Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative DNA-directed RNA polymerase III subunit RPC8.

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_3 g2268 g2268.t2 TSS g2268.t2 16347268 16347268
chr_3 g2268 g2268.t2 isoform g2268.t2 16347318 16348041
chr_3 g2268 g2268.t2 exon g2268.t2.exon1 16347318 16347507
chr_3 g2268 g2268.t2 cds g2268.t2.CDS1 16347318 16347507
chr_3 g2268 g2268.t2 exon g2268.t2.exon2 16347566 16347634
chr_3 g2268 g2268.t2 cds g2268.t2.CDS2 16347566 16347634
chr_3 g2268 g2268.t2 exon g2268.t2.exon3 16347710 16348041
chr_3 g2268 g2268.t2 cds g2268.t2.CDS3 16347710 16348041
chr_3 g2268 g2268.t2 TTS g2268.t2 16348102 16348102

Sequences

>g2268.t2 Gene=g2268 Length=591
ATGTTTATTATAACAGAATTAAAGAGTACAATTAAAGTTGATCCATCACAGTTTAATAAA
AGTTTAGCTGAAGTCAGTAAAAATGAGTTGAATAAAAAATTAGCAAACAAAGTACTTCAT
AATGTTGGTCTATGCATAAGTTTTCGAGAAGTTGTCTCTTTTGGTGATTCTTGTATTTTG
CCAGTTGATGGCTCCTCTCATACTGATGTCATTTTTAGATACATAGTTTTTCGTCCAGAA
ATCAGTAGCTTGATTACCGATGAACTTCAGCATCCATCTCGCTTTGATGAAGTTGAAAAT
GCTTGGGTTTGGGAATATCCTTTAGAAGATGGTGCAAAGCATGATCTATTTATGGATGTC
GGAGAAACAATTAAATTTAGAGTAATTGATGAAGAATTTGTTGAATCTGAGCCAACTGGT
CCACCTGAGACAAATAGCGAGAGCACTTCAACAAATACAAACACTGATAATATGAAACCT
CCATACAAAATTTTTGGTGCAATCAATGAAAGTGGATTAGGACTTGATTCTTGGTGGACA
CAAAATTCTGGTGAAGTTGAAGATGAAGAAGATGATGAAGAAGAGTCATAA

>g2268.t2 Gene=g2268 Length=196
MFIITELKSTIKVDPSQFNKSLAEVSKNELNKKLANKVLHNVGLCISFREVVSFGDSCIL
PVDGSSHTDVIFRYIVFRPEISSLITDELQHPSRFDEVENAWVWEYPLEDGAKHDLFMDV
GETIKFRVIDEEFVESEPTGPPETNSESTSTNTNTDNMKPPYKIFGAINESGLGLDSWWT
QNSGEVEDEEDDEEES

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g2268.t2 CDD cd04330 RNAP_III_Rpc25_N 2 79 2.17273E-30
11 g2268.t2 Gene3D G3DSA:3.30.1490.120 - 1 77 1.0E-26
12 g2268.t2 Gene3D G3DSA:2.40.50.140 - 78 180 6.6E-25
10 g2268.t2 MobiDBLite mobidb-lite consensus disorder prediction 133 163 -
8 g2268.t2 MobiDBLite mobidb-lite consensus disorder prediction 139 159 -
9 g2268.t2 MobiDBLite mobidb-lite consensus disorder prediction 175 196 -
3 g2268.t2 PANTHER PTHR12709:SF1 DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC8 1 86 1.0E-39
5 g2268.t2 PANTHER PTHR12709 DNA-DIRECTED RNA POLYMERASE II, III 1 86 1.0E-39
4 g2268.t2 PANTHER PTHR12709:SF1 DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC8 86 181 1.0E-39
6 g2268.t2 PANTHER PTHR12709 DNA-DIRECTED RNA POLYMERASE II, III 86 181 1.0E-39
2 g2268.t2 Pfam PF03876 SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 10 64 1.1E-7
1 g2268.t2 Pfam PF08292 RNA polymerase III subunit Rpc25 86 179 8.7E-24
7 g2268.t2 SUPERFAMILY SSF88798 N-terminal, heterodimerisation domain of RBP7 (RpoE) 1 78 3.27E-18

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: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