Samd5 (sterile alpha motif domain containing 5) - Rat Genome Database

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Gene: Samd5 (sterile alpha motif domain containing 5) Rattus norvegicus
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Symbol: Samd5
Name: sterile alpha motif domain containing 5
RGD ID: 1311012
Description: Predicted to be involved in regulation of intracellular signal transduction. Predicted to be located in cytoplasm. Orthologous to human SAMD5 (sterile alpha motif domain containing 5); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC365038; RGD1311012; similar to RIKEN cDNA E130306M17 gene; sterile alpha motif domain-containing protein 5
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
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
GRCr815,861,793 - 5,911,153 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl15,497,567 - 5,911,064 (-)EnsemblGRCr8
mRatBN7.214,041,547 - 4,090,909 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl13,677,784 - 4,091,120 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx13,716,317 - 3,765,463 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.019,716,740 - 9,765,890 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.013,998,446 - 4,047,596 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.013,713,750 - 3,763,392 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl13,713,750 - 3,763,392 (-)Ensemblrn6Rnor6.0
Rnor_5.015,388,579 - 5,437,905 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.414,269,126 - 4,333,486 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera12,582,110 - 2,631,436 (-)NCBICelera
RGSC_v3.114,293,531 - 4,333,198 (-)NCBI
Cytogenetic Map1p13NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IEA,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:28388653  


Genomics

Comparative Map Data
Samd5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr815,861,793 - 5,911,153 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl15,497,567 - 5,911,064 (-)EnsemblGRCr8
mRatBN7.214,041,547 - 4,090,909 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl13,677,784 - 4,091,120 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx13,716,317 - 3,765,463 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.019,716,740 - 9,765,890 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.013,998,446 - 4,047,596 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.013,713,750 - 3,763,392 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl13,713,750 - 3,763,392 (-)Ensemblrn6Rnor6.0
Rnor_5.015,388,579 - 5,437,905 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.414,269,126 - 4,333,486 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera12,582,110 - 2,631,436 (-)NCBICelera
RGSC_v3.114,293,531 - 4,333,198 (-)NCBI
Cytogenetic Map1p13NCBI
SAMD5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386147,508,690 - 147,954,680 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6147,508,690 - 147,737,547 (+)Ensemblhg38GRCh38
GRCh376147,829,826 - 147,891,157 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366147,871,756 - 147,932,850 (+)NCBIBuild 36Build 36hg18NCBI36
Celera6148,570,287 - 148,631,616 (+)NCBICelera
Cytogenetic Map6q24.3NCBI
HuRef6145,393,492 - 145,454,849 (+)NCBIHuRef
CHM1_16148,093,227 - 148,154,560 (+)NCBICHM1_1
T2T-CHM13v2.06148,701,984 - 149,150,652 (+)NCBIT2T-CHM13v2.0
Samd5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39109,138,205 - 9,551,670 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl109,400,709 - 9,550,952 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38109,262,461 - 9,675,926 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl109,622,936 - 9,675,208 (-)Ensemblmm10GRCm38
MGSCv37109,347,057 - 9,395,006 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36109,317,452 - 9,365,398 (-)NCBIMGSCv36mm8
Celera109,528,592 - 9,578,286 (-)NCBICelera
Cytogenetic Map10A1NCBI
cM Map103.15NCBI
Samd5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049558672,559 - 3,011 (-)Ensembl
ChiLan1.0NW_0049558672,559 - 3,237 (-)NCBIChiLan1.0ChiLan1.0
SAMD5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v25167,525,064 - 167,586,443 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16165,418,761 - 165,480,537 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06145,318,564 - 145,379,936 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
SAMD5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_Tasha139,412,325 - 39,469,502 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0138,687,085 - 38,744,721 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl138,687,297 - 38,743,365 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1138,561,879 - 38,619,257 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0138,432,212 - 38,489,628 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0138,771,531 - 38,828,974 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Samd5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946133,605,444 - 133,657,005 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936489859,056 - 908,953 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936489858,839 - 908,998 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SAMD5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl118,231,494 - 18,290,021 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1117,883,397 - 18,290,021 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2120,431,070 - 20,487,260 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SAMD5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Vero_WHO_p1.0NW_023666040199,739,114 - 200,199,762 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Samd5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462478510,527,402 - 10,578,481 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Samd5
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v12227,414,071 - 227,824,210 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Samd5
872 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:608
Count of miRNA genes:276
Interacting mature miRNAs:352
Transcripts:ENSRNOT00000034744
Prediction methods:Microtar, Miranda, 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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1600360Mcs16Mammary carcinoma susceptibility QTL 162.4mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1126564886Rat
2313090Bmd69Bone mineral density QTL 694.40.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)1529322934184556Rat
70179Xhs2X-ray hypersensitivity QTL 23.2intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)1143965634Rat
1354647Despr8Despair related QTL 80.0000341locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)1126564886Rat
2317755Glom22Glomerulus QTL 223.8urine protein amount (VT:0005160)urine protein level (CMO:0000591)1134184556Rat
1300170Rf6Renal function QTL 63.14renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)1128483164Rat
2313070Bss52Bone structure and strength QTL 524.40.0001body length (VT:0001256)body length (CMO:0000013)1529322934184556Rat
2313053Bss51Bone structure and strength QTL 513.80.0001tibia length (VT:0004357)tibia length (CMO:0000450)1529322934184556Rat


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
15 10 64 134 91 90 59 62 59 6 312 151 3 119 79 91 31 12 12

Sequence


Ensembl Acc Id: ENSRNOT00000034744   ⟹   ENSRNOP00000058700
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl14,041,547 - 4,090,909 (-)Ensembl
Rnor_6.0 Ensembl13,713,750 - 3,763,392 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000098127   ⟹   ENSRNOP00000089535
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl15,497,567 - 5,911,064 (-)Ensembl
mRatBN7.2 Ensembl13,677,784 - 4,091,120 (-)Ensembl
RefSeq Acc Id: NM_001108901   ⟹   NP_001102371
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr815,861,793 - 5,911,153 (-)NCBI
mRatBN7.214,041,547 - 4,090,909 (-)NCBI
Rnor_6.013,713,750 - 3,763,392 (-)NCBI
Rnor_5.015,388,579 - 5,437,905 (-)NCBI
RGSC_v3.414,269,126 - 4,333,486 (-)RGD
Celera12,582,110 - 2,631,436 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001102371 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL93698 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000089535.1
RefSeq Acc Id: NP_001102371   ⟸   NM_001108901
- UniProtKB: D3ZLM9 (UniProtKB/TrEMBL),   A6JP26 (UniProtKB/TrEMBL),   A0A8I6ABZ6 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000058700   ⟸   ENSRNOT00000034744
Ensembl Acc Id: ENSRNOP00000089535   ⟸   ENSRNOT00000098127
Protein Domains
SAM

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZLM9-F1-model_v2 AlphaFold D3ZLM9 1-173 view protein structure

Transcriptome

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

Promoters
RGD ID:13689484
Promoter ID:EPDNEW_R9
Type:single initiation site
Name:Samd5_1
Description:sterile alpha motif domain containing 5
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_6.013,763,314 - 3,763,374EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311012 AgrOrtholog
BioCyc Gene G2FUF-62426 BioCyc
Ensembl Genes ENSRNOG00000023549 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000098127.3 UniProtKB/TrEMBL
Gene3D-CATH 1.10.150.50 UniProtKB/TrEMBL
InterPro SAM UniProtKB/TrEMBL
  SAM-SH3_domain_protein UniProtKB/TrEMBL
  SAM_type UniProtKB/TrEMBL
KEGG Report rno:365038 UniProtKB/TrEMBL
NCBI Gene 365038 ENTREZGENE
PANTHER SAM-DOMAIN, SH3 AND NUCLEAR LOCALIZATION SIGNALS PROTEIN RELATED UniProtKB/TrEMBL
  STERILE ALPHA MOTIF DOMAIN-CONTAINING PROTEIN 5 UniProtKB/TrEMBL
Pfam SAM_1 UniProtKB/TrEMBL
PhenoGen Samd5 PhenoGen
PROSITE SAM_DOMAIN UniProtKB/TrEMBL
RatGTEx ENSRNOG00000023549 RatGTEx
SMART SAM UniProtKB/TrEMBL
Superfamily-SCOP SAM_homology UniProtKB/TrEMBL
UniProt A0A8I6ABZ6 ENTREZGENE, UniProtKB/TrEMBL
  A6JP26 ENTREZGENE, UniProtKB/TrEMBL
  D3ZLM9 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-27 Samd5  sterile alpha motif domain containing 5  RGD1311012_predicted  similar to RIKEN cDNA E130306M17 gene (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 RGD1311012_predicted  similar to RIKEN cDNA E130306M17 gene (predicted)  LOC365038_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC365038_predicted  similar to RIKEN cDNA E130306M17 gene (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL