General information for g5144.t3
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 g5144 is located on chr_2: 7276993..7279664 (- 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 | g5144 | g5144.t3 | TTS | g5144.t3 | 7274932 | 7274932 |
| chr_2 | g5144 | g5144.t3 | isoform | g5144.t3 | 7275198 | 7276732 |
| chr_2 | g5144 | g5144.t3 | exon | g5144.t3.exon1 | 7275198 | 7275348 |
| chr_2 | g5144 | g5144.t3 | cds | g5144.t3.CDS1 | 7275198 | 7275348 |
| chr_2 | g5144 | g5144.t3 | exon | g5144.t3.exon2 | 7275405 | 7275693 |
| chr_2 | g5144 | g5144.t3 | cds | g5144.t3.CDS2 | 7275405 | 7275693 |
| chr_2 | g5144 | g5144.t3 | exon | g5144.t3.exon3 | 7275762 | 7275980 |
| chr_2 | g5144 | g5144.t3 | cds | g5144.t3.CDS3 | 7275762 | 7275980 |
| chr_2 | g5144 | g5144.t3 | exon | g5144.t3.exon4 | 7276044 | 7276190 |
| chr_2 | g5144 | g5144.t3 | cds | g5144.t3.CDS4 | 7276044 | 7276190 |
| chr_2 | g5144 | g5144.t3 | exon | g5144.t3.exon5 | 7276246 | 7276732 |
| chr_2 | g5144 | g5144.t3 | cds | g5144.t3.CDS5 | 7276246 | 7276723 |
| chr_2 | g5144 | g5144.t3 | TSS | g5144.t3 | NA | NA |
Sequences
>g5144.t3 Gene=g5144 Length=1293
AAAGGAGCAATGTTGTGTCATGATAATTTTACGTGGATAACAAATAGTGTGACTGAATAT
TTGCCGAATTTGGAAATGGGGAAGGAAATCCTCGTATCATATCTTCCACTCTCACACGTT
GCTGCACAAACTTTAGATATTTATGTTACATTAGCATTAGCTGCAACTGTATATTTTGCT
GATCGTGATGCATTGAAAGGAACACTATTAAAAACTCTCACTGAAGCGCGACCAACTGTT
TTCTTGGGTGTGCCGAGAGTGTATGAAAAAATTCAGGAAAAGATGATGCAAGCTGGCTCA
CAATCAGGCGCTTTGAAACGTACACTTGGTTCATGGGCTAAAAGCGTCACTCTTCAATAT
CATTTGGATTGCATGGCTGGTAATTATTATACTGGATTCCAATATAAACTTGCAACAAAG
TTGTTACTTAGCAAAGTCAAACATGCACTTGGCTTTGACCGAATCAAATTCATGATAACT
GGTGCAGCACCGATGAGTGTCGAAACGAAAAAATACTTTCTGAGTCTTGATATGCCTATT
ATTGAAGCATACGGAATGTCCGAATCAAGCGGTGCCCACTCAGTTGCTAAAGTGCATGAT
CCATCTTTTGAATCTATTGGAAAAACACTACCAGGTATCGAGACAAAAATCGATAATCCA
AATGAGGAAGGTCATGGTGAAATTTGCAAACGTGGTAGAAATGTTTTTATGGGATATATT
GGGGAACTTGATAAAACTTTAGAGGCATTAGATGATGATGGATGGTTACATACAGGCGAT
ATCGGATATGTAGATGAAAATGGCTACCTTTTCATTACTGGCCGAATTAAAGAGCTTGTT
ATTACTGCAGGAGGTGAAAATATTCCACCGGTACATATTGAGAATTTAGTCAAGGCGGAA
TGCTCAGCAATTTCAAATGCATTTCTCGTTGGTGATAATCGTAAATTCCTTACAATTTTG
ATTTCTCTTAAGACTGAAGTCGATAAAGAAGGTGCTCCATTGGATGAACTTGCACCTGAA
TCTCTTAAATTAATGAAATCGCTTAATTTAAATTATACAAAATTGAGTGAAGTTCTCAAT
GCAGGTCCTGATGTGAAGGTTTCACAAGCCATACAAGACGCAATTGTTCGTGCCAACAAA
AGTTCCATTTCCAACGCTCAAAAAGTTCAAAAGTTTGCATTTTTACCACATGATTTTAGC
ATTCCTACAGGAGAGTTAGGACCAACACTTAAAATAAAAAGAAGCTACATCTCAGAAAAG
TACAAAGAGATCATCAATAAACTTTATCATTAG
>g5144.t3 Gene=g5144 Length=427
MLCHDNFTWITNSVTEYLPNLEMGKEILVSYLPLSHVAAQTLDIYVTLALAATVYFADRD
ALKGTLLKTLTEARPTVFLGVPRVYEKIQEKMMQAGSQSGALKRTLGSWAKSVTLQYHLD
CMAGNYYTGFQYKLATKLLLSKVKHALGFDRIKFMITGAAPMSVETKKYFLSLDMPIIEA
YGMSESSGAHSVAKVHDPSFESIGKTLPGIETKIDNPNEEGHGEICKRGRNVFMGYIGEL
DKTLEALDDDGWLHTGDIGYVDENGYLFITGRIKELVITAGGENIPPVHIENLVKAECSA
ISNAFLVGDNRKFLTILISLKTEVDKEGAPLDELAPESLKLMKSLNLNYTKLSEVLNAGP
DVKVSQAIQDAIVRANKSSISNAQKVQKFAFLPHDFSIPTGELGPTLKIKRSYISEKYKE
IINKLYH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g5144.t3 | Gene3D | G3DSA:3.40.50.12780 | - | 1 | 118 | 0 |
| 6 | g5144.t3 | Gene3D | G3DSA:3.40.50.12780 | - | 133 | 272 | 0 |
| 2 | g5144.t3 | PANTHER | PTHR43272 | LONG-CHAIN-FATTY-ACID–COA LIGASE | 1 | 426 | 0 |
| 3 | g5144.t3 | PANTHER | PTHR43272:SF32 | LONG-CHAIN-FATTY-ACID–COA LIGASE ACSBG2 | 1 | 426 | 0 |
| 1 | g5144.t3 | Pfam | PF00501 | AMP-binding enzyme | 1 | 279 | 0 |
| 4 | g5144.t3 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 1 | 426 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5144/g5144.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5144.t3.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.
