General information for g5884.t2
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.t2 | TSS | g5884.t2 | 12578293 | 12578293 |
| chr_2 | g5884 | g5884.t2 | isoform | g5884.t2 | 12578386 | 12584366 |
| chr_2 | g5884 | g5884.t2 | exon | g5884.t2.exon1 | 12578386 | 12578388 |
| chr_2 | g5884 | g5884.t2 | exon | g5884.t2.exon2 | 12583062 | 12583476 |
| chr_2 | g5884 | g5884.t2 | cds | g5884.t2.CDS1 | 12583124 | 12583476 |
| chr_2 | g5884 | g5884.t2 | exon | g5884.t2.exon3 | 12583546 | 12584366 |
| chr_2 | g5884 | g5884.t2 | cds | g5884.t2.CDS2 | 12583546 | 12584365 |
| chr_2 | g5884 | g5884.t2 | TTS | g5884.t2 | NA | NA |
Sequences
>g5884.t2 Gene=g5884 Length=1239
TAGATATATATTGAAAAATTAGTGACTTTTCTGCGTAATATAATTAAACAAAAAAATTAA
ACAACATGGCAAAACACGTTGCATTACGCGAAACGAAAGAATTTCGCATAACAGATCCAT
CAAAACCCGTGAGAATATTTCAAAATCCACGTGATAAAACAGCATCGGTCGATCCTATTA
CAGTTCCAGCTCTCATGAATCGTACAGTAGAAAATTATGGTAATCATCCAGCTCTCAAAT
ACAAAGATCCTGTCACAGGAAAGTGGCAGACAATTACTTATAAAGAATACAAAGAACGCG
TTGAGAAGATGGCTAAAGTTTTCATAAAACTTGGTCTCGAACGCTATGGCACTGTCGCAG
TTCTCGCATTCAATAGTGTTGAATGGTTTGTCTCTGAATTAGCGGCAATTCATGCCGGTG
GAAATATTGCTGGTGTATACACAACAAATTCTGTCGATTCAGTGTTTTATGTACTTGATA
GTTGTAAAGCAAATATTGTCGTTGTTGATGATGCTAAACAAATGGAAAAGATTCATGCAA
TTAAAGACAAATTGCCTCATTTAAAGGCCATCATTCAAACAATTTCACCTTATGCACCTT
ATGTTAAACGTGCTGATGGTTATTGGCGATGGAGTGAACTCCAAGAAATGAAGACTGATG
ATGTCGAAGAAGAATATCAGCGAAGACTCAAGAGTATAGTTGCAAACGAATGCTGTTGTT
TAGTTTATACATCAGGCACAACAGGCACACCAAAAGGTGCAATGTTATCGCACGATAATT
TTACATGGGATGCTTACAGTTTCACAGTTTATGTGGATAATTTACAAATGGGAAAGGAAG
TTATAGTTAGTTATCTTCCACTTTCACATGTTGCTGCACAGATTATTGATATTTTCATTT
CAATGACAATTGCTGCTACTGTATATTTTGCTGATAAAGATACATTAAAAGGATCACTCG
TCAAAACACTCATTGATGCACGACCAACAAATTTTTTGGGTGTTCCACGTGTTTATGAAA
AAATTCAAGAAAAAATGATGGCTATTGGATCACAGTCGGGTGCATTAAAAAGAGCAATTG
CATCATGGGCAAAAAGTGCAACATTAAAACATCATATGGAGAAAATGGCTGGTCGACCTT
CAGCATCTTTGCAATACAAATTAGCAAATAAGATTGTAATGAGCAAAGTTAAGCAAGCAC
TTGGTCTTAATCGATGCAAAAACTTTATCACTGGTGCAG
>g5884.t2 Gene=g5884 Length=391
MAKHVALRETKEFRITDPSKPVRIFQNPRDKTASVDPITVPALMNRTVENYGNHPALKYK
DPVTGKWQTITYKEYKERVEKMAKVFIKLGLERYGTVAVLAFNSVEWFVSELAAIHAGGN
IAGVYTTNSVDSVFYVLDSCKANIVVVDDAKQMEKIHAIKDKLPHLKAIIQTISPYAPYV
KRADGYWRWSELQEMKTDDVEEEYQRRLKSIVANECCCLVYTSGTTGTPKGAMLSHDNFT
WDAYSFTVYVDNLQMGKEVIVSYLPLSHVAAQIIDIFISMTIAATVYFADKDTLKGSLVK
TLIDARPTNFLGVPRVYEKIQEKMMAIGSQSGALKRAIASWAKSATLKHHMEKMAGRPSA
SLQYKLANKIVMSKVKQALGLNRCKNFITGA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5884.t2 | Gene3D | G3DSA:3.40.50.12780 | - | 33 | 362 | 1.4E-51 |
| 2 | g5884.t2 | PANTHER | PTHR43272 | LONG-CHAIN-FATTY-ACID–COA LIGASE | 9 | 391 | 1.8E-127 |
| 3 | g5884.t2 | PANTHER | PTHR43272:SF32 | LONG-CHAIN-FATTY-ACID–COA LIGASE ACSBG2 | 9 | 391 | 1.8E-127 |
| 1 | g5884.t2 | Pfam | PF00501 | AMP-binding enzyme | 46 | 338 | 8.7E-56 |
| 5 | g5884.t2 | ProSitePatterns | PS00455 | Putative AMP-binding domain signature. | 219 | 230 | - |
| 4 | g5884.t2 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 35 | 338 | 2.75E-55 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5884/g5884.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5884.t2.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.
