Gene loci information

Transcript annotation

  • This transcript has been annotated as DNA-directed RNA polymerases I and III subunit RPAC1.

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_2 g5425 g5425.t4 TSS g5425.t4 9521770 9521770
chr_2 g5425 g5425.t4 isoform g5425.t4 9521851 9522918
chr_2 g5425 g5425.t4 exon g5425.t4.exon1 9521851 9522059
chr_2 g5425 g5425.t4 cds g5425.t4.CDS1 9522047 9522059
chr_2 g5425 g5425.t4 exon g5425.t4.exon2 9522236 9522441
chr_2 g5425 g5425.t4 cds g5425.t4.CDS2 9522236 9522441
chr_2 g5425 g5425.t4 exon g5425.t4.exon3 9522502 9522918
chr_2 g5425 g5425.t4 cds g5425.t4.CDS3 9522502 9522918
chr_2 g5425 g5425.t4 TTS g5425.t4 9522933 9522933

Sequences

>g5425.t4 Gene=g5425 Length=832
ATGGCAAAAATAGGTGACAAAAAGCCTAAAGTGATCTTGGAAGAGTTTAAAATTAAAGAA
AATTCAGAGGATTACGGTTTTGCAGATGAACAATTCAACCGAGAAGATTTTAAGCGAAAT
TTTAAGCTTAAAGTTATTAAGAAATCAAATTTAGATATTGAATTTGATTTAATAGGAATA
ACACCTGCTATTGCAAATGCATTTCGTAGATACACTAGAATTCAAACTTGAGATTAAATG
CACATGGAAGAATAAAGATGTAAAAGATTCTCGAAACTTTGATGCTATGTACAAAAATCA
TAACATTTATAGTGAACACATTAAATGGGTACCAAGAGGAAAACAAGGTACACTCTATAA
TGAAGCAAATATTGGACCATGTGATGACAAGATTTTAATCTCTAAAATGAGACCGGGACA
CGAGTTCAATATTAAATTACTTGCAGTGAAAGGGATTGGAAAAGATCATGCAAAATTTAG
TCCGGTTTCGCTTGCCACTTACAGATTATTGCCGGAAATCACATTGTTAAAAGAAATTCG
TGGAAAGGATGCACAACTTCTTCAGAAATGTTTCTCACCAGGAGTAATTGAAATCGATAA
AAGTGGCATTGCTTATGTCAAAAATGCAAGATATGATAATTGCAGCCGAAACGTATATCG
ATATCCTGAATTATCAAAAAACGTTGAAATATCACGAGTTCGCAATCATTTCATTTTTAA
TATTGAGTCTCTGGGTGCTTATAAACCAGAAGAAATTTTCATACTCGCAGTAAAGACCCT
CAAAAATAAATGCGATGTATTATTGGAAGAATTGAATTTTGAAAATAAATGA

>g5425.t4 Gene=g5425 Length=211
MHFVDTLEFKLEIKCTWKNKDVKDSRNFDAMYKNHNIYSEHIKWVPRGKQGTLYNEANIG
PCDDKILISKMRPGHEFNIKLLAVKGIGKDHAKFSPVSLATYRLLPEITLLKEIRGKDAQ
LLQKCFSPGVIEIDKSGIAYVKNARYDNCSRNVYRYPELSKNVEISRVRNHFIFNIESLG
AYKPEEIFILAVKTLKNKCDVLLEELNFENK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g5425.t4 CDD cd07032 RNAP_I_II_AC40 5 205 2.22402E-99
9 g5425.t4 Coils Coil Coil 192 211 -
8 g5425.t4 Gene3D G3DSA:3.30.1360.270 - 74 206 4.7E-44
3 g5425.t4 PANTHER PTHR11800 DNA-DIRECTED RNA POLYMERASE 5 207 9.3E-72
4 g5425.t4 PANTHER PTHR11800:SF13 DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC1 5 207 9.3E-72
1 g5425.t4 Pfam PF01000 RNA polymerase Rpb3/RpoA insert domain 6 95 7.3E-11
2 g5425.t4 Pfam PF01193 RNA polymerase Rpb3/Rpb11 dimerisation domain 106 199 1.3E-9
7 g5425.t4 SMART SM00662 rpoldneu2 4 205 8.3E-26
5 g5425.t4 SUPERFAMILY SSF56553 Insert subdomain of RNA polymerase alpha subunit 6 96 3.31E-15
6 g5425.t4 SUPERFAMILY SSF55257 RBP11-like subunits of RNA polymerase 123 207 1.88E-18

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5425/g5425.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5425.t4.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0003899 DNA-directed 5’-3’ RNA polymerase activity MF
GO:0001056 RNA polymerase III activity MF
GO:0006351 transcription, DNA-templated BP
GO:0001054 RNA polymerase I activity MF
GO:0046983 protein dimerization 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