General information for g1600.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable DNA-directed RNA polymerase III subunit RPC6.
Parent gene
- The parent gene g1600 is located on chr_3: 12084684..12085867 (- strand)
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.t1 | TTS | g1600.t1 | 12084666 | 12084666 |
| chr_3 | g1600 | g1600.t1 | isoform | g1600.t1 | 12084684 | 12085559 |
| chr_3 | g1600 | g1600.t1 | exon | g1600.t1.exon1 | 12084684 | 12085559 |
| chr_3 | g1600 | g1600.t1 | cds | g1600.t1.CDS1 | 12084684 | 12085559 |
| chr_3 | g1600 | g1600.t1 | TSS | g1600.t1 | 12085830 | 12085830 |
Sequences
>g1600.t1 Gene=g1600 Length=876
ATGGCTGATGCTGAAGCACAATTATTACAATTGGCAACATCCAAGCCAACTGGAATTTCT
AATGACGACATTAAAGCTAAATTGAGTGATATTCCACTCGAGATTCGTCTGAAAGCAATC
AATAAATTAATTCAAACAGAGATGCTTGAGGTATTAAAGAAAGGAGAGACACTTATTTAT
AGACTCAAGGATCCATCAAAATCCTCTGCGTCAATGAACATGGATAATGACGAAAAAATT
ATTTATGATATCATTGCAGCCGGTGAGAATACAGGTGTATGGGTAAAAGACATTAGAACA
AAATCGAATCTTATAATGACACATTTAACAAAAATATTGAGGACTCTCGAGAATAAGAAA
CTAATTAAAGCTGTGAAATCAGTAAATGCTAGCAAAAAGAAGGTGTATATGCTTTACAAT
CTTGAACCAGCGCGTTCGGTTACTGGTGGTGCATGGTATCAAGATTCTGACTTTGAAGCT
GAATTTGTAGATGTTCTTAATCAACAGTGTCTTAGATTCTTACAAATGAAGCGTACAGAA
GCTAAAAAGATCAAAGATGGTCCTTACAATGTTCAATTAAAATCTCTCTGTTCTGTCAAA
GAAGTTCACGATTTTATTACACAACTCGGCATTAGTAAAATCAAACTCGAAGAAGACGAT
CTCGATACGATATTAAAGACAATTGTCTATGACGGAAAAGCGCAGAGAATTCTTCAAGCT
GATGGAAAATACTTGTATAAAGCTGTTGAATCATTACTCCCGCCTGAAGGTCTCGTTCAG
ACGCCATGTGGAATTTGTCCTGTTATACATAATTGTAGCGATGTTGGAAATATAACGCCA
AAAACATGTGTTTATATGAACGAATGGTTGGAATAA
>g1600.t1 Gene=g1600 Length=291
MADAEAQLLQLATSKPTGISNDDIKAKLSDIPLEIRLKAINKLIQTEMLEVLKKGETLIY
RLKDPSKSSASMNMDNDEKIIYDIIAAGENTGVWVKDIRTKSNLIMTHLTKILRTLENKK
LIKAVKSVNASKKKVYMLYNLEPARSVTGGAWYQDSDFEAEFVDVLNQQCLRFLQMKRTE
AKKIKDGPYNVQLKSLCSVKEVHDFITQLGISKIKLEEDDLDTILKTIVYDGKAQRILQA
DGKYLYKAVESLLPPEGLVQTPCGICPVIHNCSDVGNITPKTCVYMNEWLE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g1600.t1 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 1 | 63 | 0 |
| 5 | g1600.t1 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 75 | 140 | 0 |
| 2 | g1600.t1 | PANTHER | PTHR12780 | RNA POLYMERASE III DNA DIRECTED , 39KD SUBUNIT-RELATED | 1 | 290 | 0 |
| 7 | g1600.t1 | PIRSF | PIRSF028763 | RNAP3_C34/C39 | 2 | 291 | 0 |
| 1 | g1600.t1 | Pfam | PF05158 | RNA polymerase Rpc34 subunit | 4 | 291 | 0 |
| 4 | g1600.t1 | SUPERFAMILY | SSF46785 | Winged helix DNA-binding domain | 2 | 64 | 0 |
| 3 | g1600.t1 | 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 transcript has been annotated with K03025 (DNA-directed RNA polymerase III subunit RPC6)
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.
