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.t4 TTS g2253.t4 16295137 16295137
chr_3 g2253 g2253.t4 isoform g2253.t4 16295325 16297144
chr_3 g2253 g2253.t4 exon g2253.t4.exon1 16295325 16295366
chr_3 g2253 g2253.t4 exon g2253.t4.exon2 16295474 16295575
chr_3 g2253 g2253.t4 exon g2253.t4.exon3 16295727 16295838
chr_3 g2253 g2253.t4 cds g2253.t4.CDS1 16295815 16295838
chr_3 g2253 g2253.t4 exon g2253.t4.exon4 16296063 16296095
chr_3 g2253 g2253.t4 cds g2253.t4.CDS2 16296063 16296095
chr_3 g2253 g2253.t4 exon g2253.t4.exon5 16296184 16296525
chr_3 g2253 g2253.t4 cds g2253.t4.CDS3 16296184 16296525
chr_3 g2253 g2253.t4 exon g2253.t4.exon6 16296631 16296764
chr_3 g2253 g2253.t4 cds g2253.t4.CDS4 16296631 16296711
chr_3 g2253 g2253.t4 exon g2253.t4.exon7 16297017 16297144
chr_3 g2253 g2253.t4 TSS g2253.t4 16297144 16297144

Sequences

>g2253.t4 Gene=g2253 Length=893
ATTCGGTCGCGAGTTGCTTAACTGCTTTGTTGAAATTTTTCTTTCGTTAATAAGTAAATT
AGCACGTCGTTTTGGGATCATCATTATTTGTGCGTTGAGTTTTTTGTTTTTAACTACTTG
CATTAAAGAAAATAATAAATAAATAATTAAAATAGTCACCGGAGCATCAACTCCAATTGG
AATGGCAATTTGTAAAGCTCTTGTAACACATGGACTTAAAGTATGTGCGATAGCAAAGAA
ATCAGGAGTTGCTAAATTAGATGCATTAAACACGACATTTTTTGATGTCAAAGGAAAGAT
GCTCACATATGAGTGTGATTTAACGGATGAAGAGCAAGTTAAGGCAGTTTTTAGACATAT
TGGTGAAAAATATGATGGAATCGATTTACTTGTAAATAATGCCAATGTGATGAAAAAAGG
ACTTTTATTAGATCAAAATAACACCAATGATATGCATTATATAATGAACACAAATGTTCT
CGCTCTATGCATTGTCACGAGAGAGGCAGTAAAATTAATGCGACAGCGAACGATGGAGAG
AAAAGATGTAGCTCATATAGTGAACATAAATTCGATTTTCGGACACAAAATTATGGCCAC
TGTGCCTGGTACCACTCCAATGAACGGTCTATATCCTATATGCTTCAACTGCAATAACTG
AATGTGTGCGACAAGAACTTTTATTTTTGGACGAAACTGTCAAAGTAACAAGTATCTCAC
CAGGATTAGTTGAGAGCGATATAATTCATGCAAATGCACATGACGAAATTTTAAAATTGA
TGCCTGCACTTAAACCGGATGATGTTGCAGGTGCAGTGATTTTTGCACTTGGCGCAAAAG
AAGGTGTTGAGGTTCATGAGATTGTAATTAAGCCAGTTGGTGAATATCTGTAA

>g2253.t4 Gene=g2253 Length=159
MAICKALVTHGLKVCAIAKKSGVAKLDALNTTFFDVKGKMLTYECDLTDEEQVKAVFRHI
GEKYDGIDLLVNNANVMKKGLLLDQNNTNDMHYIMNTNVLALCIVTREAVKLMRQRTMER
KDVAHIVNINSIFGHKIMATVPGTTPMNGLYPICFNCNN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g2253.t4 Gene3D G3DSA:3.40.50.720 - 1 151 0
2 g2253.t4 PANTHER PTHR43115 DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 2 138 0
3 g2253.t4 PANTHER PTHR43115:SF4 DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 2 138 0
1 g2253.t4 Pfam PF00106 short chain dehydrogenase 2 140 0
4 g2253.t4 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 2 139 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