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.t8 TTS g9967.t8 6289701 6289701
chr_1 g9967 g9967.t8 isoform g9967.t8 6289804 6290898
chr_1 g9967 g9967.t8 exon g9967.t8.exon1 6289804 6290570
chr_1 g9967 g9967.t8 cds g9967.t8.CDS1 6289804 6290570
chr_1 g9967 g9967.t8 exon g9967.t8.exon2 6290643 6290756
chr_1 g9967 g9967.t8 cds g9967.t8.CDS2 6290643 6290756
chr_1 g9967 g9967.t8 exon g9967.t8.exon3 6290823 6290898
chr_1 g9967 g9967.t8 cds g9967.t8.CDS3 6290823 6290898
chr_1 g9967 g9967.t8 TSS g9967.t8 6291000 6291000

Sequences

>g9967.t8 Gene=g9967 Length=957
ATGATAATCATCTTGGTAATTTTCTTTCATATTATTATTTTTCAATGGCTTACACGAAAG
AAGAAAAATGTTGATGGAAAACACGTCGTTGTAACTGGTGGAAGTTCTGGCATCGGTCTA
TGGGTTGCAATAAATGCTGTTCGCAAAGGTGCTGATGTTACAATCGTTGCAAGAAACGTA
CGAATTTTAGCTGTTGCTGTCATTAAAGAAAACTGTATAAGAGATGATCAAAAAGTGGAA
TATTATTCGTTAGATTTGTCAAAAGAGCATGAAATCATTGAAAAAGGATTTAACGACATT
GAAGCAAAATTAGGTGATATTTATATGCTTGTGAACTGTGCTGGACAGGCATTATGCGGA
GTAATTGAGGATGTGAAACCAGAAGATGCTCGATTTTTAATGAATCTAAATTACTTTGGA
ACTTTATACCCAATTCAATATGTTTTGCCCAAAATGAAAGTTAAAAAAGATGGTATCATT
GTACTTACATCCTCACAAGCTGGTTTAATGGGAATTTATGGCTTGGGCCCTTACTCTGCT
GCTAAGTTTGCTCTTCGTGGTTTGGCTGAAGCTCTTTCAATGGAAACAAAGCATTTAGGA
ATCAACGTGACTTTGGGATTACCTGCTGACACAGATACACCAGGATTTGCAAATGAACAA
AAATCAAAGCCAAAAATTACACAAGAAATTTGTAGTGGTGGTGGTCTCTTTAAACCTGAA
GATGTCGGAAAGAAACTTTTTGAAGATGCATTGAAAGGAAATTTCTTTTCAATTTTAGGC
TTTGAAAGTTGGATTTTATCAATTTTGTGCGTGGGAATGTCTCCCTGGAAAAATCCTCTT
CTTGGTATTCTTCAATCTTATGTCATGGGCGCATTGAGAATGATAAGTTTTGTCATTCAA
TGGAATTTTGGAAGAATAGTCAAGAAATATTATCAACCAAAGGAAAAAACAAATTGA

>g9967.t8 Gene=g9967 Length=318
MIIILVIFFHIIIFQWLTRKKKNVDGKHVVVTGGSSGIGLWVAINAVRKGADVTIVARNV
RILAVAVIKENCIRDDQKVEYYSLDLSKEHEIIEKGFNDIEAKLGDIYMLVNCAGQALCG
VIEDVKPEDARFLMNLNYFGTLYPIQYVLPKMKVKKDGIIVLTSSQAGLMGIYGLGPYSA
AKFALRGLAEALSMETKHLGINVTLGLPADTDTPGFANEQKSKPKITQEICSGGGLFKPE
DVGKKLFEDALKGNFFSILGFESWILSILCVGMSPWKNPLLGILQSYVMGALRMISFVIQ
WNFGRIVKKYYQPKEKTN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g9967.t8 CDD cd08939 KDSR-like_SDR_c 26 256 1.28946E-86
9 g9967.t8 Gene3D G3DSA:3.40.50.720 - 17 263 3.0E-49
2 g9967.t8 PANTHER PTHR43550 3-KETODIHYDROSPHINGOSINE REDUCTASE 4 317 8.5E-102
3 g9967.t8 PANTHER PTHR43550:SF3 3-KETODIHYDROSPHINGOSINE REDUCTASE 4 317 8.5E-102
4 g9967.t8 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 28 45 2.7E-14
7 g9967.t8 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 105 116 2.7E-14
6 g9967.t8 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 152 168 2.7E-14
5 g9967.t8 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 178 197 2.7E-14
1 g9967.t8 Pfam PF00106 short chain dehydrogenase 27 221 3.9E-41
11 g9967.t8 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 253 -
14 g9967.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 254 274 -
12 g9967.t8 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 275 279 -
13 g9967.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 280 299 -
10 g9967.t8 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 300 318 -
20 g9967.t8 ProSitePatterns PS00061 Short-chain dehydrogenases/reductases family signature. 165 193 -
8 g9967.t8 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 22 281 6.62E-51
19 g9967.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 2 19 -
18 g9967.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 29 48 -
17 g9967.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 254 276 -
16 g9967.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 281 303 -

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

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