General information for g9821.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 g9821 is located on chr_1: 5387981..5388649 (+ 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 | g9821 | g9821.t1 | TSS | g9821.t1 | 5386333 | 5386333 |
| chr_1 | g9821 | g9821.t1 | isoform | g9821.t1 | 5386601 | 5388463 |
| chr_1 | g9821 | g9821.t1 | exon | g9821.t1.exon1 | 5386601 | 5387130 |
| chr_1 | g9821 | g9821.t1 | cds | g9821.t1.CDS1 | 5386601 | 5387130 |
| chr_1 | g9821 | g9821.t1 | exon | g9821.t1.exon2 | 5387223 | 5387298 |
| chr_1 | g9821 | g9821.t1 | cds | g9821.t1.CDS2 | 5387223 | 5387298 |
| chr_1 | g9821 | g9821.t1 | exon | g9821.t1.exon3 | 5387356 | 5387919 |
| chr_1 | g9821 | g9821.t1 | cds | g9821.t1.CDS3 | 5387356 | 5387919 |
| chr_1 | g9821 | g9821.t1 | exon | g9821.t1.exon4 | 5387981 | 5388463 |
| chr_1 | g9821 | g9821.t1 | cds | g9821.t1.CDS4 | 5387981 | 5388463 |
| chr_1 | g9821 | g9821.t1 | TTS | g9821.t1 | 5388808 | 5388808 |
Sequences
>g9821.t1 Gene=g9821 Length=1653
ATGGCTTCATTTGATTCGGATTTAAAAATTTGGAATGGATTGGAATTAAGATATGGATTT
AGTTATAATACATCAATCGGTGCAGAATTGTTGAAAAAATTATCGGAATCACCAGAGCGA
GTGTTAAGTATTTGTCATGATGAGGAGACGTCATTGACATGTCATGAAACAAAATTGGCA
AGTATTCGAATCGCACAAAATTTAACAAAACTCGGTTATCAGAAAGGAGATGTGATTGGA
TTTATGTGCAGCAATAGCACATATTTGCCAGCAGTACTTTATGCTTCCATAATGATAGGG
ACACCAGTTAACCCTCTCGATACTGGATTTAAAAAGGTTGATATTATGCATATGTTTGAT
ATAACTCAGCCAAAATTAGTCTTCTGCGATTATGACGTTTATGAAAGAGTTAAATTATCT
CTTGATGAGATGAAGAGTAATGCTAAAATTATTACGCTGCGACAGGCAATTGATGGAGTT
ACATTCGTTGATGAATTACTCGCGATAACAGGAAATGAAGATTCCTTTGAGCCAACTGAT
CTCGGTGACTCTAGAGAAGCGTGTGCTGTTATTATGTGCTCATCAGGAACAAGTGGTGAA
ATTAAAGGTGTTTGTTTGTCACATGCCAATATTTTATCCCAGCTCACAACATTTGACATG
TCATTTGCTTTTATTTCATTGAGCTTTAGTCCTATTTACTGGACAACTGGATTGCTGACA
ACAATTTTGACAGCACTTCGATCGCGCGATACACGTATTATGACAATTCAACCATTTAGT
GTAGAGCTCTTTTTACAACTTGTTAAAAAATATGACATCAACGTCTTTAAAGCTGCTCCA
TATCAACTTACTTTGCTTCTTCAACATCCTGCATTCAATGCTAAAGACTATGAAAGAATT
TTAATATTTTTTGCTATGGGCAGTTTAGTCTCAGAGTCGTTAAGAAAAGAATTTCGTCAT
GCATTTCCTAACCATCCACTTGTTATTGGCTATGGCATGACTGAAGCATGCATTACAATT
TCTGCAAATGGTCCGGGCGATTCTATAGAAGGTTTAACTGTAGGTAGAATTTCTCATAAT
GTAAAAGTGAAAGTCATCGGTAAAAATGGACAACCTGTTGACATCAGTGTAACTGGAGAA
ATTTTTGCTAAACCACAATTCCCTTTTCTGGGATATTATAAGAATGAAGAGGCTACAAGA
AATGCAATTGATGAAGATGGATATCTTAAAACGGGTGACATAGGTTTTGTAGATGAAGAA
GGAAATATATTTTTGATAGATAAAAAGAAAGAAGTATTGAAGTACAAAAATTATCAAGTT
TGTACAACAGAAATTGAGGAAATTGTTCAAGAAATTGAAGGTGTAGAACAAGTTTCAGTT
GTAGGAATTCCCGATCCACTTTACACAACTTTGCCTGCTGCAGTGGTTGTCAAAAAGCCA
GAATTTGAAGATCTCAATGAACAATTTATAATGGATTATGTTGCAGAAAAATTACCGGAA
TATAATCAACTTCATGGTGGAGTATATTTTGTCGAAGAAATGCCCATGACGGCATCAGGT
CAAATACAAAAACGTTTTGTGAAGGTCATTGCAATTAGAGAGTATAAAAGTCGTATGGTA
CAAGAGGACGATGATGAAGAATATTCACAATAA
>g9821.t1 Gene=g9821 Length=550
MASFDSDLKIWNGLELRYGFSYNTSIGAELLKKLSESPERVLSICHDEETSLTCHETKLA
SIRIAQNLTKLGYQKGDVIGFMCSNSTYLPAVLYASIMIGTPVNPLDTGFKKVDIMHMFD
ITQPKLVFCDYDVYERVKLSLDEMKSNAKIITLRQAIDGVTFVDELLAITGNEDSFEPTD
LGDSREACAVIMCSSGTSGEIKGVCLSHANILSQLTTFDMSFAFISLSFSPIYWTTGLLT
TILTALRSRDTRIMTIQPFSVELFLQLVKKYDINVFKAAPYQLTLLLQHPAFNAKDYERI
LIFFAMGSLVSESLRKEFRHAFPNHPLVIGYGMTEACITISANGPGDSIEGLTVGRISHN
VKVKVIGKNGQPVDISVTGEIFAKPQFPFLGYYKNEEATRNAIDEDGYLKTGDIGFVDEE
GNIFLIDKKKEVLKYKNYQVCTTEIEEIVQEIEGVEQVSVVGIPDPLYTTLPAAVVVKKP
EFEDLNEQFIMDYVAEKLPEYNQLHGGVYFVEEMPMTASGQIQKRFVKVIAIREYKSRMV
QEDDDEEYSQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g9821.t1 | Gene3D | G3DSA:3.40.50.12780 | - | 10 | 431 | 3.3E-90 |
| 8 | g9821.t1 | Gene3D | G3DSA:3.30.300.30 | - | 432 | 533 | 3.3E-21 |
| 3 | g9821.t1 | PANTHER | PTHR24096:SF353 | GH16244P-RELATED | 4 | 533 | 1.5E-134 |
| 4 | g9821.t1 | PANTHER | PTHR24096 | LONG-CHAIN-FATTY-ACID–COA LIGASE | 4 | 533 | 1.5E-134 |
| 2 | g9821.t1 | Pfam | PF00501 | AMP-binding enzyme | 36 | 435 | 3.1E-70 |
| 1 | g9821.t1 | Pfam | PF13193 | AMP-binding enzyme C-terminal domain | 444 | 520 | 4.2E-12 |
| 10 | g9821.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 221 | - |
| 11 | g9821.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 222 | 246 | - |
| 9 | g9821.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 247 | 550 | - |
| 6 | g9821.t1 | ProSitePatterns | PS00455 | Putative AMP-binding domain signature. | 191 | 202 | - |
| 5 | g9821.t1 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 25 | 533 | 7.98E-107 |
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.
