Gene loci information

Transcript annotation

  • This transcript has been annotated as Replication factor C subunit 3.

Parent gene

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.t9 TTS g3527.t9 26202623 26202623
chr_3 g3527 g3527.t9 isoform g3527.t9 26202659 26203906
chr_3 g3527 g3527.t9 exon g3527.t9.exon1 26202659 26203141
chr_3 g3527 g3527.t9 cds g3527.t9.CDS1 26202659 26203141
chr_3 g3527 g3527.t9 exon g3527.t9.exon2 26203199 26203906
chr_3 g3527 g3527.t9 cds g3527.t9.CDS2 26203199 26203336
chr_3 g3527 g3527.t9 TSS g3527.t9 26203981 26203981

Sequences

>g3527.t9 Gene=g3527 Length=1191
ATGTCATTGTGGGTTGATAAATATCGTCCTCGTGAGTTATCAAAGCTAGATTATCATAAA
GAACAAGCTGCCGACTTAAAGAGATTATGTGAACAGCAAGATTTTCCACATTTGATGTTC
TTTGGTCCTAGTGGTTCAGGAAAAAAAGTAATTGTCATAAAATTAAAAAATTGTTATTCC
ATTTTTATTCATTATTTATTTAAATAGACAAGAATACAATGTATGTTAAGAGAACTTTAT
GGAACATCAGCTGAGAGACTTCGAAATGAAACAATGACATTTACCACTCCATCAAATAAG
AAAGTAGATATAATGACTGTATCAAGCAATTATCATATCGAGTGTGAGTAAAAATATAAA
AATAAATAACAAACTTACTAATTGAAACCTTTGATTATAGTAAATCCTTCTGATGCAGGA
ATATATGATCGAGTTATCATTACTGATATAATTAAGCAAATTGCACAAACAGCAAATATT
GATAGCGGTTCTGAGCGAGATTTTAAAGTGATTGTATTAACAGAAATCGATGATTTAACA
AAAGATGCTCAACATGCTCTAAGACGAACAATGGAAAAATATGTAGCCACTTGTCGAATC
ATTCTTTGTGTGAATTCAACTTCTCGAGTTATTCCAGCAATTAAAAGTCGTTGTTTAGGA
ATTCGCGTTTCAGCGCCATCAATTGAAGAGATTGTAGCAATTCTCCATAAAATTTGTCGA
AAAGAAAACTTGACACTTCCTAATGAATTAGCATTGAATATTGCAAAAACATCTGATAGA
AATTTGAGAAGAGCGATTTTGATGCTTGAAGCTGCTAAAGTTCAAAAATATCCATTCACT
TCGAATCAGCAAGTACCGGACGTTGATTGGAAAATTTTTCTTCATGAAACTGCTAACGTA
ATCATGCGTGAACAGACACCAGCTAATTTAGAAAAAATTCGAGATCGTTTATATGAATTG
CTTTCTCATGGAATTCCATCAGATATCATATTTCGAGAGTTAGTCAAAATTTTAACAACA
AAATGCGATTCAGAAGTTAAATCTCAAATTTACGGATATGCAAGTCTCTATGAACATCGA
ATGCTTTCTGGTAACAAACCTATTTATCATCTTGAAGCATTTGTAGCACAGTTTATGAGT
ATTTATAAAAAGTATCTTAACGACATTACGATGGATTTTGATGATGATTAA

>g3527.t9 Gene=g3527 Length=206
MEKYVATCRIILCVNSTSRVIPAIKSRCLGIRVSAPSIEEIVAILHKICRKENLTLPNEL
ALNIAKTSDRNLRRAILMLEAAKVQKYPFTSNQQVPDVDWKIFLHETANVIMREQTPANL
EKIRDRLYELLSHGIPSDIIFRELVKILTTKCDSEVKSQIYGYASLYEHRMLSGNKPIYH
LEAFVAQFMSIYKKYLNDITMDFDDD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g3527.t9 Gene3D G3DSA:3.40.50.300 - 1 36 7.1e-06
8 g3527.t9 Gene3D G3DSA:1.10.8.60 - 37 93 0.0e+00
7 g3527.t9 Gene3D G3DSA:1.20.272.10 - 99 193 0.0e+00
2 g3527.t9 PANTHER PTHR11669 REPLICATION FACTOR C / DNA POLYMERASE III GAMMA-TAU SUBUNIT 1 193 0.0e+00
3 g3527.t9 PANTHER PTHR11669:SF1 REPLICATION FACTOR C SUBUNIT 3 1 193 0.0e+00
1 g3527.t9 Pfam PF08542 Replication factor C C-terminal domain 114 187 0.0e+00
5 g3527.t9 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 1 85 0.0e+00
4 g3527.t9 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.

Raw TPM values