General information for g17099.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 4-coumarate–CoA ligase-like 9.
Parent gene
- The parent gene g17099 is located on chr_4: 12463387..12465066 (- 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 | g17099 | g17099.t1 | isoform | g17099.t1 | 12463387 | 12465066 |
| chr_4 | g17099 | g17099.t1 | exon | g17099.t1.exon1 | 12463387 | 12463932 |
| chr_4 | g17099 | g17099.t1 | cds | g17099.t1.CDS1 | 12463387 | 12463932 |
| chr_4 | g17099 | g17099.t1 | exon | g17099.t1.exon2 | 12463990 | 12465066 |
| chr_4 | g17099 | g17099.t1 | cds | g17099.t1.CDS2 | 12463990 | 12465066 |
| chr_4 | g17099 | g17099.t1 | TSS | g17099.t1 | NA | NA |
| chr_4 | g17099 | g17099.t1 | TTS | g17099.t1 | NA | NA |
Sequences
>g17099.t1 Gene=g17099 Length=1623
ATGTATAAACCAATTTTTGATAAAAAAACAAAAGTTTGGAGTGGTCCAAAAGTTCCACCA
ATTTTCAATCCTGATCAAAATCTTGGCCAGCTTATTTTGAGAATTCTTAAAATTTCACCA
GAATCTGTGACACAAATTTCAGCTGACACAAAAGTTTCAGTCACTTGCGGTCAAATGCGA
GAAAGAATTGAAAAATTCGCGAAATATTTGAACAGTCTTGGACTCAAGCAAGGCGATGTT
GTTAGAATTGTTGCTGCAAATACTGAAAATCTTGCTCCAGCTGTTTTTGCTTGCTTTCTA
CTTGGACTTTCTGTTAATCCATTGGCACCAATCATGATTGAAAGTGATATTGTGCATATG
TTTGACAAAACTAAACCAAAATTGATTCTGTGCGATGAGAATAATTTAAAAATTGTTCAA
AATGCTGTGAATATGATGAAAAGTGATGCAAAAATTATTACAGTGATGGAAGATGTTGAA
AATTATGATTCAGTGACAAAAATATTAAACAGAAAAGCAGAAAAAGAATTTAATTATCCT
AAAATTGATTCGAATTCAGTTTTGGTAATTTTATGTTCATCAGGTTCAACTGGAATACCA
AAAGGAATTTGCAAGACACTCAAAGAATTCATCATTGCTTCAGACTTTCTTGATTATAAT
GTAATAGAAAGTTTAGTCATTTTCCAAACTACAACAATATTTTGGATTACTGGTTTATAT
TTCCTGATTTATTCAACAATTCATCGATTAACTCGTGTCATTACTGCTCAATTTTATCAA
CCAAAACATTTTGCTGAAATTTTTATGAATTATAAAGTGGGAATGGCAATAACACCTCCT
GTAATTGTTGAAACTTTAATAAAAAGTGGACATTTAAAACCACTTAAACACATGAGATGT
TGGTTAATTGGTGGTGCAAAAGTAACCACAAAACTTATAGAAAAATTTAAGCCATTTGTT
CCAAATGCTCTGTTGGTCAACACTTATGCTTGCACAGAAGCAAATTTGATTGCTTTTAAT
TTACATGGAAGAAAATTTGAAAGTTCTGGTCAACCTGTTACAAATACCAGCATTAAAATT
GTCGATGATGATGGAAATGCTTTGGATAATTTTCAACAAGGTGAAATTTGTGTCAAACAT
GAAGTACCATTTGCTGGTTATATTGATGATCTTGAGAAGACTAAAGAAGCTTATGATGGT
GAATGGTTTAAGACAGGTGACATTGGTTATTTTGATGATGAAGGATTTCTTTATTTTATT
GAAAGACAGAAGGATTTAATAAAATATGAAGGAATTAAAACTGCACCATCAGAATTAGAA
GCAATCATAAATGAAATTGATGGAGTTGTCAGCAGTTGTGTTGTTGGAGTTCATAAGGAA
AATTCTGAAAATGACATCATTCATGCTTTTGTAATTGTTGATGAATCTATAAATTTAACA
GAAATTCAAATTGAAAATTTCTTTAATTCAAAAGTTATAGAACAAAGAAAACTTCGTGGT
GGTGTTCATTTTGTGAAAAAATTTCCATTGCTTCTGTCTGGAAAAATTAATAAGAAAATT
ATGAAAGCAAAATGTGAAGAATTTATGAAGGAAAAAATATTAAATGAAAGATTTAGAGCC
TAA
>g17099.t1 Gene=g17099 Length=540
MYKPIFDKKTKVWSGPKVPPIFNPDQNLGQLILRILKISPESVTQISADTKVSVTCGQMR
ERIEKFAKYLNSLGLKQGDVVRIVAANTENLAPAVFACFLLGLSVNPLAPIMIESDIVHM
FDKTKPKLILCDENNLKIVQNAVNMMKSDAKIITVMEDVENYDSVTKILNRKAEKEFNYP
KIDSNSVLVILCSSGSTGIPKGICKTLKEFIIASDFLDYNVIESLVIFQTTTIFWITGLY
FLIYSTIHRLTRVITAQFYQPKHFAEIFMNYKVGMAITPPVIVETLIKSGHLKPLKHMRC
WLIGGAKVTTKLIEKFKPFVPNALLVNTYACTEANLIAFNLHGRKFESSGQPVTNTSIKI
VDDDGNALDNFQQGEICVKHEVPFAGYIDDLEKTKEAYDGEWFKTGDIGYFDDEGFLYFI
ERQKDLIKYEGIKTAPSELEAIINEIDGVVSSCVVGVHKENSENDIIHAFVIVDESINLT
EIQIENFFNSKVIEQRKLRGGVHFVKKFPLLLSGKINKKIMKAKCEEFMKEKILNERFRA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g17099.t1 | Gene3D | G3DSA:3.40.50.12780 | - | 10 | 424 | 9.9E-86 |
| 9 | g17099.t1 | Gene3D | G3DSA:3.30.300.30 | - | 425 | 529 | 2.2E-15 |
| 2 | g17099.t1 | PANTHER | PTHR24096:SF353 | GH16244P-RELATED | 6 | 527 | 2.8E-128 |
| 3 | g17099.t1 | PANTHER | PTHR24096 | LONG-CHAIN-FATTY-ACID–COA LIGASE | 6 | 527 | 2.8E-128 |
| 1 | g17099.t1 | Pfam | PF00501 | AMP-binding enzyme | 45 | 429 | 1.8E-71 |
| 11 | g17099.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 224 | - |
| 12 | g17099.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 225 | 243 | - |
| 10 | g17099.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 244 | 540 | - |
| 7 | g17099.t1 | ProSitePatterns | PS00455 | Putative AMP-binding domain signature. | 190 | 201 | - |
| 6 | g17099.t1 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 11 | 525 | 3.14E-97 |
| 5 | g17099.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 91 | 113 | - |
| 4 | g17099.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 225 | 247 | - |
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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
