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[173260_s_at]

Description C51978_rc /REP_DB=TREMBL Accession /GB=C51978 /FEA=Transcript Cluster /DEF=C.elegans cDNA clone yk224a10 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 77      6grp_high1_10_10 > 77      4grp_highest_8_8 > 09      4grp_high_8_8 > 53      6grp_highest_nonorm > 95      6grp_total > 77      4grp_total > 58      6grp_highest_sub > Da      6grp_cgc > 48      6grp_high1_sub > Da      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 579
1 2 3 4 range
A 526.6
(-0)
P 		764
(2.7)
P 		793.6
(3)
P 		266.1
(-3)
P 		528
B 357.6
(-2.6)
P 		806.5
(3)
P 		729
(2)
P 		328.5
(-3)
P 		478
C 548.2
(0.2)
P 		708.8
(1.9)
P 		819.6
(3)
P 		241.1
(-3)
P 		579
avr 477.5
(-0.6) 		759.8
(2.8) 		780.7
(3) 		278.6
(-3) 		502

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1541
1 2 3 4 5 6 range
A 340.1
(-3)
P 		447.1
(-2.6)
P 		460.4
(-2.5)
P 		414.1
(-2.7)
P 		788.1
(-1.3)
P 		1880.8
(3)
P 		1541
B 518.1
(-2.6)
P 		442.9
(-3)
P 		558.6
(-2.4)
P 		690.1
(-1.7)
P 		729.8
(-1.5)
P 		1605.3
(3)
P 		1162
C 562.1
(-2.5)
P 		452.9
(-3)
P 		614.4
(-2.2)
P 		778.8
(-1.4)
P 		770.6
(-1.5)
P 		1688.7
(3)
P 		1236
avr 473.4
(-2.9) 		447.6
(-3) 		544.5
(-2.5) 		627.7
(-2.2) 		762.8
(-1.5) 		1724.9
(3) 		1277
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 247
1 2 3 4 range
A 191.7
(2.4)
P 		165.8
(1.5)
P 		207.5
(3)
P 		39
(-3)
P 		169
B 114
(-1)
P 		199.2
(3)
P 		168.9
(1.6)
P 		70
(-3)
P 		129
C 181.5
(0.4)
P 		203.8
(1)
P 		285.6
(3)
P 		40.7
(-3)
P 		245
avr 162.4
(1) 		189.6
(1.9) 		220.7
(3) 		49.9
(-3) 		171

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 536
1 2 3 4 5 6 range
A 62.7
(-3)
P 		159
(-1.5)
P 		100.3
(-2.4)
P 		105
(-2.4)
P 		237.8
(-0.3)
P 		457.9
(3)
P 		395
B 180.3
(-2.4)
P 		147.4
(-2.8)
P 		135.6
(-3)
P 		182.8
(-2.4)
P 		296.5
(-0.9)
P 		598.6
(3)
P 		463
C 208.3
(-2)
P 		138.2
(-3)
P 		156.4
(-2.7)
P 		156.6
(-2.7)
P 		249.4
(-1.4)
P 		565.3
(3)
P 		427
avr 150.4
(-2.7) 		148.2
(-2.7) 		130.8
(-3) 		148.1
(-2.7) 		261.2
(-1.1) 		540.6
(3) 		410
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173260_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.28007
Sequence Type Exemplar sequence
Representative Public ID C51978 NCBI
Target Description C51978_rc /REP_DB=TREMBL Accession /GB=C51978 /FEA=Transcript Cluster /DEF=C.elegans cDNA clone yk224a10 : 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 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_073088(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073088 NCBI Caenorhabditis elegans HoloCentric chromosome binding Protein family member (hcp-2) (hcp-2) mRNA, complete cds. 11/11 A 
SNAP00000007444 ENSEMBL cdna:SNAP chromosome:CEL140:V:9643239:9652688:1 11/11 None
GENEFINDER00000007457 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:9648445:9652688:1 11/11 None
T06E4.1 ENSEMBL cdna:known chromosome:CEL140:V:9648424:9652881:1 gene:T06E4.1 11/11 A 
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
chrV:9652464-9652697(+) 75.82 75.82
Public Domain and Genome References
Gene Title
Gene Symbol hcp-2
Ensembl T06E4.1
Entrez Gene 179353 Entrez gene
SwissProt Q22257 EMBL-EBI
WormBase CE06368 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAA94789 Hypothetical protein T06E4.1 [Caenorhabditis elegans] ref|NP_505489.1| HoloCentric chromosome binding Protein family member (hcp-2) [Caenorhabditis elegans] 0.0
blast CAE70092 Hypothetical protein CBG16534 [Caenorhabditis briggsae] 0.0
blast AAC19259 Holocentric chromosome binding protein protein 1 [Caenorhabditis elegans] ref|NP_504677.1| HoloCentric chromosome binding Protein family member (hcp-1) [Caenorhabditis elegans] 1.0E-141
Sequence
Target Sequence 
>C. ELEGANS:173260_S_AT
gccgctgagtcgtgaacattctcatgcggagccaccagagcctgttgttgaggacaagtt
cgaagatgctcaggattcgttccaagaagagttttcccattcgccagatgatatcacgtc
atctacggtactccatccagatgatcatnttcaagaaacaactgcagttgaaacgccgtc
gaagaaggcgaaccgctcaaactgcaaccagcaata

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
GCCGCTGAGTCGTGAACATTCTCAT 668 285 63 Antisense
CGTGAACATTCTCATGCGGAGCCAC 678 243 73 Antisense
GCCACCAGAGCCTGTTGTTGAGGAC 298 279 93 Antisense
GAAGATGCTCAGGATTCGTTCCAAG 132 339 124 Antisense
CAAGAAGAGTTTTCCCATTCGCCAG 648 185 145 Antisense
TATCACGTCATCTACGGTACTCCAT 522 657 174 Antisense
TCTACGGTACTCCATCCAGATGATC 140 615 184 Antisense
ACAACTGCAGTTGAAACGCCGTCGA 146 111 220 Antisense
TGAAACGCCGTCGAAGAAGGCGAAC 594 571 231 Antisense
GAAGGCGAACCGCTCAAACTGCAAC 390 333 246 Antisense
ACCGCTCAAACTGCAACCAGCAATA 489 89 254 Antisense
Sequence Source Affymetrix Proprietary Database