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[190665_at] Zinc finger, CCHC class

Description Y38H6C.5 /REP_DB=WormBase Gene ID /WP=CE19099 /TR=Q9XX53 /GB=CAA20985.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Zinc finger, CCHC class
Cluster 6grp_total > 82      4grp_total > 58      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 68
1 2 3 4 range
A 33.9
(0.9)
A 		36.6
(1.3)
A 		48.7
(3)
A 		6.5
(-3)
A 		42
B 19.5
(-1.6)
A 		72.2
(3)
A 		66
(2.5)
A 		3.9
(-3)
A 		68
C 31.6
(-3)
A 		47.5
(2.1)
A 		50.3
(3)
A 		33.1
(-2.5)
A 		19
avr 28.3
(-1) 		52.1
(2.6) 		55
(3) 		14.5
(-3) 		41

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 48
1 2 3 4 5 6 range
A 9.5
(-3)
A 		38.2
(1.6)
A 		28.5
(0)
A 		15.8
(-2)
A 		47.2
(3)
A 		29.8
(0.2)
A 		38
B 3
(-3)
A 		23.9
(0.4)
A 		34.1
(2.1)
A 		39.6
(3)
A 		18.2
(-0.5)
A 		13.5
(-1.3)
A 		37
C 22.5
(-0.8)
A 		10.2
(-2.5)
A 		12.8
(-2.2)
A 		50.6
(3)
A 		28.6
(-0)
A 		6.7
(-3)
A 		44
avr 11.7
(-3) 		24.1
(0.2) 		25.1
(0.4) 		35.3
(3) 		31.3
(2) 		16.7
(-1.7) 		24
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 17
1 2 3 4 range
A 12.3
(2.8)
A 		7.9
(0.5)
A 		12.7
(3)
A 		1
(-3)
A 		12
B 6.2
(-1.1)
A 		17.8
(3)
A 		15.3
(2.1)
A 		0.8
(-3)
A 		17
C 10.5
(-0.5)
A 		13.6
(1)
A 		17.5
(3)
A 		5.6
(-3)
A 		12
avr 9.7
(0.4) 		13.1
(2) 		15.2
(3) 		2.5
(-3) 		13

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 13
1 2 3 4 5 6 range
A 1.7
(-3)
A 		13.6
(2.7)
A 		6.2
(-0.9)
A 		4
(-1.9)
A 		14.3
(3)
A 		7.3
(-0.3)
A 		13
B 1
(-3)
A 		7.9
(1.4)
A 		8.3
(1.6)
A 		10.5
(3)
A 		7.4
(1)
A 		5
(-0.5)
A 		10
C 8.4
(1.6)
A 		3.1
(-2.4)
A 		3.3
(-2.2)
A 		10.2
(3)
A 		9.2
(2.2)
A 		2.3
(-3)
A 		8
avr 3.7
(-3) 		8.2
(1.1) 		5.9
(-1) 		8.2
(1.1) 		10.3
(3) 		4.9
(-1.9) 		7
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190665_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.12578
Sequence Type Exemplar sequence
Representative Public ID Y38H6C.5 NCBI
Target Description Y38H6C.5 /REP_DB=WormBase Gene ID /WP=CE19099 /TR=Q9XX53 /GB=CAA20985.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Zinc finger, CCHC class
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_075547(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_075547 NCBI Caenorhabditis elegans Y38H6C.5 (Y38H6C.5) mRNA, complete cds. 11/11 None
SNAP00000041319 ENSEMBL cdna:SNAP chromosome:CEL140:V:20507432:20508058:1 11/11 None
GENEFINDER00000041348 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:20503690:20508058:1 11/11 None
Y38H6C.5 ENSEMBL cdna:known chromosome:CEL140:V:20503690:20508058:1 gene:Y38H6C.5 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
chrV:20503689-20508058(+) 84.46 100.0
Public Domain and Genome References
Gene Title Zinc finger, CCHC class
Ensembl Y38H6C.5
Entrez Gene 189686 Entrez gene
SwissProt Q9XX53 EMBL-EBI
WormBase CE19099 Wormbase
Functional Annotations
Gene Ontology
GO Molecular Function (view graph)
ID Description Evidence Links
3676 nucleic acid binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA20985 Hypothetical protein Y38H6C.5 [Caenorhabditis elegans] ref|NP_507948.1| Y38H6C.5 [Caenorhabditis elegans] 0.0
blast CAA20985 Hypothetical protein Y38H6C.5 [Caenorhabditis elegans] ref|NP_507948.1| Y38H6C.5 [Caenorhabditis elegans] 1.0E-117
blast AAC02594 Hypothetical protein F58H7.6 [Caenorhabditis elegans] ref|NP_500013.1| F58H7.6 [Caenorhabditis elegans] 2.0E-79
blast CAB60574 Hypothetical protein Y37H2A.3 [Caenorhabditis elegans] ref|NP_507535.1| Y37H2A.3 [Caenorhabditis elegans] 6.0E-74
Protein Domains
Database ID Description E-Value
Pfam IPR001878 EMBL-EBI Zn-finger, CCHC type 2.0E-5
Pfam IPR005162 EMBL-EBI Retrotransposon gag protein 2.4E-21
Sequence
Target Sequence 
>C. ELEGANS:190665_AT
tcatccacccacatggctagacgaaaacgatcgagagctcttcggcacgcaaggcttgga
caatcggccgggacccagtgcccagccggtccaagtcgccgtcgagcaaattttaaatga
aacgaatactcctgctgatccagcaaatccaaagatgcttatttcggagcgacttaaaga
ggtccacgaaggagtcctcaaggatctcgccgaagcccttctcaacacgaagagacgtct
caccccgccttcacatagagcgcccggtgccggagaagaagtcactttggccgcaattgg
aaccgattacgcaagaggaccgacgtcctttgtagaagagatggagttcatcgacgtgaa
gctggctatccagagcaacatcactcgagtcttggctcatcgacaaaagaaattcccgcc
acagaaacttgcttggttccacatcatcggaaagatcaccaagttggatactcgtaaacc
gctggcgtcgctcaagctgaccaacgccgcgccaccaagcatcattatcgatttcatgaa
cgaaaagtttggatcacgtctctactggttcaaggtcttcac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCATCCACCCACATGGCTAGACGAA 211 621 2142 Antisense
AAACGATCGAGAGCTCTTCGGCACG 415 125 2166 Antisense
GCAAGGCTTGGACAATCGGCCGGGA 417 319 2190 Antisense
TGAAACGAATACTCCTGCTGATCCA 111 573 2259 Antisense
GAAGGAGTCCTCAAGGATCTCGCCG 613 333 2329 Antisense
GTCACTTTGGCCGCAATTGGAACCG 529 463 2422 Antisense
GAGCAACATCACTCGAGTCTTGGCT 573 389 2514 Antisense
GAAACTTGCTTGGTTCCACATCATC 363 357 2565 Antisense
GCGCCACCAAGCATCATTATCGATT 253 287 2650 Antisense
AAGTTTGGATCACGTCTCTACTGGT 542 155 2686 Antisense
GTCTCTACTGGTTCAAGGTCTTCAC 411 469 2699 Antisense
Sequence Source Affymetrix Proprietary Database