Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Very-long-chain 3-oxoacyl-CoA reductase.

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 g4623 g4623.t5 TTS g4623.t5 3660496 3660496
chr_2 g4623 g4623.t5 isoform g4623.t5 3661309 3662176
chr_2 g4623 g4623.t5 exon g4623.t5.exon1 3661309 3661406
chr_2 g4623 g4623.t5 cds g4623.t5.CDS1 3661309 3661406
chr_2 g4623 g4623.t5 exon g4623.t5.exon2 3661462 3661584
chr_2 g4623 g4623.t5 cds g4623.t5.CDS2 3661462 3661584
chr_2 g4623 g4623.t5 exon g4623.t5.exon3 3662017 3662176
chr_2 g4623 g4623.t5 cds g4623.t5.CDS3 3662017 3662176
chr_2 g4623 g4623.t5 TSS g4623.t5 3662315 3662315

Sequences

>g4623.t5 Gene=g4623 Length=381
ATGTTTGAAACATTTTTAATTTGTGTTGGTATTTATGCCACAATTTGGTATTTGTATGAA
AATTTATCATCACCTATTTTGATAATTGTCAATACTCTATTGGAACTTTTTATTCCTTCA
AAGAAGAAAAGTTTTAAGGAAAAATATGGTGAATGGGCAGTTGTTACTGGCGCAACTGAT
GGCATTGGTAAGCAATATGCAAAGGAACTAGCAAAACATGGCATGAATATCGTTCTAATC
TCAAGAACTGAGTCAAAATTGATTGAAGTCGCTAAAGAAATTGAGTCAATGTACTCGGTA
AAGACAAAGTATGTGGCTGTTGACTTTGGCAATGGCAAAAAAATCTATGAAAAAATAAAA
GAAGAATTAAAGTCAATGGAT

>g4623.t5 Gene=g4623 Length=127
MFETFLICVGIYATIWYLYENLSSPILIIVNTLLELFIPSKKKSFKEKYGEWAVVTGATD
GIGKQYAKELAKHGMNIVLISRTESKLIEVAKEIESMYSVKTKYVAVDFGNGKKIYEKIK
EELKSMD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g4623.t5 Gene3D G3DSA:3.40.50.720 - 44 127 2.1E-17
2 g4623.t5 PANTHER PTHR43899:SF9 MIP25013P-RELATED 2 127 1.7E-45
3 g4623.t5 PANTHER PTHR43899 RH59310P 2 127 1.7E-45
1 g4623.t5 Pfam PF00106 short chain dehydrogenase 52 127 1.0E-13
8 g4623.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 21 -
9 g4623.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 22 38 -
7 g4623.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 39 127 -
5 g4623.t5 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 50 121 3.8E-17
4 g4623.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 15 37 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

## [1] "No matching GO terms"

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