General information for g2668.t1
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.t1 | TSS | g2668.t1 | 19473800 | 19473800 |
| chr_3 | g2668 | g2668.t1 | isoform | g2668.t1 | 19473930 | 19477707 |
| chr_3 | g2668 | g2668.t1 | exon | g2668.t1.exon1 | 19473930 | 19473948 |
| chr_3 | g2668 | g2668.t1 | cds | g2668.t1.CDS1 | 19473930 | 19473948 |
| chr_3 | g2668 | g2668.t1 | exon | g2668.t1.exon2 | 19474021 | 19474241 |
| chr_3 | g2668 | g2668.t1 | cds | g2668.t1.CDS2 | 19474021 | 19474241 |
| chr_3 | g2668 | g2668.t1 | exon | g2668.t1.exon3 | 19474299 | 19477188 |
| chr_3 | g2668 | g2668.t1 | cds | g2668.t1.CDS3 | 19474299 | 19477188 |
| chr_3 | g2668 | g2668.t1 | exon | g2668.t1.exon4 | 19477247 | 19477551 |
| chr_3 | g2668 | g2668.t1 | cds | g2668.t1.CDS4 | 19477247 | 19477551 |
| chr_3 | g2668 | g2668.t1 | exon | g2668.t1.exon5 | 19477618 | 19477707 |
| chr_3 | g2668 | g2668.t1 | cds | g2668.t1.CDS5 | 19477618 | 19477707 |
| chr_3 | g2668 | g2668.t1 | TTS | g2668.t1 | NA | NA |
Sequences
>g2668.t1 Gene=g2668 Length=3525
ATGTATGACAACGACGATGTTTACAATGATGAAGAGGATCAAGAAATTTCAGATGAATTG
TGGCAAGAAGCCTGTTGGATCGTTATTAATGCATATTTTGACGACAAAGGTCTTGTACGT
CAACAATTAGATAGTTTTGATGAATTTATTCAAATGTCTGTGCAGAGTATTGTAGCAGAA
TCACCTGCGATTGAATTGCAAGCAGAAGCACAACATACATCCGGAGAAATTGAAACTCCA
CCACGATATGTTTTGAAATTTGAACAAATTTATCTCTCAAAACCAACACATTGGGAAAAA
GATGGTGCACCATCTCCAATGATGCCTAATCAAGCTCGTCTCCGAAATTTGACTTACTCT
GCACCGCTTTATGTTGACATTACTAAAACTAAACACATTGAAGGACAAAAGCCAATTGAA
ACACAACATCAAAAGACATTCATTGGAAAAATTCCTATTATGCTTCGATCAGCCTATTGT
CTTTTAAATAATCTATCAGATCGTGACTTGACTGAATTGAATGAATGTCCTCTTGATCCA
GGCGGATATTTTATTATCAACGGCTCTGAAAAAGTTTTGATTGCTCAAGAGAAAATGGCA
ACTAATACTGTCTATGTTTTCAGCATGAAAGATGGAAAGTATGCATATAAAGCTGAAATT
AGATCATGTTTAGAGCATAGTTCAAGACCTACATCTACTCTCTGGGTTAATATGTTTGCA
AAAGGTGGAAGTAATGCTAAGAAATCAGCAATTGGACAAAGGATCATAGCAATTCTACCA
TATATTAAACAAGAAATTCCAATTATGATCGTTTTTCGAGCTCTGGGATTTGTGGCTGAT
CGTGATATTCTTGAACATATTATTTACGATTTCGATGATCCAGAGATGATGGAAATGGTT
AAACCATCACTCGATGAAGCTTTTGTAGTTCAGGAACAAAATGTTGCATTGAATTTTATT
GGTTCCAGAGGTGCTAGACCTGGTGTAACAAAAGAAAAACGTATTAAATATGCTAAGGAA
ATTTTACAAAGAGAAATGTTGCCACATGTTGGTATTTCTGATTTTTGCGAAACAAAGAAG
GCATATTTTCTCGGATATATGGTTCATCGTCTTCTTCTCGCTGCTCTCGGACGACGTGAA
TTGGATGATCGTGATCATTACGGAAATAAACGTTTGGATCTCGCTGGACCTTTGCTTGCT
TTCCTATTTAGAGGATTGTTTAAGAATTTAATGAAAGAAGTGCGAATGTATGCACAAAAA
TTTATTGATCGTGGAAAAGATTTCAATTTGGAGTTGGCAATCAAGACTAAAATTATCACA
GACGGTTTACGTTATTCACTTGCTACTGGAAATTGGGGTGATCAGAAAAAAGCACATCAA
GCTCGTGCTGGAGTATCTCAAGTCTTGAATCGTTTAACTTTCGCATCAACTCTTTCACAT
TTGCGTCGTGTTAATTCACCAATTGGTAGAGATGGAAAATTGGCAAAACCTCGTCAATTA
CACAACACTTTATGGGGAATGTTGTGTCCAGCTGAGACACCTGAAGGTGCTGCTGTAGGA
TTAGTAAAGAATCTTGCTTTAATGGCGTACATTTCTGTCGGTTCACAACCAGTGCCAATT
CTTGAATTCTTAGAAGAATGGTCAATGGAAAATTTAGAAGAAATTGCTCCTTCAGCTATT
GCTGATGCAACAAAAATTTTCGTCAATGGATGTTGGGTAGGAATTCATCGTGATCCTGAA
CAACTCATGTCAACTCTTCGAAAACTTAGACGTCAAATGGACATCATTGTATCTGAAGTA
TCAATGATTAGAGATATTCGAGATCGTGAAATTCGAATTTACACTGATGCTGGTCGCATT
TGTCGTCCACTTTTGATTGTCGAAAATGGAAATTTGTTGCTTAAAAGAAGTCATATTGAT
AATTTGAAAGAACGTTATGAAACAAATTACGGTTGGCAAGTACTTGTTGCTTCTGGTGTT
GTTGAATATATAGATACACTTGAGGAAGAAACAGTTATGATTGCCATGACTGTGAGTGAT
TTGAAGCAAGAAAAAGAATTTGCCTATTGTACGACATATACTCATTGTGAAATTCATCCA
GCTATGATTCTTGGAGTTTGTGCTTCAATTATTCCTTTTCCTGATCACAACCAATCTCCT
CGTAATACCTATCAAAGTGCTATGGGTAAACAAGCAATGGGTGTTTACATTACAAATTAT
CACGTGCGCATGGATACATTGGCTCATGTTCTTTATTATCCAATGAAACCTTTGGTAACA
ACACGCTCAATGGAATATCTTCGTTTCCGTGAATTGCCTGCTGGTATTAATTCAATCGTA
GCAATTCTCTGTTATACTGGTTACAATCAAGAAGATTCTGTCATTCTCAATGCATCAGCT
GTCGAGCGCGGTTTCTTCAGATCAGTTTTCTATCGTTCATATAAAGATTCTGAATGCAAA
AGAATTGGTGATCAAGAAGAACAATTTGAAAAACCTAATCGTCAAACTTGTCAAGGAATG
CGAAATGCTTTATACGATAAATTAGATGAAGATGGAATTATTGCTCCAGGTTTGCGTGTA
TCTGGAGATGATGTTGTTATTGGTAAAACAATCACTTTGCCAGAAAATGATGATGATCTT
GAAGGTACGACTGTTCGTTATACAAAGAGAGATGCTTCAACATTCTTACGTAATTCTGAA
ACTGGAATTGTCGATCAAGTTATGTTGACATTAAATAGTGAAGGTTACAAGTTTTGTAAA
ATTCGTGTGCGCTCAGTGAGAATTCCTCAAATTGGTGATAAATTTGCTTCACGTCACGGT
CAAAAAGGAACATGTGGTATTCAATATCGACAAGAAGATATGCCTTTTACTTGTGAAGGT
TTAACTCCGGATATCATAATTAATCCTCACGCTATTCCGTCTCGTATGACAATTGGGCAT
TTAATTGAATGTATTCAGGGCAAACTTGGCTCAAATAAAGGTGAAATTGGTGATGCTACA
CCTTTTAACGATGCTGTCAATGTACAGAAAATTTCTACTTTCCTGCAAGAATATGGTTAT
CACTTGAGAGGCAATGAAGTGATGTATAACGGTCATACTGGACGAAAAATTAATGCACAA
GTTTTCTTAGGTCCAACATACTATCAACGTCTCAAACACATGGTAGATGATAAAATTCAC
TCTCGTGCTCGTGGTCCTGTTCAAATTCTCGTTCGACAACCTATGGAAGGTCGTGCTCGT
GATGGTGGTTTGCGTTTCGGTGAAATGGAACGTGATTGTCAAATTTCTCATGGCGCTGCT
CAATTTTTGCGTGAGCGTTTATTCGAAGTCTCTGATCCTTATCGTATTCATGTTTGTAAT
TTTTGTGGATTGATTGCTATTGCTAATTTGAGAAATAATACTTTTGAATGCAAAGGATGT
AAAAATAAGACACAGATTTCTCAAGTCAAACTTCCTTATGCTGCAAAATTGTTATTCCAA
GAGTTGATGGCAATGAATATTGCACCAAGATTGATGGTTGTCTAA
>g2668.t1 Gene=g2668 Length=1174
MYDNDDVYNDEEDQEISDELWQEACWIVINAYFDDKGLVRQQLDSFDEFIQMSVQSIVAE
SPAIELQAEAQHTSGEIETPPRYVLKFEQIYLSKPTHWEKDGAPSPMMPNQARLRNLTYS
APLYVDITKTKHIEGQKPIETQHQKTFIGKIPIMLRSAYCLLNNLSDRDLTELNECPLDP
GGYFIINGSEKVLIAQEKMATNTVYVFSMKDGKYAYKAEIRSCLEHSSRPTSTLWVNMFA
KGGSNAKKSAIGQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMV
KPSLDEAFVVQEQNVALNFIGSRGARPGVTKEKRIKYAKEILQREMLPHVGISDFCETKK
AYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQK
FIDRGKDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSH
LRRVNSPIGRDGKLAKPRQLHNTLWGMLCPAETPEGAAVGLVKNLALMAYISVGSQPVPI
LEFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMSTLRKLRRQMDIIVSEV
SMIRDIRDREIRIYTDAGRICRPLLIVENGNLLLKRSHIDNLKERYETNYGWQVLVASGV
VEYIDTLEEETVMIAMTVSDLKQEKEFAYCTTYTHCEIHPAMILGVCASIIPFPDHNQSP
RNTYQSAMGKQAMGVYITNYHVRMDTLAHVLYYPMKPLVTTRSMEYLRFRELPAGINSIV
AILCYTGYNQEDSVILNASAVERGFFRSVFYRSYKDSECKRIGDQEEQFEKPNRQTCQGM
RNALYDKLDEDGIIAPGLRVSGDDVVIGKTITLPENDDDLEGTTVRYTKRDASTFLRNSE
TGIVDQVMLTLNSEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEG
LTPDIIINPHAIPSRMTIGHLIECIQGKLGSNKGEIGDATPFNDAVNVQKISTFLQEYGY
HLRGNEVMYNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRAR
DGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRIHVCNFCGLIAIANLRNNTFECKGC
KNKTQISQVKLPYAAKLLFQELMAMNIAPRLMVV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 18 | g2668.t1 | CDD | cd00653 | RNA_pol_B_RPB2 | 38 | 1172 | 0.0 |
| 17 | g2668.t1 | Gene3D | G3DSA:3.90.1100.10 | - | 29 | 201 | 3.4E-14 |
| 13 | g2668.t1 | Gene3D | G3DSA:3.90.1110.10 | - | 202 | 383 | 1.3E-78 |
| 14 | g2668.t1 | Gene3D | G3DSA:3.90.1070.20 | - | 534 | 616 | 8.0E-39 |
| 15 | g2668.t1 | Gene3D | G3DSA:2.40.270.10 | - | 708 | 1066 | 1.6E-155 |
| 16 | g2668.t1 | Gene3D | G3DSA:2.40.50.150 | - | 738 | 928 | 1.6E-155 |
| 12 | g2668.t1 | Gene3D | G3DSA:3.90.1800.10 | RNA polymerase alpha subunit dimerisation domain | 1067 | 1174 | 1.9E-45 |
| 8 | g2668.t1 | PANTHER | PTHR20856:SF7 | DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 | 22 | 1173 | 0.0 |
| 9 | g2668.t1 | PANTHER | PTHR20856 | DNA-DIRECTED RNA POLYMERASE I SUBUNIT 2 | 22 | 1173 | 0.0 |
| 7 | g2668.t1 | Pfam | PF04563 | RNA polymerase beta subunit | 37 | 440 | 1.3E-68 |
| 2 | g2668.t1 | Pfam | PF04561 | RNA polymerase Rpb2, domain 2 | 200 | 393 | 1.5E-53 |
| 5 | g2668.t1 | Pfam | PF04565 | RNA polymerase Rpb2, domain 3 | 467 | 531 | 1.6E-24 |
| 1 | g2668.t1 | Pfam | PF04566 | RNA polymerase Rpb2, domain 4 | 566 | 628 | 4.8E-24 |
| 4 | g2668.t1 | Pfam | PF04567 | RNA polymerase Rpb2, domain 5 | 652 | 700 | 3.5E-16 |
| 3 | g2668.t1 | Pfam | PF00562 | RNA polymerase Rpb2, domain 6 | 707 | 1080 | 2.0E-124 |
| 6 | g2668.t1 | Pfam | PF04560 | RNA polymerase Rpb2, domain 7 | 1082 | 1172 | 3.1E-33 |
| 11 | g2668.t1 | ProSitePatterns | PS01166 | RNA polymerases beta chain signature. | 932 | 944 | - |
| 10 | g2668.t1 | SUPERFAMILY | SSF64484 | beta and beta-prime subunits of DNA dependent RNA-polymerase | 18 | 1172 | 0.0 |
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 transcript has been annotated with K03010 (DNA-directed RNA polymerase II subunit RPB2)
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.
