Samd11 (sterile alpha motif domain containing 11) - Rat Genome Database

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Gene: Samd11 (sterile alpha motif domain containing 11) Rattus norvegicus
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Symbol: Samd11
Name: sterile alpha motif domain containing 11
RGD ID: 1310271
Description: Predicted to enable several functions, including DNA-binding transcription repressor activity, RNA polymerase II-specific; histone binding activity; and protein domain specific binding activity. Predicted to be involved in negative regulation of DNA-templated transcription and retinal rod cell development. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II. Predicted to be part of PRC1 complex. Predicted to be active in nucleus. Orthologous to human SAMD11 (sterile alpha motif domain containing 11); INTERACTS WITH 1-naphthyl isothiocyanate; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC102549710; LOC313778; RGD1310271; similar to hypothetical protein MGC45873; sterile alpha motif domain-containing protein 11; sterile alpha motif domain-containing protein 11-like
RGD Orthologs
Human
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85172,113,900 - 172,142,026 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl5172,113,654 - 172,131,927 (-)EnsemblGRCr8
mRatBN7.25166,831,681 - 166,859,805 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5166,831,663 - 166,850,009 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx5169,533,801 - 169,542,492 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05171,355,185 - 171,363,878 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05171,317,745 - 171,326,438 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.05173,672,413 - 173,689,360 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5173,672,810 - 173,680,290 (-)Ensemblrn6Rnor6.0
Rnor_5.05177,146,471 - 177,174,525 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.45173,082,689 - 173,089,608 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera5165,033,505 - 165,042,183 (-)NCBICelera
Cytogenetic Map5q36NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleus  (IBA,ISO)
PRC1 complex  (ISO)

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:15632090   PMID:16539743  


Genomics

Comparative Map Data
Samd11
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85172,113,900 - 172,142,026 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl5172,113,654 - 172,131,927 (-)EnsemblGRCr8
mRatBN7.25166,831,681 - 166,859,805 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5166,831,663 - 166,850,009 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx5169,533,801 - 169,542,492 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05171,355,185 - 171,363,878 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05171,317,745 - 171,326,438 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.05173,672,413 - 173,689,360 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5173,672,810 - 173,680,290 (-)Ensemblrn6Rnor6.0
Rnor_5.05177,146,471 - 177,174,525 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.45173,082,689 - 173,089,608 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera5165,033,505 - 165,042,183 (-)NCBICelera
Cytogenetic Map5q36NCBI
SAMD11
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381923,923 - 944,574 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1923,923 - 944,575 (+)Ensemblhg38GRCh38
GRCh371859,303 - 879,954 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361850,984 - 869,824 (+)NCBIBuild 36Build 36hg18NCBI36
Build 341914,832 - 920,104NCBI
Celera11,711,838 - 1,728,177 (-)NCBICelera
Cytogenetic Map1p36.33NCBI
HuRef1131,531 - 149,470 (+)NCBIHuRef
CHM1_11848,155 - 866,997 (+)NCBICHM1_1
T2T-CHM13v2.01353,566 - 373,316 (+)NCBIT2T-CHM13v2.0
Samd11
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554869,763,725 - 9,779,197 (-)Ensembl
ChiLan1.0NW_0049554869,763,704 - 9,781,132 (-)NCBIChiLan1.0ChiLan1.0
SAMD11
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21227,319,485 - 227,339,362 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11226,016,974 - 226,035,943 (-)NCBINHGRI_mPanPan1
PanPan1.11823,527 - 843,433 (+)NCBIPanPan1.1PanPan1.1panPan2
SAMD11
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1556,119,207 - 56,175,267 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl556,151,171 - 56,172,055 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha556,197,020 - 56,253,328 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0556,322,212 - 56,378,556 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl556,354,439 - 56,378,552 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1556,313,372 - 56,369,650 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0556,205,328 - 56,261,585 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0556,595,401 - 56,651,599 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
SAMD11
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl663,287,713 - 63,308,482 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1663,287,449 - 63,308,231 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
SAMD11
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120130,488,810 - 130,510,621 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605435,118,720 - 35,138,086 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Samd11
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248188,563,879 - 8,581,015 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248188,563,376 - 8,581,028 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Samd11
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v114,403,870 - 4,421,966 (+)NCBIRrattus_CSIRO_v1

miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:20
Count of miRNA genes:18
Interacting mature miRNAs:20
Transcripts:ENSRNOT00000027564
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)555124766172190305Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5130249266172190305Rat
1354583Despr3Despair related QTL34.980.0002locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)5132930505172190305Rat
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5141212838172190305Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5131708216172190305Rat
61452Ciaa5CIA Autoantibody QTL 53.5blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)599905133172190305Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5133789363172190305Rat
1331803Rf32Renal function QTL 322.798kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)5134369199172190305Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5136631198172190305Rat
1354631Swd2Spike wave discharge measurement QTL 23.640.0002brain electrophysiology trait (VT:0010557)brain total spike-and-wave discharge duration (CMO:0001740)5156396728172190305Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5133081618172190305Rat
1581505Rf54Renal function QTL 54kidney physiology trait (VT:0002136)kidney 20-HETE level (CMO:0001854)5133270647172190305Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5160071170172129029Rat
2317753Glom24Glomerulus QTL 243.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)5141764300172190305Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5133081618172190305Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5133789363172190305Rat
1331721Bp210Blood pressure QTL 2103.413arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5148093485172129029Rat
1581510Cm54Cardiac mass QTL 543.40.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)5125969677172190305Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 161 91 90 59 86 59 6 350 186 11 140 81 92 31 17 17

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001415981 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006239615 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006239616 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006239617 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008764412 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008764413 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008764414 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593113 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109112 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109113 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109114 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109116 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109119 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005504352 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC097183 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473968 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000005 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSRNOT00000027564   ⟹   ENSRNOP00000027564
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl5172,113,654 - 172,131,927 (-)Ensembl
mRatBN7.2 Ensembl5166,831,663 - 166,840,345 (-)Ensembl
Rnor_6.0 Ensembl5173,672,810 - 173,680,290 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000096699   ⟹   ENSRNOP00000084329
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl5172,113,900 - 172,131,927 (-)Ensembl
mRatBN7.2 Ensembl5166,831,663 - 166,850,009 (-)Ensembl
RefSeq Acc Id: NM_001415981   ⟹   NP_001402910
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85172,113,900 - 172,131,927 (-)NCBI
mRatBN7.25166,831,681 - 166,849,712 (-)NCBI
RefSeq Acc Id: XM_039109112   ⟹   XP_038965040
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85172,113,900 - 172,131,580 (-)NCBI
mRatBN7.25166,831,681 - 166,849,864 (-)NCBI
RefSeq Acc Id: XM_039109113   ⟹   XP_038965041
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85172,113,900 - 172,131,580 (-)NCBI
mRatBN7.25166,831,681 - 166,849,864 (-)NCBI
RefSeq Acc Id: XM_039109114   ⟹   XP_038965042
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85172,113,900 - 172,142,026 (-)NCBI
mRatBN7.25166,831,681 - 166,859,805 (-)NCBI
RefSeq Acc Id: XM_039109116   ⟹   XP_038965044
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85172,113,900 - 172,127,635 (-)NCBI
mRatBN7.25166,831,681 - 166,845,408 (-)NCBI
RefSeq Acc Id: XM_039109119   ⟹   XP_038965047
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85172,115,546 - 172,131,580 (-)NCBI
mRatBN7.25166,833,324 - 166,849,864 (-)NCBI
RefSeq Acc Id: XR_005504352
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85172,114,381 - 172,131,580 (-)NCBI
mRatBN7.25166,832,160 - 166,849,864 (-)NCBI
Ensembl Acc Id: ENSRNOP00000027564   ⟸   ENSRNOT00000027564
RefSeq Acc Id: XP_038965042   ⟸   XM_039109114
- Peptide Label: isoform X3
- UniProtKB: D3ZMX5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038965040   ⟸   XM_039109112
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038965041   ⟸   XM_039109113
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038965044   ⟸   XM_039109116
- Peptide Label: isoform X4
- UniProtKB: D3ZMX5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038965047   ⟸   XM_039109119
- Peptide Label: isoform X5
Ensembl Acc Id: ENSRNOP00000084329   ⟸   ENSRNOT00000096699
RefSeq Acc Id: NP_001402910   ⟸   NM_001415981
- UniProtKB: A0A8I5ZXL4 (UniProtKB/TrEMBL)
Protein Domains
SAM   SAND

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZMX5-F1-model_v2 AlphaFold D3ZMX5 1-554 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310271 AgrOrtholog
BioCyc Gene G2FUF-38854 BioCyc
Ensembl Genes ENSRNOG00000020342 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000027564.8 UniProtKB/TrEMBL
  ENSRNOT00000096699 ENTREZGENE
  ENSRNOT00000096699.2 UniProtKB/TrEMBL
Gene3D-CATH 1.10.150.50 UniProtKB/TrEMBL
  3.10.390.10 UniProtKB/TrEMBL
InterPro PcG_chromatin_remod_factors UniProtKB/TrEMBL
  SAM UniProtKB/TrEMBL
  SAM_type UniProtKB/TrEMBL
  SAND-like_dom_sf UniProtKB/TrEMBL
  SAND_dom UniProtKB/TrEMBL
NCBI Gene Samd11 ENTREZGENE
PANTHER GLUCOCORTICOID MODULATORY ELEMENT-BINDING PROTEIN UniProtKB/TrEMBL
  POLYCOMB GROUP PROTEIN UniProtKB/TrEMBL
  STERILE ALPHA MOTIF DOMAIN-CONTAINING 11 UniProtKB/TrEMBL
  STERILE ALPHA MOTIF DOMAIN-CONTAINING PROTEIN 11 UniProtKB/TrEMBL
Pfam SAM_1 UniProtKB/TrEMBL
  SAND UniProtKB/TrEMBL
PhenoGen Samd11 PhenoGen
PROSITE SAM_DOMAIN UniProtKB/TrEMBL
  SAND UniProtKB/TrEMBL
RatGTEx ENSRNOG00000020342 RatGTEx
SMART SAM UniProtKB/TrEMBL
  SAND UniProtKB/TrEMBL
Superfamily-SCOP SAM_homology UniProtKB/TrEMBL
  SSF63763 UniProtKB/TrEMBL
UniProt A0A8I5ZXL4 ENTREZGENE, UniProtKB/TrEMBL
  D3ZMX5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-03-16 Samd11  sterile alpha motif domain containing 11  Samd11  sterile alpha motif domain containing 11  Type changed (type changed from [null] to [protein-coding]) 629549 APPROVED
2015-02-25 Samd11  sterile alpha motif domain containing 11  LOC102549710  sterile alpha motif domain-containing protein 11-like  Data merged from RGD:7652027 737654 APPROVED
2013-12-18 LOC102549710  sterile alpha motif domain-containing protein 11-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2011-05-26 Samd11  sterile alpha motif domain containing 11  RGD1310271  similar to hypothetical protein MGC45873  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1310271  similar to hypothetical protein MGC45873   RGD1310271_predicted  similar to hypothetical protein MGC45873 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1310271_predicted  similar to hypothetical protein MGC45873 (predicted)  LOC313778_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC313778_predicted  similar to hypothetical protein MGC45873 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL