General information for g3527.t13
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.t13 | TTS | g3527.t13 | 26202623 | 26202623 |
| chr_3 | g3527 | g3527.t13 | isoform | g3527.t13 | 26203200 | 26203906 |
| chr_3 | g3527 | g3527.t13 | exon | g3527.t13.exon1 | 26203200 | 26203506 |
| chr_3 | g3527 | g3527.t13 | cds | g3527.t13.CDS1 | 26203202 | 26203506 |
| chr_3 | g3527 | g3527.t13 | exon | g3527.t13.exon2 | 26203564 | 26203699 |
| chr_3 | g3527 | g3527.t13 | cds | g3527.t13.CDS2 | 26203564 | 26203699 |
| chr_3 | g3527 | g3527.t13 | exon | g3527.t13.exon3 | 26203760 | 26203906 |
| chr_3 | g3527 | g3527.t13 | cds | g3527.t13.CDS3 | 26203760 | 26203906 |
| chr_3 | g3527 | g3527.t13 | TSS | g3527.t13 | 26203981 | 26203981 |
Sequences
>g3527.t13 Gene=g3527 Length=590
ATGTCATTGTGGGTTGATAAATATCGTCCTCGTGAGTTATCAAAGCTAGATTATCATAAA
GAACAAGCTGCCGACTTAAAGAGATTATGTGAACAGCAAGATTTTCCACATTTGATGTTC
TTTGGTCCTAGTGGTTCAGGAAAAAAAACAAGAATACAATGTATGTTAAGAGAACTTTAT
GGAACATCAGCTGAGAGACTTCGAAATGAAACAATGACATTTACCACTCCATCAAATAAG
AAAGTAGATATAATGACTGTATCAAGCAATTATCATATCGAGTTAAATCCTTCTGATGCA
GGAATATATGATCGAGTTATCATTACTGATATAATTAAGCAAATTGCACAAACAGCAAAT
ATTGATAGCGGTTCTGAGCGAGATTTTAAAGTGATTGTATTAACAGAAATCGATGATTTA
ACAAAAGATGCTCAACATGCTCTAAGACGAACAATGGAAAAATATGTAGCCACTTGTCGA
ATCATTCTTTGTGTGAATTCAACTTCTCGAGTTATTCCAGCAATTAAAAGTCGTTGTTTA
GGAATTCGCGTTTCAGCGCCATCAATTGAAGAGATTGTAGCAATTCTCCA
>g3527.t13 Gene=g3527 Length=196
MSLWVDKYRPRELSKLDYHKEQAADLKRLCEQQDFPHLMFFGPSGSGKKTRIQCMLRELY
GTSAERLRNETMTFTTPSNKKVDIMTVSSNYHIELNPSDAGIYDRVIITDIIKQIAQTAN
IDSGSERDFKVIVLTEIDDLTKDAQHALRRTMEKYVATCRIILCVNSTSRVIPAIKSRCL
GIRVSAPSIEEIVAIL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g3527.t13 | CDD | cd00009 | AAA | 21 | 188 | 0 |
| 5 | g3527.t13 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 187 | 0 |
| 2 | g3527.t13 | PANTHER | PTHR11669 | REPLICATION FACTOR C / DNA POLYMERASE III GAMMA-TAU SUBUNIT | 3 | 196 | 0 |
| 3 | g3527.t13 | PANTHER | PTHR11669:SF1 | REPLICATION FACTOR C SUBUNIT 3 | 3 | 196 | 0 |
| 1 | g3527.t13 | Pfam | PF13177 | DNA polymerase III, delta subunit | 19 | 185 | 0 |
| 4 | g3527.t13 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 4 | 196 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
