Human Gene SLTM (uc002afp.3) Description and Page Index
  Description: Homo sapiens SAFB-like, transcription modulator (SLTM), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr15:59,171,244-59,225,852 Size: 54,609 Total Exon Count: 21 Strand: -
Coding Region
   Position: hg19 chr15:59,172,198-59,225,764 Size: 53,567 Coding Exon Count: 21 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:59,171,244-59,225,852)mRNA (may differ from genome)Protein (1034 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtPubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: SLTM_HUMAN
DESCRIPTION: RecName: Full=SAFB-like transcription modulator; AltName: Full=Modulator of estrogen-induced transcription;
FUNCTION: When overexpressed, acts as a general inhibitor of transcription that eventually leads to apoptosis (By similarity).
SUBCELLULAR LOCATION: Nucleus (By similarity). Note=Detected in punctate structures (By similarity).
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR (By similarity).
SIMILARITY: Contains 1 RRM (RNA recognition motif) domain.
SIMILARITY: Contains 1 SAP domain.
SEQUENCE CAUTION: Sequence=AAI08657.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=BAB14502.1; Type=Erroneous initiation; Sequence=BAB14971.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAB14971.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SLTM
CDC HuGE Published Literature: SLTM
Positive Disease Associations: Asperger Syndrome , Insulin
Related Studies:
  1. Asperger Syndrome
    D Salyakina et al. Autism research 2010, Variants in several genomic regions associated with asperger disorder., Autism research : official journal of the International Society for Autism Research. [PubMed 21182207]
  2. Insulin
    , , . [PubMed 0]

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 33.51 RPKM in Thyroid
Total median expression: 1137.41 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -43.5088-0.494 Picture PostScript Text
3' UTR -250.60954-0.263 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR012677 - Nucleotide-bd_a/b_plait
IPR000504 - RRM_dom
IPR003034 - SAP_DNA-bd

Pfam Domains:
PF00076 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
PF02037 - SAP domain
PF13893 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)

SCOP Domains:
68906 - SAP domain
54928 - RNA-binding domain, RBD

ModBase Predicted Comparative 3D Structure on Q9NWH9
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003690 double-stranded DNA binding
GO:0003723 RNA binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006915 apoptotic process
GO:0050684 regulation of mRNA processing

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0016604 nuclear body


-  Descriptions from all associated GenBank mRNAs
  BC046119 - Homo sapiens SAFB-like, transcription modulator, mRNA (cDNA clone IMAGE:6196843), partial cds.
AK023275 - Homo sapiens cDNA FLJ13213 fis, clone NT2RP4001126, weakly similar to TRICHOHYALIN.
JD344589 - Sequence 325613 from Patent EP1572962.
JD386243 - Sequence 367267 from Patent EP1572962.
JD206526 - Sequence 187550 from Patent EP1572962.
JD562388 - Sequence 543412 from Patent EP1572962.
JD185895 - Sequence 166919 from Patent EP1572962.
JD359359 - Sequence 340383 from Patent EP1572962.
BC040120 - Homo sapiens SAFB-like, transcription modulator, mRNA (cDNA clone IMAGE:5110622), with apparent retained intron.
AK055195 - Homo sapiens cDNA FLJ30633 fis, clone CTONG2002418, highly similar to Homo sapiens modulator of estrogen induced transcription, transcript variant 1, mRNA.
AL834297 - Homo sapiens mRNA; cDNA DKFZp762G052 (from clone DKFZp762G052).
BC014944 - Homo sapiens SAFB-like, transcription modulator, mRNA (cDNA clone IMAGE:4864860), partial cds.
JD113045 - Sequence 94069 from Patent EP1572962.
JD147430 - Sequence 128454 from Patent EP1572962.
AK291423 - Homo sapiens cDNA FLJ78261 complete cds.
JD513869 - Sequence 494893 from Patent EP1572962.
JD563023 - Sequence 544047 from Patent EP1572962.
JD180377 - Sequence 161401 from Patent EP1572962.
BC140851 - Homo sapiens SAFB-like, transcription modulator, mRNA (cDNA clone MGC:176528 IMAGE:9021719), complete cds.
JD553082 - Sequence 534106 from Patent EP1572962.
JD305202 - Sequence 286226 from Patent EP1572962.
JD173367 - Sequence 154391 from Patent EP1572962.
JD180557 - Sequence 161581 from Patent EP1572962.
AK024710 - Homo sapiens cDNA: FLJ21057 fis, clone CAS00705.
AK000867 - Homo sapiens cDNA FLJ10005 fis, clone HEMBA1000156.
AK131242 - Homo sapiens cDNA FLJ16159 fis, clone BRCAN2002854.
BC108656 - Homo sapiens SAFB-like, transcription modulator, mRNA (cDNA clone IMAGE:4520738), partial cds.

-  Other Names for This Gene
  Alternate Gene Symbols: B2RTX3, MET, NM_024755, NP_079031, Q2VPK7, Q52MB3, Q658J7, Q6ZNF2, Q86TK6, Q9H7C3, Q9H8U9, Q9NWH9, SLTM_HUMAN
UCSC ID: uc002afp.3
RefSeq Accession: NM_024755
Protein: Q9NWH9 (aka SLTM_HUMAN)
CCDS: CCDS10168.2

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_024755.2
exon count: 21CDS single in 3' UTR: no RNA size: 4164
ORF size: 3105CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 6333.00frame shift in genome: no % Coverage: 99.59
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.