Human Gene SF1 (ENST00000377390.8_8) from GENCODE V47lift37

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Description: splicing factor 1, transcript variant 1 (from RefSeq NM_004630.4)
Gencode Transcript: ENST00000377390.8_8
Gencode Gene: ENSG00000168066.22_16
Transcript (Including UTRs)
Position: hg19 chr11:64,532,078-64,546,014 Size: 13,937 Total Exon Count: 13 Strand: -
Coding Region
Position: hg19 chr11:64,533,290-64,545,864 Size: 12,575 Coding Exon Count: 13

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 (chr11:64,532,078-64,546,014)			mRNA (may differ from genome)		Protein (639 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: SF01_HUMAN DESCRIPTION: RecName: Full=Splicing factor 1; AltName: Full=Mammalian branch point-binding protein; Short=BBP; Short=mBBP; AltName: Full=Transcription factor ZFM1; AltName: Full=Zinc finger gene in MEN1 locus; AltName: Full=Zinc finger protein 162; FUNCTION: Necessary for the ATP-dependent first step of spliceosome assembly. Binds to the intron branch point sequence (BPS) 5'-UACUAAC-3' of the pre-mRNA. May act as transcription repressor. SUBUNIT: Binds U2AF2. Interacts with U1 snRNA. Binds EWSR1, FUS and TAF15. SUBCELLULAR LOCATION: Nucleus. TISSUE SPECIFICITY: Detected in lung, ovary, adrenal gland, colon, kidney, muscle, pancreas, thyroid, placenta, brain, liver and heart. PTM: Phosphorylation on Ser-20 interferes with U2AF2 binding and spliceosome assembly. Isoform 6 is phosphorylated on Ser-463. SIMILARITY: Belongs to the BBP/SF1 family. SIMILARITY: Contains 1 CCHC-type zinc finger. SIMILARITY: Contains 1 KH domain. SEQUENCE CAUTION: Sequence=AAH00773.1; Type=Erroneous initiation;

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: SF1 Diseases sorted by gene-association score: multiple endocrine neoplasia 1 (3)

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene D004041 Dietary Fats D013749 Tetrachlorodibenzodioxin D014635 Valproic Acid C006780 bisphenol A C495626 14-deoxy-11,12-didehydroandrographolide C029497 2,3-bis(3'-hydroxybenzyl)butyrolactone C016403 2,4-dinitrotoluene C023514 2,6-dinitrotoluene C035207 4-amino-2,6-dinitrotoluene D015124 8-Bromo Cyclic Adenosine Monophosphate 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: 116.65 RPKM in Ovary Total median expression: 3440.12 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	-72.50	150	-0.483	Picture	PostScript	Text
3' UTR	-409.10	1212	-0.338	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
IPR004087 - KH_dom
IPR004088 - KH_dom_type_1
IPR001878 - Znf_CCHC

Pfam Domains:
PF00013 - KH domain
PF00098 - Zinc knuckle
PF13917 - Zinc knuckle
PF16275 - Splicing factor 1 helix-hairpin domain

SCOP Domains:
56112 - Protein kinase-like (PK-like)
54791 - Eukaryotic type KH-domain (KH-domain type I)
54814 - Prokaryotic type KH domain (KH-domain type II)
57756 - Retrovirus zinc finger-like domains

Protein Data Bank (PDB) 3-D Structure
MuPIT help

1K1G - NMR MuPIT

ModBase Predicted Comparative 3D Structure on Q15637


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	Genome Browser
Gene Details	Gene Details				Gene Details
Gene Sorter	Gene Sorter				Gene Sorter
	RGD	Ensembl			SGD
					Protein Sequence
					Alignment

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0003676 nucleic acid binding GO:0003714 transcription corepressor activity GO:0003723 RNA binding GO:0005515 protein binding GO:0008270 zinc ion binding GO:0042802 identical protein binding GO:0045131 pre-mRNA branch point binding GO:0046872 metal ion binding Biological Process: GO:0000245 spliceosomal complex assembly GO:0000389 mRNA 3'-splice site recognition GO:0000398 mRNA splicing, via spliceosome GO:0006351 transcription, DNA-templated GO:0006355 regulation of transcription, DNA-templated GO:0006397 mRNA processing GO:0008380 RNA splicing GO:0030238 male sex determination GO:0030575 nuclear body organization GO:0033327 Leydig cell differentiation GO:0048662 negative regulation of smooth muscle cell proliferation GO:0050810 regulation of steroid biosynthetic process GO:1903507 negative regulation of nucleic acid-templated transcription Cellular Component: GO:0005634 nucleus GO:0005654 nucleoplasm GO:0005681 spliceosomal complex GO:0005840 ribosome GO:0016604 nuclear body

Descriptions from all associated GenBank mRNAs


	LF211197 - JP 2014500723-A/18700: Polycomb-Associated Non-Coding RNAs. L49345 - Homo sapiens transcription factor ZFM1 isoform B3 mRNA, complete cds. L49380 - Homo sapiens clone B4 transcription factor ZFM1 mRNA, complete cds. BC032676 - Homo sapiens cDNA clone IMAGE:5575272, containing frame-shift errors. BC069273 - Homo sapiens cDNA clone IMAGE:5927414, containing frame-shift errors. D26120 - Homo sapiens mRNA for ZFM1 protein, ZFM1 protein alternatively spliced product, complete cds. E10222 - cDNA of a tumor suppressing gene. BC034451 - Homo sapiens splicing factor 1, mRNA (cDNA clone IMAGE:4822403). BC038446 - Homo sapiens splicing factor 1, mRNA (cDNA clone MGC:45254 IMAGE:5493676), complete cds. BC011657 - Homo sapiens splicing factor 1, mRNA (cDNA clone IMAGE:4124268), partial cds. BC008080 - Homo sapiens splicing factor 1, mRNA (cDNA clone MGC:4482 IMAGE:2961666), complete cds. BC008724 - Homo sapiens splicing factor 1, mRNA (cDNA clone MGC:8657 IMAGE:2961666), complete cds. BC000773 - Homo sapiens, Similar to zinc finger protein 162, clone IMAGE:3506879, mRNA, partial cds. Y08765 - H.sapiens mRNA for splicing factor, SF1-HL1 isoform. BC020217 - Homo sapiens splicing factor 1, mRNA (cDNA clone MGC:31898 IMAGE:4869292), complete cds. LF344571 - JP 2014500723-A/152074: Polycomb-Associated Non-Coding RNAs. JD140264 - Sequence 121288 from Patent EP1572962. JD297840 - Sequence 278864 from Patent EP1572962. JD250453 - Sequence 231477 from Patent EP1572962. JD558881 - Sequence 539905 from Patent EP1572962. LF344570 - JP 2014500723-A/152073: Polycomb-Associated Non-Coding RNAs. JD131667 - Sequence 112691 from Patent EP1572962. AK301803 - Homo sapiens cDNA FLJ54064 complete cds, highly similar to Splicing factor 1. JD176637 - Sequence 157661 from Patent EP1572962. JD053668 - Sequence 34692 from Patent EP1572962. JD551753 - Sequence 532777 from Patent EP1572962. JD499191 - Sequence 480215 from Patent EP1572962. Y08766 - H.sapiens mRNA for splicing factor, SF1-Bo isoform. AK299705 - Homo sapiens cDNA FLJ54056 complete cds, highly similar to Splicing factor 1. JD405817 - Sequence 386841 from Patent EP1572962. JD057248 - Sequence 38272 from Patent EP1572962. EU832634 - Synthetic construct Homo sapiens clone HAIB:100067663; DKFZo008D0631 splicing factor 1 protein (SF1) gene, encodes complete protein. KJ892395 - Synthetic construct Homo sapiens clone ccsbBroadEn_01789 SF1 gene, encodes complete protein. EU832710 - Synthetic construct Homo sapiens clone HAIB:100067739; DKFZo004D0632 splicing factor 1 protein (SF1) gene, encodes complete protein. AK296237 - Homo sapiens cDNA FLJ53344 complete cds, highly similar to Splicing factor 1. AK293753 - Homo sapiens cDNA FLJ54737 complete cds, highly similar to Splicing factor 1. LF344569 - JP 2014500723-A/152072: Polycomb-Associated Non-Coding RNAs. AB489174 - Synthetic construct DNA, clone: pF1KB9453, Homo sapiens SF1 gene for splicing factor 1, without stop codon, in Flexi system. LF344566 - JP 2014500723-A/152069: Polycomb-Associated Non-Coding RNAs. LF344565 - JP 2014500723-A/152068: Polycomb-Associated Non-Coding RNAs. LF344564 - JP 2014500723-A/152067: Polycomb-Associated Non-Coding RNAs. LF344563 - JP 2014500723-A/152066: Polycomb-Associated Non-Coding RNAs. CU675923 - Synthetic construct Homo sapiens gateway clone IMAGE:100017401 5' read SF1 mRNA. LF344561 - JP 2014500723-A/152064: Polycomb-Associated Non-Coding RNAs. LF344560 - JP 2014500723-A/152063: Polycomb-Associated Non-Coding RNAs. LF344559 - JP 2014500723-A/152062: Polycomb-Associated Non-Coding RNAs. LF344558 - JP 2014500723-A/152061: Polycomb-Associated Non-Coding RNAs. D26122 - Homo sapiens mRNA for ZFM1 protein alternatively spliced product domain H, complete cds. LF344557 - JP 2014500723-A/152060: Polycomb-Associated Non-Coding RNAs. LF344556 - JP 2014500723-A/152059: Polycomb-Associated Non-Coding RNAs. LF344554 - JP 2014500723-A/152057: Polycomb-Associated Non-Coding RNAs. D26121 - Homo sapiens mRNA for ZFM1 protein alternatively spliced product domain A, B and G, complete cds. LF344549 - JP 2014500723-A/152052: Polycomb-Associated Non-Coding RNAs. JD222083 - Sequence 203107 from Patent EP1572962. JD444918 - Sequence 425942 from Patent EP1572962. JD537723 - Sequence 518747 from Patent EP1572962. MA580148 - JP 2018138019-A/152074: Polycomb-Associated Non-Coding RNAs. MA580147 - JP 2018138019-A/152073: Polycomb-Associated Non-Coding RNAs. MA580146 - JP 2018138019-A/152072: Polycomb-Associated Non-Coding RNAs. MA580143 - JP 2018138019-A/152069: Polycomb-Associated Non-Coding RNAs. MA580142 - JP 2018138019-A/152068: Polycomb-Associated Non-Coding RNAs. MA580141 - JP 2018138019-A/152067: Polycomb-Associated Non-Coding RNAs. MA580140 - JP 2018138019-A/152066: Polycomb-Associated Non-Coding RNAs. MA580138 - JP 2018138019-A/152064: Polycomb-Associated Non-Coding RNAs. MA580137 - JP 2018138019-A/152063: Polycomb-Associated Non-Coding RNAs. MA580136 - JP 2018138019-A/152062: Polycomb-Associated Non-Coding RNAs. MA580135 - JP 2018138019-A/152061: Polycomb-Associated Non-Coding RNAs. MA580134 - JP 2018138019-A/152060: Polycomb-Associated Non-Coding RNAs. MA580133 - JP 2018138019-A/152059: Polycomb-Associated Non-Coding RNAs. MA580131 - JP 2018138019-A/152057: Polycomb-Associated Non-Coding RNAs. MA580126 - JP 2018138019-A/152052: Polycomb-Associated Non-Coding RNAs. MA446774 - JP 2018138019-A/18700: Polycomb-Associated Non-Coding RNAs.

Biochemical and Signaling Pathways


	Reactome (by CSHL, EBI, and GO) Protein Q15637 (Reactome details) participates in the following event(s): R-HSA-72107 Formation of the Spliceosomal E complex R-HSA-72124 Formation of the Spliceosomal A Complex R-HSA-72163 mRNA Splicing - Major Pathway R-HSA-72172 mRNA Splicing R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA R-HSA-8953854 Metabolism of RNA

Other Names for This Gene


	Alternate Gene Symbols: B7Z1Q1, C9JJE2, ENST00000377390.1, ENST00000377390.2, ENST00000377390.3, ENST00000377390.4, ENST00000377390.5, ENST00000377390.6, ENST00000377390.7, NM_004630, Q14818, Q14819, Q15637, Q15913, Q8IY00, Q92744, Q92745, Q969H7, Q9BW01, Q9UEI0, SF01_HUMAN, uc318noq.1, uc318noq.2, ZFM1, ZNF162 UCSC ID: ENST00000377390.8_8 RefSeq Accession: NM_004630.4 Protein: Q15637 (aka SF01_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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