General information for g5167.t2
Yuki Yoshida
6/2/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Short-chain dehydrogenase/reductase family 16C member 6.
Parent gene
- The parent gene g5167 is located on chr_2: 7411505..7416724 (- 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_2 | g5167 | g5167.t2 | TTS | g5167.t2 | 7405985 | 7405985 |
| chr_2 | g5167 | g5167.t2 | isoform | g5167.t2 | 7406910 | 7409851 |
| chr_2 | g5167 | g5167.t2 | exon | g5167.t2.exon1 | 7406910 | 7407261 |
| chr_2 | g5167 | g5167.t2 | cds | g5167.t2.CDS1 | 7406910 | 7407261 |
| chr_2 | g5167 | g5167.t2 | exon | g5167.t2.exon2 | 7407356 | 7407671 |
| chr_2 | g5167 | g5167.t2 | cds | g5167.t2.CDS2 | 7407356 | 7407671 |
| chr_2 | g5167 | g5167.t2 | exon | g5167.t2.exon3 | 7407737 | 7407779 |
| chr_2 | g5167 | g5167.t2 | cds | g5167.t2.CDS3 | 7407737 | 7407779 |
| chr_2 | g5167 | g5167.t2 | exon | g5167.t2.exon4 | 7409729 | 7409851 |
| chr_2 | g5167 | g5167.t2 | cds | g5167.t2.CDS4 | 7409729 | 7409821 |
| chr_2 | g5167 | g5167.t2 | TSS | g5167.t2 | NA | NA |
Sequences
>g5167.t2 Gene=g5167 Length=834
CTAGATGAGTCTAAAAAAATAGTCGATTCAATGGGTGGCTGGTGTCGTTCACAAATAGTT
GACATATCAAAACGACAAGAAGTATACAAAGCAGCAGAAGACATCAAGAATCAATATGGC
AATGTTACATTGCTTATAAATAACGCAGGAGTATTAAGTGGTCGAGCACTGCTTGATACA
CCTGATCATTTAATAGAGAGATCTTTCAATGTCAATGTAATTGCACATTTTTGGACAGTA
AAAGCATTCCTTCCAACAATGATTGAGAAGGATCATGGACATATAGTGACAATAGCAAGT
ATGGCGGGCCATGTTGGCATTGCTAAACTTATCGACTATTGCAGTACAAAATTTGCTGCC
GTTGGCTTCGATGAGGCACTTCGACTTGAGCTTGAAGTAATGGGCATTAAAAACATTCAC
ACATCTGTAATTTGTCCGTATTTTATACAAGCCACTGGAATGTTTGATGATGTTAACTCA
AGATGGGTTAACACATTAAGTTCAAATGATGTAGCAGATCGTATTATAGAAGCAGTGAGA
AAGAATGAAAAAATGGCACTTATACCTTGGTATTTCAACATCATGCTCATTCTAAAAACT
ATCTTCCCTTGGGGCTGCACATCAGGATTTCTTCGGCGACTTGTCCCTGATGCTACACCT
CAGCATCTTCTTACAACACCCGTATCAACGCCATCAATTACAAAGCAGGAGGAAATGCAA
TTTATGAACAACAACAATCATCATGTCTTAAACAATAATAATAACAATAATGATAAAGAA
ACAACTCTGATAAAACGAATGGCTGCGACTATTGAGGGTGAACGAGTGTTGTGA
>g5167.t2 Gene=g5167 Length=267
MGGWCRSQIVDISKRQEVYKAAEDIKNQYGNVTLLINNAGVLSGRALLDTPDHLIERSFN
VNVIAHFWTVKAFLPTMIEKDHGHIVTIASMAGHVGIAKLIDYCSTKFAAVGFDEALRLE
LEVMGIKNIHTSVICPYFIQATGMFDDVNSRWVNTLSSNDVADRIIEAVRKNEKMALIPW
YFNIMLILKTIFPWGCTSGFLRRLVPDATPQHLLTTPVSTPSITKQEEMQFMNNNNHHVL
NNNNNNNDKETTLIKRMAATIEGERVL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g5167.t2 | CDD | cd05339 | 17beta-HSDXI-like_SDR_c | 1 | 196 | 0 |
| 12 | g5167.t2 | Gene3D | G3DSA:3.40.50.720 | - | 1 | 196 | 0 |
| 2 | g5167.t2 | PANTHER | PTHR24322:SF634 | FI23927P1-RELATED | 2 | 230 | 0 |
| 3 | g5167.t2 | PANTHER | PTHR24322 | PKSB | 2 | 230 | 0 |
| 4 | g5167.t2 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 30 | 41 | 0 |
| 8 | g5167.t2 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 30 | 41 | 0 |
| 7 | g5167.t2 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 77 | 93 | 0 |
| 6 | g5167.t2 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 83 | 91 | 0 |
| 5 | g5167.t2 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 103 | 122 | 0 |
| 9 | g5167.t2 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 103 | 122 | 0 |
| 10 | g5167.t2 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 127 | 144 | 0 |
| 1 | g5167.t2 | Pfam | PF00106 | short chain dehydrogenase | 10 | 150 | 0 |
| 11 | g5167.t2 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 4 | 202 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5167/g5167.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5167.t2.fa.iupred3.txt does not exist
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