Tm4sf20 (transmembrane 4 L six family member 20) - Rat Genome Database

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Gene: Tm4sf20 (transmembrane 4 L six family member 20) Rattus norvegicus
Analyze
Symbol: Tm4sf20
Name: transmembrane 4 L six family member 20
RGD ID: 1588633
Description: Predicted to be involved in negative regulation of proteolysis. Predicted to be located in endoplasmic reticulum membrane. Predicted to be active in membrane. Human ortholog(s) of this gene implicated in specific language impairment. Orthologous to human TM4SF20 (transmembrane 4 L six family member 20); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 3,7-dihydropurine-6-thione.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC108348188; LOC691066; similar to transmembrane 4 L six family member 20; transmembrane 4 L6 family member 20; transmembrane 4 L6 family member 20-like
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8991,486,847 - 91,500,745 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl991,486,847 - 91,500,745 (-)EnsemblGRCr8
mRatBN7.2984,038,715 - 84,052,615 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl984,038,715 - 84,052,615 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx992,468,952 - 92,482,852 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0997,597,439 - 97,611,337 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0995,980,372 - 95,994,274 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0988,521,193 - 88,534,710 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl988,521,193 - 88,534,710 (-)Ensemblrn6Rnor6.0
Rnor_5.0988,265,563 - 88,282,348 (-)NCBIRnor_5.0Rnor_5.0rn5
Rnor_5.0990,651,149 - 90,654,610 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4982,073,815 - 82,087,712 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera981,480,188 - 81,494,099 (-)NCBICelera
Cytogenetic Map9q34NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:25310401   PMID:27499293  


Genomics

Comparative Map Data
Tm4sf20
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8991,486,847 - 91,500,745 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl991,486,847 - 91,500,745 (-)EnsemblGRCr8
mRatBN7.2984,038,715 - 84,052,615 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl984,038,715 - 84,052,615 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx992,468,952 - 92,482,852 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0997,597,439 - 97,611,337 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0995,980,372 - 95,994,274 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0988,521,193 - 88,534,710 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl988,521,193 - 88,534,710 (-)Ensemblrn6Rnor6.0
Rnor_5.0988,265,563 - 88,282,348 (-)NCBIRnor_5.0Rnor_5.0rn5
Rnor_5.0990,651,149 - 90,654,610 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4982,073,815 - 82,087,712 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera981,480,188 - 81,494,099 (-)NCBICelera
Cytogenetic Map9q34NCBI
TM4SF20
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382227,362,038 - 227,381,647 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2227,362,038 - 227,381,995 (-)Ensemblhg38GRCh38
GRCh372228,226,754 - 228,244,022 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362227,935,116 - 227,952,264 (-)NCBIBuild 36Build 36hg18NCBI36
Celera2221,996,055 - 222,013,256 (-)NCBICelera
Cytogenetic Map2q36.3NCBI
HuRef2220,070,270 - 220,087,413 (-)NCBIHuRef
CHM1_12228,232,671 - 228,249,818 (-)NCBICHM1_1
T2T-CHM13v2.02227,844,708 - 227,864,664 (-)NCBIT2T-CHM13v2.0
Tm4sf20
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39182,734,368 - 82,746,182 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl182,734,370 - 82,746,182 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38182,756,647 - 82,768,461 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl182,756,649 - 82,768,461 (-)Ensemblmm10GRCm38
MGSCv37182,753,224 - 82,765,031 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36182,635,673 - 82,647,480 (-)NCBIMGSCv36mm8
Celera182,822,999 - 82,834,807 (-)NCBICelera
Cytogenetic Map1C5NCBI
cM Map142.48NCBI
Tm4sf20
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554537,201,738 - 7,219,322 (+)Ensembl
ChiLan1.0NW_0049554537,201,738 - 7,219,322 (+)NCBIChiLan1.0ChiLan1.0
TM4SF20
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v213129,975,774 - 129,997,617 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12B129,995,128 - 130,012,587 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B114,606,488 - 114,623,569 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12B233,418,112 - 233,435,128 (-)NCBIPanPan1.1PanPan1.1panPan2
TM4SF20
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12540,148,578 - 40,159,975 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2540,148,570 - 40,159,959 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2540,766,086 - 40,777,482 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02540,395,712 - 40,407,104 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2540,395,749 - 40,407,089 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12540,332,871 - 40,344,263 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02540,173,307 - 40,184,711 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02540,347,168 - 40,358,568 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Tm4sf20
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303182,339,298 - 182,352,540 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365258,587,236 - 8,600,313 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365258,587,236 - 8,600,780 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TM4SF20
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15128,801,849 - 128,814,177 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.115128,802,438 - 128,814,201 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215142,608,536 - 142,620,001 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TM4SF20
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110113,384,569 - 113,402,884 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl10113,383,898 - 113,402,277 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604086,050,352 - 86,067,798 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tm4sf20
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248431,663,426 - 1,677,556 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248431,665,110 - 1,677,556 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Tm4sf20
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v14155,611,776 - 155,625,978 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Tm4sf20
81 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:106
Count of miRNA genes:77
Interacting mature miRNAs:98
Transcripts:ENSRNOT00000020880
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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)956047863101047863Rat
1582203Gluco19Glucose level QTL 193.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)963376862108376862Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)965657365108376720Rat
724547Cm21Cardiac mass QTL 212.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)986720043110356905Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)94445825699506504Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)986720043121768150Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)964220169109220169Rat
6903941Pur31Proteinuria QTL 310.036urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)98672213292642305Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)964220169109220169Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)944458256121768150Rat
11353949Bp393Blood pressure QTL 393arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)99062451792642305Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)964220169109220169Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)968875497121768150Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)983161999118999486Rat
4889852Pur26Proteinuria QTL 26150.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)985262459109044727Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)985262459118999486Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)948718864108376862Rat
1578757Pur6Proteinuria QTL 63.30.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)964220169109220169Rat
4889943Bss90Bone structure and strength QTL 904.1tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)95450650499506504Rat

Markers in Region
RH127628  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2984,038,938 - 84,039,142 (+)MAPPERmRatBN7.2
Rnor_6.0990,911,752 - 90,911,955NCBIRnor6.0
Rnor_6.0988,521,417 - 88,521,620NCBIRnor6.0
Rnor_5.0988,269,073 - 88,269,276UniSTSRnor5.0
Rnor_5.0990,651,373 - 90,651,576UniSTSRnor5.0
RGSC_v3.4982,074,039 - 82,074,242UniSTSRGSC3.4
Celera981,480,412 - 81,480,615UniSTS
Cytogenetic Map9q34UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 11 26 55 76 75 44 39 44 6 227 93 6 35 66 65 31 2 2

Sequence


Ensembl Acc Id: ENSRNOT00000020880   ⟹   ENSRNOP00000020880
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl991,486,847 - 91,500,745 (-)Ensembl
mRatBN7.2 Ensembl984,038,715 - 84,052,615 (-)Ensembl
Rnor_6.0 Ensembl988,521,193 - 88,534,710 (-)Ensembl
RefSeq Acc Id: NM_001109618   ⟹   NP_001103088
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8991,486,847 - 91,500,745 (-)NCBI
mRatBN7.2984,038,715 - 84,052,615 (-)NCBI
Rnor_6.0988,521,193 - 88,534,710 (-)NCBI
Rnor_5.0990,651,149 - 90,654,610 (-)NCBI
RGSC_v3.4982,073,815 - 82,087,712 (-)RGD
Celera981,480,188 - 81,494,099 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001103088 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL75520 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000020880
  ENSRNOP00000020880.4
RefSeq Acc Id: NP_001103088   ⟸   NM_001109618
- UniProtKB: D3ZJ15 (UniProtKB/TrEMBL),   A6JWB2 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000020880   ⟸   ENSRNOT00000020880

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZJ15-F1-model_v2 AlphaFold D3ZJ15 1-226 view protein structure

Transcriptome

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

Promoters
RGD ID:13696802
Promoter ID:EPDNEW_R7325
Type:single initiation site
Name:Tm4sf20_1
Description:transmembrane 4 L six family member 20
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0988,534,702 - 88,534,762EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1588633 AgrOrtholog
BioCyc Gene G2FUF-26977 BioCyc
Ensembl Genes ENSRNOG00000015460 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000020880 ENTREZGENE
  ENSRNOT00000020880.7 UniProtKB/TrEMBL
InterPro L6_membrane UniProtKB/TrEMBL
KEGG Report rno:691066 UniProtKB/TrEMBL
NCBI Gene 691066 ENTREZGENE
PANTHER PTHR14198 UniProtKB/TrEMBL
  TRANSMEMBRANE 4 L6 FAMILY MEMBER 20 UniProtKB/TrEMBL
Pfam L6_membrane UniProtKB/TrEMBL
PhenoGen Tm4sf20 PhenoGen
RatGTEx ENSRNOG00000015460 RatGTEx
UniProt A6JWB2 ENTREZGENE, UniProtKB/TrEMBL
  D3ZJ15 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Tm4sf20  transmembrane 4 L six family member 20  LOC108348188  transmembrane 4 L6 family member 20-like  Data merged from RGD:11500321 737654 PROVISIONAL
2016-08-02 LOC108348188  transmembrane 4 L6 family member 20-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-03-06 Tm4sf20  transmembrane 4 L six family member 20  LOC691066  similar to transmembrane 4 L six family member 20  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC691066  similar to transmembrane 4 L six family member 20  LOC682510  similar to transmembrane 4 L six family member 20  Data merged from RGD:1597964 1643240 APPROVED
2006-11-20 LOC682510  similar to transmembrane 4 L six family member 20      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC691066  similar to transmembrane 4 L six family member 20      Symbol and Name status set to provisional 70820 PROVISIONAL