Gpatch11 (G patch domain containing 11) - Rat Genome Database

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Gene: Gpatch11 (G patch domain containing 11) Rattus norvegicus
Analyze
Symbol: Gpatch11
Name: G patch domain containing 11
RGD ID: 1311424
Description: Predicted to enable nucleic acid binding activity. Predicted to be active in kinetochore. Orthologous to human GPATCH11 (G-patch domain containing 11); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; amitrole.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Ccdc75; coiled-coil domain containing 75; coiled-coil domain-containing protein 75; G patch domain-containing protein 11; LOC362685; RGD1311424; similar to hypothetical protein FLJ38348
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
GRCr8621,982,074 - 21,995,562 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl621,985,202 - 21,995,381 (-)EnsemblGRCr8
mRatBN7.2616,229,933 - 16,243,305 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl616,233,059 - 16,243,238 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx616,542,293 - 16,552,463 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0616,864,501 - 16,874,671 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0616,345,431 - 16,355,636 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.061,410,461 - 1,421,506 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl61,410,507 - 1,423,041 (+)Ensemblrn6Rnor6.0
Rnor_5.061,401,697 - 1,412,259 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.461,619,937 - 1,630,116 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera615,888,195 - 15,898,395 (-)NCBICelera
RGSC_v3.161,619,941 - 1,629,692 (+)NCBI
Cytogenetic Map6q12NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
kinetochore  (IBA,ISO)
nucleoplasm  (IEA,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. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:20813266  


Genomics

Comparative Map Data
Gpatch11
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8621,982,074 - 21,995,562 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl621,985,202 - 21,995,381 (-)EnsemblGRCr8
mRatBN7.2616,229,933 - 16,243,305 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl616,233,059 - 16,243,238 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx616,542,293 - 16,552,463 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0616,864,501 - 16,874,671 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0616,345,431 - 16,355,636 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.061,410,461 - 1,421,506 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl61,410,507 - 1,423,041 (+)Ensemblrn6Rnor6.0
Rnor_5.061,401,697 - 1,412,259 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.461,619,937 - 1,630,116 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera615,888,195 - 15,898,395 (-)NCBICelera
RGSC_v3.161,619,941 - 1,629,692 (+)NCBI
Cytogenetic Map6q12NCBI
GPATCH11
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38237,084,518 - 37,099,244 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl237,084,482 - 37,099,244 (+)Ensemblhg38GRCh38
GRCh37237,311,661 - 37,326,387 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36237,165,165 - 37,177,206 (+)NCBIBuild 36Build 36hg18NCBI36
Celera237,152,623 - 37,164,767 (+)NCBICelera
Cytogenetic Map2p22.2NCBI
HuRef237,051,794 - 37,066,588 (+)NCBIHuRef
CHM1_1237,240,939 - 37,255,733 (+)NCBICHM1_1
T2T-CHM13v2.0237,091,653 - 37,106,376 (+)NCBIT2T-CHM13v2.0
Gpatch11
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391779,142,951 - 79,155,737 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1779,142,996 - 79,155,737 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381778,835,516 - 78,848,308 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1778,835,567 - 78,848,308 (+)Ensemblmm10GRCm38
MGSCv371779,234,856 - 79,247,648 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361778,740,647 - 78,753,366 (+)NCBIMGSCv36mm8
MGSCv361778,091,174 - 78,103,893 (+)NCBIMGSCv36mm8
Celera1783,152,129 - 83,164,888 (+)NCBICelera
Cytogenetic Map17E3NCBI
cM Map1749.54NCBI
Gpatch11
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554414,879,338 - 4,891,807 (+)Ensembl
ChiLan1.0NW_0049554414,879,410 - 4,890,775 (+)NCBIChiLan1.0ChiLan1.0
GPATCH11
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21289,378,452 - 89,397,011 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12A89,382,428 - 89,400,987 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02A37,110,121 - 37,125,223 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12A37,874,996 - 37,888,341 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A37,874,996 - 37,888,341 (+)EnsemblpanPan2panpan1.1
GPATCH11
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11729,478,352 - 29,489,207 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1729,293,020 - 29,306,050 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01730,128,549 - 30,141,590 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1730,128,550 - 30,141,586 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11729,356,108 - 29,369,134 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01729,419,150 - 29,432,176 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01729,637,238 - 29,650,269 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Gpatch11
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629242,500,653 - 42,511,747 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366631,167,025 - 1,177,226 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366631,167,105 - 1,177,197 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GPATCH11
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl3103,098,588 - 103,119,512 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.13103,100,083 - 103,111,998 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.23109,679,720 - 109,691,696 (-)NCBISscrofa10.2Sscrofa10.2susScr3
GPATCH11
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11470,302,399 - 70,309,392 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1470,302,511 - 70,314,491 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604541,638,281 - 41,653,325 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Gpatch11
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473818,696,583 - 18,710,669 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Gpatch11
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1714,390,511 - 14,401,596 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Gpatch11
12 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:307
Count of miRNA genes:194
Interacting mature miRNAs:226
Transcripts:ENSRNOT00000034919
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
8552962Pigfal16Plasma insulin-like growth factor 1 level QTL 169.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)6197587946975879Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6197587946975879Rat
1598843Cm63Cardiac mass QTL 632.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)6144788383Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6197587946975879Rat
8693699Alc37Alcohol consumption QTL 372.60.224drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)61371716927053860Rat
2293706Bmd20Bone mineral density QTL 204.30.0002femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)6125740059Rat
2292616Ept15Estrogen-induced pituitary tumorigenesis QTL 154.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)6144788383Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6197587946975879Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)62009763565097635Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)620859430113082285Rat
2301964Bp323Blood pressure QTL 3234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6186868070Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6323998948239989Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6323998948239989Rat
1300128Rf16Renal function QTL 163.89renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6140163351Rat
70199Coreg1Compensatory renal growth QTL 111.8kidney mass (VT:0002707)compensatory renal growth score (CMO:0001894)61459947363457687Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)62009763565097635Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6323998948239989Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)61608937261967788Rat
1358190Ept1Estrogen-induced pituitary tumorigenesis QTL 14.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)6144788383Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6323998948239989Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6197587946975879Rat
8693690Alc35Alcohol consumption QTL 352.20.606drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)61371716927053860Rat


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 12 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000034919   ⟹   ENSRNOP00000031805
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl621,985,202 - 21,995,381 (-)Ensembl
mRatBN7.2 Ensembl616,233,059 - 16,243,238 (-)Ensembl
Rnor_6.0 Ensembl61,410,507 - 1,423,041 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000107573   ⟹   ENSRNOP00000077849
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl616,233,059 - 16,239,852 (-)Ensembl
RefSeq Acc Id: NM_001108700   ⟹   NP_001102170
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8621,985,202 - 21,995,381 (-)NCBI
mRatBN7.2616,233,059 - 16,243,238 (-)NCBI
Rnor_6.061,410,562 - 1,420,741 (+)NCBI
Rnor_5.061,401,697 - 1,412,259 (+)NCBI
RGSC_v3.461,619,937 - 1,630,116 (+)RGD
Celera615,888,195 - 15,898,395 (-)RGD
Sequence:
RefSeq Acc Id: XM_006239636   ⟹   XP_006239698
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8621,982,074 - 21,995,459 (-)NCBI
mRatBN7.2616,229,933 - 16,243,276 (-)NCBI
Rnor_6.061,410,461 - 1,421,506 (+)NCBI
Rnor_5.061,401,697 - 1,412,259 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039112453   ⟹   XP_038968381
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8621,982,074 - 21,995,477 (-)NCBI
mRatBN7.2616,229,933 - 16,243,299 (-)NCBI
RefSeq Acc Id: XM_063262044   ⟹   XP_063118114
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8621,985,772 - 21,995,562 (-)NCBI
RefSeq Acc Id: XR_010052099
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8621,985,772 - 21,995,562 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001102170 (Get FASTA)   NCBI Sequence Viewer  
  XP_006239698 (Get FASTA)   NCBI Sequence Viewer  
  XP_038968381 (Get FASTA)   NCBI Sequence Viewer  
  XP_063118114 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM02809 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000031805
  ENSRNOP00000031805.6
RefSeq Acc Id: NP_001102170   ⟸   NM_001108700
- UniProtKB: F1LV52 (UniProtKB/TrEMBL),   A6H9V4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006239698   ⟸   XM_006239636
- Peptide Label: isoform X2
- UniProtKB: F1LV52 (UniProtKB/TrEMBL),   A6H9V4 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000031805   ⟸   ENSRNOT00000034919
RefSeq Acc Id: XP_038968381   ⟸   XM_039112453
- Peptide Label: isoform X2
- UniProtKB: A6H9V4 (UniProtKB/TrEMBL),   F1LV52 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000077849   ⟸   ENSRNOT00000107573
RefSeq Acc Id: XP_063118114   ⟸   XM_063262044
- Peptide Label: isoform X1
- UniProtKB: F1LV52 (UniProtKB/TrEMBL)
Protein Domains
G-patch

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LV52-F1-model_v2 AlphaFold F1LV52 1-260 view protein structure

Transcriptome

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

Promoters
RGD ID:13694353
Promoter ID:EPDNEW_R4878
Type:multiple initiation site
Name:Gpatch11_1
Description:G patch domain containing 11
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_6.061,410,523 - 1,410,583EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311424 AgrOrtholog
BioCyc Gene G2FUF-38487 BioCyc
Ensembl Genes ENSRNOG00000025317 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000034919 ENTREZGENE
  ENSRNOT00000034919.7 UniProtKB/TrEMBL
InterPro DUF4187 UniProtKB/TrEMBL
  G_patch UniProtKB/TrEMBL
  GPATCH11 UniProtKB/TrEMBL
KEGG Report rno:362685 UniProtKB/TrEMBL
NCBI Gene 362685 ENTREZGENE
PANTHER G PATCH DOMAIN-CONTAINING PROTEIN 11 UniProtKB/TrEMBL
  PTHR21032 UniProtKB/TrEMBL
Pfam DUF4187 UniProtKB/TrEMBL
  G-patch UniProtKB/TrEMBL
PhenoGen Gpatch11 PhenoGen
PROSITE G_PATCH UniProtKB/TrEMBL
RatGTEx ENSRNOG00000025317 RatGTEx
SMART DUF4187 UniProtKB/TrEMBL
  G_patch UniProtKB/TrEMBL
UniProt A6H9V4 ENTREZGENE, UniProtKB/TrEMBL
  F1LV52 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-02-06 Gpatch11  G patch domain containing 11  Ccdc75  coiled-coil domain containing 75  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-10-16 Ccdc75  coiled-coil domain containing 75  RGD1311424  similar to hypothetical protein FLJ38348   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1311424  similar to hypothetical protein FLJ38348   RGD1311424_predicted  similar to hypothetical protein FLJ38348 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1311424_predicted  similar to hypothetical protein FLJ38348 (predicted)  LOC362685_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC362685_predicted  similar to hypothetical protein FLJ38348 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL