General information for g13879.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as RNA polymerase II subunit A C-terminal domain phosphatase SSU72.
Parent gene
- The parent gene g13879 is located on chr_1: 33090610..33092679 (+ 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 | g13879 | g13879.t3 | TSS | g13879.t3 | 33089778 | 33089778 |
| chr_1 | g13879 | g13879.t3 | isoform | g13879.t3 | 33089826 | 33090610 |
| chr_1 | g13879 | g13879.t3 | exon | g13879.t3.exon1 | 33089826 | 33089924 |
| chr_1 | g13879 | g13879.t3 | cds | g13879.t3.CDS1 | 33089826 | 33089924 |
| chr_1 | g13879 | g13879.t3 | exon | g13879.t3.exon2 | 33089995 | 33090046 |
| chr_1 | g13879 | g13879.t3 | cds | g13879.t3.CDS2 | 33089995 | 33090046 |
| chr_1 | g13879 | g13879.t3 | exon | g13879.t3.exon3 | 33090110 | 33090191 |
| chr_1 | g13879 | g13879.t3 | cds | g13879.t3.CDS3 | 33090110 | 33090191 |
| chr_1 | g13879 | g13879.t3 | exon | g13879.t3.exon4 | 33090250 | 33090610 |
| chr_1 | g13879 | g13879.t3 | cds | g13879.t3.CDS4 | 33090250 | 33090610 |
| chr_1 | g13879 | g13879.t3 | TTS | g13879.t3 | 33090729 | 33090729 |
Sequences
>g13879.t3 Gene=g13879 Length=594
ATGTCTTACATTAGCAATTTATCAATAGCAGTAATATGTTCATCAAATATGAATCGTTCA
ATGGAAGCACATCATTTTCTTAATAAGAAAAACTTTAAGGTGCGCTCTTTCGGAACAGGA
GATAAAGTTAAACTGCCAGGTAAGTTTTTCACAATCGATAAACCTAATGTCTATGAATTC
GGTGTGCCTTACTCTGATATTTATGAAGACCTTTCTAGAAAAGATAAAGCATATTATACA
CAAAATGGTTTATTACATATGTTGGATAGAAATAGACGGCTAAAGTTAGCACCAGAGAGA
TTTCAGAACTGTGAAGAAAAATTTGATGTCATTATTACTTGCGAAGAAAGAGTTTATGAT
CAAGTTGTAGACTTTTTAGAAACAAAAGGCAATGTTTCTAATATACCAGTACATCTAATT
AACATAGATATTATAGACAACCATGATGAAGCTGTAAAAGGAGCATTCATAATTTCAGAT
CTTGTTACACAACTTGCAAAAGCATCAGATCTTGATAATGAAATAGATGAAATCCTATCT
TTAGTTGAAGATCATACAGAAAAAAACTTTCTTCATTGTATCATGTTTTATTAA
>g13879.t3 Gene=g13879 Length=197
MSYISNLSIAVICSSNMNRSMEAHHFLNKKNFKVRSFGTGDKVKLPGKFFTIDKPNVYEF
GVPYSDIYEDLSRKDKAYYTQNGLLHMLDRNRRLKLAPERFQNCEEKFDVIITCEERVYD
QVVDFLETKGNVSNIPVHLINIDIIDNHDEAVKGAFIISDLVTQLAKASDLDNEIDEILS
LVEDHTEKNFLHCIMFY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g13879.t3 | Coils | Coil | Coil | 168 | 188 | - |
| 4 | g13879.t3 | Gene3D | G3DSA:3.40.50.2300 | - | 2 | 76 | 1.4E-15 |
| 5 | g13879.t3 | Gene3D | G3DSA:3.40.50.2300 | - | 77 | 197 | 2.3E-39 |
| 2 | g13879.t3 | PANTHER | PTHR20383:SF11 | RNA POLYMERASE II SUBUNIT A C-TERMINAL DOMAIN PHOSPHATASE SSU72 | 5 | 197 | 1.2E-72 |
| 3 | g13879.t3 | PANTHER | PTHR20383 | RNA POLYMERASE II SUBUNIT A C-TERMINAL DOMAIN PHOSPHATASE | 5 | 197 | 1.2E-72 |
| 1 | g13879.t3 | Pfam | PF04722 | Ssu72-like protein | 7 | 197 | 7.9E-79 |
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:0005634 | nucleus | CC |
| GO:0004721 | phosphoprotein phosphatase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K15544 (RNA polymerase II subunit A C-terminal domain phosphatase SSU72)
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. There were no conditions that were differentially expressed