Human Gene SBF1 (ENST00000380817.8_11) from GENCODE V47lift37

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Description: SET binding factor 1, transcript variant 1 (from RefSeq NM_002972.4)
Gencode Transcript: ENST00000380817.8_11
Gencode Gene: ENSG00000100241.22_19
Transcript (Including UTRs)
Position: hg19 chr22:50,883,429-50,913,464 Size: 30,036 Total Exon Count: 41 Strand: -
Coding Region
Position: hg19 chr22:50,885,571-50,913,269 Size: 27,699 Coding Exon Count: 41

Page Index	Sequence and Links	UniProtKB Comments	Primers	MalaCards	CTD
Gene Alleles	RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species
GO Annotations	mRNA Descriptions	Pathways	Other Names	Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr22:50,883,429-50,913,464)			mRNA (may differ from genome)		Protein (1893 aa)
Gene Sorter	Genome Browser	Other Species FASTA	VisiGene	Gene interactions	Table Schema
AlphaFold	BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards
HGNC	Malacards	MGI	OMIM	PubMed	Reactome
UniProtKB	Wikipedia	BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: MTMR5_HUMAN DESCRIPTION: RecName: Full=Myotubularin-related protein 5; AltName: Full=SET-binding factor 1; Short=Sbf1; FUNCTION: Probable pseudophosphatase. Lacks several amino acids in the catalytic pocket which renders it catalytically inactive as a phosphatase. The pocket is however sufficiently preserved to bind phosphorylated substrates, and maybe protect them from phosphatases. Inhibits myoblast differentiation in vitro and induces oncogenic transformation in fibroblasts. According to PubMed:20937701, may function as a guanine nucleotide exchange factor (GEF) activating RAB28. Promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form. SUBUNIT: Interacts with the SET domain of MLL/HRX. Interacts with SUV39H1. SUBCELLULAR LOCATION: Nucleus. SIMILARITY: Belongs to the protein-tyrosine phosphatase family. Non-receptor class myotubularin subfamily. SIMILARITY: Contains 1 dDENN domain. SIMILARITY: Contains 1 DENN domain. SIMILARITY: Contains 1 GRAM domain. SIMILARITY: Contains 1 myotubularin phosphatase domain. SIMILARITY: Contains 1 PH domain. SIMILARITY: Contains 1 uDENN domain. SEQUENCE CAUTION: Sequence=AAC39675.1; Type=Frameshift; Positions=1603, 1627, 1631, 1864;

Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

MalaCards Disease Associations


	MalaCards Gene Search: SBF1 Diseases sorted by gene-association score: charcot-marie-tooth disease, type 4b3* (1578), charcot-marie-tooth neuropathy type 4b3* (100), tooth disease (14), charcot-marie-tooth disease (11), centronuclear myopathy (10), charcot-marie-tooth disease, type 4b2 (9), charcot-marie-tooth disease, type 4b1 (7), early-onset glaucoma (7), neuropathy, congenital hypomyelinating (4) * = Manually curated disease association

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene D000082 Acetaminophen C023514 2,6-dinitrotoluene D001151 Arsenic D001564 Benzo(a)pyrene D004997 Ethinyl Estradiol D005411 Flame Retardants D006997 Hypochlorous Acid D018817 N-Methyl-3,4-methylenedioxyamphetamine D010795 Phthalic Acids D013749 Tetrachlorodibenzodioxin 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: 87.81 RPKM in Testis Total median expression: 1375.67 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

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-120.10	195	-0.616	Picture	PostScript	Text
3' UTR	-1011.50	2142	-0.472	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
IPR005112 - dDENN_dom
IPR001194 - DENN_dom
IPR004182 - GRAM
IPR010569 - Myotub-related
IPR017906 - Myotubularin_phosphatase_dom
IPR011993 - PH_like_dom
IPR001849 - Pleckstrin_homology
IPR022096 - SBF2
IPR005113 - uDENN_dom

Pfam Domains:
PF00169 - PH domain
PF02141 - DENN (AEX-3) domain
PF02893 - GRAM domain
PF03456 - uDENN domain
PF06602 - Myotubularin-like phosphatase domain
PF12335 - Myotubularin protein

SCOP Domains:
50729 - PH domain-like
52799 - (Phosphotyrosine protein) phosphatases II

ModBase Predicted Comparative 3D Structure on O95248


Front	Top	Side

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.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	No ortholog	No ortholog
Gene Details	Gene Details
Gene Sorter	Gene Sorter
	RGD

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0005085 guanyl-nucleotide exchange factor activity GO:0008138 protein tyrosine/serine/threonine phosphatase activity GO:0017112 Rab guanyl-nucleotide exchange factor activity GO:0019208 phosphatase regulator activity Biological Process: GO:0006470 protein dephosphorylation GO:0006661 phosphatidylinositol biosynthetic process GO:0007283 spermatogenesis GO:0043087 regulation of GTPase activity Cellular Component: GO:0005634 nucleus GO:0005737 cytoplasm GO:0005789 endoplasmic reticulum membrane GO:0005829 cytosol GO:0016021 integral component of membrane GO:0016604 nuclear body

Descriptions from all associated GenBank mRNAs


	JD491079 - Sequence 472103 from Patent EP1572962. JD345115 - Sequence 326139 from Patent EP1572962. JD274835 - Sequence 255859 from Patent EP1572962. JD413937 - Sequence 394961 from Patent EP1572962. JD253224 - Sequence 234248 from Patent EP1572962. JD207307 - Sequence 188331 from Patent EP1572962. JD188721 - Sequence 169745 from Patent EP1572962. JD263890 - Sequence 244914 from Patent EP1572962. JD533527 - Sequence 514551 from Patent EP1572962. JD370705 - Sequence 351729 from Patent EP1572962. JD176991 - Sequence 158015 from Patent EP1572962. JD221445 - Sequence 202469 from Patent EP1572962. JD497051 - Sequence 478075 from Patent EP1572962. JD220194 - Sequence 201218 from Patent EP1572962. JD384363 - Sequence 365387 from Patent EP1572962. JD495508 - Sequence 476532 from Patent EP1572962. JD548934 - Sequence 529958 from Patent EP1572962. JD364870 - Sequence 345894 from Patent EP1572962. JD360555 - Sequence 341579 from Patent EP1572962. JD497303 - Sequence 478327 from Patent EP1572962. JD501172 - Sequence 482196 from Patent EP1572962. JD378808 - Sequence 359832 from Patent EP1572962. JD098098 - Sequence 79122 from Patent EP1572962. JD420386 - Sequence 401410 from Patent EP1572962. LF210403 - JP 2014500723-A/17906: Polycomb-Associated Non-Coding RNAs. BC046169 - Homo sapiens SET binding factor 1, mRNA (cDNA clone IMAGE:6192910), partial cds. BC024101 - Homo sapiens SET binding factor 1, mRNA (cDNA clone IMAGE:2960236), containing frame-shift errors. U93181 - Homo sapiens nuclear dual-specificity phosphatase (SBF1) mRNA, partial cds. BC087612 - Homo sapiens SET binding factor 1, mRNA (cDNA clone MGC:99700 IMAGE:6671883), complete cds. BC056915 - Homo sapiens SET binding factor 1, mRNA (cDNA clone IMAGE:6142405), partial cds. BC009268 - Homo sapiens SET binding factor 1, mRNA (cDNA clone IMAGE:3028662), partial cds. AK057985 - Homo sapiens cDNA FLJ25256 fis, clone STM03946, highly similar to Homo sapiens nuclear dual-specificity phosphatase (SBF1) mRNA. JD520556 - Sequence 501580 from Patent EP1572962. JD191357 - Sequence 172381 from Patent EP1572962. JD542255 - Sequence 523279 from Patent EP1572962. JD226478 - Sequence 207502 from Patent EP1572962. JD443153 - Sequence 424177 from Patent EP1572962. JD137656 - Sequence 118680 from Patent EP1572962. BC111424 - Homo sapiens cDNA clone IMAGE:40037678. JD252377 - Sequence 233401 from Patent EP1572962. JD194249 - Sequence 175273 from Patent EP1572962. EU831421 - Synthetic construct Homo sapiens clone HAIB:100066450; DKFZo008B0817 SET binding factor 1 protein (SBF1) gene, encodes complete protein. EU831514 - Synthetic construct Homo sapiens clone HAIB:100066543; DKFZo004B0818 SET binding factor 1 protein (SBF1) gene, encodes complete protein. AF072929 - Homo sapiens myotubularin related protein 5 mRNA, partial cds. CR749672 - Homo sapiens mRNA; cDNA DKFZp761D0422 (from clone DKFZp761D0422). AB209682 - Homo sapiens mRNA for SET binding factor 1 isoform a variant protein. BC040031 - Homo sapiens SET binding factor 1, mRNA (cDNA clone IMAGE:5770163). LF337647 - JP 2014500723-A/145150: Polycomb-Associated Non-Coding RNAs. LF337648 - JP 2014500723-A/145151: Polycomb-Associated Non-Coding RNAs. LF337651 - JP 2014500723-A/145154: Polycomb-Associated Non-Coding RNAs. JD282377 - Sequence 263401 from Patent EP1572962. LF337652 - JP 2014500723-A/145155: Polycomb-Associated Non-Coding RNAs. JD394208 - Sequence 375232 from Patent EP1572962. JD534366 - Sequence 515390 from Patent EP1572962. JD232960 - Sequence 213984 from Patent EP1572962. JD534365 - Sequence 515389 from Patent EP1572962. JD409432 - Sequence 390456 from Patent EP1572962. JD343002 - Sequence 324026 from Patent EP1572962. LF337653 - JP 2014500723-A/145156: Polycomb-Associated Non-Coding RNAs. JD226994 - Sequence 208018 from Patent EP1572962. LF337654 - JP 2014500723-A/145157: Polycomb-Associated Non-Coding RNAs. JD242204 - Sequence 223228 from Patent EP1572962. LF337655 - JP 2014500723-A/145158: Polycomb-Associated Non-Coding RNAs. DQ570565 - Homo sapiens piRNA piR-30677, complete sequence. JD056229 - Sequence 37253 from Patent EP1572962. JD406055 - Sequence 387079 from Patent EP1572962. JD271292 - Sequence 252316 from Patent EP1572962. JD458514 - Sequence 439538 from Patent EP1572962. JD057274 - Sequence 38298 from Patent EP1572962. JD406801 - Sequence 387825 from Patent EP1572962. JD461601 - Sequence 442625 from Patent EP1572962. JD056228 - Sequence 37252 from Patent EP1572962. JD458513 - Sequence 439537 from Patent EP1572962. JD458511 - Sequence 439535 from Patent EP1572962. JD458512 - Sequence 439536 from Patent EP1572962. JD271291 - Sequence 252315 from Patent EP1572962. JD458510 - Sequence 439534 from Patent EP1572962. MA445980 - JP 2018138019-A/17906: Polycomb-Associated Non-Coding RNAs. MA573224 - JP 2018138019-A/145150: Polycomb-Associated Non-Coding RNAs. MA573225 - JP 2018138019-A/145151: Polycomb-Associated Non-Coding RNAs. MA573228 - JP 2018138019-A/145154: Polycomb-Associated Non-Coding RNAs. MA573229 - JP 2018138019-A/145155: Polycomb-Associated Non-Coding RNAs. MA573230 - JP 2018138019-A/145156: Polycomb-Associated Non-Coding RNAs. MA573231 - JP 2018138019-A/145157: Polycomb-Associated Non-Coding RNAs. MA573232 - JP 2018138019-A/145158: Polycomb-Associated Non-Coding RNAs.

Biochemical and Signaling Pathways


	Reactome (by CSHL, EBI, and GO) Protein O95248 (Reactome details) participates in the following event(s): R-HSA-6809764 SBF1 binds MTMR2 R-HSA-6809777 PI3P is dephosphorylated to PI by MTMR2:SBF1 R-HSA-6809778 PI(3,5)P2 is dephosphorylated to PI5P by MTMR2:SBF1 R-HSA-8876837 RAB21 GEFs exchange GTP for GDP on RAB21 R-HSA-1483248 Synthesis of PIPs at the ER membrane R-HSA-1483255 PI Metabolism R-HSA-1483257 Phospholipid metabolism R-HSA-8876198 RAB GEFs exchange GTP for GDP on RABs R-HSA-556833 Metabolism of lipids R-HSA-9007101 Rab regulation of trafficking R-HSA-1430728 Metabolism R-HSA-199991 Membrane Trafficking R-HSA-5653656 Vesicle-mediated transport

Other Names for This Gene


	Alternate Gene Symbols: A0A024R4Z9, A6PVG9, ENST00000380817.1, ENST00000380817.2, ENST00000380817.3, ENST00000380817.4, ENST00000380817.5, ENST00000380817.6, ENST00000380817.7, G5E933, MTMR5, MTMR5_HUMAN, NM_002972, O60228, O95248, Q5JXD8, Q5PPM2, Q96GR9, Q9UGB8, uc318pwd.1, uc318pwd.2 UCSC ID: ENST00000380817.8_11 RefSeq Accession: NM_002972.4 Protein: O95248 (aka MTMR5_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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