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
//