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[182349_s_at]

Description Y80D3A.3 /REP_DB=WormBase Gene ID /WP=CE24675 /TR=Q9U1R1 /GB=CAB60440.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation
Cluster 6grp_total > 48      4grp_total > 13      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 31
1 2 3 4 range
A 29.1
(3)
A 		5.3
(-2.6)
A 		3.6
(-3)
A 		11.1
(-1.2)
A 		26
B 3.4
(-3)
A 		9.3
(-1.9)
A 		5.4
(-2.6)
A 		34.2
(3)
A 		31
C 4.9
(-3)
A 		5.4
(-2.6)
A 		7.8
(-0.5)
A 		12
(3)
A 		7
avr 12.5
(0.1) 		6.7
(-2.5) 		5.6
(-3) 		19.1
(3) 		14

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 9
1 2 3 4 5 6 range
A 10
(3)
A 		2.8
(-3)
A 		5.1
(-1.1)
A 		3
(-2.8)
A 		6.1
(-0.3)
A 		5.9
(-0.4)
A 		7
B 6.3
(0.5)
A 		4.5
(-1)
A 		2
(-3)
A 		5.7
(0)
A 		2.5
(-2.6)
A 		9.4
(3)
A 		7
C 8.6
(1.2)
A 		5.6
(-1)
A 		2.8
(-3)
A 		11
(3)
A 		4.2
(-2)
A 		6.6
(-0.2)
A 		8
avr 8.3
(3) 		4.3
(-1.8) 		3.3
(-3) 		6.6
(1) 		4.3
(-1.8) 		7.3
(1.8) 		5
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 10
1 2 3 4 range
A 10.6
(3)
A 		1.1
(-2.9)
A 		0.9
(-3)
A 		1.6
(-2.6)
A 		10
B 1.1
(-3)
A 		2.3
(-1.8)
A 		1.2
(-2.9)
A 		7.3
(3)
A 		6
C 1.6
(-3)
A 		1.6
(-3)
A 		2.7
(3)
A 		2
(-0.8)
A 		1
avr 4.4
(3) 		1.7
(-2.8) 		1.6
(-3) 		3.6
(1.3) 		3

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3
1 2 3 4 5 6 range
A 1.8
(3)
A 		1
(-1.8)
A 		1.1
(-1.2)
A 		0.8
(-3)
A 		1.8
(3)
A 		1.4
(0.6)
A 		1
B 2.2
(0.4)
A 		1.5
(-1)
A 		0.5
(-3)
A 		1.5
(-1)
A 		1
(-2)
A 		3.5
(3)
A 		3
C 3.2
(3)
A 		1.7
(-0.6)
A 		0.7
(-3)
A 		2.2
(0.6)
A 		1.3
(-1.6)
A 		2.2
(0.6)
A 		3
avr 2.4
(3) 		1.4
(-0.8) 		0.8
(-3) 		1.5
(-0.4) 		1.4
(-0.8) 		2.4
(3) 		2
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 182349_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.13933
Sequence Type Exemplar sequence
Representative Public ID Y80D3A.3 NCBI
Target Description Y80D3A.3 /REP_DB=WormBase Gene ID /WP=CE24675 /TR=Q9U1R1 /GB=CAB60440.1 /SUBMIT=HINXTON /CHR=5 /FEA=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_075284(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_075284 NCBI Caenorhabditis elegans Y80D3A.3 (Y80D3A.3) mRNA, complete cds. 11/11 None
GENEFINDER00000017392 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:18876706:18878723:1 11/11 None
Y80D3A.3 ENSEMBL cdna:known chromosome:CEL140:V:18876706:18878742:1 gene:Y80D3A.3 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:18876705-18878480(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Ensembl Y80D3A.3
Entrez Gene 180233 Entrez gene
SwissProt Q9U1R1 EMBL-EBI
WormBase CE24675 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
3677 DNA binding inferred from electronic annotation QuickGO AmiGO
3700 transcription factor activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB60440 Hypothetical protein Y80D3A.3 [Caenorhabditis elegans] ref|NP_507685.1| Y80D3A.3 [Caenorhabditis elegans] 1.0E-104
blast CAB60440 Hypothetical protein Y80D3A.3 [Caenorhabditis elegans] ref|NP_507685.1| Y80D3A.3 [Caenorhabditis elegans] 1.0E-103
blast CAE72977 Hypothetical protein CBG20317 [Caenorhabditis briggsae] 6.0E-16
blast CAE72977 Hypothetical protein CBG20317 [Caenorhabditis briggsae] 8.0E-16
blast AAR89086 brain-specific homeodomain protein [Gallus gallus] ref|NP_989843.1| brain-specific homeodomain protein [Gallus gallus] sp|Q6RFL5|BSH_CHICK Brain-specific homeobox protein homolog 4.0E-11
blast AAR89086 brain-specific homeodomain protein [Gallus gallus] ref|NP_989843.1| brain-specific homeodomain protein [Gallus gallus] sp|Q6RFL5|BSH_CHICK Brain-specific homeobox protein homolog 6.0E-11
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 8.99999968854031E-17
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 3.0000001167616E-17
Pfam IPR001356 EMBL-EBI Homeobox 1.1E-20
Sequence
Target Sequence 
>C. ELEGANS:182349_S_AT
agctctccgggctcaatgagctcatcgccagcctatccggcggcctatcaggctccatca
ccgtgctacgtggcggatcccaatcagctttactatcaacaacagctggctcataatggg
aatgatatgttagttcaagcccatgctcaagcctaccaagctcaatgcttcgcctggttc
cagcagcagtactcacaactctccccatcctcgtttcctcatcctatggtggctcatcac
gctggcttcatcccaccaccgccgtcttttctacatcatcagcatcagcagcatccaaga
gctccttcagaaaagcggagaggcgctcgaactccgttctccgattctcagctttacgcg
ttgagaaccagatttgagcagtgcgacacaataaaggttgacgagcgacggaagttggga
gcagtcatcggactttcgcccgagcagatcaagatttggtttcagaatcggagattcaag
ttgagaaaggagaaatacaagcagatcaagcaggacgctgtgcagcaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AGCTCTCCGGGCTCAATGAGCTCAT 12 81 136 Antisense
CGGATCCCAATCAGCTTTACTATCA 647 243 209 Antisense
TACTATCAACAACAGCTGGCTCATA 661 645 226 Antisense
TGCTCAAGCCTACCAAGCTCAATGC 107 581 279 Antisense
TCGCCTGGTTCCAGCAGCAGTACTC 299 599 305 Antisense
ATCAGCAGCATCCAAGAGCTCCTTC 184 29 419 Antisense
AGCGGAGAGGCGCTCGAACTCCGTT 598 81 449 Antisense
CCGATTCTCAGCTTTACGCGTTGAG 137 265 476 Antisense
TGGGAGCAGTCATCGGACTTTCGCC 151 553 551 Antisense
GACTTTCGCCCGAGCAGATCAAGAT 693 371 566 Antisense
GATCAAGCAGGACGCTGTGCAGCAA 420 421 639 Antisense
Sequence Source Affymetrix Proprietary Database