Gene loci information

Transcript annotation

  • This transcript has been annotated as Proliferating cell nuclear antigen.

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 g6300 g6300.t3 isoform g6300.t3 16031859 16032964
chr_2 g6300 g6300.t3 exon g6300.t3.exon1 16031859 16031997
chr_2 g6300 g6300.t3 TSS g6300.t3 16031901 16031901
chr_2 g6300 g6300.t3 exon g6300.t3.exon2 16032096 16032229
chr_2 g6300 g6300.t3 cds g6300.t3.CDS1 16032122 16032229
chr_2 g6300 g6300.t3 exon g6300.t3.exon3 16032290 16032721
chr_2 g6300 g6300.t3 cds g6300.t3.CDS2 16032290 16032721
chr_2 g6300 g6300.t3 exon g6300.t3.exon4 16032812 16032964
chr_2 g6300 g6300.t3 cds g6300.t3.CDS3 16032812 16032964
chr_2 g6300 g6300.t3 TTS g6300.t3 16033185 16033185

Sequences

>g6300.t3 Gene=g6300 Length=858
GTAACTTTACTGTAACTGTCATTTGTAAGTTGCGCGCCAAAAATTGTGTGAATTGCCCGC
TCTTTTCATTAAAATAAAGAAAATTGATTCTGCCAAAAGTACGCCTTAATAAAGCGATAA
ATTTAATTTATTCTATTCTAAAAACACAAAAATCAAATATCAAAAATGTTTGAAGCACGT
TTAGTATCAAGTGGGACACTCAAAAAGGTTCTCGATTCAATCAAAGATTTGCTCAATGAA
GCCACTTTCGACTGTTCTGACTCTGGAATTCAGCTTCAAGCTATGGACAATTCTCATGTT
TCTCTTGTTTCACTTAATCTTCGGTCTGATGGTTTCGATAAATACAGATGTGATAGAAAT
CTATCAATGGGTATGAATCTTGCAAATATGAGTAAAATTCTCAAATGCGCAAACAATAAT
GATACAGTCACAATTAAAGCTCAAGATAATGCTGATACTGTGACTTTCATGTTTGAATCA
CAAAATCAAGAAAAGATTTCTGACTATGAAATGAAATTGATGAACTTAGATCAAGAACAT
TTGGGAATTCCTGAAACAGATTACGCTTGCATCGTTCGTATGCCATCACAAGAATTTGCA
CGCATTTGCCGTGATTTGGCTCAATTTGGTGATTCGGTAAATATTCAGTGTACAAAGGAA
GGGGTTCGCTTTTCAGCAACGGGAGATTCAGGTTCTGCCAACATCTATTTGAATTCCTTC
ACAAAAGCAACTCCTCTATCGACTCAAGTAAGTTTGAGTATGTCTGCAGATGTTCCATTG
GTCGTTGAATATACAATCCCAGACTTGGGTCATATTCGCTATTACCTTGCTCCAAAGATT
GAAGACGACGACAATTAA

>g6300.t3 Gene=g6300 Length=230
MFEARLVSSGTLKKVLDSIKDLLNEATFDCSDSGIQLQAMDNSHVSLVSLNLRSDGFDKY
RCDRNLSMGMNLANMSKILKCANNNDTVTIKAQDNADTVTFMFESQNQEKISDYEMKLMN
LDQEHLGIPETDYACIVRMPSQEFARICRDLAQFGDSVNIQCTKEGVRFSATGDSGSANI
YLNSFTKATPLSTQVSLSMSADVPLVVEYTIPDLGHIRYYLAPKIEDDDN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g6300.t3 CDD cd00577 PCNA 4 226 1.46085E-94
14 g6300.t3 Gene3D G3DSA:3.10.150.10 DNA Polymerase III 1 163 3.2E-76
15 g6300.t3 Gene3D G3DSA:3.10.150.10 DNA Polymerase III 178 229 4.8E-18
7 g6300.t3 Hamap MF_00317 DNA polymerase sliding clamp [pcn]. 2 225 17.018181
3 g6300.t3 PANTHER PTHR11352 PROLIFERATING CELL NUCLEAR ANTIGEN 1 180 5.8E-105
5 g6300.t3 PANTHER PTHR11352:SF8 PROLIFERATING CELL NUCLEAR ANTIGEN 1 180 5.8E-105
4 g6300.t3 PANTHER PTHR11352 PROLIFERATING CELL NUCLEAR ANTIGEN 181 229 5.8E-105
6 g6300.t3 PANTHER PTHR11352:SF8 PROLIFERATING CELL NUCLEAR ANTIGEN 181 229 5.8E-105
9 g6300.t3 PRINTS PR00339 Proliferating cell nuclear antigen (cyclin) signature 10 29 2.6E-46
8 g6300.t3 PRINTS PR00339 Proliferating cell nuclear antigen (cyclin) signature 34 52 2.6E-46
10 g6300.t3 PRINTS PR00339 Proliferating cell nuclear antigen (cyclin) signature 56 80 2.6E-46
11 g6300.t3 PRINTS PR00339 Proliferating cell nuclear antigen (cyclin) signature 110 132 2.6E-46
1 g6300.t3 Pfam PF00705 Proliferating cell nuclear antigen, N-terminal domain 1 125 1.8E-58
2 g6300.t3 Pfam PF02747 Proliferating cell nuclear antigen, C-terminal domain 127 182 4.3E-24
17 g6300.t3 ProSitePatterns PS01251 Proliferating cell nuclear antigen signature 1. 34 57 -
18 g6300.t3 ProSitePatterns PS00293 Proliferating cell nuclear antigen signature 2. 61 79 -
12 g6300.t3 SUPERFAMILY SSF55979 DNA clamp 1 126 6.0E-46
13 g6300.t3 SUPERFAMILY SSF55979 DNA clamp 127 229 3.66E-33
19 g6300.t3 TIGRFAM TIGR00590 pcna: proliferating cell nuclear antigen (pcna) 1 180 2.4E-91

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:0003677 DNA binding MF
GO:0006275 regulation of DNA replication BP
GO:0030337 DNA polymerase processivity factor activity MF

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