General information for g13886.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Replication factor C subunit 5.
Parent gene
- The parent gene g13886 is located on chr_1: 33101088..33102148 (- 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_1 | g13886 | g13886.t1 | isoform | g13886.t1 | 33101088 | 33102148 |
| chr_1 | g13886 | g13886.t1 | exon | g13886.t1.exon1 | 33101088 | 33102054 |
| chr_1 | g13886 | g13886.t1 | cds | g13886.t1.CDS1 | 33101088 | 33102054 |
| chr_1 | g13886 | g13886.t1 | exon | g13886.t1.exon2 | 33102111 | 33102148 |
| chr_1 | g13886 | g13886.t1 | cds | g13886.t1.CDS2 | 33102111 | 33102148 |
| chr_1 | g13886 | g13886.t1 | TSS | g13886.t1 | 33103158 | 33103158 |
| chr_1 | g13886 | g13886.t1 | TTS | g13886.t1 | NA | NA |
Sequences
>g13886.t1 Gene=g13886 Length=1005
ATGGTACAAAATCAAGAGAATATTGCTAATTTGCCATGGGTTGAAAAATATCGACCTGCA
ACTTTAGATGATTTGATTTCGCATGAAGACATAATTTCAACAATTAAAAAGTTTATTGAT
CAAGATCAACTTCCACATCTTCTTTTCTATGGTCCAGCTGGTACGGGTAAGACAAGCACC
ATATTGGCATGTGCAAAAAAGCTTTATACACCTGCACAATTGAGAACAATGGTACTTGAA
TTAAATGCATCAGATGATCGTGGTATTGGAATTGTTCGCGAGCAAGTTCTTACTTTTGCC
TCTTCTAAAACAATCTTTGGTACCGGATATAAATTAATTATACTTGATGAAGCTGATGCT
ATGACTAATGATGCACAGAATGCACTACGAAGAATTATTGAAAAATATACAGACAACGTT
CGATTCTGCATCATCTGTAATTACTTGAGTAAAATTATTCCTGCATTACAATCACGTTGC
ACTCGCTTCAGATTTGCTCCACTATCTCTTAATCAAATTCTTCCACGATTAGATTATGTT
GTTGAGAAAGAAAATGTTAAAATCACAGAAGATGGAAAGAAAGCGCTTATGGATTTATCA
GATGGTGATATGCGAAAAGTATTGAATGTGCTACAAAGTACATGGATGGCTTTCAAATTA
GTAAATGAAGACAATGTCTATACTTGTGTTGGTCATCCATTAAAGAAAGATATTGAAAAT
ATTGTTTATTGGCTATTAAATGATGAAAATGTTAAAGACACTTATAAAAAGATGAATGCT
TTGAAAGTCGATAAAGGTCTCGCATTAGAAGACATTTTAAAACAAGTTCATCTTTATGTT
CAACGACTTCAATTGCCACCACGCGTCATTTCTCAATTAGTTATTAAAATGGCAAATATT
GAAGAGCGGCTTGCACATGGAACATCTGAAAATATTCAACTTGCTGCTTTTATTGCAGCT
TTTAGATTAGCAAGACAACAAGTTACAGTTGATGATGAAAATTAA
>g13886.t1 Gene=g13886 Length=334
MVQNQENIANLPWVEKYRPATLDDLISHEDIISTIKKFIDQDQLPHLLFYGPAGTGKTST
ILACAKKLYTPAQLRTMVLELNASDDRGIGIVREQVLTFASSKTIFGTGYKLIILDEADA
MTNDAQNALRRIIEKYTDNVRFCIICNYLSKIIPALQSRCTRFRFAPLSLNQILPRLDYV
VEKENVKITEDGKKALMDLSDGDMRKVLNVLQSTWMAFKLVNEDNVYTCVGHPLKKDIEN
IVYWLLNDENVKDTYKKMNALKVDKGLALEDILKQVHLYVQRLQLPPRVISQLVIKMANI
EERLAHGTSENIQLAAFIAAFRLARQQVTVDDEN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g13886.t1 | CDD | cd00009 | AAA | 26 | 167 | 0 |
| 12 | g13886.t1 | CDD | cd18140 | HLD_clamp_RFC | 168 | 230 | 0 |
| 8 | g13886.t1 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 168 | 0 |
| 10 | g13886.t1 | Gene3D | G3DSA:1.10.8.60 | - | 171 | 232 | 0 |
| 9 | g13886.t1 | Gene3D | G3DSA:1.20.272.10 | - | 233 | 333 | 0 |
| 3 | g13886.t1 | PANTHER | PTHR11669:SF9 | REPLICATION FACTOR C SUBUNIT 5 | 7 | 328 | 0 |
| 4 | g13886.t1 | PANTHER | PTHR11669 | REPLICATION FACTOR C / DNA POLYMERASE III GAMMA-TAU SUBUNIT | 7 | 328 | 0 |
| 1 | g13886.t1 | Pfam | PF00004 | ATPase family associated with various cellular activities (AAA) | 47 | 166 | 0 |
| 2 | g13886.t1 | Pfam | PF08542 | Replication factor C C-terminal domain | 234 | 320 | 0 |
| 7 | g13886.t1 | SMART | SM00382 | AAA_5 | 43 | 171 | 0 |
| 6 | g13886.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 10 | 230 | 0 |
| 5 | g13886.t1 | SUPERFAMILY | SSF48019 | post-AAA+ oligomerization domain-like | 232 | 324 | 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:0005524 | ATP binding | MF |
| GO:0006260 | DNA replication | BP |
| GO:0016887 | ATP hydrolysis activity | MF |
KEGG
Orthology
- This transcript has been annotated with K10756 (replication factor C subunit 3/5)
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.
