Vgll2 (vestigial-like family member 2) - Rat Genome Database

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Gene: Vgll2 (vestigial-like family member 2) Rattus norvegicus
Analyze
Symbol: Vgll2
Name: vestigial-like family member 2
RGD ID: 1311903
Description: Predicted to enable transcription coactivator activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within positive regulation of transcription by RNA polymerase II and skeletal muscle tissue development. Predicted to be located in cytoplasm. Predicted to be active in nucleus. Orthologous to human VGLL2 (vestigial like family member 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; all-trans-retinoic acid; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC309772; transcription cofactor vestigial-like protein 2; vestigial like 2; vestigial like 2 (Drosophila); vestigial like 2 homolog; vestigial like 2 homolog (Drosophila)
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
GRCr82031,952,214 - 31,958,100 (+)NCBIGRCr8
mRatBN7.22031,409,529 - 31,415,408 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2031,409,552 - 31,415,408 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2032,404,448 - 32,410,319 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02031,795,358 - 31,801,226 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02032,536,231 - 32,542,095 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02033,077,106 - 33,082,962 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2033,077,106 - 33,082,962 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02034,858,269 - 34,864,128 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42030,732,016 - 30,737,872 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12030,745,959 - 30,751,234 (+)NCBI
Celera2032,808,237 - 32,814,091 (+)NCBICelera
Cytogenetic Map20q11NCBI
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
cytoplasm  (ISO)
nucleus  (IBA,ISO)

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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
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:12376544   PMID:14762206   PMID:17689488  


Genomics

Comparative Map Data
Vgll2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82031,952,214 - 31,958,100 (+)NCBIGRCr8
mRatBN7.22031,409,529 - 31,415,408 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2031,409,552 - 31,415,408 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2032,404,448 - 32,410,319 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02031,795,358 - 31,801,226 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02032,536,231 - 32,542,095 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02033,077,106 - 33,082,962 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2033,077,106 - 33,082,962 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02034,858,269 - 34,864,128 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42030,732,016 - 30,737,872 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12030,745,959 - 30,751,234 (+)NCBI
Celera2032,808,237 - 32,814,091 (+)NCBICelera
Cytogenetic Map20q11NCBI
VGLL2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386117,265,558 - 117,273,630 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6117,265,558 - 117,273,565 (+)EnsemblGRCh38hg38GRCh38
GRCh376117,586,721 - 117,594,728 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366117,693,414 - 117,701,421 (+)NCBINCBI36Build 36hg18NCBI36
Celera6118,329,639 - 118,337,646 (+)NCBICelera
Cytogenetic Map6q22.1NCBI
HuRef6115,167,061 - 115,175,071 (+)NCBIHuRef
CHM1_16117,850,863 - 117,858,870 (+)NCBICHM1_1
T2T-CHM13v2.06118,449,447 - 118,457,457 (+)NCBIT2T-CHM13v2.0
Vgll2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391051,898,598 - 51,904,567 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1051,898,598 - 51,904,567 (+)EnsemblGRCm39 Ensembl
GRCm381052,022,502 - 52,028,471 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1052,022,502 - 52,028,471 (+)EnsemblGRCm38mm10GRCm38
MGSCv371051,742,492 - 51,748,277 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361051,711,101 - 51,716,886 (+)NCBIMGSCv36mm8
Celera1052,859,209 - 52,864,995 (+)NCBICelera
Cytogenetic Map10B3NCBI
cM Map1026.16NCBI
Vgll2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_004955436510,478 - 514,511 (+)NCBIChiLan1.0ChiLan1.0
VGLL2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v25137,279,472 - 137,287,765 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16135,172,311 - 135,179,233 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06115,073,919 - 115,082,212 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16119,215,683 - 119,223,541 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6119,215,683 - 119,223,541 (+)Ensemblpanpan1.1panPan2
VGLL2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1157,529,901 - 57,537,893 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl157,529,928 - 57,574,871 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha158,324,840 - 58,332,796 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0157,711,797 - 57,719,772 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl157,711,802 - 57,784,645 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1157,606,283 - 57,614,265 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0157,453,993 - 57,461,973 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0158,089,172 - 58,097,148 (+)NCBIUU_Cfam_GSD_1.0
Vgll2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946108,255,478 - 108,263,459 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936658362,296 - 370,322 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936658362,377 - 370,298 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VGLL2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl144,549,412 - 44,557,797 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1144,549,407 - 44,557,793 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2149,878,272 - 49,904,485 (-)NCBISscrofa10.2Sscrofa10.2susScr3
VGLL2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11356,576,583 - 56,584,632 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1356,577,660 - 56,584,427 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604028,911,514 - 28,920,059 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vgll2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462479812,457,614 - 12,464,090 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Vgll2
28 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:65
Count of miRNA genes:51
Interacting mature miRNAs:60
Transcripts:ENSRNOT00000000456
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201761783247606836Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201769755054435887Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)201919072154435887Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202510672254435887Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202510672254435887Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202510672254435887Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202520973454435887Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)202924438854435887Rat


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 hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3
Low 2 2 2 8 8 14 2 15 1 8
Below cutoff 16 11 8 8 29 4 8 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000000456   ⟹   ENSRNOP00000000456
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2031,409,552 - 31,415,408 (+)Ensembl
Rnor_6.0 Ensembl2033,077,106 - 33,082,962 (+)Ensembl
RefSeq Acc Id: NM_001107630   ⟹   NP_001101100
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82031,952,244 - 31,958,100 (+)NCBI
mRatBN7.22031,409,552 - 31,415,408 (+)NCBI
Rnor_6.02033,077,106 - 33,082,962 (+)NCBI
Rnor_5.02034,858,269 - 34,864,128 (+)NCBI
RGSC_v3.42030,732,016 - 30,737,872 (+)RGD
Celera2032,808,237 - 32,814,091 (+)RGD
Sequence:
RefSeq Acc Id: XM_006256448   ⟹   XP_006256510
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82031,952,214 - 31,958,100 (+)NCBI
mRatBN7.22031,409,529 - 31,415,408 (+)NCBI
Rnor_6.02033,077,110 - 33,082,962 (+)NCBI
Rnor_5.02034,858,269 - 34,864,128 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008772885   ⟹   XP_008771107
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82031,952,676 - 31,958,100 (+)NCBI
mRatBN7.22031,409,990 - 31,415,408 (+)NCBI
Rnor_6.02033,077,481 - 33,082,962 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001101100 (Get FASTA)   NCBI Sequence Viewer  
  XP_006256510 (Get FASTA)   NCBI Sequence Viewer  
  XP_008771107 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL92947 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000000456
  ENSRNOP00000000456.3
Reference Protein Sequences
RefSeq Acc Id: NP_001101100   ⟸   NM_001107630
- UniProtKB: D3ZG38 (UniProtKB/TrEMBL),   A6K475 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006256510   ⟸   XM_006256448
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008771107   ⟸   XM_008772885
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000000456   ⟸   ENSRNOT00000000456

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZG38-F1-model_v2 AlphaFold D3ZG38 1-323 view protein structure

Transcriptome

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

Promoters
RGD ID:13701621
Promoter ID:EPDNEW_R12145
Type:single initiation site
Name:Vgll2_1
Description:vestigial-like family member 2
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_6.02033,077,096 - 33,077,156EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311903 AgrOrtholog
BioCyc Gene G2FUF-3650 BioCyc
Ensembl Genes ENSRNOG00000000405 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000456 ENTREZGENE
  ENSRNOT00000000456.5 UniProtKB/TrEMBL
InterPro Vg_Tdu UniProtKB/TrEMBL
KEGG Report rno:309772 UniProtKB/TrEMBL
NCBI Gene 309772 ENTREZGENE
PANTHER PTHR15950 UniProtKB/TrEMBL
  TRANSCRIPTION COFACTOR VESTIGIAL-LIKE PROTEIN 2 UniProtKB/TrEMBL
Pfam Vg_Tdu UniProtKB/TrEMBL
PhenoGen Vgll2 PhenoGen
RatGTEx ENSRNOG00000000405 RatGTEx
UniProt A6K475 ENTREZGENE, UniProtKB/TrEMBL
  D3ZG38 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-03-13 Vgll2  vestigial-like family member 2  Vgll2  vestigial like 2 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-25 Vgll2  vestigial like 2 (Drosophila)  Vgll2  vestigial like 2 homolog (Drosophila)   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Vgll2  vestigial like 2 homolog (Drosophila)   Vgll2_predicted  vestigial like 2 homolog (Drosophila) (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Vgll2_predicted  vestigial like 2 homolog (Drosophila) (predicted)      Symbol and Name status set to approved 70820 APPROVED