General information for g11691.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as DNA-directed RNA polymerase II subunit Rpb4.
Parent gene
- The parent gene g11691 is located on chr_1: 17821028..17821404 (+ 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 | g11691 | g11691.t1 | TSS | g11691.t1 | 17820827 | 17820827 |
| chr_1 | g11691 | g11691.t1 | isoform | g11691.t1 | 17820920 | 17821404 |
| chr_1 | g11691 | g11691.t1 | exon | g11691.t1.exon1 | 17820920 | 17820983 |
| chr_1 | g11691 | g11691.t1 | cds | g11691.t1.CDS1 | 17820920 | 17820983 |
| chr_1 | g11691 | g11691.t1 | exon | g11691.t1.exon2 | 17821049 | 17821404 |
| chr_1 | g11691 | g11691.t1 | cds | g11691.t1.CDS2 | 17821049 | 17821404 |
| chr_1 | g11691 | g11691.t1 | TTS | g11691.t1 | 17821479 | 17821479 |
Sequences
>g11691.t1 Gene=g11691 Length=420
ATGACAAGCATCAATCCCGTTGAAACTGTTGAAGAAGATGCAGCAGATTTACTATTTCCA
AAAGAATTTGAAAATGCTGAAACTTTATTAATAAGTGAAGTTCATATGCTTTTGGAACAT
CGTAAACGACAAAATGAATCGAGTGAAGAAGAGCAAGAATTCAGTGAAGTTTTTTTGAAG
ACTTACAATTATACGGAAAACTTTCGAAAGTTCAAGAATAAAGAAACAATTACAGCTATT
CGTGCGCTTCTGTCCTCAAAAAAACTTCATAAATTTGAACTAGCTGCACTTGGAAATTTA
TGTCCAGAAGCTCCTGAAGAAGCAACATCGCTCATTCCATCTCTTGAGGGTAGATTTGAA
GATGAAACGTTAAGACAAATTCTTGAAGATATTGGAACAAAAAGAAGTCTTCAATATTAA
>g11691.t1 Gene=g11691 Length=139
MTSINPVETVEEDAADLLFPKEFENAETLLISEVHMLLEHRKRQNESSEEEQEFSEVFLK
TYNYTENFRKFKNKETITAIRALLSSKKLHKFELAALGNLCPEAPEEATSLIPSLEGRFE
DETLRQILEDIGTKRSLQY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g11691.t1 | Gene3D | G3DSA:1.20.1250.40 | - | 11 | 139 | 0 |
| 2 | g11691.t1 | PANTHER | PTHR21297:SF0 | DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 | 8 | 137 | 0 |
| 3 | g11691.t1 | PANTHER | PTHR21297 | DNA-DIRECTED RNA POLYMERASE II | 8 | 137 | 0 |
| 1 | g11691.t1 | Pfam | PF03874 | RNA polymerase Rpb4 | 29 | 131 | 0 |
| 5 | g11691.t1 | SMART | SM00657 | rpol4neu2 | 21 | 138 | 0 |
| 4 | g11691.t1 | SUPERFAMILY | SSF47819 | HRDC-like | 8 | 136 | 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:0000166 | nucleotide binding | MF |
| GO:0044237 | cellular metabolic process | BP |
| GO:0030880 | RNA polymerase complex | CC |
| GO:0006352 | DNA-templated transcription, initiation | BP |
KEGG
Orthology
- This transcript has been annotated with K03012 (DNA-directed RNA polymerase II subunit RPB4)
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.
