Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative RNA polymerase II subunit A C-terminal domain phosphatase SSU72.

Parent gene

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.t6 TSS g13879.t6 33089778 33089778
chr_1 g13879 g13879.t6 isoform g13879.t6 33089826 33090709
chr_1 g13879 g13879.t6 exon g13879.t6.exon1 33089826 33090709
chr_1 g13879 g13879.t6 cds g13879.t6.CDS1 33090275 33090610
chr_1 g13879 g13879.t6 TTS g13879.t6 33090729 33090729

Sequences

>g13879.t6 Gene=g13879 Length=884
ATGTCTTACATTAGCAATTTATCAATAGCAGTAATATGTTCATCAAATATGAATCGTTCA
ATGGAAGCACATCATTTTCTTAATAAGAAAAACTTTAAGGTACATAAACGAGAATAAATG
TGAGAAATATTGAGAGATAAAATGGCATTAAATTTAATGAAACTTTTAGGTGCGCTCTTT
CGGAACAGGAGATAAAGTTAAACTGCCAGGTAAGTTTTTCAGTAACTTGAGCGATTCTCA
AATTTGAATATTAAATATTTTATCTTAAAATTTATCAGGCACAGCAATCGATAAACCTAA
TGTCTATGAATTCGGTGTGCCTTACTCTGATATTTATGAAGACCTTTCTAGAAAAGATAA
AGCATAGTGAGTCAAATGGCGAAAAAATAAATATTCAAGCACTTAACACAATTTGTCTTT
TTAGTTATACACAAAATGGTTTATTACATATGTTGGATAGAAATAGACGGCTAAAGTTAG
CACCAGAGAGATTTCAGAACTGTGAAGAAAAATTTGATGTCATTATTACTTGCGAAGAAA
GAGTTTATGATCAAGTTGTAGACTTTTTAGAAACAAAAGGCAATGTTTCTAATATACCAG
TACATCTAATTAACATAGATATTATAGACAACCATGATGAAGCTGTAAAAGGAGCATTCA
TAATTTCAGATCTTGTTACACAACTTGCAAAAGCATCAGATCTTGATAATGAAATAGATG
AAATCCTATCTTTAGTTGAAGATCATACAGAAAAAAACTTTCTTCATTGTATCATGTTTT
ATTAATACGGAATTTTTTTTAAAAATTTTTCAATGAAAGAAAAAATATTCAGGACTTTTG
CAACACTTTAATATTTAAGCATAACAGTGTATATAAAGTAAAAT

>g13879.t6 Gene=g13879 Length=111
MLDRNRRLKLAPERFQNCEEKFDVIITCEERVYDQVVDFLETKGNVSNIPVHLINIDIID
NHDEAVKGAFIISDLVTQLAKASDLDNEIDEILSLVEDHTEKNFLHCIMFY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g13879.t6 Coils Coil Coil 82 102 -
4 g13879.t6 Gene3D G3DSA:3.40.50.2300 - 1 111 3.0E-38
2 g13879.t6 PANTHER PTHR20383:SF11 RNA POLYMERASE II SUBUNIT A C-TERMINAL DOMAIN PHOSPHATASE SSU72 1 111 6.6E-34
3 g13879.t6 PANTHER PTHR20383 RNA POLYMERASE II SUBUNIT A C-TERMINAL DOMAIN PHOSPHATASE 1 111 6.6E-34
1 g13879.t6 Pfam PF04722 Ssu72-like protein 1 111 2.8E-37

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 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.

Raw TPM values