General information for g11810.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Replication factor C subunit 4.
Parent gene
- The parent gene g11810 is located on chr_1: 18527567..18528478 (+ 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 | g11810 | g11810.t4 | TSS | g11810.t4 | 18526227 | 18526227 |
| chr_1 | g11810 | g11810.t4 | isoform | g11810.t4 | 18526811 | 18527623 |
| chr_1 | g11810 | g11810.t4 | exon | g11810.t4.exon1 | 18526811 | 18527623 |
| chr_1 | g11810 | g11810.t4 | cds | g11810.t4.CDS1 | 18526920 | 18527567 |
| chr_1 | g11810 | g11810.t4 | TTS | g11810.t4 | 18527649 | 18527649 |
Sequences
>g11810.t4 Gene=g11810 Length=813
TATAAGAACAAAAGTTAAAAATTTTGCACAACTTAAAGCGAGTAATATCCGACCAGATGG
AAAACCATGTCCACCTTTCAAGATAATCATTCTTGATGAAGCAGATGCAATGACAAATGC
TGCTCAAGCTGCCTTACGTCGTACAATGGAAAAAGAAACTCGCACTACAAGATTCTGTTT
GATTTGCAACTATGTATCAAAAATAATAGAACCAATCACATCACGATGTACTAAATTTCG
ATTTATTCCATTGCATGAGGAAAAAATCATTGAGAGACTAAAGTTTATTGCTGAACAAGA
AAAATTCAATATTGAAGATGAAGCATTAAAAAGTATAGTCGAAACTTCAAATGGAGACCT
CAGAAAGGCAATAACAACGCTTCAATCATGTTATCGATTAAAATGTGGATCAGACATAAA
ACATAGTCAAGTTACGCTTTTAGATGTTTTTGAAATGTCTGGAATTGTACCTGATTCATA
TTTAGAAGAGTTCATAAAAGTCGTAAAAAGTAAGGAACTTCAAGCACTGGAAAATTTTAT
AGATGCTTTTACTTATGAAGCATACAGTCTCTCACAATTCTTTGATCAACTTAGCATCAA
AATTATCATGGATGAAACTATTACAAACAATCAAAAAGCTATAATTCTCGATAAATTAGG
AGAGTCATCTTTTCGACTTTCAACTGGAGGCAGTGAATATCTTCAATTAATTGATTTTGG
TACAATTTGTATCATTGCATTTTCAAAACAAAATTAATCCTTTTTTTGTATTCATTTTTA
TTAAAAATATGTGTCAAAAAGTTATAGAATTTT
>g11810.t4 Gene=g11810 Length=215
MTNAAQAALRRTMEKETRTTRFCLICNYVSKIIEPITSRCTKFRFIPLHEEKIIERLKFI
AEQEKFNIEDEALKSIVETSNGDLRKAITTLQSCYRLKCGSDIKHSQVTLLDVFEMSGIV
PDSYLEEFIKVVKSKELQALENFIDAFTYEAYSLSQFFDQLSIKIIMDETITNNQKAIIL
DKLGESSFRLSTGGSEYLQLIDFGTICIIAFSKQN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g11810.t4 | CDD | cd18140 | HLD_clamp_RFC | 48 | 98 | 0 |
| 6 | g11810.t4 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 47 | 0 |
| 8 | g11810.t4 | Gene3D | G3DSA:1.10.8.60 | - | 49 | 119 | 0 |
| 7 | g11810.t4 | Gene3D | G3DSA:1.20.272.10 | - | 120 | 208 | 0 |
| 2 | g11810.t4 | PANTHER | PTHR11669:SF20 | REPLICATION FACTOR C SUBUNIT 4 | 1 | 203 | 0 |
| 3 | g11810.t4 | PANTHER | PTHR11669 | REPLICATION FACTOR C / DNA POLYMERASE III GAMMA-TAU SUBUNIT | 1 | 203 | 0 |
| 1 | g11810.t4 | Pfam | PF08542 | Replication factor C C-terminal domain | 121 | 203 | 0 |
| 5 | g11810.t4 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 1 | 95 | 0 |
| 4 | g11810.t4 | SUPERFAMILY | SSF48019 | post-AAA+ oligomerization domain-like | 120 | 204 | 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.
