ver.2
Home
|
Help
|
Advanced search
Previous release (v1)
2024-11-24 07:28:34, GGRNA.v2 : RefSeq release 226 (Sep, 2024)
LOCUS XM_017356688 6778 bp mRNA linear VRT 08-SEP-2024
DEFINITION PREDICTED: Danio rerio cell adhesion molecule L1-like b (chl1b),
transcript variant X3, mRNA.
ACCESSION XM_017356688
VERSION XM_017356688.3
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_017356688.2.
##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..6778
/organism="Danio rerio"
/mol_type="mRNA"
/strain="Tuebingen"
/db_xref="taxon:7955"
/chromosome="6"
gene 1..6778
/gene="chl1b"
/note="cell adhesion molecule L1-like b; Derived by
automated computational analysis using gene prediction
method: Gnomon. Supporting evidence includes similarity
to: 11 ESTs, 1 long SRA read, 2 Proteins, and 100%
coverage of the annotated genomic feature by RNAseq
alignments, including 32 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 343..4209
/gene="chl1b"
/codon_start=1
/product="neural cell adhesion molecule L1-like protein
isoform X2"
/protein_id="XP_017212177.2"
/db_xref="GeneID:100318566"
/db_xref="ZFIN:ZDB-GENE-091105-1"
/translation="
MRLLRKTLLLLAACLNMSSRYQTNALEIPLDVEQLPTITEYSPASLIAFPFEESFPVKCEATGNPEPEFRWTKNGQDFDPYQDTRLITLDDSGTFIIPNTGNLTEFQGIYRCFATNKLGTAMSEEIEFIIPNVPKFPKEIIDPIEVMEGQSVILECNPPTGIPPLQIYWMTISLQHIEQDERVSVGLNGNLYFSNTVETDSRRDYCCFAAFPRIRTIVQKTAMSMVVKSNKLMKDSSSGSGRGYANSLLERKPSLLAPTGMESHTRLVKGEDLQLECIAEGFPTPKVEWVKIGFNKLPERVVVESHGKLLTVEMVNEEDEGKYMCRAKNPHGEVVHHFHVTVEEPPEFEIEPQSQLVTIGADVLIKCVVKGNPQPTVGWRVNGRPLNEVPTSNRKILKDGTISIHNANPENSAVYQCEATNKHGTILANANIMIMNIQPLILTENNLQYMAVEGKSVVMHCKVFSSPASSITWSKADSANAVEGERFTVHQNGSLEIHNVMKEDMGEYSCFAQNTEGKVAIAATLEVKDPTRIVDPPRDLRVLAGTTIQFSCQPEFDPSFGDDFEVLWEKDGIALNGSEDGRYILEDGVLEIINVSFGDQGFYACVARTPVDQDVAVAQLSVVDVPDPPEDVILSEHNGRSVKLQWTPGDDHNSSITEFVLEFEESQHEPGSWREMMRVPGNHHSAPLKLYGHVDYRFRVSAINEVGKGRPSQSTERYKTPASAPDKNPENIKIEAHLPHEMDINWEPLSPIEHNGPGLEYKVSYRRHGSDEDWTERMVKRHSFLVKNTPTFVLYEIKIQAKNHAGWGPDPKIITAYSGEDFPSAAPDDVAVEVLNNTMVKVRWEHVHKDKIHGHLGGYRVSWWRLRSLLDSKKTHGDKHTLTFSGERNHAVVTGLKPFSEYSLIVMAFNSRGNGPGSHSVNFKTPEGVPGQAAAFSATNIQKHKVTLTWSPPVDANGVLIGYILQYQLINNTEELGPLMTLNISADSNKQHLENLEALSKYKFYLRCCTRVGCGPAVSEERTTVPEATSTDVASFNIRKSSSRFPPRKTTVSPVANATLSSIAVLNISTSVSHNYANISWIPGTEQTESELYVAFMNNREGNWKISDMLNSSKTFHIIEGLEPGTEYTVRLMTKSWVDNSSIFEDVIRTRAKGLASIHGSISNQGWFIGLMCAIALLTLIVLIACFVNRNKGGKYSVKEKEDLHPDLESQGINDDTFCEYSDNDEKPLKSSQHSLNGDLKGGDSGDSMVDYCDEDAHFNEDGSFIGEYSGRKDRASMEIKGNNQSTA"
misc_feature 448..729
/gene="chl1b"
/note="Immunoglobulin domain; Region: Ig; cl11960"
/db_xref="CDD:472250"
misc_feature 505..519
/gene="chl1b"
/note="Ig strand B [structural motif]; Region: Ig strand
B"
/db_xref="CDD:409396"
misc_feature 544..558
/gene="chl1b"
/note="Ig strand C [structural motif]; Region: Ig strand
C"
/db_xref="CDD:409396"
misc_feature 619..633
/gene="chl1b"
/note="Ig strand E [structural motif]; Region: Ig strand
E"
/db_xref="CDD:409396"
misc_feature 667..684
/gene="chl1b"
/note="Ig strand F [structural motif]; Region: Ig strand
F"
/db_xref="CDD:409396"
misc_feature 709..720
/gene="chl1b"
/note="Ig strand G [structural motif]; Region: Ig strand
G"
/db_xref="CDD:409396"
misc_feature 754..1026
/gene="chl1b"
/note="Immunoglobulin domain; Region: Ig; cl11960"
/db_xref="CDD:472250"
misc_feature 796..810
/gene="chl1b"
/note="Ig strand B [structural motif]; Region: Ig strand
B"
/db_xref="CDD:409432"
misc_feature 838..852
/gene="chl1b"
/note="Ig strand C [structural motif]; Region: Ig strand
C"
/db_xref="CDD:409432"
misc_feature 907..921
/gene="chl1b"
/note="Ig strand E [structural motif]; Region: Ig strand
E"
/db_xref="CDD:409432"
misc_feature 952..969
/gene="chl1b"
/note="Ig strand F [structural motif]; Region: Ig strand
F"
/db_xref="CDD:409432"
misc_feature 1000..1011
/gene="chl1b"
/note="Ig strand G [structural motif]; Region: Ig strand
G"
/db_xref="CDD:409432"
misc_feature 1123..1368
/gene="chl1b"
/note="Immunoglobulin domain; Region: Ig; cl11960"
/db_xref="CDD:472250"
misc_feature 1159..1173
/gene="chl1b"
/note="Ig strand B [structural motif]; Region: Ig strand
B"
/db_xref="CDD:409394"
misc_feature 1198..1212
/gene="chl1b"
/note="Ig strand C [structural motif]; Region: Ig strand
C"
/db_xref="CDD:409394"
misc_feature 1264..1278
/gene="chl1b"
/note="Ig strand E [structural motif]; Region: Ig strand
E"
/db_xref="CDD:409394"
misc_feature 1306..1323
/gene="chl1b"
/note="Ig strand F [structural motif]; Region: Ig strand
F"
/db_xref="CDD:409394"
misc_feature 1345..1356
/gene="chl1b"
/note="Ig strand G [structural motif]; Region: Ig strand
G"
/db_xref="CDD:409394"
misc_feature 1399..1638
/gene="chl1b"
/note="Immunoglobulin domain; Region: Ig; cl11960"
/db_xref="CDD:472250"
misc_feature 1429..1443
/gene="chl1b"
/note="Ig strand B [structural motif]; Region: Ig strand
B"
/db_xref="CDD:409367"
misc_feature 1468..1482
/gene="chl1b"
/note="Ig strand C [structural motif]; Region: Ig strand
C"
/db_xref="CDD:409367"
misc_feature 1540..1554
/gene="chl1b"
/note="Ig strand E [structural motif]; Region: Ig strand
E"
/db_xref="CDD:409367"
misc_feature 1582..1599
/gene="chl1b"
/note="Ig strand F [structural motif]; Region: Ig strand
F"
/db_xref="CDD:409367"
misc_feature 1621..1632
/gene="chl1b"
/note="Ig strand G [structural motif]; Region: Ig strand
G"
/db_xref="CDD:409367"
misc_feature 1663..1923
/gene="chl1b"
/note="Immunoglobulin domain; Region: Ig; cl11960"
/db_xref="CDD:472250"
misc_feature 1711..1725
/gene="chl1b"
/note="Ig strand B [structural motif]; Region: Ig strand
B"
/db_xref="CDD:409544"
misc_feature 1750..1764
/gene="chl1b"
/note="Ig strand C [structural motif]; Region: Ig strand
C"
/db_xref="CDD:409544"
misc_feature 1819..1833
/gene="chl1b"
/note="Ig strand E [structural motif]; Region: Ig strand
E"
/db_xref="CDD:409544"
misc_feature 1861..1878
/gene="chl1b"
/note="Ig strand F [structural motif]; Region: Ig strand
F"
/db_xref="CDD:409544"
misc_feature 1900..1911
/gene="chl1b"
/note="Ig strand G [structural motif]; Region: Ig strand
G"
/db_xref="CDD:409544"
misc_feature 1927..2229
/gene="chl1b"
/note="Immunoglobulin domain; Region: Ig; cl11960"
/db_xref="CDD:472250"
misc_feature 1984..1998
/gene="chl1b"
/note="Ig strand B [structural motif]; Region: Ig strand
B"
/db_xref="CDD:409359"
misc_feature 2035..2049
/gene="chl1b"
/note="Ig strand C [structural motif]; Region: Ig strand
C"
/db_xref="CDD:409359"
misc_feature 2104..2118
/gene="chl1b"
/note="Ig strand E [structural motif]; Region: Ig strand
E"
/db_xref="CDD:409359"
misc_feature 2146..2163
/gene="chl1b"
/note="Ig strand F [structural motif]; Region: Ig strand
F"
/db_xref="CDD:409359"
misc_feature 2185..2196
/gene="chl1b"
/note="Ig strand G [structural motif]; Region: Ig strand
G"
/db_xref="CDD:409359"
misc_feature 2218..2490
/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(2218..2220,2416..2418,2461..2463)
/gene="chl1b"
/note="Interdomain contacts [active]"
/db_xref="CDD:238020"
misc_feature <2428..3627
/gene="chl1b"
/note="Fibronectin type 3 domain [General function
prediction only]; Region: FN3; COG3401"
/db_xref="CDD:442628"
misc_feature order(2464..2469,2473..2478)
/gene="chl1b"
/note="Cytokine receptor motif [active]"
/db_xref="CDD:238020"
misc_feature 3532..3750
/gene="chl1b"
/note="Fibronectin type 3 domain; Region: FN3; smart00060"
/db_xref="CDD:214495"
misc_feature 3910..4161
/gene="chl1b"
/note="Bravo-like intracellular region; Region:
Bravo_FIGEY; pfam13882"
/db_xref="CDD:464016"
polyA_site 6778
/gene="chl1b"
/experiment="COORDINATES: polyA evidence [ECO:0006239]"
ORIGIN
agatctggctttgtgggagtgattgtcactcgtttaatgagcttctttgccaggcgagaggctttggcaacatatgtctccccagtcgcctctctcgctctgttagtaccgggtctgctgtggtggacgtttctctggattttcttctctttctcaagcctgtgggattagacagagcagaaaaggaagggtttgtctgtatttctgaggacgagcggactagaatgaagcagattcctgtagcgagaccacagcctgggttggagtgagatgcactgactcctggcagactgcagatttccctgtcatcctccgctctcgcctctgaaactgtggccagtcatgcggttgttacggaaaaccctgcttcttttggctgcttgccttaatatgagcagcaggtatcaaactaacgccctggaaattccacttgatgtggagcagctgcccacaattacagagtactctcctgcctcgctcatcgccttccctttcgaagagagcttccctgtgaagtgtgaggccacaggaaaccctgaaccagaattcaggtggacaaagaacggccaagactttgatccgtatcaggacaccagattgataacgttagatgattccggaacattcatcattcccaataccggaaatctcactgaattccagggcatttatcgctgttttgcaaccaacaaattggggacagccatgtcagaagaaattgagttcattattcctaatgtcccaaagttccccaaagagatcatcgatccgattgaggtgatggaaggtcagtcagtcattctagagtgcaatccacctacagggatccctccattgcaaatctactggatgacaataagtctacagcacatcgagcaggacgaaagagtgtcagtgggtctgaatggaaacctgtacttctcaaacaccgttgaaactgatagccgcagagactattgctgctttgctgccttccctcgcatccgaactatcgtccagaaaaccgctatgtccatggtggtcaaaagcaacaagttaatgaaggactcaagctctggtagcggcagaggttatgcaaactccctgttggagaggaagcccagcctgttggcgcctacaggaatggagtcacatacacgcctggtgaaaggtgaagatcttcagttggagtgtatagcagagggattccccacgccaaaggtggaatgggttaaaataggcttcaacaagcttccagaaagggttgttgtggagagtcatgggaagctgctcactgttgagatggtgaatgaggaggatgaaggcaaatatatgtgcagagccaaaaatccccacggagaggtggtgcatcattttcatgtgacagtagaggagcctcctgagtttgagattgaacctcaaagccaactggtgacgattggagctgatgtattgatcaagtgtgtcgtgaaaggaaatcctcaacctactgtaggatggagagttaacgggcggccactgaacgaggtcccaacatccaacaggaagatcttgaaagatggcacaatttccatccacaatgcaaacccagaaaacagtgctgtttaccaatgcgaggcaaccaacaaacacggcaccatcctggccaatgccaacatcatgattatgaacatccagccgctgatcttaacagaaaacaatctgcaatatatggcggtggaggggaaaagtgtggtcatgcactgcaaggtcttcagctctccagcctccagcattacgtggagtaaagctgacagtgcaaatgcagtggaaggagaacggtttactgttcaccagaatggttcactggagatccataatgtgatgaaagaggacatgggagagtattcttgctttgcacaaaacaccgaaggcaaagttgccattgctgcaacacttgaagtcaaagatcccaccagaatagtcgatcctccacgtgatttgcgggttttggcgggaaccactattcagttttcatgccagccagagtttgatccctcttttggtgatgactttgaagtcctgtgggagaaagatggcattgccctcaacggcagcgaagatggaagatatatcctggaagacggagtgctggagatcattaatgtgagtttcggagaccagggcttttacgcgtgtgtggccagaacgcccgttgaccaagacgttgcagtggcacagctttcagtcgtggatgttcctgatccaccagaggatgtgatactgtctgaacataatggccgaagtgtgaaactgcagtggactccgggagatgaccataatagctccattaccgagtttgttctagagtttgaagaaagccaacatgagccaggcagctggagggagatgatgagagtcccaggaaaccatcactcagctccgctgaagctttatggacatgtggactaccgcttcagagtctccgccatcaacgaggtgggcaaaggtcggccaagccagtccactgaaagatacaaaactccagcatcagcacccgacaagaacccagaaaatatcaagatcgaagctcatttgccacatgaaatggatatcaactgggagccgttgtcacctattgaacacaacgggcctggtctggagtacaaagtgagctacaggagacatggcagcgatgaagactggacggagcgcatggtgaagaggcactcatttctggtcaaaaacaccccgacgttcgtcctttacgagatcaaaattcaggccaagaaccacgcgggctggggtccggaccctaaaataataacagcgtactcgggagaggatttcccctcagcagctccagatgatgtagccgtagaagtgttgaacaacactatggtgaaggtcagatgggaacatgttcacaaggacaaaatacatggacatctgggtggctacagggtgagctggtggaggcttcgtagtctgctggactcaaagaaaacacacggcgacaagcacacattgacattctcaggcgagaggaaccatgcggtggtcacaggtcttaagccgttctccgaatacagcctcattgtcatggcctttaacagcagaggaaacggtcctggcagtcattcggtcaacttcaaaacccctgagggagttcctggtcaagcagctgctttcagtgctacaaacatccagaagcacaaggtcaccttgacctggtctcctccagttgacgcaaatggagtcctaattggctacatcctccaatatcagctaataaacaacacagaggaactaggccctctgatgacactcaacatctccgccgacagcaataagcagcacctcgaaaacctggaagccctgagcaaatacaaattttaccttcggtgttgcacgcgggtgggctgcggtcctgcggtcagcgaggagcgcaccaccgtccctgaagccacttcaacagatgtggcctctttcaacatcagaaaatccagctcacgatttcctccaagaaaaaccactgtttcccctgtggctaatgctactctttcttctatagcggtgttgaatattagcacctcagttagtcacaactatgcaaatatcagctggattccaggcacagaacagacggagtcagagttatatgttgcctttatgaacaaccgtgaaggtaactggaagatatccgacatgctaaactcttctaagactttccacatcattgaagggctcgaacctggaaccgaatacacagtgcgtcttatgacaaaaagctgggttgataattctagtattttcgaagacgttatcaggaccagggccaaaggtctggccagcattcatggaagcatctcaaaccagggatggttcatcggactcatgtgtgccatagcgcttctcaccctcattgtgctcatagcgtgctttgtcaaccgaaacaaaggcggcaaatactcagtaaaagagaaggaagacctccaccccgacctggagtcccagggcataaatgatgacaccttctgtgaatacagtgataatgatgagaaaccgctgaaaagcagccagcattcattgaatggcgacttgaaaggaggagacagcggagacagcatggtggactactgtgatgaggacgctcacttcaacgaggacggctcttttatcggagaatactctggacgcaaggacagggcctccatggaaatcaagggaaacaatcagagcacagcgtaatggaccacggacaatttatttgttggacaagctctcacaaaaggtcagtcaaaaggaagcggagggaataaaagtgtggcgtaacagcacccgaaggacatttttgcaattaatgtgttattgtcaaatcctcagtcatactcacatcattttttacagggcttagttgtttccatttttttctgcgtgctgttactgatcaatcatgtcagttgtgtatacttttgtgaggtgtttttgtattaaatctttgcaaatcattgatgactgccgggaaagttctgctttcaacgtcatcatgtagccaagccagtttttctgtcagggtatatgaactttgtatttttatttttcattccaggcaaatattattgacattttatatttcagacactgtatactgtgcgttcattaaatgtgggttattatgtgtacaaaaggagttgttgcttaaataatcataagttctgttaaaatccaaaaaaaatgaaagaaagcgtaaggcgatgtaagggtttacaattagtgtaaaatgctttgatgaacagtttcacattgagctatactaacaagcttaatagccatattcagcaccacataaaccctacagtgcatctgctgctgttttaaccctttacatacagtataatacagtattttatcaaaaagacacctaatgttcatacatttaaagaaaaaaaaatgcctcaattgccttataatgactttgaatctggtaagtaagatataacaatggggtatgtgcacatggagttttaatttcagccagccagcctcagtgtttccggtgaactgtctttcctttataaaatcgccacgtttaagatctggtttcgttagaaatcagtgatcctcactgcctgatagatatacaatgtgaagagggtctcagatcgaaaaaagaagcactgcatttaatttcattttccctttccatgtctttaaaatatgtacaattaatttttgtattttcaattgagtttctgcattagcctgctgatactgatggcgtgtcacagatgttttcatactgcatgactatctagggtagcattctgttagtgatgtgtttacattttaggatggattggcgacagggggtttcacactgcatgactttacagtaggaagaatcgccgttgactttgtccaaactttgtctcacaatcaaacacacaagagaagtgacatggaaaaggatgtccgcgaggtcctaaaatgtattaaaagttgattaatcaattaagagaaaattaaagcttaaaaggtatttaaaaagtcttaatcacacttttacgaggttttataaattagctcaagcattgtccaaagtgtttgattccaaaaagtataatatatttatggctcgatccacgcgattggttcaggccggggtatgtccggccaagctcctccgttcgagtgatgtcacgtaatttgcaacaaatacgggaaggtgatgctctccacatgtagcgaaaccatagagcgaaacagacggcaaaatgagaaaatgtaagtactcctggttggagaaagacgagtttaaacagtagctgaagcctgtcgtttaaaacaaccacgtaatttattctttcaagctttgtttcttcttgagttctgttgcatgattatgctctattgatttaactacaacacgtagtgtatcttgggttatcaaccatatgcctttagtggggtagcaaatgtacttatttctcctcaacattttattctttatcgatccagttgtggtgttgctcagatgacatgtcaaacagatgcgtgtgctcctgccaaatttccatagttttcctccttttcttggatccaaataaactgagattgagcgcttttaacttctccctgctgatacccatactagcggatgcagctctctcattggctgcaggtaatcgcaaatgttattttcaatcagaacacatttcacacagcatgatttgaatcgccgacagacccaaatatttagcacgccaaatatctcaagggtgtcagcgactcatctgggattctctcagatcgcgtctttgatagttcatactgtgtgattgttactcacatgaatgagcaacgattcacttttgatttcaggcatttgtctgcgatttctcaaaacctgtcggcaaaaaatctgggctaaactcttgcagtctgaactcggcataagtctatttaactgaatgtatttgaattacattataacattgatgctgtaaaaggaacattatgaaactgagaatgtctggctggaaacactagctgtgcatataccccattctcatggattccgtgatacagggttggaattctacaaattccacattggcatcctttgaaatatttctcttcacaaacggacagttctgaaagccaacaagtcttgtttgaacaattctgtatgtttttttgcaatggctccacatatagagtcaaagccagattctgtacaatgttctgtgaattctgtttgcatgttgaaagaggtctgtgtgcagatttgacattaaattgtatcatttctttcttc
//
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]