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[175228_at] zinc finger protein

Description AV182972_rc /REP_DB=TREMBL Accession /GB=AV182972 /CHR=2 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk645a1 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 70      6grp_high1_10_10 > 17      4grp_highest_8_8 > 39      4grp_high_8_8 > 20      6grp_highest_nonorm > 80      6grp_total > 06      4grp_total > 20      6grp_highest_sub > De      6grp_cgc > 12      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.
4 313
1 2 3 4 range
A 292.2
(-0.2)
P 		358
(1.3)
P 		169.2
(-3)
P 		434.4
(3)
P 		265
B 272.1
(-0.6)
P 		192.2
(-2.2)
P 		149
(-3)
P 		461.6
(3)
P 		313
C 251.4
(-1.1)
P 		194.3
(-2.3)
P 		162.4
(-3)
P 		448.9
(3)
P 		287
avr 271.9
(-0.7) 		248.2
(-1.2) 		160.2
(-3) 		448.3
(3) 		288

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 200
1 2 3 4 5 6 range
A 242.2
(3)
P 		202.9
(0.9)
P 		205
(1)
P 		166.8
(-1)
P 		190.7
(0.3)
P 		129.7
(-3)
P 		113
B 329.6
(3)
P 		222.7
(-1.6)
P 		217.4
(-1.8)
P 		191.3
(-2.9)
P 		189.7
(-3)
P 		224.2
(-1.5)
P 		140
C 302.5
(3)
P 		252.6
(1.2)
P 		136.4
(-3)
P 		183.8
(-1.3)
P 		185.3
(-1.2)
P 		149.9
(-2.5)
P 		166
avr 291.4
(3) 		226.1
(-0.2) 		186.3
(-2.1) 		180.6
(-2.4) 		188.6
(-2) 		167.9
(-3) 		124
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 72
1 2 3 4 range
A 106.4
(3)
P 		77.7
(0.2)
P 		44.2
(-3)
P 		63.6
(-1.1)
P 		62
B 86.8
(1.9)
P 		47.5
(-1.8)
P 		34.5
(-3)
P 		98.4
(3)
P 		64
C 83.2
(3)
P 		55.9
(-3)
P 		56.6
(-2.8)
P 		75.7
(1.4)
P 		27
avr 92.1
(3) 		60.4
(-1) 		45.1
(-3) 		79.2
(1.4) 		47

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 83
1 2 3 4 5 6 range
A 44.7
(-1.1)
P 		72.2
(3)
P 		44.6
(-1.1)
P 		42.3
(-1.4)
P 		57.5
(0.8)
P 		31.6
(-3)
P 		41
B 114.7
(3)
P 		74.1
(-0.8)
P 		52.8
(-2.8)
P 		50.7
(-3)
P 		77.1
(-0.5)
P 		83.6
(0.1)
P 		64
C 112.1
(3)
P 		77.1
(0.3)
P 		34.7
(-3)
P 		37
(-2.8)
P 		60
(-1)
P 		50.2
(-1.8)
P 		77
avr 90.5
(3) 		74.5
(1) 		44
(-2.9) 		43.3
(-3) 		64.9
(-0.3) 		55.1
(-1.5) 		47
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 175228_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.20819
Sequence Type Exemplar sequence
Representative Public ID AV182972 NCBI
Target Description AV182972_rc /REP_DB=TREMBL Accession /GB=AV182972 /CHR=2 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk645a1 : 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_061367(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_061367 NCBI Caenorhabditis elegans NHL (ring finger b-box coiled coil) domain containing family member (nhl-3) (nhl-3) mRNA, complete cds. 11/11 A 
GENEFINDER00000015255 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:595328:602123:-1 11/11 None
W04H10.3 ENSEMBL cdna:known chromosome:CEL140:II:595209:602126:-1 gene:W04H10.3 11/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000015252 6/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:595271-595613(-) 100.0 100.0
Public Domain and Genome References
Gene Title zinc finger protein
Gene Symbol nhl-3
Ensembl W04H10.3
Entrez Gene 173452 Entrez gene
SwissProt O44850 EMBL-EBI
WormBase CE33468 Wormbase
Functional Annotations
Gene Ontology
GO Cellular Component (view graph)
ID Description Evidence Links
5622 intracellular inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
8270 zinc ion binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAB95013 Nhl (ring finger b-box coiled coil) domain containing protein 3 [Caenorhabditis elegans] ref|NP_493768.3| NHL (ring finger b-box coiled coil) domain containing family member (nhl-3) [Caenorhabditis elegans] 0.0
blast CAE62898 Hypothetical protein CBG07087 [Caenorhabditis briggsae] 0.0
blast XP_392730 PREDICTED: similar to NHL domain containing (nhl-3) [Apis mellifera] 2.0E-84
blast XP_392730 PREDICTED: similar to NHL domain containing (nhl-3) [Apis mellifera] 2.0E-83
Protein Domains
Database ID Description E-Value
scop a.2.5.Prefoldin All alpha proteins; Long alpha-hairpin; Prefoldin; Prefoldin 0.159999996423721
scop a.4.5.SCF ubiquitin ligase complex WHB domain All alpha proteins; DNA/RNA-binding 3-helical bundle; "Winged helix" DNA-binding domain; SCF ubiquitin ligase complex WHB domain 1.89999997615814
scop a.4.5.SCF ubiquitin ligase complex WHB domain All alpha proteins; DNA/RNA-binding 3-helical bundle; "Winged helix" DNA-binding domain; SCF ubiquitin ligase complex WHB domain 2.09999990463257
Pfam IPR000315 EMBL-EBI Zn-finger, B-box 5.0E-6
Pfam IPR001841 EMBL-EBI Zn-finger, RING 9.4E-8
Sequence
Target Sequence 
>C. ELEGANS:175228_AT
cctgtgacgtcacaaccggtcaaatcgtagtaatcttcactgacaaaaagatggatcgca
cgaatattggggtaatcagctacaaaggcgacttcctgtactccatcgaaccggggccac
acgaaaagtttatggctccatgcggcatttttgtgcacaaaaataaggcatttgtgacgg
attttgagaggaacacggtgcgaagctacaagtac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CCTGTGACGTCACAACCGGTCAAAT 542 263 25 Antisense
ACCGGTCAAATCGTAGTAATCTTCA 190 87 39 Antisense
ATCGTAGTAATCTTCACTGACAAAA 544 35 48 Antisense
TGGATCGCACGAATATTGGGGTAAT 114 551 76 Antisense
GGGGTAATCAGCTACAAAGGCGACT 73 495 93 Antisense
CTACAAAGGCGACTTCCTGTACTCC 347 225 104 Antisense
AAAGTTTATGGCTCCATGCGGCATT 68 123 149 Antisense
GGCTCCATGCGGCATTTTTGTGCAC 33 541 158 Antisense
ATAAGGCATTTGTGACGGATTTTGA 167 21 187 Antisense
GACGGATTTTGAGAGGAACACGGTG 191 375 200 Antisense
GAACACGGTGCGAAGCTACAAGTAC 447 347 215 Antisense
Sequence Source Affymetrix Proprietary Database