Gene annotation query, LanceletDB: The Lancelet (Branchiostoma belcheri) Genome Sequencing and Annotation Project Database at Sun Yat-sen University

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Analysis of genomic poly(A) sites

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[1]. For APASdbs, a genome-wide database describing alternative poly(A) sites and detailing the heterogeneous cleavage sites dwonstream each poly(A) signal in various biological conditions and deseases. It supports query by using a ID (currently Ensembl or UCSC ID only), gene name, symbols or description variable in publications and databases. Searching examples: cxcl12a, cxcl, chemokine, also ENSDARG00000037116 (Ensembl id only for Danio rerio), uc009dsc.2, uc003qht.2 (UCSC id only for Mus musculus and Homo sapiens).

[2]. For Transcripts, that annotates and stores transcript sequences, querying by using a ID, gene name, symbols or description. Example: ssr4, ssr, TLR, caspase, also Bb_073760F are available for v7h2, but v15h11 and v18h27 currently only surport id query.

[3]. For Proteins, it saves proteins sequences to supports Blast, providing query by protein ID in databases, For example Bb_073760F.

[4]. For ESTs, it stores Expressed sequence tags to supports Blast, but also provides obtaining sequences by EST-ID in databases, For example est_xb_1526.

[5]. For Genomes, it collects genome sequences and also supports Blast, querying by using a chr ID in publication and databases such as Sc0000024 (only for lancelet), chr1, chr22 and so on.

[6]. For ncRNAs, that collects ncRNAs such as tRNA, snRNA, rRNA, miRNA and so on. It provides Blast and querying by Ensembl Transcript or Gene ID. For example, ENSDART00000128920.

[7]. For miRNAs, it stores miRNAs sequences and supply Blast and searching by miRBase ID and Name, like bfl-miR-2058, dre-miR-430a and MIMAT0001423.

Searching for Transcripts

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Zebrafish
Danio rerio

Database: for

Tips for searching: search using a ID, gene name, symbols or description variable in publications and databases.
Searching examples: ssr4, ssr, hox, TLR, caspase, also Bb_073760F are available for query.

1.

Transcript Detail

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Transcript Mapping

Exons Structure

Gene id:	ENSDARG00000007358
Gene name:	cxcr3.1
Chromosome:	chr16(-)
Gene locus:	chr16(-):13603464-13609316
Gene description:	chemokine (C-X-C motif) receptor 3.1 [Source:ZFIN;Acc:ZDB-GENE-060130-38 ]

Transcript id:	ENSDART00000028141
Transcript name:	cxcr3.1-201
Transcript locus:	chr16(-):13603464-13609316

Start codon:	13607981
Stop codon:	13604933
Alternative polyA sites:	Mapped to the searched transcript (containing the 5' and 3' flanking region of 1kb).
Alternative polyA sites:	13596199, 13590133, 13589653, 13589617, 13588415, 13535291, 13530754, 13510989, 13510597, 13462675, 13462216
polyA signals:	AATAAA, AATAAA, ATTAAA, ACTAAA, TATAAA, AATAAA, CATAAA, AATAAA, AATAAA, AATAAA, ATTAAA

Notes:

mRNA/CDS:

mRNA/CDS sequence ( exon splicing-sites gapped by the sympol ' / ' )

>ENSDART00000028141 2615bp
AGCACCTCTCAACCTCTGCGTGATCACTTACAAAGGTAT/TGAATGTTGACTCAAAAACAACATTCAGTATGAAGGATTTCAGTGACTACACAGACCTTTACAATTACAGTGACTACAATGACAATGAAAGCTATGGCGCAGGAGCTGTGTGCACTCAAGACTCCAGCATGTACTTTGACAGCATTTTTAAGCCAATCCTTTACTCACTGGCAGCGGTCGTGGGGCTGCTGGGAAACGGCTTGGTTCTGATTGTACTGTGGAAGAAGAGAGCAGGTTTGAATGTTACAGACATCTTCATCCTCCACCTGAGCCTGGCAGATATTTTGCTGCTGTTAACACTGCCCTTCTGGGCTGTAGAGGCGGTGAAGGAGTGGATCTTTGGCACACCACTTTGCAAACTGACTGGAGCTATGTTCAGGGTGA/ATTTCTACTGTGGCATTTACATGCTTTCCTGCATCAGTCTCGACCGCTACCTGTCCATCGTCCATGCAGTCCAAATGTACTCCCGTAAAAAGCCCATGGCGGTTCACTGTTGCTGCATGATAGTCTGGTTCTTCTGCTTTCTGCTCTCCATTCCCGATTGGATATTACTTGGTGCCAACAAGGACTCCAGACGTCAGGATAGAACAGAATGTGTTAATTCAGAAGCTCTATCTGATTTTTGGGTTCTGGTCAATCGTCTGATCTATCATTTTTTGGGTTTCATTATTCCAGCAATAATGATGGTCTTCTGCTACACTAGCATTCTGCTGCGCTTACTGCTCGGCTCCAAGTGCATGCAGAAGAAGAGGGCCATCCATGTCATTGTAGCCCTGGTACTGGCCTTCTTCATCAGCTGGACGCCCTACAACATCGCCCTCATGGCTGACACCATACATACCAACAGGACTGACAATAACCAAACGTCCTGCGAGACCAGAACCACGTTGGATGTTGCGATCACAGCCACTTCAACATTTGCCTACATGCACTGCTGTGTCAACCCAATTCTTTATGCTTTTGTGGGGGTGAAATTTCGTCAGCACCTGCTAGACATGCTACGACCTCTGGGCTTCAAGCTGAAGGGCCGCGCAGGCCTGGTTTCTCGGAAGAGCTCGGGATGGTCAGAGTCGGTGGACACTTCCCACACATCTGCTTTCTGAAGCATCAAATGCCATCAGACCATTACAGTATCTTTTCCTGTAATTGTTAACAAACATTGTTGTATTATGCAAGAGGAATCAAGAACTCAGGCGTTGTCGTTCACACCAATGACAATGACTAACAAAAGGAAAAAAGTCAGAAAAAAGTATTAGAGCTAATGGCATAAGTACCCTAATTTTGATGTGTTTACCCAGCAGGAATTGGGAATGATTTTAGTTATAGAAATCACCATTGAGGGAACTAAAAAATCACCTACTTCAAAAAATCCAGGTCTAATCCAGCTCAACTGGAACTACAACTGACATTAGTGTACACAGATTGGGTAAATGGCATGTCATACAAAATACACAGTATTTTAAAGTGTTACAAGACACATACTTGGTCTCGATGATACAGTATGTACCATTTCAAGTTGTCATATTTTGTCTCTCATTCTAATTTAGTTCTTTCAGTCACATATCTTATACGAGTATGTTCCATTTCTATTATTATGACATACACAAAATTCAAATAGAGTCCTTTGTGATTAAAAAACGACCCTAATAATTACAATTAGGACAACGGTCTAAGATGAAAATGTAGTTATTAGAGACTTTATCTTTTTTTTTCGTCACACTCATGTGATCGAAGTGTTGTGAATGTTTTGTTGAGGTGTTTTTGGTTAAAATGTGTGTAATATTGATCATTTTGAAATTTTCGCTATAGAGAAAAAATGTAGACATGTTTAGATAGACGATCTATCTATTTCACTCTAAGACTCCAAACACAGCTGTCCTCTGACAACAGAGGAATAAAATCAATGGCTAAAACAATCATACAACATCGTCAACTTCTGTTTTGGAGGTTAATGTTACTTTAGTTTTAATAAACATCGTTATTATACGTGGTTTGAGCCAGTTTTTAATGTCGAGACTGTGCTGATTAATACGCAGAATGTTTTAAAACATGAATTTAGATGTTTAAGCTCTTCACATGTGGCAGCTACCATAGGTTTTCAACTGTTTAGCTTTCTCAAGCATATTGATTGCCTGCGACTTTGGACAGAGATCAAAGTTATATTACGTTAAAATAGATCACTTTCAATTACTCAACTGGATAATGATTTTGAAAAATTGTGGGAAGCTGAAGTTTATATATTTTTAATATTTACTTTTTTATATATATTTTTTACTTTTTTATATTATTCATTATGCTTTGGAGTTTTTTATGTATTGTTTAGTAATGCTTTCTTGATATTTACTGTATGATGTTCTATTTTTTCGGTATCTTTCTTTGCTGTACATACATTTTAAAAAATCTTTTACATAATAATATGAAATAGTACCGCCAGATATACATATTGGTTTTTAATATCTGTTTTTACTTTGATATATAACATTTTCATTTGTGCTTGCATTAATCTTGTATCTATGAGGTCTGTCTCATTAATGCTGTAAAACTGCAGTACAATAAAACAGAAGCAAAATGGCTAC

Protein product:

Amino acids sequence (deduced by the coding sequence)

>ENSDART00000028141 cxcr3.1-201 358aa
RISVTTQTFTITVTTMTMKAMAQELCALKTPACTLTAFLSQSFTHWQRSWGCWETAWF*LYCGRREQV*MLQTSSSST*AWQIFCCC*HCPSGL*RR*RSGSLAHHFAN*LELCSG*ISTVAFTCFPASVSTATCPSSMQSKCTPVKSPWRFTVAA**SGSSAFCSPFPIGYYLVPTRTPDVRIEQNVLIQKLYLIFGFWSIV*SIIFWVSLFQQ**WSSATLAFCCAYCSAPSACRRRGPSMSL*PWYWPSSSAGRPTTSPSWLTPYIPTGLTITKRPARPEPRWMLRSQPLQHLPTCTAVSTQFFMLLWG*NFVSTC*TCYDLWASS*RAAQAWFLGRARDGQSRWTLPTHLLSEA

Citation:
(Leiming You, et al. Nucleic Acids Res. 2015, 43: D59-D67) APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals.

May 19, 2019. Last updated

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