Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t9 TTS g9967.t9 6289701 6289701
chr_1 g9967 g9967.t9 isoform g9967.t9 6289804 6290898
chr_1 g9967 g9967.t9 exon g9967.t9.exon1 6289804 6290576
chr_1 g9967 g9967.t9 cds g9967.t9.CDS1 6289804 6290436
chr_1 g9967 g9967.t9 exon g9967.t9.exon2 6290643 6290898
chr_1 g9967 g9967.t9 TSS g9967.t9 6291000 6291000

Sequences

>g9967.t9 Gene=g9967 Length=1029
ATGATAATCATCTTGGTAATTTTCTTTCATATTATTATTTTTCAATGGCTTACACGAAAG
AAGAAAAATGTTGATGGTGAGTCAGAAATTAATTTTCCCTAAAAAATATTTCTTCTTTAT
TAAAATAATCAATATATTACAGGAAAACACGTCGTTGTAACTGGTGGAAGTTCTGGCATC
GGTCTATGGGTTGCAATAAATGCTGTTCGCAAAGGTGCTGATGTTACAATCGTTGCAAGA
AACGTACGAATTTTAGAGAAAGCTGTTGCTGTCATTAAAGAAAACTGTATAAGAGATGAT
CAAAAAGTGGAATATTATTCGTTAGATTTGTCAAAAGAGCATGAAATCATTGAAAAAGGA
TTTAACGACATTGAAGCAAAATTAGGTGATATTTATATGCTTGTGAACTGTGCTGGACAG
GCATTATGCGGAGTAATTGAGGATGTGAAACCAGAAGATGCTCGATTTTTAATGAATCTA
AATTACTTTGGAACTTTATACCCAATTCAATATGTTTTGCCCAAAATGAAAGTTAAAAAA
GATGGTATCATTGTACTTACATCCTCACAAGCTGGTTTAATGGGAATTTATGGCTTGGGC
CCTTACTCTGCTGCTAAGTTTGCTCTTCGTGGTTTGGCTGAAGCTCTTTCAATGGAAACA
AAGCATTTAGGAATCAACGTGACTTTGGGATTACCTGCTGACACAGATACACCAGGATTT
GCAAATGAACAAAAATCAAAGCCAAAAATTACACAAGAAATTTGTAGTGGTGGTGGTCTC
TTTAAACCTGAAGATGTCGGAAAGAAACTTTTTGAAGATGCATTGAAAGGAAATTTCTTT
TCAATTTTAGGCTTTGAAAGTTGGATTTTATCAATTTTGTGCGTGGGAATGTCTCCCTGG
AAAAATCCTCTTCTTGGTATTCTTCAATCTTATGTCATGGGCGCATTGAGAATGATAAGT
TTTGTCATTCAATGGAATTTTGGAAGAATAGTCAAGAAATATTATCAACCAAAGGAAAAA
ACAAATTGA

>g9967.t9 Gene=g9967 Length=210
MLVNCAGQALCGVIEDVKPEDARFLMNLNYFGTLYPIQYVLPKMKVKKDGIIVLTSSQAG
LMGIYGLGPYSAAKFALRGLAEALSMETKHLGINVTLGLPADTDTPGFANEQKSKPKITQ
EICSGGGLFKPEDVGKKLFEDALKGNFFSILGFESWILSILCVGMSPWKNPLLGILQSYV
MGALRMISFVIQWNFGRIVKKYYQPKEKTN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g9967.t9 Gene3D G3DSA:3.40.50.720 - 1 147 1.7E-28
2 g9967.t9 PANTHER PTHR43550 3-KETODIHYDROSPHINGOSINE REDUCTASE 1 209 1.9E-71
3 g9967.t9 PANTHER PTHR43550:SF3 3-KETODIHYDROSPHINGOSINE REDUCTASE 1 209 1.9E-71
4 g9967.t9 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 44 60 7.1E-5
5 g9967.t9 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 70 89 7.1E-5
1 g9967.t9 Pfam PF00106 short chain dehydrogenase 1 113 6.0E-24
9 g9967.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 145 -
12 g9967.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 146 166 -
10 g9967.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 167 171 -
11 g9967.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 172 191 -
8 g9967.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 192 210 -
15 g9967.t9 ProSitePatterns PS00061 Short-chain dehydrogenases/reductases family signature. 57 85 -
6 g9967.t9 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 2 176 6.02E-31
14 g9967.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 146 168 -
13 g9967.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 173 195 -

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.

Raw TPM values