General information for g14478.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Long-chain-fatty-acid–CoA ligase 1.
Parent gene
- The parent gene g14478 is located on chr_4: 773434..786971 (- 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_4 | g14478 | g14478.t2 | isoform | g14478.t2 | 773434 | 780712 |
| chr_4 | g14478 | g14478.t2 | exon | g14478.t2.exon1 | 773434 | 773571 |
| chr_4 | g14478 | g14478.t2 | cds | g14478.t2.CDS1 | 773434 | 773571 |
| chr_4 | g14478 | g14478.t2 | exon | g14478.t2.exon2 | 773630 | 773803 |
| chr_4 | g14478 | g14478.t2 | cds | g14478.t2.CDS2 | 773630 | 773803 |
| chr_4 | g14478 | g14478.t2 | exon | g14478.t2.exon3 | 773858 | 774086 |
| chr_4 | g14478 | g14478.t2 | cds | g14478.t2.CDS3 | 773858 | 774086 |
| chr_4 | g14478 | g14478.t2 | exon | g14478.t2.exon4 | 774151 | 774233 |
| chr_4 | g14478 | g14478.t2 | cds | g14478.t2.CDS4 | 774151 | 774233 |
| chr_4 | g14478 | g14478.t2 | exon | g14478.t2.exon5 | 774294 | 774698 |
| chr_4 | g14478 | g14478.t2 | cds | g14478.t2.CDS5 | 774294 | 774698 |
| chr_4 | g14478 | g14478.t2 | exon | g14478.t2.exon6 | 774754 | 774905 |
| chr_4 | g14478 | g14478.t2 | cds | g14478.t2.CDS6 | 774754 | 774905 |
| chr_4 | g14478 | g14478.t2 | exon | g14478.t2.exon7 | 774963 | 775506 |
| chr_4 | g14478 | g14478.t2 | cds | g14478.t2.CDS7 | 774963 | 775506 |
| chr_4 | g14478 | g14478.t2 | exon | g14478.t2.exon8 | 775565 | 775738 |
| chr_4 | g14478 | g14478.t2 | cds | g14478.t2.CDS8 | 775565 | 775738 |
| chr_4 | g14478 | g14478.t2 | exon | g14478.t2.exon9 | 780641 | 780712 |
| chr_4 | g14478 | g14478.t2 | cds | g14478.t2.CDS9 | 780641 | 780712 |
| chr_4 | g14478 | g14478.t2 | TSS | g14478.t2 | 781232 | 781232 |
| chr_4 | g14478 | g14478.t2 | TTS | g14478.t2 | NA | NA |
Sequences
>g14478.t2 Gene=g14478 Length=1971
ATGTCGTGTTGTACGACTGTAAGACCTTTAAGGCCACCAATTGATCTTGCTAGACAAAGT
GAAAATTTAAAGGGTGCAGAGCAAATTCACACATCACGTTTTTCAAAAGATGCTCGCGAT
GGAAAATTTGTTAGTTATTTAACTGAAGATTGTCAGACACTCTACCAGACATTTAGACAT
GGCGCTTATGAATCAAATAATGGTCCATGTCTTGGATGGCGTGAATCTTTATCGTCACCA
TATCAATGGATTAATTACAATGAAGCACTTTTACGTGCTAAAAATTTCGGCTCAGGTCTA
ATCAGTCTTGGTCTTGAGCCAGGACCAAAAACTTTTGTCTGCATCTATTCACAAAATCGT
CCAGAATGGGTACTTTGTGAGCAAGGTTGTTACAATTATTCTCTTGTTCTTGTGCCGCTT
TATGACACATTAGGACCTGATGCTTGTGCTTATATCGTTACACAAACTGAATCAACTGTT
GTTGTAGTTGAAGATGATAAAAAAGTCAATTTATTACTCGACAAAGCACCCAAAAATCTC
AAAAAACTTATTATAATTAAACCATTGCGACCAGCAACAGCACAACGTGCAAAAAATCGT
GGCATTGACATTCACACTTTTGATGAAATTGAAAAACTCGGAGCGTCAAAAAATGTTCCC
GAAGTACCACCAAGACCGACAGATTTGTGCACGATTTGTTATACTTCGGGAACAACTGGT
CATCCAAAAGGAGTAATGTTGTCACATCAAAATGTGATAGCATGTATTGTTTCTGTATGC
ATGCAATTGGGTGAGCATAAGTTACGTACAGGTGATGTCATGATCTCTTTCTTACCATTG
GCTCACATGCTTGAACGTGCCTGTGAAAATGCAATGTTCTACAATGGTGGAAGCATTGGT
TATTATTCAGGCGATATTAAAGAACTGACAAATGATCTAAAGGCACTAAAACCAACAGTA
ATGCCAGCAGTACCGCGTCTTCTTAATCGAGTTTATGACAAAATTCAAGGTGAAATTGCA
AATTCACCAATAAAGAAAATGCTTTTTCGCATGGCACTTAATTCAAAAGAAGCTGAACTT
CGTCGTGGAATTATTCGAAGAAATAGTCTTTGGGATAAGCTTGTGTTTAGAAAAGTTCAA
GAAGCCTTTGGTGGTCGACTGAGATTGATGGTTGTAGGTTCAGCACCTTTGGCTGGAACT
GTTTTAACTTTCACTCGTTGTGCACTTGGATGTATTGTTGTTGAAGGTTATGGACAGACT
GAATGTGTTGCTGCTGTCACATTGACTGTGCAGGGTGACTATATGGTTGAACATGTTGGT
CCACCACTTGCTTGTGCTTGTATTAAGCTTGTTGATGTACCAGAAATGGAATATTATGCT
GCAAATCAACAAGGAGAAGTTTGCATTAAAGGATCTTGTGTTTTTCAAGGCTACTACCGC
GATCCAGAAAGAACAGCACAGACAATCGATGCAAATGGTTGGCATCATACAGGTGACATT
GGTCAATGGCTTAGCAATGGAACACTTAAAATTATCGATCGCAAAAAACATATCTTCAAG
CTGAGTCAAGGCGAATATATTGTGCCTGAAAAGATTGAAAATATTTATGTTAATTCACAG
TATGTTGATCAAGTTTTTGTGCATGGTGAAAGTCTTAAGAGTTGCATAGTAGCAATTGTT
GTGCCGAATGTTGAAACAGTAAAGGCATGGGCACAAGCTAATGATATACCAGGAACATTG
ACAGTTCTTTGTAATAATCCTGAAGTTAAGCATCTCATTATGAGTGACATGATTGCACTT
GGTAAAGAAGCTGGACTTAAATCTTTTGAACAAGTCAAAGACATTCATTTACATCCCGAT
CCATTTTCAGTTCAAAACCAACTTTTGACACCAACATTCAAATCAAGACGGCCGCAATTG
CGTAGTTACTTTAAACCCCAATTAGATGACATGTATAAGATGCTTGATTGA
>g14478.t2 Gene=g14478 Length=656
MSCCTTVRPLRPPIDLARQSENLKGAEQIHTSRFSKDARDGKFVSYLTEDCQTLYQTFRH
GAYESNNGPCLGWRESLSSPYQWINYNEALLRAKNFGSGLISLGLEPGPKTFVCIYSQNR
PEWVLCEQGCYNYSLVLVPLYDTLGPDACAYIVTQTESTVVVVEDDKKVNLLLDKAPKNL
KKLIIIKPLRPATAQRAKNRGIDIHTFDEIEKLGASKNVPEVPPRPTDLCTICYTSGTTG
HPKGVMLSHQNVIACIVSVCMQLGEHKLRTGDVMISFLPLAHMLERACENAMFYNGGSIG
YYSGDIKELTNDLKALKPTVMPAVPRLLNRVYDKIQGEIANSPIKKMLFRMALNSKEAEL
RRGIIRRNSLWDKLVFRKVQEAFGGRLRLMVVGSAPLAGTVLTFTRCALGCIVVEGYGQT
ECVAAVTLTVQGDYMVEHVGPPLACACIKLVDVPEMEYYAANQQGEVCIKGSCVFQGYYR
DPERTAQTIDANGWHHTGDIGQWLSNGTLKIIDRKKHIFKLSQGEYIVPEKIENIYVNSQ
YVDQVFVHGESLKSCIVAIVVPNVETVKAWAQANDIPGTLTVLCNNPEVKHLIMSDMIAL
GKEAGLKSFEQVKDIHLHPDPFSVQNQLLTPTFKSRRPQLRSYFKPQLDDMYKMLD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g14478.t2 | CDD | cd05927 | LC-FACS_euk | 80 | 653 | 0.0 |
| 8 | g14478.t2 | Gene3D | G3DSA:3.40.50.12780 | - | 50 | 377 | 1.2E-49 |
| 7 | g14478.t2 | Gene3D | G3DSA:3.40.50.12780 | - | 378 | 519 | 3.4E-32 |
| 3 | g14478.t2 | PANTHER | PTHR43272:SF28 | LONG-CHAIN-FATTY-ACID–COA LIGASE 1 | 5 | 654 | 4.9E-257 |
| 4 | g14478.t2 | PANTHER | PTHR43272 | LONG-CHAIN-FATTY-ACID–COA LIGASE | 5 | 654 | 4.9E-257 |
| 2 | g14478.t2 | Pfam | PF00501 | AMP-binding enzyme | 78 | 522 | 4.7E-105 |
| 1 | g14478.t2 | Pfam | PF13193 | AMP-binding enzyme C-terminal domain | 531 | 573 | 7.2E-6 |
| 6 | g14478.t2 | ProSitePatterns | PS00455 | Putative AMP-binding domain signature. | 232 | 243 | - |
| 5 | g14478.t2 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 44 | 653 | 2.49E-117 |
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 K01897 (long-chain acyl-CoA synthetase)
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.
