General information for g9646.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as DNA-directed RNA polymerase I subunit RPA1.
Parent gene
- The parent gene g9646 is located on chr_1: 4461541..4463062 (- 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_1 | g9646 | g9646.t1 | TTS | g9646.t1 | 4456626 | 4456626 |
| chr_1 | g9646 | g9646.t1 | isoform | g9646.t1 | 4456682 | 4463062 |
| chr_1 | g9646 | g9646.t1 | exon | g9646.t1.exon1 | 4456682 | 4457101 |
| chr_1 | g9646 | g9646.t1 | cds | g9646.t1.CDS1 | 4456682 | 4457101 |
| chr_1 | g9646 | g9646.t1 | exon | g9646.t1.exon2 | 4457174 | 4459937 |
| chr_1 | g9646 | g9646.t1 | cds | g9646.t1.CDS2 | 4457174 | 4459937 |
| chr_1 | g9646 | g9646.t1 | exon | g9646.t1.exon3 | 4460016 | 4460082 |
| chr_1 | g9646 | g9646.t1 | cds | g9646.t1.CDS3 | 4460016 | 4460082 |
| chr_1 | g9646 | g9646.t1 | exon | g9646.t1.exon4 | 4460256 | 4461704 |
| chr_1 | g9646 | g9646.t1 | cds | g9646.t1.CDS4 | 4460256 | 4461704 |
| chr_1 | g9646 | g9646.t1 | exon | g9646.t1.exon5 | 4461760 | 4461954 |
| chr_1 | g9646 | g9646.t1 | cds | g9646.t1.CDS5 | 4461760 | 4461954 |
| chr_1 | g9646 | g9646.t1 | exon | g9646.t1.exon6 | 4462016 | 4462173 |
| chr_1 | g9646 | g9646.t1 | cds | g9646.t1.CDS6 | 4462016 | 4462173 |
| chr_1 | g9646 | g9646.t1 | exon | g9646.t1.exon7 | 4462246 | 4462260 |
| chr_1 | g9646 | g9646.t1 | cds | g9646.t1.CDS7 | 4462246 | 4462260 |
| chr_1 | g9646 | g9646.t1 | exon | g9646.t1.exon8 | 4463049 | 4463062 |
| chr_1 | g9646 | g9646.t1 | cds | g9646.t1.CDS8 | 4463049 | 4463062 |
| chr_1 | g9646 | g9646.t1 | TSS | g9646.t1 | NA | NA |
Sequences
>g9646.t1 Gene=g9646 Length=5082
ATGCCTAGATCAGTAATCAAAAAATTACCGAAAATGCCAGTGTCTTTGGCTAAAGAGCGT
CCAGTTACGCTAAATATTGAAAATGTAGAGTTCAGTGTTTTCAATGCTGAAGAAATTCGT
AAAATCAGTGTCTGCAAAATTTTAAACCCTATTTCTTTTGATGGTCTTGGAAATTCTACT
GCTGGAGGTCTATATGACAATCGTATGGGACCTTTATCACGTCGAGAACTTTGCGGAACT
TGCAATAGTGGAGAAAATGATTGTACCGGTCATTTTGGCCACATCGATTTAGTTATGACT
GTCTATAATCCATTTTTCATGAAAAACCTAGTTTCAATATTGAAATCAGTATGTACGAAA
TGCTTCAGACTTCAAATAACTGATCGAATGAAGGAAATTGTTGAACTTCAGTTGCAATTA
ATTGATGCAGGATATGTTGCTGAAGCTTCGGATTTAGAAGATCAGAAACTTGTTTTCTGT
AAGACAAAAACAATTTCAAAGAAGTTAACAAAAGAGAATATTGAAAATAATGAAAGAGAT
GAAAAAAGAATTGAAAAGAATTATTTTAAAACTATGAAGAAACTTCGCAAACTACTCAAA
TCAAATCCAGTAAATCACTATGAAAAAACAAAAACTTCTGAATCAATTCGAAATGCTATT
ATTCACAGTACATTTGGAACTATAACAAATAATACTTCTGCAAGTAAATGCATGTATTGT
CACTTACCTTGGAAGAAAATTCGATATTCATACAAAAAATTAGTAATGAATTTAACAAAA
GCCGAAATTGATAATATCAAGGATCAAAGTATGGAAAAGAATGAACAATTAACAAAATCG
AATACAAAGGTAATTATGGCTTTAGAGTGTCGAGACATGTTGAAACAGATTTTTGAACAT
GACGGAGAATTTTTAAAATCAATTTTCCCTATTCTTAAATCGGCTAAAAATGAAGCATAT
GAAATTTTTTTAATGGATGTTCTTCCCGTTATTCCTCCTGTGTGGCGACCTCCAAATTTA
GTGCGTGATATGTTATGCGATCATCCTCAAACACGAGCTTATCTCAAAGTAGTTGAAGTT
AATAACATGCTCAGATGTATTTTAGAAAAGATAAAGATAGATAATGGTGAACAAGAACAG
TCATCAGAATTGAATGAAGATTTACTAAATGTCTACAAATTATCAAAAGGAAACACTGCA
AATGAAAAGATTTTTTTCAAATGGGAAGAATTACAATCGACAGTTGATATGATTTTAGAC
AAAGAAGCAAATATGTCTAAGTATGTCAAAGATAGTTCAATTGGTATAAAGCAGCTCTTA
GAAAAGAAGCAAGGACTCATCAGAATGAATATGATGGGAAAAAGAGTTAATTATGCTTGT
CGAACAGTTATAACACCAGATCCGTATATTGATGTAGATCAAATTGGAATTCCTGAAGCA
TTTGCACTTAAATTAACATATCCAGTTCCTGTAACACCATGGAATGTCACTCAATTGCGT
AAAATGGTTTTAAATGGTCCCGAAAAACATCCAGGTGCTTGTTTTATTGAAACTACAAAT
GGTTCAAAACGAGTAATTCCAAAAGATTTGAATAGACGCGAAGCAATGGCAGCTACATTA
TTGAAGCCTGAACCGAATGAAGGAATAAAATTTGTGCACAGACATCTTTTAAACAACGAT
ATTATGCTTCTTAATCGTCAACCAACTTTACATAGACCATCAATTATGGCTCATAAAGCA
AAAATTTTGAAGGGTGAAAAAACTTTTAGGCTTCATTATTCAAACTGCAAAAGTTATAAT
GCTGATTTTGATGGCGATGAGATGAATGCTCATTTGCTGCAAAATGAAGTCGCAAGAAGT
GAAGCTTACAATTTAGTCGGAGTTCCACATCATTACTTAGTTCCTAAAGATGGTACACCT
CTTGGAGGCCTTATTCAAGATCACATTATTTCTGGTGTAAAGTTGTCAATGCGTGGTAAA
TTTTTTACACGAGAAGACTATCAGCAATTGGTTTATCAAGGATTAAACTCGAAAACTGGA
AGAATTATAACTTTGCCACCAACAATTCTTAAACCAAGAACACTATGGAGTGGTAAACAA
GTTTTTTCAACTCTTATTCTTAACATAGTACCTGAAGGAAAACGTTTACTTAATTTAACA
TCTGTCGCAAAAATTGGAGCACATTTGTGGCAAACAGAAGAGAAAAGAAAATGGAAATAT
GGTGGAAGTGAATTGCAAGACAATGAAATGTCTGAATCTGAGGTTATTATTCGAAGTGGT
CTCTTGTTGGTTGGTGTATTAGATAAAAATCACTATGGTGCTACACCTTACAGTTTGATA
CATTGCATATATGAATTGTATGGCGGTGAGGTTTCAACAAAATTGCTTTCTGCATTCACA
CGTGTTTTCACTACTTTTCTGCAATGGGAAGGATTTACATTAGGTGTTAGAGATATTCTA
GTAATGACTTCTGCAGATAAACAACGAACTGAAATCATCAAAAAAAGTCGTCAAATTGGT
AAAAGTATAACCTGTCAAGTACTAAATTGCGATGAAAATATTTCAAATGAAGAATTATCT
GAAAGAATTGAACAAGCATATACAAATGATCCAAAGTTTAAATCAAATTTAGATAAAAAA
TACAAATCGGCAATGGATAGTTTCACAAATGATATTAACAAAACATGCTTGCCTTCAGGA
CTAATATCTAAGTTTCCCTCAAATAATTTACAATTGATGGTCATTTCTGGTGCAAAAGGA
TCTATAGTAAATACAATGCAAATTTCGTGTCTATTGGGTCAAATTGAATTAGAAGGAAAA
CGTCCACCTGTGATGATAAATGGAAAATCTTTGCCAAGTTTTCCAATATTTGATTGTTCA
CCGAAAAGTGGTGGATTCATTGATGGACGTTTTATGACTGGTATTGATCCACAAGGATTT
TTCTTTCACTGTATGGCAGGTCGTGAAGGTTTGATTGATACGGCTGTTAAAACAAGTCGT
TCAGGATATTTACAGCGTTGTCTCATTAAGCATTTAGAAGGCCTTACAGTTGCCTATGAT
GGAACTGTACGCGATAGTGATCAAAGCGTAGTGCAGTTCATGTATGGCGAAGATGGCATG
GATATTCTCAAATCTCAATTTTTGACATCTAAACAATTACCATTCTTAGTTGAAAATTTA
GATGCTATTAAAAATGACGATGAAATTGAACAACTTAGAAACCAACCAGAAGATGATGAA
AGTATGAAGAAGCATTTAAAGAAAATTAAATCATACAAGAAGAAGTTTGGTAGTACAACA
CAAAGACCTGCTCGTAATCTCTCGACTAAGAAATGTCCACCGCCGTTAACTTCAAAATAT
CCACCACATTTGTTTTTTGGTGCTATATCTGAATGTGCACAAGAAATTTTAGATAAATAC
TTGAAAAATAATAATGATGTTGATAAAGAAAGCATACATGATATGTTTTCATTGAAAAGT
ATGAAATCTTTAGCTGAACCTGGTGAACCGGTCGGTATTTTAGCAGCACAATCAATTGGT
GAACCTTCAACTCAGATGACACTCAATACTTTTCACTTTGCTGGTAGAGGTGATATGAAC
GTTACTCTCGGTATACCTCGATTGCGTGAAATTCTCATGATGGCCTCAAAAAATATTAAA
ACACCTTCAATGGAAATTCCTTTTCTTAATCAAAACTCCGAAAATTTGGACAAAATTGCT
GACAAGTTTAGAATTCGTTTAAATCAAGTTACACTTGCTGATGTGTTAACTTTTGTAAAT
GTTAAGTCATATGTGACACTAAATCCACAAAGAATAAGAAATTATGAATTTACTTTTAAC
ATTCTTCCATATAATGCATACAAAAAACAATTTATGGTGAAACCAAAGAAAATCATAAAG
CATATTGGTCAATATTTTCTCTTTAGATTATTTCGACTTATTGAAAAAGCAGCAAAAGAT
GTTGGGAGCGATTATGTTGAAAAGGAGCAAAAAGAAACACAAACTGCCGCAAAGAGAAAA
GAAGATGAAGAAAACGAGCACGAAGAGAAACAATTAGACGAAGTTGTTAAAGATTTAAAA
AATAATGATGATTCAGATGATGACCTTGATGATCCAGCTATGGACGATGATGATGCAACG
GCAGACAAAATAAAAGCAAAACATGAAGATGAACGTGATTATGAAGAACCTGAAGATAAT
GAGGAAATTAAAGATGCAGATTCTGATAAATCTGATGAGGAAGAGGATTTTGATTTGTCA
AAAGTAAAATTAGAACTTGATGATGATGTTAATGTGAAGCTATTAGAGGAGCTCGTTAGA
GAAGATCCAGATGCTGATCTCGAACAGTTGAAAAGTTTCGAGAAGAAAGAAGATGAGGAT
GATGATCAAGGTGAAGACGATATGATGAACTATTTAGAAAAAAAACTTTCAACAATCAGT
GCTAATATAATGATTCAAAGTTTTGAGAAAGATTCTAAAAAGCATAGTTGGTGTAAAATC
AAATTTTCGGTGCCAATCAAGTTTAAGAACATTGATATGACTAGTGTAATTAGAGATGCA
GCACGCACTTCTGTTATTTGGGAAATTCCAAAAATAAAACGAGCCATTACTTTCAAACAG
AATGGTTTACTTTGCATTAAAACTGAAGGCATAAATGTTGAGGCGATGTTTGAATATGAC
AAAATTTTGGACCTCAAAAAACTTTATATCAACGATATTCATGAAGTTGCAAACAGATAT
GGAATAGAGTGTGCGGCAAAAGTAATTGTAAAGGAAGTTCAAAACGTTTTCCGAGTTTAT
GGAATTACAGTCGATCCACGTCACTTGTCTCTCATTGCTGATTATATGACCTTTGATGGT
ACAATTAAACCATTAAATAGAAAAGGAATGGAATCTAATGCTTCACCGTTTCAAAAAATT
TCTTTTGAATCCGCTCTTAGTTTTCTGAAAAACGCAGTTGTCCAAGGAAACGTTGATAAT
ATCAAATCACCATCATCATGTCTCATTACTGGCGCTCCGTGTAAAATAGGAACTGGCTCA
TTCGGTCTTATCAATAATTTAAGTTACGCATTGAATTTATAA
>g9646.t1 Gene=g9646 Length=1693
MPRSVIKKLPKMPVSLAKERPVTLNIENVEFSVFNAEEIRKISVCKILNPISFDGLGNST
AGGLYDNRMGPLSRRELCGTCNSGENDCTGHFGHIDLVMTVYNPFFMKNLVSILKSVCTK
CFRLQITDRMKEIVELQLQLIDAGYVAEASDLEDQKLVFCKTKTISKKLTKENIENNERD
EKRIEKNYFKTMKKLRKLLKSNPVNHYEKTKTSESIRNAIIHSTFGTITNNTSASKCMYC
HLPWKKIRYSYKKLVMNLTKAEIDNIKDQSMEKNEQLTKSNTKVIMALECRDMLKQIFEH
DGEFLKSIFPILKSAKNEAYEIFLMDVLPVIPPVWRPPNLVRDMLCDHPQTRAYLKVVEV
NNMLRCILEKIKIDNGEQEQSSELNEDLLNVYKLSKGNTANEKIFFKWEELQSTVDMILD
KEANMSKYVKDSSIGIKQLLEKKQGLIRMNMMGKRVNYACRTVITPDPYIDVDQIGIPEA
FALKLTYPVPVTPWNVTQLRKMVLNGPEKHPGACFIETTNGSKRVIPKDLNRREAMAATL
LKPEPNEGIKFVHRHLLNNDIMLLNRQPTLHRPSIMAHKAKILKGEKTFRLHYSNCKSYN
ADFDGDEMNAHLLQNEVARSEAYNLVGVPHHYLVPKDGTPLGGLIQDHIISGVKLSMRGK
FFTREDYQQLVYQGLNSKTGRIITLPPTILKPRTLWSGKQVFSTLILNIVPEGKRLLNLT
SVAKIGAHLWQTEEKRKWKYGGSELQDNEMSESEVIIRSGLLLVGVLDKNHYGATPYSLI
HCIYELYGGEVSTKLLSAFTRVFTTFLQWEGFTLGVRDILVMTSADKQRTEIIKKSRQIG
KSITCQVLNCDENISNEELSERIEQAYTNDPKFKSNLDKKYKSAMDSFTNDINKTCLPSG
LISKFPSNNLQLMVISGAKGSIVNTMQISCLLGQIELEGKRPPVMINGKSLPSFPIFDCS
PKSGGFIDGRFMTGIDPQGFFFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLTVAYD
GTVRDSDQSVVQFMYGEDGMDILKSQFLTSKQLPFLVENLDAIKNDDEIEQLRNQPEDDE
SMKKHLKKIKSYKKKFGSTTQRPARNLSTKKCPPPLTSKYPPHLFFGAISECAQEILDKY
LKNNNDVDKESIHDMFSLKSMKSLAEPGEPVGILAAQSIGEPSTQMTLNTFHFAGRGDMN
VTLGIPRLREILMMASKNIKTPSMEIPFLNQNSENLDKIADKFRIRLNQVTLADVLTFVN
VKSYVTLNPQRIRNYEFTFNILPYNAYKKQFMVKPKKIIKHIGQYFLFRLFRLIEKAAKD
VGSDYVEKEQKETQTAAKRKEDEENEHEEKQLDEVVKDLKNNDDSDDDLDDPAMDDDDAT
ADKIKAKHEDERDYEEPEDNEEIKDADSDKSDEEEDFDLSKVKLELDDDVNVKLLEELVR
EDPDADLEQLKSFEKKEDEDDDQGEDDMMNYLEKKLSTISANIMIQSFEKDSKKHSWCKI
KFSVPIKFKNIDMTSVIRDAARTSVIWEIPKIKRAITFKQNGLLCIKTEGINVEAMFEYD
KILDLKKLYINDIHEVANRYGIECAAKVIVKEVQNVFRVYGITVDPRHLSLIADYMTFDG
TIKPLNRKGMESNASPFQKISFESALSFLKNAVVQGNVDNIKSPSSCLITGAPCKIGTGS
FGLINNLSYALNL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 19 | g9646.t1 | CDD | cd01435 | RNAP_I_RPA1_N | 31 | 1020 | 0.0 |
| 20 | g9646.t1 | CDD | cd02735 | RNAP_I_Rpa1_C | 1159 | 1684 | 4.93163E-111 |
| 16 | g9646.t1 | Coils | Coil | Coil | 167 | 187 | - |
| 18 | g9646.t1 | Coils | Coil | Coil | 256 | 276 | - |
| 17 | g9646.t1 | Coils | Coil | Coil | 1326 | 1358 | - |
| 11 | g9646.t1 | Gene3D | G3DSA:1.20.120.1280 | - | 16 | 146 | 5.0E-26 |
| 13 | g9646.t1 | Gene3D | G3DSA:2.40.40.20 | - | 443 | 623 | 5.0E-77 |
| 15 | g9646.t1 | Gene3D | G3DSA:3.30.1490.180 | RNA polymerase ii | 486 | 558 | 5.0E-77 |
| 14 | g9646.t1 | Gene3D | G3DSA:1.10.274.100 | - | 632 | 813 | 3.5E-61 |
| 12 | g9646.t1 | Gene3D | G3DSA:1.10.132.30 | - | 814 | 976 | 1.8E-55 |
| 10 | g9646.t1 | Gene3D | G3DSA:2.20.25.410 | - | 1014 | 1059 | 2.9E-11 |
| 9 | g9646.t1 | Gene3D | G3DSA:3.30.70.2850 | - | 1250 | 1441 | 2.5E-5 |
| 25 | g9646.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1323 | 1351 | - |
| 24 | g9646.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1386 | 1420 | - |
| 22 | g9646.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1394 | 1414 | - |
| 23 | g9646.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1445 | 1465 | - |
| 6 | g9646.t1 | PANTHER | PTHR19376:SF11 | DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA1 | 28 | 1679 | 4.3E-294 |
| 7 | g9646.t1 | PANTHER | PTHR19376 | DNA-DIRECTED RNA POLYMERASE | 28 | 1679 | 4.3E-294 |
| 4 | g9646.t1 | Pfam | PF04997 | RNA polymerase Rpb1, domain 1 | 25 | 370 | 4.6E-29 |
| 3 | g9646.t1 | Pfam | PF00623 | RNA polymerase Rpb1, domain 2 | 453 | 627 | 3.9E-64 |
| 2 | g9646.t1 | Pfam | PF04983 | RNA polymerase Rpb1, domain 3 | 631 | 819 | 9.9E-37 |
| 5 | g9646.t1 | Pfam | PF05000 | RNA polymerase Rpb1, domain 4 | 873 | 967 | 3.5E-22 |
| 1 | g9646.t1 | Pfam | PF04998 | RNA polymerase Rpb1, domain 5 | 974 | 1637 | 2.4E-94 |
| 21 | g9646.t1 | SMART | SM00663 | rpolaneu7 | 321 | 656 | 6.4E-126 |
| 8 | g9646.t1 | SUPERFAMILY | SSF64484 | beta and beta-prime subunits of DNA dependent RNA-polymerase | 19 | 1688 | 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:0008270 | zinc ion binding | MF |
| GO:0006351 | transcription, DNA-templated | BP |
KEGG
Orthology
- This transcript has been annotated with K02999 (DNA-directed RNA polymerase I subunit RPA1)
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.
