Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative DNA-directed RNA polymerase II subunit Rpb4.

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_1 g11691 g11691.t3 TSS g11691.t3 17820827 17820827
chr_1 g11691 g11691.t3 isoform g11691.t3 17820920 17821404
chr_1 g11691 g11691.t3 exon g11691.t3.exon1 17820920 17820953
chr_1 g11691 g11691.t3 exon g11691.t3.exon2 17821039 17821404
chr_1 g11691 g11691.t3 cds g11691.t3.CDS1 17821090 17821404
chr_1 g11691 g11691.t3 TTS g11691.t3 17821479 17821479

Sequences

>g11691.t3 Gene=g11691 Length=400
ATGACAAGCATCAATCCCGTTGAAACTGTTGAAGCTCATTTAAGAATTTGAAAATGCTGA
AACTTTATTAATAAGTGAAGTTCATATGCTTTTGGAACATCGTAAACGACAAAATGAATC
GAGTGAAGAAGAGCAAGAATTCAGTGAAGTTTTTTTGAAGACTTACAATTATACGGAAAA
CTTTCGAAAGTTCAAGAATAAAGAAACAATTACAGCTATTCGTGCGCTTCTGTCCTCAAA
AAAACTTCATAAATTTGAACTAGCTGCACTTGGAAATTTATGTCCAGAAGCTCCTGAAGA
AGCAACATCGCTCATTCCATCTCTTGAGGGTAGATTTGAAGATGAAACGTTAAGACAAAT
TCTTGAAGATATTGGAACAAAAAGAAGTCTTCAATATTAA

>g11691.t3 Gene=g11691 Length=104
MLLEHRKRQNESSEEEQEFSEVFLKTYNYTENFRKFKNKETITAIRALLSSKKLHKFELA
ALGNLCPEAPEEATSLIPSLEGRFEDETLRQILEDIGTKRSLQY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g11691.t3 Gene3D G3DSA:1.20.1250.40 - 1 104 0
2 g11691.t3 PANTHER PTHR21297:SF0 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 1 103 0
3 g11691.t3 PANTHER PTHR21297 DNA-DIRECTED RNA POLYMERASE II 1 103 0
1 g11691.t3 Pfam PF03874 RNA polymerase Rpb4 6 96 0
5 g11691.t3 SMART SM00657 rpol4neu2 1 103 0
4 g11691.t3 SUPERFAMILY SSF47819 HRDC-like 2 101 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:0000166 nucleotide binding MF
GO:0044237 cellular metabolic process BP
GO:0030880 RNA polymerase complex CC
GO:0006352 DNA-templated transcription, initiation 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. There were no conditions that were differentially expressed