General information for g15883.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Long-chain-fatty-acid–CoA ligase 3.
Parent gene
- The parent gene g15883 is located on chr_4: 7165272..7171133 (- 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 | g15883 | g15883.t1 | isoform | g15883.t1 | 7165272 | 7171133 |
| chr_4 | g15883 | g15883.t1 | exon | g15883.t1.exon1 | 7165272 | 7165696 |
| chr_4 | g15883 | g15883.t1 | cds | g15883.t1.CDS1 | 7165272 | 7165696 |
| chr_4 | g15883 | g15883.t1 | exon | g15883.t1.exon2 | 7165756 | 7166099 |
| chr_4 | g15883 | g15883.t1 | cds | g15883.t1.CDS2 | 7165756 | 7166099 |
| chr_4 | g15883 | g15883.t1 | exon | g15883.t1.exon3 | 7166256 | 7166397 |
| chr_4 | g15883 | g15883.t1 | cds | g15883.t1.CDS3 | 7166256 | 7166397 |
| chr_4 | g15883 | g15883.t1 | exon | g15883.t1.exon4 | 7166450 | 7166815 |
| chr_4 | g15883 | g15883.t1 | cds | g15883.t1.CDS4 | 7166450 | 7166815 |
| chr_4 | g15883 | g15883.t1 | exon | g15883.t1.exon5 | 7166873 | 7166881 |
| chr_4 | g15883 | g15883.t1 | cds | g15883.t1.CDS5 | 7166873 | 7166881 |
| chr_4 | g15883 | g15883.t1 | exon | g15883.t1.exon6 | 7166943 | 7166993 |
| chr_4 | g15883 | g15883.t1 | cds | g15883.t1.CDS6 | 7166943 | 7166993 |
| chr_4 | g15883 | g15883.t1 | exon | g15883.t1.exon7 | 7167416 | 7168058 |
| chr_4 | g15883 | g15883.t1 | cds | g15883.t1.CDS7 | 7167416 | 7168058 |
| chr_4 | g15883 | g15883.t1 | exon | g15883.t1.exon8 | 7171002 | 7171133 |
| chr_4 | g15883 | g15883.t1 | cds | g15883.t1.CDS8 | 7171002 | 7171133 |
| chr_4 | g15883 | g15883.t1 | TSS | g15883.t1 | 7171228 | 7171228 |
| chr_4 | g15883 | g15883.t1 | TTS | g15883.t1 | NA | NA |
Sequences
>g15883.t1 Gene=g15883 Length=2112
ATGTCGATTGGAGCAGCAATTTTTATTGGAATTGTCGCCGTTATTTCCTTTTTTTACACT
ATCCTTACATTTCCTTTTTACTTCTTAGTACAACAACCCTGGAAAGTTAAGAAAAAGGCT
AATGAAGTTAAGGCAAAAGCAATAGGCTCAGATAGAACATCAATAACTTACCAATCAGTC
CGTCCATTTGGACCAGTCCACAAGAAATTAGATCAAGCTGGCATTCAAACATTGGAACAA
ATCCTAAAATATGTTTCACTTCAATTCAAAAACAAACGTTGCCTTGGCACACGTGAAATC
CTTTCCGAAGAAGACGAAAAGCAACCGGATGGAAAAATATTTAAAAAAGCTAGAATGGGC
AAATACAATTGGCGAACATTTGATGAAGTTGACAATGAAGCTCAACATTTTGGCAAAGGA
ATGCGAGAATTAGGCGTCGATCCACGTGATAAAGTTGTAATTTTTGCAGAAACACGAGCT
GAATGGATGATTGCTGTTCATGGATTGTTTAAGCAAGCATGCACAGTCTGTACAATTTAT
GCAACTCTTGGTGAAGATGGTGTGACATTTGGTGTAAATGAAACAGAAGTTAAATATGTG
ATTACTTCACATGAATTGATGCCGAAAATTAGAAATATTTTGAAGGATATTCCAAATGTT
CATACTGTTGTTTATTTTGAAGATCAATTGCATCCAACTGATGTTAGTGGATTTGGAAAT
GTTCGTGTTGTGCCTTATAAGGAAGTTGTTAGGAAAGGAAGCATGAATAAATTTGATCAA
CATTCACCACATCGTGATGATACTGCAATTTTGATGTACACAAGTGGTTCAACAGGTGTT
CCAAAGGGTGTCATGCTCAGTCATTGGAATTGTGTATCAGCTTTAAAAGGTTTTGTTGAT
GGCCTTGAAGTTTATGACAATGATGTTTTCCTTGGTTTACTTCCACTTGCTCATGTTTAT
GAACTTCTTGCTGAAAGCGCTATAATGTTAGTTGGTGTTCCAATTGGTTATTCAACACCA
CTAACTTTGCTTGATTCGAGTCCAAGAATTATGACTGGAACTATGGGTGATGGAAGAGTT
TTGTCACCAACAGCAATGACCTCTGTTCCTTTGATTCTTGATCGTGTTCGAAAAGGAATT
TTTGACAAAATTAGTAAAGAATCACCAATTAAAAAAGCATTGTTTGAATATTGTCTGAAA
TATAAAACAAGATGGGTTCGAAGAGGTTATAGAACACCAATTGTTGATGGTGTAGTATTT
AAAAAAGTTGCTGCTTTACTTGGTGGAAGAATGCGTGCTATGGTTAGTGGAGGTGCTCCT
TTGAGTCCTGATACTCATGAAGTGATTCGGAATTGCCTATGTTTGTCAGTAGTACAAGGC
TATGGTTTAACAGAAACAACTGCTGGAGCAACAGTAATGGAAGTTGATGATCCAACAACA
GGTCGTTCAGGTGCACCAACTACAATGTCATTGATTCGTCTTGTAAATTGGGAAGAAGGC
AATTATATGGTAACAAACAATCCATTTCCACAAGGTGAAGTGCTTGTTGGTGGTGATAAT
GTTGCAATGGGCTATTTCAAACGACCTGAATTAACTGAAGAAAGTTTCTTTGAAGAAAAT
GGAAGAAGATGGTTTAGAACTGGAGATATTGGTGAAATACATGCTGATGGAAGTTTGAAA
ATTATTGATCGTAAGAAAGATTTAGTAAAACTTCAACATGGCGAATATATTTCACTAGGC
AAAGTTGAATCAGAATTAAAAACTTGTCCATTTATTGAAAATATTTGTGTCTATGCTGAT
TCAACAAAAACCTATTGTGTTGCACTTGTCGCTCCTGCTGAAGTTGGTTTTAAAAATTTA
GCAGAAAGTATCGGAATTACAGGTGAATTTGAACAACTTTGTGTCAATCGTGAAGTTATC
AAAGCAGCAACAAAAGGACTCCATGATTATGCTAAAAAATGCAATCTTGCTAAATTTGAA
GTGCCAACAATGATTTATCTTTGTCCTGATTTTTGGACACCGGAATCAGGACTCGTTACT
GCTGCATTTAAAATTAAAAGAAAGGAAATTCTTGAAAAATATAAAAGTGAAATTACCCGA
ATGTATTCTTAG
>g15883.t1 Gene=g15883 Length=703
MSIGAAIFIGIVAVISFFYTILTFPFYFLVQQPWKVKKKANEVKAKAIGSDRTSITYQSV
RPFGPVHKKLDQAGIQTLEQILKYVSLQFKNKRCLGTREILSEEDEKQPDGKIFKKARMG
KYNWRTFDEVDNEAQHFGKGMRELGVDPRDKVVIFAETRAEWMIAVHGLFKQACTVCTIY
ATLGEDGVTFGVNETEVKYVITSHELMPKIRNILKDIPNVHTVVYFEDQLHPTDVSGFGN
VRVVPYKEVVRKGSMNKFDQHSPHRDDTAILMYTSGSTGVPKGVMLSHWNCVSALKGFVD
GLEVYDNDVFLGLLPLAHVYELLAESAIMLVGVPIGYSTPLTLLDSSPRIMTGTMGDGRV
LSPTAMTSVPLILDRVRKGIFDKISKESPIKKALFEYCLKYKTRWVRRGYRTPIVDGVVF
KKVAALLGGRMRAMVSGGAPLSPDTHEVIRNCLCLSVVQGYGLTETTAGATVMEVDDPTT
GRSGAPTTMSLIRLVNWEEGNYMVTNNPFPQGEVLVGGDNVAMGYFKRPELTEESFFEEN
GRRWFRTGDIGEIHADGSLKIIDRKKDLVKLQHGEYISLGKVESELKTCPFIENICVYAD
STKTYCVALVAPAEVGFKNLAESIGITGEFEQLCVNREVIKAATKGLHDYAKKCNLAKFE
VPTMIYLCPDFWTPESGLVTAAFKIKRKEILEKYKSEITRMYS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g15883.t1 | Gene3D | G3DSA:3.40.50.12780 | - | 83 | 385 | 4.6E-45 |
| 8 | g15883.t1 | Gene3D | G3DSA:3.40.50.12780 | - | 415 | 565 | 7.6E-32 |
| 9 | g15883.t1 | Gene3D | G3DSA:3.30.300.30 | - | 566 | 702 | 8.2E-5 |
| 2 | g15883.t1 | PANTHER | PTHR43272:SF13 | LONG-CHAIN-FATTY-ACID–COA LIGASE 3 | 26 | 702 | 5.5E-217 |
| 3 | g15883.t1 | PANTHER | PTHR43272 | LONG-CHAIN-FATTY-ACID–COA LIGASE | 26 | 702 | 5.5E-217 |
| 1 | g15883.t1 | Pfam | PF00501 | AMP-binding enzyme | 105 | 572 | 1.1E-94 |
| 11 | g15883.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 5 | - |
| 12 | g15883.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 6 | 30 | - |
| 10 | g15883.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 31 | 703 | - |
| 6 | g15883.t1 | ProSitePatterns | PS00455 | Putative AMP-binding domain signature. | 271 | 282 | - |
| 5 | g15883.t1 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 64 | 702 | 7.98E-107 |
| 4 | g15883.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 7 | 29 | - |
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. There were no conditions that were differentially expressed