Ssmem1 (serine-rich single-pass membrane protein 1) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Ssmem1 (serine-rich single-pass membrane protein 1) Rattus norvegicus
Analyze
Symbol: Ssmem1
Name: serine-rich single-pass membrane protein 1
RGD ID: 1559502
Description: Orthologous to human SSMEM1 (serine rich single-pass membrane protein 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: hypothetical protein LOC500068; LOC500068; RGD1559502; similar to RIKEN cDNA 1700025E21; uncharacterized protein LOC500068
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
mRatBN7.2459,128,730 - 59,139,029 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl459,128,730 - 59,145,007 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx464,106,804 - 64,116,985 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0460,022,989 - 60,033,170 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0458,424,906 - 58,435,087 (+)NCBIRnor_WKY
Rnor_6.0457,823,411 - 57,833,706 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl457,823,411 - 57,834,115 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0457,585,320 - 57,595,615 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4457,419,710 - 57,429,788 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera454,227,803 - 54,238,004 (+)NCBICelera
Cytogenetic Map4q22NCBI
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

Cellular Component
membrane  (IEA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Ssmem1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2459,128,730 - 59,139,029 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl459,128,730 - 59,145,007 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx464,106,804 - 64,116,985 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0460,022,989 - 60,033,170 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0458,424,906 - 58,435,087 (+)NCBIRnor_WKY
Rnor_6.0457,823,411 - 57,833,706 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl457,823,411 - 57,834,115 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0457,585,320 - 57,595,615 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4457,419,710 - 57,429,788 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera454,227,803 - 54,238,004 (+)NCBICelera
Cytogenetic Map4q22NCBI
SSMEM1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh387130,205,410 - 130,216,844 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl7130,206,344 - 130,216,844 (+)EnsemblGRCh38hg38GRCh38
GRCh377129,847,700 - 129,856,684 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 367129,634,954 - 129,644,733 (+)NCBINCBI36Build 36hg18NCBI36
Celera7124,643,463 - 124,652,445 (+)NCBICelera
Cytogenetic Map7q32.2NCBI
HuRef7124,210,101 - 124,219,083 (+)NCBIHuRef
CHM1_17129,781,282 - 129,790,267 (+)NCBICHM1_1
T2T-CHM13v2.07131,521,250 - 131,530,235 (+)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v27129,233,070 - 129,242,052 (+)NCBI
Ssmem1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39630,509,790 - 30,520,253 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl630,509,848 - 30,520,253 (+)EnsemblGRCm39 Ensembl
GRCm38630,509,791 - 30,520,254 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl630,509,849 - 30,520,254 (+)EnsemblGRCm38mm10GRCm38
MGSCv37630,462,304 - 30,469,963 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36630,462,314 - 30,469,973 (+)NCBIMGSCv36mm8
Celera630,522,345 - 30,530,004 (+)NCBICelera
Cytogenetic Map6A3.3NCBI
Ssmem1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495547910,864,278 - 10,875,072 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495547910,864,515 - 10,875,033 (+)NCBIChiLan1.0ChiLan1.0
SSMEM1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.17134,692,338 - 134,700,857 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl7134,692,392 - 134,700,857 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v07122,174,764 - 122,183,708 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
SSMEM1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1146,665,645 - 6,697,345 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl146,687,138 - 6,694,722 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha146,351,628 - 6,384,011 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0146,425,952 - 6,458,619 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl146,447,414 - 6,455,069 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1146,631,438 - 6,663,831 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0146,376,112 - 6,408,514 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0146,519,749 - 6,552,158 (-)NCBIUU_Cfam_GSD_1.0
Ssmem1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511824,882,901 - 24,889,656 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049365795,015,859 - 5,022,179 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SSMEM1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1818,603,390 - 18,613,430 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11818,604,054 - 18,613,285 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21819,683,306 - 19,692,423 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SSMEM1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12198,844,390 - 98,854,345 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2198,844,809 - 98,853,994 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660424,550,065 - 4,559,708 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ssmem1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247836,060,554 - 6,069,173 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247836,060,360 - 6,069,608 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
619616Bp79Blood pressure QTL 790.0292arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4521460278882945Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
1358203Stl19Serum triglyceride level QTL 192.80.002blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829465958103Rat
631261Tcas3Tongue tumor susceptibility QTL 36.88tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)41081417091360527Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
2303585Bw86Body weight QTL 864body mass (VT:0001259)body weight (CMO:0000012)41467806559678065Rat
2313401Anxrr27Anxiety related response QTL 27aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)41793350862933508Rat
61412Pia2Pristane induced arthritis QTL 23.9joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)42133334362278020Rat
6909122Insul22Insulin level QTL 224.63blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)42690728575585128Rat
6909128Pancm4Pancreatic morphology QTL 411.35pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)42690728575585128Rat
8655906Rf60Renal function QTL 603.8blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)42949419581006281Rat
12798520Anxrr55Anxiety related response QTL 554.450.01locomotor behavior trait (VT:0001392)number of rearing movements with lid-pushing in an experimental apparatus (CMO:0002715)432583980114627242Rat
8552782Vie1Viral induced encephalitis QTL 126.4brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)43443048482490359Rat
8552801Bw143Body weight QTL 1437.3body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)43443048482490359Rat
8552809Vie5Viral induced encephalitis QTL 525.3brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)43443048482490359Rat
8655961Kidm43Kidney mass QTL 4318kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)436303261103194984Rat
1358352Srcrt3Stress Responsive Cort QTL 32.29blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)438465774146803430Rat
61475Aia2Adjuvant induced arthritis QTL 25.8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)43950527573892441Rat
1331807Rf31Renal function QTL 312.988urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)43952426474726312Rat
1300139Hrtrt6Heart rate QTL 62.85heart pumping trait (VT:2000009)heart rate (CMO:0000002)439524264116179656Rat
61445Strs3Sensitivity to stroke QTL 33cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)44043338885433388Rat
8694439Bw168Body weight QTL 1689.570.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)44043341485433414Rat
6893678Bw108Body weight QTL 1082.60.006body mass (VT:0001259)body weight (CMO:0000012)44345797688457976Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)444463720155883716Rat
1354612Foco1Food consumption QTL 18.87eating behavior trait (VT:0001431)food intake rate (CMO:0000427)444463908148090542Rat
1354660Salc1Saline consumption QTL 111.26drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)444463908148090542Rat
2312567Glom19Glomerulus QTL 191.90.006kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)445456990146803430Rat
1298082Stresp4Stress response QTL 4blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)450119848146803430Rat
4889969Bss96Bone structure and strength QTL 964.9tibia size trait (VT:0100001)tibia cortical bone volume (CMO:0001725)45664777678882945Rat
4889972Bss97Bone structure and strength QTL 975.6tibia size trait (VT:0100001)tibia total bone volume (CMO:0001724)45664777678882945Rat
5685009Bmd86Bone mineral density QTL 863.7tibia mineral mass (VT:1000283)bone mineral density (CMO:0001226)45664777678882945Rat
5685012Bmd87Bone mineral density QTL 875.1tibia mineral mass (VT:1000283)bone mineral content (CMO:0001554)45664777678882945Rat
70200Alc18Alcohol consumption QTL 189.2drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)456647873149491524Rat
1641833Alc21Alcohol consumption QTL 218.60.0001drinking behavior trait (VT:0001422)ethanol drink intake rate (CMO:0001407)456698790126192555Rat
631546Bp86Blood pressure QTL 863.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)45711443291360801Rat
634311Sach7Saccharin preference QTL 7taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)457114432102114432Rat
61336Bp21Blood pressure QTL 214.6arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)45711470578881294Rat
1358363Sradr3Stress Responsive Adrenal Weight QTL 36.19adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)457486946102486946Rat
1558651Swd3Spike wave discharge measurement QTL 34.620.000024brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)45843213392991462Rat
631671Iddm11Insulin dependent diabetes mellitus QTL 113.60.0012blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)45863587778886137Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:181
Count of miRNA genes:130
Interacting mature miRNAs:143
Transcripts:ENSRNOT00000030462
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 7
Low 2 38 41 25 18 25 8 11 74 31 34 11 8
Below cutoff 1 5 16 16 1 16 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000030462   ⟹   ENSRNOP00000036034
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl459,128,730 - 59,139,028 (+)Ensembl
Rnor_6.0 Ensembl457,823,411 - 57,833,706 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000088235   ⟹   ENSRNOP00000074526
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl459,128,730 - 59,145,007 (+)Ensembl
Rnor_6.0 Ensembl457,823,412 - 57,834,115 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093932   ⟹   ENSRNOP00000081177
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl459,131,207 - 59,139,026 (+)Ensembl
RefSeq Acc Id: NM_001109228   ⟹   NP_001102698
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2459,128,730 - 59,139,028 (+)NCBI
Rnor_6.0457,823,411 - 57,833,706 (+)NCBI
Rnor_5.0457,585,320 - 57,595,615 (+)NCBI
RGSC_v3.4457,419,710 - 57,429,788 (+)RGD
Celera454,227,803 - 54,238,004 (+)RGD
Sequence:
RefSeq Acc Id: XM_006236228   ⟹   XP_006236290
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2459,131,259 - 59,139,029 (+)NCBI
Rnor_6.0457,825,897 - 57,833,479 (+)NCBI
Rnor_5.0457,585,320 - 57,595,615 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039108119   ⟹   XP_038964047
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2459,136,825 - 59,139,029 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001102698 (Get FASTA)   NCBI Sequence Viewer  
  NP_001385839 (Get FASTA)   NCBI Sequence Viewer  
  XP_006236290 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964047 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM15252 (Get FASTA)   NCBI Sequence Viewer  
  EDM15253 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001102698   ⟸   NM_001109228
- UniProtKB: D3ZDF5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006236290   ⟸   XM_006236228
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000036034   ⟸   ENSRNOT00000030462
RefSeq Acc Id: ENSRNOP00000074526   ⟸   ENSRNOT00000088235
RefSeq Acc Id: XP_038964047   ⟸   XM_039108119
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000081177   ⟸   ENSRNOT00000093932

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZDF5-F1-model_v2 AlphaFold D3ZDF5 1-197 view protein structure

Transcriptome

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

Promoters
RGD ID:13692938
Promoter ID:EPDNEW_R3460
Type:initiation region
Name:Ssmem1_1
Description:serine-rich single-pass membrane protein 1
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_6.0457,823,432 - 57,823,492EPDNEW

Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
4 57823858 57823859 C T snv LH/MavRrrc (RGD), WAG/RijCrl (2020), LH/MavRrrcAek (2020), WN/N (2020), CDR, CDS, COP/CrCrl (MCW & UW), FHL/EurMcwi (MCW), SBN/Ygl (MCW), SS/JrHsdMcwi (MCW), Buf/N (MCW), WN/N (MCW), FHL/EurMcwi (RGD), LEW/Crl (RGD), LEW/NCrlBR (RGD), LL/MavRrrc (RGD), MHS/Gib (RGD), SBN/Ygl (RGD), SS/Jr (RGD), SS/JrHsdMcwi (RGD), WAG/Rij (RGD), BUF/N (2020), LEW/Crl (2019), LL/MavRrrcAek (2020), MWF/Hsd (2019), SS/JrHsdMcwi (2019), MNS/Gib (RGD)


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
4 57585767 57585768 C T snv COP/CrCrl (MCW & UW), ZFDM (KyushuU), SBN/Ygl (MCW), SS/JrHsdMcwi (MCW), WN/N (KNAW), LH/MavRrrc (KNAW), LL/MavRrrc (KNAW), MHS/Gib (KNAW), SS/Jr (KNAW), SS/JrHsdMcwi (KNAW), WAG/Rij (KNAW), BUF/N (KNAW), FHL/EurMcwi (KNAW), LEW/Crl (KNAW), LEW/NCrl (KNAW), MNS/Gib (KNAW), SBN/Ygl (KNAW), SDLEF7/Barth (UDEL), Crl:SD (UDEL), NIG-III/Hok (KyushuU), HTX/Kyo (KyushuU), HWY/Slc (KyushuU), ZF (KyushuU), FHL/EurMcwi (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
4 57420157 57420158 C T snv FHL/EurMcwi (MCW), WAG/Rij (ICL), SS/JrHsdMcwi (MDC), BUF/N (KNAW), WN/N (KNAW), COP/CrCrl (MCW & UW), FHL/EurMcwi (ICL), LEW/Crl (ICL), LEW/NCrl (ICL), LH/MavRrrc (ICL), LL/MavRrrc (ICL), MHS/Gib (ICL), MNS/Gib (ICL), SBN/Ygl (ICL), SS/Jr (ICL), SS/JrHsdMcwi (ICL), SS/JrHsdMcwi (MCW)


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
4 59129177 59129178 C T snv BUF/N (2020), LEW/Crl (2019), LH/MavRrrcAek (2020), WN/N (2020), MWF/Hsd (2019), SS/JrHsdMcwi (2019), WAG/RijCrl (2020), LL/MavRrrcAek (2020)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1559502 AgrOrtholog
BioCyc Gene G2FUF-45351 BioCyc
Ensembl Genes ENSRNOG00000010345 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000036034 ENTREZGENE
  ENSRNOP00000036034.4 UniProtKB/TrEMBL
  ENSRNOP00000074526.2 UniProtKB/TrEMBL
  ENSRNOP00000081177 ENTREZGENE
  ENSRNOP00000081177.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000030462 ENTREZGENE
  ENSRNOT00000030462.6 UniProtKB/TrEMBL
  ENSRNOT00000088235.2 UniProtKB/TrEMBL
  ENSRNOT00000093932 ENTREZGENE
  ENSRNOT00000093932.1 UniProtKB/TrEMBL
InterPro DUF4636 UniProtKB/TrEMBL
KEGG Report rno:500068 UniProtKB/TrEMBL
NCBI Gene 500068 ENTREZGENE
PANTHER PTHR31822 UniProtKB/TrEMBL
Pfam DUF4636 UniProtKB/TrEMBL
PhenoGen Ssmem1 PhenoGen
UniProt A0A0G2K8A0_RAT UniProtKB/TrEMBL
  A0A8I5ZUI6_RAT UniProtKB/TrEMBL
  D3ZDF5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-03-20 Ssmem1  serine-rich single-pass membrane protein 1  RGD1559502  similar to RIKEN cDNA 1700025E21  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1559502  similar to RIKEN cDNA 1700025E21   RGD1559502_predicted  similar to RIKEN cDNA 1700025E21 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1559502_predicted  similar to RIKEN cDNA 1700025E21 (predicted)  LOC500068  similar to RIKEN cDNA 1700025E21  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC500068  similar to RIKEN cDNA 1700025E21      Symbol and Name status set to provisional 70820 PROVISIONAL