Gene loci information

Transcript annotation

  • This transcript has been annotated as DNA-directed RNA polymerase II subunit RPB9.

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_2 g4702 g4702.t2 isoform g4702.t2 4278157 4278894
chr_2 g4702 g4702.t2 exon g4702.t2.exon1 4278157 4278394
chr_2 g4702 g4702.t2 TSS g4702.t2 4278237 4278237
chr_2 g4702 g4702.t2 exon g4702.t2.exon2 4278454 4278650
chr_2 g4702 g4702.t2 cds g4702.t2.CDS1 4278463 4278650
chr_2 g4702 g4702.t2 exon g4702.t2.exon3 4278705 4278894
chr_2 g4702 g4702.t2 cds g4702.t2.CDS2 4278705 4278894
chr_2 g4702 g4702.t2 TTS g4702.t2 4278980 4278980

Sequences

>g4702.t2 Gene=g4702 Length=625
GAGTAGAAATTTTTATATGTAACGGTCACAAAAAATTTAAAAGTCGAAGGGATATTTTTA
ACGCTACGCCTTTGCAACATAAAAATTAGTAAACAAAACTTAAATAGAAATTTTTATAAT
TTTTCTCAAATTCAGAGGAAAATACTTTATTTAGTGAAATAAAAATCATTAAAAAAGAAG
GTAAATTAAAATCGTATAAGAATAAGTTAAAGTTTGCAGTATAATCAATTAAATAAAGAA
TTAAAAGATGGAACGAGTCTATGAAAATGAATTAGGATTTGTTGGTATTCGTTTCTGTCA
AGAATGCAATAACATGTTATATCCGAAAGAAGACAAAGACAACAAAATTCTCTTGTATGC
ATGCAGAAATTGTGACTACAAAACAGAAGCTGACAGCTATTGCATTTATGTAAATAAAAT
TATGCACGAAATTGACGAATTGACTCATATTGTCCCTGATGTAATTTCTGATCCAACATT
GCCACGGACTGAAGAACATCCTTGTCCAAAATGCGGTCATCGTGAAGCTGTGTTCTTTCA
AGCTCAAACTCGTCGCGCTGAAGAAGAAATGAGACTTTATTATGTCTGTACAAATCAAAA
TTGCTCTCACAGATGGACCGAATAA

>g4702.t2 Gene=g4702 Length=125
MERVYENELGFVGIRFCQECNNMLYPKEDKDNKILLYACRNCDYKTEADSYCIYVNKIMH
EIDELTHIVPDVISDPTLPRTEEHPCPKCGHREAVFFQAQTRRAEEEMRLYYVCTNQNCS
HRWTE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g4702.t2 CDD cd10508 Zn-ribbon_RPB9 74 124 4.99771E-29
7 g4702.t2 Gene3D G3DSA:2.20.25.10 - 1 56 7.9E-27
8 g4702.t2 Gene3D G3DSA:2.20.25.10 - 57 125 2.1E-33
3 g4702.t2 PANTHER PTHR11239 DNA-DIRECTED RNA POLYMERASE 13 124 1.3E-51
4 g4702.t2 PANTHER PTHR11239:SF1 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 13 124 1.3E-51
9 g4702.t2 PIRSF PIRSF005586 RNApol_RpoM 14 125 3.3E-25
1 g4702.t2 Pfam PF02150 RNA polymerases M/15 Kd subunit 14 50 2.8E-16
2 g4702.t2 Pfam PF01096 Transcription factor S-II (TFIIS) 84 124 1.9E-17
12 g4702.t2 ProSitePatterns PS01030 RNA polymerases M / 15 Kd subunits signature. 16 42 -
11 g4702.t2 ProSitePatterns PS00466 Zinc finger TFIIS-type signature. 86 123 -
15 g4702.t2 ProSiteProfiles PS51133 Zinc finger TFIIS-type profile. 82 124 15.23
14 g4702.t2 SMART SM00661 rpol9cneu 15 68 1.4E-20
13 g4702.t2 SMART SM00440 Cys4_2 84 125 4.6E-21
6 g4702.t2 SUPERFAMILY SSF57783 Zinc beta-ribbon 12 58 4.08E-18
5 g4702.t2 SUPERFAMILY SSF57783 Zinc beta-ribbon 60 125 9.07E-23

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:0008270 zinc ion binding MF
GO:0006379 mRNA cleavage BP
GO:0006351 transcription, DNA-templated BP
GO:0003676 nucleic acid binding MF

KEGG

Orthology

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.

Raw TPM values