Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Replication factor C subunit 4.

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_1 g11810 g11810.t2 TSS g11810.t2 18526227 18526227
chr_1 g11810 g11810.t2 isoform g11810.t2 18526296 18527567
chr_1 g11810 g11810.t2 exon g11810.t2.exon1 18526296 18526736
chr_1 g11810 g11810.t2 exon g11810.t2.exon2 18526792 18527567
chr_1 g11810 g11810.t2 cds g11810.t2.CDS1 18526920 18527567
chr_1 g11810 g11810.t2 TTS g11810.t2 18527649 18527649

Sequences

>g11810.t2 Gene=g11810 Length=1217
ATGCAAGCATTTTTACAAGGCCATAAATTGTCAGCTCAAAAACCAGCTTCATTTAATAGT
CAGAGAAAAGAGAAAAAGAGTCGAGAAAAGCCGATTCCTTGGGTAGAAAAGGTAAGAAAG
ACTTGGCGCCAAAAAATTAGAAAACTTCTAAACATGTTTTTATCTACCAATGCAATTTGT
AGTATCGGCCAAAGAAAGTTGATGATGTTGTAGAGCAAAATGAAGTGTGTGCTGTTCTGA
GAGAAAGTATGCAAACTTCAGACTTACCTAATTTATTATTATATGGTCCTCCAGGTTTGT
TTATTTTATTTACACAAAAAAATATCAATATTACGTTTAATTAATATGCAGGCACTGGAA
AAACATCGACAATCTTAGCAGCAGCTCGTCAACTTTTTGGTGAATTTATAAAAGAACGTG
TGCTTGAGCTTAATGCATCAGATGATCGTGGAATTTCGGTTATAAGAACAAAAGTTAAAA
ATTTTGCACAACTTAAAGCGAGTAATATCCGACCAGATGGAAAACCATGTCCACCTTTCA
AGATAATCATTCTTGATGAAGCAGATGCAATGACAAATGCTGCTCAAGCTGCCTTACGTC
GTACAATGGAAAAAGAAACTCGCACTACAAGATTCTGTTTGATTTGCAACTATGTATCAA
AAATAATAGAACCAATCACATCACGATGTACTAAATTTCGATTTATTCCATTGCATGAGG
AAAAAATCATTGAGAGACTAAAGTTTATTGCTGAACAAGAAAAATTCAATATTGAAGATG
AAGCATTAAAAAGTATAGTCGAAACTTCAAATGGAGACCTCAGAAAGGCAATAACAACGC
TTCAATCATGTTATCGATTAAAATGTGGATCAGACATAAAACATAGTCAAGTTACGCTTT
TAGATGTTTTTGAAATGTCTGGAATTGTACCTGATTCATATTTAGAAGAGTTCATAAAAG
TCGTAAAAAGTAAGGAACTTCAAGCACTGGAAAATTTTATAGATGCTTTTACTTATGAAG
CATACAGTCTCTCACAATTCTTTGATCAACTTAGCATCAAAATTATCATGGATGAAACTA
TTACAAACAATCAAAAAGCTATAATTCTCGATAAATTAGGAGAGTCATCTTTTCGACTTT
CAACTGGAGGCAGTGAATATCTTCAATTAATTGATTTTGGTACAATTTGTATCATTGCAT
TTTCAAAACAAAATTAA

>g11810.t2 Gene=g11810 Length=215
MTNAAQAALRRTMEKETRTTRFCLICNYVSKIIEPITSRCTKFRFIPLHEEKIIERLKFI
AEQEKFNIEDEALKSIVETSNGDLRKAITTLQSCYRLKCGSDIKHSQVTLLDVFEMSGIV
PDSYLEEFIKVVKSKELQALENFIDAFTYEAYSLSQFFDQLSIKIIMDETITNNQKAIIL
DKLGESSFRLSTGGSEYLQLIDFGTICIIAFSKQN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g11810.t2 CDD cd18140 HLD_clamp_RFC 48 98 0
6 g11810.t2 Gene3D G3DSA:3.40.50.300 - 1 47 0
8 g11810.t2 Gene3D G3DSA:1.10.8.60 - 49 119 0
7 g11810.t2 Gene3D G3DSA:1.20.272.10 - 120 208 0
2 g11810.t2 PANTHER PTHR11669:SF20 REPLICATION FACTOR C SUBUNIT 4 1 203 0
3 g11810.t2 PANTHER PTHR11669 REPLICATION FACTOR C / DNA POLYMERASE III GAMMA-TAU SUBUNIT 1 203 0
1 g11810.t2 Pfam PF08542 Replication factor C C-terminal domain 121 203 0
5 g11810.t2 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 1 95 0
4 g11810.t2 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.

Raw TPM values