Gdf6 (growth differentiation factor 6) - Rat Genome Database

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Pathways
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Gene: Gdf6 (growth differentiation factor 6) Rattus norvegicus
Analyze
Symbol: Gdf6
Name: growth differentiation factor 6
RGD ID: 620104
Description: Predicted to enable cytokine activity and identical protein binding activity. Predicted to be involved in several processes, including cell surface receptor protein serine/threonine kinase signaling pathway; positive regulation of chondrocyte differentiation; and positive regulation of intracellular signal transduction. Predicted to act upstream of or within with a positive effect on cell migration involved in metanephros development and epithelial cell migration. Predicted to act upstream of or within positive regulation of neuron differentiation. Predicted to be active in extracellular space. Human ortholog(s) of this gene implicated in Leber congenital amaurosis 17; bone disease (multiple); cleft lip; cleft palate; and isolated microphthalmia 4. Orthologous to human GDF6 (growth differentiation factor 6); PARTICIPATES IN transforming growth factor-beta superfamily mediated signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; ammonium chloride; beta-naphthoflavone.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: BMP-13; bone morphogenetic protein 13; GDF-6; gdf16; growth differentiation factor 16; growth/differentiation factor 16; growth/differentiation factor 6
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
GRCr8527,793,561 - 27,809,884 (+)NCBIGRCr8
mRatBN7.2522,996,246 - 23,012,567 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl522,996,246 - 23,012,567 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx525,230,195 - 25,246,549 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0526,816,190 - 26,832,510 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0526,596,487 - 26,612,805 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0523,056,345 - 23,072,666 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl523,056,347 - 23,074,599 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0527,786,775 - 27,803,096 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4523,739,175 - 23,756,140 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1523,755,784 - 23,755,986 (+)NCBI
Celera522,249,415 - 22,265,738 (+)NCBICelera
Cytogenetic Map5q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Genomic screening identifies novel linkages and provides further evidence for a role of MYH9 in nonsyndromic cleft lip and palate. Chiquet BT, etal., Eur J Hum Genet. 2009 Feb;17(2):195-204. doi: 10.1038/ejhg.2008.149. Epub 2008 Aug 20.
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. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
4. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
5. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
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. Gene expression of growth differentiation factors in the developing periodontium of rat molars. Sena K, etal., J Dent Res 2003 Mar;82(3):166-71.
Additional References at PubMed
PMID:9786991   PMID:16049014   PMID:21469182   PMID:24006456   PMID:26643732   PMID:26774823  


Genomics

Comparative Map Data
Gdf6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8527,793,561 - 27,809,884 (+)NCBIGRCr8
mRatBN7.2522,996,246 - 23,012,567 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl522,996,246 - 23,012,567 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx525,230,195 - 25,246,549 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0526,816,190 - 26,832,510 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0526,596,487 - 26,612,805 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0523,056,345 - 23,072,666 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl523,056,347 - 23,074,599 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0527,786,775 - 27,803,096 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4523,739,175 - 23,756,140 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1523,755,784 - 23,755,986 (+)NCBI
Celera522,249,415 - 22,265,738 (+)NCBICelera
Cytogenetic Map5q13NCBI
GDF6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38896,142,333 - 96,160,806 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl896,142,333 - 96,160,806 (-)EnsemblGRCh38hg38GRCh38
GRCh37897,154,561 - 97,173,034 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36897,223,734 - 97,242,196 (-)NCBINCBI36Build 36hg18NCBI36
Build 34897,223,737 - 97,242,196NCBI
Celera893,340,541 - 93,359,001 (-)NCBICelera
Cytogenetic Map8q22.1NCBI
HuRef892,360,118 - 92,378,582 (-)NCBIHuRef
CHM1_1897,194,809 - 97,213,265 (-)NCBICHM1_1
T2T-CHM13v2.0897,267,652 - 97,286,137 (-)NCBIT2T-CHM13v2.0
Gdf6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3949,844,372 - 9,862,345 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl49,844,372 - 9,862,345 (+)EnsemblGRCm39 Ensembl
GRCm3849,844,372 - 9,862,345 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl49,844,372 - 9,862,345 (+)EnsemblGRCm38mm10GRCm38
MGSCv3749,771,519 - 9,789,492 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3649,771,519 - 9,789,492 (+)NCBIMGSCv36mm8
Celera49,660,031 - 9,677,998 (+)NCBICelera
Cytogenetic Map4A1NCBI
cM Map44.35NCBI
Gdf6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541712,152,448 - 12,169,362 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541712,152,448 - 12,169,173 (-)NCBIChiLan1.0ChiLan1.0
GDF6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v27113,474,794 - 113,493,871 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1889,013,655 - 89,032,096 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0892,767,401 - 92,785,955 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1894,965,399 - 94,984,456 (-)NCBIpanpan1.1PanPan1.1panPan2
GDF6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12940,676,851 - 40,694,174 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2940,676,851 - 40,694,174 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2940,676,851 - 40,694,174 (-)NCBICanFam3.1canFam3CanFam3.1
ROS_Cfam_1.02940,868,628 - 40,885,256 (-)NCBIROS_Cfam_1.0
UNSW_CanFamBas_1.02940,880,805 - 40,897,837 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02941,342,023 - 41,361,005 (-)NCBIUU_Cfam_GSD_1.0
Gdf6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530338,894,428 - 38,952,490 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647046,361,451 - 46,377,594 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647046,361,528 - 46,379,576 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GDF6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl440,472,935 - 40,490,033 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1440,473,015 - 40,491,142 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
GDF6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1891,105,663 - 91,124,059 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl891,107,857 - 91,123,874 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603949,663,846 - 49,682,176 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Gdf6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247633,474,671 - 3,490,297 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247633,473,047 - 3,490,346 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Gdf6
105 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:76
Count of miRNA genes:71
Interacting mature miRNAs:76
Transcripts:ENSRNOT00000010266
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
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
2312562Pur18Proteinuria QTL 182.60.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5213896532656739Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5228222669540447Rat
2313085Bss59Bone structure and strength QTL 592.90.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)5384401826141981Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5384401847869213Rat
61462Niddm10Non-insulin dependent diabetes mellitus QTL 103.90.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)5511215947171491Rat
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)5894822853948228Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat
1641903Alcrsp3Alcohol response QTL 3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)51268928557689285Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat
1600358Mamtr5Mammary tumor resistance QTL 5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)51887394763873947Rat
1358353Srcrtb2Stress Responsive Cort Basal QTL 23.480.003blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)51887394774251464Rat
8552954Pigfal14Plasma insulin-like growth factor 1 level QTL 149blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)52122674466226744Rat


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 10 6 6 6 7
Low 19 8 8 11 8 8 8 17 2
Below cutoff 3 8 35 25 5 25 4 7 52 17 13 9 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000010266   ⟹   ENSRNOP00000010266
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl523,056,347 - 23,074,599 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000101359   ⟹   ENSRNOP00000082414
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl522,996,246 - 23,012,567 (+)Ensembl
RefSeq Acc Id: NM_001013038   ⟹   NP_001013056
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8527,793,561 - 27,809,884 (+)NCBI
mRatBN7.2522,996,246 - 23,012,567 (+)NCBI
Rnor_6.0523,056,345 - 23,072,666 (+)NCBI
Rnor_5.0527,786,775 - 27,803,096 (+)NCBI
RGSC_v3.4523,739,175 - 23,756,140 (+)RGD
Celera522,249,415 - 22,265,738 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001013056 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAC02714 (Get FASTA)   NCBI Sequence Viewer  
  CAD60936 (Get FASTA)   NCBI Sequence Viewer  
  EDM11664 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000082414
  ENSRNOP00000082414.1
  ENSRNOP00055027705
  ENSRNOP00065019648
GenBank Protein Q6HA10 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001013056   ⟸   NM_001013038
- Peptide Label: precursor
- UniProtKB: Q8K4X4 (UniProtKB/Swiss-Prot),   Q6HA10 (UniProtKB/Swiss-Prot),   A6JFR8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000010266   ⟸   ENSRNOT00000010266
RefSeq Acc Id: ENSRNOP00000082414   ⟸   ENSRNOT00000101359
Protein Domains
TGF-beta family profile

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6HA10-F1-model_v2 AlphaFold Q6HA10 1-452 view protein structure

Transcriptome

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

Promoters
RGD ID:13693559
Promoter ID:EPDNEW_R4083
Type:multiple initiation site
Name:Gdf6_1
Description:growth differentiation factor 6
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_6.0523,056,332 - 23,056,392EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620104 AgrOrtholog
BioCyc Gene G2FUF-41990 BioCyc
Ensembl Genes ENSRNOG00000007810 Ensembl
  ENSRNOG00000067800 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055020007 UniProtKB/Swiss-Prot
  ENSRNOG00065015165 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000101359 ENTREZGENE
  ENSRNOT00000101359.1 UniProtKB/Swiss-Prot
  ENSRNOT00055034153 UniProtKB/Swiss-Prot
  ENSRNOT00065025106 UniProtKB/Swiss-Prot
Gene3D-CATH 2.10.90.10 UniProtKB/Swiss-Prot
  2.60.120.970 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cystine-knot cytokines UniProtKB/TrEMBL
InterPro Cystine-knot_cytokine UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TGF-b_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TGF-b_propeptide UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TGF-beta-rel UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TGFb_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:252834 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 252834 ENTREZGENE
PANTHER GROWTH/DIFFERENTIATION FACTOR 6 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR11848 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam TGF_beta UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TGFb_propeptide UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Gdf6 PhenoGen
PRINTS INHIBINA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE TGF_BETA_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TGF_BETA_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000007810 RatGTEx
  ENSRNOG00000067800 RatGTEx
  ENSRNOG00055020007 RatGTEx
  ENSRNOG00065015165 RatGTEx
SMART TGFB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP Cystine-knot cytokines UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
UniProt A6JFR8 ENTREZGENE, UniProtKB/TrEMBL
  GDF6_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q8K4X4 ENTREZGENE
UniProt Secondary Q8K4X4 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-01-20 Gdf6  growth differentiation factor 6      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Gdf6  growth differentiation factor 6      Symbol and Name status set to provisional 70820 PROVISIONAL