General information for g11872.t12
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Protein suppressor of forked.
Parent gene
- The parent gene g11872 is located on chr_1: 18882825..18886305 (- 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_1 | g11872 | g11872.t12 | TTS | g11872.t12 | 18881827 | 18881827 |
| chr_1 | g11872 | g11872.t12 | isoform | g11872.t12 | 18882825 | 18883225 |
| chr_1 | g11872 | g11872.t12 | exon | g11872.t12.exon1 | 18882825 | 18883128 |
| chr_1 | g11872 | g11872.t12 | cds | g11872.t12.CDS1 | 18882826 | 18883128 |
| chr_1 | g11872 | g11872.t12 | exon | g11872.t12.exon2 | 18883190 | 18883225 |
| chr_1 | g11872 | g11872.t12 | cds | g11872.t12.CDS2 | 18883190 | 18883225 |
| chr_1 | g11872 | g11872.t12 | TSS | g11872.t12 | 18883566 | 18883566 |
Sequences
>g11872.t12 Gene=g11872 Length=340
ATGTCTACAGAAAGTAGCTTGATAAAAATTGATATTGAATGGGGACATGAACGTCTAGTT
AGAGCTCAACAAACCGTTGAATTACGTCCATACGATATAGAATCTTGGTCAATTTTATTG
AGAGAAGCACAATCGAGAAACTGCAATGAAGTTAGATCGCTTTATGAATCTCTTGTTTCT
GTATTTCCCACAACTGCACGTTATTGGAAGATTTATATTGAGCAGGAAATGAAAGCTCGT
AATTTTGAGAGAGTAGAAAAACTTTTTCAAAGATGCTTAGTAAAAATTTTGAACATTGAT
CTTTGGAAGCTATATTTGACATATGTAAAAGAAAACAAGG
>g11872.t12 Gene=g11872 Length=113
MSTESSLIKIDIEWGHERLVRAQQTVELRPYDIESWSILLREAQSRNCNEVRSLYESLVS
VFPTTARYWKIYIEQEMKARNFERVEKLFQRCLVKILNIDLWKLYLTYVKENK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g11872.t12 | Gene3D | G3DSA:1.25.40.1040 | - | 15 | 113 | 0.00000 |
| 1 | g11872.t12 | PANTHER | PTHR19980 | RNA CLEAVAGE STIMULATION FACTOR | 18 | 113 | 0.00000 |
| 3 | g11872.t12 | SMART | SM00386 | hat_new_1 | 46 | 78 | 0.12000 |
| 4 | g11872.t12 | SMART | SM00386 | hat_new_1 | 80 | 111 | 0.00045 |
| 2 | g11872.t12 | SUPERFAMILY | SSF48452 | TPR-like | 22 | 112 | 0.00000 |
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:0006396 | RNA processing | BP |
| 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.
