Spocd1 (SPOC domain containing 1) - Rat Genome Database

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Gene: Spocd1 (SPOC domain containing 1) Rattus norvegicus
Analyze
Symbol: Spocd1
Name: SPOC domain containing 1
RGD ID: 1560989
Description: Predicted to be involved in DNA methylation; retrotransposon silencing; and spermatogenesis. Predicted to be located in nucleus. Orthologous to human SPOCD1 (SPOC domain containing 1); INTERACTS WITH bisphenol A; 17beta-estradiol (ortholog); 2,2',4,4'-Tetrabromodiphenyl ether (ortholog).
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC313060; RGD1560989; similar to SPOC domain containing 1; SPOC domain containing 1, pseudogene 1; SPOC domain-containing protein 1; Spocd1-ps1
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
GRCr85147,573,460 - 147,581,165 (+)NCBIGRCr8
mRatBN7.25142,288,822 - 142,297,113 (+)NCBImRatBN7.2mRatBN7.2
Rnor_6.05148,138,309 - 148,166,567 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.05151,863,962 - 151,886,106 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45148,970,198 - 148,979,672 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera5140,738,589 - 140,766,618 (+)NCBICelera
Cytogenetic Map5q36NCBI
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

Biological Process

Cellular Component
nucleus  (ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. GOA pipeline RGD automated data pipeline
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:19389623  


Genomics

Comparative Map Data
Spocd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85147,573,460 - 147,581,165 (+)NCBIGRCr8
mRatBN7.25142,288,822 - 142,297,113 (+)NCBImRatBN7.2mRatBN7.2
Rnor_6.05148,138,309 - 148,166,567 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.05151,863,962 - 151,886,106 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45148,970,198 - 148,979,672 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera5140,738,589 - 140,766,618 (+)NCBICelera
Cytogenetic Map5q36NCBI
SPOCD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38131,790,422 - 31,816,022 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl131,790,422 - 31,816,022 (-)EnsemblGRCh38hg38GRCh38
GRCh37132,256,023 - 32,281,623 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36132,028,612 - 32,054,167 (-)NCBINCBI36Build 36hg18NCBI36
Build 34131,925,117 - 31,950,673NCBI
Celera130,525,263 - 30,551,501 (-)NCBICelera
Cytogenetic Map1p35.2NCBI
HuRef130,373,146 - 30,398,177 (-)NCBIHuRef
CHM1_1132,371,716 - 32,397,303 (-)NCBICHM1_1
T2T-CHM13v2.0131,648,071 - 31,674,002 (-)NCBIT2T-CHM13v2.0
Spocd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394129,822,560 - 129,850,908 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl4129,823,042 - 129,850,908 (+)EnsemblGRCm39 Ensembl
GRCm384129,928,767 - 129,957,115 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4129,929,249 - 129,957,115 (+)EnsemblGRCm38mm10GRCm38
MGSCv374129,624,974 - 129,634,237 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv364129,449,851 - 129,474,477 (+)NCBIMGSCv36mm8
Celera4128,254,853 - 128,291,833 (+)NCBICelera
Cytogenetic Map4D2.2NCBI
cM Map463.43NCBI
Spocd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495545210,192,076 - 10,214,914 (-)NCBIChiLan1.0ChiLan1.0
SPOCD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21195,011,449 - 195,039,381 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11194,133,173 - 194,161,073 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0131,074,169 - 31,100,378 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1132,091,296 - 32,116,993 (-)NCBIpanpan1.1PanPan1.1panPan2
SPOCD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1269,254,343 - 69,326,588 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl269,289,328 - 69,326,595 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha265,834,359 - 65,906,031 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0269,820,558 - 69,892,087 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1266,656,573 - 66,728,022 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0267,652,653 - 67,724,147 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0268,652,370 - 68,723,679 (+)NCBIUU_Cfam_GSD_1.0
LOC101963659
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505849,066,533 - 49,089,586 (-)NCBIHiC_Itri_2
SpeTri2.0NW_00493647414,894,564 - 14,918,088 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SPOCD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl688,323,080 - 88,349,963 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1688,323,119 - 88,349,194 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2682,187,353 - 82,211,609 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SPOCD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120101,052,445 - 101,080,826 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl20101,052,823 - 101,080,648 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603315,610,820 - 15,638,954 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Spocd1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476415,025,755 - 15,052,718 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Spocd1
27 total Variants

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1298089Scl14Serum cholesterol level QTL 145.80.0004blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)5108845856153845856Rat
631562Apr2Acute phase response QTL 23.7blood murinoglobulin 1 amount (VT:0010597)plasma murinoglobulin 1 level (CMO:0001931)5135927956166875058Rat
738018Anxrr4Anxiety related response QTL 45.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)5130130159166875058Rat
8657050Bw146Body weight QTL 14619.840.001body mass (VT:0001259)body weight gain (CMO:0000420)5108938288153938288Rat
8694441Bw169Body weight QTL 16917.610.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)5111416838156416838Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5131345754166875058Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5128506074166875058Rat
8694198Abfw3Abdominal fat weight QTL 316.130.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)5111416838156416838Rat
8694389Bw160Body weight QTL 1606.170.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)5111416838156416838Rat
631505Bp103Blood pressure QTL 1033.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5132717196165560427Rat
634349Bp139Blood pressure QTL 1390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5128924607166875058Rat
8552960Pigfal15Plasma insulin-like growth factor 1 level QTL 15blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5111416838156416838Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5128506074166875058Rat
7207488Bss110Bone structure and strength QTL 18.4femur strength trait (VT:0010010)femur stiffness (CMO:0001674)5106906205151906205Rat
7207491Bss112Bone structure and strength QTL 1127femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)5106906205151906205Rat
7207481Bss106Bone structure and strength QTL 1067.9femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5106906205151906205Rat
7207486Bss109Bone structure and strength QTL 109femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)5106906205151906205Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5124965598166875058Rat
1331803Rf32Renal function QTL 322.798kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)5129132428143070159Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)569540295151018848Rat
1549838Bss4Bone structure and strength QTL 49.2femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)5106906205151906205Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540128307148607290Rat
1358187Emca1Estrogen-induced mammary cancer QTL 14.4mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)599216724148607142Rat
1581510Cm54Cardiac mass QTL 543.40.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)5120740824143608494Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5127798274166875058Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)546711509161317411Rat
1578673Bmd13Bone mineral density QTL 134.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)5103689353148689353Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)560293434161481680Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)559793399143070159Rat
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5135929696166875058Rat
70156Niddm30Non-insulin dependent diabetes mellitus QTL 303.98blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)5129132447151006154Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5126424772166875058Rat
2317056Wbc3White blood cell count QTL 32.510.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)5105999803150999803Rat
2293642Bss37Bone structure and strength QTL 374.640.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5120740824151018848Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5121846814166846814Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5127798274166875058Rat
1331796Thshl2Thyroid stimulating hormone level QTL 22.3blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)597059760147465714Rat
1598847Cm62Cardiac mass QTL 623.4heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5108845856153845856Rat
61452Ciaa5CIA Autoantibody QTL 53.5blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)594858972143070159Rat

Markers in Region
D4Wehi5  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25142,296,190 - 142,296,358 (+)MAPPERmRatBN7.2
Rnor_6.05148,165,645 - 148,165,812NCBIRnor6.0
Rnor_5.05151,885,184 - 151,885,351UniSTSRnor5.0
Celera5140,765,695 - 140,765,863UniSTS
Cytogenetic Map5q36UniSTS


Expression


Sequence


RefSeq Acc Id: XM_063261356   ⟹   XP_063117426
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85147,573,460 - 147,581,165 (+)NCBI
Protein Sequences
Protein RefSeqs XP_063117426 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL80576 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: XP_063117426   ⟸   XM_063261356


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1560989 AgrOrtholog
BioCyc Gene G2FUF-39771 BioCyc
NCBI Gene 313060 ENTREZGENE
PhenoGen Spocd1 PhenoGen


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-03-07 Spocd1  SPOC domain containing 1  Spocd1-ps1  SPOC domain containing 1, pseudogene 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-06-09 Spocd1-ps1  SPOC domain containing 1, pseudogene 1  Spocd1  SPOC domain containing 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-04-23 Spocd1  SPOC domain containing 1  RGD1560989  similar to SPOC domain containing 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1560989  similar to SPOC domain containing 1   RGD1560989_predicted  similar to SPOC domain containing 1 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1560989_predicted  similar to SPOC domain containing 1 (predicted)  LOC313060  similar to SPOC domain containing 1  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC313060  similar to SPOC domain containing 1      Symbol and Name status set to provisional 70820 PROVISIONAL