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[192833_at] nuclear hormone receptor

Description F55D12.4 /REP_DB=WormBase Gene ID /WP=CE05957 /GEN=unc-55 /TR=Q20832 /GB=CAA99861.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=nuclear hormone receptor
Cluster 6grp_total > 42      4grp_total > 26      6grp_cgc > 70      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 63
1 2 3 4 range
A 1.8
(-3)
A 		25.6
(3)
A 		2.3
(-2.9)
A 		7.8
(-1.5)
A 		24
B 1.7
(-3)
A 		34.2
(3)
A 		33.1
(2.8)
A 		6
(-2.2)
A 		33
C 22.5
(-1.1)
A 		3.6
(-3)
A 		7.6
(-2.6)
A 		64.5
(3)
A 		61
avr 8.7
(-3) 		21.1
(1.3) 		14.3
(-1.1) 		26.1
(3) 		17

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 42
1 2 3 4 5 6 range
A 43.3
(3)
A 		4.8
(-2.5)
A 		16.3
(-0.9)
A 		7
(-2.2)
A 		1.3
(-3)
A 		4.3
(-2.6)
A 		42
B 2.7
(-3)
A 		22.3
(3)
A 		16.2
(1.1)
A 		5.5
(-2.1)
A 		21.5
(2.8)
A 		4.4
(-2.5)
A 		20
C 7.9
(-2.1)
A 		18.4
(-0.3)
A 		37.9
(3)
A 		22
(0.3)
A 		4.3
(-2.7)
A 		2.3
(-3)
A 		36
avr 18
(1.3) 		15.2
(0.5) 		23.5
(3) 		11.5
(-0.6) 		9
(-1.4) 		3.7
(-3) 		20
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 10
1 2 3 4 range
A 0.7
(-2.9)
A 		5.6
(3)
A 		0.6
(-3)
A 		1.1
(-2.4)
A 		5
B 0.5
(-3)
A 		8.4
(3)
A 		7.7
(2.5)
A 		1.3
(-2.4)
A 		8
C 7.5
(0.9)
A 		1
(-3)
A 		2.6
(-2)
A 		10.9
(3)
A 		10
avr 2.9
(-3) 		5
(3) 		3.6
(-1) 		4.4
(1.3) 		2

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 9
1 2 3 4 5 6 range
A 8
(3)
A 		1.7
(-2)
A 		3.6
(-0.5)
A 		1.8
(-1.9)
A 		0.4
(-3)
A 		1
(-2.5)
A 		8
B 0.9
(-3)
A 		7.4
(2)
A 		3.9
(-0.7)
A 		1.5
(-2.5)
A 		8.7
(3)
A 		1.6
(-2.5)
A 		8
C 2.9
(-1.6)
A 		5.6
(0.3)
A 		9.6
(3)
A 		4.4
(-0.5)
A 		1.4
(-2.6)
A 		0.8
(-3)
A 		9
avr 3.9
(0.7) 		4.9
(2) 		5.7
(3) 		2.6
(-1) 		3.5
(0.1) 		1.1
(-3) 		5
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192833_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.838
Sequence Type Exemplar sequence
Representative Public ID F55D12.4 NCBI
Target Description F55D12.4 /REP_DB=WormBase Gene ID /WP=CE05957 /GEN=unc-55 /TR=Q20832 /GB=CAA99861.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=nuclear hormone receptor
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_059780(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059780 NCBI Caenorhabditis elegans UNCoordinated family member (unc-55) (unc-55) mRNA, complete cds. 11/11 None
F55D12.4 ENSEMBL cdna:known chromosome:CEL140:I:7907169:7911909:-1 gene:F55D12.4 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
GENEFINDER00000016637 8/11 Cross Hyb Matching Probes None
SNAP00000016629 8/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrI:7907099-7911840(-) 100.0 100.0
Public Domain and Genome References
Gene Title nuclear hormone receptor
Gene Symbol unc-55
Ensembl F55D12.4
Entrez Gene 192082 Entrez gene
SwissProt Q20832 EMBL-EBI
WormBase CE05957 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1588306_AT similar to nuclear receptor subfamily 2, group F, member 2 cfa
CANINE_2:CFA.12293.1.A1_AT similar to nuclear receptor subfamily 2, group F, member 2 cfa
CANINE_2:CFA.12293.1.A1_S_AT similar to nuclear receptor subfamily 2, group F, member 2 cfa
CANINE_2:CFAAFFX.17039.1.S1_AT similar to nuclear receptor subfamily 2, group F, member 2 cfa
CHICKEN:GGA.4445.1.S1_AT nuclear receptor subfamily 2, group F, member 2 gga
HG-U133A:209121_X_AT nuclear receptor subfamily 2, group F, member 2 hs
HG-U133_PLUS_2:209121_X_AT nuclear receptor subfamily 2, group F, member 2 hs
HG-U133A_2:209121_X_AT nuclear receptor subfamily 2, group F, member 2 hs
HG-U133_PLUS_2:215073_S_AT nuclear receptor subfamily 2, group F, member 2 hs
HG-U133A_2:215073_S_AT nuclear receptor subfamily 2, group F, member 2 hs
HG-U133A:215073_S_AT nuclear receptor subfamily 2, group F, member 2 hs
HU35KSUBA:RC_AA393876_S_AT nuclear receptor subfamily 2, group F, member 2 hs
HU35KSUBD:RC_AA418544_AT nuclear receptor subfamily 2, group F, member 2 hs
HUGENEFL:M64497_AT nuclear receptor subfamily 2, group F, member 2 hs
U133_X3P:G179023_3P_A_AT nuclear receptor subfamily 2, group F, member 2 hs
U133_X3P:HS.288869.1.S1_3P_A_AT nuclear receptor subfamily 2, group F, member 2 hs
U133_X3P:HS.288869.0.S3_3P_AT nuclear receptor subfamily 2, group F, member 2 hs
U133_X3P:HS.288869.0.S1_3P_X_AT nuclear receptor subfamily 2, group F, member 2 hs
U133_X3P:HS.288869.0.S1_3P_A_AT nuclear receptor subfamily 2, group F, member 2 hs
HG-U133A_2:209119_X_AT nuclear receptor subfamily 2, group F, member 2 hs
HG-U133_PLUS_2:209119_X_AT nuclear receptor subfamily 2, group F, member 2 hs
HG-U133A:209119_X_AT nuclear receptor subfamily 2, group F, member 2 hs
HG-U133A_2:209120_AT nuclear receptor subfamily 2, group F, member 2 hs
HG-U133_PLUS_2:209120_AT nuclear receptor subfamily 2, group F, member 2 hs
HG-U133A:209120_AT nuclear receptor subfamily 2, group F, member 2 hs
HG-U95AV2:39397_AT nuclear receptor subfamily 2, group F, member 2 hs
HG-U95D:78413_AT Nuclear receptor subfamily 2, group F, member 2 hs
HG-U95C:62283_S_AT Nuclear receptor subfamily 2, group F, member 2 hs
HG-U95C:62284_R_AT Nuclear receptor subfamily 2, group F, member 2 hs
MOUSE430_2:1431237_AT nuclear receptor subfamily 2, group F, member 2 mm
MOE430B:1431237_AT nuclear receptor subfamily 2, group F, member 2 mm
MU11KSUBB:X76653_S_AT nuclear receptor subfamily 2, group F, member 2 mm
MG-U74AV2:103052_R_AT nuclear receptor subfamily 2, group F, member 2 mm
MG-U74BV2:106526_AT nuclear receptor subfamily 2, group F, member 2 mm
MG-U74AV2:161792_F_AT nuclear receptor subfamily 2, group F, member 2 mm
MOE430A:1416159_AT nuclear receptor subfamily 2, group F, member 2 mm
MOUSE430A_2:1416159_AT nuclear receptor subfamily 2, group F, member 2 mm
MOUSE430_2:1416159_AT nuclear receptor subfamily 2, group F, member 2 mm
MOE430A:1416160_AT nuclear receptor subfamily 2, group F, member 2 mm
MOUSE430A_2:1416160_AT nuclear receptor subfamily 2, group F, member 2 mm
MOUSE430_2:1416160_AT nuclear receptor subfamily 2, group F, member 2 mm
MOE430A:1416158_AT nuclear receptor subfamily 2, group F, member 2 mm
MOUSE430A_2:1416158_AT nuclear receptor subfamily 2, group F, member 2 mm
MOUSE430_2:1416158_AT nuclear receptor subfamily 2, group F, member 2 mm
MG-U74CV2:134006_AT Nuclear receptor subfamily 2, group F, member 2 (Nr2f2), transcript variant 1, mRNA mm
MOUSE430_2:1436475_AT Nuclear receptor subfamily 2, group F, member 2 (Nr2f2), transcript variant 1, mRNA mm
MOE430B:1436475_AT Nuclear receptor subfamily 2, group F, member 2 (Nr2f2), transcript variant 1, mRNA mm
MOE430B:1444229_AT Nuclear receptor subfamily 2, group F, member 2 (Nr2f2), transcript variant 1, mRNA mm
MOUSE430_2:1444229_AT Nuclear receptor subfamily 2, group F, member 2 (Nr2f2), transcript variant 1, mRNA mm
MU19KSUBB:TC29518_S_AT Nuclear receptor subfamily 2, group F, member 2 (Nr2f2), transcript variant 1, mRNA mm
MU19KSUBC:TC40059_AT Nuclear receptor subfamily 2, group F, member 2 (Nr2f2), transcript variant 1, mRNA mm
RG-U34A:RC_AI012183_AT nuclear receptor subfamily 2, group F, member 2 rn
RAE230A:1370063_AT nuclear receptor subfamily 2, group F, member 2 rn
RAT230_2:1370063_AT nuclear receptor subfamily 2, group F, member 2 rn
RAE230A:1389554_AT Nuclear receptor subfamily 2, group F, member 2 rn
RAT230_2:1389554_AT Nuclear receptor subfamily 2, group F, member 2 rn
RAE230A:1389998_AT Nuclear receptor subfamily 2, group F, member 2 rn
RAT230_2:1389998_AT Nuclear receptor subfamily 2, group F, member 2 rn
RAE230B:1392624_AT Nuclear receptor subfamily 2, group F, member 2 rn
RAT230_2:1392624_AT Nuclear receptor subfamily 2, group F, member 2 rn
RG-U34B:RC_AA850038_AT Nuclear receptor subfamily 2, group F, member 2 rn
RG-U34C:RC_AI071284_AT Nuclear receptor subfamily 2, group F, member 2 rn
RG-U34C:RC_AI103202_AT Nuclear receptor subfamily 2, group F, member 2 rn
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
3677 DNA binding inferred from electronic annotation QuickGO AmiGO
3700 transcription factor activity inferred from electronic annotation QuickGO AmiGO
3707 steroid hormone receptor activity inferred from electronic annotation QuickGO AmiGO
4879 ligand-dependent nuclear receptor activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA99861 Hypothetical protein F55D12.4 [Caenorhabditis elegans] ref|NP_492181.1| UNCoordinated family member (unc-55) [Caenorhabditis elegans] 0.0
blast CAE63721 Hypothetical protein CBG08244 [Caenorhabditis briggsae] 2.0E-71
blast XP_849497 PREDICTED: similar to nuclear receptor subfamily 2, group F, member 2 isoform 2 [Canis familiaris] 7.0E-48
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 2.5E-18
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 6.1E-47
Sequence
Target Sequence 
>C. ELEGANS:192833_AT
ttgcactggctcaatcgaatttcgcactcaatctttcaacccatttaactgcagttacgg
caacggcggcgtcaacagaaaatggatcttcttcgttgggttcaaagtcagaagatgagg
aaaagagtgaagaaaaaccggaaagagtatttgatgagccacagtttcagggatttcagg
cgaaaattgataagatccgtgactttcatttggatgtcgttgaaagctcgtctcttcgag
cggttcttctttttagttgcggataccgaaatatacattactttgaagtagcttctgtca
ttttgataatcggtttaatttcagatgaagaagcattggaggagaagggaaaaattgaag
aaattgttgagaaattgaaaagtgcagtggatgaatattgcaaaatgaataaacgtagtg
agagatatcatcaaatctgtgaatgtcttcaacttctcaaatcaactcgaaatcttccaa
tttctcgtcttttcttttctcgacttcttggtacaactcctcttgaaacaattttatcag
atcttttaattactccacctc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTGCACTGGCTCAATCGAATTTCGC 10 703 683 Antisense
GAATTTCGCACTCAATCTTTCAACC 649 325 699 Antisense
ATCTTTCAACCCATTTAACTGCAGT 347 19 713 Antisense
TAACTGCAGTTACGGCAACGGCGGC 699 633 728 Antisense
AATGGATCTTCTTCGTTGGGTTCAA 505 161 763 Antisense
GATGAGCCACAGTTTCAGGGATTTC 575 411 835 Antisense
TGTCGTTGAAAGCTCGTCTCTTCGA 538 557 897 Antisense
TCTTCGAGCGGTTCTTCTTTTTAGT 411 615 915 Antisense
GAAGTAGCTTCTGTCATTTTGATAA 324 337 967 Antisense
TTTTCTCGACTTCTTGGTACAACTC 64 677 1177 Antisense
TCAGATCTTTTAATTACTCCACCTC 52 625 1219 Antisense
Sequence Source Affymetrix Proprietary Database