General information for g5781.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been not been annotated.
Parent gene
- The parent gene g5781 is located on chr_2: 11918963..11919268 (- 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 | g5781 | g5781.t1 | TTS | g5781.t1 | 11918679 | 11918679 |
| chr_2 | g5781 | g5781.t1 | isoform | g5781.t1 | 11918963 | 11919268 |
| chr_2 | g5781 | g5781.t1 | exon | g5781.t1.exon1 | 11918963 | 11919075 |
| chr_2 | g5781 | g5781.t1 | cds | g5781.t1.CDS1 | 11918963 | 11919075 |
| chr_2 | g5781 | g5781.t1 | exon | g5781.t1.exon2 | 11919145 | 11919268 |
| chr_2 | g5781 | g5781.t1 | cds | g5781.t1.CDS2 | 11919145 | 11919268 |
| chr_2 | g5781 | g5781.t1 | TSS | g5781.t1 | 11919366 | 11919366 |
Sequences
>g5781.t1 Gene=g5781 Length=237
ATGGCATCAGATACACACAGAGAAGCAATTCAACGTCAGATTCATCAAGATTGGGCAAAT
AGAGAGTACATAGAAGTGATAACAAATTCGATTAAGAAAATTACGGCTTTCTTGAATTCA
TTTGACATGTCTTGCCGCTCTCGATTAGCATCATTAAACGAGAAACTCACGCTTTTGGAA
CGTAAAATAGATCATTTGGAAGCGTGTATAAACAAAGATTCGATTGTAAGACCATAA
>g5781.t1 Gene=g5781 Length=78
MASDTHREAIQRQIHQDWANREYIEVITNSIKKITAFLNSFDMSCRSRLASLNEKLTLLE
RKIDHLEACINKDSIVRP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g5781.t1 | Coils | Coil | Coil | 49 | 69 | - |
| 2 | g5781.t1 | Gene3D | G3DSA:1.20.5.110 | - | 3 | 70 | 3.5E-33 |
| 1 | g5781.t1 | PANTHER | PTHR33668 | PROTEIN BRICK1 | 1 | 72 | 3.0E-27 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5781/g5781.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5781.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0031209 | SCAR complex | CC |
| GO:0007015 | actin filament organization | BP |
| GO:0044877 | protein-containing complex binding | MF |
KEGG
Orthology
- This transcript has been annotated with K05752 (chromosome 3 open reading frame 10)
Pathway
- This transcript belongs to the following pathways
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.
