General information for g11872.t1
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.t1 | TTS | g11872.t1 | 18880028 | 18880028 |
| chr_1 | g11872 | g11872.t1 | isoform | g11872.t1 | 18880104 | 18883225 |
| chr_1 | g11872 | g11872.t1 | exon | g11872.t1.exon1 | 18880104 | 18880321 |
| chr_1 | g11872 | g11872.t1 | cds | g11872.t1.CDS1 | 18880104 | 18880321 |
| chr_1 | g11872 | g11872.t1 | exon | g11872.t1.exon2 | 18880389 | 18880493 |
| chr_1 | g11872 | g11872.t1 | cds | g11872.t1.CDS2 | 18880389 | 18880493 |
| chr_1 | g11872 | g11872.t1 | exon | g11872.t1.exon3 | 18880646 | 18881345 |
| chr_1 | g11872 | g11872.t1 | cds | g11872.t1.CDS3 | 18880646 | 18881345 |
| chr_1 | g11872 | g11872.t1 | exon | g11872.t1.exon4 | 18881410 | 18881601 |
| chr_1 | g11872 | g11872.t1 | cds | g11872.t1.CDS4 | 18881410 | 18881601 |
| chr_1 | g11872 | g11872.t1 | exon | g11872.t1.exon5 | 18882010 | 18882070 |
| chr_1 | g11872 | g11872.t1 | cds | g11872.t1.CDS5 | 18882010 | 18882070 |
| chr_1 | g11872 | g11872.t1 | exon | g11872.t1.exon6 | 18882129 | 18882259 |
| chr_1 | g11872 | g11872.t1 | cds | g11872.t1.CDS6 | 18882129 | 18882259 |
| chr_1 | g11872 | g11872.t1 | exon | g11872.t1.exon7 | 18882316 | 18882483 |
| chr_1 | g11872 | g11872.t1 | cds | g11872.t1.CDS7 | 18882316 | 18882483 |
| chr_1 | g11872 | g11872.t1 | exon | g11872.t1.exon8 | 18882536 | 18882755 |
| chr_1 | g11872 | g11872.t1 | cds | g11872.t1.CDS8 | 18882536 | 18882755 |
| chr_1 | g11872 | g11872.t1 | exon | g11872.t1.exon9 | 18882806 | 18883128 |
| chr_1 | g11872 | g11872.t1 | cds | g11872.t1.CDS9 | 18882806 | 18883128 |
| chr_1 | g11872 | g11872.t1 | exon | g11872.t1.exon10 | 18883190 | 18883225 |
| chr_1 | g11872 | g11872.t1 | cds | g11872.t1.CDS10 | 18883190 | 18883225 |
| chr_1 | g11872 | g11872.t1 | TSS | g11872.t1 | 18883566 | 18883566 |
Sequences
>g11872.t1 Gene=g11872 Length=2154
ATGTCTACAGAAAGTAGCTTGATAAAAATTGATATTGAATGGGGACATGAACGTCTAGTT
AGAGCTCAACAAACCGTTGAATTACGTCCATACGATATAGAATCTTGGTCAATTTTATTG
AGAGAAGCACAATCGAGAAACTGCAATGAAGTTAGATCGCTTTATGAATCTCTTGTTTCT
GTATTTCCCACAACTGCACGTTATTGGAAGATTTATATTGAGCAGGAAATGAAAGCTCGT
AATTTTGAGAGAGTAGAAAAACTTTTTCAAAGATGCTTAGTAAAAATTTTGAACATTGAT
CTTTGGAAGCTATATTTGACATATGTAAAAGAAAACAAGGCTGGATTGAGTACTCATAAA
GAGAAACTGGCACAAGCATACGATTTTGCACTTGAAAAAATTGGAATGGATCTTCATTCA
TATTCAATTTGGTCGGACTATATTGTATTTCTAAAAAGTTTTGAACCTATTGGTAGTTTT
GCGGAAAATCAACAAATTACTGCTATTCGAAGGGTTTATCAAAAAGCGGTTCTTACGCCA
ATAATCGGAATCGAAGTTCTTTGGAAGGAGTATATACAGTTTGAGCACAAAATTAATCCA
GTTATTTCGGAAAAGATGAGTTTGGAACGATCTCGTGATTACATGAATGCACGTCGTGTA
GCAAAAGAACTTGAGCATATTACAAAAGGTTTGAACAAAAACTTACCAGCCGTTCAACCT
ACTTTAACTAAAGAAGAATTTAAACAAGCTGAATTATGGAGAAAATTCATTAATTTTGAA
AAATCAAATCCTTTAAGAAGTGAAGATACAGCTCTCGTATCAAGACGAGTAATGTTTGCA
ACTGAACAATGTCTACTTGTAATGTGTCATCATCCATCTTTCTGGATAATGGCCGCTCAA
TATTTGGACAGTACAGCTAAACATTTAACAGAGAAAGCAGATGTAAATGCAGCCAAAATA
TTTTATGATGAAGTAGCAAATATACTTGAGAGAGCAATCAACGGTGTGATGAGTAGAAAT
ACATTACTTTACTTTACATATACTGATTTCGAAGAAGGAAGATTAAAATATGAAAAAGTC
CATCAAATGTACAACAAATTTCTTGCTATACCCGATATCGATCCGACTTTGGTCTATGTT
CAATATATGAAGTTTACAAGAAGAGCAGAAGGAATTAAATCTGCTCGTGCCATATTCAAA
CGCGCAAGAGAAGATGTTCGTTCCCGATATCATGTTTTCGTAGCTGCTGCATTAATGGAA
TATTATTGCAGCAAAGATAAAGATATTGCATTTCGTATTTTCGAGTTAGGCTTGAAACGA
TTTGGAGGAAGTCCTGAATATGTTATGTGTTATATTGACTATTTATCTCATTTAAATGAA
GATAATAACACAAGAGTTCTCTTTGAAAGAGTTTTATCTTCTGGAGGTTTAACTAATCAG
CTTTCTGTGCAGATTTGGAATAAATTTTTAGAATTTGAATCAAACATTGGCGATTTGTCA
TCAATCGTGAAAGTAGAACGGCGTCGCAGTGCAGTTCTAGAAAATTTAAAAGAATACGAA
GGAAAGGAAACTGCACAATTGATTGATCGTTACAAGTTTTTGGATCTTTATCCTTGTAGT
CAAGCTGAACTGAAATCAGTTGGTTATTACGAAATATCATCCATCAGTAGTGGAGGACAA
AAAGTAGTCCAACAGAATCAAGAAGAAGAAGAATCTCAAAAAGTTCTTCCTCGTCCTGAT
TTTTCTCAGATGATTCCATTTAAGCCCAAGTCAAATGCATATCCTGGTGAACATCCAATG
GGTAGTGGAGGCACTTTTCCGCAACCAATAGCTCTTGCGGCTCTCTGTGCAACTTTGCCG
CCACCAATTTGCTTTAGAGGACCATTTGTATCAGTTGATAAGCTGATTGATGTATTTAAC
CGAATCAAAATTGATGCACCTGTTCCATCTGAAAATGGCTTGGATACAAAATTGTTTGAC
CTTGCAAAATCTGTTCATTGGATTGTTGATGAAAGTCATCAATATGAAGGAATCAAAAGA
AGGAGAATTTTGCCAGGAGGTGGTGAAGACTCTGATGACGAAACAACAAATACTGCTAAT
CCACCAGTCAATGACATTTATCGTTTAAGACAACAAAAAAAATTTAATAAATAA
>g11872.t1 Gene=g11872 Length=717
MSTESSLIKIDIEWGHERLVRAQQTVELRPYDIESWSILLREAQSRNCNEVRSLYESLVS
VFPTTARYWKIYIEQEMKARNFERVEKLFQRCLVKILNIDLWKLYLTYVKENKAGLSTHK
EKLAQAYDFALEKIGMDLHSYSIWSDYIVFLKSFEPIGSFAENQQITAIRRVYQKAVLTP
IIGIEVLWKEYIQFEHKINPVISEKMSLERSRDYMNARRVAKELEHITKGLNKNLPAVQP
TLTKEEFKQAELWRKFINFEKSNPLRSEDTALVSRRVMFATEQCLLVMCHHPSFWIMAAQ
YLDSTAKHLTEKADVNAAKIFYDEVANILERAINGVMSRNTLLYFTYTDFEEGRLKYEKV
HQMYNKFLAIPDIDPTLVYVQYMKFTRRAEGIKSARAIFKRAREDVRSRYHVFVAAALME
YYCSKDKDIAFRIFELGLKRFGGSPEYVMCYIDYLSHLNEDNNTRVLFERVLSSGGLTNQ
LSVQIWNKFLEFESNIGDLSSIVKVERRRSAVLENLKEYEGKETAQLIDRYKFLDLYPCS
QAELKSVGYYEISSISSGGQKVVQQNQEEEESQKVLPRPDFSQMIPFKPKSNAYPGEHPM
GSGGTFPQPIALAALCATLPPPICFRGPFVSVDKLIDVFNRIKIDAPVPSENGLDTKLFD
LAKSVHWIVDESHQYEGIKRRRILPGGGEDSDDETTNTANPPVNDIYRLRQQKKFNK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g11872.t1 | Coils | Coil | Coil | 502 | 522 | - |
| 16 | g11872.t1 | Gene3D | G3DSA:1.25.40.1040 | - | 15 | 547 | 3.3E-173 |
| 15 | g11872.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 681 | 707 | - |
| 14 | g11872.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 691 | 705 | - |
| 2 | g11872.t1 | PANTHER | PTHR19980 | RNA CLEAVAGE STIMULATION FACTOR | 18 | 715 | 1.5E-230 |
| 1 | g11872.t1 | Pfam | PF05843 | Suppressor of forked protein (Suf) | 376 | 644 | 1.4E-79 |
| 10 | g11872.t1 | SMART | SM00386 | hat_new_1 | 46 | 78 | 0.12 |
| 12 | g11872.t1 | SMART | SM00386 | hat_new_1 | 80 | 111 | 4.5E-4 |
| 5 | g11872.t1 | SMART | SM00386 | hat_new_1 | 118 | 153 | 2.6 |
| 6 | g11872.t1 | SMART | SM00386 | hat_new_1 | 164 | 197 | 0.0057 |
| 9 | g11872.t1 | SMART | SM00386 | hat_new_1 | 230 | 262 | 46.0 |
| 4 | g11872.t1 | SMART | SM00386 | hat_new_1 | 320 | 353 | 110.0 |
| 11 | g11872.t1 | SMART | SM00386 | hat_new_1 | 355 | 388 | 54.0 |
| 8 | g11872.t1 | SMART | SM00386 | hat_new_1 | 390 | 422 | 56.0 |
| 13 | g11872.t1 | SMART | SM00386 | hat_new_1 | 425 | 457 | 0.74 |
| 7 | g11872.t1 | SMART | SM00386 | hat_new_1 | 459 | 495 | 0.022 |
| 3 | g11872.t1 | SUPERFAMILY | SSF48452 | TPR-like | 22 | 551 | 1.49E-147 |
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 transcript has been annotated with K14408 (cleavage stimulation factor subunit 3)
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.
