Sec16a (SEC16 homolog A, endoplasmic reticulum export factor) - Rat Genome Database

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Gene: Sec16a (SEC16 homolog A, endoplasmic reticulum export factor) Rattus norvegicus
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Symbol: Sec16a
Name: SEC16 homolog A, endoplasmic reticulum export factor
RGD ID: 2322350
Description: Predicted to be involved in several processes, including Golgi vesicle transport; protein localization to endoplasmic reticulum exit site; and protein stabilization. Predicted to localize to several cellular components, including ER to Golgi transport vesicle membrane; endoplasmic reticulum; and perinuclear region of cytoplasm. Orthologous to human SEC16A (SEC16 homolog A, endoplasmic reticulum export factor); PARTICIPATES IN inositol phosphate metabolic pathway; phosphatidylinositol 3-kinase signaling pathway; INTERACTS WITH bisphenol A; Brodifacoum; cadmium dichloride.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: LOC100360302; SEC16 homolog A; SEC16 homolog A (S. cerevisiae); SEC16 homolog A-like
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.239,229,687 - 9,264,837 (-)NCBI
Rnor_6.0 Ensembl33,856,218 - 3,890,758 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.033,856,218 - 3,890,785 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.039,217,446 - 9,252,578 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.434,583,882 - 4,613,980 (-)NCBIRGSC3.4rn4RGSC3.4
Celera34,049,023 - 4,084,074 (-)NCBICelera
Cytogenetic Map3p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:8889548   PMID:11596118   PMID:17428803   PMID:19638414   PMID:21768384   PMID:22355596   PMID:22740409   PMID:22926577   PMID:25002582   PMID:25201882   PMID:27354378   PMID:28067262  
PMID:28442536   PMID:29300766  


Genomics

Comparative Map Data
Sec16a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.239,229,687 - 9,264,837 (-)NCBI
Rnor_6.0 Ensembl33,856,218 - 3,890,758 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.033,856,218 - 3,890,785 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.039,217,446 - 9,252,578 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.434,583,882 - 4,613,980 (-)NCBIRGSC3.4rn4RGSC3.4
Celera34,049,023 - 4,084,074 (-)NCBICelera
Cytogenetic Map3p13NCBI
SEC16A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl9136,440,096 - 136,483,759 (-)EnsemblGRCh38hg38GRCh38
GRCh389136,440,096 - 136,484,552 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh379139,334,557 - 139,378,235 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369138,454,369 - 138,497,328 (-)NCBINCBI36hg18NCBI36
Celera9109,849,015 - 109,891,964 (-)NCBI
Cytogenetic Map9q34.3NCBI
HuRef9108,793,635 - 108,837,485 (-)NCBIHuRef
CHM1_19139,482,991 - 139,526,945 (-)NCBICHM1_1
Sec16a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39226,299,443 - 26,336,138 (-)NCBIGRCm39mm39
GRCm39 Ensembl226,299,443 - 26,335,228 (-)Ensembl
GRCm38226,409,431 - 26,446,293 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl226,409,431 - 26,445,216 (-)EnsemblGRCm38mm10GRCm38
MGSCv37226,264,951 - 26,300,736 (-)NCBIGRCm37mm9NCBIm37
MGSCv36226,231,445 - 26,250,355 (-)NCBImm8
Celera226,127,145 - 26,163,053 (-)NCBICelera
Cytogenetic Map2A3NCBI
Sec16a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555134,273,581 - 4,303,157 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555134,272,623 - 4,304,314 (+)NCBIChiLan1.0ChiLan1.0
SEC16A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.19136,493,957 - 136,533,672 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9136,493,957 - 136,533,655 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v09107,516,556 - 107,560,930 (-)NCBIMhudiblu_PPA_v0panPan3
SEC16A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1949,027,190 - 49,060,858 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl949,031,669 - 49,060,848 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha948,277,816 - 48,311,534 (+)NCBI
ROS_Cfam_1.0949,903,885 - 49,937,614 (+)NCBI
UMICH_Zoey_3.1948,684,649 - 48,718,370 (+)NCBI
UNSW_CanFamBas_1.0948,978,370 - 49,012,325 (+)NCBI
UU_Cfam_GSD_1.0949,026,101 - 49,059,830 (+)NCBI
Sec16a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947201,999,577 - 202,031,070 (-)NCBI
SpeTri2.0NW_0049366691,344,019 - 1,375,483 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SEC16A
(Sus scrofa - pig)
No map positions available.
SEC16A
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1121,718,520 - 1,763,562 (+)NCBI
ChlSab1.1 Ensembl121,724,838 - 1,761,941 (+)Ensembl
Vero_WHO_p1.0NW_0236660583,452,828 - 3,498,315 (-)NCBI
Sec16a
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247601,595,021 - 1,628,985 (-)NCBI

Position Markers
RH143614  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.239,237,586 - 9,237,839 (+)MAPPER
Rnor_6.033,864,118 - 3,864,368NCBIRnor6.0
Rnor_5.039,225,346 - 9,225,596UniSTSRnor5.0
RGSC_v3.434,590,817 - 4,591,067UniSTSRGSC3.4
Celera34,056,923 - 4,057,173UniSTS
AU049181  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.239,237,476 - 9,237,744 (+)MAPPER
Rnor_6.033,864,008 - 3,864,273NCBIRnor6.0
Rnor_5.039,225,236 - 9,225,501UniSTSRnor5.0
RGSC_v3.434,590,707 - 4,590,972UniSTSRGSC3.4
Celera34,056,813 - 4,057,078UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3125786001Rat
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3128136884Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3128500807Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)3128500807Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)3128500807Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3128500807Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3132972944Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3137891710Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3139773425Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3195176874Rat
1358185Ept6Estrogen-induced pituitary tumorigenesis QTL 66.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)35711366000866Rat
2292615Ept17Estrogen-induced pituitary tumorigenesis QTL 176.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)35711366000866Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)3263142133477544Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3263142148562146Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)3328592928136884Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)3328592928136884Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:119
Count of miRNA genes:91
Interacting mature miRNAs:103
Transcripts:ENSRNOT00000064083
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.


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 3 38 57 41 19 41 2 4 74 35 41 11 2
Low 5 6 7 6
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001276417 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233662 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233663 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233664 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233666 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104081 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104083 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005501745 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005501746 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AA964568 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC129824 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AI029484 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BF559738 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB693657 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB697736 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB748595 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB769991 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB796406 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CK478543 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CR754440 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DY309886 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EV776567 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ142479 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ238789 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000115 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000064083   ⟹   ENSRNOP00000060572
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl33,856,218 - 3,890,758 (-)Ensembl
RefSeq Acc Id: NM_001276417   ⟹   NP_001263346
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.239,229,687 - 9,264,233 (-)NCBI
Rnor_6.033,856,218 - 3,890,758 (-)NCBI
Rnor_5.039,217,446 - 9,252,578 (-)NCBI
Celera34,049,023 - 4,084,074 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006233662   ⟹   XP_006233724
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.239,229,687 - 9,264,266 (-)NCBI
Rnor_6.033,856,218 - 3,890,785 (-)NCBI
Rnor_5.039,217,446 - 9,252,578 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006233663   ⟹   XP_006233725
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.239,229,687 - 9,264,266 (-)NCBI
Rnor_6.033,856,218 - 3,890,785 (-)NCBI
Rnor_5.039,217,446 - 9,252,578 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006233664   ⟹   XP_006233726
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.239,229,687 - 9,263,855 (-)NCBI
Rnor_6.033,856,218 - 3,890,429 (-)NCBI
Rnor_5.039,217,446 - 9,252,578 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006233666   ⟹   XP_006233728
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.239,229,687 - 9,264,265 (-)NCBI
Rnor_6.033,856,218 - 3,890,784 (-)NCBI
Rnor_5.039,217,446 - 9,252,578 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039104081   ⟹   XP_038960009
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.239,229,687 - 9,264,837 (-)NCBI
RefSeq Acc Id: XM_039104083   ⟹   XP_038960011
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.239,234,314 - 9,264,266 (-)NCBI
RefSeq Acc Id: XR_005501745
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.239,230,914 - 9,264,264 (-)NCBI
RefSeq Acc Id: XR_005501746
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.239,230,902 - 9,264,264 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001263346   ⟸   NM_001276417
- UniProtKB: D3ZN76 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006233725   ⟸   XM_006233663
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006233728   ⟸   XM_006233666
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006233724   ⟸   XM_006233662
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006233726   ⟸   XM_006233664
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000060572   ⟸   ENSRNOT00000064083
RefSeq Acc Id: XP_038960009   ⟸   XM_039104081
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038960011   ⟸   XM_039104083
- Peptide Label: isoform X2
Protein Domains
Sec16   Sec16_C

Transcriptome

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

Promoters
RGD ID:13691907
Promoter ID:EPDNEW_R2432
Type:initiation region
Name:Sec16a_1
Description:SEC16 homolog A, endoplasmic reticulum export factor
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_6.033,890,760 - 3,890,820EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2322350 AgrOrtholog
Ensembl Genes ENSRNOG00000019122 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000060572 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000064083 ENTREZGENE, UniProtKB/TrEMBL
InterPro ACE1_Sec16_Sec31 UniProtKB/TrEMBL
  Sec16 UniProtKB/TrEMBL
  Sec16_CCD UniProtKB/TrEMBL
KEGG Report rno:100360302 UniProtKB/TrEMBL
NCBI Gene 100360302 ENTREZGENE
PANTHER PTHR13402 UniProtKB/TrEMBL
Pfam Sec16 UniProtKB/TrEMBL
  Sec16_C UniProtKB/TrEMBL
PhenoGen Sec16a PhenoGen
UniProt D3ZN76 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-30 Sec16a  SEC16 homolog A, endoplasmic reticulum export factor  Sec16a  SEC16 homolog A (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-08-06 Sec16a  SEC16 homolog A (S. cerevisiae)  LOC100360302  SEC16 homolog A-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-06 LOC100360302  SEC16 homolog A-like      Symbol and Name status set to provisional 70820 PROVISIONAL