Barhl1 (BarH-like homeobox 1) - Rat Genome Database

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Gene: Barhl1 (BarH-like homeobox 1) Rattus norvegicus
Analyze
Symbol: Barhl1
Name: BarH-like homeobox 1
RGD ID: 620648
Description: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including negative regulation of outer hair cell apoptotic process; nervous system development; and sensory perception of sound. Predicted to be active in nucleus. Orthologous to human BARHL1 (BarH like homeobox 1); INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: bar-class homeodomain protein MBH2; BarH-like 1 (Drosophila); barH-like 1 homeobox protein; BarH-like 2; BarH-like 2 (Drosophila); barH-related homeobox protein 1; Barhl2; Mbh2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8332,639,283 - 32,646,605 (-)NCBIGRCr8
mRatBN7.2312,241,327 - 12,248,649 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl312,241,327 - 12,248,649 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx315,314,424 - 15,321,756 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0323,899,395 - 23,906,727 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0322,153,843 - 22,161,175 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.037,491,234 - 7,498,555 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl37,491,234 - 7,498,555 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0312,841,460 - 12,848,781 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.437,917,842 - 7,925,164 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.137,918,141 - 7,925,464 (-)NCBI
Celera37,020,613 - 7,027,935 (-)NCBICelera
Cytogenetic Map3p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

References - curated
# Reference Title Reference Citation
1. BARHL1 Is Downregulated in Alzheimer's Disease and May Regulate Cognitive Functions through ESR1 and Multiple Pathways. Barh D, etal., Genes (Basel). 2017 Sep 28;8(10). pii: genes8100245. doi: 10.3390/genes8100245.
2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. Hearing loss caused by progressive degeneration of cochlear hair cells in mice deficient for the Barhl1 homeobox gene. Li S, etal., Development. 2002 Jul;129(14):3523-32.
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
6. GOA pipeline RGD automated data pipeline
7. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
9. Information Derived from GenBank Report RGD, Sept. 2003
Additional References at PubMed
PMID:15044550   PMID:16752387   PMID:18212062  


Genomics

Comparative Map Data
Barhl1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8332,639,283 - 32,646,605 (-)NCBIGRCr8
mRatBN7.2312,241,327 - 12,248,649 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl312,241,327 - 12,248,649 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx315,314,424 - 15,321,756 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0323,899,395 - 23,906,727 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0322,153,843 - 22,161,175 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.037,491,234 - 7,498,555 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl37,491,234 - 7,498,555 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0312,841,460 - 12,848,781 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.437,917,842 - 7,925,164 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.137,918,141 - 7,925,464 (-)NCBI
Celera37,020,613 - 7,027,935 (-)NCBICelera
Cytogenetic Map3p12NCBI
BARHL1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389132,582,606 - 132,590,252 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9132,582,606 - 132,590,252 (+)EnsemblGRCh38hg38GRCh38
GRCh379135,457,993 - 135,465,639 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369134,447,814 - 134,455,461 (+)NCBINCBI36Build 36hg18NCBI36
Build 349132,487,546 - 132,495,194NCBI
Celera9105,999,743 - 106,007,390 (+)NCBICelera
Cytogenetic Map9q34.13NCBI
HuRef9104,951,812 - 104,959,454 (+)NCBIHuRef
CHM1_19135,608,371 - 135,616,013 (+)NCBICHM1_1
T2T-CHM13v2.09144,793,810 - 144,801,451 (+)NCBIT2T-CHM13v2.0
Barhl1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39228,797,692 - 28,807,996 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl228,797,691 - 28,806,680 (-)EnsemblGRCm39 Ensembl
GRCm38228,907,680 - 28,917,984 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl228,907,679 - 28,916,668 (-)EnsemblGRCm38mm10GRCm38
MGSCv37228,763,200 - 28,771,960 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36228,729,682 - 28,738,430 (-)NCBIMGSCv36mm8
Celera228,613,544 - 28,622,304 (-)NCBICelera
Cytogenetic Map2A3NCBI
cM Map219.38NCBI
Barhl1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555131,959,634 - 1,966,247 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555131,955,906 - 1,970,110 (+)NCBIChiLan1.0ChiLan1.0
BARHL1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2116,768,517 - 6,778,456 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan196,770,853 - 6,780,706 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v09103,698,024 - 103,709,834 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19132,331,662 - 132,343,116 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9132,331,770 - 132,338,661 (+)Ensemblpanpan1.1panPan2
BARHL1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1951,704,590 - 51,711,726 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl951,703,936 - 51,712,093 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha950,968,439 - 50,976,455 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0952,596,767 - 52,604,794 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl952,597,590 - 52,604,205 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1951,376,679 - 51,384,690 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0951,701,143 - 51,709,148 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0951,780,866 - 51,788,879 (-)NCBIUU_Cfam_GSD_1.0
Barhl1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947199,343,376 - 199,351,136 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648719,111,726 - 19,119,677 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493648719,112,479 - 19,119,677 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
BARHL1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1272,373,402 - 272,381,224 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11272,373,125 - 272,380,223 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21306,405,596 - 306,412,475 (+)NCBISscrofa10.2Sscrofa10.2susScr3
BARHL1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1125,549,484 - 5,557,348 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl125,549,234 - 5,556,945 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366607910,081,270 - 10,089,322 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Barhl1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247603,765,714 - 3,772,315 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247603,765,938 - 3,772,347 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Barhl1
16 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:365
Count of miRNA genes:183
Interacting mature miRNAs:211
Transcripts:ENSRNOT00000017725
Prediction methods:Microtar, 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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1558647Cm46Cardiac mass QTL 465.40.0000055heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)3865816227494778Rat
6893355Bw101Body weight QTL 1010.40.38body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3136847613Rat
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3822719447233430Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)3822719433703538Rat
1558650Cm48Cardiac mass QTL 4840.0001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)31077882330356773Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31086191289878372Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)31077870450302886Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3133278763Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3131158234Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1558657Cm43Cardiac mass QTL 436.63e-08heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3139874793Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)3865816227494778Rat
6893363Bw105Body weight QTL 1052.60.0036body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3127494778Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3138710544Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3133278763Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3133230976Rat

Markers in Region
BE120051  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2312,241,351 - 12,241,501 (+)MAPPERmRatBN7.2
Rnor_6.037,491,259 - 7,491,408NCBIRnor6.0
Rnor_5.0312,841,485 - 12,841,634UniSTSRnor5.0
RGSC_v3.437,917,867 - 7,918,016UniSTSRGSC3.4
Celera37,020,638 - 7,020,787UniSTS
RH 3.4 Map321.9UniSTS
Cytogenetic Map3p12UniSTS


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 appendage
High
Medium 23
Low 32 16 2
Below cutoff 1 4 18 6 12 6 2 3 19 19 18 9 2

Sequence


RefSeq Acc Id: ENSRNOT00000017725   ⟹   ENSRNOP00000017725
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl312,241,327 - 12,248,649 (-)Ensembl
Rnor_6.0 Ensembl37,491,234 - 7,498,555 (-)Ensembl
RefSeq Acc Id: NM_057109   ⟹   NP_476450
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,639,283 - 32,646,605 (-)NCBI
mRatBN7.2312,241,327 - 12,248,649 (-)NCBI
Rnor_6.037,491,234 - 7,498,555 (-)NCBI
Rnor_5.0312,841,460 - 12,848,781 (-)NCBI
RGSC_v3.437,917,842 - 7,925,164 (-)RGD
Celera37,020,613 - 7,027,935 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_476450 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAB18600 (Get FASTA)   NCBI Sequence Viewer  
  EDL93393 (Get FASTA)   NCBI Sequence Viewer  
  EDL93394 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000017725.1
  ENSRNOP00055008460
  ENSRNOP00060043701
  ENSRNOP00065031300
GenBank Protein P63156 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_476450   ⟸   NM_057109
- UniProtKB: P63156 (UniProtKB/Swiss-Prot),   A6JTQ3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000017725   ⟸   ENSRNOT00000017725
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P63156-F1-model_v2 AlphaFold P63156 1-327 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620648 AgrOrtholog
BioCyc Gene G2FUF-50266 BioCyc
Ensembl Genes ENSRNOG00000013209 Ensembl, UniProtKB/Swiss-Prot
  ENSRNOG00055006666 UniProtKB/Swiss-Prot
  ENSRNOG00060030267 UniProtKB/Swiss-Prot
  ENSRNOG00065022611 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000017725.4 UniProtKB/Swiss-Prot
  ENSRNOT00055010876 UniProtKB/Swiss-Prot
  ENSRNOT00060052541 UniProtKB/Swiss-Prot
  ENSRNOT00065038591 UniProtKB/Swiss-Prot
Gene3D-CATH Homeodomain-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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 rno:117232 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 117232 ENTREZGENE
PANTHER HOMEO BOX HB9 LIKE A-RELATED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HOMEOBOX DOMAIN-CONTAINING PROTEIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Homeodomain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Barhl1 PhenoGen
PRINTS HOMEOBOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE HOMEOBOX_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000013209 RatGTEx
  ENSRNOG00055006666 RatGTEx
  ENSRNOG00060030267 RatGTEx
  ENSRNOG00065022611 RatGTEx
SMART HOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain-like UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
UniProt A6JTQ3 ENTREZGENE, UniProtKB/TrEMBL
  BARH1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q9JK26 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-25 Barhl1  BarH-like homeobox 1  Barhl1  BarH-like 1 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Barhl1  BarH-like 1 (Drosophila)  Barhl2  BarH-like 2 (Drosophila)  Symbol and Name updated 1299863 APPROVED
2002-08-07 Barhl2        Symbol and Name status set to provisional 70820 PROVISIONAL