General information for g5884.t10
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.t10 | isoform | g5884.t10 | 12583568 | 12585866 |
| chr_2 | g5884 | g5884.t10 | exon | g5884.t10.exon1 | 12583568 | 12584366 |
| chr_2 | g5884 | g5884.t10 | cds | g5884.t10.CDS1 | 12583649 | 12584366 |
| chr_2 | g5884 | g5884.t10 | exon | g5884.t10.exon2 | 12584434 | 12585866 |
| chr_2 | g5884 | g5884.t10 | cds | g5884.t10.CDS2 | 12584434 | 12585239 |
| chr_2 | g5884 | g5884.t10 | TTS | g5884.t10 | 12585868 | 12585868 |
| chr_2 | g5884 | g5884.t10 | TSS | g5884.t10 | NA | NA |
Sequences
>g5884.t10 Gene=g5884 Length=2232
ACAACAAATTCTGTCGATTCAGTGTTTTATGTACTTGATAGTTGTAAAGCAAATATTGTC
GTTGTTGATGATGCTAAACAAATGGAAAAGATTCATGCAATTAAAGACAAATTGCCTCAT
TTAAAGGCCATCATTCAAACAATTTCACCTTATGCACCTTATGTTAAACGTGCTGATGGT
TATTGGCGATGGAGTGAACTCCAAGAAATGAAGACTGATGATGTCGAAGAAGAATATCAG
CGAAGACTCAAGAGTATAGTTGCAAACGAATGCTGTTGTTTAGTTTATACATCAGGCACA
ACAGGCACACCAAAAGGTGCAATGTTATCGCACGATAATTTTACATGGGATGCTTACAGT
TTCACAGTTTATGTGGATAATTTACAAATGGGAAAGGAAGTTATAGTTAGTTATCTTCCA
CTTTCACATGTTGCTGCACAGATTATTGATATTTTCATTTCAATGACAATTGCTGCTACT
GTATATTTTGCTGATAAAGATACATTAAAAGGATCACTCGTCAAAACACTCATTGATGCA
CGACCAACAAATTTTTTGGGTGTTCCACGTGTTTATGAAAAAATTCAAGAAAAAATGATG
GCTATTGGATCACAGTCGGGTGCATTAAAAAGAGCAATTGCATCATGGGCAAAAAGTGCA
ACATTAAAACATCATATGGAGAAAATGGCTGGTCGACCTTCAGCATCTTTGCAATACAAA
TTAGCAAATAAGATTGTAATGAGCAAAGTTAAGCAAGCACTTGGTCTTAATCGATGCAAA
AACTTTATCACTGGTGCAGCTCCAATGAGCGTAGACACAAAGAAATATTTTATGAGTTTA
GATATGCCAATTGTAGAAGCATTTGGTATGAGTGAATCTACTGGTGGACATTGTATGGGA
AATGTACATGATCCAACATTTGAGTCAATTGGTAGAAATGCACCCGGTACACAGACAAAA
ATTGTGAATGCAGATGAAAAAGGACATGGAGAGATCTGCTTGCGAGGCCGTCATGTTTTT
ATGGGCTATATTAATGAAATTGAAAAGACAATTGATGCTGTTGATGATGAAGGATGGCTT
CATACAGGCGATATTGGATATGTTGACAATGATGGTTATATTTTCATCACTGGAAGACTA
AAGGAAATAATCATCACAGCTGGTGGAGAAAATATTCCTCCAGTTCACATCGAAAACCTC
GTCAAGAGTGAATGTTCAGCCATTTCAAATGCAATACTTATTGGTGATAAAAGAAAATTC
CTTAGTATGTTGATTACATTGAAGACTGAAGTTGATGCAGAAGGAGCACCAAAAAATGAA
CTCACACAAGAAACAATGAAATGGATTCAATCGATGGACTTGAAATACACATCATTAAAA
GAAATTCTCGCAGCAGGACCAGATCCAAAAGTTATGAATGCTATACAAGAAGCTATCAAT
AGAGCTAACAAAAACTCTATTTCAAATGCACAAAAAGTTCAAAAGTTTGCAATTTTACCG
CACGATTTCAGCATACCAACTGGAGAAATCGGACCAACAATGAAAATTAAGCGCAGTTTC
ATTGCAGAAAAATATAAGGAAGTCATCGATAAATTTTATCAATAAGTAATCTCAAAATTT
TTTACGTGTGTCCTTAATTGTGAAACATTCTATTATACTGCTTAAGAACAATGCCAAAAT
TACATCACTTACACACTTTAACTGCCTCACATGATTTTTTGTGAGTCCTTTTATGTTAAT
TTTTTTTCTCATTTTTCTTGGGTTTGATTTTAACTTTTTTTGCTTATGCTCATACCTACC
TATTTATAAATTATCATGAAAGGATCGATTTTTATTAAACTTATTCAATAAGTGTCATTG
TTTTTAAATCATAAATTAATTTATATTGTATATATTTATAGTTATAATGATATGAAGGTA
ATTTGAGCCATTAATTATTATATAAAGAAAAATTTAGAAAATTTTGCTATGCGCTCTGGG
AACTGATATGGGTTAATATTTAATAAATGAGAAAATTTTGAATATACCTATAGCTAGAAG
ATAAGAGTAGTGATGAAAGCCTAAAAGTTGAATCATAAAAGATAGATCTAAATATTAAAG
AAAATTTGTAATAATCTAGTTAATTGAAAAACTTACTTAAGATAATTTTTGTCATTTATC
TTCTTTGTAATGAAGAAAAAATAATCTTATAAATTGATAATAAAATAAAAATCATTGATA
TTGCTAATAAAA
>g5884.t10 Gene=g5884 Length=507
MEKIHAIKDKLPHLKAIIQTISPYAPYVKRADGYWRWSELQEMKTDDVEEEYQRRLKSIV
ANECCCLVYTSGTTGTPKGAMLSHDNFTWDAYSFTVYVDNLQMGKEVIVSYLPLSHVAAQ
IIDIFISMTIAATVYFADKDTLKGSLVKTLIDARPTNFLGVPRVYEKIQEKMMAIGSQSG
ALKRAIASWAKSATLKHHMEKMAGRPSASLQYKLANKIVMSKVKQALGLNRCKNFITGAA
PMSVDTKKYFMSLDMPIVEAFGMSESTGGHCMGNVHDPTFESIGRNAPGTQTKIVNADEK
GHGEICLRGRHVFMGYINEIEKTIDAVDDEGWLHTGDIGYVDNDGYIFITGRLKEIIITA
GGENIPPVHIENLVKSECSAISNAILIGDKRKFLSMLITLKTEVDAEGAPKNELTQETMK
WIQSMDLKYTSLKEILAAGPDPKVMNAIQEAINRANKNSISNAQKVQKFAILPHDFSIPT
GEIGPTMKIKRSFIAEKYKEVIDKFYQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5884.t10 | Gene3D | G3DSA:3.40.50.12780 | - | 1 | 206 | 1.6E-25 |
| 7 | g5884.t10 | Gene3D | G3DSA:3.40.50.12780 | - | 209 | 352 | 5.5E-35 |
| 2 | g5884.t10 | PANTHER | PTHR43272 | LONG-CHAIN-FATTY-ACID–COA LIGASE | 2 | 506 | 2.1E-199 |
| 3 | g5884.t10 | PANTHER | PTHR43272:SF32 | LONG-CHAIN-FATTY-ACID–COA LIGASE ACSBG2 | 2 | 506 | 2.1E-199 |
| 1 | g5884.t10 | Pfam | PF00501 | AMP-binding enzyme | 41 | 359 | 7.3E-66 |
| 5 | g5884.t10 | ProSitePatterns | PS00455 | Putative AMP-binding domain signature. | 67 | 78 | - |
| 4 | g5884.t10 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 3 | 506 | 8.77E-76 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5884/g5884.t10; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5884.t10.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.
