General information for g3527.t12
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.t12 | TTS | g3527.t12 | 26202623 | 26202623 |
| chr_3 | g3527 | g3527.t12 | isoform | g3527.t12 | 26202659 | 26203906 |
| chr_3 | g3527 | g3527.t12 | exon | g3527.t12.exon1 | 26202659 | 26203141 |
| chr_3 | g3527 | g3527.t12 | cds | g3527.t12.CDS1 | 26202659 | 26203141 |
| chr_3 | g3527 | g3527.t12 | exon | g3527.t12.exon2 | 26203199 | 26203506 |
| chr_3 | g3527 | g3527.t12 | cds | g3527.t12.CDS2 | 26203199 | 26203336 |
| chr_3 | g3527 | g3527.t12 | exon | g3527.t12.exon3 | 26203566 | 26203699 |
| chr_3 | g3527 | g3527.t12 | exon | g3527.t12.exon4 | 26203760 | 26203906 |
| chr_3 | g3527 | g3527.t12 | TSS | g3527.t12 | 26203981 | 26203981 |
Sequences
>g3527.t12 Gene=g3527 Length=1072
ATGTCATTGTGGGTTGATAAATATCGTCCTCGTGAGTTATCAAAGCTAGATTATCATAAA
GAACAAGCTGCCGACTTAAAGAGATTATGTGAACAGCAAGATTTTCCACATTTGATGTTC
TTTGGTCCTAGTGGTTCAGGAAAAAAAACAAGAATACAATGTATGTTAAGAGAACTTTAT
GGAACATCAGCTGAGAGACTTCGAAATGAAACAATGACATTTACCACTCCATCAAATAAG
AAAGTAGATATAATGACTGTATCAAGCAATTATCATATCGATAAATCCTTCTGATGCAGG
AATATATGATCGAGTTATCATTACTGATATAATTAAGCAAATTGCACAAACAGCAAATAT
TGATAGCGGTTCTGAGCGAGATTTTAAAGTGATTGTATTAACAGAAATCGATGATTTAAC
AAAAGATGCTCAACATGCTCTAAGACGAACAATGGAAAAATATGTAGCCACTTGTCGAAT
CATTCTTTGTGTGAATTCAACTTCTCGAGTTATTCCAGCAATTAAAAGTCGTTGTTTAGG
AATTCGCGTTTCAGCGCCATCAATTGAAGAGATTGTAGCAATTCTCCATAAAATTTGTCG
AAAAGAAAACTTGACACTTCCTAATGAATTAGCATTGAATATTGCAAAAACATCTGATAG
AAATTTGAGAAGAGCGATTTTGATGCTTGAAGCTGCTAAAGTTCAAAAATATCCATTCAC
TTCGAATCAGCAAGTACCGGACGTTGATTGGAAAATTTTTCTTCATGAAACTGCTAACGT
AATCATGCGTGAACAGACACCAGCTAATTTAGAAAAAATTCGAGATCGTTTATATGAATT
GCTTTCTCATGGAATTCCATCAGATATCATATTTCGAGAGTTAGTCAAAATTTTAACAAC
AAAATGCGATTCAGAAGTTAAATCTCAAATTTACGGATATGCAAGTCTCTATGAACATCG
AATGCTTTCTGGTAACAAACCTATTTATCATCTTGAAGCATTTGTAGCACAGTTTATGAG
TATTTATAAAAAGTATCTTAACGACATTACGATGGATTTTGATGATGATTAA
>g3527.t12 Gene=g3527 Length=206
MEKYVATCRIILCVNSTSRVIPAIKSRCLGIRVSAPSIEEIVAILHKICRKENLTLPNEL
ALNIAKTSDRNLRRAILMLEAAKVQKYPFTSNQQVPDVDWKIFLHETANVIMREQTPANL
EKIRDRLYELLSHGIPSDIIFRELVKILTTKCDSEVKSQIYGYASLYEHRMLSGNKPIYH
LEAFVAQFMSIYKKYLNDITMDFDDD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g3527.t12 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 36 | 7.1e-06 |
| 8 | g3527.t12 | Gene3D | G3DSA:1.10.8.60 | - | 37 | 93 | 0.0e+00 |
| 7 | g3527.t12 | Gene3D | G3DSA:1.20.272.10 | - | 99 | 193 | 0.0e+00 |
| 2 | g3527.t12 | PANTHER | PTHR11669 | REPLICATION FACTOR C / DNA POLYMERASE III GAMMA-TAU SUBUNIT | 1 | 193 | 0.0e+00 |
| 3 | g3527.t12 | PANTHER | PTHR11669:SF1 | REPLICATION FACTOR C SUBUNIT 3 | 1 | 193 | 0.0e+00 |
| 1 | g3527.t12 | Pfam | PF08542 | Replication factor C C-terminal domain | 114 | 187 | 0.0e+00 |
| 5 | g3527.t12 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 1 | 85 | 0.0e+00 |
| 4 | g3527.t12 | SUPERFAMILY | SSF48019 | post-AAA+ oligomerization domain-like | 98 | 193 | 0.0e+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 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.
