General information for g3561.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g3561 is located on chr_3: 26449802..26450380 (- 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 | g3561 | g3561.t1 | TTS | g3561.t1 | 26449743 | 26449743 |
| chr_3 | g3561 | g3561.t1 | isoform | g3561.t1 | 26449802 | 26450380 |
| chr_3 | g3561 | g3561.t1 | exon | g3561.t1.exon1 | 26449802 | 26449953 |
| chr_3 | g3561 | g3561.t1 | cds | g3561.t1.CDS1 | 26449802 | 26449953 |
| chr_3 | g3561 | g3561.t1 | exon | g3561.t1.exon2 | 26450012 | 26450167 |
| chr_3 | g3561 | g3561.t1 | cds | g3561.t1.CDS2 | 26450012 | 26450167 |
| chr_3 | g3561 | g3561.t1 | exon | g3561.t1.exon3 | 26450371 | 26450380 |
| chr_3 | g3561 | g3561.t1 | cds | g3561.t1.CDS3 | 26450371 | 26450380 |
| chr_3 | g3561 | g3561.t1 | TSS | g3561.t1 | 26450399 | 26450399 |
Sequences
>g3561.t1 Gene=g3561 Length=318
ATGTCAACTGAAGATAATTTCTTGCTAAGCAGCGAAAACTTACGCTCATCGCCTGAGTTA
TGGCCAGAGAAAATACCCGGTAGTGAGAATTATAAAAAGGCAGCAATTAAAAACATAAAA
GATAATCCAAACGGTTTGACTCAAGATGATATCAGGAAAATTTATCAGCTCGGTAGTTTA
CCTAAATCTGAAATTGTTGCTGAAATAAAGAGATTATATGATGAAGGATACCAACTTGGA
GTAGAAGAAGCAAAAGAAGTCACACGAGGGAAATATCTCAATATATTCACTAATACGTCA
ATCATTAAAAGAAAATAA
>g3561.t1 Gene=g3561 Length=105
MSTEDNFLLSSENLRSSPELWPEKIPGSENYKKAAIKNIKDNPNGLTQDDIRKIYQLGSL
PKSEIVAEIKRLYDEGYQLGVEEAKEVTRGKYLNIFTNTSIIKRK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g3561.t1 | PANTHER | PTHR31489 | LIN52 FAMILY MEMBER | 5 | 99 | 0 |
| 1 | g3561.t1 | Pfam | PF10044 | Retinal tissue protein | 8 | 96 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0070176 | DRM complex | CC |
| GO:0006351 | transcription, DNA-templated | BP |
KEGG
Orthology
- This transcript has been annotated with K21775 (protein lin-52)
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.
