General information for g9804.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Probable 4-coumarate–CoA ligase 1.
Parent gene
- The parent gene g9804 is located on chr_1: 5309848..5311516 (+ 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_1 | g9804 | g9804.t1 | isoform | g9804.t1 | 5309848 | 5311516 |
| chr_1 | g9804 | g9804.t1 | exon | g9804.t1.exon1 | 5309848 | 5310930 |
| chr_1 | g9804 | g9804.t1 | cds | g9804.t1.CDS1 | 5309848 | 5310930 |
| chr_1 | g9804 | g9804.t1 | exon | g9804.t1.exon2 | 5310998 | 5311516 |
| chr_1 | g9804 | g9804.t1 | cds | g9804.t1.CDS2 | 5310998 | 5311516 |
| chr_1 | g9804 | g9804.t1 | TSS | g9804.t1 | NA | NA |
| chr_1 | g9804 | g9804.t1 | TTS | g9804.t1 | NA | NA |
Sequences
>g9804.t1 Gene=g9804 Length=1602
ATGCATCATTCGACATTTAATAAAATCACAAAAATCTGGAGTGGTCCAAAAGTGCTTCCA
ATTTTCAATCCTGATCAAAATCTTGGTGAATTAATTGTGAAAGTTCTTGAACAAACTCCT
GATGCCATAACCCAAATTTCAGCTGACACAAATGTCTCATTAACTTGTGGCGAAATGCGA
AATAGAATCCTTAAAATTGCATTTCATTTAAATGATCTTGAACTTAAACAAGGCGATGTA
GTTGGAGTTATAACTGAAAACACTGAAAATATTGCTCCAGTTGTTTTTGCTTGTTTTTTA
CTTGGACTACCGGTTAATCCATTAGCATCAGTGATGATTGAAAGTGATATTGCACAAATA
TACTCTAAAACTAAACCAAAATTAATCTTTTGTGATGAGAAAAATTTAAAAACTGTGCAA
AATGCTGTGAAAATAATGAAAAGTGAAGCCAAAATTTATACAGTGATGGAAAAAGTTGAT
GGCTATGAATCAGTGACAAAAGTCCTTGAAAAAATTGTGAATTTTGAAGATTTCATTTAT
CCAGAAGTTGATCCTAATTCAATTATTTTTATTCCTTGTACATCAGGTTCAACTGGTTTG
GCTAAAGGAATAGGAAAAACTCATAAAGAAATAATATTTCGATTTGTTCCATCATCTTTA
TATAATCCAAATGGACCAAATGTTTTATTTCAGTCTACAGCAATCTTTTGGTTCAGTGGA
ATTTATTTTCTTATTTATGGCGCACTTTATAAATGTTTGAGAATAACTACAGCTCAATCA
GTGACGCCTGAGCTTATTGTTGAAATAATCAAAAAATATAAAGTTACAAATGTCTCTACT
GCTCCATATCTCATTGTTAATTTACTTCAATTAACAAATTTAAAACCATTTGAGACAATA
AAAATGTGGATGATTCCAGGAGCAACCGCAACTCAAAATCTTTGTGAAAGATTAAAGAAA
TACGTACCCAATGGTGTTGTAAGCAGCTTTTATGGATCGACTGAATGTGACATTATTTCA
AGCAATTCACGCGAGAAAAAATTTGGAAGTTGCGGTGAAATTTTCTATAACAATGAAGTT
AAGATAATTAATGATAATGAAAATTCGATTGATTGCAATCAAAAAGGAGAAATTTGTGTC
AAAAATATTGTAAAATTTACCGGTTATTATAATGATATTGAGAAAACTAACGAAGTATAT
GATGGTGAATGGTTTAAAACAGGAGACATTGGCTATATTGATGATGAAGGACTTCTTTAT
GTTATTGATCGTAAGAAGGACATTTTAAAATATAATAATATGCAAGTGGCTCCATTAGAA
CTTGAAGCAATAATTAATGAAATTGATGGAGTTATAAATTGTTGTGTTGTTGGAGTTTCA
GAAAAAAATACTGGAAATGATATAATTCATGCTTTTGTGATTACTAATGAATCAAAAAAT
TTAACTAGCACAGGAATTGAAGATTATATAAATTCAAAAGTCATTGATGTTAAGAAAATT
CGAGGTGGTGTTCATTTTATTAAAAATATTCCTTTAACAGCATCAGGAAAAATTGACAGA
AAAATGCTGAGAAAATTGGCAAGTGAAAAGTTTACAAAATAA
>g9804.t1 Gene=g9804 Length=533
MHHSTFNKITKIWSGPKVLPIFNPDQNLGELIVKVLEQTPDAITQISADTNVSLTCGEMR
NRILKIAFHLNDLELKQGDVVGVITENTENIAPVVFACFLLGLPVNPLASVMIESDIAQI
YSKTKPKLIFCDEKNLKTVQNAVKIMKSEAKIYTVMEKVDGYESVTKVLEKIVNFEDFIY
PEVDPNSIIFIPCTSGSTGLAKGIGKTHKEIIFRFVPSSLYNPNGPNVLFQSTAIFWFSG
IYFLIYGALYKCLRITTAQSVTPELIVEIIKKYKVTNVSTAPYLIVNLLQLTNLKPFETI
KMWMIPGATATQNLCERLKKYVPNGVVSSFYGSTECDIISSNSREKKFGSCGEIFYNNEV
KIINDNENSIDCNQKGEICVKNIVKFTGYYNDIEKTNEVYDGEWFKTGDIGYIDDEGLLY
VIDRKKDILKYNNMQVAPLELEAIINEIDGVINCCVVGVSEKNTGNDIIHAFVITNESKN
LTSTGIEDYINSKVIDVKKIRGGVHFIKNIPLTASGKIDRKMLRKLASEKFTK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g9804.t1 | Gene3D | G3DSA:3.40.50.12780 | - | 10 | 427 | 1.2E-85 |
| 10 | g9804.t1 | Gene3D | G3DSA:3.30.300.30 | - | 428 | 532 | 4.4E-21 |
| 3 | g9804.t1 | PANTHER | PTHR24096:SF353 | GH16244P-RELATED | 4 | 529 | 6.2E-130 |
| 4 | g9804.t1 | PANTHER | PTHR24096 | LONG-CHAIN-FATTY-ACID–COA LIGASE | 4 | 529 | 6.2E-130 |
| 2 | g9804.t1 | Pfam | PF00501 | AMP-binding enzyme | 36 | 431 | 3.6E-67 |
| 1 | g9804.t1 | Pfam | PF13193 | AMP-binding enzyme C-terminal domain | 440 | 517 | 2.4E-10 |
| 12 | g9804.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 227 | - |
| 13 | g9804.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 228 | 249 | - |
| 11 | g9804.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 250 | 533 | - |
| 8 | g9804.t1 | ProSitePatterns | PS00455 | Putative AMP-binding domain signature. | 191 | 202 | - |
| 7 | g9804.t1 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 14 | 528 | 1.26E-97 |
| 6 | g9804.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 91 | 113 | - |
| 5 | g9804.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 228 | 250 | - |
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. There were no conditions that were differentially expressed