Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Probable 4-coumarate–CoA ligase 1.

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_3 g1086 g1086.t2 TSS g1086.t2 8063942 8063942
chr_3 g1086 g1086.t2 isoform g1086.t2 8063978 8065059
chr_3 g1086 g1086.t2 exon g1086.t2.exon1 8063978 8065059
chr_3 g1086 g1086.t2 cds g1086.t2.CDS1 8063978 8065057
chr_3 g1086 g1086.t2 TTS g1086.t2 8065758 8065758

Sequences

>g1086.t2 Gene=g1086 Length=1082
ATGTTCAAACCAACATACGATAAAGCTACAAAAGTCTGGAGCGGTCCAAAAGTACCACCA
ATCTTCAATCCTGATCAAAATCTTGGTCAATTAATTGTGAAAGTTCTTGAGCAAACTCCA
GATGCTGTGACACAAATTTCAGCTGATACAAATGTTTCAGTAACTTGTGGTGAAATGCGA
GAAAGAATTTTGAAATTCGCTGTTCATTTGAATAATCTTGGACTTAAACAAGGCGATGTT
ATTGGTGTTGTAGCTGGAAATACTGAAAATATTGCTCCAACTGTTTTTGCTTGCTTCTTT
CTCGGACTTCCTGTTAATCCGCTTACTCCGGTTATGGTCAAAAGCAATATTGTACAAATG
TATTCGAAAACTAAACCAAAATTGATCTTTTGTGATGAGAAAAATTTAAAAATAGTTCAA
AATTCAGTAGACATGATGAAAAGTGAAGCAAAAATTTATACAGTGATGGAAAAAGTTGAA
AATTATGAATGTGTAACTGAAATACTTAAAGAAAATGTTAATTTTGACGAGTTCATTTTT
CCTAAAGTTGATCCAAACACAACATTAATAATTCTTTGCTCATCTGGAACATCGGGACCT
TTGAAAGGAATTTGCAAATCACATCGTGAAGTCTTATCAGCAATGTTTCCACTCTACGAT
CGTTATTTGATGAATAATCCAAGATTTTACGTCATTTCTGCAGTTTTCTGGGCAAGTGGT
TTTCATTTTCTTTTGATGACTTCTTTATTCAATTATACAAGAATTATAACAGCTGAACCA
TATGAGCCTAAACGTTTTGTTGACATTTTAGTGAAATATAAAATAAATTCCTTAATGACG
CCACCATTTATGATTATCAATCTCGTACAAAATGACGCATTTCAAATTCTAGAACATATG
AGGTTGTGGTTTTTCGCTGGTGCAATTGTTACAAAAGAAATTTTTAAAAAACTTCGACCT
TTTATTCCAAATGCAATGTTTGTAAATGGTTATGGAATTTCTGAAGTTAATTTACTTGCT
ATAAATTATGAAATGAAAAAACCAGAAAGTAGTGGATATCCTGTTCAAAATGTTGATATT
AT

>g1086.t2 Gene=g1086 Length=360
MFKPTYDKATKVWSGPKVPPIFNPDQNLGQLIVKVLEQTPDAVTQISADTNVSVTCGEMR
ERILKFAVHLNNLGLKQGDVIGVVAGNTENIAPTVFACFFLGLPVNPLTPVMVKSNIVQM
YSKTKPKLIFCDEKNLKIVQNSVDMMKSEAKIYTVMEKVENYECVTEILKENVNFDEFIF
PKVDPNTTLIILCSSGTSGPLKGICKSHREVLSAMFPLYDRYLMNNPRFYVISAVFWASG
FHFLLMTSLFNYTRIITAEPYEPKRFVDILVKYKINSLMTPPFMIINLVQNDAFQILEHM
RLWFFAGAIVTKEIFKKLRPFIPNAMFVNGYGISEVNLLAINYEMKKPESSGYPVQNVDI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g1086.t2 Gene3D G3DSA:3.40.50.12780 - 10 360 1.7E-61
2 g1086.t2 PANTHER PTHR24096:SF353 GH16244P-RELATED 4 359 1.1E-72
3 g1086.t2 PANTHER PTHR24096 LONG-CHAIN-FATTY-ACID–COA LIGASE 4 359 1.1E-72
1 g1086.t2 Pfam PF00501 AMP-binding enzyme 36 360 5.3E-40
8 g1086.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 228 -
10 g1086.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 229 250 -
9 g1086.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 251 360 -
6 g1086.t2 ProSitePatterns PS00455 Putative AMP-binding domain signature. 191 202 -
5 g1086.t2 SUPERFAMILY SSF56801 Acetyl-CoA synthetase-like 12 359 2.22E-52
4 g1086.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 229 251 -

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