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[189079_s_at]

Description C25A11.3 /REP_DB=WormBase Gene ID /WP=CE04073 /CHR=X /FEA=Sanger Annotation /DEF=locus:jam-1 (ST.LOUIS) TR:Q18139 protein_id:AAA80390.1
Cluster 6grp_highest_10_10 > 71      6grp_high1_10_10 > 18      4grp_highest_8_8 > 50      4grp_high_8_8 > 40      6grp_highest_nonorm > 50      6grp_total > 18      4grp_total > 55      6grp_highest_sub > De      6grp_cgc > 13      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 492
1 2 3 4 range
A 758
(3)
P 		413.6
(-2.1)
P 		449.8
(-1.6)
P 		355.6
(-3)
P 		402
B 766.2
(3)
P 		431.8
(-1.5)
P 		422.2
(-1.6)
P 		321.1
(-3)
P 		445
C 734.7
(3)
P 		361.1
(-1.9)
P 		394.3
(-1.4)
P 		274.3
(-3)
P 		460
avr 753
(3) 		402.2
(-1.8) 		422.1
(-1.6) 		317
(-3) 		436

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 787
1 2 3 4 5 6 range
A 668.3
(3)
P 		657.7
(2.9)
P 		229
(-3)
P 		393.7
(-0.8)
P 		320.8
(-1.7)
P 		453
(0.1)
P 		439
B 669.6
(3)
P 		468.9
(-0)
P 		291.2
(-2.7)
P 		349.1
(-1.8)
P 		273.1
(-3)
P 		343.1
(-1.9)
P 		397
C 1016.3
(3)
P 		379.9
(-2.3)
P 		350.3
(-2.5)
P 		336.8
(-2.6)
P 		441.3
(-1.8)
P 		290.2
(-3)
P 		726
avr 784.7
(3) 		502.2
(-0.4) 		290.2
(-3) 		359.9
(-2.2) 		345.1
(-2.3) 		362.1
(-2.1) 		495
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 230
1 2 3 4 range
A 276
(3)
P 		89.8
(-2)
P 		117.6
(-1.2)
P 		52.1
(-3)
P 		224
B 244.4
(3)
P 		106.7
(-1.7)
P 		97.8
(-2)
P 		68.4
(-3)
P 		176
C 243.2
(3)
P 		103.8
(-1.2)
P 		137.4
(-0.2)
P 		46.3
(-3)
P 		197
avr 254.5
(3) 		100.1
(-1.7) 		117.6
(-1.1) 		55.6
(-3) 		199

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 327
1 2 3 4 5 6 range
A 123.2
(-0.6)
P 		233.9
(3)
P 		49.9
(-3)
P 		99.8
(-1.4)
P 		96.8
(-1.5)
P 		110.3
(-1)
P 		184
B 233
(3)
P 		156.1
(0.2)
P 		70.7
(-3)
P 		92.5
(-2.2)
P 		111
(-1.5)
P 		128
(-0.9)
P 		162
C 376.7
(3)
P 		115.9
(-2.1)
P 		89.1
(-2.6)
P 		67.7
(-3)
P 		142.8
(-1.5)
P 		97.2
(-2.4)
P 		309
avr 244.3
(3) 		168.6
(0.4) 		69.9
(-3) 		86.7
(-2.4) 		116.9
(-1.4) 		111.8
(-1.6) 		174
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 189079_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17118
Sequence Type Exemplar sequence
Representative Public ID C25A11.3 NCBI
Target Description C25A11.3 /REP_DB=WormBase Gene ID /WP=CE04073 /CHR=X /FEA=Sanger Annotation /DEF=locus:jam-1 (ST.LOUIS) TR:Q18139 protein_id:AAA80390.1
Cluster Evidence This cluster is supported by a 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(11), NM_077135(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. 11/11 A 
NM_077135 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 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 2 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:9111423-9113257(+) 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
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:189079_S_AT
agaaccagagaactatccgcagctagactcttttttgtgtcctgcaagcactgctacaca
tactactgctctagagaatgcaggcataacaattggccaaaccactcgggaagatgttct
tttgcacgaattaatacattatgtaaagatgttatcatgaaagttcgagaggatgaacag
gctcaagctttcatgtcgaaagtcgccagagacggtttttcagttagtgggagaggaagt
gtgaatattcgtctgtcatccccacaactcgcacaggcatacgtcagcaacggatggaga
gcactttccgcttatccaaatgaccaacttctctattactacactgtcaaagctttgatt
gctgaaaggaaagaaccttctttgattgccctttgtaatcggtatgaaccaagagaaaag
ttcattctttccgtgtctatcattgctgacatcgagcactgcccagagactccacctcca
gagacacgcgaactctcagccgtccaattctcctctcctagatcccgctacgaagccatt
cagaat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AGAACCAGAGAACTATCCGCAGCTA 609 73 463 Antisense
GCTAGACTCTTTTTTGTGTCCTGCA 520 303 484 Antisense
GCAAGCACTGCTACACATACTACTG 212 321 506 Antisense
GAACAGGCTCAAGCTTTCATGTCGA 684 351 637 Antisense
GTCGCCAGAGACGGTTTTTCAGTTA 505 475 664 Antisense
TGTGAATATTCGTCTGTCATCCCCA 250 557 702 Antisense
CACAACTCGCACAGGCATACGTCAG 105 195 725 Antisense
ACTTTCCGCTTATCCAAATGACCAA 45 101 765 Antisense
CCAACTTCTCTATTACTACACTGTC 189 277 786 Antisense
TTCTTTCCGTGTCTATCATTGCTGA 433 691 887 Antisense
ATCCCGCTACGAAGCCATTCAGAAT 280 39 984 Antisense
Sequence Source Affymetrix Proprietary Database