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Danio rerio strain Tuebingen chromosome 18 genomic scaffold, GRCz11 alternate locus group ALT_DRER_TU_2 ALT_CTG18_2_1

NCBI Reference Sequence: NW_018395333.1

FASTA Graphics 

LOCUS       NW_018395333            1106 bp    DNA     linear   CON 08-SEP-2024
DEFINITION  Danio rerio strain Tuebingen chromosome 18 genomic scaffold, GRCz11
            alternate locus group ALT_DRER_TU_2 ALT_CTG18_2_1.
ACCESSION   NW_018395333 REGION: 201..1306
VERSION     NW_018395333.1
DBLINK      BioProject: PRJNA13922
            BioSample: SAMN06930106
            Assembly: GCF_000002035.6
KEYWORDS    RefSeq; ALTERNATE_LOCUS.
SOURCE      Danio rerio (zebrafish)
  ORGANISM  Danio rerio
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Actinopterygii; Neopterygii; Teleostei; Ostariophysi;
            Cypriniformes; Danionidae; Danioninae; Danio.
REFERENCE   1  (bases 1 to 1106)
  AUTHORS   Howe,K., Clark,M.D., Torroja,C.F., Torrance,J., Berthelot,C.,
            Muffato,M., Collins,J.E., Humphray,S., McLaren,K., Matthews,L.,
            McLaren,S., Sealy,I., Caccamo,M., Churcher,C., Scott,C.,
            Barrett,J.C., Koch,R., Rauch,G.J., White,S., Chow,W., Kilian,B.,
            Quintais,L.T., Guerra-Assuncao,J.A., Zhou,Y., Gu,Y., Yen,J.,
            Vogel,J.H., Eyre,T., Redmond,S., Banerjee,R., Chi,J., Fu,B.,
            Langley,E., Maguire,S.F., Laird,G.K., Lloyd,D., Kenyon,E.,
            Donaldson,S., Sehra,H., Almeida-King,J., Loveland,J., Trevanion,S.,
            Jones,M., Quail,M., Willey,D., Hunt,A., Burton,J., Sims,S.,
            McLay,K., Plumb,B., Davis,J., Clee,C., Oliver,K., Clark,R.,
            Riddle,C., Elliot,D., Threadgold,G., Harden,G., Ware,D., Begum,S.,
            Mortimore,B., Kerry,G., Heath,P., Phillimore,B., Tracey,A.,
            Corby,N., Dunn,M., Johnson,C., Wood,J., Clark,S., Pelan,S.,
            Griffiths,G., Smith,M., Glithero,R., Howden,P., Barker,N.,
            Lloyd,C., Stevens,C., Harley,J., Holt,K., Panagiotidis,G.,
            Lovell,J., Beasley,H., Henderson,C., Gordon,D., Auger,K.,
            Wright,D., Collins,J., Raisen,C., Dyer,L., Leung,K., Robertson,L.,
            Ambridge,K., Leongamornlert,D., McGuire,S., Gilderthorp,R.,
            Griffiths,C., Manthravadi,D., Nichol,S., Barker,G., Whitehead,S.,
            Kay,M., Brown,J., Murnane,C., Gray,E., Humphries,M., Sycamore,N.,
            Barker,D., Saunders,D., Wallis,J., Babbage,A., Hammond,S.,
            Mashreghi-Mohammadi,M., Barr,L., Martin,S., Wray,P., Ellington,A.,
            Matthews,N., Ellwood,M., Woodmansey,R., Clark,G., Cooper,J.,
            Tromans,A., Grafham,D., Skuce,C., Pandian,R., Andrews,R.,
            Harrison,E., Kimberley,A., Garnett,J., Fosker,N., Hall,R.,
            Garner,P., Kelly,D., Bird,C., Palmer,S., Gehring,I., Berger,A.,
            Dooley,C.M., Ersan-Urun,Z., Eser,C., Geiger,H., Geisler,M.,
            Karotki,L., Kirn,A., Konantz,J., Konantz,M., Oberlander,M.,
            Rudolph-Geiger,S., Teucke,M., Lanz,C., Raddatz,G., Osoegawa,K.,
            Zhu,B., Rapp,A., Widaa,S., Langford,C., Yang,F., Schuster,S.C.,
            Carter,N.P., Harrow,J., Ning,Z., Herrero,J., Searle,S.M.,
            Enright,A., Geisler,R., Plasterk,R.H., Lee,C., Westerfield,M., de
            Jong,P.J., Zon,L.I., Postlethwait,J.H., Nusslein-Volhard,C.,
            Hubbard,T.J., Roest Crollius,H., Rogers,J. and Stemple,D.L.
  TITLE     The zebrafish reference genome sequence and its relationship to the
            human genome
  JOURNAL   Nature 496 (7446), 498-503 (2013)
   PUBMED   23594743
  REMARK    Erratum:[Nature. 2014 Jan 9;505(7482):248. Cooper, James [corrected
            to Cooper, James D]; Eliott, David [corrected to Elliot, David];
            Mortimer, Beverly [corrected to Mortimore, Beverley]; Begum,
            Sharmin [added]; Lloyd, Christine [added]; Lanz, Christa [added];
            Raddatz, Gunter [added]; Schuster, Stephan C [added]]
REFERENCE   2  (bases 1 to 1106)
  CONSRTM   Genome Reference Consortium
  TITLE     Genome Reference Consortium reference assembly of the zebrafish
            genome
  JOURNAL   Unpublished
REFERENCE   3  (bases 1 to 1106)
  CONSRTM   Genome Reference Consortium
  TITLE     Direct Submission
  JOURNAL   Submitted (09-MAY-2017) NCBI, NIH, Bethesda, MD 20892, USA
COMMENT     REFSEQ INFORMATION: The reference sequence is identical to
            KZ114958.1.
            Assembly Name: GRCz11 ALT_DRER_TU_2
            The GRCz11 sequence is composed of genomic sequence, primarily
            finished clones that were sequenced as part of Zebrafish Genome
            Project at the Wellcome Trust Sanger Institute. PCR products and
            WGS shotgun sequence from mainly the WGS31 assembly
            (CABZ00000000.1) but also WGS29 (CAAK00000000.1) and WGS32
            (CZQB00000000.1) have been added where necessary to fill gaps. In
            addition, unplaced sequences from WGS31 were added if they featured
            at least 5 kb of non-repetitive sequence, or if alignments with a
            cDNA could be detected that were not already covered by the placed
            sequences. For more information see: https://genomereference.org.
            This assembly includes sequences that are considered alternate loci
            to the primary reference assembly. They are sourced from those
            finished clones that were found to be haplotypic to the primary
            assembly but differ by at least 5 kb of insertion or deletion.
            Region: region272.
            
            ##Genome-Annotation-Data-START##
            Annotation Provider         :: NCBI RefSeq
            Annotation Status           :: Full annotation
            Annotation Name             :: GCF_000002035.6-RS_2024_08
            Annotation Pipeline         :: NCBI eukaryotic genome annotation
                                           pipeline
            Annotation Software Version :: 10.3
            Annotation Method           :: Best-placed RefSeq; Gnomon;
                                           cmsearch; tRNAscan-SE
            Features Annotated          :: Gene; mRNA; CDS; ncRNA
            Annotation Date             :: 08/15/2024
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..1106
                     /organism="Danio rerio"
                     /mol_type="genomic DNA"
                     /strain="Tuebingen"
                     /db_xref="taxon:7955"
                     /chromosome="18"
                     /map="unlocalized"
     misc_feature    <1..>1106
                     /note="Anchor sequence. This sequence is derived from alt
                     loci or patch scaffold components that are also components
                     of the primary assembly unit. It was included to ensure a
                     robust alignment of this scaffold to the primary assembly
                     unit. Anchor component: CR318588.10"
     gene            <1..1106
                     /gene="arf5"
                     /gene_synonym="cb445; cb789; sb:cb445; wu:fa06c04;
                     wu:fb16f02"
                     /note="ADP-ribosylation factor 5; Derived by automated
                     computational analysis using gene prediction method:
                     BestRefSeq."
                     /db_xref="GeneID:378724"
                     /db_xref="ZFIN:ZDB-GENE-030910-5"
     mRNA            <1..1106
                     /gene="arf5"
                     /gene_synonym="cb445; cb789; sb:cb445; wu:fa06c04;
                     wu:fb16f02"
                     /product="ADP-ribosylation factor 5"
                     /inference="similar to RNA sequence, mRNA (same
                     species):RefSeq:NM_199275.1"
                     /exception="annotated by transcript or proteomic data"
                     /note="The RefSeq transcript has 4 substitutions, 2
                     non-frameshifting indels and aligns at 63% coverage
                     compared to this genomic sequence; Derived by automated
                     computational analysis using gene prediction method:
                     BestRefSeq."
                     /transcript_id="NM_199275.1"
                     /db_xref="GeneID:378724"
                     /db_xref="ZFIN:ZDB-GENE-030910-5"
     CDS             <1..88
                     /gene="arf5"
                     /gene_synonym="cb445; cb789; sb:cb445; wu:fa06c04;
                     wu:fb16f02"
                     /inference="similar to AA sequence (same
                     species):RefSeq:NP_954969.1"
                     /exception="annotated by transcript or proteomic data"
                     /note="The RefSeq protein aligns at 16% coverage compared
                     to this genomic sequence; Derived by automated
                     computational analysis using gene prediction method:
                     BestRefSeq."
                     /codon_start=2
                     /product="ADP-ribosylation factor 5"
                     /protein_id="NP_954969.1"
                     /db_xref="GeneID:378724"
                     /db_xref="ZFIN:ZDB-GENE-030910-5"
                     /translation="MGLTISSLFGRLFGKKQMRILMVGLDAAGKTTILYKLKLGEIVT
                     TIPTIGFNVETVEYKNICFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVAE
                     SAEELSKMLQEDELRDAVLLVFANKQDLPNAMAVSELTDKLGLQSLRSRTWYVQATCA
                     TQGTGLYEGLDWLSNELSKR"
ORIGIN      
        1 gtggtacgtt caagcgacct gcgcaacaca gggcactgga ctctatgaag gactggactg
       61 gttatcaaat gagctctcca aacgctagtg tgtgcctgtt agggtcccag atgtgtgtga
      121 actttagaaa gacggagtgt gtccattgat cgactctgtc ttgaagaact tgtgtgaatg
      181 tgtgtgtgtg tgtgtgtgtg tggaggagct atcaagtgtt cagcatcatg tctaatctat
      241 cttatctgtc ttttttctat gctgtattcc tactaatgtt cttttaattt tgtttctcct
      301 tacaaatctg attgttttct tgactgtaag ataatgctta aattgcacgt ttacttgata
      361 actgtgagag cattatggca caaaggggag gaattccagc tcggggcgtc cctctcatgc
      421 aagtctggag tatttgtagc ttaaaaacaa atgataggat tgagtaaatg ccaggaagaa
      481 gctgttgtgc attaacgctc actttgagat ctcggttgca gtgctgccta atttgactag
      541 ccaatcacag gactcgccgc cctatgaaca ttccctttca tggctgttca ttttattcca
      601 ggagctacat gctaactttt gttgcaggga cagctttgag aagtgacaac agaatggtac
      661 atgaagtatt gatagcaata tggagtcatc cattgattag cccaatgttc tttgatatga
      721 aatacctcca ctgaacaata tggaagtaaa tgtttgagtt gaaagcattt ttgaacagat
      781 cacattagct tgcttgattt tcggacatgg tggattggac gaggatgatt agtttccttt
      841 ttttttccag ctttctccat gtttcttttc atgtcaaaca gatgcgtgta tgtatttgtg
      901 ctggcgcctt ttaatatcag cgatcgaggt gcattgggtg agaattttgt atcggacact
      961 ccagtaaaaa cgatactgtc ctcatttcct gagcaggact ttctgatctt gtacacttcc
     1021 ctactgcggc aaatgccgta ctcttgcttg aactgtgcca caaggtccac ccctgtgaga
     1081 aaataaagat ctggtaaaaa cccaaa
//
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