Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Probable very-long-chain enoyl-CoA reductase art-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 g3472 g3472.t6 TSS g3472.t6 25772089 25772089
chr_3 g3472 g3472.t6 isoform g3472.t6 25772160 25773395
chr_3 g3472 g3472.t6 exon g3472.t6.exon1 25772160 25772165
chr_3 g3472 g3472.t6 cds g3472.t6.CDS1 25772160 25772165
chr_3 g3472 g3472.t6 exon g3472.t6.exon2 25772226 25772256
chr_3 g3472 g3472.t6 cds g3472.t6.CDS2 25772226 25772256
chr_3 g3472 g3472.t6 exon g3472.t6.exon3 25772417 25773016
chr_3 g3472 g3472.t6 cds g3472.t6.CDS3 25772417 25772751
chr_3 g3472 g3472.t6 exon g3472.t6.exon4 25773075 25773395
chr_3 g3472 g3472.t6 TTS g3472.t6 25773546 25773546

Sequences

>g3472.t6 Gene=g3472 Length=958
ATGGAGATTGAAATTCTTGATGCACGAAATTCAAAAGTTATAACAAAATGTAATGTTCAA
TCCAGCACAACGATAAAAGATTTGAAATCCAGTGTATATGCGGCAAATAAAAAATTAAAT
GTTCATCGTCAATCATTTAAGCTGGAAGTAAAAGGAAAAACACTTAAGGATAGTGACACA
ATTGAATCATTGAACTTAAGAAATGGTAGTAAATTGTATGTTAAAGATCTTGGTCCGCAA
ATTGGTTGGTCAACTGTTTTCCTTTGCGAATATGCTGGTCCACTTGTTGTTTATTTATGG
GTTTATACTCGTCCTTGGTTGTTTTATGGTGACACATCGTCATCAGCTGAAATCAGTCAA
ACAGCACAGTAAGTATTTGTGTAAATTAAGATTATTAAAGCTAATTAATTTTGTTTTTAG
TATTGCTGCTGCATGCTACACATTGCATTATGCTAAACGATTACTTGAAACAATTTTCGT
TCATCGCTTTTCACATGCGACAATGCCTATGAGAAATTTGTTCAAAAACTGCATCTACTA
TTGGGGATTTACTGCTTACGTTGCCTATCACGTTAATCATCCTCTTTTTACATCACCATC
TACTGCTCAAGTTTATGCTAGTCTTGCCGCATTCTTGTTATGTGAACTTGGTAACTTTTC
AATACATATCAATTTGAGAAATTTAAGACCACCAGGAACATCTGTAAGAAAAATTCCAAT
GTCTGATTCAAATCCGCTAACTGCTCTCTTTAACTTCGTTTCGTGTCCAAATTATACTTA
CGAGTTCGGAGCTTGGCTTTCATTTTCTATCATGACTCAATGCTTGCCTGCTTTCCTTTT
TGCTGCTGCTGGAATGTATCAAATGACAATGTGGGCTATCGGAAAACATAAGAACTACAA
AAAAGAATTCAAAGAATATCCAAAGCAAAGAAAAGCTATTATTCCATTTTTATTGTAA

>g3472.t6 Gene=g3472 Length=123
MEIEILDARNSKVITKCNVQSSTTIKDLKSSVYAANKKLNVHRQSFKLEVKGKTLKDSDT
IESLNLRNGSKLYVKDLGPQIGWSTVFLCEYAGPLVVYLWVYTRPWLFYGDTSSSAEISQ
TAQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g3472.t6 CDD cd01801 Ubl_TECR_like 2 77 1.79398E-22
5 g3472.t6 Gene3D G3DSA:3.10.20.90 - 1 77 3.6E-23
2 g3472.t6 PANTHER PTHR10556:SF28 SC2 1 120 1.7E-23
3 g3472.t6 PANTHER PTHR10556 3-OXO-5-ALPHA-STEROID 4-DEHYDROGENASE 1 120 1.7E-23
1 g3472.t6 Pfam PF00240 Ubiquitin family 16 74 3.2E-8
9 g3472.t6 ProSiteProfiles PS50053 Ubiquitin domain profile. 1 74 11.442
8 g3472.t6 SMART SM00213 ubq_7 3 77 4.9E-4
4 g3472.t6 SUPERFAMILY SSF54236 Ubiquitin-like 12 74 1.37E-9
7 g3472.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 81 103 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005515 protein binding MF

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