General information for g2715.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t1 | TSS | g2715.t1 | 19846898 | 19846898 |
| chr_3 | g2715 | g2715.t1 | isoform | g2715.t1 | 19847040 | 19847657 |
| chr_3 | g2715 | g2715.t1 | exon | g2715.t1.exon1 | 19847040 | 19847051 |
| chr_3 | g2715 | g2715.t1 | cds | g2715.t1.CDS1 | 19847040 | 19847051 |
| chr_3 | g2715 | g2715.t1 | exon | g2715.t1.exon2 | 19847148 | 19847657 |
| chr_3 | g2715 | g2715.t1 | cds | g2715.t1.CDS2 | 19847148 | 19847657 |
| chr_3 | g2715 | g2715.t1 | TTS | g2715.t1 | 19847758 | 19847758 |
Sequences
>g2715.t1 Gene=g2715 Length=522
ATGTTTTATCACATTTCTCTTGAACATGAAATTCTACTTCATCCGCGATATTTCGGTCCA
CAATTACTTGATACAGTGCGACAGAAACTCTATACAGAAGTTGAAGGAACATGCACAGGC
AAATATGGCTTTGTGATAGCAGTTACAACGATTATTGATATTGGGGCAGGAATTATACAA
GCTGGACAAGGATTTGTTGTTTATCCAGTGAAATATAAAGCCATAGTTTTCCGCCCATTT
AAAGGAGAAGTGCTTGATGCTGTAGTAAAGCAGGTTAACAAAGTTGGAATGTTCGCAGAA
ATTGGGCCTCTCTCTTGCTTCATTTCACATCACTCTATTCCCGCCGACATGCAATTTTGT
CCAAACAGTAATCCAGCATGCTATAAATCTAAAGATGAAGATATTGTCATAGCTGCCGAA
GATAAGATTCGCTTGAAAATTGTCGGAACAAGAGTCGATGCTACTGGTATTTTTGCTATC
GGGACATTAATGGACGATTATCTCGGTTTGGTTCTTAATTGA
>g2715.t1 Gene=g2715 Length=173
MFYHISLEHEILLHPRYFGPQLLDTVRQKLYTEVEGTCTGKYGFVIAVTTIIDIGAGIIQ
AGQGFVVYPVKYKAIVFRPFKGEVLDAVVKQVNKVGMFAEIGPLSCFISHHSIPADMQFC
PNSNPACYKSKDEDIVIAAEDKIRLKIVGTRVDATGIFAIGTLMDDYLGLVLN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g2715.t1 | CDD | cd04329 | RNAP_II_Rpb7_N | 2 | 81 | 0 |
| 10 | g2715.t1 | CDD | cd04462 | S1_RNAPII_Rpb7 | 81 | 169 | 0 |
| 7 | g2715.t1 | Gene3D | G3DSA:3.30.1490.120 | - | 1 | 80 | 0 |
| 8 | g2715.t1 | Gene3D | G3DSA:2.40.50.140 | - | 81 | 171 | 0 |
| 3 | g2715.t1 | PANTHER | PTHR12709 | DNA-DIRECTED RNA POLYMERASE II, III | 1 | 169 | 0 |
| 4 | g2715.t1 | PANTHER | PTHR12709:SF4 | DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 | 1 | 169 | 0 |
| 2 | g2715.t1 | Pfam | PF03876 | SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 | 11 | 64 | 0 |
| 1 | g2715.t1 | Pfam | PF00575 | S1 RNA binding domain | 78 | 157 | 0 |
| 5 | g2715.t1 | SUPERFAMILY | SSF88798 | N-terminal, heterodimerisation domain of RBP7 (RpoE) | 1 | 78 | 0 |
| 6 | g2715.t1 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 78 | 169 | 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:0006351 | transcription, DNA-templated | BP |
| GO:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K03015 (DNA-directed RNA polymerase II subunit RPB7)
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.
