Sohlh1 (spermatogenesis and oogenesis specific basic helix-loop-helix 1) - Rat Genome Database

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Gene: Sohlh1 (spermatogenesis and oogenesis specific basic helix-loop-helix 1) Rattus norvegicus
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Symbol: Sohlh1
Name: spermatogenesis and oogenesis specific basic helix-loop-helix 1
RGD ID: 1564440
Description: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and protein dimerization activity. Predicted to be involved in oocyte differentiation and positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including ovarian follicle development; positive regulation of DNA-templated transcription; and spermatogenesis. Predicted to be located in cytoplasm and male germ cell nucleus. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in ovarian dysgenesis 5 and spermatogenic failure 32. Orthologous to human SOHLH1 (spermatogenesis and oogenesis specific basic helix-loop-helix 1); INTERACTS WITH azoxystrobin; bisphenol A; chlorpyrifos.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC362085; RGD1564440; similar to helix-loop-helix protein NOHLH; spermatogenesis- and oogenesis-specific basic helix-loop-helix-containing protein 1
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
GRCr8329,061,267 - 29,065,588 (-)NCBIGRCr8
mRatBN7.238,662,995 - 8,667,521 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl38,663,318 - 8,667,388 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx311,717,563 - 11,721,579 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0320,300,777 - 20,304,793 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0318,556,095 - 18,560,111 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.033,290,766 - 3,295,226 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl33,291,084 - 3,295,101 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.038,653,008 - 8,657,322 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.434,015,651 - 4,019,668 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera33,486,441 - 3,490,458 (-)NCBICelera
Cytogenetic Map3p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Cellular Component

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:16564520   PMID:16690745   PMID:18753606   PMID:22056784   PMID:22328502   PMID:28504655  


Genomics

Comparative Map Data
Sohlh1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8329,061,267 - 29,065,588 (-)NCBIGRCr8
mRatBN7.238,662,995 - 8,667,521 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl38,663,318 - 8,667,388 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx311,717,563 - 11,721,579 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0320,300,777 - 20,304,793 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0318,556,095 - 18,560,111 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.033,290,766 - 3,295,226 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl33,291,084 - 3,295,101 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.038,653,008 - 8,657,322 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.434,015,651 - 4,019,668 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera33,486,441 - 3,490,458 (-)NCBICelera
Cytogenetic Map3p13NCBI
SOHLH1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389135,693,407 - 135,702,112 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9135,693,407 - 135,704,498 (-)EnsemblGRCh38hg38GRCh38
GRCh379138,585,253 - 138,591,327 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369137,725,074 - 137,731,195 (-)NCBINCBI36Build 36hg18NCBI36
Celera9109,103,027 - 109,109,205 (-)NCBICelera
Cytogenetic Map9q34.3NCBI
HuRef9108,046,733 - 108,052,911 (-)NCBIHuRef
CHM1_19138,733,602 - 138,739,721 (-)NCBICHM1_1
T2T-CHM13v2.09147,920,187 - 147,928,960 (-)NCBIT2T-CHM13v2.0
Sohlh1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39225,733,007 - 25,737,347 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl225,733,007 - 25,737,260 (-)EnsemblGRCm39 Ensembl
GRCm38225,842,995 - 25,847,248 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl225,842,995 - 25,847,248 (-)EnsemblGRCm38mm10GRCm38
MGSCv37225,698,515 - 25,702,768 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36225,665,004 - 25,669,257 (-)NCBIMGSCv36mm8
Celera225,562,491 - 25,566,744 (-)NCBICelera
Cytogenetic Map2A3NCBI
cM Map218.21NCBI
Sohlh1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049555134,767,591 - 4,771,654 (+)NCBIChiLan1.0ChiLan1.0
SOHLH1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2113,671,894 - 3,693,534 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan193,673,522 - 3,695,867 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v09106,765,101 - 106,786,836 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19135,755,100 - 135,768,736 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9135,755,100 - 135,761,228 (-)Ensemblpanpan1.1panPan2
SOHLH1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1949,593,740 - 49,598,279 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl949,593,703 - 49,599,113 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha948,846,147 - 48,850,679 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0950,472,938 - 50,477,471 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl950,472,933 - 50,477,545 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1949,252,908 - 49,257,430 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0949,547,156 - 49,551,680 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0949,595,299 - 49,599,829 (+)NCBIUU_Cfam_GSD_1.0
Sohlh1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947201,462,874 - 201,468,044 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049366691,901,892 - 1,912,184 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SOHLH1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa10.21308,722,662 - 308,726,787 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SOHLH1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1122,493,066 - 2,508,396 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660582,652,074 - 2,658,421 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sohlh1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247601,154,848 - 1,159,341 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Sohlh1
13 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:232
Count of miRNA genes:172
Interacting mature miRNAs:190
Transcripts:ENSRNOT00000051729
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
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3127494778Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3131158234Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3133230976Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3133278763Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3133278763Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3136847613Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3138710544Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3139874793Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1358185Ept6Estrogen-induced pituitary tumorigenesis QTL 66.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3653764510778823Rat
2292615Ept17Estrogen-induced pituitary tumorigenesis QTL 176.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3653764510778823Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)3822719433703538Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3822719447233430Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)3865816227494778Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)3865816227494778Rat


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

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 15
Low 14
Below cutoff 1 7 1 9 1 3 3 36 1 9 5 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000051729   ⟹   ENSRNOP00000042351
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl38,663,318 - 8,667,388 (-)Ensembl
Rnor_6.0 Ensembl33,291,084 - 3,295,101 (-)Ensembl
RefSeq Acc Id: NM_001413659   ⟹   NP_001400588
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8329,061,267 - 29,065,588 (-)NCBI
mRatBN7.238,663,154 - 8,667,475 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001400588 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL93534 (Get FASTA)   NCBI Sequence Viewer  
  EDL93535 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000042351
  ENSRNOP00000042351.4
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000042351   ⟸   ENSRNOT00000051729
RefSeq Acc Id: NP_001400588   ⟸   NM_001413659
- UniProtKB: D4A4L1 (UniProtKB/TrEMBL)
Protein Domains
bHLH

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A4L1-F1-model_v2 AlphaFold D4A4L1 1-357 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:1564440 AgrOrtholog
BioCyc Gene G2FUF-50410 BioCyc
Ensembl Genes ENSRNOG00000033983 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000051729 ENTREZGENE
  ENSRNOT00000051729.5 UniProtKB/TrEMBL
InterPro HLH_DNA-bd UniProtKB/TrEMBL
  HLH_DNA-bd_sf UniProtKB/TrEMBL
  TCFL5/SOLH1/2 UniProtKB/TrEMBL
KEGG Report rno:362085 UniProtKB/TrEMBL
NCBI Gene 362085 ENTREZGENE
PANTHER SPERMATOGENESIS- AND OOGENESIS-SPECIFIC BASIC HELIX-LOOP-HELIX-CONTAINING PROTEIN 1 UniProtKB/TrEMBL
  TRANSCRIPTION FACTOR-LIKE 5 PROTEIN UniProtKB/TrEMBL
Pfam HLH UniProtKB/TrEMBL
PhenoGen Sohlh1 PhenoGen
PROSITE HLH UniProtKB/TrEMBL
RatGTEx ENSRNOG00000033983 RatGTEx
Superfamily-SCOP HLH_basic UniProtKB/TrEMBL
UniProt D4A4L1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-06 Sohlh1  spermatogenesis and oogenesis specific basic helix-loop-helix 1  RGD1564440_predicted  similar to helix-loop-helix protein NOHLH (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1564440_predicted  similar to helix-loop-helix protein NOHLH (predicted)  LOC362085  similar to helix-loop-helix protein NOHLH  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC362085  similar to helix-loop-helix protein NOHLH      Symbol and Name status set to provisional 70820 PROVISIONAL