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[194245_x_at]

Description CEK071F8R_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F42F12.1 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D65968 /WB_GENE_ID=F42F12.1 /WP=CE03312 /CHR=X /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk71f8 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 57      6grp_high1_10_10 > 85      4grp_highest_8_8 > 18      4grp_high_8_8 > 62      6grp_highest_nonorm > 28      6grp_total > 75      4grp_total > 58      6grp_cgc > 57      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 11431
1 2 3 4 range
A 5130
(-0.6)
P 		7441.2
(0.6)
P 		11923.1
(3)
P 		716.4
(-3)
P 		11207
B 4272.8
(-0.3)
P 		7117.1
(1.7)
P 		8930.6
(3)
P 		492.1
(-3)
P 		8439
C 3610.3
(-0.9)
P 		7580.8
(1.9)
P 		9063.8
(3)
P 		726
(-3)
P 		8338
avr 4337.7
(-0.6) 		7379.7
(1.3) 		9972.5
(3) 		644.8
(-3) 		9328

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 14801
1 2 3 4 5 6 range
A 5778.3
(-3)
P 		6732.1
(-2.5)
P 		13224.8
(1)
P 		12044.8
(0.3)
P 		9642.5
(-0.9)
P 		17073.4
(3)
P 		11295
B 3757
(-3)
P 		8839.5
(-0.8)
P 		12180.1
(0.7)
P 		10009
(-0.2)
P 		9701.1
(-0.4)
P 		17375.5
(3)
P 		13619
C 3088
(-3)
P 		9302.8
(-0.5)
P 		10719
(0.1)
P 		12275.9
(0.7)
P 		8706.3
(-0.7)
P 		17888.8
(3)
P 		14801
avr 4207.8
(-3) 		8291.5
(-1.1) 		12041.3
(0.6) 		11443.2
(0.3) 		9350
(-0.7) 		17445.9
(3) 		13238
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 3054
1 2 3 4 range
A 1867.8
(0.5)
P 		1615.3
(0)
P 		3116.9
(3)
P 		104.9
(-3)
P 		3012
B 1362.6
(0.8)
P 		1757.8
(2)
P 		2069.4
(3)
P 		104.9
(-3)
P 		1965
C 1195.1
(-0.9)
P 		2179.5
(1.1)
P 		3159
(3)
P 		122.4
(-3)
P 		3037
avr 1475.2
(0.1) 		1850.9
(0.9) 		2781.8
(3) 		110.7
(-3) 		2671

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 5414
1 2 3 4 5 6 range
A 1065.2
(-3)
P 		2394.3
(-0.4)
P 		2880.1
(0.5)
P 		3054.8
(0.9)
P 		2909.7
(0.6)
P 		4156.8
(3)
P 		3092
B 1307.3
(-3)
P 		2942.3
(-1.1)
P 		2957.7
(-1.1)
P 		2651
(-1.4)
P 		3941.4
(0.1)
P 		6479.2
(3)
P 		5172
C 1144.6
(-3)
P 		2838.6
(-0.9)
P 		2728.2
(-1)
P 		2468.7
(-1.4)
P 		2817.2
(-0.9)
P 		5988.4
(3)
P 		4844
avr 1172.4
(-3) 		2725.1
(-0.9) 		2855.3
(-0.7) 		2724.8
(-0.9) 		3222.8
(-0.2) 		5541.5
(3) 		4369
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 194245_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.25760
Sequence Type Exemplar sequence
Representative Public ID CEK071F8R NCBI
Target Description CEK071F8R_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F42F12.1 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D65968 /WB_GENE_ID=F42F12.1 /WP=CE03312 /CHR=X /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk71f8 : 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 Genome Target Overlap based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade B annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_077672, NM_001029176
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
GENEFINDER00000001338 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:12340490:12343777:-1 None
GENEFINDER00000001336 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:12356006:12361042:1 None
NM_001029176 NCBI Caenorhabditis elegans Nematode Specific Peptide family, group C family member (nspc-3) (nspc-3) mRNA, complete cds. None
F42F12.6 ENSEMBL cdna:known chromosome:CEL140:X:12357429:12357779:1 gene:F42F12.6 A 
SNAP00000001333 ENSEMBL cdna:SNAP chromosome:CEL140:X:12356179:12356668:-1 None
NM_077672 NCBI Caenorhabditis elegans Nematode Specific Peptide family, group C family member (nspc-13) (nspc-13) mRNA, complete cds. A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_001029179 2/11 Cross Hyb Matching Probes None
NM_001029178 2/11 Cross Hyb Matching Probes None
NM_001029177 2/11 Cross Hyb Matching Probes None
NM_171744 2/11 Cross Hyb Matching Probes B 
NM_001029182 2/11 Cross Hyb Matching Probes None
NM_001029181 2/11 Cross Hyb Matching Probes None
NM_077669 8/11 Cross Hyb Matching Probes None
NM_182450 5/11 Cross Hyb Matching Probes None
NM_001029486 6/11 Cross Hyb Matching Probes None
NM_182449 6/11 Cross Hyb Matching Probes None
NM_077673 6/11 Cross Hyb Matching Probes None
SNAP00000001329 4/11 Cross Hyb Matching Probes None
GENEFINDER00000026294 2/11 Cross Hyb Matching Probes None
GENEFINDER00000026296 3/11 Cross Hyb Matching Probes None
GENEFINDER00000026297 2/11 Cross Hyb Matching Probes None
GENEFINDER00000026295 2/11 Cross Hyb Matching Probes None
C03G5.8 2/11 Cross Hyb Matching Probes None
C03G5.2 2/11 Cross Hyb Matching Probes None
F42F12.1 8/11 Cross Hyb Matching Probes None
F42F12.9 5/11 Cross Hyb Matching Probes None
F42F12.10 6/11 Cross Hyb Matching Probes None
F42F12.7 6/11 Cross Hyb Matching Probes None
F42F12.8.2 6/11 Cross Hyb Matching Probes B 
F42F12.8.1 6/11 Cross Hyb Matching Probes B 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrX:12356306-12357780(+) 90.09 90.09
chrX:12342886-12343778(-) 100.0 100.0
chrX:12358546-12360914(-) 97.2 97.2
chrX:12353422-12357651(-) 92.15 92.15
Public Domain and Genome References
Gene Title

Gene Symbol nspc-3
nspc-13
Ensembl F42F12.6
Entrez Gene 185671 Entrez gene
3565449 Entrez gene
SwissProt Q20342 EMBL-EBI
WormBase CE38675 Wormbase
CE31939 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAA92170 Hypothetical protein F42F12.2 [Caenorhabditis elegans] ref|NP_510069.1| 2 (Zwei) IG-domain protein family member (zig-2) [Caenorhabditis elegans] gb|AAL59607.1| secreted 2-immunoglobulin-domain protein ZIG-2 [Caenorhabditis elegans] 1.0E-124
blast AAY55843 Nematode specific peptide family, group c protein 3 [Caenorhabditis elegans] ref|NP_001024347.1| Nematode Specific Peptide family, group C family member (nspc-3) [Caenorhabditis elegans] 4.0E-57
blast CAA92172 Hypothetical protein F42F12.6 [Caenorhabditis elegans] emb|CAA92171.2| Hypothetical protein F42F12.7 [Caenorhabditis elegans] ref|NP_510073.2| Nematode Specific Peptide family, group C family member (nspc-13) [Caenorhabditis elegans] ref|NP_872249.1| Nematode Specific Peptide family, group C family member (nspc-14) [Caenorhabditis elegans] 1.0E-56
blast AAU05596 Nematode specific peptide family, group c protein 1 [Caenorhabditis elegans] ref|NP_001024352.1| Nematode Specific Peptide family, group C family member (nspc-1) [Caenorhabditis elegans] 2.0E-56
blast CAH60761 Hypothetical protein F42F12.10 [Caenorhabditis elegans] emb|CAD54144.1| Hypothetical protein F42F12.8 [Caenorhabditis elegans] ref|NP_510074.2| Nematode Specific Peptide family, group C family member (nspc-15) [Caenorhabditis elegans] ref|NP_001024657.1| Nematode Specific Peptide family, group C family member (nspc-12) [Caenorhabditis elegans] 3.0E-56
blast CAA92174 Hypothetical protein F42F12.1 [Caenorhabditis elegans] ref|NP_510070.2| Nematode Specific Peptide family, group C family member (nspc-9) [Caenorhabditis elegans] 6.0E-56
blast AAL65774 Nematode specific peptide family, group c protein 7 [Caenorhabditis elegans] ref|NP_741862.1| Nematode Specific Peptide family, group C family member (nspc-7) [Caenorhabditis elegans] 1.0E-55
blast CAH60761 Hypothetical protein F42F12.10 [Caenorhabditis elegans] emb|CAD54144.1| Hypothetical protein F42F12.8 [Caenorhabditis elegans] ref|NP_510074.2| Nematode Specific Peptide family, group C family member (nspc-15) [Caenorhabditis elegans] ref|NP_001024657.1| Nematode Specific Peptide family, group C family member (nspc-12) [Caenorhabditis elegans] 3.0E-55
Protein Domains
Database ID Description E-Value
Pfam IPR007110 EMBL-EBI Immunoglobulin-like 0.043
Pfam IPR007110 EMBL-EBI Immunoglobulin-like 0.0015
Trans Membrane
ID Number Of Domains Domain Boundaries
SNAP00000001333 1 15-37
Sequence
Target Sequence 
>C. ELEGANS:194245_X_AT
gtaagattcaccaccattgacaccagcacagaactcttgacagagttgcaaggtgatgga
gctgatggcagaaacaaggcaaaggacaacgagggtgcgaaggaactgcaaggatattca
atgttacttcgcaccctcgttgccctttgcttggtttctgccatcagctccatcaccttg
caactctgtcaagagttctgtgctggtgtcaatggtggtgaatcttacgcattctgctct
ccatggatcagttttgccactcaaaccaacaaaacttgctacaatctctgtgttcataac
tgtgctgctgtctatgatggttcctgcacaactgatcctgacttcagatgctgcttgaaa
accactcca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTAAGATTCACCACCATTGACACCA 92 463 83 Antisense
TTGACACCAGCACAGAACTCTTGAC 347 703 99 Antisense
ATATTCAATGTTACTTCGCACCCTC 511 19 196 Antisense
TCCATCACCTTGCAACTCTGTCAAG 394 591 251 Antisense
GTCAAGAGTTCTGTGCTGGTGTCAA 405 463 270 Antisense
GTGGTGAATCTTACGCATTCTGCTC 566 489 297 Antisense
CATTCTGCTCTCCATGGATCAGTTT 376 217 312 Antisense
AACTTGCTACAATCTCTGTGTTCAT 331 139 355 Antisense
GTGTTCATAACTGTGCTGCTGTCTA 217 485 372 Antisense
TGCTGTCTATGATGGTTCCTGCACA 320 579 388 Antisense
CAGATGCTGCTTGAAAACCACTCCA 235 207 427 Antisense
Sequence Source Affymetrix Proprietary Database