General information for g3527.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Replication factor C subunit 3.
Parent gene
- The parent gene g3527 is located on chr_3: 26203200..26203906 (- 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_3 | g3527 | g3527.t1 | TTS | g3527.t1 | 26202623 | 26202623 |
| chr_3 | g3527 | g3527.t1 | isoform | g3527.t1 | 26202659 | 26203906 |
| chr_3 | g3527 | g3527.t1 | exon | g3527.t1.exon1 | 26202659 | 26203141 |
| chr_3 | g3527 | g3527.t1 | cds | g3527.t1.CDS1 | 26202659 | 26203141 |
| chr_3 | g3527 | g3527.t1 | exon | g3527.t1.exon2 | 26203199 | 26203506 |
| chr_3 | g3527 | g3527.t1 | cds | g3527.t1.CDS2 | 26203199 | 26203506 |
| chr_3 | g3527 | g3527.t1 | exon | g3527.t1.exon3 | 26203564 | 26203699 |
| chr_3 | g3527 | g3527.t1 | cds | g3527.t1.CDS3 | 26203564 | 26203699 |
| chr_3 | g3527 | g3527.t1 | exon | g3527.t1.exon4 | 26203760 | 26203906 |
| chr_3 | g3527 | g3527.t1 | cds | g3527.t1.CDS4 | 26203760 | 26203906 |
| chr_3 | g3527 | g3527.t1 | TSS | g3527.t1 | 26203981 | 26203981 |
Sequences
>g3527.t1 Gene=g3527 Length=1074
ATGTCATTGTGGGTTGATAAATATCGTCCTCGTGAGTTATCAAAGCTAGATTATCATAAA
GAACAAGCTGCCGACTTAAAGAGATTATGTGAACAGCAAGATTTTCCACATTTGATGTTC
TTTGGTCCTAGTGGTTCAGGAAAAAAAACAAGAATACAATGTATGTTAAGAGAACTTTAT
GGAACATCAGCTGAGAGACTTCGAAATGAAACAATGACATTTACCACTCCATCAAATAAG
AAAGTAGATATAATGACTGTATCAAGCAATTATCATATCGAGTTAAATCCTTCTGATGCA
GGAATATATGATCGAGTTATCATTACTGATATAATTAAGCAAATTGCACAAACAGCAAAT
ATTGATAGCGGTTCTGAGCGAGATTTTAAAGTGATTGTATTAACAGAAATCGATGATTTA
ACAAAAGATGCTCAACATGCTCTAAGACGAACAATGGAAAAATATGTAGCCACTTGTCGA
ATCATTCTTTGTGTGAATTCAACTTCTCGAGTTATTCCAGCAATTAAAAGTCGTTGTTTA
GGAATTCGCGTTTCAGCGCCATCAATTGAAGAGATTGTAGCAATTCTCCATAAAATTTGT
CGAAAAGAAAACTTGACACTTCCTAATGAATTAGCATTGAATATTGCAAAAACATCTGAT
AGAAATTTGAGAAGAGCGATTTTGATGCTTGAAGCTGCTAAAGTTCAAAAATATCCATTC
ACTTCGAATCAGCAAGTACCGGACGTTGATTGGAAAATTTTTCTTCATGAAACTGCTAAC
GTAATCATGCGTGAACAGACACCAGCTAATTTAGAAAAAATTCGAGATCGTTTATATGAA
TTGCTTTCTCATGGAATTCCATCAGATATCATATTTCGAGAGTTAGTCAAAATTTTAACA
ACAAAATGCGATTCAGAAGTTAAATCTCAAATTTACGGATATGCAAGTCTCTATGAACAT
CGAATGCTTTCTGGTAACAAACCTATTTATCATCTTGAAGCATTTGTAGCACAGTTTATG
AGTATTTATAAAAAGTATCTTAACGACATTACGATGGATTTTGATGATGATTAA
>g3527.t1 Gene=g3527 Length=357
MSLWVDKYRPRELSKLDYHKEQAADLKRLCEQQDFPHLMFFGPSGSGKKTRIQCMLRELY
GTSAERLRNETMTFTTPSNKKVDIMTVSSNYHIELNPSDAGIYDRVIITDIIKQIAQTAN
IDSGSERDFKVIVLTEIDDLTKDAQHALRRTMEKYVATCRIILCVNSTSRVIPAIKSRCL
GIRVSAPSIEEIVAILHKICRKENLTLPNELALNIAKTSDRNLRRAILMLEAAKVQKYPF
TSNQQVPDVDWKIFLHETANVIMREQTPANLEKIRDRLYELLSHGIPSDIIFRELVKILT
TKCDSEVKSQIYGYASLYEHRMLSGNKPIYHLEAFVAQFMSIYKKYLNDITMDFDDD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g3527.t1 | CDD | cd00009 | AAA | 21 | 188 | 0e+00 |
| 7 | g3527.t1 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 187 | 0e+00 |
| 9 | g3527.t1 | Gene3D | G3DSA:1.10.8.60 | - | 188 | 243 | 0e+00 |
| 8 | g3527.t1 | Gene3D | G3DSA:1.20.272.10 | - | 250 | 344 | 0e+00 |
| 3 | g3527.t1 | PANTHER | PTHR11669 | REPLICATION FACTOR C / DNA POLYMERASE III GAMMA-TAU SUBUNIT | 3 | 344 | 0e+00 |
| 4 | g3527.t1 | PANTHER | PTHR11669:SF1 | REPLICATION FACTOR C SUBUNIT 3 | 3 | 344 | 0e+00 |
| 1 | g3527.t1 | Pfam | PF13177 | DNA polymerase III, delta subunit | 19 | 185 | 0e+00 |
| 2 | g3527.t1 | Pfam | PF08542 | Replication factor C C-terminal domain | 265 | 338 | 1e-07 |
| 6 | g3527.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 4 | 236 | 0e+00 |
| 5 | g3527.t1 | SUPERFAMILY | SSF48019 | post-AAA+ oligomerization domain-like | 249 | 344 | 0e+00 |
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 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.
