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[192550_at] Replication factor C

Description F31E3.3 /REP_DB=WormBase Gene ID /WP=CE01268 /GEN=rfc-4 /TR=SW:P53016 /GB=AAA81689.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=Replication factor C
Cluster 6grp_highest_10_10 > 69      6grp_high1_10_10 > 98      4grp_highest_8_8 > 03      4grp_high_8_8 > 46      6grp_highest_nonorm > 89      6grp_total > 96      4grp_total > 49      6grp_highest_sub > In      6grp_cgc > 68      6grp_high1_sub > In      6grp_cgc_sub > In      6grp_total_sub > Increase      6grp_rule_based > S6      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 669
1 2 3 4 range
A 954.6
(-3)
P 		1195.7
(1.4)
P 		1280.2
(3)
P 		1050.1
(-1.2)
P 		326
B 922.9
(-3)
P 		1592
(3)
P 		1461.4
(1.8)
P 		1165.3
(-0.8)
P 		669
C 1062
(-3)
P 		1345.6
(2.1)
P 		1397.6
(3)
P 		1079.5
(-2.7)
P 		336
avr 979.8
(-3) 		1377.8
(3) 		1379.7
(3) 		1098.3
(-1.2) 		400

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1512
1 2 3 4 5 6 range
A 849.6
(-3)
P 		921
(-2.7)
P 		1047.4
(-2.1)
P 		1535.7
(-0)
P 		1915.9
(1.6)
P 		2237.7
(3)
P 		1388
B 874
(-3)
P 		910.8
(-2.8)
P 		1104.2
(-2.1)
P 		1420.2
(-0.8)
P 		2178.3
(2.4)
P 		2331.4
(3)
P 		1457
C 867.9
(-3)
P 		933.4
(-2.7)
P 		1110.5
(-2)
P 		1762
(0.6)
P 		1520.6
(-0.4)
P 		2361.5
(3)
P 		1494
avr 863.8
(-3) 		921.7
(-2.8) 		1087.4
(-2.1) 		1572.6
(-0.1) 		1871.6
(1.2) 		2310.2
(3) 		1446
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 333
1 2 3 4 range
A 347.6
(3)
P 		259.5
(0.3)
P 		334.7
(2.6)
P 		153.7
(-3)
P 		194
B 294.3
(-1.1)
P 		393.2
(3)
P 		338.6
(0.7)
P 		248.3
(-3)
P 		145
C 351.5
(0.3)
P 		386.9
(1)
P 		487.1
(3)
P 		182
(-3)
P 		305
avr 331.1
(1.3) 		346.5
(1.7) 		386.8
(3) 		194.7
(-3) 		192

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 728
1 2 3 4 5 6 range
A 156.6
(-3)
P 		327.6
(-0.6)
P 		228.1
(-2)
P 		389.5
(0.3)
P 		578.1
(3)
P 		544.8
(2.5)
P 		422
B 304.1
(-2.6)
P 		303.2
(-2.7)
P 		268.1
(-3)
P 		376.2
(-1.9)
P 		885
(3)
P 		869.4
(2.8)
P 		617
C 321.7
(-2.5)
P 		284.8
(-3)
P 		282.7
(-3)
P 		354.3
(-2.2)
P 		492
(-0.5)
P 		790.5
(3)
P 		508
avr 260.8
(-3) 		305.2
(-2.4) 		259.6
(-3) 		373.3
(-1.6) 		651.7
(1.9) 		734.9
(3) 		475
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192550_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6616
Sequence Type Exemplar sequence
Representative Public ID F31E3.3 NCBI
Target Description F31E3.3 /REP_DB=WormBase Gene ID /WP=CE01268 /GEN=rfc-4 /TR=SW:P53016 /GB=AAA81689.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=Replication factor C
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_066120(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066120 NCBI Caenorhabditis elegans RFC (DNA replication factor) family member (rfc-4) (rfc-4) mRNA, complete cds. 11/11 None
SNAP00000009454 ENSEMBL cdna:SNAP chromosome:CEL140:III:6969474:6973546:1 11/11 None
GENEFINDER00000009464 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:6972191:6973546:1 11/11 None
F31E3.3 ENSEMBL cdna:known chromosome:CEL140:III:6972191:6973586:1 gene:F31E3.3 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
chrIII:6972188-6973544(+) 100.0 100.0
Public Domain and Genome References
Gene Title Replication factor C
Gene Symbol rfc-4
Ensembl F31E3.3
Entrez Gene 175976 Entrez gene
SwissProt P53016 EMBL-EBI
WormBase CE01268 Wormbase
Functional Annotations
Gene Ontology
GO Molecular Function (view graph)
ID Description Evidence Links
166 nucleotide binding inferred from electronic annotation QuickGO AmiGO
5524 ATP binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAA81689 Rfc (dna replication factor) family protein 4 [Caenorhabditis elegans] ref|NP_498521.1| RFC (DNA replication factor) family member (rfc-4) [Caenorhabditis elegans] sp|P53016|RFC4_CAEEL Probable activator 1 37 kDa subunit (Replication factor C 37 kDa subunit) (A1 37 kDa subunit) (RF-C 37 kDa subunit) (RFC37) 1.0E-179
blast AAA81689 Rfc (dna replication factor) family protein 4 [Caenorhabditis elegans] ref|NP_498521.1| RFC (DNA replication factor) family member (rfc-4) [Caenorhabditis elegans] sp|P53016|RFC4_CAEEL Probable activator 1 37 kDa subunit (Replication factor C 37 kDa subunit) (A1 37 kDa subunit) (RF-C 37 kDa subunit) (RFC37) 1.0E-178
blast CAE70058 Hypothetical protein CBG16492 [Caenorhabditis briggsae] emb|CAE56764.1| Hypothetical protein CBG24567 [Caenorhabditis briggsae] 1.0E-154
blast XP_881694 PREDICTED: similar to Activator 1 37 kDa subunit (Replication factor C 37 kDa subunit) (A1 37 kDa subunit) (RF-C 37 kDa subunit) (RFC37) isoform 6 [Bos taurus] 3.0E-65
Protein Domains
Database ID Description E-Value
Pfam IPR003959 EMBL-EBI AAA ATPase, central region 5.3E-21
Pfam IPR003959 EMBL-EBI AAA ATPase, central region 5.3E-21
Trans Membrane
ID Number Of Domains Domain Boundaries
SNAP00000009454 1 105-127
Sequence
Target Sequence 
>C. ELEGANS:192550_AT
gcgatgacccgagaagcacaagcagcaatgcgcagagttattgaagatttttccaaaact
actcgcttcattctcatctgcaactatgtttcccgattgattcctccagttgtgagccgt
tgtgccaagttccgattcaaatcacttccagccgagattcaagttcaaagattgagaaca
atttgtgatgcagaaggaactcccatgagtgatgatgaactgaaacaagttatggaatat
tcagaaggtgatttgagacgagctgtatgtacacttcagtcattggctccaattttgaaa
agtggcgatgacaatgctcgaaattgctatctccgtggttcttcggacagtttactcatt
tcaaacgtttgcaaatcaatcctgactgctgatgttccccaaataattgcattgacaaag
gatatcacaaaatcgtgcactggtgttgctttcattcgtcgttgtttccaacagttgatg
gatgaagatgttatcaatgacgagaatattggagtaatggggaaactggttgcgacttgc
gaaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCGATGACCCGAGAAGCACAAGCAG 155 291 397 Antisense
GCTTCATTCTCATCTGCAACTATGT 661 305 461 Antisense
TTGATTCCTCCAGTTGTGAGCCGTT 267 705 493 Antisense
CCGTTGTGCCAAGTTCCGATTCAAA 135 265 513 Antisense
TCAAATCACTTCCAGCCGAGATTCA 307 629 533 Antisense
TACACTTCAGTCATTGGCTCCAATT 165 643 666 Antisense
AATGCTCGAAATTGCTATCTCCGTG 464 165 709 Antisense
CTATCTCCGTGGTTCTTCGGACAGT 593 221 723 Antisense
ATCAATCCTGACTGCTGATGTTCCC 281 27 771 Antisense
GCTTTCATTCGTCGTTGTTTCCAAC 341 303 844 Antisense
GGGAAACTGGTTGCGACTTGCGAAA 459 493 916 Antisense
Sequence Source Affymetrix Proprietary Database