General information for g10820.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative DNA-directed RNA polymerase III subunit RPC3.
Parent gene
- The parent gene g10820 is located on chr_1: 12143244..12145776 (- 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_1 | g10820 | g10820.t1 | TTS | g10820.t1 | 12141428 | 12141428 |
| chr_1 | g10820 | g10820.t1 | isoform | g10820.t1 | 12142252 | 12143244 |
| chr_1 | g10820 | g10820.t1 | exon | g10820.t1.exon1 | 12142252 | 12143025 |
| chr_1 | g10820 | g10820.t1 | cds | g10820.t1.CDS1 | 12142252 | 12143025 |
| chr_1 | g10820 | g10820.t1 | exon | g10820.t1.exon2 | 12143098 | 12143244 |
| chr_1 | g10820 | g10820.t1 | cds | g10820.t1.CDS2 | 12143098 | 12143244 |
| chr_1 | g10820 | g10820.t1 | TSS | g10820.t1 | 12143308 | 12143308 |
Sequences
>g10820.t1 Gene=g10820 Length=921
ATGTCCATAACAGCTATGAAATTATGCAGTATGATACTGCAAGAAAATTTTGGTGATGTT
GTTAGAACAGTAGGCGATGATCTATTCTGTACAAAATCAAGAACTATATATGAAATAATT
AAGAAAACAAACTTATCAAGAAAGCAGGTAACTTCAAGTCTTGCGATTCTCACACAATAT
CGACTGGTTAGCTATTCTTCAATTGAAAACAATGAACAGATAGCCGAGTATATGCTTCAT
TATGATAAAATATTGCTTTTTCTTCGTTATCCACGATATATGTATTTCATTCAAAAGAAG
AAAGGAGATTTGGGAGCATTATTGCTTGAAGAATTGTTAAGATCAGGGATGGCAATCGCA
CACTCTGTTATTATTCAAGCATACGCTAATACAGATGTTAAAAATGACCAAACTCTGATT
GAACTTAGAGATACATTTATAGATATGGTAGGTGAAAAATTCTTCATTCGATGTCCTGAA
ATGTCTGATGATCCAGTACCTAAAATATTAAATGAAAAAAATGGAAATTTTCAAGTATCG
AATATTGAAATTAAAGAAATTAAACAATTGATTGATAGCAACAAAGACCCAGAAAATGTT
GTTAGTGAAAAAGTTTATTGGACTGTAAATTTTGACAAATTACATCAATGTTTTCGTGAT
AAAGTTCTTATAGATGCAATCGAACGTCAAATTGATGCAAATGCAGCCGAGTGTTTTCAA
TTTATCATATCACTCATGTACAAAACAACGGAAGCATGGGAACCAGTGTCAAATGCAATT
TCAATAGGTGAAATCAAGCGTGTCATTGAAAAGAAGTCAAACAACACTGAACTTTTAAGA
CACTTGGAGCAGTATGTGTCGATAATTGAAAAGGATGAATGTGGATTTTTGAAAAAAGAC
GAAACTGGAAATGCAGTTTAA
>g10820.t1 Gene=g10820 Length=306
MSITAMKLCSMILQENFGDVVRTVGDDLFCTKSRTIYEIIKKTNLSRKQVTSSLAILTQY
RLVSYSSIENNEQIAEYMLHYDKILLFLRYPRYMYFIQKKKGDLGALLLEELLRSGMAIA
HSVIIQAYANTDVKNDQTLIELRDTFIDMVGEKFFIRCPEMSDDPVPKILNEKNGNFQVS
NIEIKEIKQLIDSNKDPENVVSEKVYWTVNFDKLHQCFRDKVLIDAIERQIDANAAECFQ
FIISLMYKTTEAWEPVSNAISIGEIKRVIEKKSNNTELLRHLEQYVSIIEKDECGFLKKD
ETGNAV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g10820.t1 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 1 | 79 | 0 |
| 4 | g10820.t1 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 81 | 164 | 0 |
| 5 | g10820.t1 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 210 | 305 | 0 |
| 3 | g10820.t1 | PANTHER | PTHR12949 | RNA POLYMERASE III DNA DIRECTED -RELATED | 1 | 301 | 0 |
| 1 | g10820.t1 | Pfam | PF08221 | RNA polymerase III subunit RPC82 helix-turn-helix domain | 7 | 66 | 0 |
| 2 | g10820.t1 | Pfam | PF05645 | RNA polymerase III subunit RPC82 | 193 | 299 | 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:0003697 | single-stranded DNA binding | MF |
| GO:0003677 | DNA binding | MF |
| GO:0006351 | transcription, DNA-templated | BP |
| GO:0005666 | RNA polymerase III complex | CC |
KEGG
Orthology
- This transcript has been annotated with K03023 (DNA-directed RNA polymerase III subunit RPC3)
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.
