[Home] | [Total List]

[172268_x_at] --- /// --- /// ---

Description D1025.4 /REP_DB=WormBase Gene ID /WP=CE17612 /TR=O62121 /GB=CAB05471.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 46      6grp_high1_10_10 > 64      4grp_highest_8_8 > 25      4grp_high_8_8 > 60      6grp_highest_nonorm > 29      6grp_total > 64      4grp_total > 60      6grp_cgc > 56      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 16205
1 2 3 4 range
A 13628.4
(2.2)
P 		14337.2
(2.5)
P 		15339.4
(3)
P 		2059.3
(-3)
P 		13280
B 13019.4
(1.2)
P 		14700.2
(1.8)
P 		17950.4
(3)
P 		1745.2
(-3)
P 		16205
C 13550.4
(2.4)
P 		14785.4
(3)
P 		13526.8
(2.4)
P 		2054.7
(-3)
P 		12731
avr 13399.4
(2) 		14607.6
(2.6) 		15605.5
(3) 		1953.1
(-3) 		13652

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 9405
1 2 3 4 5 6 range
A 13286.5
(-1.8)
P 		13051.5
(-2)
P 		19963.8
(3)
P 		13914.9
(-1.4)
P 		11665.7
(-3)
P 		16373.4
(0.4)
P 		8298
B 10558.8
(-3)
P 		13971.6
(-0.5)
P 		18813
(3)
P 		13329.7
(-1)
P 		10657.7
(-2.9)
P 		14655.6
(-0)
P 		8254
C 10699.5
(-3)
P 		13945.5
(0.7)
P 		14411.7
(1.3)
P 		15916.3
(3)
P 		11044
(-2.6)
P 		15853.6
(2.9)
P 		5217
avr 11514.9
(-2.6) 		13656.2
(-0.7) 		17729.5
(3) 		14387
(-0) 		11122.5
(-3) 		15627.5
(1.1) 		6607
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 4661
1 2 3 4 range
A 4962.1
(3)
P 		3112.2
(0.6)
P 		4010
(1.8)
P 		301.4
(-3)
P 		4661
B 4151.8
(3)
P 		3630.6
(2.2)
P 		4159.5
(3)
P 		371.9
(-3)
P 		3788
C 4485.6
(2.7)
P 		4250.9
(2.4)
P 		4714.5
(3)
P 		346.4
(-3)
P 		4368
avr 4533.2
(3) 		3664.6
(1.8) 		4294.7
(2.7) 		339.9
(-3) 		4193

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3016
1 2 3 4 5 6 range
A 2449.3
(-3)
P 		4641.8
(3)
P 		4347.7
(2.2)
P 		3529.1
(-0)
P 		3520.2
(-0.1)
P 		3986.4
(1.2)
P 		2193
B 3674
(-2.6)
P 		4650.6
(0.5)
P 		4568.4
(0.2)
P 		3530.6
(-3)
P 		4330.1
(-0.5)
P 		5465
(3)
P 		1934
C 3965.8
(-0.8)
P 		4255.2
(0)
P 		3668
(-1.7)
P 		3200.8
(-3)
P 		3573.7
(-1.9)
P 		5307.1
(3)
P 		2106
avr 3363
(-3) 		4515.9
(1.4) 		4194.7
(0.2) 		3420.2
(-2.8) 		3808
(-1.3) 		4919.5
(3) 		1557
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172268_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17916
Sequence Type Exemplar sequence
Representative Public ID D1025.4 NCBI
Target Description D1025.4 /REP_DB=WormBase Gene ID /WP=CE17612 /TR=O62121 /GB=CAB05471.1 /SUBMIT=HINXTON /CHR=X /FEA=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_001029341(9), NM_078016(11), NM_078015(10)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001029341 NCBI Caenorhabditis elegans Nematode Specific Peptide family, group C family member (nspc-19) (nspc-19) mRNA, complete cds. 9/11 None
NM_078016 NCBI Caenorhabditis elegans Nematode Specific Peptide family, group C family member (nspc-20) (nspc-20) mRNA, complete cds. 11/11 None
NM_078015 NCBI Caenorhabditis elegans Nematode Specific Peptide family, group C family member (nspc-16) (nspc-16) mRNA, complete cds. 10/11 None
GENEFINDER00000016231 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:14520697:14523875:1 10/11 None
SNAP00000016223 ENSEMBL cdna:SNAP chromosome:CEL140:X:14523522:14523875:1 10/11 None
SNAP00000016227 ENSEMBL cdna:SNAP chromosome:CEL140:X:14528489:14528993:1 9/11 None
SNAP00000016228 ENSEMBL cdna:SNAP chromosome:CEL140:X:14529745:14530150:-1 10/11 None
D1025.6 ENSEMBL cdna:known chromosome:CEL140:X:14523494:14523892:1 gene:D1025.6 10/11 None
D1025.9 ENSEMBL cdna:known chromosome:CEL140:X:14528572:14529117:1 gene:D1025.9 9/11 None
D1025.4 ENSEMBL cdna:known chromosome:CEL140:X:14529704:14530128:-1 gene:D1025.4 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_001029340 8/11 Cross Hyb Matching Probes None
NM_171801 6/11 Cross Hyb Matching Probes None
SNAP00000016224 8/11 Cross Hyb Matching Probes None
GENEFINDER00000016233 8/11 Cross Hyb Matching Probes None
SNAP00000016225 6/11 Cross Hyb Matching Probes None
D1025.8 8/11 Cross Hyb Matching Probes None
D1025.7 6/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrX:14523521-14523875(+) 98.4 98.4
chrX:14528635-14528988(+) 96.79 96.79
chrX:14529744-14530098(-) 100.0 100.0
chrX:14524719-14525072(-) 96.47 96.47
chrX:14527135-14527488(-) 94.87 94.87
Public Domain and Genome References
Gene Title


Gene Symbol nspc-20
nspc-16
nspc-19
Ensembl D1025.6
D1025.9
D1025.4
Entrez Gene 181549 Entrez gene
183904 Entrez gene
3565534 Entrez gene
SwissProt O62121 EMBL-EBI
Q7YST5 EMBL-EBI
WormBase CE17612 Wormbase
CE17612 Wormbase
CE34779 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAB05474 Hypothetical protein D1025.1 [Caenorhabditis elegans] ref|NP_510415.1| D1025.1 [Caenorhabditis elegans] 1.0E-148
blast CAE17765 Hypothetical protein D1025.9 [Caenorhabditis elegans] emb|CAE17764.1| Hypothetical protein D1025.8 [Caenorhabditis elegans] ref|NP_001024512.1| Nematode Specific Peptide family, group C family member (nspc-19) [Caenorhabditis elegans] ref|NP_001024511.1| Nematode Specific Peptide family, group C family member (nspc-17) [Caenorhabditis elegans] 7.0E-58
blast CAE17765 Hypothetical protein D1025.9 [Caenorhabditis elegans] emb|CAE17764.1| Hypothetical protein D1025.8 [Caenorhabditis elegans] ref|NP_001024512.1| Nematode Specific Peptide family, group C family member (nspc-19) [Caenorhabditis elegans] ref|NP_001024511.1| Nematode Specific Peptide family, group C family member (nspc-17) [Caenorhabditis elegans] 8.0E-58
blast CAC42279 Hypothetical protein D1025.6 [Caenorhabditis elegans] emb|CAB05471.1| Hypothetical protein D1025.4 [Caenorhabditis elegans] ref|NP_510416.1| Nematode Specific Peptide family, group C family member (nspc-16) [Caenorhabditis elegans] ref|NP_510417.1| Nematode Specific Peptide family, group C family member (nspc-20) [Caenorhabditis elegans] 8.0E-58
blast CAD44104 Hypothetical protein D1025.7 [Caenorhabditis elegans] ref|NP_741930.1| Nematode Specific Peptide family, group C family member (nspc-18) [Caenorhabditis elegans] 2.0E-57
Protein Domains
Trans Membrane
ID Number Of Domains Domain Boundaries
SNAP00000016227 1 33-55
Sequence
Target Sequence 
>C. ELEGANS:172268_X_AT
ttcttactgccgtagctaccataaccttgaacctctgtcaagagttttgtgcaggtgtca
acggtggagaatcatacgaaaactgttctccatggttgagttatgctactgctaagaaca
agacttgctacaatctctgtgtgcataactgtgctgctgtctatgatggatcgtgtatca
atgaccgtagattcaagtgctgtcttgcaacattcccagca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTCTTACTGCCGTAGCTACCATAAC 66 685 47 Antisense
CTACCATAACCTTGAACCTCTGTCA 580 225 62 Antisense
GAACCTCTGTCAAGAGTTTTGTGCA 64 347 75 Antisense
GTGCAGGTGTCAACGGTGGAGAATC 108 481 95 Antisense
TACGAAAACTGTTCTCCATGGTTGA 511 647 121 Antisense
GACTTGCTACAATCTCTGTGTGCAT 575 371 168 Antisense
GTGTGCATAACTGTGCTGCTGTCTA 560 487 185 Antisense
GTGCTGCTGTCTATGATGGATCGTG 307 479 197 Antisense
GATGGATCGTGTATCAATGACCGTA 334 407 211 Antisense
ATGACCGTAGATTCAAGTGCTGTCT 186 45 227 Antisense
GTGCTGTCTTGCAACATTCCCAGCA 537 479 243 Antisense
Sequence Source Affymetrix Proprietary Database