General information for g5516.t17
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5516 is located on chr_2: 10031743..10032883 (+ 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 | g5516 | g5516.t17 | isoform | g5516.t17 | 10031743 | 10032582 |
| chr_2 | g5516 | g5516.t17 | exon | g5516.t17.exon1 | 10031743 | 10031885 |
| chr_2 | g5516 | g5516.t17 | exon | g5516.t17.exon2 | 10031945 | 10032582 |
| chr_2 | g5516 | g5516.t17 | cds | g5516.t17.CDS1 | 10032061 | 10032147 |
| chr_2 | g5516 | g5516.t17 | TTS | g5516.t17 | 10032590 | 10032590 |
| chr_2 | g5516 | g5516.t17 | TSS | g5516.t17 | NA | NA |
Sequences
>g5516.t17 Gene=g5516 Length=781
CATATCACCATTTGGTTATAAACGCGGTGAAGGAATTGATGCTGGTTCTGGAGAAATTGA
TTGGATTTGTGAACGTGATAGAGCACGTACTGATCCAATCTTTGAATCACTCAATCCTGT
TGATGGAAAAATTAGTGGCGCTGCCGCCAAGAGTGAATTGATCAAATCAAAATTACCTAA
TTCAGTACTTTCTAAAATCTGGAAATTATCAGATGTTGATTGTGATGGTTTCCTGGATAT
TGAAGAATTTGCACTCGCTATGCATTTAATAAATGTAAAAATTGACGGAAATGAATTGCC
CAACATTTTACCGGATCATTTAATTCCACCATCACACAGAGTATGAACATTGTCGTTGAC
ATTCATCATAATTTGCACATCACAGTTATAATCACTTTTGTTAGTAACAATTTCCTTCTA
TCATCTTTATGAATGTGAAAATGTCAACTAATCATTTGTGTGCATCACTTGAGTAATTTT
CTACTTGGAGAAAAATATATATATATTTTTTGATCAAAAATCATCCAAACGACAACAATG
GACAAATCATCCTTTTTTTTGAATTTAGAACCACACGGGCTTATTTTCTTCCTTCCTTAG
TAAAATTCAATACGCATATTATATACTTTAAAATAAAGAAAGAAACAATTCATATAGTTT
ACAGTTTACTCTTATATAAGATATACACCCTAAATATTATTATTATATTATATACACATA
TTTTATTAAAATACCATTTTGAATTATTTATAAATTTATGAATAATAAAGTTCACAAAAT
G
>g5516.t17 Gene=g5516 Length=28
MHLINVKIDGNELPNILPDHLIPPSHRV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value |
|---|---|---|---|---|---|---|
| g5516.t17 | Gene3D | G3DSA:1.10.238.10 | - | 1 | 28 | 0.000046 |
| g5516.t17 | ProSiteProfiles | PS50031 | EH domain profile. | 1 | 28 | 9.072000 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5516/g5516.t17; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5516.t17.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005515 | protein binding | MF |
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.
