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:	ENSDARG00000090890
Gene name:	cmklr1
Chromosome:	chr5(+)
Gene locus:	chr5(+):22353901-22373896
Gene description:	chemokine-like receptor 1 [Source:ZFIN;Acc:ZDB-GENE-060526-126 ]

Transcript id:	ENSDART00000137019
Transcript name:	cmklr1-001
Transcript locus:	chr5(+):22353901-22373896

Start codon:	22372835
Stop codon:	22373894
Alternative polyA sites:	Mapped to the searched transcript (containing the 5' and 3' flanking region of 1kb).
Alternative polyA sites:	22392153, 22392336, 22392453, 22392981, 22393099, 22393240, 22393455, 22394915, 22395564, 22397061, 22397438, 22587185, 22587282, 22604862, 22605376, 22779890, 22779947, 22781734, 22885933, 22886053, 22888748, 22965536, 22971859, 22973139, 22973533, 22973643, 22973749, 22973939, 22974191, 22974276, 22974334, 22980726, 22981989, 22982267, 22991805, 22992092, 22997201, 22997429, 23002012, 23013492, 23013614, 23019732, 23062133, 23133333, 23143201, 23502829, 23518992, 23525382, 23525407, 23525542, 23528310, 23529045, 23803199, 23820638, 23820924, 23821275, 23821801, 23822439, 23822571, 23823122, 23922571, 23922764, 23933219, 23935246, 23936268, 23990983, 24129092, 24130814, 24131056, 24234533, 24288637, 24333755, 24541868, 24541963, 24543030, 24543115, 24759619, 24786975, 24833416, 24857788, 24858030, 25056402, 25059485, 25059547, 25059701, 25059741, 25059813, 25430989, 25431351, 25432717, 25432945, 25524215, 25527227, 25537431, 25554135, 25554491, 25554602, 25554640, 25554707, 25554753, 25554837, 25554900, 25555067, 25555522, 25555589, 25555622, 25556036, 25556591, 25557263, 25557478, 25558440, 25558592, 25558750, 25559179, 25627909, 25638318, 25638421, 25638575, 25638772, 25639359, 25640135, 25644637, 25671768, 25671841, 25730376, 25730812, 25730948, 25735645, 25736076, 25736741, 25736949, 25763948, 25764029, 25764202, 25764693, 25764860, 25765027, 25765327, 25766978, 25776205, 25776355, 25777914, 25778363, 25796110, 25796237, 25796304, 25796440, 25796564, 25796888, 25797002, 25797286, 25797532, 25797627, 25797749, 25797883, 25798232, 25798373, 25798412, 25798832, 25857624, 25958938, 26002291, 26045191, 26048671, 26048767, 26048806, 26048899, 26074684, 26075213, 26103698, 26103934, 26114651, 26114711, 26114762, 26115049, 26115785, 26115846, 26131955, 26140926, 26140972, 26141042, 26141423, 26141580, 26141730, 26141851, 26141939, 26143414, 26143576, 26143732, 26154917, 26155125, 26155187, 26155268, 26158679, 26162254, 26164076, 26167541, 26187823, 26187917, 26200936, 26202306, 26202394, 26202607, 26202750, 26202886, 26203874, 26212501, 26212783, 26212885, 26213006, 26213728, 26216411, 26219010, 26219087, 26219495, 26219646, 26219810, 26230388, 26230448, 26230500, 26230758, 26230802, 26233379, 26233532, 26348242, 26448647, 26764135, 26885874, 26886040, 26888448, 26923640, 26932000, 26934570, 26934737, 26934869, 26935180, 26936333, 26962906, 26963272, 26972438, 26972612, 26973027, 26980697, 26981107, 26981208, 26981332, 26981428, 26981618, 27027700, 27115424, 27124936, 27137622, 27137971
polyA signals:	AATAAA, AATAAA, ACTAAA, AATAGA, none, none, AATAAA, AATAAA, none, AATAAA, CATAAA, none, none, ATTAAA, AATAAA, AATAAA, AATAAA, AATAAA, AATAAA, AATAAA, ATTAAA, AATAAA, ATTAAA, AATAAA, AATGAA, ACTAAA, ATTAAA, ATTAAA, AATAAA, AATAAA, ATTAAA, none, AGTAAA, AATAAA, TATAAA, multi, none, AATAAA, AATAAA, AATAAA, ATTAAA, AAGAAA, multi, AATAAA, AATAAA, AATAAA, none, none, none, AATAAA, AATACA, AATAAA, AATAAA, none, TATAAA, AATAAA, none, none, AATAAA, TATAAA, AATGAA, AATAAA, AATAAA, ATTAAA, AATAAA, AATAAA, none, AATAAA, ATTAAA, AATAAA, AATAAA, AATAAA, CATAAA, multi, TATAAA, ATTAAA, AATAAA, AATAAA, none, AATAAA, AATAAA, AATAAA, ATTAAA, none, AATAAA, AATGAA, none, AATAAA, ATTAAA, AATAAA, none, ATTAAA, AATAAA, AATAAA, none, AGTAAA, none, none, none, none, none, multi, AGTAAA, ACTAAA, none, none, GATAAA, GATAAA, TATAAA, none, multi, AATAAA, none, none, ATTAAA, AATAAA, none, AATAAA, none, AATAAA, AATAAA, AATAAA, none, multi, AATAAA, AATATA, GATAAA, AATACA, GATAAA, none, ATTAAA, none, ACTAAA, ATTAAA, AATAAA, none, TATAAA, AATACA, AATAAA, none, none, none, none, AGTAAA, AATGAA, AATAAA, AATGAA, AATATA, AATAAA, ATTAAA, TATAAA, none, ACTAAA, ATTAAA, AGTAAA, AATAAA, AATAAA, AGTAAA, AATAAA, AATAAA, AATAAA, AATAAA, AATAAA, ATTAAA, none, none, AATAAA, AATAAA, AATAAA, AATAGA, AATAAA, multi, multi, ATTAAA, AATAAA, none, AATAAA, none, ATTAAA, AATAGA, ATTAAA, AATACA, none, AGTAAA, multi, AGTAAA, TATAAA, CATAAA, AATATA, ATTAAA, AATACA, none, multi, AATAAA, AATAAA, TATAAA, none, AATAAA, AATAAA, none, none, GATAAA, AATAAA, multi, multi, AATAAA, none, ATTAAA, AATACA, multi, AATAAA, AATAAA, none, none, none, multi, ATTAAA, AATAAA, AATAAA, AATATA, AATACA, AATAAA, AATAAA, AATAAA, AATAAA, multi, TATAAA, AATAAA, AATAAA, TATAAA, none, none, ATTAAA, AAGAAA, none, multi, AATAAA, ATTAAA, AATAAA, TATAAA, multi, CATAAA, AATAAA, multi, ATTAAA, AATAAA, AGTAAA, AATAAA, ATTAAA, none, none, TATAAA, AATAAA

Notes:

mRNA/CDS:

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

>ENSDART00000137019 1157bp
TGGCTTGAGCTGTTGCTTGCTGAACATTCCGGCAAACAAGCTGTTAGATGTTATGGATCAGTGGACGGGTAAGAG/GAAATTGAAATAAAATCACAATGGATTTACTAGACTTAACATATGATTACGAAGACTATGGAAATGTCACCGACTATGGAAATTTCACCTTTGGCAATGTAACACATGAAGAAACTTATTACCACCACACAGCCCAAAACATGTGCTTCACTCAGGTCCTCTGCGTGCTGTTGCTGGTGATCAACATGCTCATCTGTCTGCTGGGTCTTAGTGGAAACGGCGTGGTCATCTGGATCGCAGGGTTTGCCATGAAGAAGTCAGTCAACACCACCTGGTACCTGAGTCTGGCTGTGTCTGACTTCATATTTTGCGCCTTTTTGCCTTTTAACATTGCCTACAGTGCCACATCCAACTGGATCTTCGGCCTCTTCATGTGCAAGTTCACTTCGTTCGTCATGTTCCTCAACATGTTCAGCAGCATCTTCATCCTGGTCATCATCAGCGTGGACCGTTGCGTCGCCGTCATGTTCCCCGTTTGGGCACAAAATCACCGCACCATTGGAAAAGCATCGGTGTTGATCATACTTGCCTGGATCGCCTCCGCAGCTTTAAGCATCCCATCAATTGTGTACCGTGACGTCCAGAATTATCTGGGCACAAACGATTGCATGAACAACTACACGTCCAGCAGGTACGGCCATAAAGTCATTGCTGTGAGCCGCTTTATTTTTGGCTTTATAATTCCATTCATCCTCATCATCCTTTGCTACACGGTCATTATCGTCAGGCTGAGAGCTTCCAAAATGGCCAAATCCAACAAGCCATTTAAGATCATGACAGCTCTCATCCTGACCTTCTTCCTTTGCTGGTTGCCGTACCATACATTTGTGCTGATCGAATTTAACCAGACCTTTGAGAATGGCATCATTCGTCTTGGGATGCAAATAGGCACCATCACTGCTGCCGCAAACAGCTTCCTGAACCCTGTGTTGTACGTGTTCATGGGCAATGACTTCAGAAAGAGGTTCAAGAGTTCCATCTTATCCAAGATTGAGAATGCTATTGGAGAAGAAGGACGAACCATCAGTCGCTATCTGTCCCGCTCCAGCTCGGTGGACGCCAGGGCTTCCACTCATATCTGA

Protein product:

Amino acids sequence (deduced by the coding sequence)

>ENSDART00000137019 cmklr1-001 354aa
MDLLDLTYDYEDYGNVTDYGNFTFGNVTHEETYYHHTAQNMCFTQVLCVLLLVINMLICLLGLSGNGVVIWIAGFAMKKSVNTTWYLSLAVSDFIFCAFLPFNIAYSATSNWIFGLFMCKFTSFVMFLNMFSSIFILVIISVDRCVAVMFPVWAQNHRTIGKASVLIILAWIASAALSIPSIVYRDVQNYLGTNDCMNNYTSSRYGHKVIAVSRFIFGFIIPFILIILCYTVIIVRLRASKMAKSNKPFKIMTALILTFFLCWLPYHTFVLIEFNQTFENGIIRLGMQIGTITAAANSFLNPVLYVFMGNDFRKRFKSSILSKIENAIGEEGRTISRYLSRSSSVDARASTHI*

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.

Jan 11, 2021. Last updated

Copyright© Laboratory of Molecular Medicine, Sun Yat-Sen University, High Education Mega Center, Guangzhou 510006 China.