General information for g6300.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Proliferating cell nuclear antigen.
Parent gene
- The parent gene g6300 is located on chr_2: 16032330..16037313 (+ strand)
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.t1 | TSS | g6300.t1 | 16031901 | 16031901 |
| chr_2 | g6300 | g6300.t1 | isoform | g6300.t1 | 16032122 | 16032964 |
| chr_2 | g6300 | g6300.t1 | exon | g6300.t1.exon1 | 16032122 | 16032229 |
| chr_2 | g6300 | g6300.t1 | cds | g6300.t1.CDS1 | 16032122 | 16032229 |
| chr_2 | g6300 | g6300.t1 | exon | g6300.t1.exon2 | 16032290 | 16032964 |
| chr_2 | g6300 | g6300.t1 | cds | g6300.t1.CDS2 | 16032290 | 16032964 |
| chr_2 | g6300 | g6300.t1 | TTS | g6300.t1 | 16033185 | 16033185 |
Sequences
>g6300.t1 Gene=g6300 Length=783
ATGTTTGAAGCACGTTTAGTATCAAGTGGGACACTCAAAAAGGTTCTCGATTCAATCAAA
GATTTGCTCAATGAAGCCACTTTCGACTGTTCTGACTCTGGAATTCAGCTTCAAGCTATG
GACAATTCTCATGTTTCTCTTGTTTCACTTAATCTTCGGTCTGATGGTTTCGATAAATAC
AGATGTGATAGAAATCTATCAATGGGTATGAATCTTGCAAATATGAGTAAAATTCTCAAA
TGCGCAAACAATAATGATACAGTCACAATTAAAGCTCAAGATAATGCTGATACTGTGACT
TTCATGTTTGAATCACAAAATCAAGAAAAGATTTCTGACTATGAAATGAAATTGATGAAC
TTAGATCAAGAACATTTGGGAATTCCTGAAACAGATTACGCTTGCATCGTTCGTATGCCA
TCACAAGAATTTGCACGCATTTGCCGTGATTTGGCTCAATTTGGTGATTCGGTAAATATT
CAGTGTACAAAGGAAGGGGTTCGCTTTTCAGCAACGGGAGATTCAGGTTCTGCCAACATC
AAACTTTCACAGACATCATCAGTGGACAAAGAGGAAGAAGCAGTCAGCATTGAAATGCAA
GAACCAGTGTCATTGACTTTTGCATGTCAGTATTTGAATTCCTTCACAAAAGCAACTCCT
CTATCGACTCAAGTAAGTTTGAGTATGTCTGCAGATGTTCCATTGGTCGTTGAATATACA
ATCCCAGACTTGGGTCATATTCGCTATTACCTTGCTCCAAAGATTGAAGACGACGACAAT
TAA
>g6300.t1 Gene=g6300 Length=260
MFEARLVSSGTLKKVLDSIKDLLNEATFDCSDSGIQLQAMDNSHVSLVSLNLRSDGFDKY
RCDRNLSMGMNLANMSKILKCANNNDTVTIKAQDNADTVTFMFESQNQEKISDYEMKLMN
LDQEHLGIPETDYACIVRMPSQEFARICRDLAQFGDSVNIQCTKEGVRFSATGDSGSANI
KLSQTSSVDKEEEAVSIEMQEPVSLTFACQYLNSFTKATPLSTQVSLSMSADVPLVVEYT
IPDLGHIRYYLAPKIEDDDN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g6300.t1 | CDD | cd00577 | PCNA | 4 | 256 | 3.81067E-106 |
| 14 | g6300.t1 | Gene3D | G3DSA:3.70.10.10 | - | 1 | 260 | 2.5E-114 |
| 5 | g6300.t1 | Hamap | MF_00317 | DNA polymerase sliding clamp [pcn]. | 2 | 255 | 21.073847 |
| 3 | g6300.t1 | PANTHER | PTHR11352 | PROLIFERATING CELL NUCLEAR ANTIGEN | 1 | 259 | 1.8E-124 |
| 4 | g6300.t1 | PANTHER | PTHR11352:SF8 | PROLIFERATING CELL NUCLEAR ANTIGEN | 1 | 259 | 1.8E-124 |
| 7 | g6300.t1 | PRINTS | PR00339 | Proliferating cell nuclear antigen (cyclin) signature | 10 | 29 | 5.7E-66 |
| 6 | g6300.t1 | PRINTS | PR00339 | Proliferating cell nuclear antigen (cyclin) signature | 34 | 52 | 5.7E-66 |
| 10 | g6300.t1 | PRINTS | PR00339 | Proliferating cell nuclear antigen (cyclin) signature | 56 | 80 | 5.7E-66 |
| 11 | g6300.t1 | PRINTS | PR00339 | Proliferating cell nuclear antigen (cyclin) signature | 110 | 132 | 5.7E-66 |
| 9 | g6300.t1 | PRINTS | PR00339 | Proliferating cell nuclear antigen (cyclin) signature | 203 | 217 | 5.7E-66 |
| 8 | g6300.t1 | PRINTS | PR00339 | Proliferating cell nuclear antigen (cyclin) signature | 241 | 258 | 5.7E-66 |
| 1 | g6300.t1 | Pfam | PF00705 | Proliferating cell nuclear antigen, N-terminal domain | 1 | 125 | 2.4E-58 |
| 2 | g6300.t1 | Pfam | PF02747 | Proliferating cell nuclear antigen, C-terminal domain | 127 | 254 | 4.3E-61 |
| 16 | g6300.t1 | ProSitePatterns | PS01251 | Proliferating cell nuclear antigen signature 1. | 34 | 57 | - |
| 17 | g6300.t1 | ProSitePatterns | PS00293 | Proliferating cell nuclear antigen signature 2. | 61 | 79 | - |
| 12 | g6300.t1 | SUPERFAMILY | SSF55979 | DNA clamp | 1 | 126 | 8.28E-46 |
| 13 | g6300.t1 | SUPERFAMILY | SSF55979 | DNA clamp | 127 | 255 | 2.04E-46 |
| 18 | g6300.t1 | 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
- This transcript has been annotated with K04802 (proliferating cell nuclear antigen)
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.
