Gene loci information

Transcript annotation

  • This transcript has been annotated as Very long-chain-fatty-acid–CoA ligase bubblegum.

Parent gene

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_1 g9356 g9356.t2 isoform g9356.t2 2207909 2209636
chr_1 g9356 g9356.t2 exon g9356.t2.exon1 2207909 2209636
chr_1 g9356 g9356.t2 cds g9356.t2.CDS1 2209032 2209625
chr_1 g9356 g9356.t2 TSS g9356.t2 NA NA
chr_1 g9356 g9356.t2 TTS g9356.t2 NA NA

Sequences

>g9356.t2 Gene=g9356 Length=1728
GTCGTGGTAGAATGACATTTATGGGATATTTGAATGATATTGAGAAGACAATGGAAGTTA
TTGATAAAGATTTTTGGTTTAATACTGGCGATGTTGGATATTTTGATGATGAAGGATTTT
TATTTATAACTGGAAGAACTAAAGAGCTGATAGTATCATCAGGTGGTGAAAATATTCCTT
ATCTTTTGATTGAAAACACTGTGAAAAATGAATGTGAAGCAATTTCAAATGCTTTCTTAG
TTGGTGACAAAAGAAAATTTCTCACAATGTTGATAACTTTGAAAACAAAAATGGACCAAA
ATGGTGCACCGATTGATGAACTTGCTGATGAAAGTTTGAGTTTAATGAATGATTTAGGCT
TGAATTATGTTTCATTGAGTGAAATTCTCAATGCTGGACCTGATAAGAAAGTTTTAGCTG
CAATTCAATCAGCAATCGATCGTGCAAATGAAAAAGCAATTTCAAGAGCTCAGAAAGTTC
AGAAATTTGCAATTTTACCAAATGATTTTAGTTTATCAACTGGAGAATTGAGTTCAACAT
TGAAACTGAAAAGACATTTTGTGCTTGAAAAATATAAGAATATTATTGATGAATTTTATT
TGTGAAAATTGGCTGTGTTTAATTAAAAAGGAATAAAATAAAATTATCAGAACCGTCTTT
AAAACAGATTTTATAAATTTGAAAATATTGAAAAAAATAAATTTGTTGCGTGTGACAAAA
AAATGTTAAGCGACAAAAAGATTTGTCATATGTAAATAAATTAAAATTATCGATTGATAT
TTTTCAAGATAGCCAGCAAAAGCCTGTATAAATAATGAAGATAAAATTCTGTTCTGTTCT
CAGCAAAATGAATCGAACAAATGACGGAAATTGCACAGCAAAAAATGTTGAAAGCACTTA
AAATTGAATTGCATCAATAATTAAAACACATAAAAAATATTTTCAGACATCAGCGGCTGA
AAATTTTTCTTCTTGATTGTTCACAGACAATTTTTTATGTTGTGATCATCAAAAATGAGT
TTTTTGTGCTTATAATTAAAATGTCAGGGGAGCTAGTGTAGGAAAGTTTTGTGTTGCAAT
GAAAAATCATGAAAAGTTTCAGTTTTTGAAGTTTTAAAGAATTTTAAAATTTAACGGTTA
TTTTAAATTTAAATATATTTTTTATGTTTATAAATTTTATAAAAAATTCTTTTTAAATAA
ATTTTCGTAAAATAAACATAGGATAGAAAAATTTTGAGCAGAAATACAAAAAATTGTCCA
CAAAAGATAAAATTGTCAAAAAATTGAAAATTTTTTTGAAATAATTTTAAGTTTTTCATT
CTTAATTGAAGTTTTTTCTAAATTTTTTAAATAAAATGAATGTAGAAAATTCTACGTGAT
AAAATGATGATGATCATTTTAAAATTTTATTGCTGTCGCAATTTTCAAAAACAAAACTTT
TTTACACAACAAGACACGAGTTAAGCTCTTTGAAAGTTTTTGCTTTTGCAATTTTTCTCT
TCATATCTAGTCTCGCTAAATGGCTACAAAAAAAAACTTAGATTGGATTTTCATGAAGTT
TTACAATTTTACTTATGTCTCAGTCATATCCATTAGAAGTGAGTGTGAGTAGCAACACAG
TAATGGCTTTAAGTTGATGACTTTCTTTTTACTAAATCCACATGTATTGTTTCCATCGTT
TTATGTCAATAAAAAATAAGAGCGAGGTTGAGAAACTTGTTGAAATGA

>g9356.t2 Gene=g9356 Length=197
MTFMGYLNDIEKTMEVIDKDFWFNTGDVGYFDDEGFLFITGRTKELIVSSGGENIPYLLI
ENTVKNECEAISNAFLVGDKRKFLTMLITLKTKMDQNGAPIDELADESLSLMNDLGLNYV
SLSEILNAGPDKKVLAAIQSAIDRANEKAISRAQKVQKFAILPNDFSLSTGELSSTLKLK
RHFVLEKYKNIIDEFYL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g9356.t2 Gene3D G3DSA:3.40.50.12780 - 1 45 0
2 g9356.t2 PANTHER PTHR43272 LONG-CHAIN-FATTY-ACID–COA LIGASE 3 196 0
3 g9356.t2 PANTHER PTHR43272:SF32 LONG-CHAIN-FATTY-ACID–COA LIGASE ACSBG2 3 196 0
1 g9356.t2 Pfam PF00501 AMP-binding enzyme 2 49 0
4 g9356.t2 SUPERFAMILY SSF56801 Acetyl-CoA synthetase-like 2 196 0

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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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. There were no conditions that were differentially expressed