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[177583_at]

Description T22C8.8 /REP_DB=WormBase Gene ID /WP=CE16439 /TR=O18108 /GB=CAA88880.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 0      6grp_high1_10_10 > 08      4grp_highest_8_8 > 52      4grp_high_8_8 > 17      6grp_highest_nonorm > 71      6grp_total > 09      4grp_total > 31      6grp_cgc > 10      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 140
1 2 3 4 range
A 332
(3)
P 		238.3
(-2.3)
P 		226.1
(-3)
P 		313.8
(2)
P 		106
B 365.6
(3)
P 		227.5
(-3)
P 		250.2
(-2)
P 		281.4
(-0.7)
P 		138
C 350.8
(3)
P 		350.2
(2.9)
P 		291.1
(-3)
P 		298.6
(-2.2)
P 		60
avr 349.5
(3) 		272
(-2) 		255.8
(-3) 		297.9
(-0.3) 		94

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 297
1 2 3 4 5 6 range
A 384.2
(1.4)
P 		347.2
(0.3)
P 		322.4
(-0.5)
P 		437.3
(3)
P 		281.2
(-1.7)
P 		238.4
(-3)
P 		199
B 398.5
(3)
P 		319
(-0.1)
P 		310.7
(-0.4)
P 		292.9
(-1.1)
P 		318.2
(-0.1)
P 		243.6
(-3)
P 		155
C 535.3
(3)
P 		328.9
(-1.5)
P 		330.1
(-1.5)
P 		346.9
(-1.1)
P 		343
(-1.2)
P 		262.8
(-3)
P 		273
avr 439.3
(3) 		331.7
(-0.4) 		321.1
(-0.7) 		359
(0.5) 		314.1
(-0.9) 		248.3
(-3) 		191
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 75
1 2 3 4 range
A 120.9
(3)
P 		51.7
(-2.5)
P 		59.1
(-1.9)
P 		45.9
(-3)
P 		75
B 116.6
(3)
P 		56.2
(-3)
P 		58
(-2.8)
P 		60
(-2.6)
P 		60
C 116.1
(3)
P 		100.7
(1.6)
P 		101.5
(1.7)
P 		50.3
(-3)
P 		66
avr 117.9
(3) 		69.5
(-1.4) 		72.9
(-1.1) 		52.1
(-3) 		66

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 140
1 2 3 4 5 6 range
A 70.8
(-1.8)
P 		123.5
(3)
P 		70.2
(-1.9)
P 		110.9
(1.8)
P 		84.8
(-0.5)
P 		58
(-3)
P 		66
B 138.7
(3)
P 		106.2
(-0.1)
P 		75.4
(-3)
P 		77.6
(-2.8)
P 		129.3
(2.1)
P 		90.8
(-1.5)
P 		63
C 198.4
(3)
P 		100.4
(-1.6)
P 		84
(-2.3)
P 		69.8
(-3)
P 		111
(-1.1)
P 		88
(-2.2)
P 		129
avr 136
(3) 		110
(0.4) 		76.5
(-3) 		86.1
(-2) 		108.4
(0.2) 		78.9
(-2.8) 		60
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 177583_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3174
Sequence Type Exemplar sequence
Representative Public ID T22C8.8 NCBI
Target Description T22C8.8 /REP_DB=WormBase Gene ID /WP=CE16439 /TR=O18108 /GB=CAA88880.1 /SUBMIT=HINXTON /CHR=2 /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_063435(10)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063435 NCBI Caenorhabditis elegans Variable ABnormal morphology family member (vab-9) (vab-9) mRNA, complete cds. 10/11 None
SNAP00000014913 ENSEMBL cdna:SNAP chromosome:CEL140:II:8636411:8637595:-1 10/11 None
GENEFINDER00000014919 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:8636411:8637632:-1 10/11 None
T22C8.8 ENSEMBL cdna:known chromosome:CEL140:II:8636155:8637632:-1 gene:T22C8.8 10/11 None
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:8636407-8637592(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol vab-9
Ensembl T22C8.8
Entrez Gene 188736 Entrez gene
SwissProt O18108 EMBL-EBI
WormBase CE32938 Wormbase
Functional Annotations
Ortholog
ID Title Organism
DROSGENOME1:150396_AT dm
DROSOPHILA_2:1630752_AT dm
Protein Similarities
Method ID Description E-Value
blast CAA88880 Hypothetical protein T22C8.8 [Caenorhabditis elegans] ref|NP_495836.2| Variable ABnormal morphology family member (vab-9) [Caenorhabditis elegans] gb|AAP31908.1| cell junction protein VAB-9 [Caenorhabditis elegans] 3.0E-99
blast CAA88880 Hypothetical protein T22C8.8 [Caenorhabditis elegans] ref|NP_495836.2| Variable ABnormal morphology family member (vab-9) [Caenorhabditis elegans] gb|AAP31908.1| cell junction protein VAB-9 [Caenorhabditis elegans] 4.0E-99
blast CAE57544 Hypothetical protein CBG00522 [Caenorhabditis briggsae] 5.0E-82
blast AAR88558 LD08231p [Drosophila melanogaster] gb|AAF56054.1| CG6982-PA [Drosophila melanogaster] ref|NP_651089.1| CG6982-PA [Drosophila melanogaster] 7.0E-31
Protein Domains
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_495836.2 4 21-43,88-110,131-153,168-187
T22C8.8 4 21-43,88-110,131-153,168-187
SNAP00000014913 4 21-43,88-110,131-153,168-187
GENEFINDER00000014919 4 34-56,101-123,144-166,181-200
Sequence
Target Sequence 
>C. ELEGANS:177583_AT
ggatcattcagaacgggtctcttcaaagaatgcacatcaacaaatgagccaactcatgct
gctccattccctggtgcacctgctcctggttcatgtcacaagccatcgaggaattctgga
ttccttaccgcagcagctgttcttctcattgttgctctattcctcactgcactttctacc
attttcaatattgttggactcagcaaatcagatgtccgtggaaaatatcgatggtaccga
attgcgacaatgatttctggattttctggtgagtttttcagagttttttttttttttttt
ttgcaaattaatcaaattggtataatttcaaagcgacataatgaaattttaatgaccgtc
actgaatttttaaaaattcaatttgtctttctactggaattgaccgctttgattatgttc
ccagctgcattctacgtaaaaataagtgactacggtagccgcaggaactg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGATCATTCAGAACGGGTCTCTTCA 420 511 148 Antisense
AAATGAGCCAACTCATGCTGCTCCA 463 119 189 Antisense
TGCTCCTGGTTCATGTCACAAGCCA 364 581 228 Antisense
GGAATTCTGGATTCCTTACCGCAGC 639 533 257 Antisense
TTACCGCAGCAGCTGTTCTTCTCAT 505 681 272 Antisense
GACTCAGCAAATCAGATGTCCGTGG 612 371 344 Antisense
CGATGGTACCGAATTGCGACAATGA 446 247 376 Antisense
GTCTTTCTACTGGAATTGACCGCTT 476 467 532 Antisense
TTGACCGCTTTGATTATGTTCCCAG 56 705 547 Antisense
TGTTCCCAGCTGCATTCTACGTAAA 131 563 563 Antisense
GTGACTACGGTAGCCGCAGGAACTG 467 481 593 Antisense
Sequence Source Affymetrix Proprietary Database