Gene loci information

Transcript annotation

  • This transcript has been annotated as 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.t3 TSS g2268.t3 16347268 16347268
chr_3 g2268 g2268.t3 isoform g2268.t3 16347318 16357739
chr_3 g2268 g2268.t3 exon g2268.t3.exon1 16347318 16347507
chr_3 g2268 g2268.t3 cds g2268.t3.CDS1 16347318 16347507
chr_3 g2268 g2268.t3 exon g2268.t3.exon2 16347566 16348126
chr_3 g2268 g2268.t3 cds g2268.t3.CDS2 16347566 16348041
chr_3 g2268 g2268.t3 exon g2268.t3.exon3 16357708 16357739
chr_3 g2268 g2268.t3 TTS g2268.t3 16357725 16357725

Sequences

>g2268.t3 Gene=g2268 Length=783
ATGTTTATTATAACAGAATTAAAGAGTACAATTAAAGTTGATCCATCACAGTTTAATAAA
AGTTTAGCTGAAGTCAGTAAAAATGAGTTGAATAAAAAATTAGCAAACAAAGTACTTCAT
AATGTTGGTCTATGCATAAGTTTTCGAGAAGTTGTCTCTTTTGGTGATTCTTGTATTTTG
CCAGTTGATGGCTCCTCTCATACTGATGTCATTTTTAGATACATAGTTTTTCGTCCAGAA
ATCAGTAGCTTGATTACCGGTAAAATCAAAAGCTGTACACGTGATGGTATATTTGTAACA
TTAGGATTTTTTGATGATATTTTCATACCCAAAGATGAACTTCAGCATCCATCTCGCTTT
GATGAAGTTGAAAATGCTTGGGTTTGGGAATATCCTTTAGAAGATGGTGCAAAGCATGAT
CTATTTATGGATGTCGGAGAAACAATTAAATTTAGAGTAATTGATGAAGAATTTGTTGAA
TCTGAGCCAACTGGTCCACCTGAGACAAATAGCGAGAGCACTTCAACAAATACAAACACT
GATAATATGAAACCTCCATACAAAATTTTTGGTGCAATCAATGAAAGTGGATTAGGACTT
GATTCTTGGTGGACACAAAATTCTGGTGAAGTTGAAGATGAAGAAGATGATGAAGAAGAG
TCATAAAAATTATTTTAAACTTTTATTCAATTATGACGATTAATAAAATTATTTTTTAAG
AAATATTTGAATTACGTTGTTTTACATAGAGACAAAAAGAAGTGAGTCGAAAAAAAAAAA
AAA

>g2268.t3 Gene=g2268 Length=221
MFIITELKSTIKVDPSQFNKSLAEVSKNELNKKLANKVLHNVGLCISFREVVSFGDSCIL
PVDGSSHTDVIFRYIVFRPEISSLITGKIKSCTRDGIFVTLGFFDDIFIPKDELQHPSRF
DEVENAWVWEYPLEDGAKHDLFMDVGETIKFRVIDEEFVESEPTGPPETNSESTSTNTNT
DNMKPPYKIFGAINESGLGLDSWWTQNSGEVEDEEDDEEES

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g2268.t3 CDD cd04330 RNAP_III_Rpc25_N 2 79 3.02221E-29
10 g2268.t3 Gene3D G3DSA:3.30.1490.120 - 1 79 1.3E-26
11 g2268.t3 Gene3D G3DSA:2.40.50.140 - 81 205 1.0E-40
9 g2268.t3 MobiDBLite mobidb-lite consensus disorder prediction 158 188 -
8 g2268.t3 MobiDBLite mobidb-lite consensus disorder prediction 164 184 -
7 g2268.t3 MobiDBLite mobidb-lite consensus disorder prediction 200 221 -
3 g2268.t3 PANTHER PTHR12709:SF1 DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC8 1 206 1.0E-59
4 g2268.t3 PANTHER PTHR12709 DNA-DIRECTED RNA POLYMERASE II, III 1 206 1.0E-59
2 g2268.t3 Pfam PF03876 SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 10 64 1.4E-7
1 g2268.t3 Pfam PF08292 RNA polymerase III subunit Rpc25 84 204 7.3E-40
5 g2268.t3 SUPERFAMILY SSF88798 N-terminal, heterodimerisation domain of RBP7 (RpoE) 1 78 4.19E-18
6 g2268.t3 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 79 164 6.47E-16

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

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.

Raw TPM values