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[187353_s_at]

Description Y110A2AL.8 /REP_DB=WormBase Gene ID /WP=CE25194 /TR=Q9N4A1 /GB=AAF60405.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 09      6grp_high1_10_10 > 90      4grp_highest_8_8 > 01      4grp_high_8_8 > 45      6grp_highest_nonorm > 54      6grp_total > 92      4grp_total > 50      6grp_cgc > 97      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1648
1 2 3 4 range
A 861.1
(-2.1)
P 		2170.7
(3)
P 		1869.3
(1.8)
P 		617.1
(-3)
P 		1554
B 652.2
(-2.7)
P 		2077.8
(3)
P 		1735.8
(1.6)
P 		572.1
(-3)
P 		1506
C 618.6
(-2.6)
P 		1874.6
(3)
P 		1737.9
(2.4)
P 		522.3
(-3)
P 		1352
avr 710.6
(-2.4) 		2041
(3) 		1781
(1.9) 		570.5
(-3) 		1471

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1457
1 2 3 4 5 6 range
A 1032.4
(-0.9)
P 		1291.4
(0.6)
P 		999.8
(-1.1)
P 		1078.6
(-0.6)
P 		1705.7
(3)
P 		662.4
(-3)
P 		1043
B 1223.1
(0.9)
P 		1418.2
(2.1)
P 		840.3
(-1.6)
P 		1551
(3)
P 		1488.8
(2.6)
P 		615.7
(-3)
P 		935
C 1054.9
(-0.4)
P 		1304.1
(0.7)
P 		864.6
(-1.1)
P 		1196.9
(0.2)
P 		1870
(3)
P 		412.9
(-3)
P 		1457
avr 1103.5
(-0.1) 		1337.9
(1.1) 		901.6
(-1.2) 		1275.5
(0.8) 		1688.2
(3) 		563.7
(-3) 		1125
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 518
1 2 3 4 range
A 313.5
(0.4)
P 		471.2
(2.7)
P 		488.7
(3)
P 		90.3
(-3)
P 		398
B 208
(-1.7)
P 		513.2
(3)
P 		402.2
(1.3)
P 		121.9
(-3)
P 		391
C 204.8
(-1.6)
P 		539
(2.2)
P 		605.7
(3)
P 		88.1
(-3)
P 		518
avr 242.1
(-0.9) 		507.8
(3) 		498.9
(2.9) 		100.1
(-3) 		408

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 467
1 2 3 4 5 6 range
A 190.3
(-2.5)
P 		459.3
(2.1)
P 		217.7
(-2)
P 		273.6
(-1.1)
P 		514.7
(3)
P 		161.3
(-3)
P 		353
B 425.6
(0.3)
P 		472
(1)
P 		204
(-3)
P 		410.8
(0.1)
P 		604.9
(3)
P 		229.6
(-2.6)
P 		401
C 391
(0.2)
P 		397.9
(0.3)
P 		220.1
(-1.9)
P 		240.7
(-1.7)
P 		605.1
(3)
P 		138.2
(-3)
P 		467
avr 335.6
(-0.6) 		443.1
(1) 		213.9
(-2.4) 		308.4
(-1) 		574.9
(3) 		176.4
(-3) 		399
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 187353_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.4857
Sequence Type Exemplar sequence
Representative Public ID Y110A2AL.8 NCBI
Target Description Y110A2AL.8 /REP_DB=WormBase Gene ID /WP=CE25194 /TR=Q9N4A1 /GB=AAF60405.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=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_061983(11), NM_061982(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_061983 NCBI Caenorhabditis elegans PaTChed family member (ptc-3) (ptc-3) mRNA, complete cds. 11/11 None
NM_061982 NCBI Caenorhabditis elegans PaTChed family member (ptc-3) (ptc-3) mRNA, complete cds. 11/11 None
SNAP00000036281 ENSEMBL cdna:SNAP chromosome:CEL140:II:2844397:2852127:-1 11/11 None
GENEFINDER00000036299 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:2845615:2863268:-1 11/11 None
Y110A2AL.8a ENSEMBL cdna:known chromosome:CEL140:II:2845393:2852592:-1 gene:Y110A2AL.8 11/11 None
Y110A2AL.8b ENSEMBL cdna:known chromosome:CEL140:II:2845615:2852511:-1 gene:Y110A2AL.8 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
chrII:2845613-2852126(-) 100.0 100.0
Public Domain and Genome References
Ensembl Y110A2AL.8
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAT92058 Patched family protein 3, isoform a [Caenorhabditis elegans] ref|NP_494384.2| PaTChed family member (ptc-3) [Caenorhabditis elegans] 0.0
blast AAT92059 Patched family protein 3, isoform b [Caenorhabditis elegans] ref|NP_494383.2| PaTChed family member (ptc-3) [Caenorhabditis elegans] 0.0
blast CAE72420 Hypothetical protein CBG19582 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR003392 EMBL-EBI Patched family 6.5E-9
Pfam IPR003392 EMBL-EBI Patched family 4.1E-15
Pfam IPR003392 EMBL-EBI Patched family 2.9E-6
Pfam IPR003392 EMBL-EBI Patched family 4.1E-15
Pfam IPR003392 EMBL-EBI Patched family 6.5E-9
Pfam IPR003392 EMBL-EBI Patched family 4.1E-15
Pfam IPR003392 EMBL-EBI Patched family 6.5E-9
Pfam IPR003392 EMBL-EBI Patched family 4.1E-15
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_494384.2 10 616-638,650-672,682-704,725-747,757-779,1133-1155,1159-1181,1188-1210,1230-1252,1259-1281
NP_494383.2 10 616-638,650-672,682-704,725-747,757-779,1136-1158,1162-1184,1191-1213,1233-1255,1262-1284
Y110A2AL.8a 10 616-638,650-672,682-704,725-747,757-779,1133-1155,1159-1181,1188-1210,1230-1252,1259-1281
Y110A2AL.8b 10 616-638,650-672,682-704,725-747,757-779,1136-1158,1162-1184,1191-1213,1233-1255,1262-1284
SNAP00000036281 10 625-647,659-681,691-713,734-756,766-788,1142-1164,1168-1190,1197-1219,1239-1261,1268-1290
GENEFINDER00000036299 10 650-672,684-706,716-738,759-781,791-813,1167-1189,1193-1215,1222-1244,1264-1286,1293-1315
Sequence
Target Sequence 
>C. ELEGANS:187353_S_AT
gcagccactcttatcatgtgcatcgtagtgatcactaccatcgagctgggaggattcatg
gggcttatgggcatcaagatgaacccgatttccgctgtaaccctcatctgtgccgtcgga
atcggtgtcgagttcactgctcacgtcgagttggccttcctgacagctctaggaaccatc
gatcaacgcctggagtcttgcctccagcacatgttcgtgccagtctatcacggagccatc
tcaacgttcctcggagttgtgatgcttgtgttctccgagttcgacttcgtcgtcacctac
ttcttctacacaatgacgttgctggtagcgttgggtgtgttcaacgggttgtgtgttctt
ccagtgatccttacgctggtcggcccgaagcctgagctgacaccaaccgatggtagcagt
gtgcttccaccacctccaccattgcggcagcagtacgctg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCAGCCACTCTTATCATGTGCATCG 126 315 3577 Antisense
TCAAGATGAACCCGATTTCCGCTGT 159 631 3650 Antisense
TGCCGTCGGAATCGGTGTCGAGTTC 679 585 3687 Antisense
GGCCTTCCTGACAGCTCTAGGAACC 164 543 3729 Antisense
GAACCATCGATCAACGCCTGGAGTC 672 345 3749 Antisense
GTTCGTGCCAGTCTATCACGGAGCC 655 441 3789 Antisense
CCATCTCAACGTTCCTCGGAGTTGT 541 271 3812 Antisense
CACCTACTTCTTCTACACAATGACG 568 201 3870 Antisense
TCAACGGGTTGTGTGTTCTTCCAGT 523 607 3917 Antisense
TCCAGTGATCCTTACGCTGGTCGGC 295 589 3936 Antisense
CCACCATTGCGGCAGCAGTACGCTG 110 273 4012 Antisense
Sequence Source Affymetrix Proprietary Database