General information for g11872.t8
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t8 | TTS | g11872.t8 | 18881827 | 18881827 |
| chr_1 | g11872 | g11872.t8 | isoform | g11872.t8 | 18882010 | 18883225 |
| chr_1 | g11872 | g11872.t8 | exon | g11872.t8.exon1 | 18882010 | 18882070 |
| chr_1 | g11872 | g11872.t8 | cds | g11872.t8.CDS1 | 18882010 | 18882070 |
| chr_1 | g11872 | g11872.t8 | exon | g11872.t8.exon2 | 18882129 | 18882259 |
| chr_1 | g11872 | g11872.t8 | cds | g11872.t8.CDS2 | 18882129 | 18882259 |
| chr_1 | g11872 | g11872.t8 | exon | g11872.t8.exon3 | 18882316 | 18882483 |
| chr_1 | g11872 | g11872.t8 | cds | g11872.t8.CDS3 | 18882316 | 18882483 |
| chr_1 | g11872 | g11872.t8 | exon | g11872.t8.exon4 | 18882536 | 18883128 |
| chr_1 | g11872 | g11872.t8 | cds | g11872.t8.CDS4 | 18882536 | 18882709 |
| chr_1 | g11872 | g11872.t8 | exon | g11872.t8.exon5 | 18883190 | 18883225 |
| chr_1 | g11872 | g11872.t8 | TSS | g11872.t8 | 18883566 | 18883566 |
Sequences
>g11872.t8 Gene=g11872 Length=989
ATGTCTACAGAAAGTAGCTTGATAAAAATTGATATTGAATGGGGACATGAACGTCTAGTT
AGAGCTCAACAAACCGTTGAATTACGTCCATACGATATAGAATCTTGGTCAATTTTATTG
AGAGAAGCACAATCGAGAAACTGCAATGAAGTTAGATCGCTTTATGAATCTCTTGTTTCT
GTATTTCCCACAACTGCACGTTATTGGAAGATTTATATTGAGCAGGAAATGAAAGCTCGT
AATTTTGAGAGAGTAGAAAAACTTTTTCAAAGATGCTTAGTAAAAATTTTGAACATTGAT
CTTTGGAAGCTATATTTGACATATGTAAAAGAAAACAAGGCTGGATTGAGTACTCATAAG
TATGTTATAATTTTCATTAATTGAAGATTTCTTATTATTATATTTTTAGAGAGAAACTGG
CACAAGCATACGATTTTGCACTTGAAAAAATTGGAATGGATCTTCATTCATATTCAATTT
GGTCGGACTATATTGTATTTCTAAAAAGTTTTGAACCTATTGGTAGTTTTGCGGAAAATC
AACAAATTACTGCTATTCGAAGGGTTTATCAAAAAGCGGTTCTTACGCCAATAATCGGAA
TCGAAGTTCTTTGGAAGGAGTATATACAGTTTGAGCACAAAATTAATCCAGTTATTTCGG
AAAAGATGAGTTTGGAACGATCTCGTGATTACATGAATGCACGTCGTGTAGCAAAAGAAC
TTGAGCATATTACAAAAGGTTTGAACAAAAACTTACCAGCCGTTCAACCTACTTTAACTA
AAGAAGAATTTAAACAAGCTGAATTATGGAGAAAATTCATTAATTTTGAAAAATCAAATC
CTTTAAGAAGTGAAGATACAGCTCTCGTATCAAGACGAGTAATGTTTGCAACTGAACAAT
GTCTACTTGTAATGTGTCATCATCCATCTTTCTGGATAATGGCCGCTCAATATTTGGACA
GTACAGCTAAACATTTAACAGAGAAAGCA
>g11872.t8 Gene=g11872 Length=178
MDLHSYSIWSDYIVFLKSFEPIGSFAENQQITAIRRVYQKAVLTPIIGIEVLWKEYIQFE
HKINPVISEKMSLERSRDYMNARRVAKELEHITKGLNKNLPAVQPTLTKEEFKQAELWRK
FINFEKSNPLRSEDTALVSRRVMFATEQCLLVMCHHPSFWIMAAQYLDSTAKHLTEKA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g11872.t8 | Gene3D | G3DSA:1.25.40.1040 | - | 1 | 178 | 0.0000 |
| 1 | g11872.t8 | PANTHER | PTHR19980 | RNA CLEAVAGE STIMULATION FACTOR | 1 | 172 | 0.0000 |
| 4 | g11872.t8 | SMART | SM00386 | hat_new_1 | 29 | 62 | 0.0057 |
| 3 | g11872.t8 | SMART | SM00386 | hat_new_1 | 95 | 127 | 46.0000 |
| 2 | g11872.t8 | SUPERFAMILY | SSF48452 | TPR-like | 1 | 177 | 0.0000 |
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.
