General information for g8693.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative DNA-directed RNA polymerase II subunit RPB7.
Parent gene
- The parent gene g8693 is located on chr_2: 32299250..32299835 (- 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 | g8693 | g8693.t1 | TTS | g8693.t1 | 32299197 | 32299197 |
| chr_2 | g8693 | g8693.t1 | isoform | g8693.t1 | 32299250 | 32299835 |
| chr_2 | g8693 | g8693.t1 | exon | g8693.t1.exon1 | 32299250 | 32299753 |
| chr_2 | g8693 | g8693.t1 | cds | g8693.t1.CDS1 | 32299250 | 32299753 |
| chr_2 | g8693 | g8693.t1 | exon | g8693.t1.exon2 | 32299824 | 32299835 |
| chr_2 | g8693 | g8693.t1 | cds | g8693.t1.CDS2 | 32299824 | 32299835 |
| chr_2 | g8693 | g8693.t1 | TSS | g8693.t1 | 32299886 | 32299886 |
Sequences
>g8693.t1 Gene=g8693 Length=516
ATGTTTTATCACATGCAGTTAACTCATGAAACTGTAGTTCATCCAATTTATTTTGGTCCT
GAATTGATGGATATTGTTTTGAAAAAGATTTACACGGAAGTTGAAGGATCTTGTCATGGA
AATATTGGCTATGTTATTTCGATCACATCAATTACAGAAATAGAAAGAGGCTTACTCGTT
GATAGCGGAATGGCTTTATATTATGCAAAATATTTTGCAATTGTTTTTCGACCTTTCAAA
AATGAAATTCTTGATGGAATCGTCAAAAATGTGAATTCAATTGGCTTTTTTGCTGAAATT
GGTCCAATATTATGCTTTGTTTCTCATCAGTCAATGCCTCAAGGATTCAGGTTTATTTCT
AAAGAATTTCCAAACTATTTTAAATCAGAAGATAATGAAGTAATCACAATTGGAGATCCT
ATTCGTATTCGAATCATTGGAGTTCGTGTAGACCAAAATAAGATGTTTTGCATTGGAACA
ATTGTGGATGATTATTTAGGACTTCTTGTTAAATAA
>g8693.t1 Gene=g8693 Length=171
MFYHMQLTHETVVHPIYFGPELMDIVLKKIYTEVEGSCHGNIGYVISITSITEIERGLLV
DSGMALYYAKYFAIVFRPFKNEILDGIVKNVNSIGFFAEIGPILCFVSHQSMPQGFRFIS
KEFPNYFKSEDNEVITIGDPIRIRIIGVRVDQNKMFCIGTIVDDYLGLLVK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g8693.t1 | Gene3D | G3DSA:3.30.1490.120 | - | 1 | 79 | 0.000 |
| 8 | g8693.t1 | Gene3D | G3DSA:2.40.50.140 | - | 80 | 169 | 0.000 |
| 3 | g8693.t1 | PANTHER | PTHR12709 | DNA-DIRECTED RNA POLYMERASE II, III | 1 | 167 | 0.000 |
| 4 | g8693.t1 | PANTHER | PTHR12709:SF4 | DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 | 1 | 167 | 0.000 |
| 2 | g8693.t1 | Pfam | PF03876 | SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 | 13 | 63 | 0.000 |
| 1 | g8693.t1 | Pfam | PF00575 | S1 RNA binding domain | 77 | 155 | 0.000 |
| 9 | g8693.t1 | ProSiteProfiles | PS50126 | S1 domain profile. | 81 | 161 | 8.727 |
| 5 | g8693.t1 | SUPERFAMILY | SSF88798 | N-terminal, heterodimerisation domain of RBP7 (RpoE) | 1 | 77 | 0.000 |
| 6 | g8693.t1 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 78 | 168 | 0.000 |
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:0006351 | transcription, DNA-templated | BP |
| GO:0003676 | nucleic acid binding | MF |
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. There were no conditions that were differentially expressed