General information for g2715.t2
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 g2715 is located on chr_3: 19847657..19848511 (+ 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 | g2715 | g2715.t2 | TSS | g2715.t2 | 19846898 | 19846898 |
| chr_3 | g2715 | g2715.t2 | isoform | g2715.t2 | 19847031 | 19847657 |
| chr_3 | g2715 | g2715.t2 | exon | g2715.t2.exon1 | 19847031 | 19847032 |
| chr_3 | g2715 | g2715.t2 | exon | g2715.t2.exon2 | 19847148 | 19847657 |
| chr_3 | g2715 | g2715.t2 | cds | g2715.t2.CDS1 | 19847424 | 19847657 |
| chr_3 | g2715 | g2715.t2 | TTS | g2715.t2 | 19847758 | 19847758 |
Sequences
>g2715.t2 Gene=g2715 Length=512
ACATTTCTCTTGAACATGAAATTCTACTTCATCCGCGATATTTCGGTCCACAATTACTTG
ATACAGTGCGACAGAAACTCTATACAGAAGTTGAAGGAACATGCACAGGCAAATATGGCT
TTGTGATAGCAGTTACAACGATTATTGATATTGGGGCAGGAATTATACAAGCTGGACAAG
GATTTGTTGTTTATCCAGTGAAATATAAAGCCATAGTTTTCCGCCCATTTAAAGGAGAAG
TGCTTGATGCTGTAGTAAAGCAGGTTAACAAAGTTGGAATGTTCGCAGAAATTGGGCCTC
TCTCTTGCTTCATTTCACATCACTCTATTCCCGCCGACATGCAATTTTGTCCAAACAGTA
ATCCAGCATGCTATAAATCTAAAGATGAAGATATTGTCATAGCTGCCGAAGATAAGATTC
GCTTGAAAATTGTCGGAACAAGAGTCGATGCTACTGGTATTTTTGCTATCGGGACATTAA
TGGACGATTATCTCGGTTTGGTTCTTAATTGA
>g2715.t2 Gene=g2715 Length=77
MFAEIGPLSCFISHHSIPADMQFCPNSNPACYKSKDEDIVIAAEDKIRLKIVGTRVDATG
IFAIGTLMDDYLGLVLN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g2715.t2 | CDD | cd04462 | S1_RNAPII_Rpb7 | 1 | 73 | 0e+00 |
| 5 | g2715.t2 | Gene3D | G3DSA:2.40.50.140 | - | 1 | 75 | 0e+00 |
| 2 | g2715.t2 | PANTHER | PTHR12709 | DNA-DIRECTED RNA POLYMERASE II, III | 1 | 73 | 0e+00 |
| 3 | g2715.t2 | PANTHER | PTHR12709:SF4 | DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 | 1 | 73 | 0e+00 |
| 1 | g2715.t2 | Pfam | PF00575 | S1 RNA binding domain | 1 | 61 | 1e-06 |
| 4 | g2715.t2 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 1 | 73 | 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: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.
