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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

SAMD13 Gene

protein-coding   GIFtS: 37
GCID: GC01P084764

Sterile Alpha Motif Domain Containing 13

  Search for SAMD13
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Sterile Alpha Motif Domain Containing 131 2
SAM Domain-Containing Protein 132 3
RP11-376N17.12
Dnaj-Like Protein (LOC148418)2
Sterile Alpha Motif Domain-Containing Protein 132

External Ids:    HGNC: 245821   Entrez Gene: 1484182   Ensembl: ENSG000002039437   UniProtKB: Q5VXD33   

Export aliases for SAMD13 gene to outside databases

Previous GC identifers: GC01P084477 GC01P084536 GC01P082874


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for SAMD13 Gene: 
SAMD13 (sterile alpha motif domain containing 13) is a protein-coding gene. An important paralog of this gene is SAMD1.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000001.10  NC_018912.2  NT_032977.9  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SAMD13 gene promoter:
         POU2F1   POU2F1a   HFH-1   Nkx2-5   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSAMD13 promoter sequence
   Search SABiosciences Chromatin IP Primers for SAMD13

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SAMD13


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 1p31.1   Ensembl cytogenetic band:  1p31.1   HGNC cytogenetic band: 1p31.1

SAMD13 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SAMD13 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P084764:  view genomic region     (about GC identifiers)

Start:
84,764,049 bp from pter      End:
84,855,640 bp from pter
Size:
91,592 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: SAM13_HUMAN, Q5VXD3 (See protein sequence)
Recommended Name: Sterile alpha motif domain-containing protein 13  
Size: 122 amino acids; 13570 Da
Secondary accessions: B3KPW8 D3DT11 Q53AI4 Q5VXD2 Q5VXD4
Alternative splicing: 4 isoforms:  Q5VXD3-1   Q5VXD3-2   Q5VXD3-3   Q5VXD3-4   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SAMD13: NX_Q5VXD3

Explore proteomics data for SAMD13 at MOPED 

SAMD13 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

SAMD13 Protein Expression

REFSEQ proteins (3 alternative transcripts): 
NP_001010971.1  NP_001128135.1  NP_001128136.1  

ENSEMBL proteins: 
 ENSP00000359707   ENSP00000359705   ENSP00000378311   ENSP00000359703   ENSP00000359702  
 ENSP00000359704   ENSP00000391978   ENSP00000359701  

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Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005634nucleus ----

SAMD13 for ontologies           About GeneDecksing



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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
HGNC Gene Families: 
SAMD: Sterile alpha motif (SAM) domain containing

3 InterPro protein domains:
 IPR013761 SAM/pointed
 IPR001660 SAM
 IPR021129 SAM_type1

Graphical View of Domain Structure for InterPro Entry Q5VXD3

ProtoNet protein and cluster: Q5VXD3

1 Blocks protein domain: IPB001660 Sterile alpha motif SAM

UniProtKB/Swiss-Prot: SAM13_HUMAN, Q5VXD3
Similarity: Contains 1 SAM (sterile alpha motif) domain


SAMD13 for domains           About GeneDecksing


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section

     Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005515protein binding ----
GO:0043565sequence-specific DNA binding ----
     
SAMD13 for ontologies           About GeneDecksing


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(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SAMD13

STRING Interaction Network Preview (showing 4 interactants - click image to see more details)

4 Interacting proteins for SAMD13 (ENSP000003597074) via UniProtKB, MINT, STRING, and/or I2D
InteractantInteraction Details
GeneCardExternal ID(s)
ENSG00000206324ENSP000003827234STRING: ENSP00000382723
SRSF4ENSP000003629004STRING: ENSP00000362900
TRNAU1APENSP000003629364STRING: ENSP00000362936
--ENSP000003727674STRING: ENSP00000372767
About this table

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
Browse Small Molecules at EMD Millipore
Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for SAMD13 (SAM13)

Search CenterWatch for drugs/clinical trials and news about SAMD13 / SAM13

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for SAMD13 gene (3 alternative transcripts): 
NM_001010971.2  NM_001134663.1  NM_001134664.1  

Unigene Cluster for SAMD13:

Sterile alpha motif domain containing 13
Hs.591445  [show with all ESTs]
Unigene Representative Sequence: NM_001010971
10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000370673(uc001djr.3) ENST00000370671 ENST00000394834 ENST00000463429
ENST00000370669 ENST00000479082 ENST00000370668(uc010orw.2 uc010orx.2)
ENST00000370670 ENST00000454967 ENST00000370667(uc001djs.3)
miRNA
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SwitchGear 3'UTR luciferase reporter plasmidSAMD13 3' UTR sequence
Inhib. RNA
Products:
     
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Additional mRNA sequence: 

AK056937.1 AK311207.1 AY604569.1 AY604570.1 BC037973.1 

6 DOTS entries:

DT.408382  DT.100016382  DT.65287831  DT.121454623  DT.99999749  DT.303134 

24/41 AceView cDNA sequences (see all 41):

CR615899 BC037973 CK821788 CK821789 AA913464 BX281193 CD107636 CR617905 
BX092540 AI631824 BI759190 CB047557 BM926925 BX325328 AK056937 AA846694 
BU853107 BF000472 AA609154 BU680318 AW262750 AA496252 AA465293 AI696679 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

SAMD13 expression in normal human tissues (normalized intensities)      SAMD13 embryonic expression: see
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: ATGGTGTAAT
SAMD13 Expression
About this image


SAMD13 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database 
 5/1 selected tissues (see all 1) fully expand
 
 Pancreas (Endocrine System)
         Pancreatic endoderm/endocrine precursor-like cells ( A scalable, suspension protocol...

See SAMD13 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for SAMD13

SOURCE GeneReport for Unigene cluster: Hs.591445
    SABiosciences Custom PCR Arrays for SAMD13
Primer
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SAMD13

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section

This gene was present in the common ancestor of animals.

Orthologs for SAMD13 gene from 6/11 species (see all 11)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Samd135 sterile alpha motif domain containing 13   --   3 (72.28 cM) -
chicken
(Gallus gallus)
Aves DNASE2B6
dnaj-like protein
36(a)
1 ↔ 1
8(15564994-15576789)
lizard
(Anolis carolinensis)
Reptilia SAMD136
sterile alpha motif domain containing 13
86(a)
1 ↔ 1
GL343194.1(9459665-9480652)
African clawed frog
(Xenopus laevis)
Amphibia Xl.324702 Xenopus laevis transcribed sequence with weak similarity more 78.3(n)    BJ618989.1 
zebrafish
(Danio rerio)
Actinopterygii samd131 sterile alpha motif domain containing 13 73.54(n)
80.41(a)
  767772  NM_001168317.1  NP_001161789.1 
fruit fly
(Drosophila melanogaster)
Insecta CG26626
--
7(a)
1 → many
X(2592737-2594951)


ENSEMBL Gene Tree for SAMD13 (if available)
TreeFam Gene Tree for SAMD13 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
Paralogs for SAMD13 gene
SAMD12  
13 SIMAP similar genes for SAMD13 using alignment to 3 protein entries:     SAM13_HUMAN (see all proteins):
RNF113A    HPH1    L3MBTL4    PHC3    PHC1    L3MBTL1
PHC2    RNF113B    SAMD1    SCMH1    SFMBT2    L3MBTL3
SAMD11

SAMD13 for paralogs           About GeneDecksing



(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

10/928 SNPs in SAMD13 are shown (see all 928)    About this table     
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 1 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs12465741,2
C,F,H--84780634(+) gcaccA/Ggacgt 1 -- us2k123Minor allele frequency- G:0.14NS EA NA CSA WA 2094
rs1401461691,2
--84780676(+) CCTTCC/TTCACT 1 -- us2k10--------
rs1859753751,2
--84780787(+) TTTCAA/GTATTG 1 -- us2k10--------
rs1503253631,2
C--84780882(+) ATTTAC/TAGATT 1 -- us2k10--------
rs1900877711,2
--84780927(+) CAATCA/GTAACA 1 -- us2k10--------
rs7848341,2
F,A--84780950(+) gatcaC/Tagatc 1 -- us2k12Minor allele frequency- T:0.00NA 4
rs1826752591,2
--84781021(+) GACACA/TGAGAC 1 -- us2k10--------
rs1494695991,2
--84781032(+) ATGAAA/GTGAGC 1 -- us2k10--------
rs1468975971,2
--84781046(+) TACTGA/CTGGAA 1 -- us2k10--------
rs800723071,2
C,F--84781068(+) ATAGAC/TTTGTT 1 -- us2k11Minor allele frequency- T:0.14WA 118

HapMap Linkage Disequilibrium report for SAMD13 (84764049 - 84855640 bp)

Structural Variations
     Database of Genomic Variants (DGV) 3 variations for SAMD13:    About this table     
Variant IDTypeSubtypePubMed ID
nsv1744CNV Insertion18451855
nsv830414CNV Gain17160897
nsv830426CNV Gain17160897

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section
  --

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
About This Section

PubMed articles for SAMD13 gene integrated from 9 sources:
(articles sorted by number of sources associating them with SAMD13)
    Utopia: connect your pdf to the dynamic
world of online information

  1. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (2006)
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
  3. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. (PubMed id 23251661)1 Comuzzie A.G....Butte N.F. (2012)
  4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)
  5. Hepatitis C virus core protein interacts with 14-3-3 protein and activates the kinase Raf-1. (PubMed id )2 Aoki H.... Hino O. (2000)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section
Entrez Gene: 148418 HGNC: 24582 AceView: LOC148418 Ensembl:ENSG00000203943 euGenes: HUgn148418
ECgene: SAMD13 H-InvDB: SAMD13

(According to HUGE)
About This Section
  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
NameDescription
PharmGKB entry for SAMD13 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
Patent Information for SAMD13 gene:
Search GeneIP for patents involving SAMD13

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
About This Section

 
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GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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