Barhl2 (BarH-like homeobox 2) - Rat Genome Database

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Gene: Barhl2 (BarH-like homeobox 2) Rattus norvegicus
Analyze
Symbol: Barhl2
Name: BarH-like homeobox 2
RGD ID: 620726
Description: Enables DNA-binding transcription factor activity. Involved in nervous system development and regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in oral squamous cell carcinoma. Orthologous to human BARHL2 (BarH like homeobox 2); INTERACTS WITH 6-propyl-2-thiouracil; ammonium chloride; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: bar-class homeodomain protein MBH1; Barh; BarH-class homeodomain transcription factor; BarH-like 2 (Drosophila); barH-like 2 homeobox protein; homeobox protein B-H1; LOC65050; MBH1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8143,485,309 - 3,490,206 (+)NCBIGRCr8
mRatBN7.2143,340,465 - 3,345,362 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl143,340,465 - 3,345,353 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx143,212,127 - 3,217,012 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0144,513,629 - 4,518,514 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0143,213,991 - 3,218,875 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0144,362,717 - 4,367,614 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl144,362,717 - 4,367,605 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0144,356,650 - 4,361,547 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4143,888,153 - 3,893,050 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1143,888,152 - 3,893,041 (+)NCBI
Celera143,342,723 - 3,347,622 (+)NCBICelera
Cytogenetic Map14p22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleus  (IBA,ISO)

References

References - curated
# Reference Title Reference Citation
1. 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.
2. Up-regulation of miR-187 modulates the advances of oral carcinoma by targeting BARX2 tumor suppressor. Lin SC, etal., Oncotarget. 2016 Sep 20;7(38):61355-61365. doi: 10.18632/oncotarget.11349.
3. Down-regulation of Barx2 predicts poor survival in colorectal cancer. Mi Y, etal., Biochem Biophys Res Commun. 2016 Sep 9;478(1):67-73. doi: 10.1016/j.bbrc.2016.07.091. Epub 2016 Jul 22.
4. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
5. GOA pipeline RGD automated data pipeline
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Mammalian BarH homologue is a potential regulator of neural bHLH genes. Saito T, etal., Dev Biol 1998 Jul 15;199(2):216-25.
8. BARHL2 Methylation Using Gastric Wash DNA or Gastric Juice Exosomal DNA is a Useful Marker For Early Detection of Gastric Cancer in an H. pylori-Independent Manner. Yamamoto H, etal., Clin Transl Gastroenterol. 2016 Jul 21;7(7):e184. doi: 10.1038/ctg.2016.40.
Additional References at PubMed
PMID:12657654   PMID:14998930   PMID:18212062  


Genomics

Comparative Map Data
Barhl2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8143,485,309 - 3,490,206 (+)NCBIGRCr8
mRatBN7.2143,340,465 - 3,345,362 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl143,340,465 - 3,345,353 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx143,212,127 - 3,217,012 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0144,513,629 - 4,518,514 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0143,213,991 - 3,218,875 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0144,362,717 - 4,367,614 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl144,362,717 - 4,367,605 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0144,356,650 - 4,361,547 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4143,888,153 - 3,893,050 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1143,888,152 - 3,893,041 (+)NCBI
Celera143,342,723 - 3,347,622 (+)NCBICelera
Cytogenetic Map14p22NCBI
BARHL2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38190,711,539 - 90,717,302 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl190,711,539 - 90,717,302 (-)EnsemblGRCh38hg38GRCh38
GRCh37191,177,096 - 91,182,859 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36190,950,167 - 90,955,382 (-)NCBINCBI36Build 36hg18NCBI36
Build 34190,889,599 - 90,894,815NCBI
Celera189,425,682 - 89,430,897 (-)NCBICelera
Cytogenetic Map1p22.2NCBI
HuRef189,296,413 - 89,301,629 (-)NCBIHuRef
CHM1_1191,292,732 - 91,297,947 (-)NCBICHM1_1
T2T-CHM13v2.0190,555,903 - 90,561,666 (-)NCBIT2T-CHM13v2.0
Barhl2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395106,600,389 - 106,606,032 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl5106,600,389 - 106,606,032 (-)EnsemblGRCm39 Ensembl
GRCm385106,452,523 - 106,458,166 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5106,452,523 - 106,458,166 (-)EnsemblGRCm38mm10GRCm38
MGSCv375106,881,542 - 106,887,185 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv365106,881,542 - 106,887,185 (-)NCBIMGSCv36mm8
Celera5103,565,328 - 103,570,954 (-)NCBICelera
Cytogenetic Map5E5NCBI
cM Map551.43NCBI
Barhl2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554233,516,660 - 3,522,536 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554233,516,973 - 3,522,459 (+)NCBIChiLan1.0ChiLan1.0
BARHL2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21136,306,017 - 136,313,430 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11135,461,979 - 135,468,959 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0193,373,317 - 93,378,667 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1192,121,017 - 92,126,036 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl192,121,017 - 92,126,036 (-)Ensemblpanpan1.1panPan2
BARHL2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1657,971,077 - 57,977,197 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl657,971,018 - 57,977,211 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha660,675,782 - 60,681,623 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0658,355,942 - 58,361,782 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl658,355,347 - 58,361,798 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1658,029,710 - 58,035,547 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0658,005,081 - 58,010,922 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0658,485,088 - 58,490,931 (+)NCBIUU_Cfam_GSD_1.0
Barhl2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405058100,812,786 - 100,818,760 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365378,129,207 - 8,135,237 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365378,129,213 - 8,134,744 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
BARHL2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4126,029,437 - 126,036,210 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.14126,030,373 - 126,035,662 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24137,708,728 - 137,715,018 (+)NCBISscrofa10.2Sscrofa10.2susScr3
BARHL2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12042,743,465 - 42,757,833 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2042,743,888 - 42,749,876 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603375,223,048 - 75,228,743 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Barhl2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247427,027,069 - 7,034,308 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247427,027,122 - 7,033,342 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Barhl2
17 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:111
Count of miRNA genes:83
Interacting mature miRNAs:91
Transcripts:ENSRNOT00000002887
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
2300159Bmd61Bone mineral density QTL 615.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
2300183Bmd60Bone mineral density QTL 605.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
619619Rf4Renal disease susceptibility QTL 44.10.002urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14132754612Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
71115Niddm15Non-insulin dependent diabetes mellitus QTL 154.8blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14121760611030812Rat
70204Niddm20Non-insulin dependent diabetes mellitus QTL 205.10.000008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)14121760616960180Rat

Markers in Region
Barhl2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2143,340,987 - 3,341,055 (+)MAPPERmRatBN7.2
Rnor_6.0144,363,240 - 4,363,307NCBIRnor6.0
Rnor_5.0144,357,173 - 4,357,240UniSTSRnor5.0
RGSC_v3.4143,888,676 - 3,888,743UniSTSRGSC3.4
Celera143,343,246 - 3,343,313UniSTS
Cytogenetic Map14p22UniSTS
AL034195  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2143,342,122 - 3,342,260 (+)MAPPERmRatBN7.2
Rnor_6.0144,364,375 - 4,364,512NCBIRnor6.0
Rnor_5.0144,358,308 - 4,358,445UniSTSRnor5.0
RGSC_v3.4143,889,811 - 3,889,948UniSTSRGSC3.4
Celera143,344,381 - 3,344,518UniSTS
Cytogenetic Map14p22UniSTS


Expression


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

endocrine system exocrine system hepatobiliary system nervous system reproductive system respiratory system
High
Medium 39
Low 33 2
Below cutoff 1 1 1 2 14 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000002887   ⟹   ENSRNOP00000002887
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl143,340,465 - 3,345,353 (+)Ensembl
Rnor_6.0 Ensembl144,362,717 - 4,367,605 (+)Ensembl
RefSeq Acc Id: NM_022956   ⟹   NP_075245
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8143,485,309 - 3,490,206 (+)NCBI
mRatBN7.2143,340,465 - 3,345,362 (+)NCBI
Rnor_6.0144,362,717 - 4,367,614 (+)NCBI
Rnor_5.0144,356,650 - 4,361,547 (+)NCBI
RGSC_v3.4143,888,153 - 3,893,050 (+)RGD
Celera143,342,723 - 3,347,622 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_075245 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAA32474 (Get FASTA)   NCBI Sequence Viewer  
  EDL83949 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000002887
  ENSRNOP00000002887.2
  ENSRNOP00055035047
  ENSRNOP00060013524
GenBank Protein O88181 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_075245   ⟸   NM_022956
- UniProtKB: O88181 (UniProtKB/Swiss-Prot),   A6KPL6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000002887   ⟸   ENSRNOT00000002887
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O88181-F1-model_v2 AlphaFold O88181 1-384 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:620726 AgrOrtholog
BioCyc Gene G2FUF-16570 BioCyc
Ensembl Genes ENSRNOG00000002117 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055024909 UniProtKB/Swiss-Prot
  ENSRNOG00060010299 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000002887 ENTREZGENE
  ENSRNOT00000002887.4 UniProtKB/Swiss-Prot
  ENSRNOT00055042926 UniProtKB/Swiss-Prot
  ENSRNOT00060017407 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:65050 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 65050 ENTREZGENE
PANTHER BARH-LIKE 2 HOMEOBOX PROTEIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HOMEOBOX PROTEIN BARH-LIKE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Homeodomain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Barhl2 PhenoGen
PRINTS HOMEOBOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE HOMEOBOX_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000002117 RatGTEx
  ENSRNOG00055024909 RatGTEx
  ENSRNOG00060010299 RatGTEx
SMART HOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain-like UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
UniProt A6KPL6 ENTREZGENE, UniProtKB/TrEMBL
  BARH2_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-25 Barhl2  BarH-like homeobox 2  Barhl2  BarH-like 2 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-25 Barhl2  BarH-like 2 (Drosophila)  LOC65050  BarH-class homeodomain transcription factor  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-08-07 Loc65050  BarH-class homeodomain transcription factor      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_process involved in neural differentiation