General information for g517.t1
Yuki Yoshida
6/2/2022
Gene loci information
Transcript annotation
- This transcript has been not been annotated.
Parent gene
- The parent gene g517 is located on chr_3: 3865550..3866942 (+ 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 | g517 | g517.t1 | TSS | g517.t1 | 3865495 | 3865495 |
| chr_3 | g517 | g517.t1 | isoform | g517.t1 | 3865550 | 3866942 |
| chr_3 | g517 | g517.t1 | exon | g517.t1.exon1 | 3865550 | 3865599 |
| chr_3 | g517 | g517.t1 | cds | g517.t1.CDS1 | 3865550 | 3865599 |
| chr_3 | g517 | g517.t1 | exon | g517.t1.exon2 | 3866756 | 3866942 |
| chr_3 | g517 | g517.t1 | cds | g517.t1.CDS2 | 3866756 | 3866942 |
| chr_3 | g517 | g517.t1 | TTS | g517.t1 | 3867586 | 3867586 |
Sequences
>g517.t1 Gene=g517 Length=237
ATGTCGATTTCACGATGGTCTGGTCGTGTTGCGGTTGTGACAGGAGCAAGCGCTGGAATT
GGTGCTGCAACTGCAATAGAATTAGCTAAAAATGGTTTGATCACAATTGGATTAGCGAGA
AGAGTCGAAAAAGTTGAAGAACTTCGATCACACTTGACATCAGAACAACAGCAAAATTTT
CATGCCATGAAATGTGATGTTTCAGTTGAAGCTGAAATTGTTAAGAACTTTTTCTGA
>g517.t1 Gene=g517 Length=78
MSISRWSGRVAVVTGASAGIGAATAIELAKNGLITIGLARRVEKVEELRSHLTSEQQQNF
HAMKCDVSVEAEIVKNFF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g517.t1 | Gene3D | G3DSA:3.40.50.720 | - | 1 | 77 | 2.1E-18 |
| 2 | g517.t1 | PANTHER | PTHR43115 | DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 | 4 | 77 | 8.2E-29 |
| 3 | g517.t1 | PANTHER | PTHR43115:SF4 | DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 | 4 | 77 | 8.2E-29 |
| 1 | g517.t1 | Pfam | PF00106 | short chain dehydrogenase | 10 | 74 | 1.5E-13 |
| 7 | g517.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 25 | - |
| 8 | g517.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 9 | - |
| 9 | g517.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 10 | 20 | - |
| 10 | g517.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 21 | 25 | - |
| 6 | g517.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 26 | 78 | - |
| 4 | g517.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 3 | 74 | 1.52E-17 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g517/g517.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g517.t1.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