General information for g2571.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as DNA-directed RNA polymerase III subunit RPC1.
Parent gene
- The parent gene g2571 is located on chr_3: 18809720..18811540 (+ 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 | g2571 | g2571.t1 | TSS | g2571.t1 | 18805220 | 18805220 |
| chr_3 | g2571 | g2571.t1 | isoform | g2571.t1 | 18805330 | 18809720 |
| chr_3 | g2571 | g2571.t1 | exon | g2571.t1.exon1 | 18805330 | 18805764 |
| chr_3 | g2571 | g2571.t1 | cds | g2571.t1.CDS1 | 18805330 | 18805764 |
| chr_3 | g2571 | g2571.t1 | exon | g2571.t1.exon2 | 18805826 | 18806911 |
| chr_3 | g2571 | g2571.t1 | cds | g2571.t1.CDS2 | 18805826 | 18806911 |
| chr_3 | g2571 | g2571.t1 | exon | g2571.t1.exon3 | 18806970 | 18808557 |
| chr_3 | g2571 | g2571.t1 | cds | g2571.t1.CDS3 | 18806970 | 18808557 |
| chr_3 | g2571 | g2571.t1 | exon | g2571.t1.exon4 | 18808627 | 18809465 |
| chr_3 | g2571 | g2571.t1 | cds | g2571.t1.CDS4 | 18808627 | 18809465 |
| chr_3 | g2571 | g2571.t1 | exon | g2571.t1.exon5 | 18809526 | 18809720 |
| chr_3 | g2571 | g2571.t1 | cds | g2571.t1.CDS5 | 18809526 | 18809720 |
| chr_3 | g2571 | g2571.t1 | TTS | g2571.t1 | 18809826 | 18809826 |
Sequences
>g2571.t1 Gene=g2571 Length=4143
ATGCCAAAGGAGCAGTACAGAGAGGCAGATGCCATTAAGGAAATATCACATGTTTCATTT
AGTCTCGATTCAGCTGAACAAATTCAACAATCGAGTCATTTACATGTCAAAGTAAAATCT
CTATATAATCAAGATCAGAAGCGAACTCCTATGACTTCTGGAGTTCTTGATTTACGGCTT
GGAGTCAGTCAAAAAGGCGCTACTTGTGAAACATGTAATCAAGGGTTGAACGAATGTGTA
GGTCATTTTGGATATCTCGATTTAGCTTTACCAGTATTTCATATTGGTCATTTTCGAGCG
ACTATAACTATATTACAAACAATTTGTAAAACATGTAGTCGTGTTATGCTTAAAGATGAA
GAAGCCAAAACGTTTAGTAAGAAACTTATGAATCCAAATCTCTCTTATCTCACAAAAAAA
GCTATTCATCAACAGGTTTTGAAAAAAGCAAAAAAAAACACAAAATGTCCACATTGTGAT
GCAATAAATGGTCCTGTCAAAAAAGGAGTTGGATTATTGAAAATTGTCCATGAACCATTT
AGAGGAAGAAAGAAAACTGATCCATTAGTAAATGATGCTCTTGAAGAACTTCTTTCAGCA
ACAGAAGAGAACAAGGAAGTATTTCAAAATGTTGGACAACAAACTTTAATTCATGAACTC
AATCCCGTAGAAGTACTGCATTTATTTAAAAATATACCAAAATGTGATATACCTCTTCTC
GGAATGACATCAGAAAATGCAGATCCAGCAAATTTAATTGTTACTCGGGTTTATGTTCCT
CCTGCTTGTATTCGCCCTTCTGTTGTCTCCGATATCAAATCTGGAACTACTGAAGACGAC
CTAACAATGAAACAAAGTGAAATTCTTCTCATTAATGATTTTATTGCAAAACATATGAAT
ACAAGTGGCAAAATTGAAATTATAGAGGAAGATTGGGATTATTTGCAGTTACACGTAGCA
CTTTATTTCAATAGTGAAGTATCTGGAATTCCTATAAATATGATGCCAACCAAACAGACT
CGAGGCATTGTACAGCGTTTAAAAGGAAAACAAGGTCGATTTAGAGGAAATTTATCGGGC
AAGCGTGTGGACTTTTCAGCTCGTACAGTAATTTCTCCTGATCCTAATTTAATGATTCAT
GAAGTTGGTGTGCCCGATCGAGTCGCAAAAATTTTAACTTTTCCGGAACGAGTCAATCCC
TCAAATATTCAAAAACTTCGAAACATGGTACGTAATGGTCCTGATGTTCATCCCGGAGCA
AATTATGTTCAACAGAAAGGTGTCACTTTCAAAAAGTTTTTAGCTTATGGTAATCGTGAT
AAAGTAGCACAAGATTTAAAATATGGTGATATTGTTGAGAGACATTTGATTGATGGTGAT
ATTGTATTGTTTAATCGTCAACCAAGTTTACATAAATTGAGTATCATGTGTCATATAGCT
AAAGTTCAACCACAAAGAACATTTAGATTCAATGAATGTGCATGTACTCCTTATAATGCT
GATTTCGATGGAGATGAAATGAATTTGCATTTGCCTCAAACAGAAGAAGCCAGAGCAGAA
GCACTTGTATTAATGGGAAATCGTTCAAATCTCGTAACACCACGCAATGGTGAATTGTTG
ATTGCTGCAACACAAGATTTTATAACTGGTGGCTATTTAATAACACAACGAGATGAATTT
TTTACAAAAGAGAAAGCTATGCAATTGGCTTCGTGTATGTTAGCAGGACCAGATACTAAT
ATGAAAATTGATTTACCACCACCTACAATTCTCAAACCTCGCCGATTGTGGACAGGAAAA
CAAATTTTTAGTCTCATCCTTAGGCCAAACAAAAATTATCCAGTTATGGCAAATATGGCA
ACAAAAGGCAAAAACTATACTGGAAATTTAGACATGTGTGTTCGCGATTCTTATGTGATT
ATTAGAAATTCTCAACTACTTTGTGGATCAATGGATAAAAGTACATTAGGATCAGGCACA
AAAAATTGTGTTTTCTATGTGATTCTTCGTGATTTTGGTGAAGAGTATGCAACAAGAGCG
ATGTGGCGATTAGCCAGAATGGCATCATACTTTATGATGAATCGTGGTTTCTCTTTTGGA
ATTGGTGATGTTACTCCAAGTAAAAAATTGTTGGAAGAAAAACAAATATTACTTGATAAA
GGATATAGTAAATGTGATGAATATATTGCTGAAATGAAAAAAGGAACATTGCAGTGTGCG
CCTGGATGTACACCAGAACAAACATTAGAATCAATGATGTTAAAAGAGCTTTCATCGATT
CGTGAATTGGCAGCTAAAGCTTGCTTCCGTGAATTACATCCAACAAATAGTGCATTAATT
ATGGCTCAATCAGGTTCAAAAGGTTCAAATATTAACATTTCACAAATGATTGCTTGTGTG
GGACAACAAGCTATAAATGGAAAGAGAGTGCCTAATGGATTTGAAGATCGTGCATTGCCA
CACTTTGAAAAATTTTCTAAAATACCAGCAGCAAGAGGATTCGTTCAAAATTCCTTCTTT
TCTGGTCTCACACCTACTGAATTTTTCTTTCACACAATGGCCGGTCGTGAAGGACTTGTT
GATACAGCGGTCAAGACAGCGGAAACTGGTTATTTACAACGTCGTCTAGTCAAATGTCTT
GAAGACCTTGTCGTTCAATATGATGGAACAGTTAGAAGCGCTATTTCGGAAGTTGTTGAA
TTTGTATATGGGGGAGATGGCTTAGATCCATCATATATGGAAACAAAAAATCGTCCAGTT
GATATGGATCGACAACTCATGCACATTACAGCTAAATACTTGTATCGTGATCAAAAGAAA
ATAAAATCATGCGATTTAAAGAAAGCGGCAGAAGAAATTCTTTCTAGACCAGAATACAAC
AATAGTAGAGATGATTTCAAAATGGAATGTGTGACATTTTTCGATAATGTTGCAAAGAAA
AATGAAAAAGTTGAGAAGAAATATGAAAAATTTGGGAAAATAGGAGATGAATTGAATCGA
ATTACATATGGACAAATTGAACAATTTATAGATGTAGTAAACGAAAAATTCAACCGTTCT
GTTATTGAACCAGGCACTGCAGTTGGTGCATTAGGTGCACAAAGTATAGGCGAACCAGGA
ACTCAAATGACTTTGAAAACCTTTCATTTTGCTGGTGTTGCTTCGATGAATATTACAAGT
GGTGTTCCTCGTATAGTAGAAATCATAAATGCAACAAAAGTTATTTCAACACCAATTATA
ACTACTGAAATTGAAAATAACACATCAATGGAATTTGCAAGAAAAGTCAAAGCACGAATA
GAGAAGACAACTCTTGGTGAAGTTACATCATTTATTGAAGAAGTTTATCGCAATAATGAT
TGTTTTGTTCTCATTAAACTCGATTTGGAACGTATTCGTGTACTTGGATTAGATGTGACT
ATTGATACAATAAGATATTCAATTTGCATTTCAAAATTAAAGGTGAAACCAAATCAAGTT
GAAATTCATGGACCTTCTGTTATAGTAATTCAACCTGATCGTACAAAATACGGACATATG
ATAAATGTTGAAATGCAAAGACTAGCAAATTCAATTTCTCAAATTGTGATCGCAGGAATA
CCAACAGTTTCAAGAGCAGTCATTGCAATTGATGATTCAAAACAACCAGTCACATATAAA
TTGTGTGTCGAAGGATCTGGATTTCGTGAAGTTATGGCAACTTTCGGAGTTGTTGGTTCA
AAAACAAGAAGTAATAATATCTGGGAAGTATATAATACACTTGGTATCGAAGCAGCTCGT
ACTACAATTATCAATGAAATTACATCTGTTATGGAAGGTCATGGAATGCAAGTCGATTAT
CGCCATATTATGTTACTGGCCGGTCAGATGACAAGTAGAGGAGAAGTTTTAGGAATTACA
AGACATGGCTTAGCAAAAATGCGTGAATCTGTTTTTAATTTGGCTTCATTTGAAAAGACT
GCTGACCATTTGTTTGATGCTGCTTATTATGGACAAACTGACTCAATTGATGGTGTATCT
GAAAGAATTATTTTAGGAATGCCTGCTTCAATTGGCACAGGTCTATTTAAAATCCTTCAT
AAGCATGTAGATAAGCAGATTGTTCCAGCACCAACTCCTATTTTCGATAAATTTGATTGG
TAA
>g2571.t1 Gene=g2571 Length=1380
MPKEQYREADAIKEISHVSFSLDSAEQIQQSSHLHVKVKSLYNQDQKRTPMTSGVLDLRL
GVSQKGATCETCNQGLNECVGHFGYLDLALPVFHIGHFRATITILQTICKTCSRVMLKDE
EAKTFSKKLMNPNLSYLTKKAIHQQVLKKAKKNTKCPHCDAINGPVKKGVGLLKIVHEPF
RGRKKTDPLVNDALEELLSATEENKEVFQNVGQQTLIHELNPVEVLHLFKNIPKCDIPLL
GMTSENADPANLIVTRVYVPPACIRPSVVSDIKSGTTEDDLTMKQSEILLINDFIAKHMN
TSGKIEIIEEDWDYLQLHVALYFNSEVSGIPINMMPTKQTRGIVQRLKGKQGRFRGNLSG
KRVDFSARTVISPDPNLMIHEVGVPDRVAKILTFPERVNPSNIQKLRNMVRNGPDVHPGA
NYVQQKGVTFKKFLAYGNRDKVAQDLKYGDIVERHLIDGDIVLFNRQPSLHKLSIMCHIA
KVQPQRTFRFNECACTPYNADFDGDEMNLHLPQTEEARAEALVLMGNRSNLVTPRNGELL
IAATQDFITGGYLITQRDEFFTKEKAMQLASCMLAGPDTNMKIDLPPPTILKPRRLWTGK
QIFSLILRPNKNYPVMANMATKGKNYTGNLDMCVRDSYVIIRNSQLLCGSMDKSTLGSGT
KNCVFYVILRDFGEEYATRAMWRLARMASYFMMNRGFSFGIGDVTPSKKLLEEKQILLDK
GYSKCDEYIAEMKKGTLQCAPGCTPEQTLESMMLKELSSIRELAAKACFRELHPTNSALI
MAQSGSKGSNINISQMIACVGQQAINGKRVPNGFEDRALPHFEKFSKIPAARGFVQNSFF
SGLTPTEFFFHTMAGREGLVDTAVKTAETGYLQRRLVKCLEDLVVQYDGTVRSAISEVVE
FVYGGDGLDPSYMETKNRPVDMDRQLMHITAKYLYRDQKKIKSCDLKKAAEEILSRPEYN
NSRDDFKMECVTFFDNVAKKNEKVEKKYEKFGKIGDELNRITYGQIEQFIDVVNEKFNRS
VIEPGTAVGALGAQSIGEPGTQMTLKTFHFAGVASMNITSGVPRIVEIINATKVISTPII
TTEIENNTSMEFARKVKARIEKTTLGEVTSFIEEVYRNNDCFVLIKLDLERIRVLGLDVT
IDTIRYSICISKLKVKPNQVEIHGPSVIVIQPDRTKYGHMINVEMQRLANSISQIVIAGI
PTVSRAVIAIDDSKQPVTYKLCVEGSGFREVMATFGVVGSKTRSNNIWEVYNTLGIEAAR
TTIINEITSVMEGHGMQVDYRHIMLLAGQMTSRGEVLGITRHGLAKMRESVFNLASFEKT
ADHLFDAAYYGQTDSIDGVSERIILGMPASIGTGLFKILHKHVDKQIVPAPTPIFDKFDW
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 19 | g2571.t1 | CDD | cd02583 | RNAP_III_RPC1_N | 24 | 892 | 0.0 |
| 18 | g2571.t1 | CDD | cd02736 | RNAP_III_Rpc1_C | 1016 | 1356 | 5.97682E-167 |
| 17 | g2571.t1 | Coils | Coil | Coil | 190 | 211 | - |
| 11 | g2571.t1 | Gene3D | G3DSA:1.20.120.1280 | - | 1 | 131 | 2.2E-26 |
| 13 | g2571.t1 | Gene3D | G3DSA:2.40.40.20 | - | 350 | 521 | 6.7E-77 |
| 16 | g2571.t1 | Gene3D | G3DSA:3.30.1490.180 | RNA polymerase ii | 393 | 458 | 6.7E-77 |
| 14 | g2571.t1 | Gene3D | G3DSA:1.10.274.100 | - | 533 | 696 | 1.0E-110 |
| 12 | g2571.t1 | Gene3D | G3DSA:1.10.132.30 | - | 697 | 843 | 1.0E-110 |
| 10 | g2571.t1 | Gene3D | G3DSA:2.20.25.410 | - | 881 | 933 | 4.6E-15 |
| 15 | g2571.t1 | Gene3D | G3DSA:1.10.150.390 | - | 1311 | 1356 | 3.3E-18 |
| 6 | g2571.t1 | PANTHER | PTHR19376:SF32 | DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC1 | 3 | 1360 | 0.0 |
| 7 | g2571.t1 | PANTHER | PTHR19376 | DNA-DIRECTED RNA POLYMERASE | 3 | 1360 | 0.0 |
| 4 | g2571.t1 | Pfam | PF04997 | RNA polymerase Rpb1, domain 1 | 13 | 358 | 1.1E-82 |
| 3 | g2571.t1 | Pfam | PF00623 | RNA polymerase Rpb1, domain 2 | 360 | 525 | 6.1E-73 |
| 2 | g2571.t1 | Pfam | PF04983 | RNA polymerase Rpb1, domain 3 | 530 | 704 | 9.5E-39 |
| 5 | g2571.t1 | Pfam | PF05000 | RNA polymerase Rpb1, domain 4 | 733 | 835 | 4.9E-31 |
| 1 | g2571.t1 | Pfam | PF04998 | RNA polymerase Rpb1, domain 5 | 842 | 1310 | 3.5E-89 |
| 9 | g2571.t1 | SMART | SM00663 | rpolaneu7 | 250 | 555 | 1.6E-167 |
| 8 | g2571.t1 | SUPERFAMILY | SSF64484 | beta and beta-prime subunits of DNA dependent RNA-polymerase | 10 | 1361 | 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:0003677 | DNA binding | MF |
| GO:0006351 | transcription, DNA-templated | BP |
KEGG
Orthology
- This transcript has been annotated with K03018 (DNA-directed RNA polymerase III subunit RPC1)
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.
