General information for g11872.t2
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.t2 | TTS | g11872.t2 | 18880028 | 18880028 |
| chr_1 | g11872 | g11872.t2 | isoform | g11872.t2 | 18880104 | 18881340 |
| chr_1 | g11872 | g11872.t2 | exon | g11872.t2.exon1 | 18880104 | 18880321 |
| chr_1 | g11872 | g11872.t2 | cds | g11872.t2.CDS1 | 18880104 | 18880321 |
| chr_1 | g11872 | g11872.t2 | exon | g11872.t2.exon2 | 18880389 | 18880493 |
| chr_1 | g11872 | g11872.t2 | cds | g11872.t2.CDS2 | 18880389 | 18880493 |
| chr_1 | g11872 | g11872.t2 | exon | g11872.t2.exon3 | 18880646 | 18881340 |
| chr_1 | g11872 | g11872.t2 | cds | g11872.t2.CDS3 | 18880646 | 18881330 |
| chr_1 | g11872 | g11872.t2 | TSS | g11872.t2 | NA | NA |
Sequences
>g11872.t2 Gene=g11872 Length=1018
TGTTCAATATATGAAGTTTACAAGAAGAGCAGAAGGAATTAAATCTGCTCGTGCCATATT
CAAACGCGCAAGAGAAGATGTTCGTTCCCGATATCATGTTTTCGTAGCTGCTGCATTAAT
GGAATATTATTGCAGCAAAGATAAAGATATTGCATTTCGTATTTTCGAGTTAGGCTTGAA
ACGATTTGGAGGAAGTCCTGAATATGTTATGTGTTATATTGACTATTTATCTCATTTAAA
TGAAGATAATAACACAAGAGTTCTCTTTGAAAGAGTTTTATCTTCTGGAGGTTTAACTAA
TCAGCTTTCTGTGCAGATTTGGAATAAATTTTTAGAATTTGAATCAAACATTGGCGATTT
GTCATCAATCGTGAAAGTAGAACGGCGTCGCAGTGCAGTTCTAGAAAATTTAAAAGAATA
CGAAGGAAAGGAAACTGCACAATTGATTGATCGTTACAAGTTTTTGGATCTTTATCCTTG
TAGTCAAGCTGAACTGAAATCAGTTGGTTATTACGAAATATCATCCATCAGTAGTGGAGG
ACAAAAAGTAGTCCAACAGAATCAAGAAGAAGAAGAATCTCAAAAAGTTCTTCCTCGTCC
TGATTTTTCTCAGATGATTCCATTTAAGCCCAAGTCAAATGCATATCCTGGTGAACATCC
AATGGGTAGTGGAGGCACTTTTCCGCAACCAATAGCTCTTGCGGCTCTCTGTGCAACTTT
GCCGCCACCAATTTGCTTTAGAGGACCATTTGTATCAGTTGATAAGCTGATTGATGTATT
TAACCGAATCAAAATTGATGCACCTGTTCCATCTGAAAATGGCTTGGATACAAAATTGTT
TGACCTTGCAAAATCTGTTCATTGGATTGTTGATGAAAGTCATCAATATGAAGGAATCAA
AAGAAGGAGAATTTTGCCAGGAGGTGGTGAAGACTCTGATGACGAAACAACAAATACTGC
TAATCCACCAGTCAATGACATTTATCGTTTAAGACAACAAAAAAAATTTAATAAATAA
>g11872.t2 Gene=g11872 Length=335
MKFTRRAEGIKSARAIFKRAREDVRSRYHVFVAAALMEYYCSKDKDIAFRIFELGLKRFG
GSPEYVMCYIDYLSHLNEDNNTRVLFERVLSSGGLTNQLSVQIWNKFLEFESNIGDLSSI
VKVERRRSAVLENLKEYEGKETAQLIDRYKFLDLYPCSQAELKSVGYYEISSISSGGQKV
VQQNQEEEESQKVLPRPDFSQMIPFKPKSNAYPGEHPMGSGGTFPQPIALAALCATLPPP
ICFRGPFVSVDKLIDVFNRIKIDAPVPSENGLDTKLFDLAKSVHWIVDESHQYEGIKRRR
ILPGGGEDSDDETTNTANPPVNDIYRLRQQKKFNK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g11872.t2 | Coils | Coil | Coil | 120 | 140 | - |
| 9 | g11872.t2 | Gene3D | G3DSA:1.25.40.1040 | - | 1 | 165 | 2.6E-61 |
| 8 | g11872.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 299 | 325 | - |
| 7 | g11872.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 309 | 323 | - |
| 2 | g11872.t2 | PANTHER | PTHR19980 | RNA CLEAVAGE STIMULATION FACTOR | 1 | 333 | 1.2E-86 |
| 1 | g11872.t2 | Pfam | PF05843 | Suppressor of forked protein (Suf) | 1 | 262 | 2.5E-75 |
| 4 | g11872.t2 | SMART | SM00386 | hat_new_1 | 8 | 40 | 56.0 |
| 5 | g11872.t2 | SMART | SM00386 | hat_new_1 | 43 | 75 | 0.74 |
| 6 | g11872.t2 | SMART | SM00386 | hat_new_1 | 77 | 113 | 0.022 |
| 3 | g11872.t2 | SUPERFAMILY | SSF48452 | TPR-like | 1 | 169 | 5.69E-50 |
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.
