General information for g17104.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Probable 4-coumarate–CoA ligase 3.
Parent gene
- The parent gene g17104 is located on chr_4: 12483961..12485674 (- 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 | g17104 | g17104.t1 | isoform | g17104.t1 | 12483961 | 12485674 |
| chr_4 | g17104 | g17104.t1 | exon | g17104.t1.exon1 | 12483961 | 12484542 |
| chr_4 | g17104 | g17104.t1 | cds | g17104.t1.CDS1 | 12483961 | 12484542 |
| chr_4 | g17104 | g17104.t1 | exon | g17104.t1.exon2 | 12484598 | 12485674 |
| chr_4 | g17104 | g17104.t1 | cds | g17104.t1.CDS2 | 12484598 | 12485674 |
| chr_4 | g17104 | g17104.t1 | TSS | g17104.t1 | NA | NA |
| chr_4 | g17104 | g17104.t1 | TTS | g17104.t1 | NA | NA |
Sequences
>g17104.t1 Gene=g17104 Length=1659
ATGCAGAAGCCAACTTTTAATAAAATCACAAAAGTTTGGAGTGGTCCGAAAGTTCCACCA
ATTTACAATCCTGATCAAAATCTTGGTCAATTAATTCTAAAAGTTCTCGAACAAACTCCT
GAAACTGTGACACAAATTTCAGCTGACACAAAAGTTTCAGTCACTTGCGGTCAAATGCGA
GAAAGAACTGAAAAATTCGCGAAATATTTGAACAGTCTTGGACTCAAGCAAGGCGATGTT
GTTGGAATTATTGCTGCAAATACTGAAAATCTTGCTCCAGCTGTGTTTACTTGCTTTCTA
CTTGGACTTCCTGTTAATCCATTGGCACCAATAATGACTCAAAGTGACATTGTGCAAATG
TTTAGAAAAACTAAACCAAAATTGATTCTGTGTGATGGAAATAATTTAAAAATTGTTCAA
AATGCTGTGAATATGATGAAAAGTGATGCAAAAATTATCACAGTGATGGAAGATGTTGAA
AATTATGATTCAGTGACAAAAATATTAAACAGAAAAGCAGAGAAAAATTTTGATTATCCT
GAAATTGATTCGAATTCAACTGCATTAATTTTGTGTTCATCAGGATCTACTGGTTTTCCA
AAAGGAATTCCCAAAACACATAAAGAAATAATTATTCAATTTATTTCTGCATCTCCTTAC
AATTTGAATAAAAATATTTTATTTCAAACTTCATTCATTTTTTGGTTCAGTGGAATTTAT
TTTGTCATTTATGGAGCACTTTATAAATGTCTAAGAATAATCACAGCTCAAAAATTAACA
CCTGATGTTATAATTAAAATTATTCATGAATATAAAGTTACTCATGTTTTCACTGGACCT
TACATTTACATTAATTTACTTCAAAATAAAAGTTTGAAACCATTTGAAAGCATTAAACAT
TGGCGACTTGGTGGACAAAATGTGCCAAAAGAACTTTGTGAGAAATTTCAAAATTTTGTT
CCAAATGGAATTATTAGCAATGTTTATGGAAGCACTGAATGTAATTTTCATACTTGCGAT
GTATATGGAGAAAAATTTGGAAGTACAGGAAAAGTTTTGGAAAATACTGAAATTAAAATA
ATTGATGAAAATGGAAATTCACTTGACAGCAATCAGCAAGGTGAAATTTGTATCAAAAAG
TGTGTTCCATTTCTTGGTTATTTAGATGAACCGGAACAGACTAAAGAAGCTTATGATGGT
GAATGGTTTAAGACAGGCGACATTGGATACTTTGATGATGAAGGATTTTTTTATATTATT
GACCGCAAAAAAGAGATTTTAATATATCAAGGTTTTCTTACTACACCATCAGAATTAGAA
ACAATAATAAATAAAATTGATGGAGTTATGAGCAGTTGTGTTGTTGGAGTTCATCAAGAA
AGTATTGCAAGTGACATCATCCATGCTTTTGTAATTGTTGATGAATCTAAAAATTTAACA
GAATTTCAAATTGAAAATTTTGTTAATTCAAAAGTCATTGATGAAAAGAAACTTCGTGGT
GGAGTTCATTTTATTAAAGATTTTCCTCTCACTGCATCTGGGAAAGTAAGTAGAAAAGAG
CTGAAAAATTTAGCTAAAAATTCTTATACTAAAAATAGAGAAATTCAAAAGATTTTAGAA
AAATTAATTGCCAATGACATTACTTCAAGAACAGTATAA
>g17104.t1 Gene=g17104 Length=552
MQKPTFNKITKVWSGPKVPPIYNPDQNLGQLILKVLEQTPETVTQISADTKVSVTCGQMR
ERTEKFAKYLNSLGLKQGDVVGIIAANTENLAPAVFTCFLLGLPVNPLAPIMTQSDIVQM
FRKTKPKLILCDGNNLKIVQNAVNMMKSDAKIITVMEDVENYDSVTKILNRKAEKNFDYP
EIDSNSTALILCSSGSTGFPKGIPKTHKEIIIQFISASPYNLNKNILFQTSFIFWFSGIY
FVIYGALYKCLRIITAQKLTPDVIIKIIHEYKVTHVFTGPYIYINLLQNKSLKPFESIKH
WRLGGQNVPKELCEKFQNFVPNGIISNVYGSTECNFHTCDVYGEKFGSTGKVLENTEIKI
IDENGNSLDSNQQGEICIKKCVPFLGYLDEPEQTKEAYDGEWFKTGDIGYFDDEGFFYII
DRKKEILIYQGFLTTPSELETIINKIDGVMSSCVVGVHQESIASDIIHAFVIVDESKNLT
EFQIENFVNSKVIDEKKLRGGVHFIKDFPLTASGKVSRKELKNLAKNSYTKNREIQKILE
KLIANDITSRTV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g17104.t1 | Gene3D | G3DSA:3.40.50.12780 | - | 10 | 425 | 6.8E-96 |
| 9 | g17104.t1 | Gene3D | G3DSA:3.30.300.30 | - | 426 | 531 | 6.4E-18 |
| 3 | g17104.t1 | PANTHER | PTHR24096:SF353 | GH16244P-RELATED | 4 | 527 | 4.4E-135 |
| 4 | g17104.t1 | PANTHER | PTHR24096 | LONG-CHAIN-FATTY-ACID–COA LIGASE | 4 | 527 | 4.4E-135 |
| 2 | g17104.t1 | Pfam | PF00501 | AMP-binding enzyme | 36 | 429 | 1.0E-77 |
| 1 | g17104.t1 | Pfam | PF13193 | AMP-binding enzyme C-terminal domain | 438 | 515 | 1.8E-6 |
| 11 | g17104.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 225 | - |
| 12 | g17104.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 226 | 248 | - |
| 10 | g17104.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 249 | 552 | - |
| 7 | g17104.t1 | ProSitePatterns | PS00455 | Putative AMP-binding domain signature. | 190 | 201 | - |
| 6 | g17104.t1 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 11 | 527 | 1.26E-104 |
| 5 | g17104.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 226 | 248 | - |
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 K01896 (medium-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.
