General information for g5884.t4
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.t4 | TSS | g5884.t4 | 12579796 | 12579796 |
| chr_2 | g5884 | g5884.t4 | isoform | g5884.t4 | 12579975 | 12585866 |
| chr_2 | g5884 | g5884.t4 | exon | g5884.t4.exon1 | 12579975 | 12579981 |
| chr_2 | g5884 | g5884.t4 | exon | g5884.t4.exon2 | 12583062 | 12583476 |
| chr_2 | g5884 | g5884.t4 | cds | g5884.t4.CDS1 | 12583124 | 12583476 |
| chr_2 | g5884 | g5884.t4 | exon | g5884.t4.exon3 | 12583546 | 12584360 |
| chr_2 | g5884 | g5884.t4 | cds | g5884.t4.CDS2 | 12583546 | 12584360 |
| chr_2 | g5884 | g5884.t4 | exon | g5884.t4.exon4 | 12584434 | 12585866 |
| chr_2 | g5884 | g5884.t4 | cds | g5884.t4.CDS3 | 12584434 | 12585239 |
| chr_2 | g5884 | g5884.t4 | TTS | g5884.t4 | 12585868 | 12585868 |
Sequences
>g5884.t4 Gene=g5884 Length=2670
TTGATTGATATATATTGAAAAATTAGTGACTTTTCTGCGTAATATAATTAAACAAAAAAA
TTAAACAACATGGCAAAACACGTTGCATTACGCGAAACGAAAGAATTTCGCATAACAGAT
CCATCAAAACCCGTGAGAATATTTCAAAATCCACGTGATAAAACAGCATCGGTCGATCCT
ATTACAGTTCCAGCTCTCATGAATCGTACAGTAGAAAATTATGGTAATCATCCAGCTCTC
AAATACAAAGATCCTGTCACAGGAAAGTGGCAGACAATTACTTATAAAGAATACAAAGAA
CGCGTTGAGAAGATGGCTAAAGTTTTCATAAAACTTGGTCTCGAACGCTATGGCACTGTC
GCAGTTCTCGCATTCAATAGTGTTGAATGGTTTGTCTCTGAATTAGCGGCAATTCATGCC
GGTGGAAATATTGCTGGTGTATACACAACAAATTCTGTCGATTCAGTGTTTTATGTACTT
GATAGTTGTAAAGCAAATATTGTCGTTGTTGATGATGCTAAACAAATGGAAAAGATTCAT
GCAATTAAAGACAAATTGCCTCATTTAAAGGCCATCATTCAAACAATTTCACCTTATGCA
CCTTATGTTAAACGTGCTGATGGTTATTGGCGATGGAGTGAACTCCAAGAAATGAAGACT
GATGATGTCGAAGAAGAATATCAGCGAAGACTCAAGAGTATAGTTGCAAACGAATGCTGT
TGTTTAGTTTATACATCAGGCACAACAGGCACACCAAAAGGTGCAATGTTATCGCACGAT
AATTTTACATGGGATGCTTACAGTTTCACAGTTTATGTGGATAATTTACAAATGGGAAAG
GAAGTTATAGTTAGTTATCTTCCACTTTCACATGTTGCTGCACAGATTATTGATATTTTC
ATTTCAATGACAATTGCTGCTACTGTATATTTTGCTGATAAAGATACATTAAAAGGATCA
CTCGTCAAAACACTCATTGATGCACGACCAACAAATTTTTTGGGTGTTCCACGTGTTTAT
GAAAAAATTCAAGAAAAAATGATGGCTATTGGATCACAGTCGGGTGCATTAAAAAGAGCA
ATTGCATCATGGGCAAAAAGTGCAACATTAAAACATCATATGGAGAAAATGGCTGGTCGA
CCTTCAGCATCTTTGCAATACAAATTAGCAAATAAGATTGTAATGAGCAAAGTTAAGCAA
GCACTTGGTCTTAATCGATGCAAAAACTTTATCACTGCTCCAATGAGCGTAGACACAAAG
AAATATTTTATGAGTTTAGATATGCCAATTGTAGAAGCATTTGGTATGAGTGAATCTACT
GGTGGACATTGTATGGGAAATGTACATGATCCAACATTTGAGTCAATTGGTAGAAATGCA
CCCGGTACACAGACAAAAATTGTGAATGCAGATGAAAAAGGACATGGAGAGATCTGCTTG
CGAGGCCGTCATGTTTTTATGGGCTATATTAATGAAATTGAAAAGACAATTGATGCTGTT
GATGATGAAGGATGGCTTCATACAGGCGATATTGGATATGTTGACAATGATGGTTATATT
TTCATCACTGGAAGACTAAAGGAAATAATCATCACAGCTGGTGGAGAAAATATTCCTCCA
GTTCACATCGAAAACCTCGTCAAGAGTGAATGTTCAGCCATTTCAAATGCAATACTTATT
GGTGATAAAAGAAAATTCCTTAGTATGTTGATTACATTGAAGACTGAAGTTGATGCAGAA
GGAGCACCAAAAAATGAACTCACACAAGAAACAATGAAATGGATTCAATCGATGGACTTG
AAATACACATCATTAAAAGAAATTCTCGCAGCAGGACCAGATCCAAAAGTTATGAATGCT
ATACAAGAAGCTATCAATAGAGCTAACAAAAACTCTATTTCAAATGCACAAAAAGTTCAA
AAGTTTGCAATTTTACCGCACGATTTCAGCATACCAACTGGAGAAATCGGACCAACAATG
AAAATTAAGCGCAGTTTCATTGCAGAAAAATATAAGGAAGTCATCGATAAATTTTATCAA
TAAGTAATCTCAAAATTTTTTACGTGTGTCCTTAATTGTGAAACATTCTATTATACTGCT
TAAGAACAATGCCAAAATTACATCACTTACACACTTTAACTGCCTCACATGATTTTTTGT
GAGTCCTTTTATGTTAATTTTTTTTCTCATTTTTCTTGGGTTTGATTTTAACTTTTTTTG
CTTATGCTCATACCTACCTATTTATAAATTATCATGAAAGGATCGATTTTTATTAAACTT
ATTCAATAAGTGTCATTGTTTTTAAATCATAAATTAATTTATATTGTATATATTTATAGT
TATAATGATATGAAGGTAATTTGAGCCATTAATTATTATATAAAGAAAAATTTAGAAAAT
TTTGCTATGCGCTCTGGGAACTGATATGGGTTAATATTTAATAAATGAGAAAATTTTGAA
TATACCTATAGCTAGAAGATAAGAGTAGTGATGAAAGCCTAAAAGTTGAATCATAAAAGA
TAGATCTAAATATTAAAGAAAATTTGTAATAATCTAGTTAATTGAAAAACTTACTTAAGA
TAATTTTTGTCATTTATCTTCTTTGTAATGAAGAAAAAATAATCTTATAAATTGATAATA
AAATAAAAATCATTGATATTGCTAATAAAA
>g5884.t4 Gene=g5884 Length=657
MAKHVALRETKEFRITDPSKPVRIFQNPRDKTASVDPITVPALMNRTVENYGNHPALKYK
DPVTGKWQTITYKEYKERVEKMAKVFIKLGLERYGTVAVLAFNSVEWFVSELAAIHAGGN
IAGVYTTNSVDSVFYVLDSCKANIVVVDDAKQMEKIHAIKDKLPHLKAIIQTISPYAPYV
KRADGYWRWSELQEMKTDDVEEEYQRRLKSIVANECCCLVYTSGTTGTPKGAMLSHDNFT
WDAYSFTVYVDNLQMGKEVIVSYLPLSHVAAQIIDIFISMTIAATVYFADKDTLKGSLVK
TLIDARPTNFLGVPRVYEKIQEKMMAIGSQSGALKRAIASWAKSATLKHHMEKMAGRPSA
SLQYKLANKIVMSKVKQALGLNRCKNFITAPMSVDTKKYFMSLDMPIVEAFGMSESTGGH
CMGNVHDPTFESIGRNAPGTQTKIVNADEKGHGEICLRGRHVFMGYINEIEKTIDAVDDE
GWLHTGDIGYVDNDGYIFITGRLKEIIITAGGENIPPVHIENLVKSECSAISNAILIGDK
RKFLSMLITLKTEVDAEGAPKNELTQETMKWIQSMDLKYTSLKEILAAGPDPKVMNAIQE
AINRANKNSISNAQKVQKFAILPHDFSIPTGEIGPTMKIKRSFIAEKYKEVIDKFYQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g5884.t4 | Gene3D | G3DSA:3.40.50.12780 | - | 34 | 359 | 5.9E-51 |
| 6 | g5884.t4 | Gene3D | G3DSA:3.40.50.12780 | - | 360 | 503 | 1.1E-29 |
| 2 | g5884.t4 | PANTHER | PTHR43272 | LONG-CHAIN-FATTY-ACID–COA LIGASE | 9 | 656 | 3.9E-242 |
| 3 | g5884.t4 | PANTHER | PTHR43272:SF32 | LONG-CHAIN-FATTY-ACID–COA LIGASE ACSBG2 | 9 | 656 | 3.9E-242 |
| 1 | g5884.t4 | Pfam | PF00501 | AMP-binding enzyme | 46 | 509 | 3.3E-90 |
| 5 | g5884.t4 | ProSitePatterns | PS00455 | Putative AMP-binding domain signature. | 219 | 230 | - |
| 4 | g5884.t4 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 35 | 656 | 1.31E-101 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5884/g5884.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5884.t4.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K15013 (long-chain-fatty-acid–CoA ligase ACSBG)
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.
