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[193642_at] Zinc finger, C2H2 type (3 domains)

Description F52E10.1 /REP_DB=WormBase Gene ID /WP=CE03393 /GEN=sdc-1 /TR=SW:P24349 /GB=CAA91056.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=Zinc finger, C2H2 type (3 domains)
Cluster 6grp_total > 26      4grp_total > 47      6grp_cgc > 24      6grp_cgc_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 241
1 2 3 4 range
A 387.3
(3)
A 		189.9
(-2.9)
A 		187.4
(-3)
A 		189.9
(-2.9)
A 		200
B 428.5
(3)
A 		258.9
(-1.6)
A 		221.4
(-2.7)
A 		209.4
(-3)
A 		219
C 387.8
(3)
A 		261.3
(-1.4)
A 		221.7
(-2.8)
A 		215
(-3)
A 		173
avr 401.2
(3) 		236.7
(-2) 		210.2
(-2.8) 		204.8
(-3) 		196

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 237
1 2 3 4 5 6 range
A 434.4
(3)
A 		325
(0.2)
A 		229.8
(-2.2)
A 		240.4
(-1.9)
A 		197.2
(-3)
A 		229.7
(-2.2)
A 		237
B 423.8
(3)
A 		379.5
(1.8)
A 		298.5
(-0.4)
A 		228.2
(-2.4)
A 		205.7
(-3)
A 		255.4
(-1.6)
A 		218
C 327.1
(2.5)
A 		338
(3)
A 		258.6
(-0.5)
A 		201.3
(-3)
A 		207.3
(-2.7)
A 		264.1
(-0.2)
A 		137
avr 395.1
(3) 		347.5
(1.5) 		262.3
(-1.2) 		223.3
(-2.4) 		203.4
(-3) 		249.7
(-1.6) 		192
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 113
1 2 3 4 range
A 141
(3)
A 		41.2
(-2.3)
A 		49
(-1.9)
A 		27.8
(-3)
A 		113
B 136.7
(3)
A 		63.9
(-1.7)
A 		51.3
(-2.6)
A 		44.6
(-3)
A 		92
C 128.4
(3)
A 		75.1
(-0.5)
A 		77.3
(-0.3)
A 		36.3
(-3)
A 		92
avr 135.4
(3) 		60.1
(-1.6) 		59.2
(-1.6) 		36.2
(-3) 		99

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 107
1 2 3 4 5 6 range
A 80.1
(-0.2)
A 		115.6
(3)
A 		50
(-3)
A 		61
(-2)
A 		59.5
(-2.1)
A 		55.9
(-2.5)
A 		66
B 147.5
(3)
A 		126.3
(1.5)
A 		72.5
(-2.2)
A 		60.4
(-3)
A 		83.6
(-1.4)
A 		95.2
(-0.6)
A 		87
C 121.3
(3)
A 		103.1
(1.6)
A 		65.8
(-1.1)
A 		40.5
(-3)
A 		67.1
(-1)
A 		88.4
(0.6)
A 		81
avr 116.3
(3) 		115
(2.9) 		62.8
(-2.2) 		54
(-3) 		70.1
(-1.4) 		79.8
(-0.5) 		62
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193642_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17860
Sequence Type Exemplar sequence
Representative Public ID F52E10.1 NCBI
Target Description F52E10.1 /REP_DB=WormBase Gene ID /WP=CE03393 /GEN=sdc-1 /TR=SW:P24349 /GB=CAA91056.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=Zinc finger, C2H2 type (3 domains)
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_078249(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_078249 NCBI Caenorhabditis elegans Sex determination and Dosage Compensation defect family member (sdc-1) (sdc-1) mRNA, complete cds. 11/11 A 
SNAP00000003304 ENSEMBL cdna:SNAP chromosome:CEL140:X:16275686:16282213:1 11/11 None
GENEFINDER00000003308 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:16275686:16282213:1 11/11 None
F52E10.1 ENSEMBL cdna:known chromosome:CEL140:X:16275686:16282349:1 gene:F52E10.1 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:16275685-16282213(+) 100.0 100.0
Public Domain and Genome References
Gene Title Zinc finger, C2H2 type (3 domains)
Gene Symbol sdc-1
Ensembl F52E10.1
Entrez Gene 181701 Entrez gene
SwissProt P24349 EMBL-EBI
WormBase CE03393 Wormbase
Functional Annotations
Gene Ontology
GO Cellular Component (view graph)
ID Description Evidence Links
5634 nucleus inferred from electronic annotation QuickGO AmiGO
228 nuclear chromosome inferred from direct assay QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3676 nucleic acid binding inferred from electronic annotation QuickGO AmiGO
8270 zinc ion binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA91056 Hypothetical protein F52E10.1 [Caenorhabditis elegans] ref|NP_510650.1| Sex determination and Dosage Compensation defect family member (sdc-1) [Caenorhabditis elegans] 0.0
blast P24349 Zinc finger protein sdc-1 emb|CAA41410.1| zinc-finger protein [Caenorhabditis elegans] prf||1709362A Zn finger protein 0.0
blast CAE56294 Hypothetical protein CBG23946 [Caenorhabditis briggsae] 1.0E-114
Protein Domains
Database ID Description E-Value
Pfam IPR007087 EMBL-EBI Zn-finger, C2H2 type 1.7E-5
Pfam IPR007087 EMBL-EBI Zn-finger, C2H2 type 1.7E-5
Sequence
Target Sequence 
>C. ELEGANS:193642_AT
catcatcgcgttctcaccaaaatatgaaaattcgctcagcgactttcgcataagtgcaat
tggtttccgcgaaaagtatttggcggacgataaaaagaagagaaatggaattccgattcg
aaaaatgactgaggctcagaaaggtgttgcgctagactacgatacgttgatggcgcgaca
cggaggtcgtcccgacgtgataatgaacccggccggaactgtttttgtgggaggatttgt
gttcgatcggaaaccgacgtgccaggataacatgcagactgtttatgttcttcgtaatgg
ctatgcacaccggtac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CATCATCGCGTTCTCACCAAAATAT 30 213 3000 Antisense
AATTCGCTCAGCGACTTTCGCATAA 493 177 3028 Antisense
GCATAAGTGCAATTGGTTTCCGCGA 278 307 3047 Antisense
GAGGCTCAGAAAGGTGTTGCGCTAG 404 405 3130 Antisense
GTTGCGCTAGACTACGATACGTTGA 149 441 3145 Antisense
GATACGTTGATGGCGCGACACGGAG 99 425 3160 Antisense
GTCGTCCCGACGTGATAATGAACCC 548 471 3185 Antisense
GATAATGAACCCGGCCGGAACTGTT 182 423 3198 Antisense
GATCGGAAACCGACGTGCCAGGATA 147 417 3244 Antisense
CATGCAGACTGTTTATGTTCTTCGT 145 211 3270 Antisense
TCGTAATGGCTATGCACACCGGTAC 590 603 3291 Antisense
Sequence Source Affymetrix Proprietary Database