Gene loci information

Transcript annotation

  • This transcript has been annotated as DNA-directed RNA polymerase I subunit RPA1.

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 g9646 g9646.t2 TTS g9646.t2 4456626 4456626
chr_1 g9646 g9646.t2 isoform g9646.t2 4456682 4457729
chr_1 g9646 g9646.t2 exon g9646.t2.exon1 4456682 4457101
chr_1 g9646 g9646.t2 cds g9646.t2.CDS1 4456682 4457101
chr_1 g9646 g9646.t2 exon g9646.t2.exon2 4457174 4457729
chr_1 g9646 g9646.t2 cds g9646.t2.CDS2 4457174 4457716
chr_1 g9646 g9646.t2 TSS g9646.t2 NA NA

Sequences

>g9646.t2 Gene=g9646 Length=976
TGATGATCCAGCTATGGACGATGATGATGCAACGGCAGACAAAATAAAAGCAAAACATGA
AGATGAACGTGATTATGAAGAACCTGAAGATAATGAGGAAATTAAAGATGCAGATTCTGA
TAAATCTGATGAGGAAGAGGATTTTGATTTGTCAAAAGTAAAATTAGAACTTGATGATGA
TGTTAATGTGAAGCTATTAGAGGAGCTCGTTAGAGAAGATCCAGATGCTGATCTCGAACA
GTTGAAAAGTTTCGAGAAGAAAGAAGATGAGGATGATGATCAAGGTGAAGACGATATGAT
GAACTATTTAGAAAAAAAACTTTCAACAATCAGTGCTAATATAATGATTCAAAGTTTTGA
GAAAGATTCTAAAAAGCATAGTTGGTGTAAAATCAAATTTTCGGTGCCAATCAAGTTTAA
GAACATTGATATGACTAGTGTAATTAGAGATGCAGCACGCACTTCTGTTATTTGGGAAAT
TCCAAAAATAAAACGAGCCATTACTTTCAAACAGAATGGTTTACTTTGCATTAAAACTGA
AGGCATAAATGTTGAGGCGATGTTTGAATATGACAAAATTTTGGACCTCAAAAAACTTTA
TATCAACGATATTCATGAAGTTGCAAACAGATATGGAATAGAGTGTGCGGCAAAAGTAAT
TGTAAAGGAAGTTCAAAACGTTTTCCGAGTTTATGGAATTACAGTCGATCCACGTCACTT
GTCTCTCATTGCTGATTATATGACCTTTGATGGTACAATTAAACCATTAAATAGAAAAGG
AATGGAATCTAATGCTTCACCGTTTCAAAAAATTTCTTTTGAATCCGCTCTTAGTTTTCT
GAAAAACGCAGTTGTCCAAGGAAACGTTGATAATATCAAATCACCATCATCATGTCTCAT
TACTGGCGCTCCGTGTAAAATAGGAACTGGCTCATTCGGTCTTATCAATAATTTAAGTTA
CGCATTGAATTTATAA

>g9646.t2 Gene=g9646 Length=320
MDDDDATADKIKAKHEDERDYEEPEDNEEIKDADSDKSDEEEDFDLSKVKLELDDDVNVK
LLEELVREDPDADLEQLKSFEKKEDEDDDQGEDDMMNYLEKKLSTISANIMIQSFEKDSK
KHSWCKIKFSVPIKFKNIDMTSVIRDAARTSVIWEIPKIKRAITFKQNGLLCIKTEGINV
EAMFEYDKILDLKKLYINDIHEVANRYGIECAAKVIVKEVQNVFRVYGITVDPRHLSLIA
DYMTFDGTIKPLNRKGMESNASPFQKISFESALSFLKNAVVQGNVDNIKSPSSCLITGAP
CKIGTGSFGLINNLSYALNL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g9646.t2 CDD cd02735 RNAP_I_Rpa1_C 122 311 1.15118E-90
9 g9646.t2 Gene3D G3DSA:3.30.70.2850 - 49 155 6.5E-8
10 g9646.t2 Gene3D G3DSA:1.10.1790.20 - 185 285 1.6E-5
5 g9646.t2 MobiDBLite mobidb-lite consensus disorder prediction 1 20 -
6 g9646.t2 MobiDBLite mobidb-lite consensus disorder prediction 1 47 -
8 g9646.t2 MobiDBLite mobidb-lite consensus disorder prediction 21 41 -
7 g9646.t2 MobiDBLite mobidb-lite consensus disorder prediction 73 92 -
2 g9646.t2 PANTHER PTHR19376:SF11 DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA1 22 306 1.2E-39
3 g9646.t2 PANTHER PTHR19376 DNA-DIRECTED RNA POLYMERASE 22 306 1.2E-39
1 g9646.t2 Pfam PF04998 RNA polymerase Rpb1, domain 5 100 264 8.9E-27
4 g9646.t2 SUPERFAMILY SSF64484 beta and beta-prime subunits of DNA dependent RNA-polymerase 138 315 3.36E-48

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:0003899 DNA-directed 5’-3’ RNA polymerase activity MF
GO:0003677 DNA binding MF
GO:0008270 zinc ion binding MF
GO:0006351 transcription, DNA-templated BP

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