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.t8 TSS g3472.t8 25772089 25772089
chr_3 g3472 g3472.t8 isoform g3472.t8 25772160 25773395
chr_3 g3472 g3472.t8 exon g3472.t8.exon1 25772160 25772187
chr_3 g3472 g3472.t8 cds g3472.t8.CDS1 25772160 25772187
chr_3 g3472 g3472.t8 exon g3472.t8.exon2 25772417 25772747
chr_3 g3472 g3472.t8 cds g3472.t8.CDS2 25772417 25772747
chr_3 g3472 g3472.t8 exon g3472.t8.exon3 25772800 25773016
chr_3 g3472 g3472.t8 cds g3472.t8.CDS3 25772800 25773016
chr_3 g3472 g3472.t8 exon g3472.t8.exon4 25773075 25773395
chr_3 g3472 g3472.t8 cds g3472.t8.CDS4 25773075 25773395
chr_3 g3472 g3472.t8 TTS g3472.t8 25773546 25773546

Sequences

>g3472.t8 Gene=g3472 Length=897
ATGGAGGTAAACTTGTTAATCAAATACTTTATAACAAAATGTAATGTTCAATCCAGCACA
ACGATAAAAGATTTGAAATCCAGTGTATATGCGGCAAATAAAAAATTAAATGTTCATCGT
CAATCATTTAAGCTGGAAGTAAAAGGAAAAACACTTAAGGATAGTGACACAATTGAATCA
TTGAACTTAAGAAATGGTAGTAAATTGTATGTTAAAGATCTTGGTCCGCAAATTGGTTGG
TCAACTGTTTTCCTTTGCGAATATGCTGGTCCACTTGTTGTTTATTTATGGGTTTATACT
CGTCCTTGGTTGTTTTATGGTGACACATCGTCATCAGCTGAAATCAGTCAAACAGCACAT
ATTGCTGCTGCATGCTACACATTGCATTATGCTAAACGATTACTTGAAACAATTTTCGTT
CATCGCTTTTCACATGCGACAATGCCTATGAGAAATTTGTTCAAAAACTGCATCTACTAT
TGGGGATTTACTGCTTACGTTGCCTATCACGTTAATCATCCTCTTTTTACATCACCATCT
ACTGCTCAAGTTTATGCTAGTCTTGCCGCATTCTTGTTATGTGAACTTGGTAACTTTTCA
ATACATATCAATTTGAGAAATTTAAGACCACCAGGAACATCTGTAAGAAAAATTCCAATG
TCTGATTCAAATCCGCTAACTGCTCTCTTTAACTTCGTTTCGTGTCCAAATTATACTTAC
GAGTTCGGAGCTTGGCTTTCATTTTCTATCATGACTCAATGCTTGCCTGCTTTCCTTTTT
GCTGCTGCTGGAATGTATCAAATGACAATGTGGGCTATCGGAAAACATAAGAACTACAAA
AAAGAATTCAAAGAATATCCAAAGCAAAGAAAAGCTATTATTCCATTTTTATTGTAA

>g3472.t8 Gene=g3472 Length=298
MEVNLLIKYFITKCNVQSSTTIKDLKSSVYAANKKLNVHRQSFKLEVKGKTLKDSDTIES
LNLRNGSKLYVKDLGPQIGWSTVFLCEYAGPLVVYLWVYTRPWLFYGDTSSSAEISQTAH
IAAACYTLHYAKRLLETIFVHRFSHATMPMRNLFKNCIYYWGFTAYVAYHVNHPLFTSPS
TAQVYASLAAFLLCELGNFSIHINLRNLRPPGTSVRKIPMSDSNPLTALFNFVSCPNYTY
EFGAWLSFSIMTQCLPAFLFAAAGMYQMTMWAIGKHKNYKKEFKEYPKQRKAIIPFLL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g3472.t8 CDD cd01801 Ubl_TECR_like 16 74 2.51417E-19
6 g3472.t8 Gene3D G3DSA:3.10.20.90 - 3 74 2.0E-18
3 g3472.t8 PANTHER PTHR10556:SF28 SC2 10 298 6.6E-109
4 g3472.t8 PANTHER PTHR10556 3-OXO-5-ALPHA-STEROID 4-DEHYDROGENASE 10 298 6.6E-109
2 g3472.t8 Pfam PF00240 Ubiquitin family 15 71 3.3E-7
1 g3472.t8 Pfam PF02544 3-oxo-5-alpha-steroid 4-dehydrogenase 147 298 4.0E-30
11 g3472.t8 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 77 -
17 g3472.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 78 98 -
9 g3472.t8 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 99 157 -
15 g3472.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 158 176 -
12 g3472.t8 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 177 181 -
14 g3472.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 182 205 -
7 g3472.t8 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 206 225 -
16 g3472.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 226 251 -
10 g3472.t8 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 252 256 -
13 g3472.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 257 274 -
8 g3472.t8 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 275 298 -
23 g3472.t8 ProSiteProfiles PS50053 Ubiquitin domain profile. 3 71 12.074
24 g3472.t8 ProSiteProfiles PS50244 Steroid 5-alpha reductase C-terminal domain profile. 187 273 22.185
22 g3472.t8 SMART SM00213 ubq_7 1 74 3.9E-4
5 g3472.t8 SUPERFAMILY SSF54236 Ubiquitin-like 13 71 1.98E-8
20 g3472.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 77 99 -
19 g3472.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 157 176 -
21 g3472.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 242 264 -

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