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[193368_s_at] membrane protein patched (ptc) /// membrane protein patched

Description F21H12.4 /REP_DB=WormBase Gene ID /WP=CE01915 /GEN=ptc-2 /TR=Q09540 /GB=AAC46717.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=membrane protein patched (ptc)
Cluster 6grp_high1_10_10 > 28      4grp_high_8_8 > 18      6grp_total > 18      4grp_total > 30      6grp_cgc > 12      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 353
1 2 3 4 range
A 419.7
(3)
P 		154.1
(-1.5)
P 		66.7
(-3)
A 		291.3
(0.8)
P 		353
B 322.8
(2.4)
P 		124.7
(-1.9)
P 		76.4
(-3)
P 		352
(3)
P 		276
C 395.9
(3)
P 		155.8
(-1.7)
P 		89.9
(-3)
P 		298.2
(1.1)
P 		306
avr 379.5
(3) 		144.9
(-1.7) 		77.7
(-3) 		313.8
(1.7) 		302

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 457
1 2 3 4 5 6 range
A 345
(3)
P 		106.3
(-1.7)
P 		40.8
(-3)
P 		84.4
(-2.1)
A 		112.8
(-1.6)
P 		197.9
(0.1)
P 		304
B 250.9
(3)
P 		121.6
(-1.4)
P 		76.5
(-3)
A 		85.1
(-2.7)
P 		103.2
(-2.1)
P 		117.5
(-1.6)
P 		174
C 497.8
(3)
P 		190.2
(-1.3)
P 		65.8
(-3)
A 		87.9
(-2.7)
A 		78.3
(-2.8)
P 		111
(-2.4)
P 		432
avr 364.6
(3) 		139.4
(-1.5) 		61
(-3) 		85.8
(-2.5) 		98.1
(-2.3) 		142.1
(-1.4) 		304
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 135
1 2 3 4 range
A 152.8
(3)
P 		33.5
(-2.3)
P 		17.4
(-3)
A 		42.6
(-1.9)
P 		135
B 103
(3)
P 		30.8
(-2.1)
P 		17.7
(-3)
P 		75
(1)
P 		85
C 131.1
(3)
P 		44.8
(-2.2)
P 		31.3
(-3)
P 		50.3
(-1.9)
P 		100
avr 129
(3) 		36.4
(-2.2) 		22.1
(-3) 		56
(-1.1) 		107

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 176
1 2 3 4 5 6 range
A 63.6
(3)
P 		37.8
(0.2)
P 		8.9
(-3)
P 		21.4
(-1.6)
A 		34
(-0.2)
P 		48.2
(1.3)
P 		55
B 87.3
(3)
P 		40.5
(-1.1)
P 		18.6
(-3)
A 		22.5
(-2.7)
P 		41.9
(-1)
P 		43.8
(-0.8)
P 		69
C 184.5
(3)
P 		58
(-1.5)
P 		16.7
(-3)
A 		17.7
(-3)
A 		25.3
(-2.7)
P 		37.2
(-2.3)
P 		168
avr 111.8
(3) 		45.4
(-1.1) 		14.7
(-3) 		20.5
(-2.6) 		33.7
(-1.8) 		43.1
(-1.2) 		97
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 193368_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.4909
Sequence Type Exemplar sequence
Representative Public ID F21H12.4 NCBI
Target Description F21H12.4 /REP_DB=WormBase Gene ID /WP=CE01915 /GEN=ptc-2 /TR=Q09540 /GB=AAC46717.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=membrane protein patched (ptc)
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), NM_062817(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 
NM_062817 NCBI Caenorhabditis elegans PaTChed family member (ptc-2) (ptc-2) mRNA, complete cds. 11/11 None
SNAP00000015296 ENSEMBL cdna:SNAP chromosome:CEL140:II:6083582:6086217:-1 11/11 None
GENEFINDER00000015302 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:6083455:6086217:-1 10/11 None
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
F21H12.4 ENSEMBL cdna:known chromosome:CEL140:II:6083582:6085812:-1 gene:F21H12.4 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
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:7896717-7899205(+) 93.75 93.75
chrII:6083578-6086214(-) 96.6 100.0
Public Domain and Genome References
Gene Title membrane protein patched (ptc)
membrane protein patched
Gene Symbol ptc-2
ptc-1
Ensembl F21H12.4
ZK675.1
Entrez Gene 174274 Entrez gene
191745 Entrez gene
SwissProt Q09540 EMBL-EBI
Q09614 EMBL-EBI
WormBase CE36831 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
blast NP_495218 PaTChed family member (ptc-2) [Caenorhabditis elegans] gb|AAC46717.2| Patched family protein 2 [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR003392 EMBL-EBI Patched family 5.2E-13
Pfam IPR003392 EMBL-EBI Patched family 5.2E-13
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
NP_495218.2 9 144-166,170-192,218-240,250-269,335-352,548-570,577-599,609-631,644-666
F21H12.4 9 144-166,170-192,218-240,250-269,335-352,548-570,577-599,609-631,644-666
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
SNAP00000015296 9 191-213,217-239,265-287,297-316,382-399,625-647,654-676,686-708,721-743
GENEFINDER00000015302 9 191-213,217-239,265-287,297-316,377-394,543-565,572-594,604-626,647-669
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:193368_S_AT
tttccgaggatgctcgtcttgctcacgctctcatgtgctctcatggttctctatttgagt
gtgctggaagaataggaaagattcgactaattccattctacttaactggcctcacggata
ctgctgtgattgtcgatgccataaaggacatccgaagtgtttgtgaacgatttaccgatc
aaggacttccaaatttcccacaaggaatcgcattcacattctgggaacaatatcttttct
tgactggaaatcttatgcaagccatttcgatcattaccatctctgtcttctgtgtcattt
ccgttcttctttttaatccatgggctgcacttatggttgtttgtattctcggaatcatga
cttgcgaacttgccggattcatgggactcgttggaattaagctcaatccggtttcagccg
taactttgatcaccgcagttggaattggagtcgaattcactgttcatgtggttgtctcat
tcctgacggcgctcggaacaagatctcaacgaacgtcatctgcagttgatcgagttt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTTCCGAGGATGCTCGTCTTGCTCA 706 667 1553 Antisense
TCCATTCTACTTAACTGGCCTCACG 70 591 1644 Antisense
CAAGGACTTCCAAATTTCCCACAAG 236 183 1732 Antisense
GGAATCGCATTCACATTCTGGGAAC 73 533 1756 Antisense
TGCAAGCCATTTCGATCATTACCAT 650 575 1808 Antisense
ATGGGCTGCACTTATGGTTGTTTGT 669 47 1872 Antisense
TGACTTGCGAACTTGCCGGATTCAT 374 569 1910 Antisense
AGCTCAATCCGGTTTCAGCCGTAAC 13 79 1952 Antisense
TTCAGCCGTAACTTTGATCACCGCA 238 687 1965 Antisense
CTGACGGCGCTCGGAACAAGATCTC 190 239 2035 Antisense
ACGTCATCTGCAGTTGATCGAGTTT 295 95 2065 Antisense
Sequence Source Affymetrix Proprietary Database