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[171899_x_at] replication factor A

Description CEC3621_rc /REP_DB=TREMBL Accession /GB=C08362 /FEA=Transcript Cluster /DEF=C.elegans cDNA clone yk187b3 : 3prime end, single read.
Cluster 6grp_total > 78      4grp_total > 45      6grp_total_sub > Increase      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 65
1 2 3 4 range
A 52
(3)
A 		41
(-0.5)
A 		32.9
(-3)
A 		52.1
(3)
A 		19
B 48.2
(3)
A 		45
(2.6)
A 		29.5
(0.5)
A 		3.8
(-3)
A 		44
C 63.7
(2.4)
A 		68.3
(3)
A 		26.7
(-2.9)
A 		25.7
(-3)
A 		43
avr 54.6
(3) 		51.4
(2.3) 		29.7
(-2.5) 		27.2
(-3) 		27

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 79
1 2 3 4 5 6 range
A 31
(-0.8)
A 		11.4
(-2.7)
A 		35.9
(-0.3)
A 		8.9
(-3)
A 		41.1
(0.2)
A 		68.8
(3)
A 		60
B 61.6
(1.5)
A 		10.3
(-3)
A 		74.5
(2.6)
A 		59.2
(1.3)
A 		50.6
(0.5)
A 		78.8
(3)
A 		69
C 44.7
(-1.5)
A 		53
(-0.6)
A 		44.6
(-1.5)
A 		30.4
(-3)
A 		79.8
(2.2)
A 		87.9
(3)
A 		58
avr 45.8
(-0.7) 		24.9
(-3) 		51.7
(0) 		32.8
(-2.1) 		57.2
(0.6) 		78.5
(3) 		54
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 20
1 2 3 4 range
A 18.9
(3)
A 		8.9
(-2.3)
A 		8.6
(-2.5)
A 		7.6
(-3)
A 		11
B 15.4
(3)
A 		11.1
(1.2)
A 		6.8
(-0.5)
A 		0.8
(-3)
A 		15
C 21.1
(3)
A 		19.6
(2.5)
A 		9.3
(-1.2)
A 		4.3
(-3)
A 		17
avr 18.5
(3) 		13.2
(0.8) 		8.2
(-1.3) 		4.2
(-3) 		14

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 27
1 2 3 4 5 6 range
A 5.7
(-1.6)
A 		4.1
(-2.3)
A 		7.8
(-0.7)
A 		2.3
(-3)
A 		12.4
(1.2)
A 		16.7
(3)
A 		14
B 21.4
(1.2)
A 		3.4
(-3)
A 		18.1
(0.4)
A 		15.7
(-0.2)
A 		20.6
(1)
A 		29.4
(3)
A 		26
C 16.6
(-0.3)
A 		16.2
(-0.4)
A 		11.3
(-1.7)
A 		6.1
(-3)
A 		25.8
(2.1)
A 		29.4
(3)
A 		23
avr 14.6
(-0.7) 		7.9
(-3) 		12.4
(-1.4) 		8
(-3) 		19.6
(1.1) 		25.2
(3) 		17
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 171899_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.27602
Sequence Type Exemplar sequence
Representative Public ID CEC3621 NCBI
Target Description CEC3621_rc /REP_DB=TREMBL Accession /GB=C08362 /FEA=Transcript Cluster /DEF=C.elegans cDNA clone yk187b3 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Transcript Cluster.
Annotation Method Description
Annotation Description This probe set was annotated using the Genome Target Overlap based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade B annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_063205
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
SNAP00000013712 ENSEMBL cdna:SNAP chromosome:CEL140:II:7664510:7666851:1 None
F18A1.5.3 ENSEMBL cdna:known chromosome:CEL140:II:7664493:7667018:1 gene:F18A1.5 None
F18A1.5.2 ENSEMBL cdna:known chromosome:CEL140:II:7664494:7667024:1 gene:F18A1.5 None
F18A1.5.1 ENSEMBL cdna:known chromosome:CEL140:II:7664500:7667024:1 gene:F18A1.5 None
NM_063205 NCBI Caenorhabditis elegans F18A1.5 (F18A1.5) mRNA, complete cds. A 
GENEFINDER00000013722 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:7664510:7666851:1 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
chrII:7666523-7666856(+) 91.33 91.33
Public Domain and Genome References
Gene Title replication factor A
Ensembl F18A1.5
Entrez Gene 174238 Entrez gene
SwissProt Q19537 EMBL-EBI
WormBase CE04405 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:247606_AT replication protein, putative at
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6260 DNA replication inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5634 nucleus inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3676 nucleic acid binding inferred from electronic annotation QuickGO AmiGO
3677 DNA binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAB63407 Hypothetical protein F18A1.5 [Caenorhabditis elegans] ref|NP_495606.1| F18A1.5 [Caenorhabditis elegans] sp|Q19537|RFA1_CAEEL Probable replication factor A 73 kDa subunit (RP-A) (RF-A) (Replication factor-A protein 1) 0.0
blast CAA10466 F18A1.5 protein [Caenorhabditis briggsae] emb|CAA10310.1| F18A1.5 protein [Caenorhabditis briggsae] emb|CAE67510.1| Hypothetical protein CBG13026 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR004365 EMBL-EBI OB-fold nucleic acid binding domain 1.0E-10
Sequence
Target Sequence 
>C. ELEGANS:171899_X_AT
atgtcacagctttcggagatagtactgcgaagattgntggaanatcacctccggagcttg
gagaattgcacgatganagcccagatgagnacnacactattttcgtacaccttcagtttg
ttcctgagatgtggagactctcgttgccagatggattcgtacaatgaagaagttcgtcag
aagatgactgtctatggtgtggatgatgtcaatcaggacaagtacatacgcaaatctgaa
gcaaatgatcgagcagatgcttctaatg

BLASTn GenBank NR
Note: "n"'s represent regions that are not probed by the probe sequences.
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATGTCACAGCTTTCGGAGATAGTAC 706 45 15 Antisense
CCGGAGCTTGGAGAATTGCACGATG 331 263 65 Antisense
ACACTATTTTCGTACACCTTCAGTT 300 111 108 Antisense
TTTCGTACACCTTCAGTTTGTTCCT 183 671 115 Antisense
ACACCTTCAGTTTGTTCCTGAGATG 359 109 121 Antisense
GAGATGTGGAGACTCTCGTTGCCAG 684 395 140 Antisense
GAGACTCTCGTTGCCAGATGGATTC 601 393 148 Antisense
TCTCGTTGCCAGATGGATTCGTACA 472 609 153 Antisense
GATGACTGTCTATGGTGTGGATGAT 441 411 197 Antisense
ACAAGTACATACGCAAATCTGAAGC 708 111 232 Antisense
AATGATCGAGCAGATGCTTCTAATG 710 163 258 Antisense
Sequence Source Affymetrix Proprietary Database