Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Dehydrogenase/reductase SDR family member 11.

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_3 g2253 g2253.t5 TTS g2253.t5 16295137 16295137
chr_3 g2253 g2253.t5 isoform g2253.t5 16295325 16297144
chr_3 g2253 g2253.t5 exon g2253.t5.exon1 16295325 16295366
chr_3 g2253 g2253.t5 exon g2253.t5.exon2 16295474 16295575
chr_3 g2253 g2253.t5 exon g2253.t5.exon3 16295727 16295838
chr_3 g2253 g2253.t5 cds g2253.t5.CDS1 16295819 16295838
chr_3 g2253 g2253.t5 exon g2253.t5.exon4 16296059 16296095
chr_3 g2253 g2253.t5 cds g2253.t5.CDS2 16296059 16296095
chr_3 g2253 g2253.t5 exon g2253.t5.exon5 16296184 16296525
chr_3 g2253 g2253.t5 cds g2253.t5.CDS3 16296184 16296525
chr_3 g2253 g2253.t5 exon g2253.t5.exon6 16296631 16296737
chr_3 g2253 g2253.t5 cds g2253.t5.CDS4 16296631 16296737
chr_3 g2253 g2253.t5 exon g2253.t5.exon7 16296799 16296839
chr_3 g2253 g2253.t5 cds g2253.t5.CDS5 16296799 16296829
chr_3 g2253 g2253.t5 exon g2253.t5.exon8 16297017 16297144
chr_3 g2253 g2253.t5 TSS g2253.t5 16297144 16297144

Sequences

>g2253.t5 Gene=g2253 Length=911
ATTCGGTCGCGAGTTGCTTAACTGCTTTGTTGAAATTTTTCTTTCGTTAATAAGTAAATT
AGCACGTCGTTTTGGGATCATCATTATTTGTGCGTTGAGTTTTTTGTTTTTAACTACTTG
CATTAAAGTAAGAGAAAAATGTATAAATGGAATGGTCGCGTGGCAATAGTCACCGGAGCA
TCAACTCCAATTGGAATGGCAATTTGTAAAGCTCTTGTAACACATGGACTTAAAGTATGT
GCGATAGCAAAGAAATCAGGAGTTGCTAAATTAGATGCATTAAACACGACATTTTTTGAT
GTCAAAGGAAAGATGCTCACATATGAGTGTGATTTAACGGATGAAGAGCAAGTTAAGGCA
GTTTTTAGACATATTGGTGAAAAATATGATGGAATCGATTTACTTGTAAATAATGCCAAT
GTGATGAAAAAAGGACTTTTATTAGATCAAAATAACACCAATGATATGCATTATATAATG
AACACAAATGTTCTCGCTCTATGCATTGTCACGAGAGAGGCAGTAAAATTAATGCGACAG
CGAACGATGGAGAGAAAAGATGTAGCTCATATAGTGAACATAAATTCGATTTTCGGACAC
AAAATTATGGCCACTGTGCCTGGTACCACTCCAATGAACGGTCTATATCCTGTGAATATG
CTTCAACTGCAATAACTGAATGTGTGCGACAAGAACTTTTATTTTTGGACGAAACTGTCA
AAGTAACAAGTATCTCACCAGGATTAGTTGAGAGCGATATAATTCATGCAAATGCACATG
ACGAAATTTTAAAATTGATGCCTGCACTTAAACCGGATGATGTTGCAGGTGCAGTGATTT
TTGCACTTGGCGCAAAAGAAGGTGTTGAGGTTCATGAGATTGTAATTAAGCCAGTTGGTG
AATATCTGTAA

>g2253.t5 Gene=g2253 Length=178
MYKWNGRVAIVTGASTPIGMAICKALVTHGLKVCAIAKKSGVAKLDALNTTFFDVKGKML
TYECDLTDEEQVKAVFRHIGEKYDGIDLLVNNANVMKKGLLLDQNNTNDMHYIMNTNVLA
LCIVTREAVKLMRQRTMERKDVAHIVNINSIFGHKIMATVPGTTPMNGLYPVNMLQLQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g2253.t5 Gene3D G3DSA:3.40.50.720 - 4 170 0
2 g2253.t5 PANTHER PTHR43115 DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 1 157 0
3 g2253.t5 PANTHER PTHR43115:SF4 DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 1 157 0
4 g2253.t5 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 8 25 0
5 g2253.t5 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 84 95 0
6 g2253.t5 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 137 153 0
1 g2253.t5 Pfam PF00106 short chain dehydrogenase 8 159 0
7 g2253.t5 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 2 159 0

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

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