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.t7 TSS g6300.t7 16031901 16031901
chr_2 g6300 g6300.t7 isoform g6300.t7 16032330 16033175
chr_2 g6300 g6300.t7 exon g6300.t7.exon1 16032330 16033175
chr_2 g6300 g6300.t7 cds g6300.t7.CDS1 16032383 16032964
chr_2 g6300 g6300.t7 TTS g6300.t7 16033185 16033185

Sequences

>g6300.t7 Gene=g6300 Length=846
TTAATCTTCGGTCTGATGGTTTCGATAAATACAGATGTGATAGAAATCTATCAATGGGTA
TGAATCTTGCAAATATGAGTAAAATTCTCAAATGCGCAAACAATAATGATACAGTCACAA
TTAAAGCTCAAGATAATGCTGATACTGTGACTTTCATGTTTGAATCACAAAATCAAGAAA
AGATTTCTGACTATGAAATGAAATTGATGAACTTAGATCAAGAACATTTGGGAATTCCTG
AAACAGATTACGCTTGCATCGTTCGTATGCCATCACAAGAATTTGCACGCATTTGCCGTG
ATTTGGCTCAATTTGGTGATTCGGTAAATATTCAGTGTACAAAGGAAGGGGTTCGCTTTT
CAGCAACGGGAGATTCAGGTTCTGCCAACATCAAACTTTCACAGACATCATCAGTGGACA
AAGAGGAAGAAGCAGTCAGCATTGAAATGCAAGAACCAGTGTCATTGACTTTTGCATGTC
AGTATTTGAATTCCTTCACAAAAGCAACTCCTCTATCGACTCAAGTAAGTTTGAGTATGT
CTGCAGATGTTCCATTGGTCGTTGAATATACAATCCCAGACTTGGGTCATATTCGCTATT
ACCTTGCTCCAAAGATTGAAGACGACGACAATTAATCGGATTTTACGCCTTCAAACATTC
ATACAATTATGATAATTTTATTCGGCCCAGGTTTTAATTATAAAGTTGGCCATACTTTAT
TCTCTCACAATCCCCTCTTTTTTTTACAAAACACCTTTCACTCATTATCCTCTTTCTTAT
GCCCTTTTTCTTATTGTATACTCAATTATGATTTCTTTTTTGATCAAAATAAAGTTTCAA
TAGGAA

>g6300.t7 Gene=g6300 Length=193
MGMNLANMSKILKCANNNDTVTIKAQDNADTVTFMFESQNQEKISDYEMKLMNLDQEHLG
IPETDYACIVRMPSQEFARICRDLAQFGDSVNIQCTKEGVRFSATGDSGSANIKLSQTSS
VDKEEEAVSIEMQEPVSLTFACQYLNSFTKATPLSTQVSLSMSADVPLVVEYTIPDLGHI
RYYLAPKIEDDDN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g6300.t7 CDD cd00577 PCNA 1 189 0
10 g6300.t7 Gene3D G3DSA:3.70.10.10 - 1 193 0
3 g6300.t7 PANTHER PTHR11352 PROLIFERATING CELL NUCLEAR ANTIGEN 1 192 0
4 g6300.t7 PANTHER PTHR11352:SF5 PROLIFERATING CELL NUCLEAR ANTIGEN 1 192 0
6 g6300.t7 PRINTS PR00339 Proliferating cell nuclear antigen (cyclin) signature 43 65 0
5 g6300.t7 PRINTS PR00339 Proliferating cell nuclear antigen (cyclin) signature 136 150 0
7 g6300.t7 PRINTS PR00339 Proliferating cell nuclear antigen (cyclin) signature 174 191 0
1 g6300.t7 Pfam PF00705 Proliferating cell nuclear antigen, N-terminal domain 1 58 0
2 g6300.t7 Pfam PF02747 Proliferating cell nuclear antigen, C-terminal domain 60 187 0
9 g6300.t7 SUPERFAMILY SSF55979 DNA clamp 1 59 0
8 g6300.t7 SUPERFAMILY SSF55979 DNA clamp 60 188 0
11 g6300.t7 TIGRFAM TIGR00590 pcna: proliferating cell nuclear antigen (pcna) 1 192 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: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.

Raw TPM values