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[173872_at]

Description AV191230 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F57C7.3 /5_PRIME_EXT_DB=WormBase Gene ID /GB=AV191230 /WB_GENE_ID=F57C7.3 /WP=CE05996 /CHR=X /FEA=Genomic Cluster /DEF=syndecan like protein; Caenorhabditis elegans cDNA clone:yk591e2 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 60      6grp_high1_10_10 > 16      4grp_highest_8_8 > 49      4grp_high_8_8 > 41      6grp_highest_nonorm > 11      6grp_total > 07      4grp_total > 54      6grp_highest_sub > De      6grp_cgc > 13      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 2666
1 2 3 4 range
A 2783.4
(3)
P 		1626.8
(-0.4)
P 		1155.7
(-1.8)
P 		753.7
(-3)
P 		2030
B 3341.5
(3)
P 		1980.5
(-0.5)
P 		1627.3
(-1.4)
P 		1005.2
(-3)
P 		2336
C 2307.8
(3)
P 		1743.6
(0.9)
P 		1508.5
(0.1)
P 		675.7
(-3)
P 		1632
avr 2810.9
(3) 		1783.6
(-0.1) 		1430.5
(-1.1) 		811.5
(-3) 		1999

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1839
1 2 3 4 5 6 range
A 2739.4
(3)
P 		1821.5
(-0.1)
P 		1339.3
(-1.8)
P 		977.1
(-3)
P 		1279.4
(-2)
P 		1275.9
(-2)
P 		1762
B 2142.2
(3)
P 		1606.3
(0.4)
P 		1029.3
(-2.5)
P 		1774.6
(1.2)
P 		919.2
(-3)
P 		1167.4
(-1.8)
P 		1223
C 2074.7
(3)
P 		1750.7
(1.3)
P 		1468.2
(-0.1)
P 		1230.9
(-1.3)
P 		900.9
(-3)
P 		1148.1
(-1.7)
P 		1174
avr 2318.8
(3) 		1726.2
(0.2) 		1278.9
(-1.9) 		1327.5
(-1.6) 		1033.2
(-3) 		1197.1
(-2.2) 		1286
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 955
1 2 3 4 range
A 1013.4
(3)
P 		353.1
(-1.4)
P 		302.1
(-1.7)
P 		110.3
(-3)
P 		903
B 1065.6
(3)
P 		489.1
(-1.1)
P 		377.1
(-1.9)
P 		214.2
(-3)
P 		851
C 763.9
(3)
P 		501.3
(0.6)
P 		525.7
(0.8)
P 		113.9
(-3)
P 		650
avr 947.6
(3) 		447.8
(-0.7) 		401.6
(-1.1) 		146.1
(-3) 		802

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 522
1 2 3 4 5 6 range
A 505
(0.9)
P 		647.8
(3)
P 		291.7
(-2.3)
P 		247.8
(-3)
P 		386.1
(-0.9)
P 		310.6
(-2.1)
P 		400
B 745.4
(3)
P 		534.7
(0.4)
P 		249.9
(-3)
P 		470
(-0.3)
P 		373.5
(-1.5)
P 		435.3
(-0.8)
P 		496
C 769
(3)
P 		534.2
(0.3)
P 		373.7
(-1.5)
P 		247.5
(-3)
P 		291.5
(-2.5)
P 		384.3
(-1.4)
P 		522
avr 673.1
(3) 		572.2
(1.4) 		305.1
(-3) 		321.8
(-2.7) 		350.4
(-2.3) 		376.7
(-1.8) 		368
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173872_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.25876
Sequence Type Exemplar sequence
Representative Public ID AV191230 NCBI
Target Description AV191230 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F57C7.3 /5_PRIME_EXT_DB=WormBase Gene ID /GB=AV191230 /WB_GENE_ID=F57C7.3 /WP=CE05996 /CHR=X /FEA=Genomic Cluster /DEF=syndecan like protein; Caenorhabditis elegans cDNA clone:yk591e2 : 5prime 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_171972(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_171972 NCBI Caenorhabditis elegans SynDecaN family member (sdn-1) (sdn-1) mRNA, complete cds. 11/11 None
F57C7.3a.1 ENSEMBL cdna:known chromosome:CEL140:X:10589706:10593260:-1 gene:F57C7.3 11/11 None
F57C7.3a.2 ENSEMBL cdna:known chromosome:CEL140:X:10589706:10593472:-1 gene:F57C7.3 11/11 None
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
181259 2 1 NM_171972 173872_at (11)
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrX:10589731-10593205(-) 95.84 100.0
Public Domain and Genome References
Ensembl F57C7.3
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAA93474 Hypothetical protein F57C7.3a [Caenorhabditis elegans] ref|NP_741894.1| SynDecaN family member (sdn-1) [Caenorhabditis elegans] sp|P50605|SDC_CAEEL Probable syndecan precursor 1.0E-111
blast CAD44142 Hypothetical protein F57C7.3b [Caenorhabditis elegans] ref|NP_741893.1| SynDecaN family member (sdn-1) [Caenorhabditis elegans] 1.0E-109
blast CAE60807 Hypothetical protein CBG04505 [Caenorhabditis briggsae] 4.0E-75
Protein Domains
Database ID Description E-Value
Pfam IPR001050 EMBL-EBI Syndecan 1.0E-126
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_741894.1 1 230-252
F57C7.3a.1 1 230-252
F57C7.3a.2 1 230-252
Sequence
Target Sequence 
>C. ELEGANS:173872_AT
acgcgtaatctctactgtcatttgttcaaaatcttctatcactcaatcacctttcaaatc
atttttatgattctgttctcagacttcattccaatctgccatacctttcaatttgttttt
ttcccactcccatttttttcaaaccctccccccccccgccttcctttcgtaaaggtcatt
actctctgttctactcgtgataatttgataatataaactgatctgactccatggtgccaa
atatttgaatataatcttttgtagacccacttaggggtagggatgcatgtatctttgact
caatttatactatactcccttgttactataatgtgctcatattatcctattctagaaatt
tccacctaatttccaaaatccctcaacactctcacgcggtttctctggtttctgatggca
cttatctgctagagttttttgtttcaaaacttgcctcttgaaatttgtactttttcttgt
tttatccgtttacctttttctttccaataacatcttctgt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ACGCGTAATCTCTACTGTCATTTGT 181 91 873 Antisense
TTCTATCACTCAATCACCTTTCAAA 504 691 906 Antisense
TTCTGTTCTCAGACTTCATTCCAAT 360 693 943 Antisense
AAAGGTCATTACTCTCTGTTCTACT 257 121 1043 Antisense
TAAACTGATCTGACTCCATGGTGCC 185 641 1086 Antisense
GATGCATGTATCTTTGACTCAATTT 194 411 1154 Antisense
TTTATACTATACTCCCTTGTTACTA 358 673 1176 Antisense
AATGTGCTCATATTATCCTATTCTA 518 163 1202 Antisense
TAATTTCCAAAATCCCTCAACACTC 34 635 1239 Antisense
TTTCTCTGGTTTCTGATGGCACTTA 260 671 1272 Antisense
TTTTCTTTCCAATAACATCTTCTGT 614 675 1368 Antisense
Sequence Source Affymetrix Proprietary Database