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_4 g17111 g17111.t3 TSS g17111.t3 12507583 12507583
chr_4 g17111 g17111.t3 isoform g17111.t3 12510348 12511177
chr_4 g17111 g17111.t3 exon g17111.t3.exon1 12510348 12511177
chr_4 g17111 g17111.t3 cds g17111.t3.CDS1 12510512 12511069
chr_4 g17111 g17111.t3 TTS g17111.t3 12511187 12511187

Sequences

>g17111.t3 Gene=g17111 Length=830
GAACGCTCTCTAAATTGGAAACAGTTGCAAAAGAAATTAGTGAAGCTTTCAATGTTGAAA
CTGCCGTAATTGATGTCAATTTTACATCAGGACCAGAAATTTATGATAAAATAAAAGAAA
AAATTCATGGCAAGGAAATTGGAATTTTGGTCAATAATGTTGGCATGGGATATATTACAC
CTGATTATTTCTTATCAATTCCAAATCGTGATCAAATGATTAAAGACATGATTCAATGCA
ATGTATTGTCAATTCCAATGATGTGCAGCATAATTTTGCCACAAATGGTTGAACGCAAAA
AAGGCTTAGTTATCACAATTTCATCACTTTCTGCCATCATTCCTGCTGGTTGCATGACAG
TTTATTCTGCTACGAAAGCTTTTGCTCATAAATTTTCTGAAGATTTATCAATGGAATATG
GCAAGCATGGCATAAAAGTTCAAAGTATTTTACCTGGTCCAGTTGCTACAAATATGACAA
GATTAAAAAAAGGCTCATTGATGGCACCAAAAGCTGATAAATTTGTTGAATCTGCACTTT
TGACTGTTGACAGTGCTCCATATTCAACTGGTTATTTTCCACATGTAATTTTTCAAGTTA
TTACACAATTTTTGAGTTTTCTAATGCCATCATATTTGACAAGTTTGACATTGAAAACTA
TGGAAAATGTCAGAAATCGAAGTATCAAAAAAGGACTTTATACTCCTGTTGCAAGTCAAT
AAAATTTTCATTTTTTATTTGCATAATCCAAAGAATAAATTAGGAATGGAATCAAAATTT
TTATTTTTGCTTAGCTGTATGACTTTAAAAAAAATTTCGAACAAATAAAG

>g17111.t3 Gene=g17111 Length=185
MGYITPDYFLSIPNRDQMIKDMIQCNVLSIPMMCSIILPQMVERKKGLVITISSLSAIIP
AGCMTVYSATKAFAHKFSEDLSMEYGKHGIKVQSILPGPVATNMTRLKKGSLMAPKADKF
VESALLTVDSAPYSTGYFPHVIFQVITQFLSFLMPSYLTSLTLKTMENVRNRSIKKGLYT
PVASQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g17111.t3 Gene3D G3DSA:3.40.50.720 - 2 171 3.6E-23
2 g17111.t3 PANTHER PTHR43899 RH59310P 3 176 4.9E-45
3 g17111.t3 PANTHER PTHR43899:SF13 RH59310P 3 176 4.9E-45
5 g17111.t3 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 41 57 2.6E-11
6 g17111.t3 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 67 86 2.6E-11
4 g17111.t3 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 88 105 2.6E-11
1 g17111.t3 Pfam PF00106 short chain dehydrogenase 16 106 4.0E-24
11 g17111.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 47 -
15 g17111.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 48 69 -
13 g17111.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 70 140 -
14 g17111.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 141 163 -
12 g17111.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 164 185 -
9 g17111.t3 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 17 166 1.33E-24
8 g17111.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 47 69 -
7 g17111.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 141 163 -

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.

Raw TPM values