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[174162_s_at]

Description C37900_rc /REP_DB=TREMBL Accession /GB=C37900 /CHR=1 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk480e8 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 86      6grp_high1_10_10 > 67      4grp_highest_8_8 > 25      4grp_high_8_8 > 59      6grp_highest_nonorm > 92      6grp_total > 69      4grp_total > 60      6grp_highest_sub > Da      6grp_cgc > 29      6grp_high1_sub > Da      6grp_cgc_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 187
1 2 3 4 range
A 210.4
(0.3)
P 		257.3
(1.8)
P 		293.9
(3)
P 		106.9
(-3)
P 		187
B 288.7
(3)
P 		246.8
(1.6)
P 		249.5
(1.7)
P 		113.5
(-3)
P 		175
C 238.1
(3)
P 		222.2
(1.8)
P 		227
(2.2)
P 		156.8
(-3)
P 		81
avr 245.7
(2.5) 		242.1
(2.3) 		256.8
(3) 		125.7
(-3) 		131

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 471
1 2 3 4 5 6 range
A 263.4
(-0.5)
P 		194.2
(-1.7)
P 		114.5
(-3)
P 		179.9
(-1.9)
P 		222.6
(-1.2)
P 		475.4
(3)
P 		361
B 228.9
(-1.7)
P 		198.6
(-2.2)
P 		147.2
(-3)
P 		156.2
(-2.9)
P 		212
(-2)
P 		529.1
(3)
P 		382
C 247.2
(-1.3)
P 		205.3
(-1.8)
P 		110.5
(-3)
P 		120.3
(-2.9)
P 		223.7
(-1.6)
P 		581.5
(3)
P 		471
avr 246.5
(-1.2) 		199.4
(-1.9) 		124.1
(-3) 		152.1
(-2.6) 		219.4
(-1.6) 		528.7
(3) 		405
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 77
1 2 3 4 range
A 76.6
(3)
P 		55.9
(1)
P 		76.8
(3)
P 		15.6
(-3)
P 		61
B 92.1
(3)
P 		61
(0.3)
P 		57.8
(-0)
P 		24.2
(-3)
P 		68
C 78.8
(3)
P 		63.9
(1.3)
P 		79.1
(3)
P 		26.4
(-3)
P 		53
avr 82.5
(3) 		60.3
(0.8) 		71.2
(1.9) 		22.1
(-3) 		60

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 173
1 2 3 4 5 6 range
A 48.5
(-1.4)
P 		69.1
(-0.1)
P 		24.9
(-3)
P 		45.6
(-1.6)
P 		67.2
(-0.2)
P 		115.7
(3)
P 		91
B 79.6
(-1.4)
P 		66.1
(-1.9)
P 		35.8
(-3)
P 		41.4
(-2.8)
P 		86.1
(-1.1)
P 		197.3
(3)
P 		162
C 91.6
(-0.6)
P 		62.6
(-1.6)
P 		28.1
(-2.9)
P 		24.2
(-3)
P 		72.4
(-1.3)
P 		194.6
(3)
P 		170
avr 73.2
(-1.1) 		65.9
(-1.4) 		29.6
(-3) 		37.1
(-2.7) 		75.2
(-1) 		169.2
(3) 		140
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 174162_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.20393
Sequence Type Exemplar sequence
Representative Public ID C37900 NCBI
Target Description C37900_rc /REP_DB=TREMBL Accession /GB=C37900 /CHR=1 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk480e8 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_059136(11), NM_059137(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059136 NCBI Caenorhabditis elegans HoloCentric chromosome binding Protein family member (hcp-6) (hcp-6) mRNA, complete cds. 11/11 A 
NM_059137 NCBI Caenorhabditis elegans HoloCentric chromosome binding Protein family member (hcp-6) (hcp-6) mRNA, complete cds. 11/11 A 
Y110A7A.1b ENSEMBL cdna:known chromosome:CEL140:I:5165160:5171304:1 gene:Y110A7A.1 11/11 A 
Y110A7A.1a ENSEMBL cdna:known chromosome:CEL140:I:5165160:5171301:1 gene:Y110A7A.1 11/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrI:5170907-5171291(+) 100.0 100.0
Public Domain and Genome References
Ensembl Y110A7A.1
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAK68883 Holocentric chromosome binding protein protein 6, isoform b [Caenorhabditis elegans] ref|NP_491537.1| HoloCentric chromosome binding Protein family member (hcp-6) [Caenorhabditis elegans] 0.0
blast AAF60419 Holocentric chromosome binding protein protein 6, isoform a [Caenorhabditis elegans] ref|NP_491538.1| HoloCentric chromosome binding Protein family member (hcp-6) [Caenorhabditis elegans] 0.0
blast CAE56132 Hypothetical protein CBG23744 [Caenorhabditis briggsae] 0.0
Sequence
Target Sequence 
>C. ELEGANS:174162_S_AT
caagttcatctggtaacactgaaaatgatccactgtcacgcggagtgactccgttgattt
tcgatgaaagtaagcttggtgcaggacgtcattgttcaactccgattcgatcacgagaag
acgcagatccaagcgatgtcacattctcccttaatttgtcggctattaccgaaaaggaag
acttgaaaaacagaagtaagaaagtcaagcttatcaccttcacaatatcttcgaaga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CAAGTTCATCTGGTAACACTGAAAA 209 163 13 Antisense
CACTGAAAATGATCCACTGTCACGC 455 197 29 Antisense
AAAATGATCCACTGTCACGCGGAGT 188 133 34 Antisense
GATCCACTGTCACGCGGAGTGACTC 600 415 39 Antisense
CTGTCACGCGGAGTGACTCCGTTGA 442 239 45 Antisense
AAGTAAGCTTGGTGCAGGACGTCAT 362 155 80 Antisense
AAGCTTGGTGCAGGACGTCATTGTT 206 151 84 Antisense
TCGATCACGAGAAGACGCAGATCCA 318 603 119 Antisense
GACGCAGATCCAAGCGATGTCACAT 375 379 132 Antisense
AAGCTTATCACCTTCACAATATCTT 165 151 219 Antisense
ATCACCTTCACAATATCTTCGAAGA 163 29 225 Antisense
Sequence Source Affymetrix Proprietary Database