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SBF2 SET binding factor 2 [ Homo sapiens (human) ]

Gene ID: 81846, updated on 5-Aug-2018

Summary

Official Symbol
SBF2provided by HGNC
Official Full Name
SET binding factor 2provided by HGNC
Primary source
HGNC:HGNC:2135
See related
Ensembl:ENSG00000133812 MIM:607697; Vega:OTTHUMG00000165890
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CMT4B2; MTMR13; DENND7B
Summary
This gene encodes a pseudophosphatase and member of the myotubularin-related protein family. This gene maps within the CMT4B2 candidate region of chromosome 11p15 and mutations in this gene have been associated with Charcot-Marie-Tooth Disease, type 4B2. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in thyroid (RPKM 7.7), fat (RPKM 7.5) and 25 other tissues See more
Orthologs

Genomic context

See SBF2 in Genome Data Viewer
Location:
11p15.4
Exon count:
46
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 11 NC_000011.10 (9778667..10294207, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (9800214..10315754, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene RNA, 7SK small nuclear pseudogene 50 Neighboring gene switching B cell complex subunit SWAP70 Neighboring gene uncharacterized LOC105369149 Neighboring gene uncharacterized LOC440028 Neighboring gene SBF2 antisense RNA 1 Neighboring gene uncharacterized LOC101928008 Neighboring gene RNA, U7 small nuclear 28 pseudogene Neighboring gene glutamate-ammonia ligase pseudogene 2 Neighboring gene G protein subunit gamma 10 pseudogene Neighboring gene uncharacterized LOC105376544 Neighboring gene uncharacterized LOC100130460 Neighboring gene adrenomedullin Neighboring gene RNA, U6atac small nuclear 33, pseudogene

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Charcot-Marie-Tooth disease, type 4B2 Compare labs

NHGRI GWAS Catalog

Description
Genome-wide association study of smoking behaviours among Bangladeshi adults.
NHGRI GWA Catalog
Genome-wide association study of survival in patients with pancreatic adenocarcinoma.
NHGRI GWA Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of SET binding factor 2 (SBF2) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Membrane Trafficking, organism-specific biosystem (from REACTOME)
    Membrane Trafficking, organism-specific biosystemThe secretory membrane system allows a cell to regulate delivery of newly synthesized proteins, carbohydrates, and lipids to the cell surface, a necessity for growth and homeostasis. The system is ma...
  • RAB GEFs exchange GTP for GDP on RABs, organism-specific biosystem (from REACTOME)
    RAB GEFs exchange GTP for GDP on RABs, organism-specific biosystemHuman cells have more than 60 RAB proteins that are key regulators of intracellular membrane trafficking. These small GTPases contribute to trafficking specificity by localizing to the membranes of d...
  • Vesicle-mediated transport, organism-specific biosystem (from REACTOME)
    Vesicle-mediated transport, organism-specific biosystemThe transit of proteins and other cargo through the cell requires a cellular transport process in which transported substances are moved in membrane-bounded vesicles. Transported substances are enclo...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ22918, FLJ41627, KIAA1766, DKFZp779B2327

Gene Ontology Provided by GOA

Function Evidence Code Pubs
Rab guanyl-nucleotide exchange factor activity IDA
Inferred from Direct Assay
more info
PubMed 
Rab guanyl-nucleotide exchange factor activity TAS
Traceable Author Statement
more info
 
phosphatase binding IEA
Inferred from Electronic Annotation
more info
 
phosphatase regulator activity IEA
Inferred from Electronic Annotation
more info
 
phosphatidylinositol binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein homodimerization activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
myelination NAS
Non-traceable Author Statement
more info
PubMed 
protein tetramerization IEA
Inferred from Electronic Annotation
more info
 
regulation of GTPase activity IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytosol TAS
Traceable Author Statement
more info
 
membrane IDA
Inferred from Direct Assay
more info
PubMed 
vacuolar membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
myotubularin-related protein 13
Names
DENN/MADD domain containing 7B

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_008074.1 RefSeqGene

    Range
    5001..520541
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_267

mRNA and Protein(s)

  1. NM_030962.3NP_112224.1  myotubularin-related protein 13

    See identical proteins and their annotated locations for NP_112224.1

    Status: REVIEWED

    Source sequence(s)
    AI268862, AY234241, DA862574
    Consensus CDS
    CCDS31427.1
    UniProtKB/Swiss-Prot
    Q86WG5
    Related
    ENSP00000256190.8, OTTHUMP00000231444, ENST00000256190.12, OTTHUMT00000386911
    Conserved Domains (8) summary
    smart00801
    Location:352420
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:186
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    cd01235
    Location:17421847
    PH_Sbf1_hMTMR5; Set binding factor 1 (also called Human MTMR5) Pleckstrin Homology (PH) domain
    cd13339
    Location:8821000
    PH-GRAM_MTMR13; Myotubularian (MTM) related 13 protein Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
    pfam00169
    Location:17471847
    PH; PH domain
    pfam02141
    Location:116298
    DENN; DENN (AEX-3) domain
    pfam06602
    Location:11161519
    Myotub-related; Myotubularin-like phosphatase domain
    pfam12335
    Location:531754
    SBF2; Myotubularin protein

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p12 Primary Assembly

    Range
    9778667..10294207 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011520394.3XP_011518696.1  myotubularin-related protein 13 isoform X2

    Conserved Domains (8) summary
    smart00801
    Location:314382
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:186
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    cd01235
    Location:17361841
    PH_Sbf1_hMTMR5; Set binding factor 1 (also called Human MTMR5) Pleckstrin Homology (PH) domain
    cd13339
    Location:844962
    PH-GRAM_MTMR13; Myotubularian (MTM) related 13 protein Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
    pfam00169
    Location:17411841
    PH; PH domain
    pfam02141
    Location:116295
    DENN; DENN (AEX-3) domain
    pfam06602
    Location:10781513
    Myotub-related; Myotubularin-like phosphatase domain
    pfam12335
    Location:493716
    SBF2; Myotubularin protein
  2. XM_017018374.2XP_016873863.1  myotubularin-related protein 13 isoform X5

  3. XM_005253155.5XP_005253212.1  myotubularin-related protein 13 isoform X3

    Conserved Domains (8) summary
    smart00801
    Location:352421
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:186
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    cd01235
    Location:17311836
    PH_Sbf1_hMTMR5; Set binding factor 1 (also called Human MTMR5) Pleckstrin Homology (PH) domain
    cd13339
    Location:839957
    PH-GRAM_MTMR13; Myotubularian (MTM) related 13 protein Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
    pfam00169
    Location:17361836
    PH; PH domain
    pfam02141
    Location:116298
    DENN; DENN (AEX-3) domain
    pfam06602
    Location:10731508
    Myotub-related; Myotubularin-like phosphatase domain
    pfam12335
    Location:488711
    SBF2; Myotubularin protein
  4. XM_017018375.2XP_016873864.1  myotubularin-related protein 13 isoform X6

  5. XM_005253154.5XP_005253211.1  myotubularin-related protein 13 isoform X1

    Conserved Domains (8) summary
    smart00801
    Location:352420
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:186
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    cd01235
    Location:17741879
    PH_Sbf1_hMTMR5; Set binding factor 1 (also called Human MTMR5) Pleckstrin Homology (PH) domain
    cd13339
    Location:8821000
    PH-GRAM_MTMR13; Myotubularian (MTM) related 13 protein Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
    pfam00169
    Location:17791879
    PH; PH domain
    pfam02141
    Location:116298
    DENN; DENN (AEX-3) domain
    pfam06602
    Location:11161551
    Myotub-related; Myotubularin-like phosphatase domain
    pfam12335
    Location:531754
    SBF2; Myotubularin protein
  6. XM_017018373.2XP_016873862.1  myotubularin-related protein 13 isoform X4

  7. XM_017018372.2XP_016873861.1  myotubularin-related protein 13 isoform X4

  8. XM_017018376.2XP_016873865.1  myotubularin-related protein 13 isoform X7

    Conserved Domains (6) summary
    smart00801
    Location:352420
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:186
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    pfam02141
    Location:116298
    DENN; DENN (AEX-3) domain
    pfam12335
    Location:531754
    SBF2; Myotubularin protein
    cl17171
    Location:8821000
    PH-like; Pleckstrin homology-like domain
    cl21483
    Location:11161248
    PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...
  9. XM_011520395.3XP_011518697.1  myotubularin-related protein 13 isoform X7

    Conserved Domains (6) summary
    smart00801
    Location:352420
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:186
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    pfam02141
    Location:116298
    DENN; DENN (AEX-3) domain
    pfam12335
    Location:531754
    SBF2; Myotubularin protein
    cl17171
    Location:8821000
    PH-like; Pleckstrin homology-like domain
    cl21483
    Location:11161248
    PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...
  10. XM_011520396.3XP_011518698.1  myotubularin-related protein 13 isoform X8

    Conserved Domains (5) summary
    smart00801
    Location:352420
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:186
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    pfam02141
    Location:116298
    DENN; DENN (AEX-3) domain
    pfam12335
    Location:531754
    SBF2; Myotubularin protein
    cl17171
    Location:8821000
    PH-like; Pleckstrin homology-like domain
  11. XM_017018377.2XP_016873866.1  myotubularin-related protein 13 isoform X9

RNA

  1. XR_001747994.2 RNA Sequence

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