Gene loci information

Transcript annotation

  • This transcript has been annotated as 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.t17 TSS g3472.t17 25772089 25772089
chr_3 g3472 g3472.t17 isoform g3472.t17 25772160 25773395
chr_3 g3472 g3472.t17 exon g3472.t17.exon1 25772160 25772165
chr_3 g3472 g3472.t17 cds g3472.t17.CDS1 25772160 25772165
chr_3 g3472 g3472.t17 exon g3472.t17.exon2 25772392 25772747
chr_3 g3472 g3472.t17 cds g3472.t17.CDS2 25772392 25772747
chr_3 g3472 g3472.t17 exon g3472.t17.exon3 25772800 25773016
chr_3 g3472 g3472.t17 cds g3472.t17.CDS3 25772800 25773016
chr_3 g3472 g3472.t17 exon g3472.t17.exon4 25773075 25773395
chr_3 g3472 g3472.t17 cds g3472.t17.CDS4 25773075 25773395
chr_3 g3472 g3472.t17 TTS g3472.t17 25773546 25773546

Sequences

>g3472.t17 Gene=g3472 Length=900
ATGGAGTTTATCTGTCTCTTCGCTAAAACAGTTATAACAAAATGTAATGTTCAATCCAGC
ACAACGATAAAAGATTTGAAATCCAGTGTATATGCGGCAAATAAAAAATTAAATGTTCAT
CGTCAATCATTTAAGCTGGAAGTAAAAGGAAAAACACTTAAGGATAGTGACACAATTGAA
TCATTGAACTTAAGAAATGGTAGTAAATTGTATGTTAAAGATCTTGGTCCGCAAATTGGT
TGGTCAACTGTTTTCCTTTGCGAATATGCTGGTCCACTTGTTGTTTATTTATGGGTTTAT
ACTCGTCCTTGGTTGTTTTATGGTGACACATCGTCATCAGCTGAAATCAGTCAAACAGCA
CATATTGCTGCTGCATGCTACACATTGCATTATGCTAAACGATTACTTGAAACAATTTTC
GTTCATCGCTTTTCACATGCGACAATGCCTATGAGAAATTTGTTCAAAAACTGCATCTAC
TATTGGGGATTTACTGCTTACGTTGCCTATCACGTTAATCATCCTCTTTTTACATCACCA
TCTACTGCTCAAGTTTATGCTAGTCTTGCCGCATTCTTGTTATGTGAACTTGGTAACTTT
TCAATACATATCAATTTGAGAAATTTAAGACCACCAGGAACATCTGTAAGAAAAATTCCA
ATGTCTGATTCAAATCCGCTAACTGCTCTCTTTAACTTCGTTTCGTGTCCAAATTATACT
TACGAGTTCGGAGCTTGGCTTTCATTTTCTATCATGACTCAATGCTTGCCTGCTTTCCTT
TTTGCTGCTGCTGGAATGTATCAAATGACAATGTGGGCTATCGGAAAACATAAGAACTAC
AAAAAAGAATTCAAAGAATATCCAAAGCAAAGAAAAGCTATTATTCCATTTTTATTGTAA

>g3472.t17 Gene=g3472 Length=299
MEFICLFAKTVITKCNVQSSTTIKDLKSSVYAANKKLNVHRQSFKLEVKGKTLKDSDTIE
SLNLRNGSKLYVKDLGPQIGWSTVFLCEYAGPLVVYLWVYTRPWLFYGDTSSSAEISQTA
HIAAACYTLHYAKRLLETIFVHRFSHATMPMRNLFKNCIYYWGFTAYVAYHVNHPLFTSP
STAQVYASLAAFLLCELGNFSIHINLRNLRPPGTSVRKIPMSDSNPLTALFNFVSCPNYT
YEFGAWLSFSIMTQCLPAFLFAAAGMYQMTMWAIGKHKNYKKEFKEYPKQRKAIIPFLL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g3472.t17 CDD cd01801 Ubl_TECR_like 17 75 2.54982E-19
6 g3472.t17 Gene3D G3DSA:3.10.20.90 - 4 75 8.3E-19
3 g3472.t17 PANTHER PTHR10556:SF28 SC2 10 299 4.4E-109
4 g3472.t17 PANTHER PTHR10556 3-OXO-5-ALPHA-STEROID 4-DEHYDROGENASE 10 299 4.4E-109
2 g3472.t17 Pfam PF00240 Ubiquitin family 16 72 2.3E-7
1 g3472.t17 Pfam PF02544 3-oxo-5-alpha-steroid 4-dehydrogenase 148 299 4.0E-30
8 g3472.t17 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 255 -
9 g3472.t17 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 256 275 -
7 g3472.t17 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 276 299 -
15 g3472.t17 ProSiteProfiles PS50053 Ubiquitin domain profile. 4 72 11.551
16 g3472.t17 ProSiteProfiles PS50244 Steroid 5-alpha reductase C-terminal domain profile. 188 274 22.185
14 g3472.t17 SMART SM00213 ubq_7 4 75 1.3E-4
5 g3472.t17 SUPERFAMILY SSF54236 Ubiquitin-like 13 72 1.15E-8
13 g3472.t17 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 78 100 -
11 g3472.t17 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 158 177 -
12 g3472.t17 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 243 265 -

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:0016627 oxidoreductase activity, acting on the CH-CH group of donors MF
GO:0005515 protein binding MF
GO:0006629 lipid metabolic process BP

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

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