Gene loci information

Transcript annotation

  • This transcript has been annotated as 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.t1 TSS g17111.t1 12507583 12507583
chr_4 g17111 g17111.t1 isoform g17111.t1 12507703 12511069
chr_4 g17111 g17111.t1 exon g17111.t1.exon1 12507703 12507853
chr_4 g17111 g17111.t1 cds g17111.t1.CDS1 12507703 12507853
chr_4 g17111 g17111.t1 exon g17111.t1.exon2 12508914 12508960
chr_4 g17111 g17111.t1 cds g17111.t1.CDS2 12508914 12508960
chr_4 g17111 g17111.t1 exon g17111.t1.exon3 12510311 12511069
chr_4 g17111 g17111.t1 cds g17111.t1.CDS3 12510311 12511069
chr_4 g17111 g17111.t1 TTS g17111.t1 12511187 12511187

Sequences

>g17111.t1 Gene=g17111 Length=957
ATGTCTTGTTGTGGATTCATTTCAACATTTTGTGTCTTTGTAGTTTCAGTACAATTAATT
TGTGGTGTTTTTCGGTTTCTTTATCAACAATTTATTGGACCATTATTAAATGGAAAATCT
ACAGATTTTAAAAAATATGGACAATGGGCACTTGTGACAGGCGCTACTGATGGAATTGGA
AAAGAATATGCACGATCTCTTGCAAAGCGAGGATTAAACATCATTTTAGTTTCACGAACG
CTCTCTAAATTGGAAACAGTTGCAAAAGAAATTAGTGAAGCTTTCAATGTTGAAACTGCC
GTAATTGATGTCAATTTTACATCAGGACCAGAAATTTATGATAAAATAAAAGAAAAAATT
CATGGCAAGGAAATTGGAATTTTGGTCAATAATGTTGGCATGGGATATATTACACCTGAT
TATTTCTTATCAATTCCAAATCGTGATCAAATGATTAAAGACATGATTCAATGCAATGTA
TTGTCAATTCCAATGATGTGCAGCATAATTTTGCCACAAATGGTTGAACGCAAAAAAGGC
TTAGTTATCACAATTTCATCACTTTCTGCCATCATTCCTGCTGGTTGCATGACAGTTTAT
TCTGCTACGAAAGCTTTTGCTCATAAATTTTCTGAAGATTTATCAATGGAATATGGCAAG
CATGGCATAAAAGTTCAAAGTATTTTACCTGGTCCAGTTGCTACAAATATGACAAGATTA
AAAAAAGGCTCATTGATGGCACCAAAAGCTGATAAATTTGTTGAATCTGCACTTTTGACT
GTTGACAGTGCTCCATATTCAACTGGTTATTTTCCACATGTAATTTTTCAAGTTATTACA
CAATTTTTGAGTTTTCTAATGCCATCATATTTGACAAGTTTGACATTGAAAACTATGGAA
AATGTCAGAAATCGAAGTATCAAAAAAGGACTTTATACTCCTGTTGCAAGTCAATAA

>g17111.t1 Gene=g17111 Length=318
MSCCGFISTFCVFVVSVQLICGVFRFLYQQFIGPLLNGKSTDFKKYGQWALVTGATDGIG
KEYARSLAKRGLNIILVSRTLSKLETVAKEISEAFNVETAVIDVNFTSGPEIYDKIKEKI
HGKEIGILVNNVGMGYITPDYFLSIPNRDQMIKDMIQCNVLSIPMMCSIILPQMVERKKG
LVITISSLSAIIPAGCMTVYSATKAFAHKFSEDLSMEYGKHGIKVQSILPGPVATNMTRL
KKGSLMAPKADKFVESALLTVDSAPYSTGYFPHVIFQVITQFLSFLMPSYLTSLTLKTME
NVRNRSIKKGLYTPVASQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
22 g17111.t1 CDD cd05356 17beta-HSD1_like_SDR_c 47 284 1.03647E-95
13 g17111.t1 Gene3D G3DSA:3.40.50.720 - 43 272 3.4E-48
2 g17111.t1 PANTHER PTHR43899 RH59310P 12 309 5.1E-92
3 g17111.t1 PANTHER PTHR43899:SF13 RH59310P 12 309 5.1E-92
21 g17111.t1 PIRSF PIRSF000126 11-beta-HSD1 1 309 3.3E-91
11 g17111.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 49 66 1.1E-21
5 g17111.t1 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 123 134 2.0E-6
8 g17111.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 123 134 1.1E-21
9 g17111.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 174 190 1.1E-21
4 g17111.t1 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 180 188 2.0E-6
6 g17111.t1 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 200 219 2.0E-6
10 g17111.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 200 219 1.1E-21
7 g17111.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 221 238 1.1E-21
1 g17111.t1 Pfam PF00106 short chain dehydrogenase 49 239 1.1E-44
17 g17111.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 5 -
18 g17111.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 6 28 -
15 g17111.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 29 180 -
20 g17111.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 181 202 -
16 g17111.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 203 273 -
19 g17111.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 274 296 -
14 g17111.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 297 318 -
12 g17111.t1 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 47 275 2.17E-47
25 g17111.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 5 27 -
24 g17111.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 180 202 -
23 g17111.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 274 296 -

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

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