Samd4a (sterile alpha motif domain containing 4A) - Rat Genome Database

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Gene: Samd4a (sterile alpha motif domain containing 4A) Rattus norvegicus
Analyze
Symbol: Samd4a
Name: sterile alpha motif domain containing 4A
RGD ID: 1310361
Description: Predicted to enable mRNA binding activity and translation repressor activity. Predicted to be involved in nuclear-transcribed mRNA poly(A) tail shortening. Predicted to act upstream of or within positive regulation of translation. Predicted to be located in cytosol; fibrillar center; and synapse. Predicted to be active in P-body. Orthologous to human SAMD4A (sterile alpha motif domain containing 4A); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC305826; protein Smaug homolog 1; Samd4; smaug 1; sterile alpha motif domain containing 4; sterile alpha motif domain-containing protein 4A
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
mRatBN7.21520,135,994 - 20,352,131 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1520,134,377 - 20,348,380 (+)Ensembl
Rnor_6.01523,666,543 - 23,879,067 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1523,665,202 - 23,878,539 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01527,721,129 - 27,820,974 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41522,847,701 - 22,952,499 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11522,749,949 - 22,967,670 (+)NCBI
Celera1520,645,446 - 20,745,819 (+)NCBICelera
Cytogenetic Map15p14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
1,1-dichloroethene  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
aflatoxin B1  (EXP,ISO)
Aflatoxin B2 alpha  (ISO)
all-trans-retinoic acid  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
avobenzone  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bromobenzene  (EXP)
butanal  (ISO)
calyculin a  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
choline  (ISO)
cisplatin  (ISO)
cobalt dichloride  (EXP,ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
cylindrospermopsin  (ISO)
diazinon  (ISO)
dibutyl phthalate  (EXP)
dichloroacetic acid  (ISO)
dicrotophos  (ISO)
dimethylarsinic acid  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
fenamidone  (ISO)
fluoxetine  (EXP)
folic acid  (ISO)
furan  (EXP,ISO)
gentamycin  (EXP)
glutathione  (EXP)
glyphosate  (EXP)
hydralazine  (ISO)
indole-3-methanol  (EXP)
L-methionine  (ISO)
leflunomide  (ISO)
mercury dibromide  (ISO)
methotrexate  (ISO)
methylarsonic acid  (ISO)
methylmercury chloride  (ISO)
methylseleninic acid  (ISO)
N-nitrosodiethylamine  (ISO)
nickel dichloride  (EXP,ISO)
p-chloromercuribenzoic acid  (ISO)
paracetamol  (EXP,ISO)
pentachlorophenol  (ISO)
phenylmercury acetate  (ISO)
propanal  (ISO)
quercetin  (ISO)
resorcinol  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
sodium dodecyl sulfate  (ISO)
sulforaphane  (ISO)
sunitinib  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (EXP)
thioacetamide  (EXP)
trichloroethene  (EXP)
trichostatin A  (ISO)
Triptolide  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
anchoring junction  (IEA)
cell junction  (ISO)
cytoplasm  (IEA)
cytosol  (IEA,ISO)
dendrite  (IEA)
fibrillar center  (IEA,ISO)
P-body  (IBA)
synapse  (IEA,ISO)

Molecular Function

References

Additional References at PubMed
PMID:12477932   PMID:16221671   PMID:22658674   PMID:30361391  


Genomics

Comparative Map Data
Samd4a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21520,135,994 - 20,352,131 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1520,134,377 - 20,348,380 (+)Ensembl
Rnor_6.01523,666,543 - 23,879,067 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1523,665,202 - 23,878,539 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01527,721,129 - 27,820,974 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41522,847,701 - 22,952,499 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11522,749,949 - 22,967,670 (+)NCBI
Celera1520,645,446 - 20,745,819 (+)NCBICelera
Cytogenetic Map15p14NCBI
SAMD4A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381454,565,316 - 54,793,315 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1454,566,117 - 54,793,315 (+)EnsemblGRCh38hg38GRCh38
GRCh371455,033,846 - 55,260,033 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361454,104,387 - 54,325,595 (+)NCBINCBI36hg18NCBI36
Build 341454,104,386 - 54,325,595NCBI
Celera1435,084,168 - 35,309,486 (+)NCBI
Cytogenetic Map14q22.2NCBI
HuRef1435,197,040 - 35,422,619 (+)NCBIHuRef
CHM1_11454,973,048 - 55,198,669 (+)NCBICHM1_1
Samd4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391447,120,414 - 47,343,274 (+)NCBIGRCm39mm39
GRCm39 Ensembl1447,120,311 - 47,343,272 (+)Ensembl
GRCm381446,882,965 - 47,105,817 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1446,882,854 - 47,105,815 (+)EnsemblGRCm38mm10GRCm38
MGSCv371447,502,640 - 47,725,492 (+)NCBIGRCm37mm9NCBIm37
MGSCv361438,712,160 - 38,932,128 (+)NCBImm8
MGSCv361445,804,844 - 46,024,079 (+)NCBImm8
Celera1443,056,646 - 43,281,638 (+)NCBICelera
Cytogenetic Map14C1NCBI
Samd4a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554098,712,061 - 8,916,816 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554098,716,432 - 8,916,398 (-)NCBIChiLan1.0ChiLan1.0
SAMD4A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11453,432,110 - 53,658,531 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1453,566,636 - 53,654,151 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01435,153,002 - 35,380,018 (+)NCBIMhudiblu_PPA_v0panPan3
SAMD4A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1830,476,425 - 30,687,240 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl830,476,418 - 30,687,240 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha830,243,508 - 30,455,649 (+)NCBI
ROS_Cfam_1.0830,732,570 - 30,943,425 (+)NCBI
ROS_Cfam_1.0 Ensembl830,732,557 - 30,945,114 (+)Ensembl
UMICH_Zoey_3.1830,336,559 - 30,547,600 (+)NCBI
UNSW_CanFamBas_1.0830,412,983 - 30,623,593 (+)NCBI
UU_Cfam_GSD_1.0830,778,494 - 30,989,083 (+)NCBI
Samd4a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864074,558,422 - 74,768,804 (-)NCBI
SpeTri2.0NW_004936697332,577 - 543,748 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SAMD4A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1183,915,339 - 184,140,122 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11183,915,337 - 184,140,122 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21204,436,496 - 204,645,195 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SAMD4A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12431,743,735 - 31,976,009 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2431,743,560 - 31,976,053 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605319,971,620 - 20,214,772 (+)NCBIVero_WHO_p1.0
Samd4a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473114,537,063 - 14,744,703 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D15Got30  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21520,150,398 - 20,150,565 (+)MAPPERmRatBN7.2
Rnor_6.01523,680,967 - 23,681,133NCBIRnor6.0
Rnor_5.01527,624,947 - 27,625,113UniSTSRnor5.0
RGSC_v3.41522,750,252 - 22,750,419RGDRGSC3.4
RGSC_v3.41522,750,253 - 22,750,419UniSTSRGSC3.4
RGSC_v3.11522,765,953 - 22,766,119RGD
Celera1520,548,789 - 20,548,955UniSTS
RH 3.4 Map15178.0RGD
RH 3.4 Map15178.0UniSTS
Cytogenetic Map15p14UniSTS
BF386303  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21520,214,869 - 20,215,061 (+)MAPPERmRatBN7.2
Rnor_6.01523,745,243 - 23,745,434NCBIRnor6.0
Rnor_5.01527,688,531 - 27,688,722UniSTSRnor5.0
RGSC_v3.41522,815,103 - 22,815,294UniSTSRGSC3.4
Celera1520,612,853 - 20,613,044UniSTS
RH 3.4 Map15188.2UniSTS
Cytogenetic Map15p14UniSTS
BF414877  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21520,296,951 - 20,297,139 (+)MAPPERmRatBN7.2
Rnor_6.01523,827,707 - 23,827,894NCBIRnor6.0
Rnor_5.01527,771,122 - 27,771,309UniSTSRnor5.0
RGSC_v3.41522,898,103 - 22,898,290UniSTSRGSC3.4
Celera1520,694,876 - 20,695,063UniSTS
RH 3.4 Map15187.3UniSTS
Cytogenetic Map15p14UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354657Despr13Despair related QTL 130.0022locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)15129912054Rat
8552920Pigfal8Plasma insulin-like growth factor 1 level QTL 83blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)15134723002Rat
8694361Abfw6Abdominal fat weight QTL 610.20.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)15134723002Rat
9589149Insul29Insulin level QTL 299.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)15134723002Rat
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15141686771Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15142356671Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1530632945306329Rat
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)colorectal tumor number (CMO:0001794)15226636822711984Rat
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)15226636822711984Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15226636846921453Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)15553075650530756Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151249614165205939Rat
5685002Bss103Bone structure and strength QTL 1032.8tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)151448116528469888Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151672552880672115Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151736289773690657Rat
631550Bw7Body weight QTL 73.6body mass (VT:0001259)body weight (CMO:0000012)151985656634924750Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)151985656646187442Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:42
Count of miRNA genes:36
Interacting mature miRNAs:39
Transcripts:ENSRNOT00000060847
Prediction methods: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 17 6 9 6 13 9 6
Low 3 26 57 41 19 41 2 2 68 35 28 2 2
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000060847   ⟹   ENSRNOP00000057570
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1520,247,469 - 20,342,182 (+)Ensembl
Rnor_6.0 Ensembl1523,777,856 - 23,878,539 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000089226   ⟹   ENSRNOP00000069137
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1520,134,377 - 20,347,852 (+)Ensembl
Rnor_6.0 Ensembl1523,665,202 - 23,872,143 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092091   ⟹   ENSRNOP00000069646
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1520,247,469 - 20,348,380 (+)Ensembl
Rnor_6.0 Ensembl1523,792,931 - 23,877,153 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000107922   ⟹   ENSRNOP00000096104
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1520,134,377 - 20,347,852 (+)Ensembl
RefSeq Acc Id: NM_001107254   ⟹   NP_001100724
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21520,247,469 - 20,348,380 (+)NCBI
Rnor_6.01523,777,838 - 23,879,067 (+)NCBI
Rnor_5.01527,721,129 - 27,820,974 (+)NCBI
RGSC_v3.41522,847,701 - 22,952,499 (+)RGD
Celera1520,645,446 - 20,745,819 (+)RGD
Sequence:
RefSeq Acc Id: XM_039093258   ⟹   XP_038949186
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21520,135,994 - 20,349,736 (+)NCBI
RefSeq Acc Id: XM_039093259   ⟹   XP_038949187
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21520,136,394 - 20,352,131 (+)NCBI
RefSeq Acc Id: XM_039093260   ⟹   XP_038949188
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21520,246,893 - 20,347,851 (+)NCBI
RefSeq Acc Id: XM_039093261   ⟹   XP_038949189
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21520,313,697 - 20,352,131 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001100724   ⟸   NM_001107254
- Sequence:
RefSeq Acc Id: ENSRNOP00000069646   ⟸   ENSRNOT00000092091
RefSeq Acc Id: ENSRNOP00000069137   ⟸   ENSRNOT00000089226
RefSeq Acc Id: ENSRNOP00000057570   ⟸   ENSRNOT00000060847
RefSeq Acc Id: XP_038949186   ⟸   XM_039093258
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038949187   ⟸   XM_039093259
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038949188   ⟸   XM_039093260
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038949189   ⟸   XM_039093261
- Peptide Label: isoform X4
RefSeq Acc Id: ENSRNOP00000096104   ⟸   ENSRNOT00000107922
Protein Domains
SAM

Transcriptome

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

Promoters
RGD ID:13699621
Promoter ID:EPDNEW_R10131
Type:initiation region
Name:Samd4a_2
Description:sterile alpha motif domain containing 4A
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R10132  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01523,777,886 - 23,777,946EPDNEW
RGD ID:13699608
Promoter ID:EPDNEW_R10132
Type:single initiation site
Name:Samd4a_1
Description:sterile alpha motif domain containing 4A
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R10131  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01523,792,876 - 23,792,936EPDNEW

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)
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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)
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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)
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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)
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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)
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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)
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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)
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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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310361 AgrOrtholog
BioCyc Gene G2FUF-14166 BioCyc
Ensembl Genes ENSRNOG00000010489 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000057570 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000069137 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000069646 UniProtKB/TrEMBL
  ENSRNOP00000096104 ENTREZGENE
Ensembl Transcript ENSRNOT00000060847 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000089226 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000092091 UniProtKB/TrEMBL
  ENSRNOT00000107922 ENTREZGENE
Gene3D-CATH 1.10.150.50 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  1.25.40.170 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro PHAT_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SAM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SAM/pointed_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Smaug_SAM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 305826 ENTREZGENE
Pfam SAM_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Samd4a PhenoGen
SMART SAM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47769 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JUK8_RAT UniProtKB/TrEMBL
  A0A0G2JVW7_RAT UniProtKB/TrEMBL
  B5DF21 ENTREZGENE
  F1M7M7_RAT UniProtKB/TrEMBL
  SMAG1_RAT UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-18 Samd4a  sterile alpha motif domain containing 4A  Samd4  sterile alpha motif domain containing 4   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Samd4  sterile alpha motif domain containing 4   Samd4_predicted  sterile alpha motif domain containing 4 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Samd4_predicted  sterile alpha motif domain containing 4 (predicted)      Symbol and Name status set to approved 70820 APPROVED