PHF5A_MOUSE
ID PHF5A_MOUSE Reviewed; 110 AA.
AC P83870; Q3TQX7; Q9UH06;
DT 26-APR-2004, integrated into UniProtKB/Swiss-Prot.
DT 26-APR-2004, sequence version 1.
DT 03-AUG-2022, entry version 141.
DE RecName: Full=PHD finger-like domain-containing protein 5A;
DE Short=PHD finger-like domain protein 5A;
DE AltName: Full=Splicing factor 3B-associated 14 kDa protein;
DE Short=SF3b14b;
GN Name=Phf5a;
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Mus; Mus.
OX NCBI_TaxID=10090;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], SUBCELLULAR LOCATION, AND TISSUE
RP SPECIFICITY.
RX PubMed=12054543; DOI=10.1016/s0006-291x(02)00277-2;
RA Trappe R., Ahmed M., Glaeser B., Vogel C., Tascou S., Burfeind P.,
RA Engel W.;
RT "Identification and characterization of a novel murine multigene family
RT containing a PHD-finger-like motif.";
RL Biochem. Biophys. Res. Commun. 293:816-826(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=BALB/cJ, C57BL/6J, and DBA/2J; TISSUE=Egg, and Spleen;
RX PubMed=16141072; DOI=10.1126/science.1112014;
RA Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
RA Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
RA Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.,
RA Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R.,
RA Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T.,
RA Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A.,
RA Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B.,
RA Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M.,
RA Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S.,
RA Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D.,
RA Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M.,
RA Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H.,
RA Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V.,
RA Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S.,
RA Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H.,
RA Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N.,
RA Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F.,
RA Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G.,
RA Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z.,
RA Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
RA Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
RA Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S.,
RA Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K.,
RA Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R.,
RA van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H.,
RA Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M.,
RA Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C.,
RA Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S.,
RA Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K.,
RA Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M.,
RA Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C.,
RA Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
RA Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.;
RT "The transcriptional landscape of the mammalian genome.";
RL Science 309:1559-1563(2005).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=FVB/N; TISSUE=Kidney;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [4]
RP INTERACTION WITH DDX1; EP400; SRSF5 AND U2AF1, SUBCELLULAR LOCATION, AND
RP TISSUE SPECIFICITY.
RX PubMed=18758164; DOI=10.1159/000138890;
RA Rzymski T., Grzmil P., Meinhardt A., Wolf S., Burfeind P.;
RT "PHF5A represents a bridge protein between splicing proteins and ATP-
RT dependent helicases and is differentially expressed during mouse
RT spermatogenesis.";
RL Cytogenet. Genome Res. 121:232-244(2008).
RN [5]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Brain, Brown adipose tissue, Kidney, Liver, Pancreas, Spleen, and
RC Testis;
RX PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
RA Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
RA Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
RT "A tissue-specific atlas of mouse protein phosphorylation and expression.";
RL Cell 143:1174-1189(2010).
RN [6]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2 AND LYS-3, CLEAVAGE OF
RP INITIATOR METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Embryonic fibroblast;
RX PubMed=23806337; DOI=10.1016/j.molcel.2013.06.001;
RA Park J., Chen Y., Tishkoff D.X., Peng C., Tan M., Dai L., Xie Z., Zhang Y.,
RA Zwaans B.M., Skinner M.E., Lombard D.B., Zhao Y.;
RT "SIRT5-mediated lysine desuccinylation impacts diverse metabolic
RT pathways.";
RL Mol. Cell 50:919-930(2013).
RN [7]
RP FUNCTION, INTERACTION WITH CDC73; WDR61 AND RNA POLYMERASE II, SUBUNIT,
RP SUBCELLULAR LOCATION, TISSUE SPECIFICITY, AND INDUCTION.
RX PubMed=27749823; DOI=10.1038/ncb3424;
RA Strikoudis A., Lazaris C., Trimarchi T., Galvao Neto A.L., Yang Y.,
RA Ntziachristos P., Rothbart S., Buckley S., Dolgalev I., Stadtfeld M.,
RA Strahl B.D., Dynlacht B.D., Tsirigos A., Aifantis I.;
RT "Regulation of transcriptional elongation in pluripotency and cell
RT differentiation by the PHD-finger protein Phf5a.";
RL Nat. Cell Biol. 18:1127-1138(2016).
CC -!- FUNCTION: Involved with the PAF1 complex (PAF1C) in transcriptional
CC elongation by RNA polymerase II, and in regulation of development and
CC maintenance of embryonic stem cell (ESC) pluripotency. Required for
CC maintenance of ESCs self-renewal and cellular reprogramming of stem
CC cells. Maintains pluripotency by recruiting and stabilizing PAF1C on
CC pluripotency genes loci, and by regulating the expression of the
CC pluripotency genes. Regulates the deposition of elongation-associated
CC histone modifications, including dimethylated histone H3 'Lys-79'
CC (H3K79me2) and trimethylated histone H3 'Lys-36' (H3K36me3), on PAF1C
CC targets, self-renewal and pluripotency genes. Regulates RNA polymerase
CC II promoter-proximal pause release of the PAF1C targets and self-
CC renewal genes, and the levels of elongating ('Ser-2' phosphorylated)
CC RNA polymerase II in their gene bodies. Regulates muscle specification
CC in adult stem cells by stabilizing PAF1C in chromatin to promote
CC myogenic differentiation (PubMed:27749823). Involved in pre-mRNA
CC splicing as a component of the splicing factor SF3B complex. SF3B
CC complex is required for 'A' complex assembly formed by the stable
CC binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA.
CC Sequence independent binding of SF3A/SF3B complex upstream of the
CC branch site is essential, it may anchor U2 snRNP to the pre-mRNA (By
CC similarity). Acts as a transcriptional regulator by binding to the
CC GJA1/Cx43 promoter and enhancing its up-regulation by ESR1/ER-alpha (By
CC similarity). {ECO:0000250|UniProtKB:P83871,
CC ECO:0000250|UniProtKB:Q7RTV0, ECO:0000269|PubMed:27749823}.
CC -!- SUBUNIT: Interacts (via N-terminus) with U2AF1 and SRSF5; acts to
CC bridge the two. Interacts (via C-terminus) with EP400 and DDX1; acts to
CC bridge the two (PubMed:18758164). Component of splicing factor SF3B
CC complex which is composed of at least eight subunits; SF3B1, SF3B2,
CC SF3B3, SF3B4, SF3B5, SF3B6, PHF5A and DDX42. Within the SF3B complex
CC interacts directly with SF3B1 and SF3B3. The SF3B complex composed of
CC SF3B1, SF3B2, SF3B3, SF3B4, SF3B5, SF3B6 and PHF5A interacts with
CC U2AF2. SF3B associates with the splicing factor SF3A and a 12S RNA unit
CC to form the U2 small nuclear ribonucleoproteins complex (U2 snRNP).
CC Component of the U11/U12 snRNPs that are part of the U12-type
CC spliceosome (By similarity). Interacts with the PAF1 complex (PAF1C)
CC composed of CDC73, PAF1, LEO1, CTR9, RTF1 and WDR61. Within the PAF1C
CC interacts directly with CDC73 and WDR61. Interacts with RNA polymerase
CC II (PubMed:27749823). {ECO:0000250|UniProtKB:Q7RTV0,
CC ECO:0000269|PubMed:18758164, ECO:0000269|PubMed:27749823}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:12054543,
CC ECO:0000269|PubMed:18758164, ECO:0000269|PubMed:27749823}. Nucleus
CC speckle {ECO:0000269|PubMed:18758164}.
CC -!- TISSUE SPECIFICITY: Expressed in primary spermatocytes (at protein
CC level) (PubMed:18758164). Ubiquitously expressed in pre- and postnatal
CC tissues (PubMed:12054543). Highly expressed in pluripotent embryonic
CC stem cells (ESCs) (at protein level) and induced pluripotent stem cells
CC (iPSCs) (PubMed:27749823). {ECO:0000269|PubMed:12054543,
CC ECO:0000269|PubMed:18758164, ECO:0000269|PubMed:27749823}.
CC -!- INDUCTION: Expression levels are down-regulated following
CC differentiation in embryonic stem cells (ESCs) and in differentiated
CC mouse embryonic fibroblasts (MEFs). {ECO:0000269|PubMed:27749823}.
CC -!- SIMILARITY: Belongs to the PHF5 family. {ECO:0000305}.
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DR EMBL; AF479286; AAM49735.1; -; Genomic_DNA.
DR EMBL; AF479288; AAM49736.1; -; mRNA.
DR EMBL; AK003520; BAB22833.1; -; mRNA.
DR EMBL; AK143590; BAE25453.1; -; mRNA.
DR EMBL; AK163247; BAE37255.1; -; mRNA.
DR EMBL; AK167932; BAE39936.1; -; mRNA.
DR EMBL; AK167955; BAE39955.1; -; mRNA.
DR EMBL; BC025161; AAH25161.1; -; mRNA.
DR CCDS; CCDS27674.1; -.
DR PIR; JC7851; JC7851.
DR RefSeq; NP_081013.1; NM_026737.3.
DR AlphaFoldDB; P83870; -.
DR SMR; P83870; -.
DR BioGRID; 212875; 9.
DR IntAct; P83870; 2.
DR MINT; P83870; -.
DR STRING; 10090.ENSMUSP00000023117; -.
DR iPTMnet; P83870; -.
DR PhosphoSitePlus; P83870; -.
DR EPD; P83870; -.
DR MaxQB; P83870; -.
DR PaxDb; P83870; -.
DR PeptideAtlas; P83870; -.
DR PRIDE; P83870; -.
DR ProteomicsDB; 287927; -.
DR Antibodypedia; 26931; 196 antibodies from 23 providers.
DR DNASU; 68479; -.
DR Ensembl; ENSMUST00000023117; ENSMUSP00000023117; ENSMUSG00000061360.
DR GeneID; 68479; -.
DR KEGG; mmu:68479; -.
DR UCSC; uc007wxo.1; mouse.
DR CTD; 84844; -.
DR MGI; MGI:2156864; Phf5a.
DR VEuPathDB; HostDB:ENSMUSG00000061360; -.
DR eggNOG; KOG1705; Eukaryota.
DR GeneTree; ENSGT00390000018518; -.
DR HOGENOM; CLU_110369_2_0_1; -.
DR InParanoid; P83870; -.
DR OMA; AYYCWEC; -.
DR OrthoDB; 1477492at2759; -.
DR PhylomeDB; P83870; -.
DR TreeFam; TF105627; -.
DR Reactome; R-MMU-72163; mRNA Splicing - Major Pathway.
DR BioGRID-ORCS; 68479; 22 hits in 72 CRISPR screens.
DR ChiTaRS; Phf5a; mouse.
DR PRO; PR:P83870; -.
DR Proteomes; UP000000589; Chromosome 15.
DR RNAct; P83870; protein.
DR Bgee; ENSMUSG00000061360; Expressed in primitive streak and 271 other tissues.
DR Genevisible; P83870; MM.
DR GO; GO:0016363; C:nuclear matrix; IDA:MGI.
DR GO; GO:0016607; C:nuclear speck; IDA:UniProtKB.
DR GO; GO:0005654; C:nucleoplasm; ISO:MGI.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0071011; C:precatalytic spliceosome; IBA:GO_Central.
DR GO; GO:0005689; C:U12-type spliceosomal complex; ISO:MGI.
DR GO; GO:0005686; C:U2 snRNP; ISS:UniProtKB.
DR GO; GO:0071005; C:U2-type precatalytic spliceosome; ISO:MGI.
DR GO; GO:0005684; C:U2-type spliceosomal complex; ISO:MGI.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003723; F:RNA binding; ISO:MGI.
DR GO; GO:0008270; F:zinc ion binding; ISO:MGI.
DR GO; GO:0000398; P:mRNA splicing, via spliceosome; ISS:UniProtKB.
DR GO; GO:0045893; P:positive regulation of transcription, DNA-templated; ISS:UniProtKB.
DR GO; GO:0048863; P:stem cell differentiation; IEP:UniProtKB.
DR InterPro; IPR005345; PHF5.
DR PANTHER; PTHR13120; PTHR13120; 1.
DR Pfam; PF03660; PHF5; 1.
DR PIRSF; PIRSF016468; PHF5; 1.
PE 1: Evidence at protein level;
KW Acetylation; Activator; DNA-binding; Metal-binding; mRNA processing;
KW mRNA splicing; Nucleus; Phosphoprotein; Reference proteome; RNA-binding;
KW Spliceosome; Transcription; Transcription regulation; Zinc.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:23806337"
FT CHAIN 2..110
FT /note="PHD finger-like domain-containing protein 5A"
FT /id="PRO_0000218717"
FT REGION 35..51
FT /note="Interaction with SF3B1 AND SF3B3"
FT /evidence="ECO:0000250|UniProtKB:Q7RTV0"
FT REGION 79..82
FT /note="Interaction with SF3B3"
FT /evidence="ECO:0000250|UniProtKB:Q7RTV0"
FT BINDING 11
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q7RTV0"
FT BINDING 23
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q7RTV0"
FT BINDING 26
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q7RTV0"
FT BINDING 30
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q7RTV0"
FT BINDING 33
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q7RTV0"
FT BINDING 46
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q7RTV0"
FT BINDING 49
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q7RTV0"
FT BINDING 58
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q7RTV0"
FT BINDING 61
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q7RTV0"
FT BINDING 72
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q7RTV0"
FT BINDING 75
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q7RTV0"
FT BINDING 85
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q7RTV0"
FT SITE 17
FT /note="Interaction with SF3B3"
FT /evidence="ECO:0000250|UniProtKB:Q7RTV0"
FT SITE 100
FT /note="Interaction with RNA"
FT /evidence="ECO:0000250|UniProtKB:Q7RTV0"
FT MOD_RES 2
FT /note="N-acetylalanine"
FT /evidence="ECO:0007744|PubMed:23806337"
FT MOD_RES 3
FT /note="N6-acetyllysine"
FT /evidence="ECO:0007744|PubMed:23806337"
FT MOD_RES 94
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q7RTV0"
SQ SEQUENCE 110 AA; 12405 MW; 90F7469DE7292BF7 CRC64;
MAKHHPDLIF CRKQAGVAIG RLCEKCDGKC VICDSYVRPC TLVRICDECN YGSYQGRCVI
CGGPGVSDAY YCKECTIQEK DRDGCPKIVN LGSSKTDLFY ERKKYGFKKR
