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[175397_at] membrane protein patched

Description AV179000_rc /REP_DB=TREMBL Accession /GB=AV179000 /CHR=2 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk586c8 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 72      6grp_high1_10_10 > 38      4grp_highest_8_8 > 47      4grp_high_8_8 > 11      6grp_highest_nonorm > 0      6grp_total > 27      4grp_total > 13      6grp_highest_sub > Cu      6grp_cgc > 06      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1964
1 2 3 4 range
A 2300.2
(0.6)
P 		1832.4
(-1)
P 		1236.1
(-3)
P 		2999.2
(3)
P 		1763
B 2136.6
(-0.1)
P 		1570.2
(-1.9)
P 		1207.2
(-3)
P 		3155.3
(3)
P 		1948
C 2244.2
(0.7)
P 		1585.1
(-1.6)
P 		1191.1
(-3)
P 		2891.7
(3)
P 		1701
avr 2227
(0.4) 		1662.6
(-1.5) 		1211.5
(-3) 		3015.4
(3) 		1804

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2103
1 2 3 4 5 6 range
A 2690.9
(3)
P 		1580.7
(-0.3)
P 		1043.8
(-1.9)
P 		682.3
(-3)
P 		987.2
(-2.1)
P 		1471
(-0.6)
P 		2009
B 2785.7
(3)
P 		1680.8
(-0.5)
P 		1148.5
(-2.2)
P 		1069.2
(-2.5)
P 		901.4
(-3)
P 		1752.6
(-0.3)
P 		1884
C 2350.6
(3)
P 		1676.7
(0.5)
P 		1035.3
(-1.9)
P 		743.2
(-3)
P 		987.2
(-2.1)
P 		1555.6
(0)
P 		1607
avr 2609.1
(3) 		1646.1
(-0.3) 		1075.9
(-2.2) 		831.6
(-3) 		958.6
(-2.6) 		1593.1
(-0.4) 		1778
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 558
1 2 3 4 range
A 837.5
(3)
P 		397.8
(-2.1)
P 		323.1
(-3)
P 		439
(-1.6)
P 		514
B 681.4
(3)
P 		387.8
(-1.4)
P 		279.7
(-3)
P 		672.4
(2.9)
P 		402
C 742.9
(3)
P 		455.7
(-2.3)
P 		415.1
(-3)
P 		487.6
(-1.7)
P 		328
avr 753.9
(3) 		413.8
(-1.9) 		339.3
(-3) 		533
(-0.2) 		415

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 820
1 2 3 4 5 6 range
A 496
(2)
P 		562.2
(3)
P 		227.3
(-2.2)
P 		173.1
(-3)
P 		297.9
(-1.1)
P 		358.1
(-0.1)
P 		389
B 969.3
(3)
P 		559.5
(-0.6)
P 		278.9
(-3)
P 		283.2
(-3)
P 		366.2
(-2.2)
P 		653.5
(0.3)
P 		690
C 871.3
(3)
P 		511.6
(0)
P 		263.5
(-2.1)
P 		149.5
(-3)
P 		319.4
(-1.6)
P 		520.8
(0.1)
P 		722
avr 778.9
(3) 		544.4
(0.6) 		256.6
(-2.4) 		201.9
(-3) 		327.8
(-1.7) 		510.8
(0.2) 		577
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 175397_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.20808
Sequence Type Exemplar sequence
Representative Public ID AV179000 NCBI
Target Description AV179000_rc /REP_DB=TREMBL Accession /GB=AV179000 /CHR=2 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk586c8 : 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_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 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:7900071-7900351(+) 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
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
Sequence
Target Sequence 
>C. ELEGANS:175397_AT
ttgggtatttattgccacttctcaatcgaaaaaaacatgcgcataatatttactccgagt
gataaaaggggaacggtacaatttagagaaaaaagtacaattgacatatctgtattgttc
acctttttgtattgctttcaattgcacccacttggtctttttcgccgtttgttttgttcc
cctctgtgaatgatctcagcgagctttgggaatttaattatt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTGGGTATTTATTGCCACTTCTCAA 370 705 31 Antisense
TTTATTGCCACTTCTCAATCGAAAA 700 673 38 Antisense
AACATGCGCATAATATTTACTCCGA 189 137 64 Antisense
GCGCATAATATTTACTCCGAGTGAT 179 285 69 Antisense
GACATATCTGTATTGTTCACCTTTT 206 371 133 Antisense
TGTTCACCTTTTTGTATTGCTTTCA 103 563 146 Antisense
TATTGCTTTCAATTGCACCCACTTG 472 665 160 Antisense
TCAATTGCACCCACTTGGTCTTTTT 159 635 168 Antisense
GTTCCCCTCTGTGAATGATCTCAGC 522 441 206 Antisense
GAATGATCTCAGCGAGCTTTGGGAA 252 331 218 Antisense
AGCGAGCTTTGGGAATTTAATTATT 550 75 228 Antisense
Sequence Source Affymetrix Proprietary Database