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.t4 TTS g1600.t4 12084666 12084666
chr_3 g1600 g1600.t4 isoform g1600.t4 12084681 12085787
chr_3 g1600 g1600.t4 exon g1600.t4.exon1 12084681 12085579
chr_3 g1600 g1600.t4 cds g1600.t4.CDS1 12084684 12085559
chr_3 g1600 g1600.t4 exon g1600.t4.exon2 12085704 12085787
chr_3 g1600 g1600.t4 TSS g1600.t4 12085830 12085830

Sequences

>g1600.t4 Gene=g1600 Length=983
CTTTTGAAGTGATTTAGCCAATTTCTGATAATTTCTTTCTGTGATTTTGATTATATCCTC
TTTCTCATCGTCTTCCATTTCAAGTTCAATTCATTCTTTAAACAATGGCTGATGCTGAAG
CACAATTATTACAATTGGCAACATCCAAGCCAACTGGAATTTCTAATGACGACATTAAAG
CTAAATTGAGTGATATTCCACTCGAGATTCGTCTGAAAGCAATCAATAAATTAATTCAAA
CAGAGATGCTTGAGGTATTAAAGAAAGGAGAGACACTTATTTATAGACTCAAGGATCCAT
CAAAATCCTCTGCGTCAATGAACATGGATAATGACGAAAAAATTATTTATGATATCATTG
CAGCCGGTGAGAATACAGGTGTATGGGTAAAAGACATTAGAACAAAATCGAATCTTATAA
TGACACATTTAACAAAAATATTGAGGACTCTCGAGAATAAGAAACTAATTAAAGCTGTGA
AATCAGTAAATGCTAGCAAAAAGAAGGTGTATATGCTTTACAATCTTGAACCAGCGCGTT
CGGTTACTGGTGGTGCATGGTATCAAGATTCTGACTTTGAAGCTGAATTTGTAGATGTTC
TTAATCAACAGTGTCTTAGATTCTTACAAATGAAGCGTACAGAAGCTAAAAAGATCAAAG
ATGGTCCTTACAATGTTCAATTAAAATCTCTCTGTTCTGTCAAAGAAGTTCACGATTTTA
TTACACAACTCGGCATTAGTAAAATCAAACTCGAAGAAGACGATCTCGATACGATATTAA
AGACAATTGTCTATGACGGAAAAGCGCAGAGAATTCTTCAAGCTGATGGAAAATACTTGT
ATAAAGCTGTTGAATCATTACTCCCGCCTGAAGGTCTCGTTCAGACGCCATGTGGAATTT
GTCCTGTTATACATAATTGTAGCGATGTTGGAAATATAACGCCAAAAACATGTGTTTATA
TGAACGAATGGTTGGAATAAAGA

>g1600.t4 Gene=g1600 Length=291
MADAEAQLLQLATSKPTGISNDDIKAKLSDIPLEIRLKAINKLIQTEMLEVLKKGETLIY
RLKDPSKSSASMNMDNDEKIIYDIIAAGENTGVWVKDIRTKSNLIMTHLTKILRTLENKK
LIKAVKSVNASKKKVYMLYNLEPARSVTGGAWYQDSDFEAEFVDVLNQQCLRFLQMKRTE
AKKIKDGPYNVQLKSLCSVKEVHDFITQLGISKIKLEEDDLDTILKTIVYDGKAQRILQA
DGKYLYKAVESLLPPEGLVQTPCGICPVIHNCSDVGNITPKTCVYMNEWLE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g1600.t4 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 1 63 0
5 g1600.t4 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 75 140 0
2 g1600.t4 PANTHER PTHR12780 RNA POLYMERASE III DNA DIRECTED , 39KD SUBUNIT-RELATED 1 290 0
7 g1600.t4 PIRSF PIRSF028763 RNAP3_C34/C39 2 291 0
1 g1600.t4 Pfam PF05158 RNA polymerase Rpc34 subunit 4 291 0
4 g1600.t4 SUPERFAMILY SSF46785 Winged helix DNA-binding domain 2 64 0
3 g1600.t4 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

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