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[173241_at]

Description CEC758_rc /REP_DB=TREMBL Accession /GB=C07758 /FEA=Transcript Cluster /DEF=C.elegans cDNA clone yk158g9 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 52      6grp_high1_10_10 > 29      4grp_highest_8_8 > 47      4grp_high_8_8 > 03      6grp_highest_nonorm > 70      6grp_total > 27      4grp_total > 13      6grp_highest_sub > 01_02      6grp_cgc > 04      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 416
1 2 3 4 range
A 364.3
(-0.6)
P 		212.8
(-3)
P 		211.8
(-3)
P 		586.9
(3)
P 		375
B 459.3
(3)
P 		202.1
(-2.3)
P 		170.6
(-3)
P 		454.1
(2.9)
P 		289
C 340.2
(-0.9)
P 		238.2
(-2.5)
P 		210.6
(-3)
P 		578.1
(3)
P 		368
avr 387.9
(0.3) 		217.7
(-2.6) 		197.7
(-3) 		539.7
(3) 		342

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 315
1 2 3 4 5 6 range
A 411
(3)
P 		363
(1.7)
P 		198.1
(-2.6)
P 		184.3
(-3)
P 		242.4
(-1.5)
P 		261.7
(-1)
P 		227
B 374.5
(3)
P 		306.9
(1.5)
P 		96.2
(-3)
P 		206.4
(-0.6)
P 		225.6
(-0.2)
P 		245.2
(0.2)
P 		278
C 339
(1.3)
P 		403.1
(3)
P 		203.6
(-2.2)
P 		173.3
(-3)
P 		231.1
(-1.5)
P 		273.9
(-0.4)
P 		230
avr 374.8
(3) 		357.7
(2.5) 		166
(-3) 		188
(-2.4) 		233
(-1.1) 		260.3
(-0.3) 		209
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 107
1 2 3 4 range
A 132.6
(3)
P 		46.2
(-3)
P 		55.4
(-2.4)
P 		85.9
(-0.2)
P 		86
B 146.5
(3)
P 		49.9
(-2.4)
P 		39.5
(-3)
P 		96.8
(0.2)
P 		107
C 112.6
(3)
P 		68.5
(-3)
P 		73.4
(-2.3)
P 		97.5
(0.9)
P 		44
avr 130.6
(3) 		54.9
(-3) 		56.1
(-2.9) 		93.4
(0.1) 		76

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 107
1 2 3 4 5 6 range
A 75.8
(-0.7)
P 		129.1
(3)
P 		43.1
(-3)
P 		46.8
(-2.7)
P 		73.2
(-0.9)
P 		63.7
(-1.6)
P 		86
B 130.3
(3)
P 		102.2
(1.4)
P 		23.4
(-3)
P 		54.7
(-1.2)
P 		91.6
(0.8)
P 		91.4
(0.8)
P 		107
C 125.7
(3)
P 		123
(2.8)
P 		51.8
(-1.9)
P 		34.9
(-3)
P 		74.8
(-0.4)
P 		91.7
(0.8)
P 		91
avr 110.6
(2.4) 		118.1
(3) 		39.4
(-3) 		45.5
(-2.5) 		79.9
(0.1) 		82.3
(0.3) 		79
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173241_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.27767
Sequence Type Exemplar sequence
Representative Public ID CEC758 NCBI
Target Description CEC758_rc /REP_DB=TREMBL Accession /GB=C07758 /FEA=Transcript Cluster /DEF=C.elegans cDNA clone yk158g9 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Transcript Cluster.
Annotation Method Description
Annotation Description This probe set was annotated using the Genome Target Overlap based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade B annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_001029218, NM_001029217
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
C11G6.4a ENSEMBL cdna:known chromosome:CEL140:X:16354890:16359568:1 gene:C11G6.4 None
C11G6.4b.1 ENSEMBL cdna:known chromosome:CEL140:X:16355535:16359214:1 gene:C11G6.4 None
NM_001029217 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-28) (nhr-28) mRNA, complete cds. None
NM_001029218 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-28) (nhr-28) mRNA, complete cds. None
GENEFINDER00000002971 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:16354903:16359214:1 None
SNAP00000002970 ENSEMBL cdna:SNAP chromosome:CEL140:X:16358079:16359214:1 None
C11G6.4b.2 ENSEMBL cdna:known chromosome:CEL140:X:16354890:16359471:1 gene:C11G6.4 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
chrX:16358549-16359399(+) 94.06 94.06
Public Domain and Genome References
Ensembl C11G6.4
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAR11977 nuclear receptor NHR-28 [Caenorhabditis elegans] gb|AAR11976.1| nuclear receptor NHR-28 [Caenorhabditis elegans] emb|CAA94114.2| Hypothetical protein C11G6.4a [Caenorhabditis elegans] ref|NP_001024388.1| Nuclear Hormone Receptor family member (nhr-28) [Caenorhabditis elegans] sp|Q17905|NHR28_CAEEL Nuclear hormone receptor family member nhr-28 0.0
blast AAG15123 nuclear receptor NHR-28 [Caenorhabditis elegans] 0.0
blast T19202 hypothetical protein C11G6.4 - Caenorhabditis elegans 0.0
blast CAI46566 Hypothetical protein C11G6.4b [Caenorhabditis elegans] ref|NP_001024389.1| Nuclear Hormone Receptor family member (nhr-28) [Caenorhabditis elegans] 0.0
blast AAG15124 nuclear receptor NHR-28 [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 4.2E-34
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 2.4E-10
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 4.2E-34
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 2.4E-29
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 2.9E-18
Sequence
Target Sequence 
>C. ELEGANS:173241_AT
gaagttatcaaccccagaggagattgacagtgtttgggatctcaccacagggcagttggt
cgaaatgtacgaattaccaactccaccactccatacgccgaccgaaatggatccatccac
cacacagctctaaactatttcctattgctaacaatattcctccgctgacctcagttnttg
atctggcataactttctcctccacccagaatataaaangagtnnnnnaccaccgaatata
ttgatcacggttcattgttcagcttt

BLASTn GenBank NR
Note: "n"'s represent regions that are not probed by the probe sequences.
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAAGTTATCAACCCCAGAGGAGATT 378 337 13 Antisense
GACAGTGTTTGGGATCTCACCACAG 90 369 38 Antisense
TGTTTGGGATCTCACCACAGGGCAG 678 481 43 Antisense
ATCTCACCACAGGGCAGTTGGTCGA 58 33 51 Antisense
CCACACAGCTCTAAACTATTTCCTA 193 275 132 Antisense
ACACAGCTCTAAACTATTTCCTATT 93 111 134 Antisense
TATTGCTAACAATATTCCTCCGCTG 432 665 155 Antisense
TTGATCTGGCATAACTTTCTCCTCC 339 705 190 Antisense
TTTCTCCTCCACCCAGAATATAAAA 151 671 205 Antisense
ACCACCGAATATATTGATCACGGTT 473 85 240 Antisense
TGATCACGGTTCATTGTTCAGCTTT 491 565 254 Antisense
Sequence Source Affymetrix Proprietary Database