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[188333_s_at]

Description C25A11.4B /REP_DB=WormBase Gene ID /WP=CE27084 /GEN=jam-1 /TR=Q18137 /GB=AAK39186.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 40      6grp_high1_10_10 > 05      4grp_highest_8_8 > 48      4grp_high_8_8 > 42      6grp_highest_nonorm > 20      6grp_total > 05      4grp_total > 53      6grp_highest_sub > De      6grp_cgc > 22      6grp_high1_sub > De      6grp_cgc_sub > De      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1312
1 2 3 4 range
A 1651
(3)
P 		1284.4
(1)
P 		914.9
(-1)
P 		541.3
(-3)
P 		1110
B 1709.6
(3)
P 		1316.1
(0.8)
P 		1030.9
(-0.8)
P 		650.7
(-3)
P 		1059
C 1739.1
(3)
P 		1443
(1.6)
P 		1141.1
(0.3)
P 		427.6
(-3)
P 		1312
avr 1699.9
(3) 		1347.8
(1.2) 		1029
(-0.5) 		539.9
(-3) 		1160

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1465
1 2 3 4 5 6 range
A 1292.5
(1)
P 		1621.9
(3)
P 		627.2
(-3)
P 		962.7
(-1)
P 		692.7
(-2.6)
P 		707.6
(-2.5)
P 		995
B 1598.1
(3)
P 		1246.7
(1.1)
P 		848.2
(-1.1)
P 		731.2
(-1.8)
P 		640.3
(-2.3)
P 		507.3
(-3)
P 		1091
C 1896.5
(3)
P 		1037.2
(-0.5)
P 		1063.6
(-0.4)
P 		547.3
(-2.5)
P 		978
(-0.8)
P 		431.5
(-3)
P 		1465
avr 1595.7
(3) 		1301.9
(1.3) 		846.3
(-1.3) 		747.1
(-1.9) 		770.3
(-1.7) 		548.8
(-3) 		1047
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 529
1 2 3 4 range
A 601.1
(3)
P 		278.8
(-0.7)
P 		239.2
(-1.2)
P 		79.2
(-3)
P 		522
B 545.2
(3)
P 		325.1
(-0.2)
P 		238.9
(-1.5)
P 		138.7
(-3)
P 		407
C 575.7
(3)
P 		414.9
(1.1)
P 		397.7
(0.9)
P 		72.1
(-3)
P 		504
avr 574
(3) 		339.6
(0.1) 		291.9
(-0.5) 		96.7
(-3) 		477

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 593
1 2 3 4 5 6 range
A 238.3
(-1.6)
P 		576.8
(3)
P 		136.6
(-3)
P 		244.2
(-1.5)
P 		209
(-2)
P 		172.3
(-2.5)
P 		440
B 556.1
(3)
P 		415
(0.7)
P 		206
(-2.7)
P 		193.7
(-2.9)
P 		260.1
(-1.8)
P 		189.2
(-3)
P 		367
C 703
(3)
P 		316.5
(-0.9)
P 		270.7
(-1.4)
P 		110.1
(-3)
P 		316.5
(-0.9)
P 		144.4
(-2.7)
P 		593
avr 499.1
(3) 		436.1
(1.9) 		204.4
(-2.4) 		182.7
(-2.7) 		261.9
(-1.3) 		168.6
(-3) 		331
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 188333_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.16992
Sequence Type Exemplar sequence
Representative Public ID C25A11.4B NCBI
Target Description C25A11.4B /REP_DB=WormBase Gene ID /WP=CE27084 /GEN=jam-1 /TR=Q18137 /GB=AAK39186.1 /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(11), NM_077135(11), NM_077136(11), NM_077137(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 
NM_077136 NCBI Caenorhabditis elegans Apical Junction Molecule family member (ajm-1) (ajm-1) mRNA, complete cds. 11/11 A 
NM_077137 NCBI Caenorhabditis elegans Apical Junction Molecule family member (ajm-1) (ajm-1) mRNA, complete cds. 11/11 None
GENEFINDER00000000377 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:9100193:9113258:1 11/11 None
SNAP00000000370 ENSEMBL cdna:SNAP chromosome:CEL140:X:9103549:9107319:1 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 
C25A11.4c ENSEMBL cdna:known chromosome:CEL140:X:9098280:9110979:1 gene:C25A11.4 11/11 A 
C25A11.4b ENSEMBL cdna:known chromosome:CEL140:X:9098280:9108525:1 gene:C25A11.4 11/11 A 
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
chrX:9103547-9107318(+) 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
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_509538.1 1 918-940
C25A11.4b 1 918-940
Sequence
Target Sequence 
>C. ELEGANS:188333_S_AT
gatgagctggaccgaaaggcccaagagctttcggagcgggaaatgcgagaaaaggaacgt
cgtgatcgtgaacgagccaatgaagaggctcaactagctgatcttttggaacgtgaacgc
cacaatcaactcattcgtgaaaacgagcgaagagaagctgttgagcgtgccaacaatcgt
cgtctggaagacagaagatcacgcgacaagttggatcacattgtacgtgaaagatccgaa
aaggagcaatttgaactcgagaagcgcagacttcttgccgagaaggaggcaatgaacaga
aagaaaaaccatctgttgagcagtgaaactcttgcaaaacttactcagccaatgtactac
acgactcgcgaaccagaagtcaccactaaagtggaaagacaagttatcgagcgtattgac
cgtaacgtatgggttgaggatgtgccatatgctccaagccagagtgccatgggttatttg
gataatgacgagaacaaccgtgatcgtctttacaacccgaatgatttgaatagaaacgga
tccagcagaagccgctaccaacgtgccaaaaatgagaaagcccgccgcgact

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GATGAGCTGGACCGAAAGGCCCAAG 690 405 1597 Antisense
AAGGCCCAAGAGCTTTCGGAGCGGG 8 157 1612 Antisense
GAGGCTCAACTAGCTGATCTTTTGG 603 403 1681 Antisense
GAACGCCACAATCAACTCATTCGTG 269 347 1711 Antisense
GTTGAGCGTGCCAACAATCGTCGTC 217 439 1756 Antisense
TGTACTACACGACTCGCGAACCAGA 398 559 1949 Antisense
GTTGAGGATGTGCCATATGCTCCAA 134 437 2029 Antisense
TATGCTCCAAGCCAGAGTGCCATGG 567 655 2044 Antisense
CCGTGATCGTCTTTACAACCCGAAT 147 265 2094 Antisense
AACGGATCCAGCAGAAGCCGCTACC 584 143 2131 Antisense
AAAAATGAGAAAGCCCGCCGCGACT 662 127 2164 Antisense
Sequence Source Affymetrix Proprietary Database