General information for g535.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g535 is located on chr_3: 3971392..3975754 (+ 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 | g535 | g535.t3 | TSS | g535.t3 | 3970722 | 3970722 |
| chr_3 | g535 | g535.t3 | isoform | g535.t3 | 3970971 | 3973650 |
| chr_3 | g535 | g535.t3 | exon | g535.t3.exon1 | 3970971 | 3971019 |
| chr_3 | g535 | g535.t3 | cds | g535.t3.CDS1 | 3970971 | 3971019 |
| chr_3 | g535 | g535.t3 | exon | g535.t3.exon2 | 3972602 | 3972630 |
| chr_3 | g535 | g535.t3 | cds | g535.t3.CDS2 | 3972602 | 3972630 |
| chr_3 | g535 | g535.t3 | exon | g535.t3.exon3 | 3972699 | 3972892 |
| chr_3 | g535 | g535.t3 | cds | g535.t3.CDS3 | 3972699 | 3972892 |
| chr_3 | g535 | g535.t3 | exon | g535.t3.exon4 | 3972963 | 3973001 |
| chr_3 | g535 | g535.t3 | cds | g535.t3.CDS4 | 3972963 | 3973001 |
| chr_3 | g535 | g535.t3 | exon | g535.t3.exon5 | 3973444 | 3973650 |
| chr_3 | g535 | g535.t3 | cds | g535.t3.CDS5 | 3973444 | 3973648 |
| chr_3 | g535 | g535.t3 | TTS | g535.t3 | 3974186 | 3974186 |
Sequences
>g535.t3 Gene=g535 Length=518
ATGGAGAATTGTGAATATAGCATTATTGGAACGGGTCGTCAAGTAGGAGACTCAGACGTT
AGGATGACATCGAAATGGGCCAAATTTAGACTGTTGATGTGGAAAAATTACCTTCTTCAG
TATCGTCATCCATTTCAAACAATTCTTGAGATTGCTATACCAGTATTATTTTCAGCATTA
CTCGTACTCATTCGTAGCTTAGTATCACCCGACATTTTTTCAGATCCAACGATCTATCCA
CCTTTACCATTAACTGATATCAAACAGACCTTTGGCGCTAGAGGAGAGTTTGCTTTCAAA
GTTCTCTCATTTAACAAGAACATCAATATTTCACAATTTACAAACTTTTCTAATGAAATC
GTCTACTCACCGGATAACATTGAAGTCAATGCATTGATGAAAGAGTTAAATAGTTATGTG
AAACCTTTCCTTAAGGTCACTCCTGTGCCTTCATCAAATGAACTAGCTCCGTACTTAAGA
AAATCAAATGCTTATGTTGGAATTGAATTTCCTGATAA
>g535.t3 Gene=g535 Length=172
MENCEYSIIGTGRQVGDSDVRMTSKWAKFRLLMWKNYLLQYRHPFQTILEIAIPVLFSAL
LVLIRSLVSPDIFSDPTIYPPLPLTDIKQTFGARGEFAFKVLSFNKNINISQFTNFSNEI
VYSPDNIEVNALMKELNSYVKPFLKVTPVPSSNELAPYLRKSNAYVGIEFPD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g535.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 44 | - |
| 3 | g535.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 45 | 64 | - |
| 1 | g535.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 65 | 172 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g535/g535.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g535.t3.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
