Shoc1 (shortage in chiasmata 1) - Rat Genome Database

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Gene: Shoc1 (shortage in chiasmata 1) Rattus norvegicus
Analyze
Symbol: Shoc1
Name: shortage in chiasmata 1
RGD ID: 1586646
Description: Predicted to enable ATP hydrolysis activity and single-stranded DNA binding activity. Predicted to be involved in resolution of meiotic recombination intermediates and synaptonemal complex assembly. Predicted to be located in chromosome. Predicted to be active in condensed nuclear chromosome. Human ortholog(s) of this gene implicated in spermatogenic failure 75. Orthologous to human SHOC1 (shortage in chiasmata 1); INTERACTS WITH bisphenol A; 17beta-estradiol (ortholog); 2-hydroxypropanoic acid (ortholog).
Type: protein-coding
RefSeq Status: MODEL
Previously known as: AABR07048387.1; hypothetical protein LOC686050; LOC686050; uncharacterized protein C9orf84 homolog
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
GRCr8578,655,723 - 78,751,658 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl578,660,662 - 78,751,709 (-)EnsemblGRCr8
mRatBN7.2573,864,423 - 73,956,487 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl573,866,334 - 73,956,444 (-)EnsemblmRatBN7.2
Rnor_6.0576,190,486 - 76,298,723 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl576,240,167 - 76,261,198 (-)NCBIrn6Rnor6.0
Rnor_5.0580,334,292 - 80,442,339 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4577,093,824 - 77,164,496 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera572,686,689 - 72,778,720 (-)NCBICelera
Cytogenetic Map5q24NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
chromosome  (IEA,ISO)
condensed nuclear chromosome  (IBA,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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:29742103  


Genomics

Comparative Map Data
Shoc1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8578,655,723 - 78,751,658 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl578,660,662 - 78,751,709 (-)EnsemblGRCr8
mRatBN7.2573,864,423 - 73,956,487 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl573,866,334 - 73,956,444 (-)EnsemblmRatBN7.2
Rnor_6.0576,190,486 - 76,298,723 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl576,240,167 - 76,261,198 (-)NCBIrn6Rnor6.0
Rnor_5.0580,334,292 - 80,442,339 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4577,093,824 - 77,164,496 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera572,686,689 - 72,778,720 (-)NCBICelera
Cytogenetic Map5q24NCBI
SHOC1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389111,686,171 - 111,794,937 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9111,686,171 - 111,795,008 (-)Ensemblhg38GRCh38
GRCh379114,448,451 - 114,557,217 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369113,488,722 - 113,585,600 (-)NCBIBuild 36Build 36hg18NCBI36
Build 349111,579,727 - 111,636,778NCBI
Celera984,947,957 - 85,044,839 (-)NCBICelera
Cytogenetic Map9q31.3NCBI
HuRef984,047,403 - 84,144,313 (-)NCBIHuRef
CHM1_19114,595,271 - 114,692,121 (-)NCBICHM1_1
T2T-CHM13v2.09123,857,529 - 123,984,501 (-)NCBIT2T-CHM13v2.0
Shoc1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39459,041,984 - 59,138,983 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl459,043,753 - 59,138,983 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38459,041,984 - 59,138,983 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl459,043,753 - 59,138,983 (-)Ensemblmm10GRCm38
MGSCv37459,056,739 - 59,151,855 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36459,175,184 - 59,205,167 (-)NCBIMGSCv36mm8
Celera458,954,096 - 59,020,815 (-)NCBICelera
Cytogenetic Map4B3NCBI
cM Map432.36NCBI
Shoc1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541915,566,339 - 15,646,184 (+)Ensembl
ChiLan1.0NW_00495541915,563,949 - 15,644,502 (+)NCBIChiLan1.0ChiLan1.0
SHOC1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21127,635,179 - 27,750,951 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1927,637,541 - 27,746,362 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0982,816,269 - 82,916,515 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19110,978,485 - 111,085,856 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9110,978,485 - 111,085,856 (-)EnsemblpanPan2panpan1.1
SHOC1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11166,283,093 - 66,359,674 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1166,282,572 - 66,363,922 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1164,693,808 - 64,782,060 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01167,423,406 - 67,506,405 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
UMICH_Zoey_3.11165,933,499 - 66,021,936 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01165,957,013 - 66,045,252 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01166,646,988 - 66,735,531 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Shoc1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947181,594,843 - 181,649,662 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365591,612,615 - 1,671,648 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365591,616,910 - 1,671,678 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SHOC1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1252,466,222 - 252,562,066 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11252,465,893 - 252,555,063 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21283,273,032 - 283,350,699 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SHOC1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11227,716,014 - 27,820,858 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1227,720,405 - 27,821,674 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366603514,961,842 - 15,053,275 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Shoc1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476023,249,730 - 23,332,198 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462476023,220,294 - 23,332,094 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Shoc1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1192,313,667 - 92,396,325 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Shoc1
670 total Variants

QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1298067Scl15Serum cholesterol level QTL 154.80.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)53801167083011670Rat
1300115Hrtrt7Heart rate QTL 72.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)55266537294894052Rat
1357396Bw44Body weight QTL 444.19body mass (VT:0001259)body weight (CMO:0000012)573779642118779642Rat
6907115Mcs29Mammary carcinoma susceptibility QTL 29mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)53800433183004331Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)544924861153890773Rat
61380Edpm5Estrogen-dependent pituitary mass QTL 54.50.92pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)573779642103472210Rat
1358353Srcrtb2Stress Responsive Cort Basal QTL 23.480.003blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)52367149379046465Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)538207390136631402Rat
61386Bp49Blood pressure QTL 4916.6cerebrum integrity trait (VT:0010549)brain infarction volume (CMO:0001013)565089051103648916Rat
1331801Rf33Renal function QTL 334.149kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)548523123134369373Rat
2302381Bw84Body weight QTL 844.47body mass (VT:0001259)body mass index (BMI) (CMO:0000105)573779642118779642Rat
1357402Bw46Body weight QTL 464.47body mass (VT:0001259)body mass index (BMI) (CMO:0000105)573779642118779642Rat
1598807Glom12Glomerulus QTL 122.7kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)53801167083011670Rat
1302786Kidm8Kidney mass QTL 828.15kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)53801167083011670Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)565089051166764498Rat
1331782Rf36Renal function QTL 363.296kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)539019942102105896Rat
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)551657967166600247Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)555124766172190305Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)53998594884985948Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)5692228281330203Rat
7394708Emca11Estrogen-induced mammary cancer QTL 11mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)573176602118176602Rat
1576317Eutr2Estrogen induced uterine response QTL 20.01uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)53952692484526924Rat
1331773Scl26Serum cholesterol level QTL 263.065blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)54852312391770353Rat
1578673Bmd13Bone mineral density QTL 134.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)569474415114474415Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)560601597137492949Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)51001906491770353Rat
61359EaexExperimental allergic encephalomyelitis QTL x3nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)560511627105511627Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)536460764136631402Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)564589016109589016Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)574335621156302135Rat
2290005Mcs24Mammary carcinoma susceptibility QTL 24mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)569835120114835120Rat
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)51001906487027358Rat
2306971Anxrr21Anxiety related response QTL 219.47fear/anxiety-related behavior trait (VT:1000241)number of entries into a discrete space in an experimental apparatus (CMO:0000960)570969494136328156Rat
2316954Rf57Renal function QTL 570kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)56458901693503770Rat
2316959Gluco59Glucose level QTL 594.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)556546393101546393Rat
2312671Scl64Serum cholesterol level QTL 640.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)573779642118779642Rat
2316957Pur21Proteinuria QTL 216.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)56458901691762830Rat

Markers in Region
D5Got236  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr8578,749,376 - 78,749,623 (+)Marker Load Pipeline
RGSC_v3.4577,183,857 - 77,184,103UniSTSRGSC3.4
Celera572,776,625 - 72,776,851UniSTS
Cytogenetic Map5q24UniSTS
RH128541  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2573,893,961 - 73,894,178 (+)MAPPERmRatBN7.2
Rnor_6.0576,219,663 - 76,219,879NCBIRnor6.0
Rnor_5.0580,363,440 - 80,363,656UniSTSRnor5.0
RGSC_v3.4577,123,075 - 77,123,291UniSTSRGSC3.4
Celera572,716,200 - 72,716,416UniSTS
RH 3.4 Map5506.6UniSTS
Cytogenetic Map5q24UniSTS
RH130772  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr8578,713,496 - 78,713,691 (+)Marker Load Pipeline
mRatBN7.2573,918,454 - 73,918,649 (+)MAPPERmRatBN7.2
Rnor_6.0576,244,762 - 76,244,956NCBIRnor6.0
Rnor_5.0580,388,539 - 80,388,733UniSTSRnor5.0
RGSC_v3.4577,148,084 - 77,148,278UniSTSRGSC3.4
Celera572,740,779 - 72,740,973UniSTS
RH 3.4 Map5507.3UniSTS
Cytogenetic Map5q24UniSTS
RH139258  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2573,904,354 - 73,904,507 (+)MAPPERmRatBN7.2
Rnor_6.0576,230,433 - 76,230,585NCBIRnor6.0
Rnor_5.0580,374,210 - 80,374,362UniSTSRnor5.0
RGSC_v3.4577,133,984 - 77,134,136UniSTSRGSC3.4
Celera572,726,642 - 72,726,794UniSTS
Cytogenetic Map5q24UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
hemolymphoid system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
sensory system
visual system
6 1 14 42 52 106 74 9 43 26 30 14 14

Sequence


Ensembl Acc Id: ENSRNOT00000087380   ⟹   ENSRNOP00000071212
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl578,660,662 - 78,751,709 (-)Ensembl
mRatBN7.2 Ensembl573,866,334 - 73,956,444 (-)Ensembl
RefSeq Acc Id: XM_039111042   ⟹   XP_038966970
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8578,655,723 - 78,751,658 (-)NCBI
mRatBN7.2573,864,423 - 73,956,487 (-)NCBI
RefSeq Acc Id: XM_039111043   ⟹   XP_038966971
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8578,655,723 - 78,751,658 (-)NCBI
mRatBN7.2573,864,423 - 73,956,487 (-)NCBI
RefSeq Acc Id: XM_039111044   ⟹   XP_038966972
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8578,655,723 - 78,744,269 (-)NCBI
mRatBN7.2573,864,423 - 73,949,229 (-)NCBI
RefSeq Acc Id: XM_039111045   ⟹   XP_038966973
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8578,655,723 - 78,744,269 (-)NCBI
mRatBN7.2573,864,423 - 73,949,229 (-)NCBI
RefSeq Acc Id: XM_063288534   ⟹   XP_063144604
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8578,655,723 - 78,744,209 (-)NCBI
RefSeq Acc Id: XP_038966971   ⟸   XM_039111043
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038966970   ⟸   XM_039111042
- Peptide Label: isoform X1
- UniProtKB: A0A0G2JZW6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038966973   ⟸   XM_039111045
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038966972   ⟸   XM_039111044
- Peptide Label: isoform X3
Ensembl Acc Id: ENSRNOP00000071212   ⟸   ENSRNOT00000087380
RefSeq Acc Id: XP_063144604   ⟸   XM_063288534
- Peptide Label: isoform X3

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2JZW6-F1-model_v2 AlphaFold A0A0G2JZW6 1-378 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1586646 AgrOrtholog
BioCyc Gene G2FUF-41160 BioCyc
Ensembl Genes ENSRNOG00000060520 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000087380 ENTREZGENE
  ENSRNOT00000087380.3 UniProtKB/TrEMBL
InterPro SHOC1 UniProtKB/TrEMBL
NCBI Gene 686050 ENTREZGENE
PANTHER PROTEIN SHORTAGE IN CHIASMATA 1 ORTHOLOG UniProtKB/TrEMBL
  PTHR35668 UniProtKB/TrEMBL
Pfam DUF5587 UniProtKB/TrEMBL
PhenoGen Shoc1 PhenoGen
RatGTEx ENSRNOG00000060520 RatGTEx
UniProt A0A0G2JZW6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-02 Shoc1  shortage in chiasmata 1  AABR07048387.1    Data merged from RGD:15013386 737654 PROVISIONAL
2019-11-08 AABR07048387.1        Symbol and Name status set to provisional 45752 PROVISIONAL
2018-12-04 Shoc1  shortage in chiasmata 1  LOC686050  hypothetical protein LOC686050  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC686050  hypothetical protein LOC686050  LOC682456  hypothetical protein LOC682456  Data merged from RGD:1583436 1643240 APPROVED
2006-11-19 LOC686050  hypothetical protein LOC686050      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC682456  hypothetical protein LOC682456      Symbol and Name status set to provisional 70820 PROVISIONAL