Sec22c (SEC22 homolog C, vesicle trafficking protein) - Rat Genome Database

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Gene: Sec22c (SEC22 homolog C, vesicle trafficking protein) Rattus norvegicus
Analyze
Symbol: Sec22c
Name: SEC22 homolog C, vesicle trafficking protein
RGD ID: 1590146
Description: Predicted to be located in endoplasmic reticulum membrane. Orthologous to human SEC22C (SEC22 homolog C, vesicle trafficking protein); INTERACTS WITH bisphenol A; gentamycin; N,N-diethyl-m-toluamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC687022; SEC22 vesicle trafficking protein homolog C; SEC22 vesicle trafficking protein homolog C (S. cerevisiae); similar to SEC22 vesicle trafficking protein-like 3; vesicle-trafficking protein SEC22c
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
GRCr88130,223,349 - 130,249,079 (-)NCBIGRCr8
mRatBN7.28121,345,839 - 121,371,509 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8121,350,107 - 121,370,925 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.08130,319,682 - 130,345,774 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8130,324,495 - 130,338,325 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08129,503,117 - 129,526,994 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera8120,480,730 - 120,505,718 (-)NCBICelera
Cytogenetic Map8q32NCBI
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

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. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Sec22c
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88130,223,349 - 130,249,079 (-)NCBIGRCr8
mRatBN7.28121,345,839 - 121,371,509 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8121,350,107 - 121,370,925 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.08130,319,682 - 130,345,774 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8130,324,495 - 130,338,325 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08129,503,117 - 129,526,994 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera8120,480,730 - 120,505,718 (-)NCBICelera
Cytogenetic Map8q32NCBI
SEC22C
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38342,547,969 - 42,601,078 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl342,547,969 - 42,601,080 (-)EnsemblGRCh38hg38GRCh38
GRCh37342,589,461 - 42,642,570 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36342,564,476 - 42,598,432 (-)NCBINCBI36Build 36hg18NCBI36
Celera342,529,876 - 42,563,833 (-)NCBICelera
Cytogenetic Map3p22.1NCBI
HuRef342,633,575 - 42,688,134 (-)NCBIHuRef
CHM1_1342,540,655 - 42,593,764 (-)NCBICHM1_1
T2T-CHM13v2.0342,565,963 - 42,619,072 (-)NCBIT2T-CHM13v2.0
Sec22c
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399121,509,111 - 121,534,614 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl9121,509,111 - 121,534,556 (-)EnsemblGRCm39 Ensembl
GRCm389121,680,045 - 121,705,548 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9121,680,045 - 121,705,490 (-)EnsemblGRCm38mm10GRCm38
MGSCv379121,589,163 - 121,614,147 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv369121,531,726 - 121,553,657 (-)NCBIMGSCv36mm8
Celera9122,153,707 - 122,178,246 (-)NCBICelera
Cytogenetic Map9F4NCBI
cM Map972.54NCBI
Sec22c
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542028,210,790 - 28,230,444 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542028,210,912 - 28,227,015 (+)NCBIChiLan1.0ChiLan1.0
SEC22C
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2242,510,031 - 42,570,645 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1342,514,791 - 42,575,400 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0342,452,946 - 42,506,666 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1342,715,553 - 43,571,517 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl342,715,553 - 42,736,927 (-)Ensemblpanpan1.1panPan2
SEC22C
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12311,679,576 - 11,708,047 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2311,684,002 - 11,706,184 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2311,653,981 - 11,682,451 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02311,969,044 - 11,997,549 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2311,969,050 - 11,997,139 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12311,770,604 - 11,799,078 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02311,912,887 - 11,941,345 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02311,917,185 - 11,945,684 (-)NCBIUU_Cfam_GSD_1.0
Sec22c
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118200,174,482 - 200,238,975 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366952,527,205 - 2,550,293 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366952,525,662 - 2,568,691 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SEC22C
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1326,083,226 - 26,107,223 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11326,080,934 - 26,125,120 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21328,748,153 - 28,792,135 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SEC22C
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1223,995,170 - 4,029,992 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl224,000,461 - 4,029,660 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666041163,168,762 - 163,204,155 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sec22c
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473077,102,692 - 77,120,823 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473077,097,879 - 77,124,284 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Sec22c
172 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:93
Count of miRNA genes:79
Interacting mature miRNAs:85
Transcripts:ENSRNOT00000071697
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
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)876468691121468691Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)882460758122812818Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)893535351123900184Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)895718998123900184Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)895718998123900184Rat

Markers in Region
BF397064  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28121,350,218 - 121,350,343 (+)MAPPERmRatBN7.2
Rnor_6.08130,324,061 - 130,324,185NCBIRnor6.0
Rnor_5.08129,507,496 - 129,507,620UniSTSRnor5.0
Celera8120,485,109 - 120,485,233UniSTS
RH 3.4 Map81254.69UniSTS
AW534512  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28121,349,040 - 121,349,219 (+)MAPPERmRatBN7.2
Rnor_6.08130,322,883 - 130,323,061NCBIRnor6.0
Rnor_5.08129,506,318 - 129,506,496UniSTSRnor5.0
Celera8120,483,931 - 120,484,109UniSTS
RH 3.4 Map81256.1UniSTS


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 2 6 8 2 8 2 74 18 33 2
Low 1 37 49 39 11 39 8 11 17 8 9 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001427607 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006226626 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006226627 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006226628 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008757887 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008766703 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017603743 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039082760 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039082761 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039082762 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039082765 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039082766 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039082767 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039082768 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063266150 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063266151 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063266153 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH473954 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000008 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000071697   ⟹   ENSRNOP00000063993
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8121,350,107 - 121,370,925 (-)Ensembl
Rnor_6.0 Ensembl8130,324,495 - 130,338,325 (-)Ensembl
RefSeq Acc Id: NM_001427607   ⟹   NP_001414536
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88130,223,349 - 130,247,852 (-)NCBI
RefSeq Acc Id: XM_039082760   ⟹   XP_038938688
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88130,223,349 - 130,247,856 (-)NCBI
mRatBN7.28121,345,839 - 121,370,345 (-)NCBI
RefSeq Acc Id: XM_039082761   ⟹   XP_038938689
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88130,223,349 - 130,247,868 (-)NCBI
mRatBN7.28121,345,839 - 121,370,357 (-)NCBI
RefSeq Acc Id: XM_039082762   ⟹   XP_038938690
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88130,223,349 - 130,249,079 (-)NCBI
mRatBN7.28121,345,839 - 121,371,509 (-)NCBI
RefSeq Acc Id: XM_039082765   ⟹   XP_038938693
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88130,223,349 - 130,240,275 (-)NCBI
mRatBN7.28121,345,839 - 121,362,767 (-)NCBI
RefSeq Acc Id: XM_039082766   ⟹   XP_038938694
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88130,232,690 - 130,247,856 (-)NCBI
mRatBN7.28121,355,181 - 121,370,345 (-)NCBI
RefSeq Acc Id: XM_039082767   ⟹   XP_038938695
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88130,223,349 - 130,240,280 (-)NCBI
mRatBN7.28121,345,839 - 121,362,765 (-)NCBI
RefSeq Acc Id: XM_039082768   ⟹   XP_038938696
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88130,223,349 - 130,240,280 (-)NCBI
mRatBN7.28121,345,839 - 121,362,765 (-)NCBI
RefSeq Acc Id: XM_063266150   ⟹   XP_063122220
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88130,223,349 - 130,249,079 (-)NCBI
RefSeq Acc Id: XM_063266151   ⟹   XP_063122221
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88130,223,349 - 130,247,875 (-)NCBI
RefSeq Acc Id: XM_063266153   ⟹   XP_063122223
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88130,223,349 - 130,240,280 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000063993   ⟸   ENSRNOT00000071697
RefSeq Acc Id: XP_038938690   ⟸   XM_039082762
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038938689   ⟸   XM_039082761
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038938688   ⟸   XM_039082760
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038938693   ⟸   XM_039082765
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038938695   ⟸   XM_039082767
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038938696   ⟸   XM_039082768
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038938694   ⟸   XM_039082766
- Peptide Label: isoform X4
RefSeq Acc Id: XP_063122220   ⟸   XM_063266150
- Peptide Label: isoform X2
- UniProtKB: M0R3S2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063122221   ⟸   XM_063266151
- Peptide Label: isoform X2
- UniProtKB: M0R3S2 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001414536   ⟸   NM_001427607
- UniProtKB: M0R3S2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063122223   ⟸   XM_063266153
- Peptide Label: isoform X7
Protein Domains
Longin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0R3S2-F1-model_v2 AlphaFold M0R3S2 1-302 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:1590146 AgrOrtholog
BioCyc Gene G2FUF-28684 BioCyc
Ensembl Genes ENSRNOG00000047873 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000071697.3 UniProtKB/TrEMBL
Gene3D-CATH Longin domain UniProtKB/TrEMBL
InterPro Longin-like_dom UniProtKB/TrEMBL
  Longin_dom UniProtKB/TrEMBL
  Sec22a/c UniProtKB/TrEMBL
NCBI Gene 687022 ENTREZGENE
PANTHER PTHR46258 UniProtKB/TrEMBL
  VESICLE-TRAFFICKING PROTEIN SEC22C UniProtKB/TrEMBL
Pfam Longin UniProtKB/TrEMBL
PhenoGen Sec22c PhenoGen
PROSITE LONGIN UniProtKB/TrEMBL
RatGTEx ENSRNOG00000047873 RatGTEx
SMART Longin UniProtKB/TrEMBL
Superfamily-SCOP SSF64356 UniProtKB/TrEMBL
UniProt A6I449_RAT UniProtKB/TrEMBL
  M0R3S2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-08-13 Sec22c  SEC22 homolog C, vesicle trafficking protein  Sec22c  SEC22 vesicle trafficking protein homolog C (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-10-03 Sec22c  SEC22 vesicle trafficking protein homolog C (S. cerevisiae)  LOC687022  similar to SEC22 vesicle trafficking protein-like 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC687022  similar to SEC22 vesicle trafficking protein-like 3      Symbol and Name status set to provisional 70820 PROVISIONAL