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[173447_s_at]

Description g4336898 /REP_DB=GenBank Identifier /5_PRIME_EXT_ID=C35C5.1 /5_PRIME_EXT_DB=WormBase Gene ID /WB_GENE_ID=C35C5.1 /WP=CE18542 /CHR=X /FEA=Genomic Cluster /GEN=sdc-2 /DEF=SDC-2
Cluster 6grp_highest_10_10 > 42      6grp_high1_10_10 > 13      4grp_highest_8_8 > 44      4grp_high_8_8 > 16      6grp_highest_nonorm > 90      6grp_total > 25      4grp_total > 31      6grp_highest_sub > 02      6grp_cgc > 33      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 266
1 2 3 4 range
A 346.7
(3)
P 		80.6
(-3)
P 		102.4
(-2.5)
P 		183.4
(-0.7)
P 		266
B 320.7
(3)
P 		117.3
(-2.9)
P 		112.5
(-3)
P 		236.1
(0.6)
P 		208
C 314.6
(3)
P 		105.9
(-3)
P 		172.9
(-1.1)
P 		188.9
(-0.6)
P 		209
avr 327.3
(3) 		101.3
(-3) 		129.3
(-2.3) 		202.8
(-0.3) 		226

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 158
1 2 3 4 5 6 range
A 147.1
(-1.3)
P 		254.1
(3)
P 		151.1
(-1.2)
P 		166.4
(-0.5)
P 		105.4
(-3)
P 		150.8
(-1.2)
P 		149
B 206.5
(2.2)
P 		220.2
(3)
P 		177.9
(0.5)
P 		130.7
(-2.2)
P 		116.9
(-3)
P 		123.6
(-2.6)
P 		103
C 250.2
(3)
P 		237.5
(2.5)
P 		188.1
(0.6)
P 		96.4
(-3)
P 		139.6
(-1.3)
P 		109.8
(-2.5)
P 		154
avr 201.3
(1.1) 		237.3
(3) 		172.4
(-0.3) 		131.2
(-2.5) 		120.6
(-3) 		128.1
(-2.6) 		117
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 109
1 2 3 4 range
A 126.2
(3)
P 		17.5
(-3)
P 		26.8
(-2.5)
P 		26.8
(-2.5)
P 		109
B 102.3
(3)
P 		29
(-2.8)
P 		26.1
(-3)
P 		50.3
(-1.1)
P 		76
C 104.2
(3)
P 		30.5
(-3)
P 		60.3
(-0.6)
P 		31.9
(-2.9)
P 		74
avr 110.9
(3) 		25.7
(-3) 		37.7
(-2.2) 		36.3
(-2.3) 		85

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 73
1 2 3 4 5 6 range
A 27.1
(-3)
P 		90.4
(3)
P 		32.9
(-2.5)
P 		42.2
(-1.6)
P 		31.8
(-2.6)
P 		36.7
(-2.1)
P 		63
B 71.9
(2.8)
P 		73.3
(3)
P 		43.2
(-1.7)
P 		34.6
(-3)
P 		47.5
(-1)
P 		46.1
(-1.2)
P 		39
C 92.7
(3)
P 		72.5
(1.3)
P 		47.9
(-0.7)
P 		19.4
(-3)
P 		45.2
(-0.9)
P 		36.7
(-1.6)
P 		73
avr 63.9
(1.1) 		78.7
(3) 		41.3
(-1.8) 		32.1
(-3) 		41.5
(-1.8) 		39.8
(-2) 		47
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173447_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.25781
Sequence Type Exemplar sequence
Representative Public ID 4336898 NCBI
Target Description g4336898 /REP_DB=GenBank Identifier /5_PRIME_EXT_ID=C35C5.1 /5_PRIME_EXT_DB=WormBase Gene ID /WB_GENE_ID=C35C5.1 /WP=CE18542 /CHR=X /FEA=Genomic Cluster /GEN=sdc-2 /DEF=SDC-2
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_077523(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_077523 NCBI Caenorhabditis elegans Sex determination and Dosage Compensation defect family member (sdc-2) (sdc-2) mRNA, complete cds. 11/11 A 
SNAP00000005101 ENSEMBL cdna:SNAP chromosome:CEL140:X:11528427:11533045:1 11/11 None
GENEFINDER00000005119 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:11528905:11533045:1 11/11 None
C35C5.1.1 ENSEMBL cdna:known chromosome:CEL140:X:11522634:11533371:1 gene:C35C5.1 11/11 None
C35C5.1.2 ENSEMBL cdna:known chromosome:CEL140:X:11522660:11533514:1 gene:C35C5.1 11/11 None
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:11522660-11533046(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol sdc-2
Ensembl C35C5.1
Entrez Gene 181341 Entrez gene
SwissProt Q93326 EMBL-EBI
WormBase CE18542 Wormbase
Functional Annotations
Gene Ontology
GO Cellular Component (view graph)
ID Description Evidence Links
228 nuclear chromosome inferred from direct assay QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB01756 Hypothetical protein C35C5.1 [Caenorhabditis elegans] emb|CAB01693.1| Hypothetical protein C35C5.1 [Caenorhabditis elegans] ref|NP_509924.1| Sex determination and Dosage Compensation defect family member (sdc-2) [Caenorhabditis elegans] gb|AAD18003.1| SDC-2 [Caenorhabditis elegans] 0.0
blast CAE70623 Hypothetical protein CBG17307 [Caenorhabditis briggsae] 1.0E-159
blast CAE70623 Hypothetical protein CBG17307 [Caenorhabditis briggsae] 1.0E-121
blast CAE70623 Hypothetical protein CBG17307 [Caenorhabditis briggsae] 1.0E-120
Sequence
Target Sequence 
>C. ELEGANS:173447_S_AT
gatgccattgatcagtccatcatacattggaacgtctttaacttgctttgaggatgagct
cttattttctgctgttcgagaagccaaagtccatactgatactagagtggtatttcgtag
taagagctgtatgcgaccaaacgaaaaagcaggggatgcaaacttcaagacatgtaaagt
cactcttttggttaatctggaaactgcactacttagtatggttttcaagtcacgtgacca
atctgaaatcgataaagatgatcgacttgatattgatattctggatgaagaagtcattaa
accgattattgattggaataggatatttgaaactttcattcaaccaacgtacaatacttt
gttttccagaatggagaagcgtgaacgggtgagcatcttgccagaaaatccgttgggtcg
actcgaaaactatgcattcacaaatcctaaccaagataaagactgccaagcagtgttaga
gtatatcgatgttgcatcagatactgacgcagaagaatccattgaagatccattagacat
tgttgaaatgactttgaaaagagctttgccacgatctatgagcc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GATGCCATTGATCAGTCCATCATAC 46 415 8288 Antisense
GGAACGTCTTTAACTTGCTTTGAGG 189 531 8316 Antisense
GAGCTCTTATTTTCTGCTGTTCGAG 69 389 8343 Antisense
GTTCGAGAAGCCAAAGTCCATACTG 246 441 8361 Antisense
GTAAGAGCTGTATGCGACCAAACGA 672 455 8407 Antisense
AAGTCACTCTTTTGGTTAATCTGGA 499 157 8464 Antisense
GTCACGTGACCAATCTGAAATCGAT 657 465 8516 Antisense
GAAACTTTCATTCAACCAACGTACA 639 349 8616 Antisense
CAGAAAATCCGTTGGGTCGACTCGA 19 205 8689 Antisense
AACTATGCATTCACAAATCCTAACC 168 139 8715 Antisense
AGAGCTTTGCCACGATCTATGAGCC 604 69 8847 Antisense
Sequence Source GenBank