General information for g11872.t4
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.t4 | TTS | g11872.t4 | 18880028 | 18880028 |
| chr_1 | g11872 | g11872.t4 | isoform | g11872.t4 | 18880104 | 18883556 |
| chr_1 | g11872 | g11872.t4 | exon | g11872.t4.exon1 | 18880104 | 18880321 |
| chr_1 | g11872 | g11872.t4 | cds | g11872.t4.CDS1 | 18880104 | 18880321 |
| chr_1 | g11872 | g11872.t4 | exon | g11872.t4.exon2 | 18880389 | 18880493 |
| chr_1 | g11872 | g11872.t4 | cds | g11872.t4.CDS2 | 18880389 | 18880493 |
| chr_1 | g11872 | g11872.t4 | exon | g11872.t4.exon3 | 18880646 | 18881345 |
| chr_1 | g11872 | g11872.t4 | cds | g11872.t4.CDS3 | 18880646 | 18881345 |
| chr_1 | g11872 | g11872.t4 | exon | g11872.t4.exon4 | 18881410 | 18881601 |
| chr_1 | g11872 | g11872.t4 | cds | g11872.t4.CDS4 | 18881410 | 18881532 |
| chr_1 | g11872 | g11872.t4 | exon | g11872.t4.exon5 | 18883492 | 18883556 |
| chr_1 | g11872 | g11872.t4 | TSS | g11872.t4 | 18883566 | 18883566 |
Sequences
>g11872.t4 Gene=g11872 Length=1280
TTTTAAAAATAAAATAAGTCAAGCATTATTTTTAAAAAAATTACCTAAAAAGAAATAAAT
TTAATGATGTAAATGCAGCCAAAATATTTTATGATGAAGTAGCAAATATACTTGAGAGAG
CAATCAACGGTGTGATGAGTAGAAATACATTACTTTACTTTACATATACTGATTTCGAAG
AAGGAAGATTAAAATATGAAAAAGTCCATCAAATGTACAACAAATTTCTTGCTATACCCG
ATATCGATCCGACTTTGGTCTATGTTCAATATATGAAGTTTACAAGAAGAGCAGAAGGAA
TTAAATCTGCTCGTGCCATATTCAAACGCGCAAGAGAAGATGTTCGTTCCCGATATCATG
TTTTCGTAGCTGCTGCATTAATGGAATATTATTGCAGCAAAGATAAAGATATTGCATTTC
GTATTTTCGAGTTAGGCTTGAAACGATTTGGAGGAAGTCCTGAATATGTTATGTGTTATA
TTGACTATTTATCTCATTTAAATGAAGATAATAACACAAGAGTTCTCTTTGAAAGAGTTT
TATCTTCTGGAGGTTTAACTAATCAGCTTTCTGTGCAGATTTGGAATAAATTTTTAGAAT
TTGAATCAAACATTGGCGATTTGTCATCAATCGTGAAAGTAGAACGGCGTCGCAGTGCAG
TTCTAGAAAATTTAAAAGAATACGAAGGAAAGGAAACTGCACAATTGATTGATCGTTACA
AGTTTTTGGATCTTTATCCTTGTAGTCAAGCTGAACTGAAATCAGTTGGTTATTACGAAA
TATCATCCATCAGTAGTGGAGGACAAAAAGTAGTCCAACAGAATCAAGAAGAAGAAGAAT
CTCAAAAAGTTCTTCCTCGTCCTGATTTTTCTCAGATGATTCCATTTAAGCCCAAGTCAA
ATGCATATCCTGGTGAACATCCAATGGGTAGTGGAGGCACTTTTCCGCAACCAATAGCTC
TTGCGGCTCTCTGTGCAACTTTGCCGCCACCAATTTGCTTTAGAGGACCATTTGTATCAG
TTGATAAGCTGATTGATGTATTTAACCGAATCAAAATTGATGCACCTGTTCCATCTGAAA
ATGGCTTGGATACAAAATTGTTTGACCTTGCAAAATCTGTTCATTGGATTGTTGATGAAA
GTCATCAATATGAAGGAATCAAAAGAAGGAGAATTTTGCCAGGAGGTGGTGAAGACTCTG
ATGACGAAACAACAAATACTGCTAATCCACCAGTCAATGACATTTATCGTTTAAGACAAC
AAAAAAAATTTAATAAATAA
>g11872.t4 Gene=g11872 Length=381
MSRNTLLYFTYTDFEEGRLKYEKVHQMYNKFLAIPDIDPTLVYVQYMKFTRRAEGIKSAR
AIFKRAREDVRSRYHVFVAAALMEYYCSKDKDIAFRIFELGLKRFGGSPEYVMCYIDYLS
HLNEDNNTRVLFERVLSSGGLTNQLSVQIWNKFLEFESNIGDLSSIVKVERRRSAVLENL
KEYEGKETAQLIDRYKFLDLYPCSQAELKSVGYYEISSISSGGQKVVQQNQEEEESQKVL
PRPDFSQMIPFKPKSNAYPGEHPMGSGGTFPQPIALAALCATLPPPICFRGPFVSVDKLI
DVFNRIKIDAPVPSENGLDTKLFDLAKSVHWIVDESHQYEGIKRRRILPGGGEDSDDETT
NTANPPVNDIYRLRQQKKFNK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g11872.t4 | Coils | Coil | Coil | 166 | 186 | - |
| 10 | g11872.t4 | Gene3D | G3DSA:1.25.40.10 | - | 1 | 216 | 2.1E-71 |
| 8 | g11872.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 345 | 371 | - |
| 9 | g11872.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 355 | 369 | - |
| 2 | g11872.t4 | PANTHER | PTHR19980 | RNA CLEAVAGE STIMULATION FACTOR | 3 | 379 | 8.0E-103 |
| 1 | g11872.t4 | Pfam | PF05843 | Suppressor of forked protein (Suf) | 40 | 308 | 4.8E-80 |
| 4 | g11872.t4 | SMART | SM00386 | hat_new_1 | 19 | 52 | 54.0 |
| 5 | g11872.t4 | SMART | SM00386 | hat_new_1 | 54 | 86 | 56.0 |
| 7 | g11872.t4 | SMART | SM00386 | hat_new_1 | 89 | 121 | 0.74 |
| 6 | g11872.t4 | SMART | SM00386 | hat_new_1 | 123 | 159 | 0.022 |
| 3 | g11872.t4 | SUPERFAMILY | SSF48452 | TPR-like | 3 | 215 | 9.1E-64 |
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:0006397 | mRNA processing | BP |
| GO:0006396 | RNA processing | BP |
| GO:0005634 | nucleus | CC |
| 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.
