General information for g475.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as DNA-directed RNA polymerase I subunit RPA2.
Parent gene
- The parent gene g475 is located on chr_3: 3567391..3570188 (- 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 | g475 | g475.t1 | TTS | g475.t1 | 3566223 | 3566223 |
| chr_3 | g475 | g475.t1 | isoform | g475.t1 | 3566277 | 3569584 |
| chr_3 | g475 | g475.t1 | exon | g475.t1.exon1 | 3566277 | 3569255 |
| chr_3 | g475 | g475.t1 | cds | g475.t1.CDS1 | 3566277 | 3569255 |
| chr_3 | g475 | g475.t1 | exon | g475.t1.exon2 | 3569315 | 3569584 |
| chr_3 | g475 | g475.t1 | cds | g475.t1.CDS2 | 3569315 | 3569584 |
| chr_3 | g475 | g475.t1 | TSS | g475.t1 | NA | NA |
Sequences
>g475.t1 Gene=g475 Length=3249
ATGCGATTGATTCTAGATAATCTTGAACCTTATGAATTTGAATTAAATAATGGCGATAGA
TTGAAAGTCAAAGTTGAAAATTGTGAAATTTTACGACCAAGATTAACTTCACAACCTGAA
GCAAAAATCCAAAAAGTTTTTCCTTCAGAAGCTCGACAAAGAGCAATTACTTATACTGGT
AATTGCATGATGACATTAGCCTGGAGTAAAAATGGACACAAAAATGCATCTATCGATTTT
GATTTAGGACCTTTACCAATTATGATTCGATCAAAAGCATGCAATCTCAACGGAATGAAA
CCGAAAGAACTGGTTGACAAGCATGAACATGAACACGAATGGGGTGGATATTTTGTAGTC
AAAGGAAATGAGAAACTCATTCGTATGCTATTAATGACAAGAAGAAACTATCCTATAATG
CTAAAAAGAAACACTTGGAAAGATCGTGCAAAATATTTTACTCCATATGGTGTGATAATA
AGATCTGTTGCAATTGACCATACATCAACAAACAATGTGCTTCATTATTTAAAAAATGGA
ACTGCAAAATTGATGATAAGTCATAGAAAAATCCTCTCATATCTTCCTGTCATTTTGGTG
CTTAAATGTTTAGCAAATTATAGCGATAAAAAAATATTTCAAGATCTTCTATCTGGACAT
GAAGATGATTTATATTATAAAACTTGCATACAGGAAATGCTTCTTGAATTACACCAACAA
AACATTCACTCACATTTTGATGCAAAAAATTATCTTGGTCAAATATTTAGAACGCGTTTT
GATAATTTGCCTGCTTGGTCACCGAATGAGACTGTTGCAGATTATTTATTGAAAAATAAT
ATATTAATTCATTTGAATGAATATATTGATAAATACAATTTACTTGTATTTATGACTAAG
AAATTATTTCAAGCAGTACAAGGCAAATCAAAAATTGAGTCAGTGGATTCTGTGATGATG
CAAGAACTTCTTACAGGAGGACATTTGTATCAGAAAATTTTCAAAGAATTTCTCGAGTCA
TGGATGAATAATTTACGATTAAATTTAAACAAGAAGCTATCTAAAGATACAAGCATGAAT
ATTACAGCACCCGACATTTCTAATGCAGGAAAATTTTGTGGTAGTTTAATAAGACATTTT
GAATATTTTCTCGCAACTGGAAATTTAATTAGCAGATCAGGTCTTGGATTAATGCAATCA
TCTGGTCTTGTTATAATGGCAGAAAACATTAACCGAATGCGCTATATGAGCCATTTTCGT
GCTGTTCATCGTGGTTCATATTTTGTCACCATGCGTACAACAGAGGCTCGTCAGTTATTG
CCTGATTCTTGGGGATTTATTTGTCCTGTCCATACGCCTGATGGTAGCCCATGCGGTTTA
CTAAATCACTTGACTGTTGATTGCGAAACTTCACCAGATATTCTTCATAAAATTGATATG
GATAATTTAATACGACTCTTTGTTGAACTTGGAATGGAAATTGTTGACTCAAATGTGATT
TTTGAATATGAAAACTACTATACAGTGATAATTGAAGGAAAAATCATTGGTTATATTCAC
GATAGTCGAATAAAAAGTTTGGAATTTAATTTGCGTGCTTACAAAATTGAAGGAGAACGG
CTTCCACGTGAAACTGAAATTGTAGTTGTGCCAAAAAAGAATGCTGGACAATATCCTGGA
TTATTCATATTTTTCGGAGCAGCAAGAATGATGAGACCTGTTTTAAATTTGGCTTTCAAT
AAGATTGAATTGATTGGAACGTTTGAACAAGTATTTCTAGAAGTGGCTATTTCAAAAGAA
GAAATTTGCGAGGGAGTCACTACACATCTTGAATTTTCGAAACTTTCGTTTCTTTCCAAC
TTAGCAAATTTGATTCCCATGCCTGATCATAATCAAGCACCTCGTAACATGTATCAGTGT
CAAATGGGAAAGCAAACAATGGGAACACCTTGTCTTAATTGGCCTTCACAAGCAGCAAAC
AAATTATATCGACTTTATACACCTGCAACGCCACTCTTTCGACCCGTACATCATGACAAA
ATTGAACTAGATAATTTTGCAATGGGAACGAATGCAATTATTGCTGTTATTGGCTATACT
GGATATGATATGGAAGATGCAATGATTCTTAACAAATTTGCTTTAGAACGAGGCTTCGCT
CATGGAACAATTTATCATACTGAATTTTTTGAGATCAAAGCCAATTCTAGTTTTCAACGT
GATCCAACAAAACCTGAACTTGCAAAGTATCTTGAGTCTGATGGACTTCCGATGACAGGA
ACGAAAATTCAACCAAATGATCCCATGTGCTGTTATTATGATGGCAATGAGGCTGCATAT
AAAGTTGAAAGATACCGTGGAAAAGAAATAGTGTTTATTGATAATGTAAAAGTACATGGC
GATTTTAGTGTTTATGGCCCAAGAAAAGCATCAATTACGGTTAGAATTCCAAGAAATCCT
AATGTGGGTGATAAATTTGCATCGCGTGCTGGACAAAAAGGAATTTTCTCACAAAGATAT
CCTGCAGAAGATATGCCATTTACTGAAAGTGGCCTTATTCCTGATATCATCTTCAATCCT
CACGGTTTCCCTAGTCGTATGACTATTGCTATGATGATCGAAATAATGGCAGGCAAAAGT
GCAGCAATTAAAGGCGATGTCTATGATGCGACTCCATTTGAATTTTCTGAAGAAGATACA
GCAATTAATCATTTTGGAAAATTACTTACAAAATTAGGATATAATTTCTTCGGAACTGAA
CGATTGTATAGTGGTTTTGATGGATGTGAAATGAAAGCAGATATTTTCTTTGGTATTGTT
CATTATCAGCGACTGCGTCATATGGTGTCTGATAAATGGCAAGTAAGATCTACTGGTCCA
ATTGATTCAATTACACATCAACCTATAAAAGGAAGAAAACGTGGTGGTGGTGTTCGTTTT
GGAGAAATGGAACGTGATGCCTTGATTTCTCACGGTTCACCTTTCACGCTACAAGATCGA
TTATTTCATTGTTCAGATAAAACAATTTCATTAGCTTGTCTTCAGTGCCAAAATTTATTA
TTTTCTTTAGATAAAATATATGTTGGTCGACAAAAGGGTGATATTGTGAGACAAATAGAA
AAATGTATGTTTTGCGGAAAATCTGATGGAATTGATATTGTTGAAATACCATATGTATTC
AAACTACTTGTTAGTGAATTATGTGCGATGAACGTCAATCTAAAAGTTTCTTTTAAAGAC
TTGAATTAA
>g475.t1 Gene=g475 Length=1082
MRLILDNLEPYEFELNNGDRLKVKVENCEILRPRLTSQPEAKIQKVFPSEARQRAITYTG
NCMMTLAWSKNGHKNASIDFDLGPLPIMIRSKACNLNGMKPKELVDKHEHEHEWGGYFVV
KGNEKLIRMLLMTRRNYPIMLKRNTWKDRAKYFTPYGVIIRSVAIDHTSTNNVLHYLKNG
TAKLMISHRKILSYLPVILVLKCLANYSDKKIFQDLLSGHEDDLYYKTCIQEMLLELHQQ
NIHSHFDAKNYLGQIFRTRFDNLPAWSPNETVADYLLKNNILIHLNEYIDKYNLLVFMTK
KLFQAVQGKSKIESVDSVMMQELLTGGHLYQKIFKEFLESWMNNLRLNLNKKLSKDTSMN
ITAPDISNAGKFCGSLIRHFEYFLATGNLISRSGLGLMQSSGLVIMAENINRMRYMSHFR
AVHRGSYFVTMRTTEARQLLPDSWGFICPVHTPDGSPCGLLNHLTVDCETSPDILHKIDM
DNLIRLFVELGMEIVDSNVIFEYENYYTVIIEGKIIGYIHDSRIKSLEFNLRAYKIEGER
LPRETEIVVVPKKNAGQYPGLFIFFGAARMMRPVLNLAFNKIELIGTFEQVFLEVAISKE
EICEGVTTHLEFSKLSFLSNLANLIPMPDHNQAPRNMYQCQMGKQTMGTPCLNWPSQAAN
KLYRLYTPATPLFRPVHHDKIELDNFAMGTNAIIAVIGYTGYDMEDAMILNKFALERGFA
HGTIYHTEFFEIKANSSFQRDPTKPELAKYLESDGLPMTGTKIQPNDPMCCYYDGNEAAY
KVERYRGKEIVFIDNVKVHGDFSVYGPRKASITVRIPRNPNVGDKFASRAGQKGIFSQRY
PAEDMPFTESGLIPDIIFNPHGFPSRMTIAMMIEIMAGKSAAIKGDVYDATPFEFSEEDT
AINHFGKLLTKLGYNFFGTERLYSGFDGCEMKADIFFGIVHYQRLRHMVSDKWQVRSTGP
IDSITHQPIKGRKRGGGVRFGEMERDALISHGSPFTLQDRLFHCSDKTISLACLQCQNLL
FSLDKIYVGRQKGDIVRQIEKCMFCGKSDGIDIVEIPYVFKLLVSELCAMNVNLKVSFKD
LN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g475.t1 | CDD | cd00653 | RNA_pol_B_RPB2 | 1 | 1076 | 0.0 |
| 12 | g475.t1 | Gene3D | G3DSA:3.90.1110.10 | - | 136 | 314 | 2.7E-56 |
| 13 | g475.t1 | Gene3D | G3DSA:3.90.1070.20 | - | 476 | 566 | 7.6E-20 |
| 14 | g475.t1 | Gene3D | G3DSA:2.40.270.10 | - | 622 | 960 | 1.1E-131 |
| 15 | g475.t1 | Gene3D | G3DSA:2.40.50.150 | - | 652 | 819 | 1.1E-131 |
| 11 | g475.t1 | Gene3D | G3DSA:3.90.1800.10 | RNA polymerase alpha subunit dimerisation domain | 961 | 1080 | 1.2E-36 |
| 7 | g475.t1 | PANTHER | PTHR20856 | DNA-DIRECTED RNA POLYMERASE I SUBUNIT 2 | 5 | 1076 | 0.0 |
| 8 | g475.t1 | PANTHER | PTHR20856:SF5 | DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA2 | 5 | 1076 | 0.0 |
| 6 | g475.t1 | Pfam | PF04563 | RNA polymerase beta subunit | 16 | 360 | 1.6E-36 |
| 2 | g475.t1 | Pfam | PF04561 | RNA polymerase Rpb2, domain 2 | 134 | 323 | 3.2E-20 |
| 4 | g475.t1 | Pfam | PF04565 | RNA polymerase Rpb2, domain 3 | 406 | 469 | 1.3E-26 |
| 1 | g475.t1 | Pfam | PF06883 | RNA polymerase I, Rpa2 specific domain | 516 | 572 | 1.3E-17 |
| 3 | g475.t1 | Pfam | PF00562 | RNA polymerase Rpb2, domain 6 | 621 | 974 | 6.7E-103 |
| 5 | g475.t1 | Pfam | PF04560 | RNA polymerase Rpb2, domain 7 | 976 | 1077 | 8.9E-21 |
| 10 | g475.t1 | ProSitePatterns | PS01166 | RNA polymerases beta chain signature. | 823 | 835 | - |
| 9 | g475.t1 | SUPERFAMILY | SSF64484 | beta and beta-prime subunits of DNA dependent RNA-polymerase | 4 | 1080 | 4.58E-291 |
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:0005634 | nucleus | CC |
| GO:0003677 | DNA binding | MF |
| GO:0006351 | transcription, DNA-templated | BP |
KEGG
Orthology
- This transcript has been annotated with K03002 (DNA-directed RNA polymerase I subunit RPA2)
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.
