Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Long-chain-fatty-acid–CoA ligase 3.

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_2 g7969 g7969.t9 isoform g7969.t9 27330568 27331735
chr_2 g7969 g7969.t9 exon g7969.t9.exon1 27330568 27330951
chr_2 g7969 g7969.t9 cds g7969.t9.CDS1 27330568 27330951
chr_2 g7969 g7969.t9 exon g7969.t9.exon2 27331028 27331163
chr_2 g7969 g7969.t9 cds g7969.t9.CDS2 27331028 27331163
chr_2 g7969 g7969.t9 exon g7969.t9.exon3 27331225 27331349
chr_2 g7969 g7969.t9 cds g7969.t9.CDS3 27331225 27331247
chr_2 g7969 g7969.t9 TTS g7969.t9 27331318 27331318
chr_2 g7969 g7969.t9 exon g7969.t9.exon4 27331526 27331735
chr_2 g7969 g7969.t9 TSS g7969.t9 27331751 27331751

Sequences

>g7969.t9 Gene=g7969 Length=855
ATGAAGTCTCAAGTGTAAGAGTAAGAATTGCAAAATATTTAATTTTAAGCATAAATAAGT
TAAAATAAGAATAAATTGTGCTGAAATATTGAAGCTAACATTACATAGATTCATCGTAAA
GCGCAGTCTTTCAAAATAAACGTCAAATCTAGTCAAAATTGATGTGTAAAACTTTAATTT
AACTACTTATAAGTCTAAAGGTTAATAGAGTTAGCCGATTTTTTCCTCAAAAACAAGAGA
GAAAGAAGAAAAAAACAAAAATAAAGCTTCTACTTCATTCATTATATCAAGTTTAAAGTA
TTCAAAGGCAAAATGTTTATCGAAAAAGATACAAATATGAATAATTTTTGGATCCAATGT
GTCATTAAGGCAATATCATATGCGGGGCTCGTCTATGACATTTTATCATTTCCTGTCTAC
TTTCTACTTCAAAGACCATGGAGCCGTCGAAGTATGTCACATCGAATAAAGGCAAAACCA
ATAAGTTCAGATAACACGCAAATTACATACAGAAGTGTTGATCCACCGCGTGAAATTCAT
TTGAAAATGGTGCAAGCCAATATTGATACGCTTGAAAAGATGCTAAAATATATGAAAGAG
ACACATCAAGAAAAATTATGTCTCGGCACGCGTCAAGTCCTAAGTGAGGAAGATGAAGTG
CAAGCTAATGGAAAAGTTTTCAAAAAATATAAAATGGGTGACTATACATGGCGCAATTTT
ATTGAGACCGAACAAGAGGCTTGCAACTTTGGATATGGCATTCGAAAGTTGGGTGTTAAA
CCAAAGGACAATGTTGTTATTTTCTCAGAGACTCGTGCCGAATGGATGATTGCTGCTCAT
GGTTTATGTAAGATG

>g7969.t9 Gene=g7969 Length=181
MFIEKDTNMNNFWIQCVIKAISYAGLVYDILSFPVYFLLQRPWSRRSMSHRIKAKPISSD
NTQITYRSVDPPREIHLKMVQANIDTLEKMLKYMKETHQEKLCLGTRQVLSEEDEVQANG
KVFKKYKMGDYTWRNFIETEQEACNFGYGIRKLGVKPKDNVVIFSETRAEWMIAAHGLCK
M

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g7969.t9 Coils Coil Coil 77 97 -
6 g7969.t9 Gene3D G3DSA:3.40.50.12780 - 88 181 5.4E-8
2 g7969.t9 PANTHER PTHR43272:SF22 LONG-CHAIN-FATTY-ACID–COA LIGASE 4 29 177 9.4E-37
3 g7969.t9 PANTHER PTHR43272 LONG-CHAIN-FATTY-ACID–COA LIGASE 29 177 9.4E-37
1 g7969.t9 Pfam PF00501 AMP-binding enzyme 126 180 2.5E-8
9 g7969.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 11 -
10 g7969.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 39 -
8 g7969.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 40 181 -
5 g7969.t9 SUPERFAMILY SSF56801 Acetyl-CoA synthetase-like 61 180 1.7E-8
4 g7969.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 20 39 -

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.

Raw TPM values