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.t11 TTS g9967.t11 6289701 6289701
chr_1 g9967 g9967.t11 isoform g9967.t11 6289804 6290898
chr_1 g9967 g9967.t11 exon g9967.t11.exon1 6289804 6290756
chr_1 g9967 g9967.t11 cds g9967.t11.CDS1 6289804 6290756
chr_1 g9967 g9967.t11 exon g9967.t11.exon2 6290823 6290898
chr_1 g9967 g9967.t11 cds g9967.t11.CDS2 6290823 6290898
chr_1 g9967 g9967.t11 TSS g9967.t11 6291000 6291000

Sequences

>g9967.t11 Gene=g9967 Length=1029
ATGATAATCATCTTGGTAATTTTCTTTCATATTATTATTTTTCAATGGCTTACACGAAAG
AAGAAAAATGTTGATGGAAAACACGTCGTTGTAACTGGTGGAAGTTCTGGCATCGGTCTA
TGGGTTGCAATAAATGCTGTTCGCAAAGGTGCTGATGTTACAATCGTTGCAAGAAACGTA
CGAATTTTAGGTAGCACCCATAATTTTCTTATCATTAAGTCAACAAATTGCACTATGAAA
TTGTGTCGTTTTTTAGAGAAAGCTGTTGCTGTCATTAAAGAAAACTGTATAAGAGATGAT
CAAAAAGTGGAATATTATTCGTTAGATTTGTCAAAAGAGCATGAAATCATTGAAAAAGGA
TTTAACGACATTGAAGCAAAATTAGGTGATATTTATATGCTTGTGAACTGTGCTGGACAG
GCATTATGCGGAGTAATTGAGGATGTGAAACCAGAAGATGCTCGATTTTTAATGAATCTA
AATTACTTTGGAACTTTATACCCAATTCAATATGTTTTGCCCAAAATGAAAGTTAAAAAA
GATGGTATCATTGTACTTACATCCTCACAAGCTGGTTTAATGGGAATTTATGGCTTGGGC
CCTTACTCTGCTGCTAAGTTTGCTCTTCGTGGTTTGGCTGAAGCTCTTTCAATGGAAACA
AAGCATTTAGGAATCAACGTGACTTTGGGATTACCTGCTGACACAGATACACCAGGATTT
GCAAATGAACAAAAATCAAAGCCAAAAATTACACAAGAAATTTGTAGTGGTGGTGGTCTC
TTTAAACCTGAAGATGTCGGAAAGAAACTTTTTGAAGATGCATTGAAAGGAAATTTCTTT
TCAATTTTAGGCTTTGAAAGTTGGATTTTATCAATTTTGTGCGTGGGAATGTCTCCCTGG
AAAAATCCTCTTCTTGGTATTCTTCAATCTTATGTCATGGGCGCATTGAGAATGATAAGT
TTTGTCATTCAATGGAATTTTGGAAGAATAGTCAAGAAATATTATCAACCAAAGGAAAAA
ACAAATTGA

>g9967.t11 Gene=g9967 Length=342
MIIILVIFFHIIIFQWLTRKKKNVDGKHVVVTGGSSGIGLWVAINAVRKGADVTIVARNV
RILGSTHNFLIIKSTNCTMKLCRFLEKAVAVIKENCIRDDQKVEYYSLDLSKEHEIIEKG
FNDIEAKLGDIYMLVNCAGQALCGVIEDVKPEDARFLMNLNYFGTLYPIQYVLPKMKVKK
DGIIVLTSSQAGLMGIYGLGPYSAAKFALRGLAEALSMETKHLGINVTLGLPADTDTPGF
ANEQKSKPKITQEICSGGGLFKPEDVGKKLFEDALKGNFFSILGFESWILSILCVGMSPW
KNPLLGILQSYVMGALRMISFVIQWNFGRIVKKYYQPKEKTN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g9967.t11 CDD cd08939 KDSR-like_SDR_c 26 280 1.47997E-84
8 g9967.t11 Gene3D G3DSA:3.40.50.720 - 17 287 9.2E-49
2 g9967.t11 PANTHER PTHR43550 3-KETODIHYDROSPHINGOSINE REDUCTASE 4 341 4.0E-100
3 g9967.t11 PANTHER PTHR43550:SF3 3-KETODIHYDROSPHINGOSINE REDUCTASE 4 341 4.0E-100
5 g9967.t11 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 28 45 1.4E-11
6 g9967.t11 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 176 192 1.4E-11
4 g9967.t11 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 202 221 1.4E-11
1 g9967.t11 Pfam PF00106 short chain dehydrogenase 81 245 9.8E-31
10 g9967.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 277 -
13 g9967.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 278 298 -
11 g9967.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 299 303 -
12 g9967.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 304 323 -
9 g9967.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 324 342 -
19 g9967.t11 ProSitePatterns PS00061 Short-chain dehydrogenases/reductases family signature. 189 217 -
7 g9967.t11 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 22 305 1.53E-49
18 g9967.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 2 19 -
15 g9967.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 29 48 -
16 g9967.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 278 300 -
17 g9967.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 305 327 -

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.

Raw TPM values