Gene loci information

Transcript annotation

  • This transcript has been annotated as Probable DNA-directed RNA polymerase III subunit RPC6.

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 g1600 g1600.t3 TTS g1600.t3 12084666 12084666
chr_3 g1600 g1600.t3 isoform g1600.t3 12084681 12085787
chr_3 g1600 g1600.t3 exon g1600.t3.exon1 12084681 12085069
chr_3 g1600 g1600.t3 cds g1600.t3.CDS1 12084684 12085069
chr_3 g1600 g1600.t3 exon g1600.t3.exon2 12085115 12085579
chr_3 g1600 g1600.t3 cds g1600.t3.CDS2 12085115 12085559
chr_3 g1600 g1600.t3 exon g1600.t3.exon3 12085704 12085787
chr_3 g1600 g1600.t3 TSS g1600.t3 12085830 12085830

Sequences

>g1600.t3 Gene=g1600 Length=938
CTTTTGAAGTGATTTAGCCAATTTCTGATAATTTCTTTCTGTGATTTTGATTATATCCTC
TTTCTCATCGTCTTCCATTTCAAGTTCAATTCATTCTTTAAACAATGGCTGATGCTGAAG
CACAATTATTACAATTGGCAACATCCAAGCCAACTGGAATTTCTAATGACGACATTAAAG
CTAAATTGAGTGATATTCCACTCGAGATTCGTCTGAAAGCAATCAATAAATTAATTCAAA
CAGAGATGCTTGAGGTATTAAAGAAAGGAGAGACACTTATTTATAGACTCAAGGATCCAT
CAAAATCCTCTGCGTCAATGAACATGGATAATGACGAAAAAATTATTTATGATATCATTG
CAGCCGGTGAGAATACAGGTGTATGGGTAAAAGACATTAGAACAAAATCGAATCTTATAA
TGACACATTTAACAAAAATATTGAGGACTCTCGAGAATAAGAAACTAATTAAAGCTGTGA
AATCAGTAAATGCTAGCAAAAAGAAGGTGTATATGCTTTACAATCTTGAACCAGCGCGTT
CGGTTACTGATGTTCTTAATCAACAGTGTCTTAGATTCTTACAAATGAAGCGTACAGAAG
CTAAAAAGATCAAAGATGGTCCTTACAATGTTCAATTAAAATCTCTCTGTTCTGTCAAAG
AAGTTCACGATTTTATTACACAACTCGGCATTAGTAAAATCAAACTCGAAGAAGACGATC
TCGATACGATATTAAAGACAATTGTCTATGACGGAAAAGCGCAGAGAATTCTTCAAGCTG
ATGGAAAATACTTGTATAAAGCTGTTGAATCATTACTCCCGCCTGAAGGTCTCGTTCAGA
CGCCATGTGGAATTTGTCCTGTTATACATAATTGTAGCGATGTTGGAAATATAACGCCAA
AAACATGTGTTTATATGAACGAATGGTTGGAATAAAGA

>g1600.t3 Gene=g1600 Length=276
MADAEAQLLQLATSKPTGISNDDIKAKLSDIPLEIRLKAINKLIQTEMLEVLKKGETLIY
RLKDPSKSSASMNMDNDEKIIYDIIAAGENTGVWVKDIRTKSNLIMTHLTKILRTLENKK
LIKAVKSVNASKKKVYMLYNLEPARSVTDVLNQQCLRFLQMKRTEAKKIKDGPYNVQLKS
LCSVKEVHDFITQLGISKIKLEEDDLDTILKTIVYDGKAQRILQADGKYLYKAVESLLPP
EGLVQTPCGICPVIHNCSDVGNITPKTCVYMNEWLE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g1600.t3 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 1 63 0
6 g1600.t3 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 75 140 0
3 g1600.t3 PANTHER PTHR12780 RNA POLYMERASE III DNA DIRECTED , 39KD SUBUNIT-RELATED 1 275 0
8 g1600.t3 PIRSF PIRSF028763 RNAP3_C34/C39 2 276 0
1 g1600.t3 Pfam PF05158 RNA polymerase Rpc34 subunit 4 148 0
2 g1600.t3 Pfam PF05158 RNA polymerase Rpc34 subunit 163 276 0
5 g1600.t3 SUPERFAMILY SSF46785 Winged helix DNA-binding domain 2 64 0
4 g1600.t3 SUPERFAMILY SSF46785 Winged helix DNA-binding domain 69 141 0

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:0005666 RNA polymerase III complex CC
GO:0006383 transcription by RNA polymerase III 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