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[192350_at] Zinc finger, C4 type (two domains)

Description R08H2.9 /REP_DB=WormBase Gene ID /WP=CE12610 /TR=O17991 /GB=CAB04634.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Zinc finger, C4 type (two domains)
Cluster 6grp_total > 61      4grp_total > 35      6grp_cgc > 94      6grp_cgc_sub > 04      6grp_total_sub > Hat      6grp_rule_based > S4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 44
1 2 3 4 range
A 4.7
(3)
A 		3.8
(0.8)
A 		3.4
(-0.1)
A 		2.2
(-3)
A 		3
B 26.4
(3)
A 		20.8
(1.4)
A 		4.8
(-3)
A 		9.4
(-1.7)
A 		22
C 1.8
(-3)
A 		46.1
(3)
A 		13.2
(-1.5)
A 		28.5
(0.6)
A 		44
avr 11
(-1.6) 		23.6
(3) 		7.1
(-3) 		13.4
(-0.7) 		17

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 73
1 2 3 4 5 6 range
A 40.2
(2.1)
A 		17.3
(-1)
A 		33.9
(1.3)
M 		46.8
(3)
P 		42.7
(2.5)
A 		2
(-3)
A 		45
B 2.8
(-3)
A 		19.5
(-1.6)
A 		60.8
(1.8)
P 		74.8
(3)
P 		24
(-1.2)
A 		31.3
(-0.6)
A 		72
C 23.1
(-1.3)
A 		19.7
(-1.6)
A 		47.9
(0.8)
A 		74.3
(3)
M 		4.7
(-2.8)
A 		2.6
(-3)
A 		72
avr 22
(-1.9) 		18.8
(-2.2) 		47.5
(1) 		65.3
(3) 		23.8
(-1.7) 		12
(-3) 		53
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 13
1 2 3 4 range
A 1.7
(3)
A 		0.8
(-0.9)
A 		0.9
(-0.4)
A 		0.3
(-3)
A 		1
B 8.4
(3)
A 		5.1
(0.3)
A 		1.1
(-3)
A 		2
(-2.3)
A 		7
C 0.6
(-3)
A 		13.3
(3)
A 		4.6
(-1.1)
A 		4.8
(-1)
A 		13
avr 3.6
(-1) 		6.4
(3) 		2.2
(-3) 		2.4
(-2.7) 		4

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 19
1 2 3 4 5 6 range
A 7.4
(0.3)
A 		6.2
(-0.2)
A 		7.4
(0.3)
M 		11.9
(2.5)
P 		12.9
(3)
A 		0.5
(-3)
A 		12
B 1
(-3)
A 		6.5
(-1.2)
A 		14.8
(1.4)
P 		19.8
(3)
P 		9.7
(-0.2)
A 		11.7
(0.4)
A 		19
C 8.6
(0.3)
A 		6
(-0.8)
A 		12.2
(1.8)
A 		15
(3)
M 		1.5
(-2.7)
A 		0.9
(-3)
A 		14
avr 5.7
(-2.3) 		6.2
(-2) 		11.5
(0.8) 		15.6
(3) 		8
(-1.1) 		4.4
(-3) 		11
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192350_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.12967
Sequence Type Exemplar sequence
Representative Public ID R08H2.9 NCBI
Target Description R08H2.9 /REP_DB=WormBase Gene ID /WP=CE12610 /TR=O17991 /GB=CAB04634.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Zinc finger, C4 type (two 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_074412(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_074412 NCBI Caenorhabditis elegans R08H2.9 (R08H2.9) mRNA, complete cds. 11/11 None
GENEFINDER00000012534 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:15369745:15377387:-1 9/11 None
R08H2.9 ENSEMBL cdna:known chromosome:CEL140:V:15371056:15372801:-1 gene:R08H2.9 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000012521 8/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrV:15371055-15372801(-) 100.0 100.0
Public Domain and Genome References
Gene Title Zinc finger, C4 type (two domains)
Gene Symbol nhr-269
Ensembl R08H2.9
Entrez Gene 187716 Entrez gene
SwissProt O17991 EMBL-EBI
WormBase CE12610 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6118 electron transport inferred from electronic annotation QuickGO AmiGO
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
5489 electron transporter activity inferred from electronic annotation QuickGO AmiGO
20037 heme binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB04634 Hypothetical protein R08H2.9 [Caenorhabditis elegans] ref|NP_506813.1| R08H2.9 [Caenorhabditis elegans] 0.0
blast CAB04638 Hypothetical protein R08H2.8 [Caenorhabditis elegans] ref|NP_506814.1| R08H2.8 [Caenorhabditis elegans] 0.0
blast CAB04634 Hypothetical protein R08H2.9 [Caenorhabditis elegans] ref|NP_506813.1| R08H2.9 [Caenorhabditis elegans] 1.0E-133
blast CAB03504 Hypothetical protein ZK1037.5 [Caenorhabditis elegans] ref|NP_506798.1| ZK1037.5 [Caenorhabditis elegans] 2.0E-62
blast CAB03505 Hypothetical protein ZK1037.6 [Caenorhabditis elegans] ref|NP_506799.1| ZK1037.6 [Caenorhabditis elegans] 1.0E-59
blast CAE74295 Hypothetical protein CBG21997 [Caenorhabditis briggsae] 7.0E-48
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 5.0E-5
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 6.6E-7
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 2.5E-9
Pfam IPR003366 EMBL-EBI Protein of unknown function DUF141 1.7E-12
Pfam IPR003003 EMBL-EBI 7TM chemoreceptor, subfamily 2 1.2E-21
Pfam IPR003003 EMBL-EBI 7TM chemoreceptor, subfamily 2 4.9E-30
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 5.0E-5
Pfam IPR000535 EMBL-EBI Major sperm protein (MSP) domain 6.3E-15
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 1.1E-14
Trans Membrane
ID Number Of Domains Domain Boundaries
GENEFINDER00000012534 3 988-1010,1031-1053,1063-1085
Sequence
Target Sequence 
>C. ELEGANS:192350_AT
gacggctactgatattcgatttgtgatgagcttgggattccagaacgccactgtatgggc
taaccattttgaaccattttggagtctatcaaacgacgaaaaaacttcagttttatcaga
atacggaattgcatttattcttatggaacaagctatcaaaacagttaatgaaggaatcaa
aggagtgtggctactgcaaactggtacatcattgttatctcctgtaccatgtgaaactga
gcaagagaagttctttatcttctgttcaatccgtatattaattgtgattacatttaagaa
ttcaccaaaaatttcatcacatcaaaaaaatgttcacttgacaggttcaaagctacttcg
agaaaaatgcctgtcagaactaatgaaatatactacaaacatctctccaagtagtggact
tgagaaattcggtgaaatattgcttctaatgggatcaatacggtgtgctgtgaagctttt
ctt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GACGGCTACTGATATTCGATTTGTG 152 377 756 Antisense
GAGCTTGGGATTCCAGAACGCCACT 313 387 783 Antisense
GAACGCCACTGTATGGGCTAACCAT 517 345 798 Antisense
GGGCTAACCATTTTGAACCATTTTG 20 487 812 Antisense
GAGTGTGGCTACTGCAAACTGGTAC 466 401 938 Antisense
ACTGGTACATCATTGTTATCTCCTG 275 97 955 Antisense
TTATCTCCTGTACCATGTGAAACTG 77 681 970 Antisense
ATCTTCTGTTCAATCCGTATATTAA 443 31 1012 Antisense
GACAGGTTCAAAGCTACTTCGAGAA 411 367 1095 Antisense
GAAATATACTACAAACATCTCTCCA 331 363 1140 Antisense
TACGGTGTGCTGTGAAGCTTTTCTT 413 647 1214 Antisense
Sequence Source Affymetrix Proprietary Database