Gene loci information

Transcript annotation

  • This transcript has been annotated as 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.t3 TSS g11810.t3 18526227 18526227
chr_1 g11810 g11810.t3 isoform g11810.t3 18526476 18527567
chr_1 g11810 g11810.t3 exon g11810.t3.exon1 18526476 18526589
chr_1 g11810 g11810.t3 cds g11810.t3.CDS1 18526544 18526589
chr_1 g11810 g11810.t3 exon g11810.t3.exon2 18526647 18526736
chr_1 g11810 g11810.t3 cds g11810.t3.CDS2 18526647 18526736
chr_1 g11810 g11810.t3 exon g11810.t3.exon3 18526792 18527567
chr_1 g11810 g11810.t3 cds g11810.t3.CDS3 18526792 18527567
chr_1 g11810 g11810.t3 TTS g11810.t3 18527649 18527649

Sequences

>g11810.t3 Gene=g11810 Length=980
AGTATCGGCCAAAGAAAGTTGATGATGTTGTAGAGCAAAATGAAGTGTGTGCTGTTCTGA
GAGAAAGTATGCAAACTTCAGACTTACCTAATTTATTATTATATGGTCCTCCAGGCACTG
GAAAAACATCGACAATCTTAGCAGCAGCTCGTCAACTTTTTGGTGAATTTATAAAAGAAC
GTGTGCTTGAGCTTAATGCATCAGATGATCGTGGAATTTCGGTTATAAGAACAAAAGTTA
AAAATTTTGCACAACTTAAAGCGAGTAATATCCGACCAGATGGAAAACCATGTCCACCTT
TCAAGATAATCATTCTTGATGAAGCAGATGCAATGACAAATGCTGCTCAAGCTGCCTTAC
GTCGTACAATGGAAAAAGAAACTCGCACTACAAGATTCTGTTTGATTTGCAACTATGTAT
CAAAAATAATAGAACCAATCACATCACGATGTACTAAATTTCGATTTATTCCATTGCATG
AGGAAAAAATCATTGAGAGACTAAAGTTTATTGCTGAACAAGAAAAATTCAATATTGAAG
ATGAAGCATTAAAAAGTATAGTCGAAACTTCAAATGGAGACCTCAGAAAGGCAATAACAA
CGCTTCAATCATGTTATCGATTAAAATGTGGATCAGACATAAAACATAGTCAAGTTACGC
TTTTAGATGTTTTTGAAATGTCTGGAATTGTACCTGATTCATATTTAGAAGAGTTCATAA
AAGTCGTAAAAAGTAAGGAACTTCAAGCACTGGAAAATTTTATAGATGCTTTTACTTATG
AAGCATACAGTCTCTCACAATTCTTTGATCAACTTAGCATCAAAATTATCATGGATGAAA
CTATTACAAACAATCAAAAAGCTATAATTCTCGATAAATTAGGAGAGTCATCTTTTCGAC
TTTCAACTGGAGGCAGTGAATATCTTCAATTAATTGATTTTGGTACAATTTGTATCATTG
CATTTTCAAAACAAAATTAA

>g11810.t3 Gene=g11810 Length=303
MQTSDLPNLLLYGPPGTGKTSTILAAARQLFGEFIKERVLELNASDDRGISVIRTKVKNF
AQLKASNIRPDGKPCPPFKIIILDEADAMTNAAQAALRRTMEKETRTTRFCLICNYVSKI
IEPITSRCTKFRFIPLHEEKIIERLKFIAEQEKFNIEDEALKSIVETSNGDLRKAITTLQ
SCYRLKCGSDIKHSQVTLLDVFEMSGIVPDSYLEEFIKVVKSKELQALENFIDAFTYEAY
SLSQFFDQLSIKIIMDETITNNQKAIILDKLGESSFRLSTGGSEYLQLIDFGTICIIAFS
KQN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g11810.t3 CDD cd00009 AAA 1 136 0
12 g11810.t3 CDD cd18140 HLD_clamp_RFC 136 186 0
8 g11810.t3 Gene3D G3DSA:3.40.50.300 - 1 136 0
10 g11810.t3 Gene3D G3DSA:1.10.8.60 - 137 207 0
9 g11810.t3 Gene3D G3DSA:1.20.272.10 - 208 296 0
3 g11810.t3 PANTHER PTHR11669:SF20 REPLICATION FACTOR C SUBUNIT 4 2 291 0
4 g11810.t3 PANTHER PTHR11669 REPLICATION FACTOR C / DNA POLYMERASE III GAMMA-TAU SUBUNIT 2 291 0
1 g11810.t3 Pfam PF00004 ATPase family associated with various cellular activities (AAA) 9 135 0
2 g11810.t3 Pfam PF08542 Replication factor C C-terminal domain 209 291 0
7 g11810.t3 SMART SM00382 AAA_5 5 139 0
6 g11810.t3 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 4 183 0
5 g11810.t3 SUPERFAMILY SSF48019 post-AAA+ oligomerization domain-like 208 292 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:0005524 ATP binding MF
GO:0006260 DNA replication BP
GO:0016887 ATP hydrolysis activity MF

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