General information for g2668.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as DNA-directed RNA polymerase II subunit RPB2.
Parent gene
- The parent gene g2668 is located on chr_3: 19477707..19479055 (+ 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 | g2668 | g2668.t3 | TSS | g2668.t3 | 19473800 | 19473800 |
| chr_3 | g2668 | g2668.t3 | isoform | g2668.t3 | 19473930 | 19475379 |
| chr_3 | g2668 | g2668.t3 | exon | g2668.t3.exon1 | 19473930 | 19473948 |
| chr_3 | g2668 | g2668.t3 | cds | g2668.t3.CDS1 | 19473930 | 19473948 |
| chr_3 | g2668 | g2668.t3 | exon | g2668.t3.exon2 | 19474021 | 19474241 |
| chr_3 | g2668 | g2668.t3 | cds | g2668.t3.CDS2 | 19474021 | 19474241 |
| chr_3 | g2668 | g2668.t3 | exon | g2668.t3.exon3 | 19474299 | 19475379 |
| chr_3 | g2668 | g2668.t3 | cds | g2668.t3.CDS3 | 19474299 | 19475378 |
| chr_3 | g2668 | g2668.t3 | TTS | g2668.t3 | NA | NA |
Sequences
>g2668.t3 Gene=g2668 Length=1321
ATGTATGACAACGACGATGTTTACAATGATGAAGAGGATCAAGAAATTTCAGATGAATTG
TGGCAAGAAGCCTGTTGGATCGTTATTAATGCATATTTTGACGACAAAGGTCTTGTACGT
CAACAATTAGATAGTTTTGATGAATTTATTCAAATGTCTGTGCAGAGTATTGTAGCAGAA
TCACCTGCGATTGAATTGCAAGCAGAAGCACAACATACATCCGGAGAAATTGAAACTCCA
CCACGATATGTTTTGAAATTTGAACAAATTTATCTCTCAAAACCAACACATTGGGAAAAA
GATGGTGCACCATCTCCAATGATGCCTAATCAAGCTCGTCTCCGAAATTTGACTTACTCT
GCACCGCTTTATGTTGACATTACTAAAACTAAACACATTGAAGGACAAAAGCCAATTGAA
ACACAACATCAAAAGACATTCATTGGAAAAATTCCTATTATGCTTCGATCAGCCTATTGT
CTTTTAAATAATCTATCAGATCGTGACTTGACTGAATTGAATGAATGTCCTCTTGATCCA
GGCGGATATTTTATTATCAACGGCTCTGAAAAAGTTTTGATTGCTCAAGAGAAAATGGCA
ACTAATACTGTCTATGTTTTCAGCATGAAAGATGGAAAGTATGCATATAAAGCTGAAATT
AGATCATGTTTAGAGCATAGTTCAAGACCTACATCTACTCTCTGGGTTAATATGTTTGCA
AAAGGTGGAAGTAATGCTAAGAAATCAGCAATTGGACAAAGGATCATAGCAATTCTACCA
TATATTAAACAAGAAATTCCAATTATGATCGTTTTTCGAGCTCTGGGATTTGTGGCTGAT
CGTGATATTCTTGAACATATTATTTACGATTTCGATGATCCAGAGATGATGGAAATGGTT
AAACCATCACTCGATGAAGCTTTTGTAGTTCAGGAACAAAATGTTGCATTGAATTTTATT
GGTTCCAGAGGTGCTAGACCTGGTGTAACAAAAGAAAAACGTATTAAATATGCTAAGGAA
ATTTTACAAAGAGAAATGTTGCCACATGTTGGTATTTCTGATTTTTGCGAAACAAAGAAG
GCATATTTTCTCGGATATATGGTTCATCGTCTTCTTCTCGCTGCTCTCGGACGACGTGAA
TTGGATGATCGTGATCATTACGGAAATAAACGTTTGGATCTCGCTGGACCTTTGCTTGCT
TTCCTATTTAGAGGATTGTTTAAGAATTTAATGAAAGAAGTGCGAATGTATGCACAAAAA
TTTATTGATCGTGGAAAAGATTTCAATTTGGAGTTGGCAATCAAGACTAAAATTATCACA
G
>g2668.t3 Gene=g2668 Length=440
MYDNDDVYNDEEDQEISDELWQEACWIVINAYFDDKGLVRQQLDSFDEFIQMSVQSIVAE
SPAIELQAEAQHTSGEIETPPRYVLKFEQIYLSKPTHWEKDGAPSPMMPNQARLRNLTYS
APLYVDITKTKHIEGQKPIETQHQKTFIGKIPIMLRSAYCLLNNLSDRDLTELNECPLDP
GGYFIINGSEKVLIAQEKMATNTVYVFSMKDGKYAYKAEIRSCLEHSSRPTSTLWVNMFA
KGGSNAKKSAIGQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMV
KPSLDEAFVVQEQNVALNFIGSRGARPGVTKEKRIKYAKEILQREMLPHVGISDFCETKK
AYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQK
FIDRGKDFNLELAIKTKIIT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g2668.t3 | Gene3D | G3DSA:3.90.1100.10 | - | 29 | 201 | 0 |
| 6 | g2668.t3 | Gene3D | G3DSA:3.90.1110.10 | - | 202 | 383 | 0 |
| 3 | g2668.t3 | PANTHER | PTHR20856:SF23 | DNA-DIRECTED RNA POLYMERASE SUBUNIT BETA | 14 | 440 | 0 |
| 4 | g2668.t3 | PANTHER | PTHR20856 | DNA-DIRECTED RNA POLYMERASE I SUBUNIT 2 | 14 | 440 | 0 |
| 2 | g2668.t3 | Pfam | PF04563 | RNA polymerase beta subunit | 37 | 440 | 0 |
| 1 | g2668.t3 | Pfam | PF04561 | RNA polymerase Rpb2, domain 2 | 200 | 393 | 0 |
| 5 | g2668.t3 | SUPERFAMILY | SSF64484 | beta and beta-prime subunits of DNA dependent RNA-polymerase | 18 | 440 | 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:0003899 | DNA-directed 5’-3’ RNA polymerase activity | MF |
| GO:0032549 | ribonucleoside binding | MF |
| GO:0003677 | DNA binding | MF |
| GO:0006351 | transcription, DNA-templated | BP |
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