Gene loci information

Transcript annotation

  • This transcript has been annotated as 3-ketodihydrosphingosine 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_1 g9967 g9967.t10 TTS g9967.t10 6289701 6289701
chr_1 g9967 g9967.t10 isoform g9967.t10 6289804 6290898
chr_1 g9967 g9967.t10 exon g9967.t10.exon1 6289804 6290576
chr_1 g9967 g9967.t10 cds g9967.t10.CDS1 6289804 6290576
chr_1 g9967 g9967.t10 exon g9967.t10.exon2 6290823 6290898
chr_1 g9967 g9967.t10 cds g9967.t10.CDS2 6290823 6290898
chr_1 g9967 g9967.t10 TSS g9967.t10 6291000 6291000

Sequences

>g9967.t10 Gene=g9967 Length=849
ATGATAATCATCTTGGTAATTTTCTTTCATATTATTATTTTTCAATGGCTTACACGAAAG
AAGAAAAATGTTGATGAGAAAGCTGTTGCTGTCATTAAAGAAAACTGTATAAGAGATGAT
CAAAAAGTGGAATATTATTCGTTAGATTTGTCAAAAGAGCATGAAATCATTGAAAAAGGA
TTTAACGACATTGAAGCAAAATTAGGTGATATTTATATGCTTGTGAACTGTGCTGGACAG
GCATTATGCGGAGTAATTGAGGATGTGAAACCAGAAGATGCTCGATTTTTAATGAATCTA
AATTACTTTGGAACTTTATACCCAATTCAATATGTTTTGCCCAAAATGAAAGTTAAAAAA
GATGGTATCATTGTACTTACATCCTCACAAGCTGGTTTAATGGGAATTTATGGCTTGGGC
CCTTACTCTGCTGCTAAGTTTGCTCTTCGTGGTTTGGCTGAAGCTCTTTCAATGGAAACA
AAGCATTTAGGAATCAACGTGACTTTGGGATTACCTGCTGACACAGATACACCAGGATTT
GCAAATGAACAAAAATCAAAGCCAAAAATTACACAAGAAATTTGTAGTGGTGGTGGTCTC
TTTAAACCTGAAGATGTCGGAAAGAAACTTTTTGAAGATGCATTGAAAGGAAATTTCTTT
TCAATTTTAGGCTTTGAAAGTTGGATTTTATCAATTTTGTGCGTGGGAATGTCTCCCTGG
AAAAATCCTCTTCTTGGTATTCTTCAATCTTATGTCATGGGCGCATTGAGAATGATAAGT
TTTGTCATTCAATGGAATTTTGGAAGAATAGTCAAGAAATATTATCAACCAAAGGAAAAA
ACAAATTGA

>g9967.t10 Gene=g9967 Length=282
MIIILVIFFHIIIFQWLTRKKKNVDEKAVAVIKENCIRDDQKVEYYSLDLSKEHEIIEKG
FNDIEAKLGDIYMLVNCAGQALCGVIEDVKPEDARFLMNLNYFGTLYPIQYVLPKMKVKK
DGIIVLTSSQAGLMGIYGLGPYSAAKFALRGLAEALSMETKHLGINVTLGLPADTDTPGF
ANEQKSKPKITQEICSGGGLFKPEDVGKKLFEDALKGNFFSILGFESWILSILCVGMSPW
KNPLLGILQSYVMGALRMISFVIQWNFGRIVKKYYQPKEKTN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g9967.t10 Gene3D G3DSA:3.40.50.720 - 12 226 5.2E-35
2 g9967.t10 PANTHER PTHR43550 3-KETODIHYDROSPHINGOSINE REDUCTASE 26 281 4.7E-81
3 g9967.t10 PANTHER PTHR43550:SF3 3-KETODIHYDROSPHINGOSINE REDUCTASE 26 281 4.7E-81
4 g9967.t10 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 69 80 2.2E-7
6 g9967.t10 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 116 132 2.2E-7
5 g9967.t10 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 142 161 2.2E-7
1 g9967.t10 Pfam PF00106 short chain dehydrogenase 28 185 1.1E-30
11 g9967.t10 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 217 -
13 g9967.t10 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 218 238 -
12 g9967.t10 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 239 243 -
14 g9967.t10 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 244 263 -
10 g9967.t10 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 264 282 -
15 g9967.t10 ProSitePatterns PS00061 Short-chain dehydrogenases/reductases family signature. 129 157 -
7 g9967.t10 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 27 245 7.86E-37
8 g9967.t10 SignalP_EUK SignalP-noTM SignalP-noTM 1 20 -

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:0055114 NA NA
GO:0016491 oxidoreductase activity MF

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. There were no conditions that were differentially expressed