Gene loci information

Transcript annotation

  • This transcript has been annotated as DNA-directed RNA polymerase I subunit RPA2.

Parent gene

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.t3 isoform g475.t3 3567391 3570188
chr_3 g475 g475.t3 exon g475.t3.exon1 3567391 3568832
chr_3 g475 g475.t3 cds g475.t3.CDS1 3567393 3568829
chr_3 g475 g475.t3 exon g475.t3.exon2 3568919 3569255
chr_3 g475 g475.t3 exon g475.t3.exon3 3569315 3569644
chr_3 g475 g475.t3 exon g475.t3.exon4 3569694 3570188
chr_3 g475 g475.t3 TSS g475.t3 NA NA
chr_3 g475 g475.t3 TTS g475.t3 NA NA

Sequences

>g475.t3 Gene=g475 Length=2604
TTGCGTACTAAATTTATGCGTCAGAATTACTATAAAGTTACTAAAAGACTGCGAAAATAA
GAGAAATTTTCTTTGCAAACCTTTGCAAAGATGATTTTCCAAAATTGTTGTTGTTGATTT
TTTGGTAGCTATTTTGAATAATAAATACCGTTACATAGAAAAGTAAATAATAACAGTTTT
TAGGATTATTAAAGATTGTCATCTTAAATTTTGGTAATATTATTGCAAGTTTTGATAATT
ATTATGTCATGAAATATATCCATTTATCATCTTCTTATTATTAAAAAGAGAATTTGAAAA
TCATAATAAACCATAACGGTTAGAGAATATTTTTAAAAATTTTAAGTTTGAACTCCACAA
CCTCAAATTTTTAAATGCTAAACACATTTATTTATGTTTTTGAAGAAATATAATAATTCT
ATTAAAATGATTGAAAAACCAATTTTAACGAATACACATCCAATATTCTACGAAATAAAG
AAGGATAGAAACAAGATTTTAGAAAGTCTCGGTGCTCCTCATGTTTCTTCATTTAATCAT
TTTCTTACTGATGGAATGCGATTGATTCTAGATAATCTTGAACCTTATGAATTTGAATTA
AATAATGGCGATAGATTGAAAGTCAAAGTTGAAAATTGTGAAATTTTACGACCAAGATTA
ACTTCACAACCTGAAGCAAAAATCCAAAAAGTTTTTCCTTCAGAAGCTCGACAAAGAGCA
ATTACTTATACTGGTAATTGCATGATGACATTAGCCTGGAGTAAAAATGGACACAAAAAT
GCATCTATCGATTTTGATTTAGGACCTTTACCAATTATGATTCGATCAAAAGCATGCAAT
CTCAACGGAATGAAACCGAAAGAACTGGTTGACAAGCATGAACATGAACACGAATGGGGT
GGATATTTTGTAGTCAAAGGAAATGAGAAACTCATTCGTATGCTATTAATGACAAGAAGA
AACTATCCTATAATGCTAAAAAGAAACACTTGGAAAGATCGTGCAAAATATTTTACTCCA
TATGGTGTGATAATAAGATCTGTTGCAATTGACCATACATCAACAAACAATGTGCTTCAT
TATTTAAAAAATGGAACTGCAAAATTGATGATAAGTCATAGAAAAATCCTCTCATATCTT
CCTGTCATTTTGGTGCTTAAATGAAATGCTTCTTGAATTACACCAACAAAACATTCACTC
ACATTTTGATGCAAAAAATTATCTTGGTCAAATATTTAGAACGCGTTTTGATAATTTGCC
TGCTTGGTCACCGAATGAGACTGTTGCAGATTATTTATTGAAAAATAATATATTAATTCA
TTTGAATGAATATATTGATAAATACAATTTACTTGTATTTATGACTAAGAAATTATTTCA
AGCAGTACAAGGCAAATCAAAAATTGAGTCAGTGGATTCTGTGATGATGCAAGAACTTCT
TACAGGAGGACATTTGTATCAGAAAATTTTCAAAGAATTTCTCGAGTCATGGATGAATAA
TTTACGATTAAATTTAAACAAGAAGCTATCTAAAGATACAAGCATGAATATTACAGCACC
CGACATTTCTAATGCAGGAAAATTTTGTGGTAGTTTAATAAGACATTTTGAATATTTTCT
CGCAACTGGAAATTTAATTAGCAGATCAGGTCTTGGATTAATGCAATCATCTGGTCTTGT
TATAATGGCAGAAAACATTAACCGAATGCGCTATATGAGCCATTTTCGTGCTGTTCATCG
TGGTTCATATTTTGTCACCATGCGTACAACAGAGGCTCGTCAGTTATTGCCTGATTCTTG
GGGATTTATTTGTCCTGTCCATACGCCTGATGGTAGCCCATGCGGTTTACTAAATCACTT
GACTGTTGATTGCGAAACTTCACCAGATATTCTTCATAAAATTGATATGGATAATTTAAT
ACGACTCTTTGTTGAACTTGGAATGGAAATTGTTGACTCAAATGTGATTTTTGAATATGA
AAACTACTATACAGTGATAATTGAAGGAAAAATCATTGGTTATATTCACGATAGTCGAAT
AAAAAGTTTGGAATTTAATTTGCGTGCTTACAAAATTGAAGGAGAACGGCTTCCACGTGA
AACTGAAATTGTAGTTGTGCCAAAAAAGAATGCTGGACAATATCCTGGATTATTCATATT
TTTCGGAGCAGCAAGAATGATGAGACCTGTTTTAAATTTGGCTTTCAATAAGATTGAATT
GATTGGAACGTTTGAACAAGTATTTCTAGAAGTGGCTATTTCAAAAGAAGAAATTTGCGA
GGGAGTCACTACACATCTTGAATTTTCGAAACTTTCGTTTCTTTCCAACTTAGCAAATTT
GATTCCCATGCCTGATCATAATCAAGCACCTCGTAACATGTATCAGTGTCAAATGGGAAA
GCAAACAATGGGAACACCTTGTCTTAATTGGCCTTCACAAGCAGCAAACAAATTATATCG
ACTTTATACACCTGCAACGCCACTCTTTCGACCCGTACATCATGACAAAATTGAACTAGA
TAATTTTGCAATGGGAACGAATGCAATTATTGCTGTTATTGGCTATACTGGATATGATAT
GGAAGATGCAATGATTCTTAACAA

>g475.t3 Gene=g475 Length=479
MLLELHQQNIHSHFDAKNYLGQIFRTRFDNLPAWSPNETVADYLLKNNILIHLNEYIDKY
NLLVFMTKKLFQAVQGKSKIESVDSVMMQELLTGGHLYQKIFKEFLESWMNNLRLNLNKK
LSKDTSMNITAPDISNAGKFCGSLIRHFEYFLATGNLISRSGLGLMQSSGLVIMAENINR
MRYMSHFRAVHRGSYFVTMRTTEARQLLPDSWGFICPVHTPDGSPCGLLNHLTVDCETSP
DILHKIDMDNLIRLFVELGMEIVDSNVIFEYENYYTVIIEGKIIGYIHDSRIKSLEFNLR
AYKIEGERLPRETEIVVVPKKNAGQYPGLFIFFGAARMMRPVLNLAFNKIELIGTFEQVF
LEVAISKEEICEGVTTHLEFSKLSFLSNLANLIPMPDHNQAPRNMYQCQMGKQTMGTPCL
NWPSQAANKLYRLYTPATPLFRPVHHDKIELDNFAMGTNAIIAVIGYTGYDMEDAMILN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g475.t3 Gene3D G3DSA:3.90.1110.10 - 1 82 0.0e+00
9 g475.t3 Gene3D G3DSA:3.90.1070.20 - 244 334 0.0e+00
10 g475.t3 Gene3D G3DSA:2.40.270.10 - 389 479 0.0e+00
5 g475.t3 PANTHER PTHR20856 DNA-DIRECTED RNA POLYMERASE I SUBUNIT 2 7 479 0.0e+00
6 g475.t3 PANTHER PTHR20856:SF5 DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA2 7 479 0.0e+00
2 g475.t3 Pfam PF04561 RNA polymerase Rpb2, domain 2 6 91 4.4e-06
4 g475.t3 Pfam PF04565 RNA polymerase Rpb2, domain 3 174 237 0.0e+00
1 g475.t3 Pfam PF06883 RNA polymerase I, Rpa2 specific domain 284 340 0.0e+00
3 g475.t3 Pfam PF00562 RNA polymerase Rpb2, domain 6 389 479 0.0e+00
7 g475.t3 SUPERFAMILY SSF64484 beta and beta-prime subunits of DNA dependent RNA-polymerase 5 479 0.0e+00

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 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.

Raw TPM values