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[172334_x_at] --- /// --- /// --- /// --- /// --- /// --- /// --- /// ---

Description F42F12.6 /REP_DB=WormBase Gene ID /WP=CE03317 /TR=Q20343 /GB=CAA92172.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 57      6grp_high1_10_10 > 85      4grp_highest_8_8 > 17      4grp_high_8_8 > 61      6grp_highest_nonorm > 28      6grp_total > 75      4grp_total > 59      6grp_cgc > 57      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 10859
1 2 3 4 range
A 7229.9
(0.6)
P 		9767.4
(2)
P 		11461.4
(3)
P 		855
(-3)
P 		10606
B 6291.6
(0.4)
P 		9065.1
(2)
P 		10761.2
(3)
P 		602.9
(-3)
P 		10158
C 5047.3
(-0.4)
P 		8909.5
(2)
P 		10472
(3)
P 		919.9
(-3)
P 		9552
avr 6189.6
(0.2) 		9247.3
(2) 		10898.2
(3) 		792.6
(-3) 		10106

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 15098
1 2 3 4 5 6 range
A 6318.7
(-3)
P 		8731.1
(-1.9)
P 		14269.7
(0.7)
P 		12504.7
(-0.1)
P 		10542.1
(-1)
P 		19057
(3)
P 		12738
B 4391.7
(-3)
P 		9618.3
(-0.6)
P 		13911.8
(1.4)
P 		10737.9
(-0)
P 		10231.6
(-0.3)
P 		17230.8
(3)
P 		12839
C 3959.5
(-3)
P 		9648.5
(-0.5)
P 		12429
(0.8)
P 		12937.8
(1)
P 		9933.6
(-0.3)
P 		17413.4
(3)
P 		13454
avr 4890
(-3) 		9332.6
(-1) 		13536.8
(1) 		12060.1
(0.3) 		10235.8
(-0.5) 		17900.4
(3) 		13010
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 3525
1 2 3 4 range
A 2632.4
(2.2)
P 		2120.2
(1.2)
P 		2996.2
(3)
P 		125.2
(-3)
P 		2871
B 2006.3
(1.8)
P 		2238.9
(2.4)
P 		2493.6
(3)
P 		128.5
(-3)
P 		2365
C 1670.8
(-0.4)
P 		2561.5
(1.1)
P 		3649.8
(3)
P 		155.1
(-3)
P 		3495
avr 2103.2
(1.1) 		2306.9
(1.5) 		3046.5
(3) 		136.3
(-3) 		2910

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 5261
1 2 3 4 5 6 range
A 1164.8
(-3)
P 		3105.2
(0.4)
P 		3107.6
(0.4)
P 		3171.5
(0.5)
P 		3181.1
(0.5)
P 		4639.8
(3)
P 		3475
B 1528.1
(-3)
P 		3201.5
(-0.9)
P 		3378.2
(-0.7)
P 		2844.1
(-1.4)
P 		4157
(0.2)
P 		6425.3
(3)
P 		4897
C 1467.6
(-3)
P 		2944
(-1)
P 		3163.4
(-0.7)
P 		2601.8
(-1.4)
P 		3214.4
(-0.6)
P 		5829.3
(3)
P 		4362
avr 1386.8
(-3) 		3083.6
(-0.6) 		3216.4
(-0.4) 		2872.5
(-0.9) 		3517.5
(0) 		5631.5
(3) 		4245
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172334_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.16980
Sequence Type Exemplar sequence
Representative Public ID F42F12.6 NCBI
Target Description F42F12.6 /REP_DB=WormBase Gene ID /WP=CE03317 /TR=Q20343 /GB=CAA92172.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation
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_001029177, NM_001029178, NM_001029176, NM_001029179, NM_077672, NM_182450, NM_001029486, NM_077673
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
GENEFINDER00000026294 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:8534545:8535756:1 None
GENEFINDER00000026295 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:8541083:8542013:-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 None
NM_077672 NCBI Caenorhabditis elegans Nematode Specific Peptide family, group C family member (nspc-13) (nspc-13) mRNA, complete cds. None
F42F12.9 ENSEMBL cdna:known chromosome:CEL140:X:12343550:12343906:1 gene:F42F12.9 B 
NM_182450 NCBI Caenorhabditis elegans Nematode Specific Peptide family, group C family member (nspc-10) (nspc-10) mRNA, complete cds. B 
NM_077673 NCBI Caenorhabditis elegans Nematode Specific Peptide family, group C family member (nspc-15) (nspc-15) mRNA, complete cds. B 
NM_001029486 NCBI Caenorhabditis elegans Nematode Specific Peptide family, group C family member (nspc-12) (nspc-12) mRNA, complete cds. None
F42F12.10 ENSEMBL cdna:known chromosome:CEL140:X:12356077:12356534:-1 gene:F42F12.10 None
GENEFINDER00000001336 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:12356006:12361042:1 None
SNAP00000001333 ENSEMBL cdna:SNAP chromosome:CEL140:X:12356179:12356668:-1 None
F42F12.8.2 ENSEMBL cdna:known chromosome:CEL140:X:12360665:12361142:1 gene:F42F12.8 B 
F42F12.8.1 ENSEMBL cdna:known chromosome:CEL140:X:12360665:12361144:1 gene:F42F12.8 B 
F42F12.9 ENSEMBL cdna:known chromosome:CEL140:X:12343550:12343906:1 gene:F42F12.9 B 
NM_182450 NCBI Caenorhabditis elegans Nematode Specific Peptide family, group C family member (nspc-10) (nspc-10) mRNA, complete cds. B 
NM_077672 NCBI Caenorhabditis elegans Nematode Specific Peptide family, group C family member (nspc-13) (nspc-13) mRNA, complete cds. None
NM_001029179 NCBI Caenorhabditis elegans Nematode Specific Peptide family, group C family member (nspc-6) (nspc-6) mRNA, complete cds. None
NM_001029176 NCBI Caenorhabditis elegans Nematode Specific Peptide family, group C family member (nspc-3) (nspc-3) mRNA, complete cds. None
GENEFINDER00000026296 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:8536921:8537395:1 None
F42F12.6 ENSEMBL cdna:known chromosome:CEL140:X:12357429:12357779:1 gene:F42F12.6 None
NM_001029178 NCBI Caenorhabditis elegans Nematode Specific Peptide family, group C family member (nspc-5) (nspc-5) mRNA, complete cds. None
NM_001029177 NCBI Caenorhabditis elegans Nematode Specific Peptide family, group C family member (nspc-4) (nspc-4) mRNA, complete cds. None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_171744 1/11 Cross Hyb Matching Probes B 
NM_001029182 1/11 Cross Hyb Matching Probes None
NM_001029181 1/11 Cross Hyb Matching Probes None
NM_077669 7/11 Cross Hyb Matching Probes B 
NM_182449 7/11 Cross Hyb Matching Probes B 
SNAP00000001329 3/11 Cross Hyb Matching Probes None
GENEFINDER00000026297 1/11 Cross Hyb Matching Probes None
C03G5.8 1/11 Cross Hyb Matching Probes None
C03G5.2 1/11 Cross Hyb Matching Probes None
F42F12.1 7/11 Cross Hyb Matching Probes None
F42F12.7 7/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrX:12356307-12357779(+) 100.0 100.0
chrX:12358714-12361042(+) 95.73 95.73
chrX:12343054-12343906(+) 95.33 95.33
chrX:8534791-8537394(+) 91.87 91.87
chrX:12358585-12360913(-) 98.78 98.78
chrX:12342925-12343777(-) 98.17 98.17
chrX:12356178-12357650(-) 96.14 96.14
chrX:8534662-8537265(-) 91.87 91.87
Public Domain and Genome References
Gene Title







Gene Symbol nspc-3
nspc-4
nspc-5
nspc-6
nspc-12
nspc-13
nspc-15
nspc-10
Ensembl F42F12.9
F42F12.10
F42F12.6
F42F12.8
Entrez Gene 181392 Entrez gene
181394 Entrez gene
181396 Entrez gene
185671 Entrez gene
3564795 Entrez gene
3565092 Entrez gene
3565449 Entrez gene
3566000 Entrez gene
SwissProt Q8I4J1 EMBL-EBI
Q20342 EMBL-EBI
Q8I4J0 EMBL-EBI
WormBase CE38675 Wormbase
CE38676 Wormbase
CE38677 Wormbase
CE38677 Wormbase
CE31940 Wormbase
CE31939 Wormbase
CE31940 Wormbase
CE31941 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 CAD54145 Hypothetical protein F42F12.9 [Caenorhabditis elegans] ref|NP_872250.1| Nematode Specific Peptide family, group C family member (nspc-10) [Caenorhabditis elegans] 5.0E-57
blast AAY55844 Nematode specific peptide family, group c protein 4 [Caenorhabditis elegans] ref|NP_001024348.1| Nematode Specific Peptide family, group C family member (nspc-4) [Caenorhabditis elegans] 7.0E-57
blast AAY55847 Nematode specific peptide family, group c protein 2 [Caenorhabditis elegans] gb|AAY55846.1| Nematode specific peptide family, group c protein 6 [Caenorhabditis elegans] gb|AAY55845.1| Nematode specific peptide family, group c protein 5 [Caenorhabditis elegans] ref|NP_001024350.1| Nematode Specific Peptide family, group C family member (nspc-6) [Caenorhabditis elegans] ref|NP_001024353.1| Nematode Specific Peptide family, group C family member (nspc-2) [Caenorhabditis elegans] ref|NP_001024349.1| Nematode Specific Peptide family, group C family member (nspc-5) [Caenorhabditis elegans] 9.0E-57
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] 9.0E-57
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:172334_X_AT
gcaagtcttgtttctgtgagtggcaaaactgatccatggagagcagaatgcgtaagattc
accaccattgacaccagcacagaactcttgacagagttgcaaggtgatggagctgatggc
agaaacaaggcaaagggcaacgagggtgcgaaggaactgcaaggatattcattccttcgc
accctcgttgccctttgccttgtttctgccatcagctccatcaccttgcaactctgtcaa
gagttctgtgctggtgtcaatggtggtgaatcttacgcattctgctctccatggatcagt
tttgccactcaaaccaacaaaacttgctacaatctctgtgttcataattgtgctgctgtc
tatgatggttcctgcacaactgaccctgacttcagatgctgct

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCAAGTCTTGTTTCTGTGAGTGGCA 424 321 31 Antisense
GTAAGATTCACCACCATTGACACCA 91 463 82 Antisense
TTGACACCAGCACAGAACTCTTGAC 346 703 98 Antisense
TCCATCACCTTGCAACTCTGTCAAG 393 591 247 Antisense
GTCAAGAGTTCTGTGCTGGTGTCAA 404 463 266 Antisense
GTGGTGAATCTTACGCATTCTGCTC 565 489 293 Antisense
CATTCTGCTCTCCATGGATCAGTTT 375 217 308 Antisense
GGATCAGTTTTGCCACTCAAACCAA 237 511 323 Antisense
AACTTGCTACAATCTCTGTGTTCAT 330 139 351 Antisense
TGTGCTGCTGTCTATGATGGTTCCT 434 555 379 Antisense
ACTGACCCTGACTTCAGATGCTGCT 77 97 409 Antisense
Sequence Source Affymetrix Proprietary Database