Gene loci information

Transcript annotation

  • This transcript has been annotated as Dehydrogenase/reductase SDR family member 4 .

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_2 g6939 g6939.t1 TTS g6939.t1 20067424 20067424
chr_2 g6939 g6939.t1 isoform g6939.t1 20067475 20068275
chr_2 g6939 g6939.t1 exon g6939.t1.exon1 20067475 20068275
chr_2 g6939 g6939.t1 cds g6939.t1.CDS1 20067475 20068275
chr_2 g6939 g6939.t1 TSS g6939.t1 20068363 20068363

Sequences

>g6939.t1 Gene=g6939 Length=801
ATGATTCGAAGAACCTTTGCAACAATGTCGAACAATTTTGGAAAAAGATTAGACGGTCGT
GTTTGTATTGTGACAGCTTCCACTGACGGAATTGGCTTTGCAATTGCCAAGAGATTGGGA
TTAGAAGGAGGGAAAGTTATAGTAAGTTCAAGAAAGCAAAAAAATGTTGACGATGCAATT
CAAGAATTAAAAAAAGAAGGTGTGAATGAAGTTATTGGTACAACTTGTCATGTAGCAATT
TCTGAAGATCGCAAGAAACTTTTCAATTTAGCGATTGAGAAATATGGAAAAATTGATGTT
TTAGTGTCAAACGCTGCAGTTAATCCAGAAGTTGGATGTGTAACAGATACAAGTGAAAAA
GCTTGGGATAAAATTTTTGATGTAAATGTCAAATCAGCTTATTTACTAGCCAAAGAGGTC
AAGCCATATTTGCAGCAAAACAAAGGTGGATCAATTGTTTTTGTTAGCTCCATTGGAGGA
TATTCACCATTTGATTTGCTTGGAGCTTATTCAGTAAGCAAAACTGCTTTATTTGGATTA
ACAAAAGCACTTGCTGTTGAACTTGTTCACGACAATATTCGAGTGAATTGTATAGCGCCA
GGAGTAATAGAAACCAAATTTTCTTCCGCACTCTACGAATCAGAGAGTGCAAAAGAGGAA
ACATTGTCAAGAATTCCAATGAAAAGGATGGGTAAAGCTGATGAGATTGGATCAGTATGT
GCATTTTTGTGTAGTGATGATGCTAGTTACATGACTGGTGAAACTATTGCTGCCGCAGGT
GGAATGTTATCAAGGCTGTGA

>g6939.t1 Gene=g6939 Length=266
MIRRTFATMSNNFGKRLDGRVCIVTASTDGIGFAIAKRLGLEGGKVIVSSRKQKNVDDAI
QELKKEGVNEVIGTTCHVAISEDRKKLFNLAIEKYGKIDVLVSNAAVNPEVGCVTDTSEK
AWDKIFDVNVKSAYLLAKEVKPYLQQNKGGSIVFVSSIGGYSPFDLLGAYSVSKTALFGL
TKALAVELVHDNIRVNCIAPGVIETKFSSALYESESAKEETLSRIPMKRMGKADEIGSVC
AFLCSDDASYMTGETIAAAGGMLSRL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g6939.t1 Gene3D G3DSA:3.40.50.720 - 8 265 5.2E-78
2 g6939.t1 PANTHER PTHR43943 DEHYDROGENASE/REDUCTASE (SDR FAMILY) MEMBER 4 10 266 3.4E-109
9 g6939.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 21 38 1.5E-39
5 g6939.t1 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 96 107 7.6E-10
11 g6939.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 96 107 1.5E-39
8 g6939.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 144 160 1.5E-39
4 g6939.t1 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 150 158 7.6E-10
3 g6939.t1 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 170 189 7.6E-10
7 g6939.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 170 189 1.5E-39
10 g6939.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 191 208 1.5E-39
6 g6939.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 226 246 1.5E-39
1 g6939.t1 Pfam PF13561 Enoyl-(Acyl carrier protein) reductase 29 262 1.2E-65
13 g6939.t1 ProSitePatterns PS00061 Short-chain dehydrogenases/reductases family signature. 157 185 -
12 g6939.t1 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 18 263 4.88E-78

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