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[188324_at]

Description C25A11.4A /REP_DB=WormBase Gene ID /WP=CE27083 /GEN=jam-1 /TR=Q18138 /GB=AAK39187.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 40      6grp_high1_10_10 > 15      4grp_highest_8_8 > 40      4grp_high_8_8 > 43      6grp_highest_nonorm > 40      6grp_total > 15      4grp_total > 53      6grp_highest_sub > De      6grp_cgc > 32      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_total_sub > Decrease      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 674
1 2 3 4 range
A 800.2
(3)
P 		740.7
(2.3)
P 		546.1
(0.1)
P 		265.6
(-3)
P 		535
B 822.7
(3)
P 		739.6
(2.1)
P 		582.9
(0.5)
P 		245.6
(-3)
P 		577
C 876.2
(3)
P 		850.7
(2.8)
P 		558.2
(0.2)
P 		202.5
(-3)
P 		674
avr 833
(3) 		777
(2.4) 		562.4
(0.3) 		237.9
(-3) 		595

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 663
1 2 3 4 5 6 range
A 712.5
(0.1)
P 		1009.8
(3)
P 		390.5
(-3)
P 		546.6
(-1.5)
P 		558.9
(-1.4)
P 		526.3
(-1.7)
P 		619
B 781.6
(3)
P 		657.2
(1)
P 		526.7
(-1)
P 		432.5
(-2.5)
P 		432.8
(-2.5)
P 		399.8
(-3)
P 		382
C 990.3
(3)
P 		656.7
(-0.1)
P 		729.5
(0.6)
P 		409.3
(-2.4)
P 		622
(-0.4)
P 		346.4
(-3)
P 		644
avr 828.1
(3) 		774.6
(2.2) 		548.9
(-1.1) 		462.8
(-2.4) 		537.9
(-1.3) 		424.2
(-3) 		404
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 257
1 2 3 4 range
A 291.3
(3)
P 		160.8
(-0.1)
P 		142.8
(-0.5)
P 		38.9
(-3)
P 		252
B 262.4
(3)
P 		182.7
(0.7)
P 		135.1
(-0.6)
P 		52.3
(-3)
P 		210
C 290.1
(3)
P 		244.6
(1.9)
P 		194.5
(0.8)
P 		34.2
(-3)
P 		256
avr 281.3
(3) 		196
(0.9) 		157.5
(-0.1) 		41.8
(-3) 		240

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 285
1 2 3 4 5 6 range
A 131.3
(-2)
P 		359.1
(3)
P 		85
(-3)
P 		138.6
(-1.8)
P 		168.7
(-1.2)
P 		128.1
(-2.1)
P 		274
B 271.9
(3)
P 		218.8
(1)
P 		127.9
(-2.5)
P 		114.6
(-3)
P 		175.9
(-0.7)
P 		149.1
(-1.7)
P 		157
C 367.1
(3)
P 		200.4
(-0.5)
P 		185.7
(-0.8)
P 		82.3
(-3)
P 		201.3
(-0.5)
P 		116
(-2.3)
P 		285
avr 256.8
(2.9) 		259.4
(3) 		132.9
(-2.1) 		111.8
(-3) 		182
(-0.1) 		131.1
(-2.2) 		148
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188324_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17008
Sequence Type Exemplar sequence
Representative Public ID C25A11.4A NCBI
Target Description C25A11.4A /REP_DB=WormBase Gene ID /WP=CE27083 /GEN=jam-1 /TR=Q18138 /GB=AAK39187.1 /SUBMIT=ST.LOUIS /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_171966(9), NM_077135(11), NM_077136(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_171966 NCBI Caenorhabditis elegans Apical Junction Molecule family member (ajm-1) (ajm-1) mRNA, complete cds. 9/11 A 
NM_077135 NCBI Caenorhabditis elegans Apical Junction Molecule family member (ajm-1) (ajm-1) mRNA, complete cds. 11/11 A 
NM_077136 NCBI Caenorhabditis elegans Apical Junction Molecule family member (ajm-1) (ajm-1) mRNA, complete cds. 11/11 A 
GENEFINDER00000000377 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:9100193:9113258:1 11/11 None
SNAP00000000371 ENSEMBL cdna:SNAP chromosome:CEL140:X:9109171:9113258:1 11/11 None
C25A11.4a ENSEMBL cdna:known chromosome:CEL140:X:9098280:9113258:1 gene:C25A11.4 11/11 A 
C25A11.4d ENSEMBL cdna:known chromosome:CEL140:X:9098280:9113534:1 gene:C25A11.4 9/11 A 
C25A11.4c ENSEMBL cdna:known chromosome:CEL140:X:9098280:9110979:1 gene:C25A11.4 11/11 A 
Annotation Notes
There are no noteworthy cross hybridizing mRNAs found for this probe set.
Splice Variants
Entrez Total Refseq Isoforms Total Detected By This Probeset Refseq Probesets
181148 4 3 NM_077135 188324_at (11), 189079_s_at (11)
NM_077136 188324_at (11), 194256_x_at (11)
NM_077137 175053_at (9)
NM_171966 188324_at (9), 189079_s_at (11)
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrX:9103547-9110630(+) 100.0 100.0
Public Domain and Genome References
Ensembl C25A11.4
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAM51517 Apical junction molecule protein 1, isoform d [Caenorhabditis elegans] ref|NP_741868.1| Apical Junction Molecule family member (ajm-1) [Caenorhabditis elegans] 0.0
blast AAK39187 Apical junction molecule protein 1, isoform a [Caenorhabditis elegans] ref|NP_509536.1| Apical Junction Molecule family member (ajm-1) [Caenorhabditis elegans] 0.0
blast CAE57282 Hypothetical protein CBG00187 [Caenorhabditis briggsae] 0.0
blast AAK39188 Apical junction molecule protein 1, isoform c [Caenorhabditis elegans] ref|NP_509537.1| Apical Junction Molecule family member (ajm-1) [Caenorhabditis elegans] 0.0
blast T15598 hypothetical protein C25A11.4a - Caenorhabditis elegans 0.0
Protein Domains
Database ID Description E-Value
scop a.2.7.Seryl-tRNA synthetase (SerRS) All alpha proteins; Long alpha-hairpin; tRNA-binding arm; Seryl-tRNA synthetase (SerRS) 4.80000019073486
scop a.2.7.Seryl-tRNA synthetase (SerRS) All alpha proteins; Long alpha-hairpin; tRNA-binding arm; Seryl-tRNA synthetase (SerRS) 4.09999990463257
scop a.2.7.Seryl-tRNA synthetase (SerRS) All alpha proteins; Long alpha-hairpin; tRNA-binding arm; Seryl-tRNA synthetase (SerRS) 3.90000009536743
Sequence
Target Sequence 
>C. ELEGANS:188324_AT
cgtctatttaccagtcaagccgttattactatccggagaggcatggacagccacagcaca
cggacaatactcgtgccgagtccgtagttgcctacgaacgtgagagccgccgtgaatcac
cagcagaccaagctcacatcagaagccgttctgcagattatctcatggatagaagaatcc
gtgaagaaaccgaggttccagagaaccaacttcaaaaaactcgcgtggaacctcatgatc
agtcaccacgggaatctcgtatttcagaatatgaaatgcgcttccgcaaatcaaccgaga
agctaaccgttcctgactggtaccgtgaaaacagaccacagggtcaaactgctcaaactt
caacctaccgatatggaaatggagttgagccaatgagcaccacaacaacaaccactactg
ttattaatggaacatcttctcatcagcaagcaccccctccagtaccaccacaaccaattg
gaaacattggactgccgcgtggcatgt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CGTCTATTTACCAGTCAAGCCGTTA 396 241 2456 Antisense
AGAGGCATGGACAGCCACAGCACAC 511 67 2492 Antisense
GTTGCCTACGAACGTGAGAGCCGCC 472 439 2542 Antisense
AATCACCAGCAGACCAAGCTCACAT 154 171 2570 Antisense
GAAGCCGTTCTGCAGATTATCTCAT 176 345 2597 Antisense
AACTCGCGTGGAACCTCATGATCAG 234 141 2673 Antisense
GATCAGTCACCACGGGAATCTCGTA 196 421 2692 Antisense
CAACCGAGAAGCTAACCGTTCCTGA 592 185 2747 Antisense
GTCAAACTGCTCAAACTTCAACCTA 346 465 2798 Antisense
TGGAACATCTTCTCATCAGCAAGCA 507 547 2883 Antisense
AACATTGGACTGCCGCGTGGCATGT 619 137 2938 Antisense
Sequence Source Affymetrix Proprietary Database