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[174665_at]

Description CEK047G3R_rc /REP_DB=TREMBL Accession /GB=D64228 /CHR=2 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk47g3 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 41      6grp_high1_10_10 > 04      4grp_high_8_8 > 17      6grp_highest_nonorm > 40      6grp_total > 15      4grp_total > 31      6grp_highest_sub > De      6grp_cgc > 31      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 602
1 2 3 4 range
A 943.3
(3)
P 		516.5
(-1.4)
P 		362.7
(-3)
P 		648.3
(-0)
P 		581
B 918.9
(3)
P 		494.8
(-1.4)
P 		341.5
(-3)
A 		670
(0.4)
P 		577
C 932
(3)
P 		518.2
(-1.8)
P 		414.6
(-3)
P 		646.1
(-0.3)
P 		517
avr 931.4
(3) 		509.8
(-1.5) 		372.9
(-3) 		654.8
(0) 		559

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 816
1 2 3 4 5 6 range
A 833.1
(3)
P 		727.5
(1.8)
P 		566.8
(0.1)
P 		400.2
(-1.7)
P 		475.9
(-0.9)
P 		283
(-3)
P 		550
B 1099.1
(3)
P 		874.1
(1.2)
P 		592.2
(-1.1)
P 		560.5
(-1.4)
P 		382
(-2.8)
P 		357
(-3)
P 		742
C 752
(1.4)
P 		909.3
(3)
P 		561.7
(-0.5)
P 		515.9
(-0.9)
P 		309.1
(-3)
P 		386.4
(-2.2)
P 		600
avr 894.7
(3) 		837
(2.4) 		573.6
(-0.5) 		492.2
(-1.4) 		389
(-2.5) 		342.1
(-3) 		553
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 264
1 2 3 4 range
A 343.5
(3)
P 		112.1
(-2.6)
P 		94.8
(-3)
P 		94.9
(-3)
P 		249
B 293
(3)
P 		122.2
(-1.8)
P 		79.1
(-3)
A 		142.8
(-1.2)
P 		214
C 308.5
(3)
P 		149
(-1.8)
P 		144.5
(-1.9)
P 		108.9
(-3)
P 		200
avr 315
(3) 		127.8
(-2.4) 		106.1
(-3) 		115.5
(-2.7) 		209

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 314
1 2 3 4 5 6 range
A 153.6
(-0.3)
P 		258.7
(3)
P 		123.4
(-1.3)
P 		101.5
(-2)
P 		143.6
(-0.6)
P 		68.9
(-3)
P 		190
B 382.4
(3)
P 		290.9
(0.8)
P 		143.8
(-2.7)
P 		148.4
(-2.6)
P 		155.2
(-2.5)
P 		133.1
(-3)
P 		249
C 278.7
(3)
P 		277.5
(3)
P 		143
(-1.6)
P 		103.7
(-2.9)
P 		100
(-3)
P 		129.4
(-2)
P 		179
avr 271.6
(2.9) 		275.7
(3) 		136.7
(-2) 		117.9
(-2.7) 		132.9
(-2.2) 		110.5
(-3) 		165
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 174665_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.20754
Sequence Type Exemplar sequence
Representative Public ID CEK047G3R NCBI
Target Description CEK047G3R_rc /REP_DB=TREMBL Accession /GB=D64228 /CHR=2 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk47g3 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_063191(11), NM_001026977(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063191 NCBI Caenorhabditis elegans SYnapse Defective family member (syd-1) (syd-1) mRNA, complete cds. 11/11 A 
NM_001026977 NCBI Caenorhabditis elegans SYnapse Defective family member (syd-1) (syd-1) mRNA, complete cds. 11/11 None
F35D2.5c.2 ENSEMBL cdna:known chromosome:CEL140:II:7585650:7591237:-1 gene:F35D2.5 11/11 None
F35D2.5c.1 ENSEMBL cdna:known chromosome:CEL140:II:7585653:7589486:-1 gene:F35D2.5 11/11 None
F35D2.5b ENSEMBL cdna:known chromosome:CEL140:II:7585691:7591946:-1 gene:F35D2.5 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
174230 3 2 NM_001026977 174665_at (11)
NM_063191 174665_at (11), 194043_at (11)
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:7585697-7585997(-) 100.0 100.0
Public Domain and Genome References
Ensembl F35D2.5
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAO21428 Synapse defective protein 1, isoform b [Caenorhabditis elegans] ref|NP_495592.2| SYnapse Defective family member (syd-1) [Caenorhabditis elegans] gb|AAN38752.1| axon identity specification protein SYD-1 [Caenorhabditis elegans] 0.0
blast T16275 hypothetical protein F35D2.5 - Caenorhabditis elegans 0.0
blast AAO38644 Synapse defective protein 1, isoform a [Caenorhabditis elegans] ref|NP_001022146.1| SYnapse Defective family member (syd-1) [Caenorhabditis elegans] 0.0
blast AAO38645 Synapse defective protein 1, isoform c [Caenorhabditis elegans] ref|NP_001022148.1| SYnapse Defective family member (syd-1) [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR001478 EMBL-EBI PDZ/DHR/GLGF domain 4.8E-7
Pfam IPR000008 EMBL-EBI C2 domain 0.0020
Pfam IPR000198 EMBL-EBI RhoGAP domain 8.2E-28
Pfam IPR000008 EMBL-EBI C2 domain 0.0020
Pfam IPR000198 EMBL-EBI RhoGAP domain 8.2E-28
Sequence
Target Sequence 
>C. ELEGANS:174665_AT
atttgtttcaatctctaggtgcattttctcttgtcccgttcctttctattaaaataccgg
taatctacagaaatgttatacgttgatttcatgcctaatccctcgcctttacttttcaaa
ccatgaatactccctttttatcctgatattttcaatttattcgtttttattcaaataatg
tttaccatcattgtctttccctttccgagcaatatagacagtttttgtcagtgctctttg
agtcctcatgggt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATTTGTTTCAATCTCTAGGTGCATT 564 15 28 Antisense
TCTCTAGGTGCATTTTCTCTTGTCC 354 611 39 Antisense
AATACCGGTAATCTACAGAAATGTT 63 145 80 Antisense
ACGTTGATTTCATGCCTAATCCCTC 42 93 107 Antisense
CTCGCCTTTACTTTTCAAACCATGA 643 231 129 Antisense
CAAACCATGAATACTCCCTTTTTAT 287 189 144 Antisense
ATACTCCCTTTTTATCCTGATATTT 690 23 154 Antisense
ATGTTTACCATCATTGTCTTTCCCT 692 45 205 Antisense
CTTTCCCTTTCCGAGCAATATAGAC 277 223 222 Antisense
GTTTTTGTCAGTGCTCTTTGAGTCC 397 449 248 Antisense
CAGTGCTCTTTGAGTCCTCATGGGT 670 205 256 Antisense
Sequence Source Affymetrix Proprietary Database