365..159119707 [GRCh37]
Chr7:7p22.3-q36.3
pathogenic
NM_005522.5(HOXA1):c.510C>T (p.Ser170=) single nucleotide variant not provided [RCV000876334] Chr7:27095403 [GRCh38]
Chr7:27135022 [GRCh37]
Chr7:7p15.2
likely benign
GRCh37/hg19 7p15.3-14.3(chr7:23877135-33139446)x1 copy number loss not provided [RCV001005924] Chr7:23877135..33139446 [GRCh37]
Chr7:7p15.3-14.3
pathogenic
NM_005522.5(HOXA1):c.218= (p.Arg73=) variation not provided [RCV000869481] Chr7:27095695 [GRCh38]
Chr7:27135314 [GRCh37]
Chr7:7p15.2
benign
NC_000007.13:g.23236782_30690453del7453672 deletion Silver Russell Syndrome-related disorder [RCV000785664] Chr7:23236782..30690453 [GRCh37]
Chr7:7p15.3-14.3
pathogenic
NM_005522.5(HOXA1):c.*1437A>G single nucleotide variant Human HOXA1 syndromes [RCV001163923] Chr7:27093003 [GRCh38]
Chr7:27132622 [GRCh37]
Chr7:7p15.2
likely benign
NM_005522.5(HOXA1):c.*1090C>T single nucleotide variant Human HOXA1 syndromes [RCV001158982] Chr7:27093350 [GRCh38]
Chr7:27132969 [GRCh37]
Chr7:7p15.2
benign
NM_005522.5(HOXA1):c.*820A>G single nucleotide variant Human HOXA1 syndromes [RCV001158985] Chr7:27093620 [GRCh38]
Chr7:27133239 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.5(HOXA1):c.*232G>A single nucleotide variant Human HOXA1 syndromes [RCV001160322] Chr7:27094208 [GRCh38]
Chr7:27133827 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.5(HOXA1):c.*183G>C single nucleotide variant Human HOXA1 syndromes [RCV001160323] Chr7:27094257 [GRCh38]
Chr7:27133876 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.5(HOXA1):c.215_223del (p.His72_His74del) deletion not provided [RCV001572891] Chr7:27095690..27095698 [GRCh38]
Chr7:27135309..27135317 [GRCh37]
Chr7:7p15.2
likely benign
NM_005522.5(HOXA1):c.*980C>G single nucleotide variant Human HOXA1 syndromes [RCV001158984] Chr7:27093460 [GRCh38]
Chr7:27133079 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.5(HOXA1):c.210C>T (p.His70=) single nucleotide variant Human HOXA1 syndromes [RCV001159078] Chr7:27095703 [GRCh38]
Chr7:27135322 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.5(HOXA1):c.813C>T (p.Thr271=) single nucleotide variant Human HOXA1 syndromes [RCV001161979] Chr7:27094635 [GRCh38]
Chr7:27134254 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.5(HOXA1):c.*337G>A single nucleotide variant Human HOXA1 syndromes [RCV001160320] Chr7:27094103 [GRCh38]
Chr7:27133722 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.5(HOXA1):c.*281C>G single nucleotide variant Human HOXA1 syndromes [RCV001160321] Chr7:27094159 [GRCh38]
Chr7:27133778 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.5(HOXA1):c.122C>T (p.Ala41Val) single nucleotide variant Human HOXA1 syndromes [RCV001160431] Chr7:27095791 [GRCh38]
Chr7:27135410 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.5(HOXA1):c.686C>A (p.Pro229His) single nucleotide variant Human HOXA1 syndromes [RCV001161980] Chr7:27094762 [GRCh38]
Chr7:27134381 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.5(HOXA1):c.*1058T>A single nucleotide variant Human HOXA1 syndromes [RCV001158983] Chr7:27093382 [GRCh38]
Chr7:27133001 [GRCh37]
Chr7:7p15.2
uncertain significance
NC_000007.14:g.27096002T>C single nucleotide variant Human HOXA1 syndromes [RCV001160436] Chr7:27096002 [GRCh38]
Chr7:27135621 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.5(HOXA1):c.294C>G (p.Ser98Arg) single nucleotide variant Human HOXA1 syndromes [RCV001163996] Chr7:27095619 [GRCh38]
Chr7:27135238 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.5(HOXA1):c.*345C>T single nucleotide variant Human HOXA1 syndromes [RCV001160319] Chr7:27094095 [GRCh38]
Chr7:27133714 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.5(HOXA1):c.63G>A (p.Gly21=) single nucleotide variant Human HOXA1 syndromes [RCV001160432] Chr7:27095850 [GRCh38]
Chr7:27135469 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.5(HOXA1):c.-26C>A single nucleotide variant Human HOXA1 syndromes [RCV001160433] Chr7:27095938 [GRCh38]
Chr7:27135557 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.5(HOXA1):c.-86C>A single nucleotide variant Human HOXA1 syndromes [RCV001160434] Chr7:27095998 [GRCh38]
Chr7:27135617 [GRCh37]
Chr7:7p15.2
uncertain significance
NC_000007.14:g.27096001A>G single nucleotide variant Human HOXA1 syndromes [RCV001160435] Chr7:27096001 [GRCh38]
Chr7:27135620 [GRCh37]
Chr7:7p15.2
uncertain significance
NM_005522.5(HOXA1):c.151G>C (p.Asp51His) single nucleotide variant Intellectual disability [RCV001252525] Chr7:27095762 [GRCh38]
Chr7:27135381 [GRCh37]
Chr7:7p15.2
likely benign
NM_005522.5(HOXA1):c.562C>A (p.Gln188Lys) single nucleotide variant Intellectual disability [RCV001252524] Chr7:27095351 [GRCh38]
Chr7:27134970 [GRCh37]
Chr7:7p15.2
likely benign
NM_005522.5(HOXA1):c.972del (p.Ser325fs) deletion Human HOXA1 syndromes [RCV001292600] Chr7:27094476 [GRCh38]
Chr7:27134095 [GRCh37]
Chr7:7p15.2
pathogenic
NM_005522.5(HOXA1):c.36C>G (p.Tyr12Ter) single nucleotide variant Human HOXA1 syndromes [RCV001292794] Chr7:27095877 [GRCh38]
Chr7:27135496 [GRCh37]
Chr7:7p15.2
pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:5099 AgrOrtholog
COSMIC HOXA1 COSMIC
Ensembl Genes ENSG00000105991 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSP00000347851 ENTREZGENE, UniProtKB/TrEMBL
  ENSP00000494260 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENST00000355633 ENTREZGENE, UniProtKB/TrEMBL
  ENST00000643460 ENTREZGENE, UniProtKB/TrEMBL
GTEx ENSG00000105991 GTEx
HGNC ID HGNC:5099 ENTREZGENE
Human Proteome Map HOXA1 Human Proteome Map
InterPro Homeobox-like_sf 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
KEGG Report hsa:3198 UniProtKB/Swiss-Prot
NCBI Gene 3198 ENTREZGENE
OMIM 142955 OMIM
  601536 OMIM
Pfam Homeodomain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA29376 PharmGKB
PRINTS HOMEOBOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE 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 A0A2R8Y4R9_HUMAN UniProtKB/TrEMBL
  A4D185_HUMAN UniProtKB/TrEMBL
  E7ERT8_HUMAN UniProtKB/TrEMBL
  HXA1_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary A4D184 UniProtKB/Swiss-Prot
  B2R8U7 UniProtKB/Swiss-Prot
  O43363 UniProtKB/Swiss-Prot