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.t18 TSS g3472.t18 25772089 25772089
chr_3 g3472 g3472.t18 isoform g3472.t18 25772160 25773395
chr_3 g3472 g3472.t18 exon g3472.t18.exon1 25772160 25772165
chr_3 g3472 g3472.t18 cds g3472.t18.CDS1 25772160 25772165
chr_3 g3472 g3472.t18 exon g3472.t18.exon2 25772226 25772256
chr_3 g3472 g3472.t18 cds g3472.t18.CDS2 25772226 25772256
chr_3 g3472 g3472.t18 exon g3472.t18.exon3 25772417 25772747
chr_3 g3472 g3472.t18 cds g3472.t18.CDS3 25772417 25772747
chr_3 g3472 g3472.t18 exon g3472.t18.exon4 25772812 25773016
chr_3 g3472 g3472.t18 cds g3472.t18.CDS4 25772812 25773016
chr_3 g3472 g3472.t18 exon g3472.t18.exon5 25773075 25773395
chr_3 g3472 g3472.t18 cds g3472.t18.CDS5 25773075 25773395
chr_3 g3472 g3472.t18 TTS g3472.t18 25773546 25773546

Sequences

>g3472.t18 Gene=g3472 Length=894
ATGGAGATTGAAATTCTTGATGCACGAAATTCAAAAGTTATAACAAAATGTAATGTTCAA
TCCAGCACAACGATAAAAGATTTGAAATCCAGTGTATATGCGGCAAATAAAAAATTAAAT
GTTCATCGTCAATCATTTAAGCTGGAAGTAAAAGGAAAAACACTTAAGGATAGTGACACA
ATTGAATCATTGAACTTAAGAAATGGTAGTAAATTGTATGTTAAAGATCTTGGTCCGCAA
ATTGGTTGGTCAACTGTTTTCCTTTGCGAATATGCTGGTCCACTTGTTGTTTATTTATGG
GTTTATACTCGTCCTTGGTTGTTTTATGGTGACACATCGTCATCAGCTGAAATCAGTCAA
ACAGCACAATGCTACACATTGCATTATGCTAAACGATTACTTGAAACAATTTTCGTTCAT
CGCTTTTCACATGCGACAATGCCTATGAGAAATTTGTTCAAAAACTGCATCTACTATTGG
GGATTTACTGCTTACGTTGCCTATCACGTTAATCATCCTCTTTTTACATCACCATCTACT
GCTCAAGTTTATGCTAGTCTTGCCGCATTCTTGTTATGTGAACTTGGTAACTTTTCAATA
CATATCAATTTGAGAAATTTAAGACCACCAGGAACATCTGTAAGAAAAATTCCAATGTCT
GATTCAAATCCGCTAACTGCTCTCTTTAACTTCGTTTCGTGTCCAAATTATACTTACGAG
TTCGGAGCTTGGCTTTCATTTTCTATCATGACTCAATGCTTGCCTGCTTTCCTTTTTGCT
GCTGCTGGAATGTATCAAATGACAATGTGGGCTATCGGAAAACATAAGAACTACAAAAAA
GAATTCAAAGAATATCCAAAGCAAAGAAAAGCTATTATTCCATTTTTATTGTAA

>g3472.t18 Gene=g3472 Length=297
MEIEILDARNSKVITKCNVQSSTTIKDLKSSVYAANKKLNVHRQSFKLEVKGKTLKDSDT
IESLNLRNGSKLYVKDLGPQIGWSTVFLCEYAGPLVVYLWVYTRPWLFYGDTSSSAEISQ
TAQCYTLHYAKRLLETIFVHRFSHATMPMRNLFKNCIYYWGFTAYVAYHVNHPLFTSPST
AQVYASLAAFLLCELGNFSIHINLRNLRPPGTSVRKIPMSDSNPLTALFNFVSCPNYTYE
FGAWLSFSIMTQCLPAFLFAAAGMYQMTMWAIGKHKNYKKEFKEYPKQRKAIIPFLL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g3472.t18 CDD cd01801 Ubl_TECR_like 2 77 4.24141E-24
6 g3472.t18 Gene3D G3DSA:3.10.20.90 - 1 77 2.8E-22
3 g3472.t18 PANTHER PTHR10556:SF28 SC2 1 297 4.4E-107
4 g3472.t18 PANTHER PTHR10556 3-OXO-5-ALPHA-STEROID 4-DEHYDROGENASE 1 297 4.4E-107
2 g3472.t18 Pfam PF00240 Ubiquitin family 18 74 2.0E-7
1 g3472.t18 Pfam PF02544 3-oxo-5-alpha-steroid 4-dehydrogenase 146 297 3.9E-30
8 g3472.t18 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 253 -
9 g3472.t18 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 254 273 -
7 g3472.t18 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 274 297 -
15 g3472.t18 ProSiteProfiles PS50053 Ubiquitin domain profile. 1 74 11.442
16 g3472.t18 ProSiteProfiles PS50244 Steroid 5-alpha reductase C-terminal domain profile. 186 272 22.185
14 g3472.t18 SMART SM00213 ubq_7 3 77 4.9E-4
5 g3472.t18 SUPERFAMILY SSF54236 Ubiquitin-like 12 74 9.46E-9
11 g3472.t18 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 80 102 -
12 g3472.t18 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 156 175 -
13 g3472.t18 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 241 263 -

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. There were no conditions that were differentially expressed