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[192416_at] DNA replication factor

Description F58F6.4 /REP_DB=WormBase Gene ID /WP=CE17139 /GEN=rfc-2 /TR=O44175 /GB=AAB88360.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=DNA replication factor
Cluster 6grp_highest_10_10 > 98      6grp_high1_10_10 > 89      4grp_highest_8_8 > 10      4grp_high_8_8 > 54      6grp_highest_nonorm > 92      6grp_total > 89      4grp_total > 57      6grp_highest_sub > Cu      6grp_cgc > 69      6grp_high1_sub > Cu      6grp_cgc_sub > Da      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 275
1 2 3 4 range
A 329.7
(-3)
P 		455.8
(1.5)
P 		499.1
(3)
P 		379.2
(-1.2)
P 		169
B 355.4
(-1.4)
P 		445.5
(2.1)
P 		468.9
(3)
P 		314.5
(-3)
P 		154
C 375.2
(0.2)
P 		491.5
(2.8)
P 		501.9
(3)
P 		227.1
(-3)
P 		275
avr 353.4
(-1.5) 		464.3
(2.2) 		490
(3) 		306.9
(-3) 		183

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 341
1 2 3 4 5 6 range
A 280.1
(-2.3)
P 		324.7
(-1.4)
P 		247.5
(-3)
P 		325.4
(-1.4)
P 		392.7
(0.1)
P 		533
(3)
P 		286
B 281.4
(-1.9)
P 		259.8
(-2.3)
P 		221.6
(-2.9)
P 		217.3
(-3)
P 		496.7
(1.9)
P 		558.5
(3)
P 		341
C 463.2
(1.8)
P 		250.7
(-3)
P 		343
(-0.9)
P 		331.2
(-1.2)
P 		513
(2.9)
P 		519
(3)
P 		268
avr 341.6
(-1.4) 		278.4
(-2.8) 		270.7
(-3) 		291.3
(-2.5) 		467.5
(1.4) 		536.8
(3) 		266
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 137
1 2 3 4 range
A 120.1
(2.2)
P 		98.9
(0.5)
P 		130.5
(3)
P 		55.5
(-3)
P 		75
B 113.3
(3)
P 		110
(2.6)
P 		108.6
(2.4)
P 		67
(-3)
P 		46
C 124.2
(0.8)
P 		141.3
(1.5)
P 		174.9
(3)
P 		38.3
(-3)
P 		137
avr 119.2
(1.7) 		116.7
(1.5) 		138
(3) 		53.6
(-3) 		84

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 157
1 2 3 4 5 6 range
A 51.6
(-3)
P 		115.5
(1.9)
P 		53.9
(-2.8)
P 		82.5
(-0.6)
P 		118.5
(2.1)
P 		129.8
(3)
P 		78
B 97.9
(-1.3)
P 		86.5
(-1.7)
P 		53.8
(-3)
P 		57.6
(-2.9)
P 		201.8
(2.7)
P 		208.3
(3)
P 		155
C 171.7
(2.9)
P 		76.5
(-2.4)
P 		87.3
(-1.8)
P 		66.6
(-3)
P 		166
(2.6)
P 		173.7
(3)
P 		107
avr 107.1
(-0.6) 		92.8
(-1.4) 		65
(-3) 		68.9
(-2.8) 		162.1
(2.5) 		170.6
(3) 		106
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192416_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11219
Sequence Type Exemplar sequence
Representative Public ID F58F6.4 NCBI
Target Description F58F6.4 /REP_DB=WormBase Gene ID /WP=CE17139 /GEN=rfc-2 /TR=O44175 /GB=AAB88360.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=DNA replication factor
Cluster Evidence This cluster is supported by a Sanger Annotation.
Annotation Method Description
Annotation Description This probe set was annotated using the Matching Probes based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade A annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_067668(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067668 NCBI Caenorhabditis elegans RFC (DNA replication factor) family member (rfc-2) (rfc-2) mRNA, complete cds. 11/11 None
SNAP00000017982 ENSEMBL cdna:SNAP chromosome:CEL140:IV:1347318:1355213:1 10/11 None
GENEFINDER00000017988 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:1347318:1352882:1 11/11 None
F58F6.4.2 ENSEMBL cdna:known chromosome:CEL140:IV:1347314:1352882:1 gene:F58F6.4 11/11 None
F58F6.4.1 ENSEMBL cdna:known chromosome:CEL140:IV:1347316:1352956:1 gene:F58F6.4 11/11 None
Annotation Notes
There are no noteworthy cross hybridizing mRNAs found for this probe set.
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIV:1347323-1352888(+) 100.0 100.0
Public Domain and Genome References
Gene Title DNA replication factor
Gene Symbol rfc-2
Ensembl F58F6.4
Entrez Gene 176946 Entrez gene
SwissProt O44175 EMBL-EBI
WormBase CE17139 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:259690_AT replication factor C 40 kDa, putative at
CANINE_2:CFA.18363.1.S1_S_AT similar to replication factor C 2 (40kD) isoform 2 cfa
CANINE_2:CFAAFFX.18598.1.S1_S_AT similar to replication factor C 2 (40kD) isoform 2 cfa
DROSOPHILA_2:1634943_AT Replication-factor-C 40kD subunit dm
DROSGENOME1:154910_AT Replication-factor-C 40kD subunit dm
CHICKEN:GGA.883.1.S1_AT replication factor C (activator 1) 2, 40kDa gga
CHICKEN:GGA.883.2.A1_AT Replication factor C (activator 1) 2, 40kDa gga
HG-U95AV2:1053_AT replication factor C (activator 1) 2, 40kDa hs
HG-U133_PLUS_2:1053_AT replication factor C (activator 1) 2, 40kDa hs
HG-U133A_2:1053_AT replication factor C (activator 1) 2, 40kDa hs
HC-G110:1053_AT replication factor C (activator 1) 2, 40kDa hs
HG-U133A:1053_AT replication factor C (activator 1) 2, 40kDa hs
HG-FOCUS:1053_AT replication factor C (activator 1) 2, 40kDa hs
HG-U133_PLUS_2:203696_S_AT replication factor C (activator 1) 2, 40kDa hs
HG-U133A:203696_S_AT replication factor C (activator 1) 2, 40kDa hs
HG-U133A_2:203696_S_AT replication factor C (activator 1) 2, 40kDa hs
HU35KSUBD:RC_R60181_AT replication factor C (activator 1) 2, 40kDa hs
HUGENEFL:M87338_AT replication factor C (activator 1) 2, 40kDa hs
U133_X3P:G4506486_3P_X_AT replication factor C (activator 1) 2, 40kDa hs
U133_X3P:M87338_3P_X_AT replication factor C (activator 1) 2, 40kDa hs
U133_X3P:203696_3P_S_AT replication factor C (activator 1) 2, 40kDa hs
U133_X3P:1053_3P_AT replication factor C (activator 1) 2, 40kDa hs
RG-U34B:RC_AA899195_AT replication factor C (activator 1) 2 rn
RAE230A:1370910_AT replication factor C (activator 1) 2 rn
RAT230_2:1370910_AT replication factor C (activator 1) 2 rn
YEAST_2:1778831_AT Subunit of heteropentameric Replication factor C (RF-C), which is a DNA binding protein and ATPase that acts as a clamp loader of the proliferating cell nuclear antigen (PCNA) processivity factor for DNA polymerases delta and epsilon Sc
Gene Ontology
GO Molecular Function (view graph)
ID Description Evidence Links
166 nucleotide binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAB88360 Rfc (dna replication factor) family protein 2 [Caenorhabditis elegans] ref|NP_500069.1| RFC (DNA replication factor) family member (rfc-2) [Caenorhabditis elegans] 0.0
blast AAB88360 Rfc (dna replication factor) family protein 2 [Caenorhabditis elegans] ref|NP_500069.1| RFC (DNA replication factor) family member (rfc-2) [Caenorhabditis elegans] 1.0E-166
blast CAE75096 Hypothetical protein CBG23018 [Caenorhabditis briggsae] 1.0E-165
blast CAE75096 Hypothetical protein CBG23018 [Caenorhabditis briggsae] 1.0E-159
blast CAE75096 Hypothetical protein CBG23018 [Caenorhabditis briggsae] 1.0E-149
Sequence
Target Sequence 
>C. ELEGANS:192416_AT
gacgacaagatttgcgttggcctgcaatcaatccgagaagattattgagcccattcaatc
ccgttgtgccctgctccgctacacaaaattgagccccgtacagctgttgacacgtgtcaa
ggaggttgcaaaagccgagaaggtcaactatgacgacgggggtcttgaagcgattctgtt
cactgcacagggtgatatgcgacaggcgttgaacaatttacaggcaacagtgaacgctta
cgagcttgtgaacaaggaaaatgtgctgaaagtctgtgatgagccacacccggaccttat
gatcaaaatgctccattactgtacggatcgcaaattcttcgaggcatccaagattattca
cgagtttcatcggcttggcttctcctcagacgatattgtatcaacgttgttccgtgtggt
aaagactgtcgagctgtcgaaaaatgtgtccgaacagctgagaatggagtatattcggca
aatcgccatgtgccatatgcgtatcgtgc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GACGACAAGATTTGCGTTGGCCTGC 668 379 423 Antisense
GTTGGCCTGCAATCAATCCGAGAAG 660 435 438 Antisense
AAAATTGAGCCCCGTACAGCTGTTG 62 133 507 Antisense
GACGGGGGTCTTGAAGCGATTCTGT 529 375 577 Antisense
GCGATTCTGTTCACTGCACAGGGTG 101 291 592 Antisense
CCACACCCGGACCTTATGATCAAAA 294 275 706 Antisense
ATGCTCCATTACTGTACGGATCGCA 26 43 730 Antisense
GATCGCAAATTCTTCGAGGCATCCA 308 417 748 Antisense
TTCACGAGTTTCATCGGCTTGGCTT 603 687 779 Antisense
TGGCTTCTCCTCAGACGATATTGTA 143 545 798 Antisense
GCCATGTGCCATATGCGTATCGTGC 160 279 907 Antisense
Sequence Source Affymetrix Proprietary Database