General information for g17529.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Very long-chain-fatty-acid–CoA ligase bubblegum.
Parent gene
- The parent gene g17529 is located on chr_4: 13790011..13792041 (- strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_4 | g17529 | g17529.t1 | isoform | g17529.t1 | 13790011 | 13792041 |
| chr_4 | g17529 | g17529.t1 | exon | g17529.t1.exon1 | 13790011 | 13791305 |
| chr_4 | g17529 | g17529.t1 | cds | g17529.t1.CDS1 | 13790011 | 13791305 |
| chr_4 | g17529 | g17529.t1 | exon | g17529.t1.exon2 | 13791363 | 13791682 |
| chr_4 | g17529 | g17529.t1 | cds | g17529.t1.CDS2 | 13791363 | 13791682 |
| chr_4 | g17529 | g17529.t1 | exon | g17529.t1.exon3 | 13791737 | 13792041 |
| chr_4 | g17529 | g17529.t1 | cds | g17529.t1.CDS3 | 13791737 | 13792041 |
| chr_4 | g17529 | g17529.t1 | TSS | g17529.t1 | 13792086 | 13792086 |
| chr_4 | g17529 | g17529.t1 | TTS | g17529.t1 | NA | NA |
Sequences
>g17529.t1 Gene=g17529 Length=1920
ATGAAGTGCATTAGAACAACAAAATTGAATAAAAAAGTTGACATTATTCGACATAAAGAT
GATTTTGAACCAATAACTGTTATTGACTTTTTCAAAGAAACTGTAGAAAAATTTCCCAAC
ACAAATGCTCTTGTAAATTTCAGTGAAAATAAACATTTTATCTCTTATCAAATTTATCAA
ACTTATGTTGAGAAGATCGCTAAAATTTTTATTAAATTAGGACTTGAGAGACATGGAGTT
GTTGCTATTTTAGCTTGGAATTCTTCTGAGTGGGTCATATCAGCGTTAGGTGCTATTCAT
AGTGGTGGAATTGTGACTGGAATTTATACAACAAACAGCTCAGAAGCTTGTCAATATATT
CTTGAATCATCAAAAGCTCAAATTTTGATAGTTGAAGATTCAAAACAATTACAAAAGATC
AATGAAATCAAGACAGATTTGCCGTTTTTAAAGTACATCATTCAAATTAAAAATTCAAAT
TATTTAAACCCTGAAAACCTCATTCTTGATTGGAATGAATTATTGCAAATTGACACAAGT
GATGTTGAAGAAGAATATGAAAAAAGATTGAAAGAAATTACACCAAATGAGTGTTGTGCT
TTAATTTATACTTCTGGTACATCAGGTTTTCCAAAAGCTGCAATGCTCTCACATGATAAT
TTAATTTGGAATGCAAAAAAGGGCGTTGAAACGATGAAGGTTGCTGAAATAGGAAATGAA
AATTTAATGTCTTATCTTCCGCTTTCACATTTAGCTGCATTTATGTCTGATATTTTCATT
GCTATTCAATGTGCTGCAACTGTTCATTTTATTGATTTAAAAACTTTAAAAACTTCGCTT
GTTGAAGCTCTTAAAGAAATTCAACCAACAGTTTTTATTGGTGTGCCTCGAGTTTATGAG
AAAATTGAAGAGAAAATTAATGAAAAATTGCAAGAACAAAATTTTCTTAAAAAAAAACTT
TTTTTTTGGTGTCAAAATTTTATGTTAAATTCTTATTTCAATCCTGAAAATTCAACATCA
TCCATAAAGTATAAACTTGCTCAATTTATCATAACACAAGTCAAAGAAGCTCTAGGATTT
CAACATTGTAAAATTTTCATCACTGGAAGTGCACCAATGAGTGAAACAACGAAGAAATTT
TTTATTTCTTTAAATATGGCAATATATGAAGCTTATGGAATGACTGAATCATCAACTGTT
CATACATTAACATCACATGAAATTCAAATTTATTCATTAAATACTGTCGGAAGAAGTTTA
CAATTTGCGGAAACAAAAATTATTAAAAATAAAAGTGATGAAGAAGGAGAAATTTGCATA
AAAGGGCGTCATGTGTTTATGGGCTATTTGAATAACATTGAAAAAACTTTTGAAACTATT
GATACTGATGGATGGCTTCATACTGGTGATATTGGAAATATTGAAAATGATTTACTTTAT
GTGACAGGAAGATTAAAAGAAATTTTAATAACAAGTGGTGGTGAAAATATTCCTGCAGTT
CGTATTGAAAATCTTGTTAAAAATGAATGCAATGCAATTTCGAATGCAGTTTTAATTGGC
GATAAAAGAAAATTTCTTTCAATTTTATTAACTTTGAAAACTGAAATTGATAAAGAAGAA
ATTCCTTCTGATGAATTAAGCAGTGAAACTTGCAAATGGTTGAAATTGAATGATCTAAAT
TTTACTAAAATGAGTCAAGTTTATAAAGCAAGAAATGACCAAAAATTAATTGATGCTTTT
CAAAATGTAATTGATCGTGTTAATGAAAAAGCAATTGCAAATCCACAAAAAATTCAAAAA
TTTGCTATTTTGCCTCAAGATTTTAGCATTGCAAGTGATGAATTGACACCAACTATGAAA
GTTAAAAGATTTTTTGTTGTAGAAAAATACAAAGATGTTATTGAGAAATTTTATGAATAA
>g17529.t1 Gene=g17529 Length=639
MKCIRTTKLNKKVDIIRHKDDFEPITVIDFFKETVEKFPNTNALVNFSENKHFISYQIYQ
TYVEKIAKIFIKLGLERHGVVAILAWNSSEWVISALGAIHSGGIVTGIYTTNSSEACQYI
LESSKAQILIVEDSKQLQKINEIKTDLPFLKYIIQIKNSNYLNPENLILDWNELLQIDTS
DVEEEYEKRLKEITPNECCALIYTSGTSGFPKAAMLSHDNLIWNAKKGVETMKVAEIGNE
NLMSYLPLSHLAAFMSDIFIAIQCAATVHFIDLKTLKTSLVEALKEIQPTVFIGVPRVYE
KIEEKINEKLQEQNFLKKKLFFWCQNFMLNSYFNPENSTSSIKYKLAQFIITQVKEALGF
QHCKIFITGSAPMSETTKKFFISLNMAIYEAYGMTESSTVHTLTSHEIQIYSLNTVGRSL
QFAETKIIKNKSDEEGEICIKGRHVFMGYLNNIEKTFETIDTDGWLHTGDIGNIENDLLY
VTGRLKEILITSGGENIPAVRIENLVKNECNAISNAVLIGDKRKFLSILLTLKTEIDKEE
IPSDELSSETCKWLKLNDLNFTKMSQVYKARNDQKLIDAFQNVIDRVNEKAIANPQKIQK
FAILPQDFSIASDELTPTMKVKRFFVVEKYKDVIEKFYE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g17529.t1 | Coils | Coil | Coil | 299 | 319 | - |
| 7 | g17529.t1 | Gene3D | G3DSA:3.40.50.12780 | - | 19 | 322 | 5.9E-52 |
| 6 | g17529.t1 | Gene3D | G3DSA:3.40.50.12780 | - | 338 | 487 | 4.7E-32 |
| 2 | g17529.t1 | PANTHER | PTHR43272 | LONG-CHAIN-FATTY-ACID–COA LIGASE | 19 | 638 | 1.8E-216 |
| 3 | g17529.t1 | PANTHER | PTHR43272:SF32 | LONG-CHAIN-FATTY-ACID–COA LIGASE ACSBG2 | 19 | 638 | 1.8E-216 |
| 1 | g17529.t1 | Pfam | PF00501 | AMP-binding enzyme | 31 | 491 | 3.1E-87 |
| 5 | g17529.t1 | ProSitePatterns | PS00455 | Putative AMP-binding domain signature. | 201 | 212 | - |
| 4 | g17529.t1 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 15 | 638 | 3.27E-94 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K01897 (long-chain acyl-CoA synthetase)
Pathway
- This transcript belongs to the following pathways
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.
