EuRBPDB

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  • Description
  • RBDs
  • RBPome
  • Literatures
  • Expression
  • Transcripts
  • Gene Model
  • Pathways
  • Phenotypes
  • GWAS
  • PPI
  • Orthologs
  • Gene Ontology
Description
Ensembl ID
ENSG00000100410 (Gene tree)
Gene ID
84844
Gene Symbol
PHF5A
Alias
MGC1346|SF3b14b|INI|bK223H9.2|Rds3|SAP14b|SF3B7
Full Name
PHD finger protein 5A
Gene Type
protein_coding
Species
Homo_sapiens
Status
confidence
Strand
Minus strand
Length
9,009 bases
Position
chr22:41,459,717-41,468,725
Accession
18000
RBP type
canonical RBP
Summary
This gene encodes a subunit of the splicing factor 3b protein complex. Splicing factor 3b, together with splicing factor 3a and a 12S RNA unit, forms the U2 small nuclear ribonucleoproteins complex (U2 snRNP). The splicing factor 3b/3a complex binds pre-mRNA upstream of the intron's branch site in a sequence-independent manner and may anchor the U2 snRNP to the pre-mRNA. The protein encoded by this gene contains a PHD-finger-like domain that is flanked by highly basic N- and C-termini. This protein belongs to the PHD-finger superfamily and may act as a chromatin-associated protein. This gene has several pseudogenes on different chromosomes. [provided by RefSeq, Jul 2008]
RNA binding domains(RBDs)
Protein IDDomain Pfam IDE-value Domain number Total number
ENSP00000216252PHF5PF03660.145.9e-4911
RNA binding proteome (RBPome)
PIDTitleMethod TimeAuthorDoi
22681889The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts4SURIC & HEK2932012 MayBaltz AGDOI: 10.1016/j.molcel.2012.05.021
30607034Comprehensive identification of RNA protein interactions in any organism using orthogonal organic phase separation (OOPS)OOPS & HEK2932019 Jan 3Queiroz RMLDOI: 10.1038/s41587-018-0001-2
30528433The Human RNA-Binding Proteome and Its Dynamics during Translational ArrestXRNAX & HEK2932018 Dec 6Trendel JDOI: 10.1016/j.cell.2018.11.004
22658674Insights into RNA biology from an atlas of mammalian mRNA-binding proteinsRIC & Hela2012 May 31Castello ADOI: 10.1016/j.cell.2012.04.031
30528433The Human RNA-Binding Proteome and Its Dynamics during Translational ArrestXRNAX & Hela2018 Dec 6Trendel JDOI: 10.1016/j.cell.2018.11.004
30528433The Human RNA-Binding Proteome and Its Dynamics during Translational ArrestXRNAX & MCF72018 Dec 6Trendel JDOI: 10.1016/j.cell.2018.11.004
30352994Discovery of RNA-binding proteins and characterization of their dynamic responses by enhanced RNA interactome captureRIC & Jurkat2018 Oct 23Perez-Perri JIDOI:10.1038/s41467-018-06557-8

Literatures on RNA binding capacity
PIDTitleArticle TimeAuthorDoi
27720643Molecular Architecture of SF3b and Structural Consequences of Its Cancer-Related Mutations.Mol Cell2016 Oct 20Cretu Cdoi: 10.1016/j.molcel.2016.08.036
29700004PHF5A Epigenetically Inhibits Apoptosis to Promote Breast Cancer Progression.Cancer Res2018 Jun 15Zheng YZdoi: 10.1158/0008-5472.CAN-17-3514
Expression
Transcripts
Transcript IDNameLengthRefSeq ID Protein IDLengthRefSeq IDUniportKB ID
ENST00000491254PHF5A-203292--- (aa)--
ENST00000459687PHF5A-202504--- (aa)--
ENST00000216252PHF5A-2011086-ENSP00000216252110 (aa)-Q7RTV0
Gene Model
Click here to download ENSG00000100410's gene model file
Pathways
Pathway IDPathway NameSource
hsa03040SpliceosomeKEGG
Phenotypes
ensgIDTraitpValuePubmed ID
ENSG00000100410Platelet Function Tests1.5454300E-005-
ENSG00000100410Platelet Function Tests1.5454300E-005-
GWAS
ensgIDSNPChromosomePositionSNP-risk TraitPubmedID95% CIOr or BEAT EFO ID
ENSG00000100410rs60023862241463657AHighest math class taken30038396[0.017-0.028] unit decrease0.0227EFO_0004875
ENSG00000100410rs96115972241468186AEducational attainment (years of education)30038396[0.007-0.0144] unit decrease0.0107EFO_0004784
ENSG00000100410rs96115972241468186AChronotype306968231.0381082EFO_0008328
Protein-Protein Interaction (PPI)

Clik here to download ENSG00000100410's network

* RBP PPI network refers to all genes directly bind to RBP
Orthologs
Ensembl IDGene SymbolCoverageIdentiy OrthologGene SymbolCoverageIdentiy Species
ENSG00000100410PHF5A100100.000ENSAPOG00000017805phf5a100100.000Acanthochromis_polyacanthus
ENSG00000100410PHF5A74100.000ENSAMEG00000015687PHF5A100100.000Ailuropoda_melanoleuca
ENSG00000100410PHF5A10091.818ENSACIG00000021628phf5a10091.818Amphilophus_citrinellus
ENSG00000100410PHF5A100100.000ENSAOCG00000020917phf5a100100.000Amphiprion_ocellaris
ENSG00000100410PHF5A100100.000ENSAPEG00000020260phf5a100100.000Amphiprion_percula
ENSG00000100410PHF5A100100.000ENSATEG00000006506phf5a100100.000Anabas_testudineus
ENSG00000100410PHF5A100100.000ENSATEG00000007455phf5a100100.000Anabas_testudineus
ENSG00000100410PHF5A100100.000ENSACAG00000004775PHF5A100100.000Anolis_carolinensis
ENSG00000100410PHF5A9987.156ENSANAG00000020141-9287.156Aotus_nancymaae
ENSG00000100410PHF5A100100.000ENSANAG00000028988-100100.000Aotus_nancymaae
ENSG00000100410PHF5A10081.818ENSANAG00000022538-10081.818Aotus_nancymaae
ENSG00000100410PHF5A10082.727ENSANAG00000036831-10082.727Aotus_nancymaae
ENSG00000100410PHF5A100100.000ENSACLG00000019161phf5a10091.818Astatotilapia_calliptera
ENSG00000100410PHF5A100100.000ENSAMXG00000035422phf5a100100.000Astyanax_mexicanus
ENSG00000100410PHF5A100100.000ENSBTAG00000006423PHF5A100100.000Bos_taurus
ENSG00000100410PHF5A9990.826WBGene00004016phf-59990.826Caenorhabditis_elegans
ENSG00000100410PHF5A100100.000ENSCJAG00000004999PHF5A100100.000Callithrix_jacchus
ENSG00000100410PHF5A100100.000ENSCAFG00000001090PHF5A100100.000Canis_familiaris
ENSG00000100410PHF5A100100.000ENSCAFG00020001984PHF5A100100.000Canis_lupus_dingo
ENSG00000100410PHF5A10092.727ENSCHIG00000015826PHF5A10092.727Capra_hircus
ENSG00000100410PHF5A100100.000ENSTSYG00000001082PHF5A100100.000Carlito_syrichta
ENSG00000100410PHF5A77100.000ENSCAPG00000007769PHF5A87100.000Cavia_aperea
ENSG00000100410PHF5A100100.000ENSCPOG00000033309PHF5A100100.000Cavia_porcellus
ENSG00000100410PHF5A100100.000ENSCCAG00000037141-100100.000Cebus_capucinus
ENSG00000100410PHF5A10083.636ENSCCAG00000037275-10083.636Cebus_capucinus
ENSG00000100410PHF5A10067.273ENSCCAG00000009204-10067.273Cebus_capucinus
ENSG00000100410PHF5A100100.000ENSCATG00000012251PHF5A100100.000Cercocebus_atys
ENSG00000100410PHF5A100100.000ENSCLAG00000016714-100100.000Chinchilla_lanigera
ENSG00000100410PHF5A10069.369ENSCLAG00000014324-10069.369Chinchilla_lanigera
ENSG00000100410PHF5A100100.000ENSCSAG00000005811PHF5A100100.000Chlorocebus_sabaeus
ENSG00000100410PHF5A10090.909ENSCHOG00000003545PHF5A10090.909Choloepus_hoffmanni
ENSG00000100410PHF5A100100.000ENSCPBG00000020547PHF5A100100.000Chrysemys_picta_bellii
ENSG00000100410PHF5A10097.273ENSCSAVG00000007539-10097.273Ciona_savignyi
ENSG00000100410PHF5A100100.000ENSCANG00000032125PHF5A100100.000Colobus_angolensis_palliatus
ENSG00000100410PHF5A100100.000ENSCGRG00001017936Phf5a100100.000Cricetulus_griseus_chok1gshd
ENSG00000100410PHF5A100100.000ENSCGRG00000012081Phf5a100100.000Cricetulus_griseus_crigri
ENSG00000100410PHF5A10091.818ENSCSEG00000020499phf5a10091.818Cynoglossus_semilaevis
ENSG00000100410PHF5A100100.000ENSCVAG00000006090phf5a100100.000Cyprinodon_variegatus
ENSG00000100410PHF5A100100.000ENSDARG00000045155phf5a100100.000Danio_rerio
ENSG00000100410PHF5A74100.000ENSDNOG00000034362PHF5A70100.000Dasypus_novemcinctus
ENSG00000100410PHF5A100100.000ENSDORG00000002205Phf5a100100.000Dipodomys_ordii
ENSG00000100410PHF5A9996.330FBgn0031822Phf5a9896.330Drosophila_melanogaster
ENSG00000100410PHF5A100100.000ENSETEG00000010741PHF5A100100.000Echinops_telfairi
ENSG00000100410PHF5A10092.727ENSEBUG00000009125-10092.727Eptatretus_burgeri
ENSG00000100410PHF5A100100.000ENSEASG00005001560PHF5A100100.000Equus_asinus_asinus
ENSG00000100410PHF5A100100.000ENSECAG00000023225PHF5A100100.000Equus_caballus
ENSG00000100410PHF5A100100.000ENSELUG00000019796phf5a100100.000Esox_lucius
ENSG00000100410PHF5A100100.000ENSFCAG00000003676PHF5A100100.000Felis_catus
ENSG00000100410PHF5A85100.000ENSFALG00000011963PHF5A100100.000Ficedula_albicollis
ENSG00000100410PHF5A100100.000ENSFDAG00000010822PHF5A100100.000Fukomys_damarensis
ENSG00000100410PHF5A100100.000ENSFHEG00000012724phf5a100100.000Fundulus_heteroclitus
ENSG00000100410PHF5A9991.743ENSGMOG00000013318phf5a9891.743Gadus_morhua
ENSG00000100410PHF5A100100.000ENSGALG00000011953PHF5A100100.000Gallus_gallus
ENSG00000100410PHF5A100100.000ENSGAFG00000008235phf5a100100.000Gambusia_affinis
ENSG00000100410PHF5A99100.000ENSGACG00000004777phf5a98100.000Gasterosteus_aculeatus
ENSG00000100410PHF5A10091.818ENSGAGG00000017494PHF5A10091.818Gopherus_agassizii
ENSG00000100410PHF5A100100.000ENSGGOG00000001104PHF5A100100.000Gorilla_gorilla
ENSG00000100410PHF5A10091.818ENSHBUG00000004040phf5a10091.818Haplochromis_burtoni
ENSG00000100410PHF5A9990.826ENSHGLG00000020143-10090.826Heterocephalus_glaber_female
ENSG00000100410PHF5A100100.000ENSHGLG00000012537PHF5A100100.000Heterocephalus_glaber_female
ENSG00000100410PHF5A7495.062ENSHGLG00100000188-8695.062Heterocephalus_glaber_male
ENSG00000100410PHF5A10080.292ENSHCOG00000010129phf5a10080.292Hippocampus_comes
ENSG00000100410PHF5A100100.000ENSIPUG00000001222phf5a100100.000Ictalurus_punctatus
ENSG00000100410PHF5A100100.000ENSSTOG00000016207PHF5A100100.000Ictidomys_tridecemlineatus
ENSG00000100410PHF5A100100.000ENSJJAG00000011261Phf5a100100.000Jaculus_jaculus
ENSG00000100410PHF5A100100.000ENSKMAG00000006739phf5a100100.000Kryptolebias_marmoratus
ENSG00000100410PHF5A100100.000ENSLBEG00000002141phf5a100100.000Labrus_bergylta
ENSG00000100410PHF5A74100.000ENSLACG00000012094PHF5A87100.000Latimeria_chalumnae
ENSG00000100410PHF5A100100.000ENSLAFG00000028840PHF5A100100.000Loxodonta_africana
ENSG00000100410PHF5A100100.000ENSMFAG00000003129PHF5A100100.000Macaca_fascicularis
ENSG00000100410PHF5A10093.636ENSMMUG00000011354-10093.636Macaca_mulatta
ENSG00000100410PHF5A7487.654ENSMMUG00000019698-10087.654Macaca_mulatta
ENSG00000100410PHF5A100100.000ENSMNEG00000045104PHF5A100100.000Macaca_nemestrina
ENSG00000100410PHF5A9784.112ENSMNEG00000010618-9684.112Macaca_nemestrina
ENSG00000100410PHF5A100100.000ENSMLEG00000037662PHF5A100100.000Mandrillus_leucophaeus
ENSG00000100410PHF5A8891.753ENSMLEG00000038352-8491.753Mandrillus_leucophaeus
ENSG00000100410PHF5A100100.000ENSMAMG00000003744phf5a100100.000Mastacembelus_armatus
ENSG00000100410PHF5A100100.000ENSMZEG00005019188phf5a74100.000Maylandia_zebra
ENSG00000100410PHF5A100100.000ENSMGAG00000012169PHF5A100100.000Meleagris_gallopavo
ENSG00000100410PHF5A100100.000ENSMAUG00000017124Phf5a100100.000Mesocricetus_auratus
ENSG00000100410PHF5A100100.000ENSMICG00000013520PHF5A100100.000Microcebus_murinus
ENSG00000100410PHF5A100100.000ENSMOCG00000015149Phf5a100100.000Microtus_ochrogaster
ENSG00000100410PHF5A10091.818ENSMMOG00000003636phf5a10091.818Mola_mola
ENSG00000100410PHF5A100100.000ENSMODG00000016556PHF5A100100.000Monodelphis_domestica
ENSG00000100410PHF5A100100.000ENSMALG00000008655phf5a100100.000Monopterus_albus
ENSG00000100410PHF5A100100.000MGP_CAROLIEiJ_G0020061Phf5a100100.000Mus_caroli
ENSG00000100410PHF5A100100.000ENSMUSG00000061360Phf5a100100.000Mus_musculus
ENSG00000100410PHF5A100100.000MGP_PahariEiJ_G0020063Phf5a100100.000Mus_pahari
ENSG00000100410PHF5A100100.000ENSMPUG00000016398PHF5A100100.000Mustela_putorius_furo
ENSG00000100410PHF5A100100.000ENSMLUG00000002465PHF5A100100.000Myotis_lucifugus
ENSG00000100410PHF5A100100.000ENSNGAG00000001430Phf5a100100.000Nannospalax_galili
ENSG00000100410PHF5A10091.818ENSNBRG00000004747phf5a10091.818Neolamprologus_brichardi
ENSG00000100410PHF5A74100.000ENSNLEG00000015481-100100.000Nomascus_leucogenys
ENSG00000100410PHF5A84100.000ENSMEUG00000002019PHF5A100100.000Notamacropus_eugenii
ENSG00000100410PHF5A100100.000ENSOPRG00000000358PHF5A100100.000Ochotona_princeps
ENSG00000100410PHF5A100100.000ENSODEG00000013125-100100.000Octodon_degus
ENSG00000100410PHF5A10085.455ENSODEG00000012449-10085.455Octodon_degus
ENSG00000100410PHF5A100100.000ENSONIG00000019693phf5a100100.000Oreochromis_niloticus
ENSG00000100410PHF5A85100.000ENSOANG00000000616-100100.000Ornithorhynchus_anatinus
ENSG00000100410PHF5A100100.000ENSOCUG00000012705PHF5A100100.000Oryctolagus_cuniculus
ENSG00000100410PHF5A100100.000ENSORLG00000002591phf5a100100.000Oryzias_latipes
ENSG00000100410PHF5A100100.000ENSORLG00020007407phf5a100100.000Oryzias_latipes_hni
ENSG00000100410PHF5A100100.000ENSORLG00015006160phf5a100100.000Oryzias_latipes_hsok
ENSG00000100410PHF5A100100.000ENSOMEG00000008564phf5a100100.000Oryzias_melastigma
ENSG00000100410PHF5A10097.273ENSOGAG00000025336-10097.273Otolemur_garnettii
ENSG00000100410PHF5A10088.182ENSOGAG00000032258-10088.182Otolemur_garnettii
ENSG00000100410PHF5A10091.818ENSOGAG00000002839-10091.818Otolemur_garnettii
ENSG00000100410PHF5A100100.000ENSOARG00000018246PHF5A99100.000Ovis_aries
ENSG00000100410PHF5A100100.000ENSPPAG00000008422PHF5A100100.000Pan_paniscus
ENSG00000100410PHF5A100100.000ENSPPRG00000006194PHF5A100100.000Panthera_pardus
ENSG00000100410PHF5A100100.000ENSPTIG00000014228PHF5A100100.000Panthera_tigris_altaica
ENSG00000100410PHF5A10074.545ENSPTRG00000050019-10074.545Pan_troglodytes
ENSG00000100410PHF5A100100.000ENSPTRG00000014427PHF5A100100.000Pan_troglodytes
ENSG00000100410PHF5A100100.000ENSPANG00000011337PHF5A100100.000Papio_anubis
ENSG00000100410PHF5A10098.182ENSPKIG00000003100phf5a10098.182Paramormyrops_kingsleyae
ENSG00000100410PHF5A100100.000ENSPSIG00000007014PHF5A100100.000Pelodiscus_sinensis
ENSG00000100410PHF5A7488.889ENSPMGG00000003502phf5a5988.889Periophthalmus_magnuspinnatus
ENSG00000100410PHF5A100100.000ENSPMAG00000002668phf5a100100.000Petromyzon_marinus
ENSG00000100410PHF5A10091.818ENSPFOG00000016814phf5a10091.818Poecilia_formosa
ENSG00000100410PHF5A100100.000ENSPLAG00000001292phf5a100100.000Poecilia_latipinna
ENSG00000100410PHF5A100100.000ENSPMEG00000010165phf5a100100.000Poecilia_mexicana
ENSG00000100410PHF5A100100.000ENSPREG00000020700phf5a100100.000Poecilia_reticulata
ENSG00000100410PHF5A100100.000ENSPPYG00000011870PHF5A100100.000Pongo_abelii
ENSG00000100410PHF5A100100.000ENSPCAG00000009709PHF5A100100.000Procavia_capensis
ENSG00000100410PHF5A100100.000ENSPCOG00000014332PHF5A100100.000Propithecus_coquereli
ENSG00000100410PHF5A100100.000ENSPVAG00000001162PHF5A100100.000Pteropus_vampyrus
ENSG00000100410PHF5A100100.000ENSPNYG00000004375phf5a100100.000Pundamilia_nyererei
ENSG00000100410PHF5A100100.000ENSPNAG00000011460phf5a100100.000Pygocentrus_nattereri
ENSG00000100410PHF5A100100.000ENSRNOG00000024170Phf5a100100.000Rattus_norvegicus
ENSG00000100410PHF5A10070.909ENSRBIG00000044640-10070.909Rhinopithecus_bieti
ENSG00000100410PHF5A74100.000ENSRBIG00000030586-92100.000Rhinopithecus_bieti
ENSG00000100410PHF5A100100.000ENSRROG00000038952PHF5A100100.000Rhinopithecus_roxellana
ENSG00000100410PHF5A9556.190YPR094W-9856.190Saccharomyces_cerevisiae
ENSG00000100410PHF5A74100.000ENSSBOG00000025096-76100.000Saimiri_boliviensis_boliviensis
ENSG00000100410PHF5A8882.474ENSSBOG00000019049-10082.474Saimiri_boliviensis_boliviensis
ENSG00000100410PHF5A8295.556ENSSHAG00000009937PHF5A8995.556Sarcophilus_harrisii
ENSG00000100410PHF5A100100.000ENSSFOG00015013765phf5a100100.000Scleropages_formosus
ENSG00000100410PHF5A10091.818ENSSMAG00000007054phf5a10091.818Scophthalmus_maximus
ENSG00000100410PHF5A100100.000ENSSDUG00000008019phf5a100100.000Seriola_dumerili
ENSG00000100410PHF5A8387.912ENSSLDG00000011535-10087.912Seriola_lalandi_dorsalis
ENSG00000100410PHF5A100100.000ENSSLDG00000009619phf5a100100.000Seriola_lalandi_dorsalis
ENSG00000100410PHF5A10099.091ENSSARG00000003769PHF5A10099.091Sorex_araneus
ENSG00000100410PHF5A10099.091ENSSPUG00000011593PHF5A10099.091Sphenodon_punctatus
ENSG00000100410PHF5A100100.000ENSSPAG00000022955phf5a100100.000Stegastes_partitus
ENSG00000100410PHF5A100100.000ENSSSCG00000035082PHF5A100100.000Sus_scrofa
ENSG00000100410PHF5A85100.000ENSTGUG00000009936PHF5A100100.000Taeniopygia_guttata
ENSG00000100410PHF5A100100.000ENSTRUG00000023867phf5a100100.000Takifugu_rubripes
ENSG00000100410PHF5A100100.000ENSTNIG00000012939phf5a100100.000Tetraodon_nigroviridis
ENSG00000100410PHF5A10090.909ENSTBEG00000010945PHF5A10090.909Tupaia_belangeri
ENSG00000100410PHF5A100100.000ENSTTRG00000003369PHF5A100100.000Tursiops_truncatus
ENSG00000100410PHF5A74100.000ENSUAMG00000022580PHF5A95100.000Ursus_americanus
ENSG00000100410PHF5A10092.727ENSUMAG00000021030PHF5A10092.727Ursus_maritimus
ENSG00000100410PHF5A84100.000ENSVPAG00000002614PHF5A100100.000Vicugna_pacos
ENSG00000100410PHF5A100100.000ENSVVUG00000003634PHF5A100100.000Vulpes_vulpes
ENSG00000100410PHF5A100100.000ENSXETG00000006893phf5a100100.000Xenopus_tropicalis
ENSG00000100410PHF5A10091.818ENSXCOG00000000364phf5a10091.818Xiphophorus_couchianus
ENSG00000100410PHF5A74100.000ENSXMAG00000000679phf5a92100.000Xiphophorus_maculatus
Gene Ontology
Go IDGo_termPubmedIDEvidenceCategory
GO:0000398mRNA splicing, via spliceosome21873635.IBAProcess
GO:0000398mRNA splicing, via spliceosome12234937.29360106.IDAProcess
GO:0000398mRNA splicing, via spliceosome-TASProcess
GO:0003677DNA binding-IEAFunction
GO:0003700DNA-binding transcription factor activity-ISSFunction
GO:0003723RNA binding22658674.22681889.HDAFunction
GO:0005634nucleus29360106.IDAComponent
GO:0005654nucleoplasm-IDAComponent
GO:0005654nucleoplasm-TASComponent
GO:0005686U2 snRNP21873635.IBAComponent
GO:0005686U2 snRNP12234937.IDAComponent
GO:0005689U12-type spliceosomal complex21873635.IBAComponent
GO:0005689U12-type spliceosomal complex15146077.IDAComponent
GO:0016363nuclear matrix-IEAComponent
GO:0016607nuclear speck-ISSComponent
GO:0045893positive regulation of transcription, DNA-templated-ISSProcess
GO:0046872metal ion binding-IEAFunction
GO:0071005U2-type precatalytic spliceosome29360106.IDAComponent

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