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Previous release (v1)
2024-11-01 14:36:44, GGRNA.v2 : RefSeq release 226 (Sep, 2024)
LOCUS XM_017356687 6622 bp mRNA linear VRT 08-SEP-2024
DEFINITION PREDICTED: Danio rerio cell adhesion molecule L1-like b (chl1b),
transcript variant X2, mRNA.
ACCESSION XM_017356687
VERSION XM_017356687.3
DBLINK BioProject: PRJNA13922
KEYWORDS RefSeq.
SOURCE Danio rerio (zebrafish)
ORGANISM Danio rerio
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Actinopterygii; Neopterygii; Teleostei; Ostariophysi;
Cypriniformes; Danionidae; Danioninae; Danio.
COMMENT MODEL REFSEQ: This record is predicted by automated computational
analysis. This record is derived from a genomic sequence
(NC_007117.7) annotated using gene prediction method: Gnomon,
supported by EST evidence.
Also see:
Documentation of NCBI's Annotation Process
On Sep 8, 2024 this sequence version replaced XM_017356687.2.
##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..6622
/organism="Danio rerio"
/mol_type="mRNA"
/strain="Tuebingen"
/db_xref="taxon:7955"
/chromosome="6"
gene 1..6622
/gene="chl1b"
/note="cell adhesion molecule L1-like b; Derived by
automated computational analysis using gene prediction
method: Gnomon. Supporting evidence includes similarity
to: 12 ESTs, 1 long SRA read, 2 Proteins, and 100%
coverage of the annotated genomic feature by RNAseq
alignments, including 40 samples with support for all
annotated introns"
/db_xref="GeneID:100318566"
/db_xref="ZFIN:ZDB-GENE-091105-1"
misc_feature 1
/gene="chl1b"
/experiment="COORDINATES: cap analysis [ECO:0007248]"
/note="transcription start site"
CDS 169..4053
/gene="chl1b"
/codon_start=1
/product="neural cell adhesion molecule L1-like protein
isoform X1"
/protein_id="XP_017212176.2"
/db_xref="GeneID:100318566"
/db_xref="ZFIN:ZDB-GENE-091105-1"
/translation="
MRLLRKTLLLLAACLNMSSRYQTNALEIPLDVLERMNMEQLPTITEYSPASLIAFPFEESFPVKCEATGNPEPEFRWTKNGQDFDPYQDTRLITLDDSGTFIIPNTGNLTEFQGIYRCFATNKLGTAMSEEIEFIIPNVPKFPKEIIDPIEVMEGQSVILECNPPTGIPPLQIYWMTISLQHIEQDERVSVGLNGNLYFSNTVETDSRRDYCCFAAFPRIRTIVQKTAMSMVVKSNKLMKDSSSGSGRGYANSLLERKPSLLAPTGMESHTRLVKGEDLQLECIAEGFPTPKVEWVKIGFNKLPERVVVESHGKLLTVEMVNEEDEGKYMCRAKNPHGEVVHHFHVTVEEPPEFEIEPQSQLVTIGADVLIKCVVKGNPQPTVGWRVNGRPLNEVPTSNRKILKDGTISIHNANPENSAVYQCEATNKHGTILANANIMIMNIQPLILTENNLQYMAVEGKSVVMHCKVFSSPASSITWSKADSANAVEGERFTVHQNGSLEIHNVMKEDMGEYSCFAQNTEGKVAIAATLEVKDPTRIVDPPRDLRVLAGTTIQFSCQPEFDPSFGDDFEVLWEKDGIALNGSEDGRYILEDGVLEIINVSFGDQGFYACVARTPVDQDVAVAQLSVVDVPDPPEDVILSEHNGRSVKLQWTPGDDHNSSITEFVLEFEESQHEPGSWREMMRVPGNHHSAPLKLYGHVDYRFRVSAINEVGKGRPSQSTERYKTPASAPDKNPENIKIEAHLPHEMDINWEPLSPIEHNGPGLEYKVSYRRHGSDEDWTERMVKRHSFLVKNTPTFVLYEIKIQAKNHAGWGPDPKIITAYSGEDFPSAAPDDVAVEVLNNTMVKVRWEHVHKDKIHGHLGGYRVSWWRLRSLLDSKKTHGDKHTLTFSGERNHAVVTGLKPFSEYSLIVMAFNSRGNGPGSHSVNFKTPEGVPGQAAAFSATNIQKHKVTLTWSPPVDANGVLIGYILQYQLINNTEELGPLMTLNISADSNKQHLENLEALSKYKFYLRCCTRVGCGPAVSEERTTVPEATSTDVASFNIRKSSSRFPPRKTTVSPVANATLSSIAVLNISTSVSHNYANISWIPGTEQTESELYVAFMNNREGNWKISDMLNSSKTFHIIEGLEPGTEYTVRLMTKSWVDNSSIFEDVIRTRAKGLASIHGSISNQGWFIGLMCAIALLTLIVLIACFVNRNKGGKYSVKEKEDLHPDLESQGINDDTFCEYSDNDEKPLKSSQHSLNGDLKGGDSGDSMVDYCDEDAHFNEDGSFIGEYSGRKDRASMEIKGNNQSTA"
misc_feature 292..573
/gene="chl1b"
/note="Immunoglobulin domain; Region: Ig; cl11960"
/db_xref="CDD:472250"
misc_feature 349..363
/gene="chl1b"
/note="Ig strand B [structural motif]; Region: Ig strand
B"
/db_xref="CDD:409396"
misc_feature 388..402
/gene="chl1b"
/note="Ig strand C [structural motif]; Region: Ig strand
C"
/db_xref="CDD:409396"
misc_feature 463..477
/gene="chl1b"
/note="Ig strand E [structural motif]; Region: Ig strand
E"
/db_xref="CDD:409396"
misc_feature 511..528
/gene="chl1b"
/note="Ig strand F [structural motif]; Region: Ig strand
F"
/db_xref="CDD:409396"
misc_feature 553..564
/gene="chl1b"
/note="Ig strand G [structural motif]; Region: Ig strand
G"
/db_xref="CDD:409396"
misc_feature 598..870
/gene="chl1b"
/note="Immunoglobulin domain; Region: Ig; cl11960"
/db_xref="CDD:472250"
misc_feature 640..654
/gene="chl1b"
/note="Ig strand B [structural motif]; Region: Ig strand
B"
/db_xref="CDD:409432"
misc_feature 682..696
/gene="chl1b"
/note="Ig strand C [structural motif]; Region: Ig strand
C"
/db_xref="CDD:409432"
misc_feature 751..765
/gene="chl1b"
/note="Ig strand E [structural motif]; Region: Ig strand
E"
/db_xref="CDD:409432"
misc_feature 796..813
/gene="chl1b"
/note="Ig strand F [structural motif]; Region: Ig strand
F"
/db_xref="CDD:409432"
misc_feature 844..855
/gene="chl1b"
/note="Ig strand G [structural motif]; Region: Ig strand
G"
/db_xref="CDD:409432"
misc_feature 967..1212
/gene="chl1b"
/note="Immunoglobulin domain; Region: Ig; cl11960"
/db_xref="CDD:472250"
misc_feature 1003..1017
/gene="chl1b"
/note="Ig strand B [structural motif]; Region: Ig strand
B"
/db_xref="CDD:409394"
misc_feature 1042..1056
/gene="chl1b"
/note="Ig strand C [structural motif]; Region: Ig strand
C"
/db_xref="CDD:409394"
misc_feature 1108..1122
/gene="chl1b"
/note="Ig strand E [structural motif]; Region: Ig strand
E"
/db_xref="CDD:409394"
misc_feature 1150..1167
/gene="chl1b"
/note="Ig strand F [structural motif]; Region: Ig strand
F"
/db_xref="CDD:409394"
misc_feature 1189..1200
/gene="chl1b"
/note="Ig strand G [structural motif]; Region: Ig strand
G"
/db_xref="CDD:409394"
misc_feature 1243..1482
/gene="chl1b"
/note="Immunoglobulin domain; Region: Ig; cl11960"
/db_xref="CDD:472250"
misc_feature 1273..1287
/gene="chl1b"
/note="Ig strand B [structural motif]; Region: Ig strand
B"
/db_xref="CDD:409367"
misc_feature 1312..1326
/gene="chl1b"
/note="Ig strand C [structural motif]; Region: Ig strand
C"
/db_xref="CDD:409367"
misc_feature 1384..1398
/gene="chl1b"
/note="Ig strand E [structural motif]; Region: Ig strand
E"
/db_xref="CDD:409367"
misc_feature 1426..1443
/gene="chl1b"
/note="Ig strand F [structural motif]; Region: Ig strand
F"
/db_xref="CDD:409367"
misc_feature 1465..1476
/gene="chl1b"
/note="Ig strand G [structural motif]; Region: Ig strand
G"
/db_xref="CDD:409367"
misc_feature 1507..1767
/gene="chl1b"
/note="Immunoglobulin domain; Region: Ig; cl11960"
/db_xref="CDD:472250"
misc_feature 1555..1569
/gene="chl1b"
/note="Ig strand B [structural motif]; Region: Ig strand
B"
/db_xref="CDD:409544"
misc_feature 1594..1608
/gene="chl1b"
/note="Ig strand C [structural motif]; Region: Ig strand
C"
/db_xref="CDD:409544"
misc_feature 1663..1677
/gene="chl1b"
/note="Ig strand E [structural motif]; Region: Ig strand
E"
/db_xref="CDD:409544"
misc_feature 1705..1722
/gene="chl1b"
/note="Ig strand F [structural motif]; Region: Ig strand
F"
/db_xref="CDD:409544"
misc_feature 1744..1755
/gene="chl1b"
/note="Ig strand G [structural motif]; Region: Ig strand
G"
/db_xref="CDD:409544"
misc_feature 1771..2073
/gene="chl1b"
/note="Immunoglobulin domain; Region: Ig; cl11960"
/db_xref="CDD:472250"
misc_feature 1828..1842
/gene="chl1b"
/note="Ig strand B [structural motif]; Region: Ig strand
B"
/db_xref="CDD:409359"
misc_feature 1879..1893
/gene="chl1b"
/note="Ig strand C [structural motif]; Region: Ig strand
C"
/db_xref="CDD:409359"
misc_feature 1948..1962
/gene="chl1b"
/note="Ig strand E [structural motif]; Region: Ig strand
E"
/db_xref="CDD:409359"
misc_feature 1990..2007
/gene="chl1b"
/note="Ig strand F [structural motif]; Region: Ig strand
F"
/db_xref="CDD:409359"
misc_feature 2029..2040
/gene="chl1b"
/note="Ig strand G [structural motif]; Region: Ig strand
G"
/db_xref="CDD:409359"
misc_feature 2062..2334
/gene="chl1b"
/note="Fibronectin type 3 domain; One of three types of
internal repeats found in the plasma protein fibronectin.
Its tenth fibronectin type III repeat contains an RGD cell
recognition sequence in a flexible loop between 2 strands.
Approximately 2% of all...; Region: FN3; cd00063"
/db_xref="CDD:238020"
misc_feature order(2062..2064,2260..2262,2305..2307)
/gene="chl1b"
/note="Interdomain contacts [active]"
/db_xref="CDD:238020"
misc_feature <2272..3471
/gene="chl1b"
/note="Fibronectin type 3 domain [General function
prediction only]; Region: FN3; COG3401"
/db_xref="CDD:442628"
misc_feature order(2308..2313,2317..2322)
/gene="chl1b"
/note="Cytokine receptor motif [active]"
/db_xref="CDD:238020"
misc_feature 3376..3594
/gene="chl1b"
/note="Fibronectin type 3 domain; Region: FN3; smart00060"
/db_xref="CDD:214495"
misc_feature 3754..4005
/gene="chl1b"
/note="Bravo-like intracellular region; Region:
Bravo_FIGEY; pfam13882"
/db_xref="CDD:464016"
polyA_site 6622
/gene="chl1b"
/experiment="COORDINATES: polyA evidence [ECO:0006239]"
ORIGIN
agacattctgctgtcgcgcgctgactaacagctccagctcttcccgcaaaaaactcctgtgaaaggtagcgagaccacagcctgggttggagtgagatgcactgactcctggcagactgcagatttccctgtcatcctccgctctcgcctctgaaactgtggccagtcatgcggttgttacggaaaaccctgcttcttttggctgcttgccttaatatgagcagcaggtatcaaactaacgccctggaaattccacttgatgttttagagcgcatgaacatggagcagctgcccacaattacagagtactctcctgcctcgctcatcgccttccctttcgaagagagcttccctgtgaagtgtgaggccacaggaaaccctgaaccagaattcaggtggacaaagaacggccaagactttgatccgtatcaggacaccagattgataacgttagatgattccggaacattcatcattcccaataccggaaatctcactgaattccagggcatttatcgctgttttgcaaccaacaaattggggacagccatgtcagaagaaattgagttcattattcctaatgtcccaaagttccccaaagagatcatcgatccgattgaggtgatggaaggtcagtcagtcattctagagtgcaatccacctacagggatccctccattgcaaatctactggatgacaataagtctacagcacatcgagcaggacgaaagagtgtcagtgggtctgaatggaaacctgtacttctcaaacaccgttgaaactgatagccgcagagactattgctgctttgctgccttccctcgcatccgaactatcgtccagaaaaccgctatgtccatggtggtcaaaagcaacaagttaatgaaggactcaagctctggtagcggcagaggttatgcaaactccctgttggagaggaagcccagcctgttggcgcctacaggaatggagtcacatacacgcctggtgaaaggtgaagatcttcagttggagtgtatagcagagggattccccacgccaaaggtggaatgggttaaaataggcttcaacaagcttccagaaagggttgttgtggagagtcatgggaagctgctcactgttgagatggtgaatgaggaggatgaaggcaaatatatgtgcagagccaaaaatccccacggagaggtggtgcatcattttcatgtgacagtagaggagcctcctgagtttgagattgaacctcaaagccaactggtgacgattggagctgatgtattgatcaagtgtgtcgtgaaaggaaatcctcaacctactgtaggatggagagttaacgggcggccactgaacgaggtcccaacatccaacaggaagatcttgaaagatggcacaatttccatccacaatgcaaacccagaaaacagtgctgtttaccaatgcgaggcaaccaacaaacacggcaccatcctggccaatgccaacatcatgattatgaacatccagccgctgatcttaacagaaaacaatctgcaatatatggcggtggaggggaaaagtgtggtcatgcactgcaaggtcttcagctctccagcctccagcattacgtggagtaaagctgacagtgcaaatgcagtggaaggagaacggtttactgttcaccagaatggttcactggagatccataatgtgatgaaagaggacatgggagagtattcttgctttgcacaaaacaccgaaggcaaagttgccattgctgcaacacttgaagtcaaagatcccaccagaatagtcgatcctccacgtgatttgcgggttttggcgggaaccactattcagttttcatgccagccagagtttgatccctcttttggtgatgactttgaagtcctgtgggagaaagatggcattgccctcaacggcagcgaagatggaagatatatcctggaagacggagtgctggagatcattaatgtgagtttcggagaccagggcttttacgcgtgtgtggccagaacgcccgttgaccaagacgttgcagtggcacagctttcagtcgtggatgttcctgatccaccagaggatgtgatactgtctgaacataatggccgaagtgtgaaactgcagtggactccgggagatgaccataatagctccattaccgagtttgttctagagtttgaagaaagccaacatgagccaggcagctggagggagatgatgagagtcccaggaaaccatcactcagctccgctgaagctttatggacatgtggactaccgcttcagagtctccgccatcaacgaggtgggcaaaggtcggccaagccagtccactgaaagatacaaaactccagcatcagcacccgacaagaacccagaaaatatcaagatcgaagctcatttgccacatgaaatggatatcaactgggagccgttgtcacctattgaacacaacgggcctggtctggagtacaaagtgagctacaggagacatggcagcgatgaagactggacggagcgcatggtgaagaggcactcatttctggtcaaaaacaccccgacgttcgtcctttacgagatcaaaattcaggccaagaaccacgcgggctggggtccggaccctaaaataataacagcgtactcgggagaggatttcccctcagcagctccagatgatgtagccgtagaagtgttgaacaacactatggtgaaggtcagatgggaacatgttcacaaggacaaaatacatggacatctgggtggctacagggtgagctggtggaggcttcgtagtctgctggactcaaagaaaacacacggcgacaagcacacattgacattctcaggcgagaggaaccatgcggtggtcacaggtcttaagccgttctccgaatacagcctcattgtcatggcctttaacagcagaggaaacggtcctggcagtcattcggtcaacttcaaaacccctgagggagttcctggtcaagcagctgctttcagtgctacaaacatccagaagcacaaggtcaccttgacctggtctcctccagttgacgcaaatggagtcctaattggctacatcctccaatatcagctaataaacaacacagaggaactaggccctctgatgacactcaacatctccgccgacagcaataagcagcacctcgaaaacctggaagccctgagcaaatacaaattttaccttcggtgttgcacgcgggtgggctgcggtcctgcggtcagcgaggagcgcaccaccgtccctgaagccacttcaacagatgtggcctctttcaacatcagaaaatccagctcacgatttcctccaagaaaaaccactgtttcccctgtggctaatgctactctttcttctatagcggtgttgaatattagcacctcagttagtcacaactatgcaaatatcagctggattccaggcacagaacagacggagtcagagttatatgttgcctttatgaacaaccgtgaaggtaactggaagatatccgacatgctaaactcttctaagactttccacatcattgaagggctcgaacctggaaccgaatacacagtgcgtcttatgacaaaaagctgggttgataattctagtattttcgaagacgttatcaggaccagggccaaaggtctggccagcattcatggaagcatctcaaaccagggatggttcatcggactcatgtgtgccatagcgcttctcaccctcattgtgctcatagcgtgctttgtcaaccgaaacaaaggcggcaaatactcagtaaaagagaaggaagacctccaccccgacctggagtcccagggcataaatgatgacaccttctgtgaatacagtgataatgatgagaaaccgctgaaaagcagccagcattcattgaatggcgacttgaaaggaggagacagcggagacagcatggtggactactgtgatgaggacgctcacttcaacgaggacggctcttttatcggagaatactctggacgcaaggacagggcctccatggaaatcaagggaaacaatcagagcacagcgtaatggaccacggacaatttatttgttggacaagctctcacaaaaggtcagtcaaaaggaagcggagggaataaaagtgtggcgtaacagcacccgaaggacatttttgcaattaatgtgttattgtcaaatcctcagtcatactcacatcattttttacagggcttagttgtttccatttttttctgcgtgctgttactgatcaatcatgtcagttgtgtatacttttgtgaggtgtttttgtattaaatctttgcaaatcattgatgactgccgggaaagttctgctttcaacgtcatcatgtagccaagccagtttttctgtcagggtatatgaactttgtatttttatttttcattccaggcaaatattattgacattttatatttcagacactgtatactgtgcgttcattaaatgtgggttattatgtgtacaaaaggagttgttgcttaaataatcataagttctgttaaaatccaaaaaaaatgaaagaaagcgtaaggcgatgtaagggtttacaattagtgtaaaatgctttgatgaacagtttcacattgagctatactaacaagcttaatagccatattcagcaccacataaaccctacagtgcatctgctgctgttttaaccctttacatacagtataatacagtattttatcaaaaagacacctaatgttcatacatttaaagaaaaaaaaatgcctcaattgccttataatgactttgaatctggtaagtaagatataacaatggggtatgtgcacatggagttttaatttcagccagccagcctcagtgtttccggtgaactgtctttcctttataaaatcgccacgtttaagatctggtttcgttagaaatcagtgatcctcactgcctgatagatatacaatgtgaagagggtctcagatcgaaaaaagaagcactgcatttaatttcattttccctttccatgtctttaaaatatgtacaattaatttttgtattttcaattgagtttctgcattagcctgctgatactgatggcgtgtcacagatgttttcatactgcatgactatctagggtagcattctgttagtgatgtgtttacattttaggatggattggcgacagggggtttcacactgcatgactttacagtaggaagaatcgccgttgactttgtccaaactttgtctcacaatcaaacacacaagagaagtgacatggaaaaggatgtccgcgaggtcctaaaatgtattaaaagttgattaatcaattaagagaaaattaaagcttaaaaggtatttaaaaagtcttaatcacacttttacgaggttttataaattagctcaagcattgtccaaagtgtttgattccaaaaagtataatatatttatggctcgatccacgcgattggttcaggccggggtatgtccggccaagctcctccgttcgagtgatgtcacgtaatttgcaacaaatacgggaaggtgatgctctccacatgtagcgaaaccatagagcgaaacagacggcaaaatgagaaaatgtaagtactcctggttggagaaagacgagtttaaacagtagctgaagcctgtcgtttaaaacaaccacgtaatttattctttcaagctttgtttcttcttgagttctgttgcatgattatgctctattgatttaactacaacacgtagtgtatcttgggttatcaaccatatgcctttagtggggtagcaaatgtacttatttctcctcaacattttattctttatcgatccagttgtggtgttgctcagatgacatgtcaaacagatgcgtgtgctcctgccaaatttccatagttttcctccttttcttggatccaaataaactgagattgagcgcttttaacttctccctgctgatacccatactagcggatgcagctctctcattggctgcaggtaatcgcaaatgttattttcaatcagaacacatttcacacagcatgatttgaatcgccgacagacccaaatatttagcacgccaaatatctcaagggtgtcagcgactcatctgggattctctcagatcgcgtctttgatagttcatactgtgtgattgttactcacatgaatgagcaacgattcacttttgatttcaggcatttgtctgcgatttctcaaaacctgtcggcaaaaaatctgggctaaactcttgcagtctgaactcggcataagtctatttaactgaatgtatttgaattacattataacattgatgctgtaaaaggaacattatgaaactgagaatgtctggctggaaacactagctgtgcatataccccattctcatggattccgtgatacagggttggaattctacaaattccacattggcatcctttgaaatatttctcttcacaaacggacagttctgaaagccaacaagtcttgtttgaacaattctgtatgtttttttgcaatggctccacatatagagtcaaagccagattctgtacaatgttctgtgaattctgtttgcatgttgaaagaggtctgtgtgcagatttgacattaaattgtatcatttctttcttc
//
by
@meso_cacase at
DBCLS
This page is licensed under a
Creative Commons Attribution 4.0 International License (CC BY 4.0).
If you use GGRNA in your work, please cite:
Naito Y, Bono H. (2012)
GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts.
Nucleic Acids Res., 40, W592-W596.
[Full Text]