General information for g4348.t1
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 g4348 is located on chr_2: 1469778..1470698 (+ 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 | g4348 | g4348.t1 | TSS | g4348.t1 | 1468204 | 1468204 |
| chr_2 | g4348 | g4348.t1 | isoform | g4348.t1 | 1468306 | 1470698 |
| chr_2 | g4348 | g4348.t1 | exon | g4348.t1.exon1 | 1468306 | 1468637 |
| chr_2 | g4348 | g4348.t1 | cds | g4348.t1.CDS1 | 1468306 | 1468637 |
| chr_2 | g4348 | g4348.t1 | exon | g4348.t1.exon2 | 1468970 | 1469781 |
| chr_2 | g4348 | g4348.t1 | cds | g4348.t1.CDS2 | 1468970 | 1469781 |
| chr_2 | g4348 | g4348.t1 | exon | g4348.t1.exon3 | 1469835 | 1470197 |
| chr_2 | g4348 | g4348.t1 | cds | g4348.t1.CDS3 | 1469835 | 1470197 |
| chr_2 | g4348 | g4348.t1 | exon | g4348.t1.exon4 | 1470253 | 1470698 |
| chr_2 | g4348 | g4348.t1 | cds | g4348.t1.CDS4 | 1470253 | 1470698 |
| chr_2 | g4348 | g4348.t1 | TTS | g4348.t1 | 1471306 | 1471306 |
Sequences
>g4348.t1 Gene=g4348 Length=1953
ATGTCCTTCACTCGAGCAAGTAACAATATTCGCGTGTCCGATATTAAACAGCCATACAAA
ATTACAAGAATTGATAATGATTTTGATCCAATAACAATACCTGATTTATTCGATCGTATT
GTTGAAAATTATGCCGAAAATCCTGCATTGGCTTATCTAGATTATGAGACAAAGAAATGG
AATTTTCTTTCTTATAAACAATACAAAGAAAAGATTGATAAATATGCAAAAATTTTCATC
AAATTGGGCCTAAAGCGATTCGGAAGCGTTGCAGTTCTCGCATTCAATTCTGTAGAGTGG
TTTATCACCGAACTTGCGGCTATTCATGCTGGCGGTGTAATAACAGGAATCTACACGACA
AACAGTGTTGATTCAACGAAATATGTTTTGGAAAAAAGTGGCGCGACTATTGTGGTTGTT
GACGATGCAAAACAAATGGAGAAGGTCAAAGAAATAAAGAAACGCATGCCGCATTTGAAG
GTAGTCATTCAAACACGTGAACCATTTTCTGAAAGCATTGATAATGGTTACTATACATGG
GACGAACTTGCTTTAATGGACACAGACGACGTTGAACAGGAATATCATGATCGTAGAGCA
GATCTTGCTGCAAATGATTGTTGTAGTTTGATATTCACTTCAGGGACGACAGGATTTCCA
AAAGGTGTTATGCTTTCTCACGACAATCTCATATTTGTGGCTAAAGCAGGAACAGAATTT
GAAAAAATGGAAGCTCCGAAAGAAAAAATTATCAGTTACTTGCCTTTATCACACATTGCA
GCACAAATTGTCGATATTTATGCATGTTTGCTTTCTGCTGGATGCACTTATTTTGCTGAA
CGTGATGCATTAAAGGGAAGTCTAGGAAAAACATTAAAAGACGTTAAACCAACAAGATTT
TTAGGTGTACCAAGAGTGTATGAAAAGATGCATGAAAAAATGCTTGAAATTGGAAGTCGT
CAAAATTGCTTAATGCGAGCTATCGGTGGTTGGGCAAAGAGAGTCACACTTCAACATCAT
CTTGATAGAATGGCCGGCAAAGAAACAAATTCATTTCAATACCAAATTGCAAAAAAATTC
ATTATCTCCAAAGTGAAAAAGGCATTAGGATTTGAAAATTGTTTAAGTTTTGCATCAGGA
GCTGCTCCTTTGAGTGTGGATACGAAAAGATATTTTTTAAGTCTCGATATTCCAATTATT
GAAATATTTGGTATGTCTGAATGCAGCGGAGGTCATTCATTTTCAGTAGTTGATTCTCCG
TCTTTTGAAACTATTGGTAAAGGATTACCAGGAACACTAACAAAATTGAGAAATCCCGAT
GCAAACGGACATGGAGAATTGATGGTTAAAGGACGACATGTTTGCATGGGGTATATTGAT
GATATGGACAAAACTTGTGAAACTATATTAGATGATGGATGGTTGGCTACAGGTGATATT
GCTTATATTGATCACGATGGATACATTTTTATTACTGGACGATTAAAGGATATAATTATA
ACAGCAGGTGGTGAAAATGTTGCACCTTATTATTGTGAACAACTTGTCAAAGCTGAGCTT
CCTGCTATCTCAAACGCTTTTCTCATAGGTGATAGAAGAAAGTATCTCACAATGCTTATC
TCATTGAAAACATTAATGGCGGCTGATTCTGGAATGCCACTTGATGAATTGGCTGATGAA
ACAATTAAATGGTTAGAAGGTTTAAATTTAAGTTATACAACATTAAGTGGCATTTTGAAT
GCTGGACCTGATCCTATTGTCTTGCGATCAATTCAAGAAGGCATTGATCGCGCCAATAAA
AAAGCTATCTCAAATGCACAGAAAATACAAAAATTCAGAATCTTGCCACATGATTTTAGC
ATTACTACAGGTGAAATTACACCAACAATGAAACTGAAAAGAAATGTTGTTGTTGAAAAG
TATAAAGATATCATTGACAGTATGTATCAATGA
>g4348.t1 Gene=g4348 Length=650
MSFTRASNNIRVSDIKQPYKITRIDNDFDPITIPDLFDRIVENYAENPALAYLDYETKKW
NFLSYKQYKEKIDKYAKIFIKLGLKRFGSVAVLAFNSVEWFITELAAIHAGGVITGIYTT
NSVDSTKYVLEKSGATIVVVDDAKQMEKVKEIKKRMPHLKVVIQTREPFSESIDNGYYTW
DELALMDTDDVEQEYHDRRADLAANDCCSLIFTSGTTGFPKGVMLSHDNLIFVAKAGTEF
EKMEAPKEKIISYLPLSHIAAQIVDIYACLLSAGCTYFAERDALKGSLGKTLKDVKPTRF
LGVPRVYEKMHEKMLEIGSRQNCLMRAIGGWAKRVTLQHHLDRMAGKETNSFQYQIAKKF
IISKVKKALGFENCLSFASGAAPLSVDTKRYFLSLDIPIIEIFGMSECSGGHSFSVVDSP
SFETIGKGLPGTLTKLRNPDANGHGELMVKGRHVCMGYIDDMDKTCETILDDGWLATGDI
AYIDHDGYIFITGRLKDIIITAGGENVAPYYCEQLVKAELPAISNAFLIGDRRKYLTMLI
SLKTLMAADSGMPLDELADETIKWLEGLNLSYTTLSGILNAGPDPIVLRSIQEGIDRANK
KAISNAQKIQKFRILPHDFSITTGEITPTMKLKRNVVVEKYKDIIDSMYQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g4348.t1 | Gene3D | G3DSA:3.40.50.12780 | - | 27 | 340 | 1.0E-51 |
| 6 | g4348.t1 | Gene3D | G3DSA:3.40.50.12780 | - | 358 | 494 | 5.8E-31 |
| 2 | g4348.t1 | PANTHER | PTHR43272 | LONG-CHAIN-FATTY-ACID–COA LIGASE | 28 | 649 | 1.2E-228 |
| 3 | g4348.t1 | PANTHER | PTHR43272:SF32 | LONG-CHAIN-FATTY-ACID–COA LIGASE ACSBG2 | 28 | 649 | 1.2E-228 |
| 1 | g4348.t1 | Pfam | PF00501 | AMP-binding enzyme | 37 | 501 | 5.5E-87 |
| 5 | g4348.t1 | ProSitePatterns | PS00455 | Putative AMP-binding domain signature. | 210 | 221 | - |
| 4 | g4348.t1 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 13 | 649 | 1.07E-105 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
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.
