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.t2 TTS g1600.t2 12080724 12080724
chr_3 g1600 g1600.t2 isoform g1600.t2 12080828 12085867
chr_3 g1600 g1600.t2 exon g1600.t2.exon1 12080828 12080839
chr_3 g1600 g1600.t2 exon g1600.t2.exon2 12084681 12085579
chr_3 g1600 g1600.t2 cds g1600.t2.CDS1 12084684 12085559
chr_3 g1600 g1600.t2 exon g1600.t2.exon3 12085704 12085867
chr_3 g1600 g1600.t2 TSS g1600.t2 12085830 12085830

Sequences

>g1600.t2 Gene=g1600 Length=1075
CCTACAAAAGAAAACAAAGTCACGTCATTAATGAACTGAGTATGAAAATAAACAAAAGAA
GTGCGTGTCTGCTATTTTACCTTTTGAAGTGATTTAGCCAATTTCTGATAATTTCTTTCT
GTGATTTTGATTATATCCTCTTTCTCATCGTCTTCCATTTCAAGTTCAATTCATTCTTTA
AACAATGGCTGATGCTGAAGCACAATTATTACAATTGGCAACATCCAAGCCAACTGGAAT
TTCTAATGACGACATTAAAGCTAAATTGAGTGATATTCCACTCGAGATTCGTCTGAAAGC
AATCAATAAATTAATTCAAACAGAGATGCTTGAGGTATTAAAGAAAGGAGAGACACTTAT
TTATAGACTCAAGGATCCATCAAAATCCTCTGCGTCAATGAACATGGATAATGACGAAAA
AATTATTTATGATATCATTGCAGCCGGTGAGAATACAGGTGTATGGGTAAAAGACATTAG
AACAAAATCGAATCTTATAATGACACATTTAACAAAAATATTGAGGACTCTCGAGAATAA
GAAACTAATTAAAGCTGTGAAATCAGTAAATGCTAGCAAAAAGAAGGTGTATATGCTTTA
CAATCTTGAACCAGCGCGTTCGGTTACTGGTGGTGCATGGTATCAAGATTCTGACTTTGA
AGCTGAATTTGTAGATGTTCTTAATCAACAGTGTCTTAGATTCTTACAAATGAAGCGTAC
AGAAGCTAAAAAGATCAAAGATGGTCCTTACAATGTTCAATTAAAATCTCTCTGTTCTGT
CAAAGAAGTTCACGATTTTATTACACAACTCGGCATTAGTAAAATCAAACTCGAAGAAGA
CGATCTCGATACGATATTAAAGACAATTGTCTATGACGGAAAAGCGCAGAGAATTCTTCA
AGCTGATGGAAAATACTTGTATAAAGCTGTTGAATCATTACTCCCGCCTGAAGGTCTCGT
TCAGACGCCATGTGGAATTTGTCCTGTTATACATAATTGTAGCGATGTTGGAAATATAAC
GCCAAAAACATGTGTTTATATGAACGAATGGTTGGAATAAAGAGTGCGCTTTACT

>g1600.t2 Gene=g1600 Length=291
MADAEAQLLQLATSKPTGISNDDIKAKLSDIPLEIRLKAINKLIQTEMLEVLKKGETLIY
RLKDPSKSSASMNMDNDEKIIYDIIAAGENTGVWVKDIRTKSNLIMTHLTKILRTLENKK
LIKAVKSVNASKKKVYMLYNLEPARSVTGGAWYQDSDFEAEFVDVLNQQCLRFLQMKRTE
AKKIKDGPYNVQLKSLCSVKEVHDFITQLGISKIKLEEDDLDTILKTIVYDGKAQRILQA
DGKYLYKAVESLLPPEGLVQTPCGICPVIHNCSDVGNITPKTCVYMNEWLE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g1600.t2 Coils Coil Coil 286 291 -
6 g1600.t2 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 1 63 5.0E-15
5 g1600.t2 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 75 140 1.0E-24
2 g1600.t2 PANTHER PTHR12780 RNA POLYMERASE III DNA DIRECTED , 39KD SUBUNIT-RELATED 1 290 5.7E-83
8 g1600.t2 PIRSF PIRSF028763 RNAP3_C34/C39 2 291 1.6E-81
1 g1600.t2 Pfam PF05158 RNA polymerase Rpc34 subunit 4 291 1.8E-67
4 g1600.t2 SUPERFAMILY SSF46785 Winged helix DNA-binding domain 2 64 2.08E-14
3 g1600.t2 SUPERFAMILY SSF46785 Winged helix DNA-binding domain 69 141 3.99E-19

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