General information for g2668.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as DNA-directed RNA polymerase II subunit RPB2.
Parent gene
- The parent gene g2668 is located on chr_3: 19477707..19479055 (+ 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 | g2668 | g2668.t4 | isoform | g2668.t4 | 19477183 | 19478557 |
| chr_3 | g2668 | g2668.t4 | exon | g2668.t4.exon1 | 19477183 | 19478557 |
| chr_3 | g2668 | g2668.t4 | cds | g2668.t4.CDS1 | 19477276 | 19477578 |
| chr_3 | g2668 | g2668.t4 | TSS | g2668.t4 | NA | NA |
| chr_3 | g2668 | g2668.t4 | TTS | g2668.t4 | NA | NA |
Sequences
>g2668.t4 Gene=g2668 Length=1375
TCTTAGGTAAGAATGATTTTTCTTATTTATTTTATAGCATTTAGTTAAACATTTTAATTT
TTAGGTCCAACATACTATCAACGTCTCAAACACATGGTAGATGATAAAATTCACTCTCGT
GCTCGTGGTCCTGTTCAAATTCTCGTTCGACAACCTATGGAAGGTCGTGCTCGTGATGGT
GGTTTGCGTTTCGGTGAAATGGAACGTGATTGTCAAATTTCTCATGGCGCTGCTCAATTT
TTGCGTGAGCGTTTATTCGAAGTCTCTGATCCTTATCGTATTCATGTTTGTAATTTTTGT
GGATTGATTGCTATTGCTAATTTGAGAAATAATACTTTTGAATGCAAAGGATGTAAAAAT
AAGACACAGGTATGTAATTTCATATATAAATATTAAAATTCAATTTCACATTGCTTTTCT
TTTTTCTTATCTTAGATTTCTCAAGTCAAACTTCCTTATGCTGCAAAATTGTTATTCCAA
GAGTTGATGGCAATGAATATTGCACCAAGATTGATGGTTGTCTAAGAATAATATAAATAA
TTAAAAAGAATTGAGCATACGTTTAAATGTCATCAATTTATTTGAAAAATCTAATAAAAT
ATCGAAATATAATTATTAGGAATTTTTAATAGCGTGTAGAGCATAATTGATGCCATCGTA
TTTTTGCCATTTTGCAACATTTCTCCAAAATTCATATCTAAAGCCATGAACTAAAATTGT
AGTGCAATTGAATTCATCTAAAATTTTAGAAACTTCTGATGGACTAATGAATTTATCAAA
ATCGTGAGTGCCTTTTGGAACAAGATTTAAAATATATTCAGCTGCAATGATTCCACCCAA
CCAAGATGCTTGTGTTTTATTCAATGTTGTCACAAAAATACTTCCACCAGGCTTAAGACA
GTTTACACATTCTTTGAGAAATGATTTTTGATTGGGAACATGTTCTAAAACTTCACTCGC
AATTACTGCGTCGTAATTTTCTCTATGATTTTCAGAATGTTCTTCAACAGTTGTACATAT
GTAATTGATTTTAAATTTTTTGTTTTGCATATGATTTTTAGCTGTTTCAAGTAATTTTTC
TGATGGATCGATTCCTACAACATTCGCTTTCAACTTTGCTAAAGACTCAGTTAATATTCC
AGCACCACAACCAACTTCTAAAATTTTTATCCCATCTAGTACATTCGATTTATTTATATT
TTCAGTTTTTACGATTCCAGTACTTATAAGACCATCACGAATCAAAGGAACACGCAACTG
ATTAATAGCATGTAGAGCTTTCATCTCTCCATTTTTGTTCCACCACTCATCGGCAAGATT
TGACAAGTGGTTAACATCTGTTTCATTTACATTTCTTGTGTGTGTCGAAAGAACT
>g2668.t4 Gene=g2668 Length=100
MVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSDP
YRIHVCNFCGLIAIANLRNNTFECKGCKNKTQVCNFIYKY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g2668.t4 | Gene3D | G3DSA:3.90.1800.10 | RNA polymerase alpha subunit dimerisation domain | 14 | 100 | 0e+00 |
| 3 | g2668.t4 | PANTHER | PTHR20856:SF7 | DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 | 1 | 95 | 0e+00 |
| 4 | g2668.t4 | PANTHER | PTHR20856 | DNA-DIRECTED RNA POLYMERASE I SUBUNIT 2 | 1 | 95 | 0e+00 |
| 1 | g2668.t4 | Pfam | PF00562 | RNA polymerase Rpb2, domain 6 | 1 | 27 | 2e-07 |
| 2 | g2668.t4 | Pfam | PF04560 | RNA polymerase Rpb2, domain 7 | 29 | 95 | 0e+00 |
| 5 | g2668.t4 | SUPERFAMILY | SSF64484 | beta and beta-prime subunits of DNA dependent RNA-polymerase | 1 | 94 | 0e+00 |
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:0003899 | DNA-directed 5’-3’ RNA polymerase activity | MF |
| GO:0032549 | ribonucleoside binding | MF |
| GO:0003677 | DNA binding | MF |
| GO:0006351 | transcription, DNA-templated | 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.
