General information for g5008.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as DNA-directed RNA polymerase II subunit RPB11.
Parent gene
- The parent gene g5008 is located on chr_2: 6403803..6404280 (+ 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_2 | g5008 | g5008.t1 | TSS | g5008.t1 | 6403708 | 6403708 |
| chr_2 | g5008 | g5008.t1 | isoform | g5008.t1 | 6403803 | 6404280 |
| chr_2 | g5008 | g5008.t1 | exon | g5008.t1.exon1 | 6403803 | 6403855 |
| chr_2 | g5008 | g5008.t1 | cds | g5008.t1.CDS1 | 6403803 | 6403855 |
| chr_2 | g5008 | g5008.t1 | exon | g5008.t1.exon2 | 6403916 | 6404005 |
| chr_2 | g5008 | g5008.t1 | cds | g5008.t1.CDS2 | 6403916 | 6404005 |
| chr_2 | g5008 | g5008.t1 | exon | g5008.t1.exon3 | 6404070 | 6404280 |
| chr_2 | g5008 | g5008.t1 | cds | g5008.t1.CDS3 | 6404070 | 6404280 |
| chr_2 | g5008 | g5008.t1 | TTS | g5008.t1 | 6404317 | 6404317 |
Sequences
>g5008.t1 Gene=g5008 Length=354
ATGAATGCTCCACCAACGTTTGAATCATTTTTGCTATATGAAGGAGAGAAAAAAATCATT
AAAGAACTTGATACAAAAGTACCAAATGCTGCTATATTTACTGTAAATAAAGAAGATCAC
ACACTTGGTAATATGATAAGAAATCAATTGTTGAAAGATCCAAGAGTATTATTCGCAGGA
TATAAAGTTCCACATCCACTTGAGCATAAATTCGTTATAAGAATTCAAACAACATCAAAT
TATTCACCAGAGGATGCTTTCATGAATGCAATTACTGATCTTATGTCAGAATTATCATTA
TTTGAAGAACGATTTAAAGATGCTATTAAAGAAAAGAGAGAGGGAGCAGATTAA
>g5008.t1 Gene=g5008 Length=117
MNAPPTFESFLLYEGEKKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPRVLFAG
YKVPHPLEHKFVIRIQTTSNYSPEDAFMNAITDLMSELSLFEERFKDAIKEKREGAD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g5008.t1 | CDD | cd06926 | RNAP_II_RPB11 | 14 | 105 | 1.37271E-56 |
| 6 | g5008.t1 | Gene3D | G3DSA:3.30.1360.10 | - | 1 | 117 | 2.1E-49 |
| 2 | g5008.t1 | PANTHER | PTHR13946:SF31 | DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11-A-RELATED | 1 | 109 | 4.4E-50 |
| 3 | g5008.t1 | PANTHER | PTHR13946 | DNA-DIRECTED RNA POLYMERASE I,II,III | 1 | 109 | 4.4E-50 |
| 1 | g5008.t1 | Pfam | PF13656 | RNA polymerase Rpb3/Rpb11 dimerisation domain | 31 | 104 | 2.0E-29 |
| 5 | g5008.t1 | ProSitePatterns | PS01154 | RNA polymerases L / 13 to 16 Kd subunits signature. | 35 | 66 | - |
| 4 | g5008.t1 | SUPERFAMILY | SSF55257 | RBP11-like subunits of RNA polymerase | 1 | 112 | 2.62E-39 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5008/g5008.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5008.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005665 | RNA polymerase II, core complex | CC |
| GO:0003899 | DNA-directed 5’-3’ RNA polymerase activity | MF |
| GO:0003677 | DNA binding | MF |
| GO:0001055 | RNA polymerase II activity | MF |
| GO:0006351 | transcription, DNA-templated | BP |
| GO:0046983 | protein dimerization activity | MF |
| GO:0006366 | transcription by RNA polymerase II | BP |
KEGG
Orthology
- This transcript has been annotated with K03008 (DNA-directed RNA polymerase II subunit RPB11)
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.
