KHDC4_MOUSE
ID KHDC4_MOUSE Reviewed; 612 AA.
AC Q3TCX3; Q69ZW1; Q8BUQ0; Q923C9; Q9CZ63; Q9D207;
DT 24-JUL-2007, integrated into UniProtKB/Swiss-Prot.
DT 11-OCT-2005, sequence version 1.
DT 03-AUG-2022, entry version 104.
DE RecName: Full=KH homology domain-containing protein 4 {ECO:0000250|UniProtKB:Q7Z7F0};
DE AltName: Full=Brings lots of money 7 {ECO:0000250|UniProtKB:Q7Z7F0};
DE AltName: Full=Pre-mRNA splicing factor protein Khdc4;
GN Name=Khdc4; Synonyms=Blom7 {ECO:0000250|UniProtKB:Q7Z7F0}, Kiaa0907;
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 [LARGE SCALE MRNA] (ISOFORM 2).
RC TISSUE=Embryonic tail;
RX PubMed=15368895; DOI=10.1093/dnares/11.3.205;
RA Okazaki N., Kikuno R., Ohara R., Inamoto S., Koseki H., Hiraoka S.,
RA Saga Y., Seino S., Nishimura M., Kaisho T., Hoshino K., Kitamura H.,
RA Nagase T., Ohara O., Koga H.;
RT "Prediction of the coding sequences of mouse homologues of KIAA gene: IV.
RT The complete nucleotide sequences of 500 mouse KIAA-homologous cDNAs
RT identified by screening of terminal sequences of cDNA clones randomly
RT sampled from size-fractionated libraries.";
RL DNA Res. 11:205-218(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1; 3 AND 4).
RC STRAIN=C57BL/6J, and NOD;
RC TISSUE=Dendritic cell, Embryo, Embryonic spinal cord,
RC Embryonic spinal ganglion, Hypothalamus, and Thymus;
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] (ISOFORM 1).
RC STRAIN=FVB/N; TISSUE=Mammary tumor;
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).
CC -!- FUNCTION: RNA-binding protein involved in pre-mRNA splicing. Interacts
CC with the PRP19C/Prp19 complex/NTC/Nineteen complex which is part of the
CC spliceosome. Involved in regulating splice site selection. Binds
CC preferentially RNA with A/C rich sequences and poly-C stretches.
CC {ECO:0000250|UniProtKB:Q7Z7F0}.
CC -!- SUBUNIT: Interacts with PRPF19. Isoform 2: Interacts with U2AF65.
CC {ECO:0000250|UniProtKB:Q7Z7F0}.
CC -!- INTERACTION:
CC Q3TCX3; Q15637: SF1; Xeno; NbExp=3; IntAct=EBI-11298408, EBI-744603;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:Q7Z7F0}. Cytoplasm
CC {ECO:0000250|UniProtKB:Q7Z7F0}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=4;
CC Name=1;
CC IsoId=Q3TCX3-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q3TCX3-2; Sequence=VSP_027248, VSP_027249;
CC Name=3;
CC IsoId=Q3TCX3-3; Sequence=VSP_027246, VSP_027247;
CC Name=4;
CC IsoId=Q3TCX3-4; Sequence=VSP_027244, VSP_027245;
CC -!- DOMAIN: The C-terminal part is necessary for the interaction with the
CC PRP19C/Prp19 complex/NTC/Nineteen complex.
CC {ECO:0000250|UniProtKB:Q7Z7F0}.
CC -!- DOMAIN: The KH domains mediate RNA-binding.
CC {ECO:0000250|UniProtKB:Q7Z7F0}.
CC -!- SIMILARITY: Belongs to the KHDC4 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAD32335.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AK173057; BAD32335.1; ALT_INIT; mRNA.
DR EMBL; AK012969; BAB28574.1; -; mRNA.
DR EMBL; AK020778; BAB32207.1; -; mRNA.
DR EMBL; AK038617; BAC30065.1; -; mRNA.
DR EMBL; AK083018; BAC38734.1; -; mRNA.
DR EMBL; AK164337; BAE37746.1; -; mRNA.
DR EMBL; AK170490; BAE41832.1; -; mRNA.
DR EMBL; BC006621; AAH06621.1; -; mRNA.
DR CCDS; CCDS17483.1; -. [Q3TCX3-1]
DR RefSeq; NP_083090.2; NM_028814.3. [Q3TCX3-1]
DR AlphaFoldDB; Q3TCX3; -.
DR SMR; Q3TCX3; -.
DR BioGRID; 216571; 2.
DR IntAct; Q3TCX3; 1.
DR STRING; 10090.ENSMUSP00000029696; -.
DR iPTMnet; Q3TCX3; -.
DR PhosphoSitePlus; Q3TCX3; -.
DR EPD; Q3TCX3; -.
DR jPOST; Q3TCX3; -.
DR MaxQB; Q3TCX3; -.
DR PaxDb; Q3TCX3; -.
DR PeptideAtlas; Q3TCX3; -.
DR PRIDE; Q3TCX3; -.
DR ProteomicsDB; 264743; -. [Q3TCX3-1]
DR ProteomicsDB; 264744; -. [Q3TCX3-2]
DR ProteomicsDB; 264746; -. [Q3TCX3-4]
DR Antibodypedia; 1657; 90 antibodies from 21 providers.
DR DNASU; 74200; -.
DR Ensembl; ENSMUST00000029696; ENSMUSP00000029696; ENSMUSG00000028060. [Q3TCX3-1]
DR Ensembl; ENSMUST00000198042; ENSMUSP00000142773; ENSMUSG00000028060. [Q3TCX3-2]
DR Ensembl; ENSMUST00000199684; ENSMUSP00000142353; ENSMUSG00000028060. [Q3TCX3-2]
DR GeneID; 74200; -.
DR KEGG; mmu:74200; -.
DR UCSC; uc008pwe.2; mouse. [Q3TCX3-4]
DR UCSC; uc008pwf.2; mouse. [Q3TCX3-3]
DR UCSC; uc008pwg.2; mouse. [Q3TCX3-1]
DR CTD; 22889; -.
DR MGI; MGI:1921450; Khdc4.
DR VEuPathDB; HostDB:ENSMUSG00000028060; -.
DR eggNOG; KOG1960; Eukaryota.
DR GeneTree; ENSGT00510000047412; -.
DR HOGENOM; CLU_032219_1_0_1; -.
DR InParanoid; Q3TCX3; -.
DR OMA; MSFCGTQ; -.
DR OrthoDB; 633868at2759; -.
DR PhylomeDB; Q3TCX3; -.
DR BioGRID-ORCS; 74200; 6 hits in 77 CRISPR screens.
DR ChiTaRS; Khdc4; mouse.
DR PRO; PR:Q3TCX3; -.
DR Proteomes; UP000000589; Chromosome 3.
DR RNAct; Q3TCX3; protein.
DR Bgee; ENSMUSG00000028060; Expressed in undifferentiated genital tubercle and 249 other tissues.
DR ExpressionAtlas; Q3TCX3; baseline and differential.
DR Genevisible; Q3TCX3; MM.
DR GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
DR GO; GO:0005654; C:nucleoplasm; ISO:MGI.
DR GO; GO:0005634; C:nucleus; ISS:UniProtKB.
DR GO; GO:0005681; C:spliceosomal complex; ISO:MGI.
DR GO; GO:0003723; F:RNA binding; IDA:MGI.
DR GO; GO:0006376; P:mRNA splice site selection; ISS:UniProtKB.
DR Gene3D; 3.30.1370.10; -; 2.
DR InterPro; IPR036612; KH_dom_type_1_sf.
DR InterPro; IPR031121; RIK/BLOM7.
DR PANTHER; PTHR15744; PTHR15744; 1.
DR SUPFAM; SSF54791; SSF54791; 2.
PE 1: Evidence at protein level;
KW Alternative splicing; Cytoplasm; mRNA processing; mRNA splicing; Nucleus;
KW Phosphoprotein; Reference proteome; RNA-binding.
FT CHAIN 1..612
FT /note="KH homology domain-containing protein 4"
FT /id="PRO_0000296670"
FT DOMAIN 102..182
FT /note="KH 1"
FT /evidence="ECO:0000250|UniProtKB:Q7Z7F0"
FT DOMAIN 237..319
FT /note="KH 2"
FT /evidence="ECO:0000250|UniProtKB:Q7Z7F0"
FT REGION 1..53
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 436..549
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 478..547
FT /note="Required for nuclear retention"
FT /evidence="ECO:0000250|UniProtKB:Q7Z7F0"
FT REGION 567..612
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 485..502
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 583..604
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 569
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q7Z7F0"
FT MOD_RES 570
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q7Z7F0"
FT VAR_SEQ 88..131
FT /note="LQAPGKSLTSNKSKDDLVVAEVEINDVPLTCRNLLTRGQTQDEI -> VLRA
FT LDALRFGIFFFLPFLHLSVAWSLGLMKMKPVRVKITFGSI (in isoform 4)"
FT /evidence="ECO:0000303|PubMed:16141072"
FT /id="VSP_027244"
FT VAR_SEQ 132..612
FT /note="Missing (in isoform 4)"
FT /evidence="ECO:0000303|PubMed:16141072"
FT /id="VSP_027245"
FT VAR_SEQ 425..430
FT /note="SPISAP -> VGCRDM (in isoform 3)"
FT /evidence="ECO:0000303|PubMed:16141072"
FT /id="VSP_027246"
FT VAR_SEQ 431..612
FT /note="Missing (in isoform 3)"
FT /evidence="ECO:0000303|PubMed:16141072"
FT /id="VSP_027247"
FT VAR_SEQ 478..487
FT /note="QHGPIHMTNL -> QVQASPVRMR (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:15368895"
FT /id="VSP_027248"
FT VAR_SEQ 488..612
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:15368895"
FT /id="VSP_027249"
FT CONFLICT 51
FT /note="Missing (in Ref. 1; BAD32335 and 3; AAH06621)"
FT /evidence="ECO:0000305"
FT CONFLICT 112
FT /note="N -> K (in Ref. 2; BAB28574)"
FT /evidence="ECO:0000305"
FT CONFLICT 533
FT /note="S -> P (in Ref. 2; BAB28574)"
FT /evidence="ECO:0000305"
FT CONFLICT 599
FT /note="Q -> K (in Ref. 2; BAB28574)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 612 AA; 64563 MW; ACCA50E066E2EC12 CRC64;
MSAGSATHPA AGGRRSKWDQ PAPAPLLFLP PTAPGGEVAG SGASPGGATT AAAPSGALDA
AAAVAAKINA MLMAKGKLKP SQNAAEKLQA PGKSLTSNKS KDDLVVAEVE INDVPLTCRN
LLTRGQTQDE ISRLSGAAVS TRGRFMTTEE KAKVGPGDRP LYLHVQGQTR ELVDRAVNRI
KEIITNGVVK AATGTSPTFN GATVTVYHQP APIAQLSPAI NQKPSFQSGM HYVQDKLFVG
LEHAVPTFNV KEKVEGPGCS YLQHIQIETG AKVFLRGKGS GCIEPASGRE AFEPMYIYIS
HPKPEGLAAA KKLCENLLQT VHAEYSRFVN QINTAVPLPG YTQPSAISSI PPQPPYYPSN
GYQSGYPVVP PPQQPVQPPY GVPSIVPPAV SLAPGVLPAL PTGVPPVPTQ YPITQVQPPA
STGQSPISAP FIPAAPVKTA LPTGPQPQPQ LPAQPQSQKR RFTEELPDER DSGLLGYQHG
PIHMTNLGTG FSSQNEIEGA GSKPASSSGK ERERDRQLMP PPAFPVTGIK TESDERNGSG
ALAGSHDYPA KKMKTAEKGF GLVAYAADSS DEEEEHGGHK NASSFPQGWS LGYQYPSSQP
RAKQQMPFWM AP
