Gene loci information

Transcript annotation

  • This transcript has been annotated as Polycomb group RING finger protein 3.

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 g10273 g10273.t1 TTS g10273.t1 8604051 8604051
chr_1 g10273 g10273.t1 isoform g10273.t1 8604274 8605346
chr_1 g10273 g10273.t1 exon g10273.t1.exon1 8604274 8604399
chr_1 g10273 g10273.t1 cds g10273.t1.CDS1 8604274 8604399
chr_1 g10273 g10273.t1 exon g10273.t1.exon2 8604469 8604764
chr_1 g10273 g10273.t1 cds g10273.t1.CDS2 8604469 8604764
chr_1 g10273 g10273.t1 exon g10273.t1.exon3 8604820 8604978
chr_1 g10273 g10273.t1 cds g10273.t1.CDS3 8604820 8604978
chr_1 g10273 g10273.t1 exon g10273.t1.exon4 8605241 8605346
chr_1 g10273 g10273.t1 cds g10273.t1.CDS4 8605241 8605346
chr_1 g10273 g10273.t1 TSS g10273.t1 8605421 8605421

Sequences

>g10273.t1 Gene=g10273 Length=687
ATGGAGAAAAAGATCAAATTAAAGACATTAAATCCATTCATAAGTTGTAAAATATGCAGA
GGATATTTAATTGATGCAACAACCATAGTAGAATGCTTGCATACGTTTTGTAAAAGTTGT
TTAGTGAAACATTTGGAAGAATCACCAAACAATGCATGTCCTGATTGCAATTTAGTAATT
CATCAAAGTCACCCTCTTCAGTATATAAGTCATGATCGCACAATGCAAGATATCGTTTAT
AAACTCGTGCCCAATTTACAAGATAATGAAATAAATCGAGAGCGAGCATTTTATAAAGCA
AGAAATCTTCCATGTCCAAAAGACATACCACAAGACAACAAAGACAATGATGATATTGAA
TCAAAATTGAATGAAGCACACCAAGAATCAGATTACCATCGAATGGACGAACAAGTTAAC
TTATGTCTAGAATGCAGCTCAAGTAGTAACTTAAAGAATTTAAAGAGACGTTTTATTCGA
TGCAGTTCACAAGCTACAATCACACAATTGAAAAAATTTGTCGCTAAGAAAGTATTAAAT
GGAATAGAAAAATATAGAGAGATTGATATTTTATGTAATGATGAATTGCTAGGCAAGGAT
CATACACTTAAATTTGTGTACGTTACTCGTTGGAGATTCAAAGACCCACCACTTAGACTT
CAATATAGAACGACAATTTTCGACTAG

>g10273.t1 Gene=g10273 Length=228
MEKKIKLKTLNPFISCKICRGYLIDATTIVECLHTFCKSCLVKHLEESPNNACPDCNLVI
HQSHPLQYISHDRTMQDIVYKLVPNLQDNEINRERAFYKARNLPCPKDIPQDNKDNDDIE
SKLNEAHQESDYHRMDEQVNLCLECSSSSNLKNLKRRFIRCSSQATITQLKKFVAKKVLN
GIEKYREIDILCNDELLGKDHTLKFVYVTRWRFKDPPLRLQYRTTIFD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g10273.t1 CDD cd16735 RING-HC_PCGF3 13 61 7.46183E-22
9 g10273.t1 CDD cd17083 RAWUL_PCGF3 138 223 2.71977E-49
7 g10273.t1 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 1 105 5.1E-25
6 g10273.t1 Gene3D G3DSA:3.10.20.90 - 119 225 1.9E-38
3 g10273.t1 PANTHER PTHR45893:SF3 POLYCOMB GROUP RING FINGER PROTEIN 3 1 225 2.0E-99
4 g10273.t1 PANTHER PTHR45893 POLYCOMB GROUP RING FINGER PROTEIN 1 225 2.0E-99
1 g10273.t1 Pfam PF00097 Zinc finger, C3HC4 type (RING finger) 16 56 3.6E-9
2 g10273.t1 Pfam PF16207 RAWUL domain RING finger- and WD40-associated ubiquitin-like 157 223 5.2E-12
10 g10273.t1 ProSitePatterns PS00518 Zinc finger RING-type signature. 32 41 -
12 g10273.t1 ProSiteProfiles PS50089 Zinc finger RING-type profile. 16 57 11.545
11 g10273.t1 SMART SM00184 ring_2 16 56 2.7E-4
5 g10273.t1 SUPERFAMILY SSF57850 RING/U-box 9 66 4.71E-11

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:0046872 metal ion 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