LOCUS       NM_001302779            2860 bp    mRNA    linear   ROD 03-JUN-2024
DEFINITION  Mus musculus intermediate filament family orphan 1 (Iffo1),
            transcript variant 4, mRNA.
ACCESSION   NM_001302779 XM_006506277
VERSION     NM_001302779.1
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Mus musculus (house mouse)
  ORGANISM  Mus musculus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Mus; Mus.
REFERENCE   1  (bases 1 to 2860)
  AUTHORS   Diez-Roux,G., Banfi,S., Sultan,M., Geffers,L., Anand,S., Rozado,D.,
            Magen,A., Canidio,E., Pagani,M., Peluso,I., Lin-Marq,N., Koch,M.,
            Bilio,M., Cantiello,I., Verde,R., De Masi,C., Bianchi,S.A.,
            Cicchini,J., Perroud,E., Mehmeti,S., Dagand,E., Schrinner,S.,
            Nurnberger,A., Schmidt,K., Metz,K., Zwingmann,C., Brieske,N.,
            Springer,C., Hernandez,A.M., Herzog,S., Grabbe,F., Sieverding,C.,
            Fischer,B., Schrader,K., Brockmeyer,M., Dettmer,S., Helbig,C.,
            Alunni,V., Battaini,M.A., Mura,C., Henrichsen,C.N.,
            Garcia-Lopez,R., Echevarria,D., Puelles,E., Garcia-Calero,E.,
            Kruse,S., Uhr,M., Kauck,C., Feng,G., Milyaev,N., Ong,C.K.,
            Kumar,L., Lam,M., Semple,C.A., Gyenesei,A., Mundlos,S., Radelof,U.,
            Lehrach,H., Sarmientos,P., Reymond,A., Davidson,D.R., Dolle,P.,
            Antonarakis,S.E., Yaspo,M.L., Martinez,S., Baldock,R.A., Eichele,G.
            and Ballabio,A.
  TITLE     A high-resolution anatomical atlas of the transcriptome in the
            mouse embryo
  JOURNAL   PLoS Biol 9 (1), e1000582 (2011)
   PUBMED   21267068
  REMARK    Publication Status: Online-Only
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            BY729723.1, AK044728.1, AK028273.1, AC166162.6, BC057601.1 and
            AK163571.1.
            
            On Nov 14, 2014 this sequence version replaced XM_006506277.1.
            
            Transcript Variant: This variant (4) lacks an in-frame exon and
            uses an alternate in-frame splice site in the coding region
            compared to variant 1. The encoded protein (isoform d) is shorter
            than isoform a.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AK028273.1, SRR7345562.2972917.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849374, SAMN00849375
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-27                BY729723.1         1-27
            28-362              AK044728.1         2-336
            363-903             AK028273.1         347-887
            904-904             AC166162.6         123098-123098
            905-1025            AK028273.1         889-1009
            1026-1026           AC166162.6         124768-124768
            1027-1067           AK028273.1         1011-1051
            1068-1068           AC166162.6         124810-124810
            1069-1830           AK028273.1         1053-1814
            1831-2858           BC057601.1         1260-2287
            2859-2860           AK163571.1         2839-2840
FEATURES             Location/Qualifiers
     source          1..2860
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="6"
                     /map="6 59.32 cM"
     gene            1..2860
                     /gene="Iffo1"
                     /gene_synonym="4733401N06Rik; A930037G23Rik; HOM-TES-103;
                     Iffo"
                     /note="intermediate filament family orphan 1"
                     /db_xref="GeneID:320678"
                     /db_xref="MGI:MGI:2444516"
     exon            1..806
                     /gene="Iffo1"
                     /gene_synonym="4733401N06Rik; A930037G23Rik; HOM-TES-103;
                     Iffo"
                     /inference="alignment:Splign:2.1.0"
     CDS             34..1716
                     /gene="Iffo1"
                     /gene_synonym="4733401N06Rik; A930037G23Rik; HOM-TES-103;
                     Iffo"
                     /note="isoform d is encoded by transcript variant 4; NHEJ
                     factor IFFO1; non-homologous end joining factor IFFO1"
                     /codon_start=1
                     /product="non-homologous end joining factor IFFO1 isoform
                     d"
                     /protein_id="NP_001289708.1"
                     /db_xref="GeneID:320678"
                     /db_xref="MGI:MGI:2444516"
                     /translation="MNPLFGPNLFLLQQEQQGLAGPLGDPLGGDHFAGGGDLASAPLA
                     SAGPSAYSPPGPGPAPPAAMALRNDLGSNINVLKTLNLRFRCFLAKVHELERRNRLLE
                     KQLQQALEEGKQGRRGLARRDQAVQTGFISPIRPLGLPLSSRPAAVCPPSARVLGSPS
                     RSPAGPLASSAACHTSSSTSTSTAFSSSTRFMPGTIWSFSHARRLGPGLEPTLVQGPG
                     LSWVHPDGVGVQIDTITPEIRALYNVLAKVKRERDEYKRRWEEEYTVRIQLQERVTEL
                     QEEAQEADACQEELAMKVEQLKAELVVFKGLMSNNLTELDTKIQEKAMKVDMDICRRI
                     DITAKLCDLAQQRNCEDMIQMFQVPSMGGRKRERKAAVEEDTSLSESDGPRQPEGAEE
                     ESTALSINEEMQRMLSQLREYDFEDDCDSLTWEETEETLLLWEDFSGYAMAAAEAQGE
                     QQEDSLEKVIKDTESLFKTREKEYQETIDQIELELATAKNDMNRHLHEYMEMCSMKRG
                     LDVQMETCRRLITQSGDRKSPAFTAVPLSDPPPPPSETEDSDRDVSSDSSMR"
     exon            807..867
                     /gene="Iffo1"
                     /gene_synonym="4733401N06Rik; A930037G23Rik; HOM-TES-103;
                     Iffo"
                     /inference="alignment:Splign:2.1.0"
     exon            868..963
                     /gene="Iffo1"
                     /gene_synonym="4733401N06Rik; A930037G23Rik; HOM-TES-103;
                     Iffo"
                     /inference="alignment:Splign:2.1.0"
     exon            964..1104
                     /gene="Iffo1"
                     /gene_synonym="4733401N06Rik; A930037G23Rik; HOM-TES-103;
                     Iffo"
                     /inference="alignment:Splign:2.1.0"
     exon            1105..1262
                     /gene="Iffo1"
                     /gene_synonym="4733401N06Rik; A930037G23Rik; HOM-TES-103;
                     Iffo"
                     /inference="alignment:Splign:2.1.0"
     exon            1263..1383
                     /gene="Iffo1"
                     /gene_synonym="4733401N06Rik; A930037G23Rik; HOM-TES-103;
                     Iffo"
                     /inference="alignment:Splign:2.1.0"
     exon            1384..1479
                     /gene="Iffo1"
                     /gene_synonym="4733401N06Rik; A930037G23Rik; HOM-TES-103;
                     Iffo"
                     /inference="alignment:Splign:2.1.0"
     exon            1480..1610
                     /gene="Iffo1"
                     /gene_synonym="4733401N06Rik; A930037G23Rik; HOM-TES-103;
                     Iffo"
                     /inference="alignment:Splign:2.1.0"
     exon            1611..2860
                     /gene="Iffo1"
                     /gene_synonym="4733401N06Rik; A930037G23Rik; HOM-TES-103;
                     Iffo"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2838..2843
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Iffo1"
                     /gene_synonym="4733401N06Rik; A930037G23Rik; HOM-TES-103;
                     Iffo"
                     /note="hexamer: AATAAA"
     polyA_site      2858
                     /gene="Iffo1"
                     /gene_synonym="4733401N06Rik; A930037G23Rik; HOM-TES-103;
                     Iffo"
                     /note="major polyA site"
ORIGIN      
        1 actggtctcc ttctcccggc agaaggcgca gccatgaatc cgttatttgg tcccaacctc
       61 ttcctcctac agcaggagca gcaaggcttg gccgggccgc tgggggaccc tctgggaggt
      121 gaccactttg ccgggggagg ggacttagcc tcggctccgc ttgcctcggc cggcccctct
      181 gcctattcgc ctccggggcc tggtccggcg ccccccgcag ccatggctct ccgcaacgac
      241 ctaggctcca acatcaacgt actgaagacc ctgaacctcc ggtttcgctg cttcctagcc
      301 aaggtgcacg agctagagcg ccgaaatcgg ctgctggaga aacagctgca gcaggctcta
      361 gaggagggta agcagggcag gcggggcctg gcccgccgtg accaggcggt acagaccggc
      421 ttcatcagcc cgatccggcc cctggggctg cccctgagct cccggccggc cgccgtgtgc
      481 cccccatcag cgcgggtgct gggctcgccc tcccgctcgc cagctggacc cttagcatcc
      541 tctgccgcct gccacacatc atcctccact tccacatcca ctgccttctc ctcgtcgacc
      601 cgcttcatgc ctggcaccat ctggtccttc tctcacgccc gccggcttgg accaggactg
      661 gaacccacgc tggtgcaagg gcctggcctg tcgtgggtac accctgacgg ggtgggcgtc
      721 cagatcgaca ccatcacccc tgagatccgt gccctgtaca acgtgctggc caaagtgaag
      781 cgggagcggg acgagtacaa gcgaaggtgg gaagaggaat acacggttcg gatacagcta
      841 caagagcgag tgactgagct ccaggaggag gcccaagagg ccgatgcctg ccaagaggag
      901 ctagccatga aggttgagca gctgaaggca gagctggtgg tcttcaaggg gctcatgagt
      961 aataatctga cagagctgga caccaagatc caggaaaagg ccatgaaagt cgacatggac
     1021 atctgccgcc gcattgacat cacggccaag ctctgtgact tggcccagca gcgcaactgt
     1081 gaggatatga tccagatgtt ccaggtcccg tccatggggg ggcggaagcg ggagcgcaag
     1141 gctgctgtgg aggaggacac ctccctgtcg gagagtgatg ggccccgcca gcctgagggt
     1201 gccgaggagg agagcacagc cctcagcatc aacgaggaga tgcagcgcat gctcagccag
     1261 ctgagggagt atgattttga ggacgactgt gacagcctga cttgggagga gactgaggag
     1321 accttgctac tttgggagga tttctcaggc tatgccatgg cagccgcaga ggcccaggga
     1381 gagcagcagg aggacagcct ggagaaggtg atcaaagaca cggagtccct gttcaaaacc
     1441 cgggagaagg agtaccagga gaccattgac cagatagagc tggagctggc cacagccaag
     1501 aacgacatga accgacacct gcatgagtac atggagatgt gcagcatgaa gcggggcctg
     1561 gacgtgcaga tggagacctg ccgccggctc atcacacagt ccggggaccg aaagtctcct
     1621 gctttcactg cggtcccgct tagcgacccg ccgccaccgc cgagtgagac tgaggactcc
     1681 gatcgagacg tctcatctga tagctccatg agatagaaac cagtgtctgg caccccagag
     1741 ctcactgggg caggggtgtg ggtctgcagg ggtgtgggtc ttctgtgcca ctgcatgaag
     1801 cctggccctg ggctgtccct ccccaggttc tggggtgtct ggagctaggc tcagccccac
     1861 cctccctgta caacgcccat gacattggga cactccttcc tgccttcctc acatgtgggt
     1921 atctgctact tctccatctt cggaatgctg ccaggacact tgtgagcctc ccttttccac
     1981 tttgtaagga atgtgatcac gggacctgcc tgtattcctt gggtatcttg gattttgtac
     2041 tggtgctaac ttgcctaggc actcgtgtga agcagattca tcatgtacct tgggataggg
     2101 ctttgctccc tagtaaggct ttggagggtg tggggtgctc tgtccacatg ctcccagctg
     2161 ttcacttgcc tcttgcagtg aacatggccg tgcaggctcg cctttgggaa gtcctgtgct
     2221 gggcccaggt cgcggctgag gaggtgaagc tgctgcccgc acatgggtgt ggcctgcagg
     2281 ttactggtgc tcggggcctg tttctccagt gagcagctga gggtatgccg ccatggctgt
     2341 cactgacaaa accaaaaggt taagatgtcc ctgacctagg gagtcagtca cgacctccca
     2401 ggagacgcta tgttgaacta ttggaatgga acctttaaaa gcaatgacgg tgtggaatac
     2461 ttcccaagca ctgagtcact gtgtgacgca cgaaccaaag catcgaccag tgctacagcc
     2521 cctcttcatg gataccacta ggttttactg tactgggcgc ccttccaatt ttatctaatt
     2581 ttacgtctgt ctgcaggagg gctgggtaca attaaccttt gtttgcagat aaaaggacac
     2641 cgatctttct caagagcagt gagctctgga agtcagtgct gtccaacaag tgagtctcag
     2701 actgcatttc ctgtcccatt gtcaagcccc accctccgca ttgccagaca tatcagctgt
     2761 tcaggacagg cgccctgggc tgggacttgg atagaatgta gccctggact tccggcaccc
     2821 agctggatgt cagagccaat aaagatacat gcacaaaagt
//
