General information for g14478.t1
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.t1 | isoform | g14478.t1 | 773434 | 786971 |
| chr_4 | g14478 | g14478.t1 | exon | g14478.t1.exon1 | 773434 | 773571 |
| chr_4 | g14478 | g14478.t1 | cds | g14478.t1.CDS1 | 773434 | 773571 |
| chr_4 | g14478 | g14478.t1 | exon | g14478.t1.exon2 | 773630 | 773803 |
| chr_4 | g14478 | g14478.t1 | cds | g14478.t1.CDS2 | 773630 | 773803 |
| chr_4 | g14478 | g14478.t1 | exon | g14478.t1.exon3 | 773858 | 774086 |
| chr_4 | g14478 | g14478.t1 | cds | g14478.t1.CDS3 | 773858 | 774086 |
| chr_4 | g14478 | g14478.t1 | exon | g14478.t1.exon4 | 774151 | 774233 |
| chr_4 | g14478 | g14478.t1 | cds | g14478.t1.CDS4 | 774151 | 774233 |
| chr_4 | g14478 | g14478.t1 | exon | g14478.t1.exon5 | 774294 | 774698 |
| chr_4 | g14478 | g14478.t1 | cds | g14478.t1.CDS5 | 774294 | 774698 |
| chr_4 | g14478 | g14478.t1 | exon | g14478.t1.exon6 | 774754 | 774905 |
| chr_4 | g14478 | g14478.t1 | cds | g14478.t1.CDS6 | 774754 | 774905 |
| chr_4 | g14478 | g14478.t1 | exon | g14478.t1.exon7 | 774963 | 775506 |
| chr_4 | g14478 | g14478.t1 | cds | g14478.t1.CDS7 | 774963 | 775506 |
| chr_4 | g14478 | g14478.t1 | exon | g14478.t1.exon8 | 775565 | 775738 |
| chr_4 | g14478 | g14478.t1 | cds | g14478.t1.CDS8 | 775565 | 775738 |
| chr_4 | g14478 | g14478.t1 | exon | g14478.t1.exon9 | 785491 | 785648 |
| chr_4 | g14478 | g14478.t1 | cds | g14478.t1.CDS9 | 785491 | 785648 |
| chr_4 | g14478 | g14478.t1 | exon | g14478.t1.exon10 | 786950 | 786971 |
| chr_4 | g14478 | g14478.t1 | cds | g14478.t1.CDS10 | 786950 | 786971 |
| chr_4 | g14478 | g14478.t1 | TSS | g14478.t1 | NA | NA |
| chr_4 | g14478 | g14478.t1 | TTS | g14478.t1 | NA | NA |
Sequences
>g14478.t1 Gene=g14478 Length=2079
ATGAACAACTCGACTGGTCTATTGGACGACATGGATAATTATTTGCAATATGTTGGTGGC
ACAACAGGTGCAATTGCATTAACAGGAATCGCTGCTGCTTCAGCATACTATTTAGCAACA
CGTCCAGTACCAGAAAAACCACTTGTGCCTCTAGATAATCAAACTACACTCGTTCTTGAG
GGTGCAGAGCAAATTCACACATCACGTTTTTCAAAAGATGCTCGCGATGGAAAATTTGTT
AGTTATTTAACTGAAGATTGTCAGACACTCTACCAGACATTTAGACATGGCGCTTATGAA
TCAAATAATGGTCCATGTCTTGGATGGCGTGAATCTTTATCGTCACCATATCAATGGATT
AATTACAATGAAGCACTTTTACGTGCTAAAAATTTCGGCTCAGGTCTAATCAGTCTTGGT
CTTGAGCCAGGACCAAAAACTTTTGTCTGCATCTATTCACAAAATCGTCCAGAATGGGTA
CTTTGTGAGCAAGGTTGTTACAATTATTCTCTTGTTCTTGTGCCGCTTTATGACACATTA
GGACCTGATGCTTGTGCTTATATCGTTACACAAACTGAATCAACTGTTGTTGTAGTTGAA
GATGATAAAAAAGTCAATTTATTACTCGACAAAGCACCCAAAAATCTCAAAAAACTTATT
ATAATTAAACCATTGCGACCAGCAACAGCACAACGTGCAAAAAATCGTGGCATTGACATT
CACACTTTTGATGAAATTGAAAAACTCGGAGCGTCAAAAAATGTTCCCGAAGTACCACCA
AGACCGACAGATTTGTGCACGATTTGTTATACTTCGGGAACAACTGGTCATCCAAAAGGA
GTAATGTTGTCACATCAAAATGTGATAGCATGTATTGTTTCTGTATGCATGCAATTGGGT
GAGCATAAGTTACGTACAGGTGATGTCATGATCTCTTTCTTACCATTGGCTCACATGCTT
GAACGTGCCTGTGAAAATGCAATGTTCTACAATGGTGGAAGCATTGGTTATTATTCAGGC
GATATTAAAGAACTGACAAATGATCTAAAGGCACTAAAACCAACAGTAATGCCAGCAGTA
CCGCGTCTTCTTAATCGAGTTTATGACAAAATTCAAGGTGAAATTGCAAATTCACCAATA
AAGAAAATGCTTTTTCGCATGGCACTTAATTCAAAAGAAGCTGAACTTCGTCGTGGAATT
ATTCGAAGAAATAGTCTTTGGGATAAGCTTGTGTTTAGAAAAGTTCAAGAAGCCTTTGGT
GGTCGACTGAGATTGATGGTTGTAGGTTCAGCACCTTTGGCTGGAACTGTTTTAACTTTC
ACTCGTTGTGCACTTGGATGTATTGTTGTTGAAGGTTATGGACAGACTGAATGTGTTGCT
GCTGTCACATTGACTGTGCAGGGTGACTATATGGTTGAACATGTTGGTCCACCACTTGCT
TGTGCTTGTATTAAGCTTGTTGATGTACCAGAAATGGAATATTATGCTGCAAATCAACAA
GGAGAAGTTTGCATTAAAGGATCTTGTGTTTTTCAAGGCTACTACCGCGATCCAGAAAGA
ACAGCACAGACAATCGATGCAAATGGTTGGCATCATACAGGTGACATTGGTCAATGGCTT
AGCAATGGAACACTTAAAATTATCGATCGCAAAAAACATATCTTCAAGCTGAGTCAAGGC
GAATATATTGTGCCTGAAAAGATTGAAAATATTTATGTTAATTCACAGTATGTTGATCAA
GTTTTTGTGCATGGTGAAAGTCTTAAGAGTTGCATAGTAGCAATTGTTGTGCCGAATGTT
GAAACAGTAAAGGCATGGGCACAAGCTAATGATATACCAGGAACATTGACAGTTCTTTGT
AATAATCCTGAAGTTAAGCATCTCATTATGAGTGACATGATTGCACTTGGTAAAGAAGCT
GGACTTAAATCTTTTGAACAAGTCAAAGACATTCATTTACATCCCGATCCATTTTCAGTT
CAAAACCAACTTTTGACACCAACATTCAAATCAAGACGGCCGCAATTGCGTAGTTACTTT
AAACCCCAATTAGATGACATGTATAAGATGCTTGATTGA
>g14478.t1 Gene=g14478 Length=692
MNNSTGLLDDMDNYLQYVGGTTGAIALTGIAAASAYYLATRPVPEKPLVPLDNQTTLVLE
GAEQIHTSRFSKDARDGKFVSYLTEDCQTLYQTFRHGAYESNNGPCLGWRESLSSPYQWI
NYNEALLRAKNFGSGLISLGLEPGPKTFVCIYSQNRPEWVLCEQGCYNYSLVLVPLYDTL
GPDACAYIVTQTESTVVVVEDDKKVNLLLDKAPKNLKKLIIIKPLRPATAQRAKNRGIDI
HTFDEIEKLGASKNVPEVPPRPTDLCTICYTSGTTGHPKGVMLSHQNVIACIVSVCMQLG
EHKLRTGDVMISFLPLAHMLERACENAMFYNGGSIGYYSGDIKELTNDLKALKPTVMPAV
PRLLNRVYDKIQGEIANSPIKKMLFRMALNSKEAELRRGIIRRNSLWDKLVFRKVQEAFG
GRLRLMVVGSAPLAGTVLTFTRCALGCIVVEGYGQTECVAAVTLTVQGDYMVEHVGPPLA
CACIKLVDVPEMEYYAANQQGEVCIKGSCVFQGYYRDPERTAQTIDANGWHHTGDIGQWL
SNGTLKIIDRKKHIFKLSQGEYIVPEKIENIYVNSQYVDQVFVHGESLKSCIVAIVVPNV
ETVKAWAQANDIPGTLTVLCNNPEVKHLIMSDMIALGKEAGLKSFEQVKDIHLHPDPFSV
QNQLLTPTFKSRRPQLRSYFKPQLDDMYKMLD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g14478.t1 | CDD | cd05927 | LC-FACS_euk | 116 | 689 | 0.0 |
| 7 | g14478.t1 | Gene3D | G3DSA:3.40.50.12780 | - | 83 | 403 | 1.5E-49 |
| 6 | g14478.t1 | Gene3D | G3DSA:3.40.50.12780 | - | 404 | 548 | 7.2E-35 |
| 3 | g14478.t1 | PANTHER | PTHR43272:SF28 | LONG-CHAIN-FATTY-ACID–COA LIGASE 1 | 19 | 690 | 2.8E-258 |
| 4 | g14478.t1 | PANTHER | PTHR43272 | LONG-CHAIN-FATTY-ACID–COA LIGASE | 19 | 690 | 2.8E-258 |
| 2 | g14478.t1 | Pfam | PF00501 | AMP-binding enzyme | 114 | 558 | 5.5E-105 |
| 1 | g14478.t1 | Pfam | PF13193 | AMP-binding enzyme C-terminal domain | 567 | 609 | 7.7E-6 |
| 9 | g14478.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 13 | - |
| 10 | g14478.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 14 | 38 | - |
| 8 | g14478.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 39 | 692 | - |
| 13 | g14478.t1 | ProSitePatterns | PS00455 | Putative AMP-binding domain signature. | 268 | 279 | - |
| 5 | g14478.t1 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 77 | 689 | 1.96E-117 |
| 12 | g14478.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 17 | 39 | - |
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.
