General information for g516.t3
Yuki Yoshida
6/2/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g516 is located on chr_3: 3862799..3863811 (+ 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 | g516 | g516.t3 | TSS | g516.t3 | 3862759 | 3862759 |
| chr_3 | g516 | g516.t3 | isoform | g516.t3 | 3862799 | 3863811 |
| chr_3 | g516 | g516.t3 | exon | g516.t3.exon1 | 3862799 | 3863418 |
| chr_3 | g516 | g516.t3 | cds | g516.t3.CDS1 | 3863254 | 3863418 |
| chr_3 | g516 | g516.t3 | exon | g516.t3.exon2 | 3863537 | 3863811 |
| chr_3 | g516 | g516.t3 | cds | g516.t3.CDS2 | 3863537 | 3863716 |
| chr_3 | g516 | g516.t3 | TTS | g516.t3 | 3863816 | 3863816 |
Sequences
>g516.t3 Gene=g516 Length=895
ATGGAAACAACATCGCGTTGGGTAAATTGTGTTGCGGTTGTGACAGGTGCAAGGTAAAAT
ATTAAAATTAAAAAAAATTATTTAAATTAAAAATTTTGAAATTCTTTAGTGCTGGAATTG
GTGCAGCAACTTGTATTGAATTAGCTAATAGTGGAATAATTACAATTGGAATAGCAAGAA
GAATTGATAAAGTTCAAGCATTAAGGTTTTGCTTAACAACTGATAAACAACGAAATTTTC
ATGCATACAAATGTGATGTCTCAAATGAAGCTGAAGTTAAACAAGTTTTTAGTGAAATTG
AAAAGAAATTTAATGGAATTGATATTTTAATTAATAATGCTGGTGTTTTTTCAAAGTCAA
CTCTAATTCAAGCTGACAATTCAGAAGATGTTCGGCGAGTTATTAATACAAATGTCATTG
GTGTTGTGAATTGCACAAGAGAAGCAGTGAAAAGTATGAAAATGAAAAATGAAGCTCACA
TAATTCACATTGGCAGCTTTTTTAATCAAAATATATCTCAAAACTTTGGAATTTATCAAG
CAAGCAAACATGCTGTTGCTGCACTCGCTGAACAGCATCGACAGGAATTTAGTAGGAAAA
AATTGAATATTAAAGTCACTACAATAATTCCAAATGCAGTTGCAACTGAATTATATGATA
ATTCATCATATGAACCACCCAAAAGCGTAGAATTATTAGCAGCAAAAGAAATTGCTGACG
TCATAGTCTTTGCTTTAGAAACACCTCGAAACGTCGTCATTACAGAACTCAAAATTCGTC
CTATGAATGACTTTAATTAAATTTTTTTAGATGGTAATTCTTTAAATTCACACATAATTA
AAAATTATTTTATAATAAGTTTAATTATCAATAAAATGTATGTCGATTGTAATAA
>g516.t3 Gene=g516 Length=114
MKMKNEAHIIHIGSFFNQNISQNFGIYQASKHAVAALAEQHRQEFSRKKLNIKVTTIIPN
AVATELYDNSSYEPPKSVELLAAKEIADVIVFALETPRNVVITELKIRPMNDFN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g516.t3 | Gene3D | G3DSA:3.40.50.720 | - | 1 | 114 | 0.0e+00 |
| 2 | g516.t3 | PANTHER | PTHR43115 | DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 | 8 | 110 | 0.0e+00 |
| 3 | g516.t3 | PANTHER | PTHR43115:SF4 | DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 | 8 | 110 | 0.0e+00 |
| 6 | g516.t3 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 1 | 14 | 2.7e-06 |
| 5 | g516.t3 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 27 | 46 | 2.7e-06 |
| 4 | g516.t3 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 50 | 67 | 2.7e-06 |
| 1 | g516.t3 | Pfam | PF00106 | short chain dehydrogenase | 1 | 70 | 0.0e+00 |
| 7 | g516.t3 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 2 | 102 | 0.0e+00 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g516/g516.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g516.t3.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