General information for g5144.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 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.t4 | TTS | g5144.t4 | 7274932 | 7274932 |
| chr_2 | g5144 | g5144.t4 | isoform | g5144.t4 | 7275198 | 7278098 |
| chr_2 | g5144 | g5144.t4 | exon | g5144.t4.exon1 | 7275198 | 7275348 |
| chr_2 | g5144 | g5144.t4 | exon | g5144.t4.exon2 | 7275405 | 7275693 |
| chr_2 | g5144 | g5144.t4 | exon | g5144.t4.exon3 | 7275762 | 7275872 |
| chr_2 | g5144 | g5144.t4 | cds | g5144.t4.CDS1 | 7275860 | 7275872 |
| chr_2 | g5144 | g5144.t4 | exon | g5144.t4.exon4 | 7276028 | 7276190 |
| chr_2 | g5144 | g5144.t4 | cds | g5144.t4.CDS2 | 7276028 | 7276190 |
| chr_2 | g5144 | g5144.t4 | exon | g5144.t4.exon5 | 7276246 | 7276740 |
| chr_2 | g5144 | g5144.t4 | cds | g5144.t4.CDS3 | 7276246 | 7276740 |
| chr_2 | g5144 | g5144.t4 | exon | g5144.t4.exon6 | 7276800 | 7277125 |
| chr_2 | g5144 | g5144.t4 | cds | g5144.t4.CDS4 | 7276800 | 7277125 |
| chr_2 | g5144 | g5144.t4 | exon | g5144.t4.exon7 | 7277185 | 7277524 |
| chr_2 | g5144 | g5144.t4 | cds | g5144.t4.CDS5 | 7277185 | 7277519 |
| chr_2 | g5144 | g5144.t4 | exon | g5144.t4.exon8 | 7277980 | 7278098 |
| chr_2 | g5144 | g5144.t4 | TSS | g5144.t4 | 7278991 | 7278991 |
Sequences
>g5144.t4 Gene=g5144 Length=1994
AACGAGTAAAAATTTTTAAAAACAAAAATTTCACAAAATAGAAAATTGTGAAAAAAGTGA
CAAAGTGAGAAATATAGACGAGAATATTTATAAGTGAGGCTAAAGAACTACAACAACAAA
TTAAATGGCTGGAACTGAAGATTTTCGTATAATTGATCCAACGAAGCGATTAAAACTTCG
CATAAATCCTGATAACAAGATTGCAAGCATCGATCCAATTTCAGTTCCTCAGTTACTATC
AAAAATTGCAGAGAGTTTTCCTAATCATCCAGCTTTAAAGCAACGAAATGCAATCACCAA
AGATTGGGAAACAGTCACTTACAGTGATTATAAGCAACGAGTTGAGAAAATGGCAAAAGT
TTTTATTAAGTTAGGTTTAGAACGTTATGGAACAGTTGCTGTTCTTGCATTTAATAGCAT
CGAATGGTTTGTGTCAGAACTTGCAGCTATTCAAGCAGGTGGAATTGCAACTGGAATTTA
TACAACAAATTCAGTTCATTCAACACATCACGTTCTTGAGACATCTCGTGCTAATATTGT
TATAGTAGATGAAGCTAAACAAATGGAAAAGATTCGTGAAATTAAAGATAAGCTTCCAAA
TTTGAAGGCAATTGTGCAGACATTACCGCCTTATGCACAGTACATTAAAAAAGAAGATGG
TTTTTGGCGTTGGAATGAAATTGAAGAGCTCAATACTGCTGATGTTGATGAAGAATATCA
ACAGAGACTTAAAAGCATTACACCAGATGAATGTTGTTGTCTAGTTTATACATCTGGAAC
AACTGGTAATCCCAAAGGAGCAATGTTGTGTCATGATAATTTTACGTGGATAACAAATAG
TGTGACTGAATATTTGCCGAATTTGGAAATGGGGAAGGAAATCCTCGTATCATATCTTCC
ACTCTCACACGTTGCTGCACAAACTTTAGATATTTATGTTACATTAGCATTAGCTGCAAC
TGTATATTTTGCTGATCGTGATGCATTGAAAGGAACACTATTAAAAACTCTCACTGAAGC
GCGACCAACTGTTTTCTTGGGTGTGCCGAGAGTGTATGAAAAAATTCAGGAAAAGATGAT
GCAAGCTGGCTCACAATCAGGCGCTTTGAAACGTACACTTGGTTCATGGGCTAAAAGCGT
CACTCTTCAATATCATTTGGATTGCATGGCTGGTAATTATTATACTGGATTCCAATATAA
ACTTGCAACAAAGTTGTTACTTAGCAAAGTCAAACATGCACTTGGCTTTGACCGAATCAA
ATTCATGATAACTGGTGCAGCACCGATGAGTGTCGAAACGAAAAAATACTTTCTGAGTCT
TGATATGCCTATTATTGAAGCATACGGAATGTCCGAATCAAGCGGTGCCCACTCAGTTGC
TAAAGTGCATGATCCATCTTTTGAATCTATTGGAAAAACACTACCAGGTATAAAAAGTGA
TGCAGGCATTAGATGATGATGGATGGTTACATACAGGCGATATCGGATATGTAGATGAAA
ATGGCTACCTTTTCATTACTGGCCGAATTAAAGAGCTTGTTATTACTGCAGGAGGTGAAA
ATATTCCACCGGTACATATTGAGAATTTAGTCAAGGCGGAATGCTCAGCAATTTCAAATG
CATTTCTCGTTGGTGATAATCGTAAATTCCTTACAATTTTGATTTCTCTTAAGACTGAAG
TCGATAAAGAAGGTGCTCCATTGGATGAACTTGCACCTGAATCTCTTAAATTAATGAAAT
CGCTTAATTTAAATTATACAAAATTGAGTGAAGTTCTCAATGCAGGTCCTGATGTGAAGG
TTTCACAAGCCATACAAGACGCAATTGTTCGTGCCAACAAAAGTTCCATTTCCAACGCTC
AAAAAGTTCAAAAGTTTGCATTTTTACCACATGATTTTAGCATTCCTACAGGAGAGTTAG
GACCAACACTTAAAATAAAAAGAAGCTACATCTCAGAAAAGTACAAAGAGATCATCAATA
AACTTTATCATTAG
>g5144.t4 Gene=g5144 Length=443
MAGTEDFRIIDPTKRLKLRINPDNKIASIDPISVPQLLSKIAESFPNHPALKQRNAITKD
WETVTYSDYKQRVEKMAKVFIKLGLERYGTVAVLAFNSIEWFVSELAAIQAGGIATGIYT
TNSVHSTHHVLETSRANIVIVDEAKQMEKIREIKDKLPNLKAIVQTLPPYAQYIKKEDGF
WRWNEIEELNTADVDEEYQQRLKSITPDECCCLVYTSGTTGNPKGAMLCHDNFTWITNSV
TEYLPNLEMGKEILVSYLPLSHVAAQTLDIYVTLALAATVYFADRDALKGTLLKTLTEAR
PTVFLGVPRVYEKIQEKMMQAGSQSGALKRTLGSWAKSVTLQYHLDCMAGNYYTGFQYKL
ATKLLLSKVKHALGFDRIKFMITGAAPMSVETKKYFLSLDMPIIEAYGMSESSGAHSVAK
VHDPSFESIGKTLPGIKSDAGIR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5144.t4 | Gene3D | G3DSA:3.40.50.12780 | - | 32 | 342 | 1.1E-52 |
| 7 | g5144.t4 | Gene3D | G3DSA:3.40.50.12780 | - | 355 | 440 | 7.4E-9 |
| 2 | g5144.t4 | PANTHER | PTHR43272 | LONG-CHAIN-FATTY-ACID–COA LIGASE | 5 | 437 | 1.4E-145 |
| 3 | g5144.t4 | PANTHER | PTHR43272:SF32 | LONG-CHAIN-FATTY-ACID–COA LIGASE ACSBG2 | 5 | 437 | 1.4E-145 |
| 1 | g5144.t4 | Pfam | PF00501 | AMP-binding enzyme | 41 | 436 | 2.3E-68 |
| 5 | g5144.t4 | ProSitePatterns | PS00455 | Putative AMP-binding domain signature. | 213 | 224 | - |
| 4 | g5144.t4 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 30 | 436 | 6.93E-68 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5144/g5144.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5144.t4.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.
