Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 4-coumarate–CoA ligase-like 5.

Parent gene

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 g9819 g9819.t3 TSS g9819.t3 5381408 5381408
chr_1 g9819 g9819.t3 isoform g9819.t3 5381446 5382715
chr_1 g9819 g9819.t3 exon g9819.t3.exon1 5381446 5382057
chr_1 g9819 g9819.t3 cds g9819.t3.CDS1 5381446 5382057
chr_1 g9819 g9819.t3 exon g9819.t3.exon2 5382108 5382596
chr_1 g9819 g9819.t3 cds g9819.t3.CDS2 5382108 5382596
chr_1 g9819 g9819.t3 exon g9819.t3.exon3 5382668 5382715
chr_1 g9819 g9819.t3 cds g9819.t3.CDS3 5382668 5382715
chr_1 g9819 g9819.t3 TTS g9819.t3 NA NA

Sequences

>g9819.t3 Gene=g9819 Length=1149
ATGGAAGCAAGTTTTAATTCTGAACTTAAAATTTGGAGAGGTCCAAAAATTCCTTATCCC
TTTTCAATGGATACAATGATAAGCGATTTAGTTTTGGAAAATTTATCAAAAACTCCTGAG
CGAATTTTGCAAATTACAAGGTCTGATGATAAAGCAATTACTTGCAATGAATTTAAAATT
TCAATGATTCGTGTCGCTCAAAATCTTGCGAAAATCGGCATAAAGGAGGAAGATGTTGTT
GGAATAATTGCCAGGCAATCACATTTGGCTTCTTATATAATAAACGGTTGTATAGCATTA
GGTGCTCTTATTAACCCTTTACATGCGGCAATGAATGAAACTGATATATGTGGAATTTTC
ACTCAGACAAGACCAAAAATTATCATCTGTGAGTTTGATATTATTCCAAAAGTTCAATGG
GCTCTGAAAAATGTTGATTTTTCTTATCAAATTTATTCAATGTCTAATGAAAATTCAGAA
CTTTTAAAAGCAGAAGACTTTTTGAAACCAACTGATAATGAAGATAATTTTAAATTACCA
AGATTCAAAAAACCTGCGAATGAAAAGATTTTTGCAATTTTATGTTCTTCTGGAACGACA
GGAATGAGTAAAGGCGTTTGTTTCTCACACTCTTCAGTGCTCTCATTGATATCAGAATTT
CCGAAAACAACATATACTACAGTATCTTACACTACAAGTCCGATTTATTGGGCTACTGGA
TTTTTTCCTAATATAACGTCAGTTTTATTACAAAATGAATTGCGTATCGTATATGAAGAT
AAGCAAGTTGAAATCCGAGAAATCTTTGAAGATATTGAAAAATATGGAATTACATCTGCA
TCAATAACACCAACGCTTTTGGCTTTAATTTTGCAAGACGAAAATATTCATAAGTATAAT
TTAAAGAGTCTTCAAAGTGTTACATCTGGAGGCTCAATTGTTTCAAAAACATTACGAGAG
AAATTTGCTGAAATATTTCCAGACAAAGTGATGATGGTTCCTTATGGATTGACTGAAATT
TTTGTTTCAATGACAAAACCAAATGAGTATAAGCAAGAATATGCTGTTGGTTCTTTATTA
TCTCCGCATAGTGAAGTTAAAGTTTGTAAAATATTACAACAATGCAGAAGCAACATCAAT
TGCATTTGA

>g9819.t3 Gene=g9819 Length=382
MEASFNSELKIWRGPKIPYPFSMDTMISDLVLENLSKTPERILQITRSDDKAITCNEFKI
SMIRVAQNLAKIGIKEEDVVGIIARQSHLASYIINGCIALGALINPLHAAMNETDICGIF
TQTRPKIIICEFDIIPKVQWALKNVDFSYQIYSMSNENSELLKAEDFLKPTDNEDNFKLP
RFKKPANEKIFAILCSSGTTGMSKGVCFSHSSVLSLISEFPKTTYTTVSYTTSPIYWATG
FFPNITSVLLQNELRIVYEDKQVEIREIFEDIEKYGITSASITPTLLALILQDENIHKYN
LKSLQSVTSGGSIVSKTLREKFAEIFPDKVMMVPYGLTEIFVSMTKPNEYKQEYAVGSLL
SPHSEVKVCKILQQCRSNINCI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g9819.t3 Gene3D G3DSA:3.40.50.12780 - 10 375 1.5E-59
2 g9819.t3 PANTHER PTHR24096:SF353 GH16244P-RELATED 5 371 4.9E-71
3 g9819.t3 PANTHER PTHR24096 LONG-CHAIN-FATTY-ACID–COA LIGASE 5 371 4.9E-71
1 g9819.t3 Pfam PF00501 AMP-binding enzyme 34 370 2.0E-43
5 g9819.t3 ProSitePatterns PS00455 Putative AMP-binding domain signature. 193 204 -
4 g9819.t3 SUPERFAMILY SSF56801 Acetyl-CoA synthetase-like 10 364 7.72E-50

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