General information for g7969.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Long-chain-fatty-acid–CoA ligase 4.
Parent gene
- The parent gene g7969 is located on chr_2: 27331028..27331735 (- 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 | g7969 | g7969.t1 | TTS | g7969.t1 | 27328362 | 27328362 |
| chr_2 | g7969 | g7969.t1 | isoform | g7969.t1 | 27328555 | 27331247 |
| chr_2 | g7969 | g7969.t1 | exon | g7969.t1.exon1 | 27328555 | 27328985 |
| chr_2 | g7969 | g7969.t1 | cds | g7969.t1.CDS1 | 27328555 | 27328985 |
| chr_2 | g7969 | g7969.t1 | exon | g7969.t1.exon2 | 27329043 | 27329351 |
| chr_2 | g7969 | g7969.t1 | cds | g7969.t1.CDS2 | 27329043 | 27329351 |
| chr_2 | g7969 | g7969.t1 | exon | g7969.t1.exon3 | 27329420 | 27329485 |
| chr_2 | g7969 | g7969.t1 | cds | g7969.t1.CDS3 | 27329420 | 27329485 |
| chr_2 | g7969 | g7969.t1 | exon | g7969.t1.exon4 | 27329551 | 27330087 |
| chr_2 | g7969 | g7969.t1 | cds | g7969.t1.CDS4 | 27329551 | 27330087 |
| chr_2 | g7969 | g7969.t1 | exon | g7969.t1.exon5 | 27330164 | 27330367 |
| chr_2 | g7969 | g7969.t1 | cds | g7969.t1.CDS5 | 27330164 | 27330367 |
| chr_2 | g7969 | g7969.t1 | exon | g7969.t1.exon6 | 27330439 | 27330501 |
| chr_2 | g7969 | g7969.t1 | cds | g7969.t1.CDS6 | 27330439 | 27330501 |
| chr_2 | g7969 | g7969.t1 | exon | g7969.t1.exon7 | 27330576 | 27330951 |
| chr_2 | g7969 | g7969.t1 | cds | g7969.t1.CDS7 | 27330576 | 27330951 |
| chr_2 | g7969 | g7969.t1 | exon | g7969.t1.exon8 | 27331028 | 27331163 |
| chr_2 | g7969 | g7969.t1 | cds | g7969.t1.CDS8 | 27331028 | 27331163 |
| chr_2 | g7969 | g7969.t1 | exon | g7969.t1.exon9 | 27331225 | 27331247 |
| chr_2 | g7969 | g7969.t1 | cds | g7969.t1.CDS9 | 27331225 | 27331247 |
| chr_2 | g7969 | g7969.t1 | TSS | g7969.t1 | 27331751 | 27331751 |
Sequences
>g7969.t1 Gene=g7969 Length=2145
ATGTTTATCGAAAAAGATACAAATATGAATAATTTTTGGATCCAATGTGTCATTAAGGCA
ATATCATATGCGGGGCTCGTCTATGACATTTTATCATTTCCTGTCTACTTTCTACTTCAA
AGACCATGGAGCCGTCGAAGTATGTCACATCGAATAAAGGCAAAACCAATAAGTTCAGAT
AACACGCAAATTACATACAGAAGTGTTGATCCACCGCGTGAAATTCATTTGAAAATGGTG
CAAGCCAATATTGATACGCTTGAAAAGATGCTAAAATATATGAAAGAGACACATCAAGAA
AAATTATGTCTCGGCACGCGTCAAGTCCTAAGTGAGGAAGATGAAGTGCAAGCTAATGGA
AAAGTTTTCAAAAAATATAAAATGGGTGACTATACATGGCGCAATTTTATTGAGACCGAA
CAAGAGGCTTGCAACTTTGGATATGGCATTCGAAAGTTGGGTGTTAAACCAAAGGACAAT
GTTGTTATTTTCTCAGAGACTCGTGCCGAATGGATGATTGCTGCTCATGGTTTATTTAAA
CATAGTTGCACCATTGTAACAATTTATGCCACACTTGGTGAAGAAGGAATCATTCATGGT
GTTAATGAGACAGAAGTATCAGTGATAATCACATCACATGAATTGATGCCAAAACTCCGA
AGCATTCTCGATAAAATTCCAAAGGTTACAACTATCATCTTCTTTGAAGATCAATTACAG
AAAACCGATACAAAGGGATTCGAGCGAATCAAAACAATTTCATATTCCAAAGTCATTGAG
GCGGGCATTAAAAATAAAGTTGAACCGGTTGCTCCGTCAACAAATGATACCGCCATAATT
ATGTATACCTCTGGAAGTACTGGAACTCCAAAAGGTGTGCTTATTTCACATGGCAATTGT
ATTGCAACTTTAAAATGCTTCTGTGATGTTGTCGAGATTCATCCCGATGATATCCTTCTT
GGCTTTTTGCCACTGGCTCATGTCTTCGAATTGCTTGCCGAGAGTGTATGTTTGCTTACT
GGCGTTCCAATTGGCTACTCTTCGCCTAATACCCTCATTGATAGTAGCACAAAAATCATG
AAGGGCAGTAAGGGCGACGCATCGGTCCTTAGACCCACTTGCATCACGGCCGTTCCACTA
ATTCTAGATAGAATTTGTAAGGGTATCACAGATAAAATTAACAAGGGATCTCCACTACAA
AAGGCTATTTTTAAGTATTGCTACGACTATAAGGTTTTATGGTGTAGACGAGGATTTAAC
ACTCCACTGTTGGACTTCATTATTTTTAAGAAAATCACAAAGCTTATGGGCGGTCGCTTA
AGATTGATGATTTCAGGAGGCGCTCCACTTAGTGCAGAAACTCATGAACAAATTCGTTTA
TGTCTCTGTGTCGATGTCTGTCAAGGCTATGGGTTGACAGAAACAACAACAGCTTCATGT
GTAATGGATAAACATGATATGACTTATGGACGTGTTGGTGCACCATCATCATTGGTTGAT
TTGCGCTTAATTAATTGGGAAGAAGGAAATTATCGTGTGACAAATAAGCCCTATCCTCAG
GGAGAAATTGTTATTGGCTCAAAGAGTGTTGCAATGGGTTATTATAAAATGCCAGAATTA
TCAAAAGAAAGCTTCTTTGAAGAAGATGGCAAAAGATGGTTTAGAACTGGTGACATTGGT
GAAATTTATCCTGATGGTGTTTTAAAAATCATTGATCGTAAAAAAGATTTAGTGAAGCTT
CAAGCCGGTGAATATGTGTCGCTCGGACGTGTCGAAGCTGAAATGAAGACATGTCCATTA
GTTGAAAATATTTGTGTTTATGGTGATCCTTCAAAACATTATTGTGTAGCTTTGGTTGTA
CCAGCTGAAAAAATGCTAATGGAATTAGCTGAGAATTTAAATATTCATAATAAAAATTTT
GAAGAGCTCTGTGCATCGCCAATAATTGAAAAAGCAGTGGCAAGGGAATTAATTGAGCAT
GCTAAAAAATGCAAATTAGAAAAGTTTGAAATTCCTGCAGCCATAACATTATGCAAAGAC
ACATGGACGACTGAAACTGGAATGGTCACAGCAGCTTTTAAGATTAAACGAAAGGTCATT
CAGGAACGTTATAAAGAGGAAATCAAGAGGATGTATGCTTCATAA
>g7969.t1 Gene=g7969 Length=714
MFIEKDTNMNNFWIQCVIKAISYAGLVYDILSFPVYFLLQRPWSRRSMSHRIKAKPISSD
NTQITYRSVDPPREIHLKMVQANIDTLEKMLKYMKETHQEKLCLGTRQVLSEEDEVQANG
KVFKKYKMGDYTWRNFIETEQEACNFGYGIRKLGVKPKDNVVIFSETRAEWMIAAHGLFK
HSCTIVTIYATLGEEGIIHGVNETEVSVIITSHELMPKLRSILDKIPKVTTIIFFEDQLQ
KTDTKGFERIKTISYSKVIEAGIKNKVEPVAPSTNDTAIIMYTSGSTGTPKGVLISHGNC
IATLKCFCDVVEIHPDDILLGFLPLAHVFELLAESVCLLTGVPIGYSSPNTLIDSSTKIM
KGSKGDASVLRPTCITAVPLILDRICKGITDKINKGSPLQKAIFKYCYDYKVLWCRRGFN
TPLLDFIIFKKITKLMGGRLRLMISGGAPLSAETHEQIRLCLCVDVCQGYGLTETTTASC
VMDKHDMTYGRVGAPSSLVDLRLINWEEGNYRVTNKPYPQGEIVIGSKSVAMGYYKMPEL
SKESFFEEDGKRWFRTGDIGEIYPDGVLKIIDRKKDLVKLQAGEYVSLGRVEAEMKTCPL
VENICVYGDPSKHYCVALVVPAEKMLMELAENLNIHNKNFEELCASPIIEKAVARELIEH
AKKCKLEKFEIPAAITLCKDTWTTETGMVTAAFKIKRKVIQERYKEEIKRMYAS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g7969.t1 | Coils | Coil | Coil | 77 | 97 | - |
| 7 | g7969.t1 | Gene3D | G3DSA:3.40.50.12780 | - | 87 | 407 | 1.1E-45 |
| 6 | g7969.t1 | Gene3D | G3DSA:3.40.50.12780 | - | 421 | 576 | 2.1E-32 |
| 8 | g7969.t1 | Gene3D | G3DSA:3.30.300.30 | - | 577 | 712 | 1.6E-7 |
| 3 | g7969.t1 | PANTHER | PTHR43272:SF13 | LONG-CHAIN-FATTY-ACID–COA LIGASE 3 | 30 | 713 | 2.5E-228 |
| 4 | g7969.t1 | PANTHER | PTHR43272 | LONG-CHAIN-FATTY-ACID–COA LIGASE | 30 | 713 | 2.5E-228 |
| 2 | g7969.t1 | Pfam | PF00501 | AMP-binding enzyme | 126 | 581 | 1.0E-96 |
| 1 | g7969.t1 | Pfam | PF13193 | AMP-binding enzyme C-terminal domain | 591 | 684 | 1.4E-6 |
| 11 | g7969.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 11 | - |
| 12 | g7969.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 39 | - |
| 10 | g7969.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 40 | 714 | - |
| 14 | g7969.t1 | ProSitePatterns | PS00455 | Putative AMP-binding domain signature. | 280 | 291 | - |
| 5 | g7969.t1 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 63 | 712 | 5.63E-112 |
| 13 | g7969.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 20 | 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.
