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SLTM SAFB like transcription modulator [ Homo sapiens (human) ]

Gene ID: 79811, updated on 4-Dec-2022

Summary

Official Symbol
SLTMprovided by HGNC
Official Full Name
SAFB like transcription modulatorprovided by HGNC
Primary source
HGNC:HGNC:20709
See related
Ensembl:ENSG00000137776 AllianceGenome:HGNC:20709
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
Met
Summary
Enables RNA binding activity. Predicted to be involved in regulation of mRNA processing and regulation of transcription by RNA polymerase II. Located in nuclear body. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in bone marrow (RPKM 26.9), thyroid (RPKM 20.0) and 25 other tissues See more
Orthologs
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Genomic context

See SLTM in Genome Data Viewer
Location:
15q22.1
Exon count:
23
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (58879050..58933679, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (56681092..56735731, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (59171249..59225878, complement)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene zinc finger protein 444 pseudogene 1 Neighboring gene ribosomal protein L21 pseudogene 14 Neighboring gene ribosome binding factor A (putative) pseudogene Neighboring gene ring finger protein 111 Neighboring gene ribosomal protein L21 pseudogene 113

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ10005, FLJ13213, DKFZp762G052

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
involved_in apoptotic process IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of mRNA processing IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
located_in nuclear body IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
SAFB-like transcription modulator
Names
modulator of estrogen-induced transcription

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_001013843.3NP_001013865.1  SAFB-like transcription modulator isoform b

    See identical proteins and their annotated locations for NP_001013865.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1, resulting in a shorter protein (isoform b).
    Source sequence(s)
    AC025918, BC046119, BC140851, DA215437
    UniProtKB/Swiss-Prot
    Q9NWH9
    Conserved Domains (6) summary
    smart00513
    Location:2256
    SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
    PTZ00121
    Location:145705
    PTZ00121; MAEBL; Provisional
    PLN03124
    Location:25168
    PLN03124; poly [ADP-ribose] polymerase; Provisional
    PHA03307
    Location:7801015
    PHA03307; transcriptional regulator ICP4; Provisional
    COG0724
    Location:271478
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    cl17169
    Location:367440
    RRM_SF; RNA recognition motif (RRM) superfamily
  2. NM_024755.4NP_079031.2  SAFB-like transcription modulator isoform a

    See identical proteins and their annotated locations for NP_079031.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and it encodes the longest isoform (a).
    Source sequence(s)
    AC025918, BC046119, BC140851, DA215437
    Consensus CDS
    CCDS10168.2
    UniProtKB/Swiss-Prot
    Q9H8U9, Q9NWH9
    Related
    ENSP00000369887.2, ENST00000380516.7
    Conserved Domains (5) summary
    smart00513
    Location:2256
    SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
    PTZ00121
    Location:34723
    PTZ00121; MAEBL; Provisional
    PHA03307
    Location:7981033
    PHA03307; transcriptional regulator ICP4; Provisional
    COG0724
    Location:289496
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    cl17169
    Location:385458
    RRM_SF; RNA recognition motif (RRM) superfamily

RNA

  1. NR_135042.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks two alternate internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC025918, AK055195, BC046119, DA215437
    Related
    ENST00000492526.5
  2. NR_135043.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks two alternate internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC025918, AK291423, BC046119, BC140851, DA215437
    Related
    ENST00000557924.5

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    58879050..58933679 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011522031.3XP_011520333.1  SAFB-like transcription modulator isoform X19

    See identical proteins and their annotated locations for XP_011520333.1

    UniProtKB/TrEMBL
    A0A024R5U7
    Conserved Domains (4) summary
    COG0724
    Location:61268
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    cl17169
    Location:157230
    RRM_SF; RNA recognition motif (RRM) superfamily
    cl26511
    Location:8495
    Neuromodulin_N; Gap junction protein N-terminal region
    cl28033
    Location:570805
    Herpes_ICP4_C; Herpesvirus ICP4-like protein C-terminal region
  2. XM_047433051.1XP_047289007.1  SAFB-like transcription modulator isoform X19

    UniProtKB/TrEMBL
    A0A024R5U7
  3. XM_047433046.1XP_047289002.1  SAFB-like transcription modulator isoform X12

  4. XM_017022578.2XP_016878067.2  SAFB-like transcription modulator isoform X10

  5. XM_047433045.1XP_047289001.1  SAFB-like transcription modulator isoform X11

  6. XM_006720686.4XP_006720749.4  SAFB-like transcription modulator isoform X8

  7. XM_017022576.2XP_016878065.1  SAFB-like transcription modulator isoform X6

  8. XM_047433043.1XP_047288999.1  SAFB-like transcription modulator isoform X4

  9. XM_011522028.2XP_011520330.2  SAFB-like transcription modulator isoform X9

  10. XM_011522027.2XP_011520329.2  SAFB-like transcription modulator isoform X7

  11. XM_047433044.1XP_047289000.1  SAFB-like transcription modulator isoform X5

  12. XM_011522023.2XP_011520325.2  SAFB-like transcription modulator isoform X2

  13. XM_011522024.2XP_011520326.2  SAFB-like transcription modulator isoform X3

  14. XM_011522022.2XP_011520324.2  SAFB-like transcription modulator isoform X1

  15. XM_047433049.1XP_047289005.1  SAFB-like transcription modulator isoform X17

  16. XM_047433048.1XP_047289004.1  SAFB-like transcription modulator isoform X15

  17. XM_017022579.2XP_016878068.1  SAFB-like transcription modulator isoform X14

    Conserved Domains (4) summary
    PHA03307
    Location:745980
    PHA03307; transcriptional regulator ICP4; Provisional
    COG0724
    Location:236443
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    COG5271
    Location:1281
    MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]
    cl17169
    Location:332405
    RRM_SF; RNA recognition motif (RRM) superfamily
  18. XM_011522029.3XP_011520331.1  SAFB-like transcription modulator isoform X13

    Conserved Domains (2) summary
    COG0724
    Location:243450
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    cl17169
    Location:339412
    RRM_SF; RNA recognition motif (RRM) superfamily
  19. XM_047433052.1XP_047289008.1  SAFB-like transcription modulator isoform X19

    UniProtKB/TrEMBL
    A0A024R5U7
  20. XM_011522030.3XP_011520332.2  SAFB-like transcription modulator isoform X16

  21. XM_047433050.1XP_047289006.1  SAFB-like transcription modulator isoform X18

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    56681092..56735731 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_017968.2: Suppressed sequence

    Description
    NM_017968.2: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.