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Non-homologous end joining factor IFFO1 (NHEJ factor IFFO1) (Intermediate filament family orphan 1)

 IFFO1_MOUSE             Reviewed;         562 AA.
Q8BXL9; Q3TQI1; Q6PFE6; Q8BXS3; Q8C1D6;
05-FEB-2008, integrated into UniProtKB/Swiss-Prot.
01-MAR-2003, sequence version 1.
23-FEB-2022, entry version 132.
RecName: Full=Non-homologous end joining factor IFFO1 {ECO:0000303|PubMed:31548606};
Short=NHEJ factor IFFO1 {ECO:0000303|PubMed:31548606};
AltName: Full=Intermediate filament family orphan 1 {ECO:0000303|PubMed:31548606};
Name=Iffo1 {ECO:0000312|MGI:MGI:2444516}; Synonyms=Iffo;
Mus musculus (Mouse).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
Murinae; Mus; Mus.
NCBI_TaxID=10090;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1; 2; 3 AND 6).
STRAIN=C57BL/6J; TISSUE=Corpora quadrigemina, Head, and Retina;
PubMed=16141072; DOI=10.1126/science.1112014;
Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.,
Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R.,
Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T.,
Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A.,
Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B.,
Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M.,
Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S.,
Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D.,
Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M.,
Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H.,
Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V.,
Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S.,
Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H.,
Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N.,
Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F.,
Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G.,
Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z.,
Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S.,
Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K.,
Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R.,
van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H.,
Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M.,
Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C.,
Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S.,
Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K.,
Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M.,
Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C.,
Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.;
"The transcriptional landscape of the mammalian genome.";
Science 309:1559-1563(2005).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 4).
STRAIN=C57BL/6J; TISSUE=Brain;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA project:
the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[3]
FUNCTION.
PubMed=31548606; DOI=10.1038/s41556-019-0388-0;
Li W., Bai X., Li J., Zhao Y., Liu J., Zhao H., Liu L., Ding M., Wang Q.,
Shi F.Y., Hou M., Ji J., Gao G., Guo R., Sun Y., Liu Y., Xu D.;
"The nucleoskeleton protein IFFO1 immobilizes broken DNA and suppresses
chromosome translocation during tumorigenesis.";
Nat. Cell Biol. 21:1273-1285(2019).
-!- FUNCTION: Nuclear matrix protein involved in the immobilization of
broken DNA ends and the suppression of chromosome translocation during
DNA double-strand breaks (DSBs) (PubMed:31548606). Interacts with the
nuclear lamina component LMNA, resulting in the formation of a
nucleoskeleton that will relocalize to the DSB sites in a XRCC4-
dependent manner and promote the immobilization of the broken ends,
thereby preventing chromosome translocation (PubMed:31548606). Acts as
a scaffold that allows the DNA repair protein XRCC4 and LMNA to
assemble into a complex at the DSB sites (PubMed:31548606).
{ECO:0000269|PubMed:31548606}.
-!- SUBUNIT: Forms a heterotetramer with XRCC4 (By similarity). The
interaction with XRCC4 is direct, involves LIG4-free XRCC4 and leads to
relocalization of IFFO1 at the double-strand break (DSB) sites (By
similarity). Interacts with LMNA; the interaction forms an interior
nucleoskeleton and the recruitment to DNA double-strand breaks (By
similarity). {ECO:0000250|UniProtKB:Q0D2I5}.
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:Q0D2I5}. Nucleus,
nucleoplasm {ECO:0000250|UniProtKB:Q0D2I5}. Nucleus inner membrane
{ECO:0000250|UniProtKB:Q0D2I5}. Nucleus matrix
{ECO:0000250|UniProtKB:Q0D2I5}. Note=Mainly soluble, the remaining is
localized in the nuclear matrix. Localized at double-strand break (DSB)
sites near the lamina and nuclear matrix structures.
{ECO:0000250|UniProtKB:Q0D2I5}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=6;
Name=1;
IsoId=Q8BXL9-1; Sequence=Displayed;
Name=2;
IsoId=Q8BXL9-2; Sequence=VSP_030786;
Name=3;
IsoId=Q8BXL9-3; Sequence=VSP_030785, VSP_030787;
Name=4;
IsoId=Q8BXL9-4; Sequence=VSP_030785, VSP_030788;
Name=5;
IsoId=Q8BXL9-5; Sequence=VSP_030787;
Name=6;
IsoId=Q8BXL9-6; Sequence=VSP_030788;
-!- SIMILARITY: Belongs to the intermediate filament family.
{ECO:0000255|PROSITE-ProRule:PRU01188}.
---------------------------------------------------------------------------
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EMBL; AK028273; BAC25852.1; -; mRNA.
EMBL; AK044382; BAC31894.1; -; mRNA.
EMBL; AK044728; BAC32053.1; -; mRNA.
EMBL; AK163571; BAE37401.1; -; mRNA.
EMBL; BC057601; AAH57601.2; -; mRNA.
CCDS; CCDS39634.1; -. [Q8BXL9-1]
CCDS; CCDS39635.1; -. [Q8BXL9-5]
RefSeq; NP_001034758.1; NM_001039669.3. [Q8BXL9-1]
RefSeq; NP_001289707.1; NM_001302778.1.
RefSeq; NP_001289708.1; NM_001302779.1.
RefSeq; NP_848902.4; NM_178787.6. [Q8BXL9-5]
SMR; Q8BXL9; -.
BioGRID; 236208; 9.
STRING; 10090.ENSMUSP00000056373; -.
iPTMnet; Q8BXL9; -.
PhosphoSitePlus; Q8BXL9; -.
MaxQB; Q8BXL9; -.
PaxDb; Q8BXL9; -.
PRIDE; Q8BXL9; -.
ProteomicsDB; 267266; -. [Q8BXL9-1]
ProteomicsDB; 267267; -. [Q8BXL9-2]
ProteomicsDB; 267268; -. [Q8BXL9-3]
ProteomicsDB; 267269; -. [Q8BXL9-4]
ProteomicsDB; 267270; -. [Q8BXL9-5]
ProteomicsDB; 267271; -. [Q8BXL9-6]
Antibodypedia; 22511; 63 antibodies from 17 providers.
DNASU; 320678; -.
Ensembl; ENSMUST00000117675; ENSMUSP00000113088; ENSMUSG00000038271. [Q8BXL9-1]
Ensembl; ENSMUST00000119527; ENSMUSP00000113376; ENSMUSG00000038271. [Q8BXL9-5]
GeneID; 320678; -.
KEGG; mmu:320678; -.
UCSC; uc009dto.2; mouse. [Q8BXL9-1]
UCSC; uc009dtp.2; mouse. [Q8BXL9-5]
UCSC; uc009dtq.2; mouse. [Q8BXL9-6]
CTD; 25900; -.
MGI; MGI:2444516; Iffo1.
VEuPathDB; HostDB:ENSMUSG00000038271; -.
eggNOG; ENOG502QRD7; Eukaryota.
GeneTree; ENSGT00510000046803; -.
HOGENOM; CLU_039629_2_1_1; -.
InParanoid; Q8BXL9; -.
OMA; NINEKHA; -.
OrthoDB; 792412at2759; -.
PhylomeDB; Q8BXL9; -.
TreeFam; TF331217; -.
BioGRID-ORCS; 320678; 2 hits in 66 CRISPR screens.
ChiTaRS; Iffo1; mouse.
PRO; PR:Q8BXL9; -.
Proteomes; UP000000589; Chromosome 6.
RNAct; Q8BXL9; protein.
Bgee; ENSMUSG00000038271; Expressed in skeletal muscle tissue and 272 other tissues.
ExpressionAtlas; Q8BXL9; baseline and differential.
Genevisible; Q8BXL9; MM.
GO; GO:0005882; C:intermediate filament; IEA:UniProtKB-KW.
GO; GO:0005637; C:nuclear inner membrane; IEA:UniProtKB-SubCell.
GO; GO:0016363; C:nuclear matrix; ISS:UniProtKB.
GO; GO:0005654; C:nucleoplasm; ISS:UniProtKB.
GO; GO:0035861; C:site of double-strand break; ISO:MGI.
GO; GO:1990683; P:DNA double-strand break attachment to nuclear envelope; ISS:UniProtKB.
GO; GO:0006303; P:double-strand break repair via nonhomologous end joining; ISS:UniProtKB.
GO; GO:1990166; P:protein localization to site of double-strand break; ISO:MGI.
InterPro; IPR039008; IF_rod_dom.
SMART; SM01391; Filament; 1.
PROSITE; PS51842; IF_ROD_2; 1.
2: Evidence at transcript level;
Alternative splicing; Coiled coil; Intermediate filament; Membrane;
Nucleus; Reference proteome.
CHAIN 1..562
/note="Non-homologous end joining factor IFFO1"
/id="PRO_0000316795"
DOMAIN 73..529
/note="IF rod"
/evidence="ECO:0000255|PROSITE-ProRule:PRU01188"
REGION 65..116
/note="LMNA binding"
/evidence="ECO:0000250|UniProtKB:Q0D2I5"
REGION 154..187
/note="Disordered"
/evidence="ECO:0000256|SAM:MobiDB-lite"
REGION 364..401
/note="Disordered"
/evidence="ECO:0000256|SAM:MobiDB-lite"
REGION 453..528
/note="XCCR4 binding. Required for localization to the
double-strand breaks (DSBs)"
/evidence="ECO:0000250|UniProtKB:Q0D2I5"
REGION 523..562
/note="Disordered"
/evidence="ECO:0000256|SAM:MobiDB-lite"
COILED 85..117
/evidence="ECO:0000255"
COILED 237..301
/evidence="ECO:0000255"
COILED 458..504
/evidence="ECO:0000255"
COMPBIAS 163..187
/note="Polar residues"
/evidence="ECO:0000256|SAM:MobiDB-lite"
COMPBIAS 364..392
/note="Basic and acidic residues"
/evidence="ECO:0000256|SAM:MobiDB-lite"
COMPBIAS 546..562
/note="Basic and acidic residues"
/evidence="ECO:0000256|SAM:MobiDB-lite"
VAR_SEQ 1..191
/note="Missing (in isoform 3 and isoform 4)"
/evidence="ECO:0000303|PubMed:15489334,
ECO:0000303|PubMed:16141072"
/id="VSP_030785"
VAR_SEQ 259..562
/note="Missing (in isoform 2)"
/evidence="ECO:0000303|PubMed:16141072"
/id="VSP_030786"
VAR_SEQ 358..360
/note="Missing (in isoform 3 and isoform 5)"
/evidence="ECO:0000303|PubMed:16141072"
/id="VSP_030787"
VAR_SEQ 358
/note="Missing (in isoform 4 and isoform 6)"
/evidence="ECO:0000303|PubMed:15489334,
ECO:0000303|PubMed:16141072"
/id="VSP_030788"
CONFLICT 291
/note="A -> P (in Ref. 1; BAC25852)"
/evidence="ECO:0000305"
CONFLICT 331
/note="C -> W (in Ref. 1; BAC25852)"
/evidence="ECO:0000305"
CONFLICT 345
/note="Q -> H (in Ref. 1; BAC25852)"
/evidence="ECO:0000305"
CONFLICT 454
/note="Q -> QQ (in Ref. 1; BAC25852 and 2; AAH57601)"
/evidence="ECO:0000305"
SEQUENCE 562 AA; 62415 MW; 4310CC2DEAC8B604 CRC64;
MNPLFGPNLF LLQQEQQGLA GPLGDPLGGD HFAGGGDLAS APLASAGPSA YSPPGPGPAP
PAAMALRNDL GSNINVLKTL NLRFRCFLAK VHELERRNRL LEKQLQQALE EGKQGRRGLA
RRDQAVQTGF ISPIRPLGLP LSSRPAAVCP PSARVLGSPS RSPAGPLASS AACHTSSSTS
TSTAFSSSTR FMPGTIWSFS HARRLGPGLE PTLVQGPGLS WVHPDGVGVQ IDTITPEIRA
LYNVLAKVKR ERDEYKRRWE EEYTVRIQLQ ERVTELQEEA QEADACQEEL AMKVEQLKAE
LVVFKGLMSN NLTELDTKIQ EKAMKVDMDI CRRIDITAKL CDLAQQRNCE DMIQMFQKKL
VPSMGGRKRE RKAAVEEDTS LSESDGPRQP EGAEEESTAL SINEEMQRML SQLREYDFED
DCDSLTWEET EETLLLWEDF SGYAMAAAEA QGEQEDSLEK VIKDTESLFK TREKEYQETI
DQIELELATA KNDMNRHLHE YMEMCSMKRG LDVQMETCRR LITQSGDRKS PAFTAVPLSD
PPPPPSETED SDRDVSSDSS MR


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Related Genes :
[NHEJ1 XLF] Non-homologous end-joining factor 1 (Protein cernunnos) (XRCC4-like factor)
[Nhej1 Xlf] Non-homologous end-joining factor 1 (Protein cernunnos) (XRCC4-like factor)
[XRCC4] DNA repair protein XRCC4 (hXRCC4) (X-ray repair cross-complementing protein 4) [Cleaved into: Protein XRCC4, C-terminus (XRCC4/C)]
[Xrcc4] DNA repair protein XRCC4 (X-ray repair cross-complementing protein 4) [Cleaved into: Protein XRCC4, C-terminus (XRCC4/C)]
[ligD PA2138] Multifunctional non-homologous end joining protein LigD (NHEJ DNA polymerase) [Includes: 3'-phosphoesterase (3'-ribonuclease/3'-phosphatase); DNA ligase D (LigD) (EC 6.5.1.1) (Polydeoxyribonucleotide synthase [ATP]); DNA repair polymerase (Pol) (Polymerase/primase)]
[ligD Rv0938 MTCY08D9.01c MTCY10D7.36c] Multifunctional non-homologous end joining DNA repair protein LigD (NHEJ DNA repair protein D) (Mt-Lig) (NHEJ DNA polymerase) [Includes: DNA repair polymerase (Pol) (Polymerase/primase); 3'-phosphoesterase (3'-ribonuclease/3'-phosphatase) (PE); DNA ligase (Lig) (EC 6.5.1.1) (Polydeoxyribonucleotide synthase [ATP])]
[ligD MSMEG_5570 MSMEI_5419] Multifunctional non-homologous end joining protein LigD (NHEJ DNA polymerase) [Includes: DNA repair polymerase (Pol) (Polymerase/primase); 3'-phosphoesterase (3'-ribonuclease/3'-phosphatase) (PE); DNA ligase (Lig) (EC 6.5.1.1) (Polydeoxyribonucleotide synthase [ATP])]
[LMNA LMN1] Prelamin-A/C [Cleaved into: Lamin-A/C (70 kDa lamin) (Renal carcinoma antigen NY-REN-32)]
[CYREN C7orf49 MRI] Cell cycle regulator of non-homologous end joining (Cell cycle regulator of NHEJ) (Modulator of retrovirus infection homolog)
[Lmna Lmn1] Prelamin-A/C [Cleaved into: Lamin-A/C]
[Lmna Lmn1] Prelamin-A/C [Cleaved into: Lamin-A/C]
[Cyren Mri] Cell cycle regulator of non-homologous end joining (Cell cycle regulator of NHEJ) (Modulator of retrovirus infection homolog)
[Nhej1 Xlf] Non-homologous end-joining factor 1 (Protein cernunnos) (XRCC4-like factor)
[ligD BQ2027_MB0963] Multifunctional non-homologous end joining protein LigD (NHEJ DNA polymerase) [Includes: DNA repair polymerase (Pol) (Polymerase/primase); 3'-phosphoesterase (3'-ribonuclease/3'-phosphatase) (PE); DNA ligase (Lig) (EC 6.5.1.1) (Polydeoxyribonucleotide synthase [ATP])]
[XRCC6 G22P1] X-ray repair cross-complementing protein 6 (EC 3.6.4.-) (EC 4.2.99.-) (5'-deoxyribose-5-phosphate lyase Ku70) (5'-dRP lyase Ku70) (70 kDa subunit of Ku antigen) (ATP-dependent DNA helicase 2 subunit 1) (ATP-dependent DNA helicase II 70 kDa subunit) (CTC box-binding factor 75 kDa subunit) (CTC75) (CTCBF) (DNA repair protein XRCC6) (Lupus Ku autoantigen protein p70) (Ku70) (Thyroid-lupus autoantigen) (TLAA) (X-ray repair complementing defective repair in Chinese hamster cells 6)
[Nr4a1 Hmr Ngfib] Nuclear receptor subfamily 4 group A member 1 (NUR77) (Nerve growth factor-induced protein I-B) (NGFI-B) (Orphan nuclear receptor HMR)
[TERF2IP DRIP5 RAP1 PP8000] Telomeric repeat-binding factor 2-interacting protein 1 (TERF2-interacting telomeric protein 1) (TRF2-interacting telomeric protein 1) (Dopamine receptor-interacting protein 5) (Repressor/activator protein 1 homolog) (RAP1 homolog) (hRap1)
[HSF1 HSTF1] Heat shock factor protein 1 (HSF 1) (Heat shock transcription factor 1) (HSTF 1)
[Hsf1] Heat shock factor protein 1 (HSF 1) (Heat shock transcription factor 1) (HSTF 1)
[HSF1] Heat shock factor protein 1 (HSF 1) (Heat shock transcription factor 1) (HSTF 1)
[Terf2ip Rap1 MNCb-0448 MNCb-0628] Telomeric repeat-binding factor 2-interacting protein 1 (TERF2-interacting telomeric protein 1) (TRF2-interacting telomeric protein 1) (Repressor/activator protein 1 homolog) (RAP1 homolog)
[APLF C2orf13 PALF XIP1] Aprataxin and PNK-like factor (EC 3.1.-.-) (Apurinic-apyrimidinic endonuclease APLF) (PNK and APTX-like FHA domain-containing protein) (XRCC1-interacting protein 1)
[CD59 MIC11 MIN1 MIN2 MIN3 MSK21] CD59 glycoprotein (1F5 antigen) (20 kDa homologous restriction factor) (HRF-20) (HRF20) (MAC-inhibitory protein) (MAC-IP) (MEM43 antigen) (Membrane attack complex inhibition factor) (MACIF) (Membrane inhibitor of reactive lysis) (MIRL) (Protectin) (CD antigen CD59)
[BFSP1] Filensin (Beaded filament structural protein 1) (Lens fiber cell beaded-filament structural protein CP 115) (CP115) (Lens intermediate filament-like heavy) (LIFL-H) [Cleaved into: Filensin C-terminal fragment; Filensin N-terminal fragment]
[Fgf13 Fhf2] Fibroblast growth factor 13 (FGF-13) (Fibroblast growth factor homologous factor 2) (FHF-2)
[Nr4a2 Hzf-3 Nurr1 Rnr1] Nuclear receptor subfamily 4 group A member 2 (NUR-related factor 1) (Nuclear orphan receptor HZF-3) (Orphan nuclear receptor NURR1) (Regenerating liver nuclear receptor 1) (RNR-1) (SL-322)
[Terf2 Trf2] Telomeric repeat-binding factor 2 (TTAGGG repeat-binding factor 2) (Telomeric DNA-binding protein)
[Rif1] Telomere-associated protein RIF1 (Rap1-interacting factor 1 homolog) (mRif1)
[Trim28 Kap1 Krip1 Tif1b] Transcription intermediary factor 1-beta (TIF1-beta) (E3 SUMO-protein ligase TRIM28) (EC 2.3.2.27) (KRAB-A-interacting protein) (KRIP-1) (RING-type E3 ubiquitin transferase TIF1-beta) (Tripartite motif-containing protein 28)
[RIF1] Telomere-associated protein RIF1 (Rap1-interacting factor 1 homolog)

Bibliography :