General information for g5884.t11
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 g5884 is located on chr_2: 12584453..12586568 (+ 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_2 | g5884 | g5884.t11 | isoform | g5884.t11 | 12584453 | 12585866 |
| chr_2 | g5884 | g5884.t11 | exon | g5884.t11.exon1 | 12584453 | 12585866 |
| chr_2 | g5884 | g5884.t11 | cds | g5884.t11.CDS1 | 12584466 | 12585239 |
| chr_2 | g5884 | g5884.t11 | TTS | g5884.t11 | 12585868 | 12585868 |
| chr_2 | g5884 | g5884.t11 | TSS | g5884.t11 | NA | NA |
Sequences
>g5884.t11 Gene=g5884 Length=1414
AAAGAAATATTTTATGAGTTTAGATATGCCAATTGTAGAAGCATTTGGTATGAGTGAATC
TACTGGTGGACATTGTATGGGAAATGTACATGATCCAACATTTGAGTCAATTGGTAGAAA
TGCACCCGGTACACAGACAAAAATTGTGAATGCAGATGAAAAAGGACATGGAGAGATCTG
CTTGCGAGGCCGTCATGTTTTTATGGGCTATATTAATGAAATTGAAAAGACAATTGATGC
TGTTGATGATGAAGGATGGCTTCATACAGGCGATATTGGATATGTTGACAATGATGGTTA
TATTTTCATCACTGGAAGACTAAAGGAAATAATCATCACAGCTGGTGGAGAAAATATTCC
TCCAGTTCACATCGAAAACCTCGTCAAGAGTGAATGTTCAGCCATTTCAAATGCAATACT
TATTGGTGATAAAAGAAAATTCCTTAGTATGTTGATTACATTGAAGACTGAAGTTGATGC
AGAAGGAGCACCAAAAAATGAACTCACACAAGAAACAATGAAATGGATTCAATCGATGGA
CTTGAAATACACATCATTAAAAGAAATTCTCGCAGCAGGACCAGATCCAAAAGTTATGAA
TGCTATACAAGAAGCTATCAATAGAGCTAACAAAAACTCTATTTCAAATGCACAAAAAGT
TCAAAAGTTTGCAATTTTACCGCACGATTTCAGCATACCAACTGGAGAAATCGGACCAAC
AATGAAAATTAAGCGCAGTTTCATTGCAGAAAAATATAAGGAAGTCATCGATAAATTTTA
TCAATAAGTAATCTCAAAATTTTTTACGTGTGTCCTTAATTGTGAAACATTCTATTATAC
TGCTTAAGAACAATGCCAAAATTACATCACTTACACACTTTAACTGCCTCACATGATTTT
TTGTGAGTCCTTTTATGTTAATTTTTTTTCTCATTTTTCTTGGGTTTGATTTTAACTTTT
TTTGCTTATGCTCATACCTACCTATTTATAAATTATCATGAAAGGATCGATTTTTATTAA
ACTTATTCAATAAGTGTCATTGTTTTTAAATCATAAATTAATTTATATTGTATATATTTA
TAGTTATAATGATATGAAGGTAATTTGAGCCATTAATTATTATATAAAGAAAAATTTAGA
AAATTTTGCTATGCGCTCTGGGAACTGATATGGGTTAATATTTAATAAATGAGAAAATTT
TGAATATACCTATAGCTAGAAGATAAGAGTAGTGATGAAAGCCTAAAAGTTGAATCATAA
AAGATAGATCTAAATATTAAAGAAAATTTGTAATAATCTAGTTAATTGAAAAACTTACTT
AAGATAATTTTTGTCATTTATCTTCTTTGTAATGAAGAAAAAATAATCTTATAAATTGAT
AATAAAATAAAAATCATTGATATTGCTAATAAAA
>g5884.t11 Gene=g5884 Length=257
MSLDMPIVEAFGMSESTGGHCMGNVHDPTFESIGRNAPGTQTKIVNADEKGHGEICLRGR
HVFMGYINEIEKTIDAVDDEGWLHTGDIGYVDNDGYIFITGRLKEIIITAGGENIPPVHI
ENLVKSECSAISNAILIGDKRKFLSMLITLKTEVDAEGAPKNELTQETMKWIQSMDLKYT
SLKEILAAGPDPKVMNAIQEAINRANKNSISNAQKVQKFAILPHDFSIPTGEIGPTMKIK
RSFIAEKYKEVIDKFYQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g5884.t11 | Gene3D | G3DSA:3.40.50.12780 | - | 1 | 102 | 0 |
| 2 | g5884.t11 | PANTHER | PTHR43272 | LONG-CHAIN-FATTY-ACID–COA LIGASE | 2 | 256 | 0 |
| 3 | g5884.t11 | PANTHER | PTHR43272:SF32 | LONG-CHAIN-FATTY-ACID–COA LIGASE ACSBG2 | 2 | 256 | 0 |
| 1 | g5884.t11 | Pfam | PF00501 | AMP-binding enzyme | 6 | 109 | 0 |
| 4 | g5884.t11 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 4 | 256 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5884/g5884.t11; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5884.t11.fa.iupred3.txt does not exist
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.
