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.t5 TSS g6300.t5 16031901 16031901
chr_2 g6300 g6300.t5 isoform g6300.t5 16031956 16032964
chr_2 g6300 g6300.t5 exon g6300.t5.exon1 16031956 16031997
chr_2 g6300 g6300.t5 exon g6300.t5.exon2 16032105 16032229
chr_2 g6300 g6300.t5 cds g6300.t5.CDS1 16032122 16032229
chr_2 g6300 g6300.t5 exon g6300.t5.exon3 16032290 16032964
chr_2 g6300 g6300.t5 cds g6300.t5.CDS2 16032290 16032964
chr_2 g6300 g6300.t5 TTS g6300.t5 16033185 16033185

Sequences

>g6300.t5 Gene=g6300 Length=842
AGTACGCCTTAATAAAGCGATAAATTTAATTTATTCTATTCTAAAATCAAATATCAAAAA
TGTTTGAAGCACGTTTAGTATCAAGTGGGACACTCAAAAAGGTTCTCGATTCAATCAAAG
ATTTGCTCAATGAAGCCACTTTCGACTGTTCTGACTCTGGAATTCAGCTTCAAGCTATGG
ACAATTCTCATGTTTCTCTTGTTTCACTTAATCTTCGGTCTGATGGTTTCGATAAATACA
GATGTGATAGAAATCTATCAATGGGTATGAATCTTGCAAATATGAGTAAAATTCTCAAAT
GCGCAAACAATAATGATACAGTCACAATTAAAGCTCAAGATAATGCTGATACTGTGACTT
TCATGTTTGAATCACAAAATCAAGAAAAGATTTCTGACTATGAAATGAAATTGATGAACT
TAGATCAAGAACATTTGGGAATTCCTGAAACAGATTACGCTTGCATCGTTCGTATGCCAT
CACAAGAATTTGCACGCATTTGCCGTGATTTGGCTCAATTTGGTGATTCGGTAAATATTC
AGTGTACAAAGGAAGGGGTTCGCTTTTCAGCAACGGGAGATTCAGGTTCTGCCAACATCA
AACTTTCACAGACATCATCAGTGGACAAAGAGGAAGAAGCAGTCAGCATTGAAATGCAAG
AACCAGTGTCATTGACTTTTGCATGTCAGTATTTGAATTCCTTCACAAAAGCAACTCCTC
TATCGACTCAAGTAAGTTTGAGTATGTCTGCAGATGTTCCATTGGTCGTTGAATATACAA
TCCCAGACTTGGGTCATATTCGCTATTACCTTGCTCCAAAGATTGAAGACGACGACAATT
AA

>g6300.t5 Gene=g6300 Length=260
MFEARLVSSGTLKKVLDSIKDLLNEATFDCSDSGIQLQAMDNSHVSLVSLNLRSDGFDKY
RCDRNLSMGMNLANMSKILKCANNNDTVTIKAQDNADTVTFMFESQNQEKISDYEMKLMN
LDQEHLGIPETDYACIVRMPSQEFARICRDLAQFGDSVNIQCTKEGVRFSATGDSGSANI
KLSQTSSVDKEEEAVSIEMQEPVSLTFACQYLNSFTKATPLSTQVSLSMSADVPLVVEYT
IPDLGHIRYYLAPKIEDDDN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g6300.t5 CDD cd00577 PCNA 4 256 3.81067E-106
14 g6300.t5 Gene3D G3DSA:3.70.10.10 - 1 260 2.5E-114
5 g6300.t5 Hamap MF_00317 DNA polymerase sliding clamp [pcn]. 2 255 21.073847
3 g6300.t5 PANTHER PTHR11352 PROLIFERATING CELL NUCLEAR ANTIGEN 1 259 1.8E-124
4 g6300.t5 PANTHER PTHR11352:SF8 PROLIFERATING CELL NUCLEAR ANTIGEN 1 259 1.8E-124
7 g6300.t5 PRINTS PR00339 Proliferating cell nuclear antigen (cyclin) signature 10 29 5.7E-66
6 g6300.t5 PRINTS PR00339 Proliferating cell nuclear antigen (cyclin) signature 34 52 5.7E-66
10 g6300.t5 PRINTS PR00339 Proliferating cell nuclear antigen (cyclin) signature 56 80 5.7E-66
11 g6300.t5 PRINTS PR00339 Proliferating cell nuclear antigen (cyclin) signature 110 132 5.7E-66
9 g6300.t5 PRINTS PR00339 Proliferating cell nuclear antigen (cyclin) signature 203 217 5.7E-66
8 g6300.t5 PRINTS PR00339 Proliferating cell nuclear antigen (cyclin) signature 241 258 5.7E-66
1 g6300.t5 Pfam PF00705 Proliferating cell nuclear antigen, N-terminal domain 1 125 2.4E-58
2 g6300.t5 Pfam PF02747 Proliferating cell nuclear antigen, C-terminal domain 127 254 4.3E-61
16 g6300.t5 ProSitePatterns PS01251 Proliferating cell nuclear antigen signature 1. 34 57 -
17 g6300.t5 ProSitePatterns PS00293 Proliferating cell nuclear antigen signature 2. 61 79 -
12 g6300.t5 SUPERFAMILY SSF55979 DNA clamp 1 126 8.28E-46
13 g6300.t5 SUPERFAMILY SSF55979 DNA clamp 127 255 2.04E-46
18 g6300.t5 TIGRFAM TIGR00590 pcna: proliferating cell nuclear antigen (pcna) 1 259 1.4E-130

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

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