General information for g2253.t2
Yuki Yoshida
6/2/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Dehydrogenase/reductase SDR family member 11.
Parent gene
- The parent gene g2253 is located on chr_3: 16295325..16297144 (- strand)
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.t2 | TTS | g2253.t2 | 16295137 | 16295137 |
| chr_3 | g2253 | g2253.t2 | isoform | g2253.t2 | 16295325 | 16297144 |
| chr_3 | g2253 | g2253.t2 | exon | g2253.t2.exon1 | 16295325 | 16295366 |
| chr_3 | g2253 | g2253.t2 | exon | g2253.t2.exon2 | 16295474 | 16295575 |
| chr_3 | g2253 | g2253.t2 | exon | g2253.t2.exon3 | 16295727 | 16295878 |
| chr_3 | g2253 | g2253.t2 | cds | g2253.t2.CDS1 | 16295876 | 16295878 |
| chr_3 | g2253 | g2253.t2 | exon | g2253.t2.exon4 | 16296187 | 16296525 |
| chr_3 | g2253 | g2253.t2 | cds | g2253.t2.CDS2 | 16296187 | 16296525 |
| chr_3 | g2253 | g2253.t2 | exon | g2253.t2.exon5 | 16296631 | 16296769 |
| chr_3 | g2253 | g2253.t2 | cds | g2253.t2.CDS3 | 16296631 | 16296711 |
| chr_3 | g2253 | g2253.t2 | exon | g2253.t2.exon6 | 16297017 | 16297144 |
| chr_3 | g2253 | g2253.t2 | TSS | g2253.t2 | 16297144 | 16297144 |
Sequences
>g2253.t2 Gene=g2253 Length=902
ATTCGGTCGCGAGTTGCTTAACTGCTTTGTTGAAATTTTTCTTTCGTTAATAAGTAAATT
AGCACGTCGTTTTGGGATCATCATTATTTGTGCGTTGAGTTTTTTGTTTTTAACTACTTG
CATTAAAGATAAGAAAATAATAAATAAATAATTAAAATAGTCACCGGAGCATCAACTCCA
ATTGGAATGGCAATTTGTAAAGCTCTTGTAACACATGGACTTAAAGTATGTGCGATAGCA
AAGAAATCAGGAGTTGCTAAATTAGATGCATTAAACACGACATTTTTTGATGTCAAAGGA
AAGATGCTCACATATGAGTGTGATTTAACGGATGAAGAGCAAGTTAAGGCAGTTTTTAGA
CATATTGGTGAAAAATATGATGGAATCGATTTACTTGTAAATAATGCCAATGTGATGAAA
AAAGGACTTTTATTAGATCAAAATAACACCAATGATATGCATTATATAATGAACACAAAT
GTTCTCGCTCTATGCATTGTCACGAGAGAGGCAGTAAAATTAATGCGACAGCGAACGATG
GAGAGAAAAGATGTAGCTCATATAGTGAACATAAATTCGATTTTCGGACACAAAATTATG
GCCACTTGAGCAATTAATTAAAATTTAAATTACAATTTTTCTTTAGATATGCTTCAACTG
CAATAACTGAATGTGTGCGACAAGAACTTTTATTTTTGGACGAAACTGTCAAAGTAACAA
GTATCTCACCAGGATTAGTTGAGAGCGATATAATTCATGCAAATGCACATGACGAAATTT
TAAAATTGATGCCTGCACTTAAACCGGATGATGTTGCAGGTGCAGTGATTTTTGCACTTG
GCGCAAAAGAAGGTGTTGAGGTTCATGAGATTGTAATTAAGCCAGTTGGTGAATATCTGT
AA
>g2253.t2 Gene=g2253 Length=140
MAICKALVTHGLKVCAIAKKSGVAKLDALNTTFFDVKGKMLTYECDLTDEEQVKAVFRHI
GEKYDGIDLLVNNANVMKKGLLLDQNNTNDMHYIMNTNVLALCIVTREAVKLMRQRTMER
KDVAHIVNINSIFGHKIMAT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g2253.t2 | Gene3D | G3DSA:3.40.50.720 | - | 1 | 140 | 0 |
| 2 | g2253.t2 | PANTHER | PTHR43115 | DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 | 2 | 138 | 0 |
| 3 | g2253.t2 | PANTHER | PTHR43115:SF4 | DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 | 2 | 138 | 0 |
| 1 | g2253.t2 | Pfam | PF00106 | short chain dehydrogenase | 2 | 136 | 0 |
| 4 | g2253.t2 | 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