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[192536_at] membrane protein patched

Description ZK675.1 /REP_DB=WormBase Gene ID /WP=CE01720 /GEN=ptc-1 /TR=Q09614 /GB=CAA86843.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=membrane protein patched
Cluster 4grp_high_8_8 > 10      6grp_total > 27      4grp_total > 22      6grp_cgc > 06      6grp_cgc_sub > Cu      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 375
1 2 3 4 range
A 432.7
(2.7)
P 		142.8
(-2.3)
M 		102.7
(-3)
P 		449.3
(3)
P 		347
B 332.5
(0.5)
P 		151.4
(-2.7)
A 		133.7
(-3)
A 		475.4
(3)
P 		342
C 391.8
(3)
P 		141.2
(-2.2)
P 		100.3
(-3)
P 		361.5
(2.4)
P 		292
avr 385.7
(2.2) 		145.1
(-2.4) 		112.2
(-3) 		428.7
(3) 		317

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 414
1 2 3 4 5 6 range
A 455.5
(3)
P 		142.1
(-1.7)
P 		73.6
(-2.7)
A 		55.6
(-3)
A 		55.4
(-3)
A 		224.5
(-0.5)
P 		400
B 329.4
(3)
P 		143.7
(-0.9)
P 		83
(-2.1)
P 		120.4
(-1.4)
A 		41.3
(-3)
A 		152.8
(-0.7)
P 		288
C 425.4
(3)
P 		146.6
(-1.7)
P 		87.8
(-2.7)
M 		70.7
(-3)
A 		75
(-2.9)
A 		205.9
(-0.7)
P 		355
avr 403.4
(3) 		144.1
(-1.5) 		81.5
(-2.6) 		82.2
(-2.6) 		57.2
(-3) 		194.4
(-0.6) 		346
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 131
1 2 3 4 range
A 157.5
(3)
P 		31
(-2.8)
M 		26.8
(-3)
P 		65.8
(-1.2)
P 		131
B 106
(3)
P 		37.4
(-2.5)
A 		31
(-3)
A 		101.3
(2.6)
P 		75
C 129.7
(3)
P 		40.6
(-2.6)
P 		34.9
(-3)
P 		61
(-1.3)
P 		95
avr 131.1
(3) 		36.3
(-2.7) 		30.9
(-3) 		76
(-0.3) 		100

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 144
1 2 3 4 5 6 range
A 84
(3)
P 		50.5
(0.1)
P 		16
(-2.8)
A 		14.1
(-3)
A 		16.7
(-2.8)
A 		54.7
(0.5)
P 		70
B 114.6
(3)
P 		47.8
(-1.1)
P 		20.2
(-2.8)
P 		31.9
(-2.1)
A 		16.8
(-3)
A 		57
(-0.5)
P 		98
C 157.7
(3)
P 		44.7
(-1.7)
P 		22.3
(-2.7)
M 		14.2
(-3)
A 		24.3
(-2.6)
A 		68.9
(-0.7)
P 		144
avr 118.8
(3) 		47.7
(-1.3) 		19.5
(-3) 		20.1
(-3) 		19.3
(-3) 		60.2
(-0.5) 		100
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192536_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.4746
Sequence Type Exemplar sequence
Representative Public ID ZK675.1 NCBI
Target Description ZK675.1 /REP_DB=WormBase Gene ID /WP=CE01720 /GEN=ptc-1 /TR=Q09614 /GB=CAA86843.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=membrane protein patched
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_063261(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063261 NCBI Caenorhabditis elegans PaTChed family member (ptc-1) (ptc-1) mRNA, complete cds. 11/11 A 
SNAP00000025888 ENSEMBL cdna:SNAP chromosome:CEL140:II:7895310:7899630:1 11/11 None
GENEFINDER00000025899 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:7893187:7899630:1 11/11 None
ZK675.1.1 ENSEMBL cdna:known chromosome:CEL140:II:7893187:7900407:1 gene:ZK675.1 11/11 A 
ZK675.1.2 ENSEMBL cdna:known chromosome:CEL140:II:7893187:7900406:1 gene:ZK675.1 11/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
GENEFINDER00000015302 1/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:7893183-7899627(+) 100.0 100.0
Public Domain and Genome References
Gene Title membrane protein patched
Gene Symbol ptc-1
Ensembl ZK675.1
Entrez Gene 174274 Entrez gene
SwissProt Q09614 EMBL-EBI
WormBase CE01720 Wormbase
Functional Annotations
Ortholog
ID Title Organism
DROSOPHILA_2:1639749_A_AT patched dm
DROSGENOME1:143395_AT patched dm
CHICKEN:GGA.474.1.S1_AT patched homolog (Drosophila) gga
HG-U95AV2:836_AT patched homolog (Drosophila) hs
HC-G110:836_AT patched homolog (Drosophila) hs
HG-U133_PLUS_2:209816_AT patched homolog (Drosophila) hs
HG-U133A:209816_AT patched homolog (Drosophila) hs
HG-U133A_2:209816_AT patched homolog (Drosophila) hs
HG-U133_PLUS_2:208522_S_AT patched homolog (Drosophila) hs
HG-U133A:208522_S_AT patched homolog (Drosophila) hs
HG-U133A_2:208522_S_AT patched homolog (Drosophila) hs
HU35KSUBA:HUM_ALU_AT patched homolog (Drosophila) hs
HU35KSUBB:HUM_ALU_AT patched homolog (Drosophila) hs
HU35KSUBC:HUM_ALU_AT patched homolog (Drosophila) hs
HU35KSUBD:HUM_ALU_AT patched homolog (Drosophila) hs
HUGENEFL:HUM_ALU_AT patched homolog (Drosophila) hs
HC-G110:HUM_ALU_AT patched homolog (Drosophila) hs
HUGENEFL:U43148_AT patched homolog (Drosophila) hs
U133_X3P:G4506246_3P_A_AT patched homolog (Drosophila) hs
U133_X3P:HS2AFFX.1.349.S1_3P_AT patched homolog (Drosophila) hs
U133_X3P:HS.159526.0.S3_3P_AT patched homolog (Drosophila) hs
U133_X3P:HS.159526.0.S2_3P_AT patched homolog (Drosophila) hs
HG-U133_PLUS_2:1555520_AT patched homolog (Drosophila) hs
HG-U133A_2:209815_AT patched homolog (Drosophila) hs
HG-FOCUS:209815_AT patched homolog (Drosophila) hs
HG-U133_PLUS_2:209815_AT patched homolog (Drosophila) hs
HG-U133A:209815_AT patched homolog (Drosophila) hs
HG-U95AV2:38214_AT patched homolog (Drosophila) hs
HG-U95C:59969_AT patched homolog (Drosophila) hs
HG-U95E:90226_AT patched homolog (Drosophila) hs
U133_X3P:HS.125230.0.A1_3P_AT Patched homolog (Drosophila) hs
HG-U133_PLUS_2:238754_AT Patched homolog (Drosophila) hs
HG-U133B:238754_AT Patched homolog (Drosophila) hs
HG-U95E:81835_AT Patched homolog (Drosophila) hs
MOE430A:1450824_AT patched homolog 1 mm
MOUSE430A_2:1450824_AT patched homolog 1 mm
MOUSE430_2:1450824_AT patched homolog 1 mm
MU11KSUBB:MSA.2054.0_S_AT patched homolog 1 mm
MG-U74AV2:104031_AT patched homolog 1 mm
MG-U74BV2:109521_AT patched homolog 1 mm
MOE430A:1428853_AT patched homolog 1 mm
MOUSE430A_2:1428853_AT patched homolog 1 mm
MOUSE430_2:1428853_AT patched homolog 1 mm
MOE430B:1439663_AT Patched homolog 1 (Ptch1), mRNA mm
MOUSE430_2:1439663_AT Patched homolog 1 (Ptch1), mRNA mm
MG-U74AV2:104030_AT Patched homolog 1 (Ptch1), mRNA mm
MG-U74BV2:116032_AT Patched homolog 1 (Ptch1), mRNA mm
MU19KSUBA:TC17247_AT Patched homolog 1 (Ptch1), mRNA mm
MU19KSUBB:TC29936_AT Patched homolog 1 (Ptch1), mRNA mm
RG-U34A:AF079162_AT patched homolog 1 (Drosophila) rn
RAE230A:1398614_AT patched homolog 1 (Drosophila) rn
RAT230_2:1398614_AT patched homolog 1 (Drosophila) rn
RAE230B:1396494_AT Patched homolog 1 (Drosophila) rn
RAT230_2:1396494_AT Patched homolog 1 (Drosophila) rn
Gene Ontology
GO Cellular Component (view graph)
ID Description Evidence Links
16020 membrane inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
8158 hedgehog receptor activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA86843 Hypothetical protein ZK675.1 [Caenorhabditis elegans] ref|NP_495662.1| PaTChed family member (ptc-1) [Caenorhabditis elegans] sp|Q09614|PTC1_CAEEL Patched protein homolog 0.0
blast CAE59824 Hypothetical protein CBG03294 [Caenorhabditis briggsae] 0.0
blast CAE72420 Hypothetical protein CBG19582 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR003392 EMBL-EBI Patched family 4.8E-14
Pfam IPR003392 EMBL-EBI Patched family 4.8E-14
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_495662.1 11 649-668,688-710,714-736,762-784,794-813,902-919,1177-1199,1206-1228,1238-1260,1273-1295,1305-1327
ZK675.1.1 11 649-668,688-710,714-736,762-784,794-813,902-919,1177-1199,1206-1228,1238-1260,1273-1295,1305-1327
ZK675.1.2 11 649-668,688-710,714-736,762-784,794-813,902-919,1177-1199,1206-1228,1238-1260,1273-1295,1305-1327
SNAP00000025888 12 42-64,559-578,598-620,624-646,672-694,704-723,812-829,1087-1109,1116-1138,1148-1170,1183-1205,1215-1237
GENEFINDER00000025899 11 649-668,688-710,714-736,762-784,794-813,902-919,1177-1199,1206-1228,1238-1260,1273-1295,1305-1327
Sequence
Target Sequence 
>C. ELEGANS:192536_AT
tgatcgagtttttgtcccagtcattcatggatcattctccacacttctcggtattttgat
gcttggattctcagagtttgaatttgttgtcaagtatttctttattgtcatgacggctct
gatttgcattggaatcataaacggactcattcttcttccagttttattatcttggtttgg
cccaaggagagagatctctcctactggtggaaagacaacattgaccctgccacctccttt
gccaaagaatgccaactcgtctcgatctggcggcgatgattctgatgaagatgacgagcc
gagtggtcttgtgatgtactcaagacaagcaccccc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGATCGAGTTTTTGTCCCAGTCATT 431 565 3825 Antisense
GTCATGACGGCTCTGATTTGCATTG 548 465 3931 Antisense
CATAAACGGACTCATTCTTCTTCCA 697 191 3960 Antisense
GGTTTGGCCCAAGGAGAGAGATCTC 686 505 3998 Antisense
AGAGAGATCTCTCCTACTGGTGGAA 48 69 4012 Antisense
GGAAAGACAACATTGACCCTGCCAC 547 527 4033 Antisense
CTGCCACCTCCTTTGCCAAAGAATG 155 237 4051 Antisense
CAAAGAATGCCAACTCGTCTCGATC 267 193 4067 Antisense
CGTCTCGATCTGGCGGCGATGATTC 138 247 4082 Antisense
ACGAGCCGAGTGGTCTTGTGATGTA 234 93 4118 Antisense
TGATGTACTCAAGACAAGCACCCCC 183 567 4136 Antisense
Sequence Source Affymetrix Proprietary Database