ZC3H4_MOUSE
ID ZC3H4_MOUSE Reviewed; 1304 AA.
AC Q6ZPZ3;
DT 02-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 02-MAY-2006, sequence version 2.
DT 03-AUG-2022, entry version 125.
DE RecName: Full=Zinc finger CCCH domain-containing protein 4 {ECO:0000305};
GN Name=Zc3h4 {ECO:0000303|PubMed:33246328, ECO:0000312|MGI:MGI:2682314};
GN Synonyms=Kiaa1064 {ECO:0000303|PubMed:14621295};
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 GENOMIC DNA].
RC STRAIN=C57BL/6J;
RX PubMed=19468303; DOI=10.1371/journal.pbio.1000112;
RA Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X.,
RA Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y.,
RA Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S.,
RA Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R.,
RA Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K.,
RA Eichler E.E., Ponting C.P.;
RT "Lineage-specific biology revealed by a finished genome assembly of the
RT mouse.";
RL PLoS Biol. 7:E1000112-E1000112(2009).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 310-1304 (ISOFORM 2).
RC TISSUE=Embryonic tail;
RX PubMed=14621295; DOI=10.1093/dnares/10.4.167;
RA Okazaki N., Kikuno R., Ohara R., Inamoto S., Koseki H., Hiraoka S.,
RA Saga Y., Nagase T., Ohara O., Koga H.;
RT "Prediction of the coding sequences of mouse homologues of KIAA gene: III.
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. 10:167-180(2003).
RN [3]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1104; SER-1109 AND SER-1276,
RP AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Liver;
RX PubMed=17242355; DOI=10.1073/pnas.0609836104;
RA Villen J., Beausoleil S.A., Gerber S.A., Gygi S.P.;
RT "Large-scale phosphorylation analysis of mouse liver.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:1488-1493(2007).
RN [4]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Embryonic fibroblast;
RX PubMed=19131326; DOI=10.1074/mcp.m800451-mcp200;
RA Sweet S.M., Bailey C.M., Cunningham D.L., Heath J.K., Cooper H.J.;
RT "Large scale localization of protein phosphorylation by use of electron
RT capture dissociation mass spectrometry.";
RL Mol. Cell. Proteomics 8:904-912(2009).
RN [5]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-816; SER-817; SER-917;
RP SER-1104; SER-1109; SER-1115; THR-1119; SER-1270 AND SER-1276, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Brain, Brown adipose tissue, Heart, Kidney, Liver, Lung, Pancreas,
RC Spleen, and 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 METHYLATION [LARGE SCALE ANALYSIS] AT ARG-599, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Embryo;
RX PubMed=24129315; DOI=10.1074/mcp.o113.027870;
RA Guo A., Gu H., Zhou J., Mulhern D., Wang Y., Lee K.A., Yang V., Aguiar M.,
RA Kornhauser J., Jia X., Ren J., Beausoleil S.A., Silva J.C., Vemulapalli V.,
RA Bedford M.T., Comb M.J.;
RT "Immunoaffinity enrichment and mass spectrometry analysis of protein
RT methylation.";
RL Mol. Cell. Proteomics 13:372-387(2014).
RN [7]
RP DISRUPTION PHENOTYPE.
RX PubMed=33246328; DOI=10.1093/biolre/ioaa215;
RA Su J., Miao X., Archambault D., Mager J., Cui W.;
RT "ZC3H4-a novel Cys-Cys-Cys-His-type zinc finger protein-is essential for
RT early embryogenesis in mice.";
RL Biol. Reprod. 104:325-335(2021).
RN [8]
RP FUNCTION, SUBCELLULAR LOCATION, AND INTERACTION WITH WDR82.
RX PubMed=33767452; DOI=10.1038/s41594-021-00572-y;
RA Austenaa L.M.I., Piccolo V., Russo M., Prosperini E., Polletti S.,
RA Polizzese D., Ghisletti S., Barozzi I., Diaferia G.R., Natoli G.;
RT "A first exon termination checkpoint preferentially suppresses extragenic
RT transcription.";
RL Nat. Struct. Mol. Biol. 28:337-346(2021).
CC -!- FUNCTION: RNA-binding protein that suppresses transcription of long
CC non-coding RNAs (lncRNAs) (PubMed:33767452). LncRNAs are defined as
CC transcripts more than 200 nucleotides that are not translated into
CC protein (PubMed:33767452). Together with WDR82, part of a transcription
CC termination checkpoint that promotes transcription termination of
CC lncRNAs and their subsequent degradation by the exosome
CC (PubMed:33767452). The transcription termination checkpoint is
CC activated by the inefficiently spliced first exon of lncRNAs
CC (PubMed:33767452). {ECO:0000269|PubMed:33767452}.
CC -!- SUBUNIT: Interacts with WDR82. {ECO:0000269|PubMed:33767452}.
CC -!- SUBCELLULAR LOCATION: Chromosome {ECO:0000269|PubMed:33767452}.
CC Note=Recruited at sites of high RNA polymerase II occupancy.
CC {ECO:0000269|PubMed:33767452}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q6ZPZ3-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q6ZPZ3-2; Sequence=VSP_018209;
CC -!- DISRUPTION PHENOTYPE: Early embryonic lethality: embryos do not survive
CC beyond bastocyst stage due to defective epiblast and primitive endoderm
CC lineages formation. {ECO:0000269|PubMed:33246328}.
CC -!- SIMILARITY: Belongs to the suppressor of sable family. {ECO:0000305}.
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DR EMBL; AC148972; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AK129275; BAC98085.1; -; mRNA.
DR RefSeq; NP_941033.2; NM_198631.2.
DR RefSeq; XP_006540165.1; XM_006540102.3. [Q6ZPZ3-1]
DR RefSeq; XP_006540169.1; XM_006540106.3. [Q6ZPZ3-2]
DR RefSeq; XP_006540170.1; XM_006540107.3. [Q6ZPZ3-1]
DR RefSeq; XP_006540171.1; XM_006540108.3. [Q6ZPZ3-1]
DR RefSeq; XP_017177799.1; XM_017322310.1.
DR AlphaFoldDB; Q6ZPZ3; -.
DR SMR; Q6ZPZ3; -.
DR BioGRID; 236971; 1.
DR DIP; DIP-61658N; -.
DR IntAct; Q6ZPZ3; 1.
DR STRING; 10090.ENSMUSP00000096386; -.
DR iPTMnet; Q6ZPZ3; -.
DR PhosphoSitePlus; Q6ZPZ3; -.
DR SwissPalm; Q6ZPZ3; -.
DR EPD; Q6ZPZ3; -.
DR jPOST; Q6ZPZ3; -.
DR MaxQB; Q6ZPZ3; -.
DR PaxDb; Q6ZPZ3; -.
DR PeptideAtlas; Q6ZPZ3; -.
DR PRIDE; Q6ZPZ3; -.
DR ProteomicsDB; 302042; -. [Q6ZPZ3-1]
DR ProteomicsDB; 302043; -. [Q6ZPZ3-2]
DR GeneID; 330474; -.
DR KEGG; mmu:330474; -.
DR UCSC; uc009fht.1; mouse. [Q6ZPZ3-2]
DR CTD; 23211; -.
DR MGI; MGI:2682314; Zc3h4.
DR eggNOG; KOG1040; Eukaryota.
DR InParanoid; Q6ZPZ3; -.
DR OrthoDB; 145192at2759; -.
DR PhylomeDB; Q6ZPZ3; -.
DR BioGRID-ORCS; 330474; 15 hits in 73 CRISPR screens.
DR ChiTaRS; Zc3h4; mouse.
DR PRO; PR:Q6ZPZ3; -.
DR Proteomes; UP000000589; Unplaced.
DR RNAct; Q6ZPZ3; protein.
DR GO; GO:0005694; C:chromosome; IEA:UniProtKB-SubCell.
DR GO; GO:0005829; C:cytosol; ISO:MGI.
DR GO; GO:0005654; C:nucleoplasm; ISO:MGI.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0003682; F:chromatin binding; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:1990841; F:promoter-specific chromatin binding; ISO:MGI.
DR GO; GO:0003723; F:RNA binding; ISO:MGI.
DR GO; GO:0006353; P:DNA-templated transcription, termination; IEA:UniProtKB-KW.
DR GO; GO:0110064; P:lncRNA catabolic process; IDA:UniProtKB.
DR GO; GO:0032785; P:negative regulation of DNA-templated transcription, elongation; IDA:UniProtKB.
DR GO; GO:0140744; P:negative regulation of lncRNA transcription; IDA:UniProtKB.
DR GO; GO:0071027; P:nuclear RNA surveillance; IDA:UniProtKB.
DR InterPro; IPR045124; Su(sable)-like.
DR InterPro; IPR041367; Znf-CCCH_4.
DR InterPro; IPR000571; Znf_CCCH.
DR InterPro; IPR036855; Znf_CCCH_sf.
DR PANTHER; PTHR13119; PTHR13119; 1.
DR Pfam; PF00642; zf-CCCH; 1.
DR Pfam; PF18044; zf-CCCH_4; 1.
DR SMART; SM00356; ZnF_C3H1; 3.
DR SUPFAM; SSF90229; SSF90229; 3.
DR PROSITE; PS50103; ZF_C3H1; 3.
PE 1: Evidence at protein level;
KW Alternative splicing; Chromosome; Coiled coil; Metal-binding; Methylation;
KW Phosphoprotein; Reference proteome; Repeat; RNA-binding; Transcription;
KW Transcription regulation; Transcription termination; Zinc; Zinc-finger.
FT CHAIN 1..1304
FT /note="Zinc finger CCCH domain-containing protein 4"
FT /id="PRO_0000234069"
FT ZN_FING 389..416
FT /note="C3H1-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00723"
FT ZN_FING 418..445
FT /note="C3H1-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00723"
FT ZN_FING 446..469
FT /note="C3H1-type 3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00723"
FT REGION 1..387
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 485..567
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 601..691
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 719..970
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 994..1304
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 94..128
FT /evidence="ECO:0000255"
FT COILED 778..809
FT /evidence="ECO:0000255"
FT COMPBIAS 1..36
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 40..54
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 55..73
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 74..100
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 101..128
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 143..159
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 163..178
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 198..216
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 217..239
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 278..302
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 303..324
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 325..342
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 370..387
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 485..501
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 504..560
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 605..626
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 630..658
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 663..691
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 740..757
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 784..811
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 817..849
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 910..924
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 929..943
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1032..1047
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1133..1149
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1161..1175
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1200..1220
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 92
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9UPT8"
FT MOD_RES 94
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9UPT8"
FT MOD_RES 155
FT /note="Phosphotyrosine"
FT /evidence="ECO:0000250|UniProtKB:Q9UPT8"
FT MOD_RES 599
FT /note="Asymmetric dimethylarginine"
FT /evidence="ECO:0007744|PubMed:24129315"
FT MOD_RES 816
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:21183079"
FT MOD_RES 817
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:21183079"
FT MOD_RES 913
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9UPT8"
FT MOD_RES 916
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9UPT8"
FT MOD_RES 917
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:21183079"
FT MOD_RES 1104
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17242355,
FT ECO:0007744|PubMed:21183079"
FT MOD_RES 1109
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17242355,
FT ECO:0007744|PubMed:21183079"
FT MOD_RES 1111
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9UPT8"
FT MOD_RES 1115
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:21183079"
FT MOD_RES 1119
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:21183079"
FT MOD_RES 1270
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:21183079"
FT MOD_RES 1276
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17242355,
FT ECO:0007744|PubMed:21183079"
FT VAR_SEQ 726..808
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14621295"
FT /id="VSP_018209"
SQ SEQUENCE 1304 AA; 140967 MW; F2D02AAC15148C8B CRC64;
MEAVPGTPPP PPSESPPPPS PPPPSTPSPP PCSPDGRAAT PHLLHHRLPL PDDREDGELE
EGELEDDGAE EVQDPPGGQE RSRKEKGEKH HSDSEEEKSH RRLKRKRKKE REKEKRRSKK
RRKSKHKRHA SSSDDFSDFS DDSDFSPSEK SHRKYRDYSP PYAPSHQQYS SSHNAPLPKK
SYSKMDSKGY SMYEDYENEQ YGEYEGDEEE DMGKEDYDDF TKELNQYRRA KEGSSRGRGS
RGRGRGYRGR GSRGGSRGRG MGRGSRGRGR GSMGEHPEDE EDLYEEEIEY GESEEPMGDD
DYDDYSKELN QYRRSKDSRG RGLSRGRGRG SRGGRGKGMG RGRGRGGRGG MSKGGMNDDE
DFYDDDMGDG GGGSYRRSDH DKPHQQSDKK GKVICKYFVE GRCTWGDHCN FSHDIELPKK
RELCKFYITG FCARAENCPY MHGDFPCKLY HTTGNCINGD DCMFSHDPLT EETRELLDKM
LADDAEAGAE DEKEVEELKK QGINPLPKPP PGVGLLPTPP RPPGPPAPTS PNGRPMQGGP
PPPPPPPPPP PGPPQMSLPT HEPLSPQQLQ QDMYNKKIPS LFEIVVRPTG QLAEKLGVRF
PGPGGPSGPM GPGPNMGPPG PMGGPMHPDM HPDMHPDMHP DMHPDMHPDM HPDMHPDMHP
DMPMGPGMNP GPPMGPGGPP MMPYGPGDSP HSGMMPPIPP AQNFYENFYP QQEGMEMEPG
LVGDAEDYGH YEELPGQPGE PLFPEHPLEP DSFPEGGPPG RPKAGAGVPD FLPSAQRALY
LRIQQKQQEE ERARRLAESS KQDRENEEGD TGNWYSSDED EGGSSVTSIL KTLRQQTSSR
PQASVGEPSS SGLGDPRLQK GHPTGSRLSD PRLSRDPRLS RHAETSGGSG PGDSGPSDPR
LARALPTSKA EGSLHSSPAG PSSSKGQPPA EEEEGERALR EKAVNIPLDP LPGHPLRDPR
SQLQQFSHIK KDVTLSKPSF ARTVLWNPED LIPLPIPKQD VPPVPAALQS LPALDPRLHR
STPPGPPNTR QRPGSTDPST SGSNLPDFEL LSRILKTVNV NTPGQSEKPS DPRVRKTPTD
PRLQKPADPV AASRAAKPCP TEASPPAASP SGDSSPPATA PYDPRVLAAG GLGQGSSSGQ
SSVLSGISLY DPRTPNAGGK TAEPASDTSA QPKGPEGNGK GSASKAKEPP FVRKSALEQP
ETGKASTDGA TATDRYNSYN RPRPKATAAP TAASSTPPPE GATPQPGVHN LPVPTLFGTV
KPAPKTGTGS PFAGNSPARE GEQDAGSLKD VFKGFDPTAS PFCQ
