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[173975_s_at] Zinc finger, C4 type (two domains)

Description AU109674 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=T06C12.6 /5_PRIME_EXT_DB=WormBase Gene ID /GB=AU109674 /WB_GENE_ID=T06C12.6 /WP=CE16356 /CHR=5 /FEA=Genomic Cluster /DEF=Zinc finger, C4 type (two domains); Caenorhabditis elegans cDNA clone:yk709h6 : 5prime end, single read.
Cluster 6grp_high1_10_10 > 27      4grp_highest_8_8 > 60      4grp_high_8_8 > 25      6grp_total > 07      4grp_total > 39      6grp_cgc > 11      6grp_high1_sub > Cu      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 248
1 2 3 4 range
A 325.4
(3)
P 		170.1
(-1.3)
P 		110
(-3)
P 		213.1
(-0.1)
P 		215
B 358
(3)
P 		180
(-1.8)
P 		137.3
(-3)
P 		175.9
(-2)
P 		221
C 334.6
(3)
P 		185.9
(-1.5)
P 		137.3
(-3)
P 		205.6
(-0.9)
P 		197
avr 339.3
(3) 		178.7
(-1.6) 		128.2
(-3) 		198.2
(-1) 		211

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 203
1 2 3 4 5 6 range
A 244.8
(3)
P 		175.2
(0.3)
P 		194.2
(1)
P 		126.7
(-1.6)
P 		142.4
(-1)
P 		91.8
(-3)
M 		153
B 289.6
(3)
P 		154.3
(-1)
P 		151.1
(-1.1)
P 		155.8
(-1)
P 		86.9
(-3)
P 		183.4
(-0.1)
P 		203
C 289
(3)
P 		216.2
(0.7)
P 		133.8
(-1.8)
P 		155.6
(-1.1)
P 		95.2
(-3)
P 		132.4
(-1.8)
P 		194
avr 274.5
(3) 		181.9
(-0.3) 		159.7
(-1.1) 		146
(-1.6) 		108.2
(-3) 		135.9
(-2) 		166
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 90
1 2 3 4 range
A 118.5
(3)
P 		36.9
(-2.5)
P 		28.8
(-3)
P 		31.2
(-2.8)
P 		90
B 114.2
(3)
P 		44.5
(-2.1)
P 		31.8
(-3)
P 		37.5
(-2.6)
P 		82
C 110.8
(3)
P 		53.4
(-1.5)
P 		47.9
(-2)
P 		34.7
(-3)
P 		76
avr 114.5
(3) 		44.9
(-2.2) 		36.2
(-2.9) 		34.5
(-3) 		80

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 85
1 2 3 4 5 6 range
A 45.1
(0.4)
P 		62.3
(3)
P 		42.3
(-0)
P 		32.1
(-1.5)
P 		43
(0.1)
P 		22.4
(-3)
M 		40
B 100.8
(3)
P 		51.4
(-1.5)
P 		36.7
(-2.9)
P 		41.3
(-2.5)
P 		35.3
(-3)
P 		68.4
(0)
P 		66
C 107.1
(3)
P 		66
(-0.2)
P 		34.1
(-2.7)
P 		31.3
(-3)
P 		30.8
(-3)
P 		44.3
(-1.9)
P 		76
avr 84.3
(3) 		59.9
(0) 		37.7
(-2.7) 		34.9
(-3) 		36.4
(-2.8) 		45
(-1.8) 		49
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173975_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.25458
Sequence Type Exemplar sequence
Representative Public ID AU109674 NCBI
Target Description AU109674 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=T06C12.6 /5_PRIME_EXT_DB=WormBase Gene ID /GB=AU109674 /WB_GENE_ID=T06C12.6 /WP=CE16356 /CHR=5 /FEA=Genomic Cluster /DEF=Zinc finger, C4 type (two domains); Caenorhabditis elegans cDNA clone:yk709h6 : 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_074566(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_074566 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-102) (nhr-102) mRNA, complete cds. 11/11 None
SNAP00000035465 ENSEMBL cdna:SNAP chromosome:CEL140:V:15876798:15878991:-1 11/11 None
GENEFINDER00000035478 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:15876309:15878991:-1 11/11 None
T06C12.6.1 ENSEMBL cdna:known chromosome:CEL140:V:15876677:15878992:-1 gene:T06C12.6 11/11 None
T06C12.6.2 ENSEMBL cdna:known chromosome:CEL140:V:15876732:15878993:-1 gene:T06C12.6 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:15876742-15878992(-) 100.0 100.0
Public Domain and Genome References
Gene Title Zinc finger, C4 type (two domains)
Gene Symbol nhr-102
Ensembl T06C12.6
Entrez Gene 180062 Entrez gene
SwissProt Q9XVJ1 EMBL-EBI
WormBase CE16356 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6355 regulation of transcription, DNA-dependent inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5634 nucleus inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3700 transcription factor activity inferred from electronic annotation QuickGO AmiGO
3707 steroid hormone receptor activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB03298 Hypothetical protein T06C12.6 [Caenorhabditis elegans] ref|NP_506967.1| Nuclear Hormone Receptor family member (nhr-102) [Caenorhabditis elegans] 0.0
blast AAO39190 nuclear receptor NHR-102 [Caenorhabditis elegans] 0.0
blast CAE74978 Hypothetical protein CBG22870 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 0.015
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 5.8E-22
Sequence
Target Sequence 
>C. ELEGANS:173975_S_AT
tgtggcggcgattcgaacgattcgaaatgtccgtgaaaatgtttggcaatgatgtcgttg
agatcaggaaattcgcgatctcaaacgaccaaatcctcacgaaagagtttacaatagatt
tttcggagattacggatgtgccaaacactactgtacaaggaatgtttcggcattcaatgt
caaaaatgcatcatcaagtcgcaaagccgttgcttgaactcagaccgtcatctattgaaa
cggcgtacatgctcactcagatgagctggcaagttgcaggtaagaaaatgcaaggaaaag
tcgtcgaaatcggtgaacgagtttgtgatgagctggcaaataatcttcacagctactatc
tgaaagaagaaatgcgatcgaattatgcaggtcgcctggttcgcctgatgagcgttgtta
attctgttaaaaagattcacatggaaagaagtatgactatggagttggccagaatttttg
aagtttttaaggtcgacttttctgaaccggacat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGTGGCGGCGATTCGAACGATTCGA 432 553 732 Antisense
GGAAATTCGCGATCTCAAACGACCA 395 525 798 Antisense
CAAACGACCAAATCCTCACGAAAGA 243 133 813 Antisense
ACGGATGTGCCAAACACTACTGTAC 591 93 863 Antisense
GCATCATCAAGTCGCAAAGCCGTTG 87 307 919 Antisense
TTGCTTGAACTCAGACCGTCATCTA 466 675 941 Antisense
TTGAAACGGCGTACATGCTCACTCA 151 705 966 Antisense
GCAAATAATCTTCACAGCTACTATC 606 317 1067 Antisense
GAATTATGCAGGTCGCCTGGTTCGC 404 325 1111 Antisense
CCTGGTTCGCCTGATGAGCGTTGTT 199 267 1126 Antisense
AGGTCGACTTTTCTGAACCGGACAT 325 1 1221 Antisense
Sequence Source Affymetrix Proprietary Database