Gene loci information

Transcript annotation

  • This transcript has been annotated as Replication factor C subunit 5.

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 g13886 g13886.t5 isoform g13886.t5 33101031 33102053
chr_1 g13886 g13886.t5 exon g13886.t5.exon1 33101031 33102053
chr_1 g13886 g13886.t5 cds g13886.t5.CDS1 33101088 33101864
chr_1 g13886 g13886.t5 TSS g13886.t5 33102208 33102208
chr_1 g13886 g13886.t5 TTS g13886.t5 NA NA

Sequences

>g13886.t5 Gene=g13886 Length=1023
GTTGAAAAATATCGACCTGCAACTTTAGATGATTTGATTTCGCATGAAGACATAATTTCA
ACAATTAAAAAGTTTATTGATCAAGATCAACTTCCACATCTTCTTTTCTATGGTCCAGCT
GGTACGGGTAAGACAAGCACCATATTGGCATGTGCAAAAAAGCTTTATACACCTGCACAA
TTGAGAACAATGGTACTTGAATTAAATGCATCAGATGATCGTGGTATTGGAATTGTTCGC
GAGCAAGTTCTTACTTTTGCCTCTTCTAAAACAATCTTTGGTACCGGATATAAATTAATT
ATACTTGATGAAGCTGATGCTATGACTAATGATGCACAGAATGCACTACGAAGAATTATT
GAAAAATATACAGACAACGTTCGATTCTGCATCATCTGTAATTACTTGAGTAAAATTATT
CCTGCATTACAATCACGTTGCACTCGCTTCAGATTTGCTCCACTATCTCTTAATCAAATT
CTTCCACGATTAGATTATGTTGTTGAGAAAGAAAATGTTAAAATCACAGAAGATGGAAAG
AAAGCGCTTATGGATTTATCAGATGGTGATATGCGAAAAGTATTGAATGTGCTACAAAGT
ACATGGATGGCTTTCAAATTAGTAAATGAAGACAATGTCTATACTTGTGTTGGTCATCCA
TTAAAGAAAGATATTGAAAATATTGTTTATTGGCTATTAAATGATGAAAATGTTAAAGAC
ACTTATAAAAAGATGAATGCTTTGAAAGTCGATAAAGGTCTCGCATTAGAAGACATTTTA
AAACAAGTTCATCTTTATGTTCAACGACTTCAATTGCCACCACGCGTCATTTCTCAATTA
GTTATTAAAATGGCAAATATTGAAGAGCGGCTTGCACATGGAACATCTGAAAATATTCAA
CTTGCTGCTTTTATTGCAGCTTTTAGATTAGCAAGACAACAAGTTACAGTTGATGATGAA
AATTAATGTTTTAATATTGAATTTCTAAGTTTATTTTACAAATAAAAGAATAATTTTTTA
AGT

>g13886.t5 Gene=g13886 Length=258
MVLELNASDDRGIGIVREQVLTFASSKTIFGTGYKLIILDEADAMTNDAQNALRRIIEKY
TDNVRFCIICNYLSKIIPALQSRCTRFRFAPLSLNQILPRLDYVVEKENVKITEDGKKAL
MDLSDGDMRKVLNVLQSTWMAFKLVNEDNVYTCVGHPLKKDIENIVYWLLNDENVKDTYK
KMNALKVDKGLALEDILKQVHLYVQRLQLPPRVISQLVIKMANIEERLAHGTSENIQLAA
FIAAFRLARQQVTVDDEN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g13886.t5 CDD cd00009 AAA 2 91 0
11 g13886.t5 CDD cd18140 HLD_clamp_RFC 92 154 0
7 g13886.t5 Gene3D G3DSA:3.40.50.300 - 1 92 0
9 g13886.t5 Gene3D G3DSA:1.10.8.60 - 95 156 0
8 g13886.t5 Gene3D G3DSA:1.20.272.10 - 157 257 0
3 g13886.t5 PANTHER PTHR11669:SF9 REPLICATION FACTOR C SUBUNIT 5 1 252 0
4 g13886.t5 PANTHER PTHR11669 REPLICATION FACTOR C / DNA POLYMERASE III GAMMA-TAU SUBUNIT 1 252 0
1 g13886.t5 Pfam PF13177 DNA polymerase III, delta subunit 23 92 0
2 g13886.t5 Pfam PF08542 Replication factor C C-terminal domain 158 244 0
6 g13886.t5 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 3 144 0
5 g13886.t5 SUPERFAMILY SSF48019 post-AAA+ oligomerization domain-like 156 248 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:0006260 DNA replication BP

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