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 have mRNA binding activity and translation repressor activity. Predicted to be involved in regulation of gene expression. Predicted to localize to several cellular components, including P-body; cytosol; and fibrillar center. 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: PROVISIONAL
Also 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: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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  (ISO)
all-trans-retinoic 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)
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)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
fenamidone  (ISO)
fluoxetine  (EXP)
folic acid  (ISO)
furan  (EXP,ISO)
glutathione  (EXP)
glyphosate  (EXP)
hydralazine  (ISO)
indole-3-methanol  (EXP)
L-methionine  (ISO)
leflunomide  (ISO)
mercury dibromide  (ISO)
methotrexate  (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 dichromate  (EXP)
sodium dodecyl sulfate  (ISO)
sulforaphane  (ISO)
sunitinib  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (EXP)
thioacetamide  (EXP)
trichloroethene  (EXP)
trichostatin A  (ISO)
valproic acid  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cell junction  (ISO)
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
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
GRCh38.p13 Ensembl1454,566,117 - 54,793,315 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl1454,567,097 - 54,793,315 (+)EnsemblGRCh38hg38GRCh38
GRCh381454,567,097 - 54,793,315 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371455,033,815 - 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
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
CanFam3.1 Ensembl830,476,418 - 30,687,240 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1830,476,425 - 30,687,240 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Samd4a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12431,743,735 - 31,976,009 (+)NCBI
ChlSab1.1 Ensembl2431,743,560 - 31,976,053 (+)Ensembl
Samd4a
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473114,537,063 - 14,744,703 (-)NCBI

Position Markers
D15Got30  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
Cytogenetic Map15p14UniSTS
RH 3.4 Map15178.0UniSTS
RH 3.4 Map15178.0RGD
BF386303  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
Cytogenetic Map15p14UniSTS
RH 3.4 Map15188.2UniSTS
BF414877  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
Cytogenetic Map15p14UniSTS
RH 3.4 Map15187.3UniSTS


QTLs in Region (Rnor_6.0)
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)15130597196Rat
9589149Insul29Insulin level QTL 299.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)15137708474Rat
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)15137708474Rat
8694361Abfw6Abdominal fat weight QTL 610.20.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)15137708474Rat
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15142844179Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15143521446Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15162301382Rat
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)colorectal tumor number (CMO:0001794)15232787726288802Rat
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)15232787726288802Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15232787753535766Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)15388113148881131Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)151071919155719191Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151549236072568189Rat
5685002Bss103Bone structure and strength QTL 1032.8tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)151582824233657761Rat
9590272Scort14Serum corticosterone level QTL 142.780.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)151698090761980907Rat
8694427Bw163Body weight QTL 1634.820.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)151698090761980907Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151724964162249641Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151724964162249641Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151724964162249641Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151809320881255430Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151851391388036354Rat
631550Bw7Body weight QTL 73.6body mass (VT:0001259)body weight (CMO:0000012)152102134241082727Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)152102134252831189Rat
10755503Bp391Blood pressure QTL 3912.37arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)152377896946825072Rat

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
Rnor_6.0 Ensembl1523,777,856 - 23,878,539 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000089226   ⟹   ENSRNOP00000069137
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1523,665,202 - 23,872,143 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092091   ⟹   ENSRNOP00000069646
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1523,792,931 - 23,877,153 (+)Ensembl
RefSeq Acc Id: NM_001107254   ⟹   NP_001100724
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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_008770515   ⟹   XP_008768737
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01523,777,003 - 23,875,015 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017599654   ⟹   XP_017455143
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01523,666,543 - 23,875,015 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017599655   ⟹   XP_017455144
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01523,666,985 - 23,875,015 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017599656   ⟹   XP_017455145
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01523,843,925 - 23,875,015 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001100724   ⟸   NM_001107254
- Sequence:
RefSeq Acc Id: XP_008768737   ⟸   XM_008770515
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017455143   ⟸   XM_017599654
- Peptide Label: isoform X1
- UniProtKB: A0A0G2JUK8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017455144   ⟸   XM_017599655
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017455145   ⟸   XM_017599656
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000069646   ⟸   ENSRNOT00000092091
RefSeq Acc Id: ENSRNOP00000069137   ⟸   ENSRNOT00000089226
RefSeq Acc Id: ENSRNOP00000057570   ⟸   ENSRNOT00000060847
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 (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)
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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)
FHH/EurMcwi (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
FHL/EurMcwi (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)
FHL/EurMcwi (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
GH/OmrMcwi (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)
GK/Ox (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
LE/Stm (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
LEW/Crl (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
LEW/NCrlBR (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
LH/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
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:1310361 AgrOrtholog
Ensembl Genes ENSRNOG00000010489 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000057570 UniProtKB/TrEMBL
  ENSRNOP00000069137 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000069646 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000060847 UniProtKB/TrEMBL
  ENSRNOT00000089226 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000092091 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.10.150.50 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro 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
UniGene Rn.224832 ENTREZGENE
UniProt A0A0G2JUK8 ENTREZGENE, 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