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sltm SAFB-like, transcription modulator [ Danio rerio (zebrafish) ]

Gene ID: 406642, updated on 27-Mar-2024

Summary

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Official Symbol
sltmprovided by ZNC
Official Full Name
SAFB-like, transcription modulatorprovided by ZNC
Primary source
ZFIN:ZDB-GENE-040426-2647
See related
Ensembl:ENSDARG00000052728 AllianceGenome:ZFIN:ZDB-GENE-040426-2647
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
zgc:65985; wu:fd12b08
Summary
Predicted to enable sequence-specific DNA binding activity. Predicted to be involved in regulation of mRNA processing and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within ribosome biogenesis. Predicted to be active in nucleus. Orthologous to human SLTM (SAFB like transcription modulator). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs
human mouse all
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Genomic context

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See sltm in Genome Data Viewer
Location:
chromosome: 7
Exon count:
20
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 7 NC_007118.7 (30538206..30560450, complement)
105 previous assembly GRCz10 (GCF_000002035.5) 7 NC_007118.6 (30267056..30289300, complement)

Chromosome 7 - NC_007118.7Genomic Context describing neighboring genes Neighboring gene lipase, hepatic a Neighboring gene ADAM metallopeptidase domain 10a Neighboring gene MINDY lysine 48 deubiquitinase 2 Neighboring gene ring finger protein 111 Neighboring gene cyclin B2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • BioProject: PRJEB1986
  • Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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Related articles in PubMed

  1. Consequences of lineage-specific gene loss on functional evolution of surviving paralogs: ALDH1A and retinoic acid signaling in vertebrate genomes. Cañestro C, et al. PLoS Genet, 2009 May. PMID 19478994, Free PMC Article
  2. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
  3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
  4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article
  5. Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database. Pasquier J, et al. BMC Genomics, 2016 May 18. PMID 27189481, Free PMC Article

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables RNA binding IEA
Inferred from Electronic Annotation
more info
  
enables nucleic acid binding IEA
Inferred from Electronic Annotation
more info
  
enables sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in regulation of mRNA processing IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
SAFB-like transcription modulator

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_213333.2 → NP_998498.2  SAFB-like transcription modulator

    Status: VALIDATED

    Source sequence(s)
    AL935053
    UniProtKB/TrEMBL
    A0A8M1PF00, F1Q6F9
    Related
    ENSDARP00000115812.1, ENSDART00000142818.4
    Conserved Domains (2) summary
    smart00513
    Location:13 → 47
    SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
    cd12678
    Location:322 → 395
    RRM_SLTM; RNA recognition motif in Scaffold attachment factor (SAF)-like transcription modulator (SLTM) and similar proteins

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007118.7 Reference GRCz11 Primary Assembly

    Range
    30538206..30560450 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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