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[180441_s_at]

Description F54A5.1 /REP_DB=WormBase Gene ID /WP=CE20859 /TR=Q9TYT0 /GB=AAC78220.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation
Cluster 6grp_total > 72      4grp_total > 56      6grp_total_sub > Hat      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 459
1 2 3 4 range
A 5.2
(-3)
A 		276.6
(0.9)
A 		422.5
(3)
A 		9.4
(-2.9)
A 		417
B 78.5
(-1.6)
A 		230
(1.2)
A 		328.9
(3)
P 		4.3
(-3)
A 		325
C 27.4
(-2.9)
A 		300.3
(0.8)
A 		463.6
(3)
P 		20.9
(-3)
A 		443
avr 37
(-2.6) 		269
(0.9) 		405
(3) 		11.5
(-3) 		394

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 181
1 2 3 4 5 6 range
A 58.2
(-3)
A 		140.2
(1)
A 		179.6
(2.9)
A 		169.2
(2.4)
A 		181.8
(3)
A 		79.7
(-2)
A 		124
B 69.2
(-2.7)
A 		136.3
(-0.4)
A 		239.1
(3)
A 		161.9
(0.4)
A 		174.8
(0.8)
A 		60
(-3)
A 		179
C 104.5
(-1.7)
A 		113.7
(-1.4)
A 		186.2
(1.2)
A 		112.1
(-1.4)
A 		236.4
(3)
A 		68.4
(-3)
A 		168
avr 77.3
(-2.6) 		130.1
(-0.2) 		201.6
(3) 		147.7
(0.6) 		197.7
(2.8) 		69.4
(-3) 		132
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 161
1 2 3 4 range
A 1.9
(-3)
A 		60.1
(0.2)
A 		110.4
(3)
A 		1.4
(-3)
A 		109
B 25
(-1.1)
A 		56.8
(1.5)
A 		76.2
(3)
P 		0.9
(-3)
A 		75
C 9.1
(-2.8)
A 		86.3
(0.1)
A 		161.6
(3)
P 		3.5
(-3)
A 		158
avr 12
(-2.5) 		67.7
(0.5) 		116.1
(3) 		1.9
(-3) 		114

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 66
1 2 3 4 5 6 range
A 10.7
(-3)
A 		49.9
(2.3)
A 		39.1
(0.9)
A 		42.9
(1.4)
A 		54.9
(3)
A 		19.4
(-1.8)
A 		44
B 24.1
(-2.8)
A 		45.4
(-0.2)
A 		58.1
(1.4)
A 		42.9
(-0.5)
A 		71
(3)
A 		22.4
(-3)
A 		49
C 38.7
(-1.2)
A 		34.7
(-1.7)
A 		47.4
(-0.2)
A 		22.6
(-3)
A 		76.5
(3)
A 		22.9
(-3)
A 		54
avr 24.5
(-2.6) 		43.3
(-0.2) 		48.2
(0.5) 		36.1
(-1.1) 		67.5
(3) 		21.6
(-3) 		46
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 180441_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11
Sequence Type Exemplar sequence
Representative Public ID F54A5.1 NCBI
Target Description F54A5.1 /REP_DB=WormBase Gene ID /WP=CE20859 /TR=Q9TYT0 /GB=AAC78220.1 /SUBMIT=ST.LOUIS /CHR=1 /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_058402(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_058402 NCBI Caenorhabditis elegans F54A5.1 (F54A5.1) mRNA, complete cds. 11/11 None
F54A5.1.2 ENSEMBL cdna:known chromosome:CEL140:I:989673:992374:1 gene:F54A5.1 11/11 None
F54A5.1.1 ENSEMBL cdna:known chromosome:CEL140:I:989673:992180:1 gene:F54A5.1 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000006753 4/11 Cross Hyb Matching Probes None
GENEFINDER00000006761 4/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrI:989684-991794(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Ensembl F54A5.1
Entrez Gene 171679 Entrez gene
SwissProt Q9TYT0 EMBL-EBI
WormBase CE20859 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1597196_AT similar to F54A5.1 cfa
CANINE_2:CFAAFFX.13080.1.S1_S_AT similar to F54A5.1 cfa
CHICKEN:GGA.11820.1.S1_AT similar to Hypothetical protein FLJ21616 gga
HG-U133_PLUS_2:219269_AT hypothetical protein FLJ21616 hs
HG-U133A:219269_AT hypothetical protein FLJ21616 hs
HG-U133A_2:219269_AT hypothetical protein FLJ21616 hs
HU35KSUBA:RC_AA282206_AT hypothetical protein FLJ21616 hs
HU35KSUBD:RC_N51223_AT hypothetical protein FLJ21616 hs
U133_X3P:G13375737_3P_AT hypothetical protein FLJ21616 hs
HG-U95B:46764_AT hypothetical protein FLJ21616 hs
HG-U95B:53846_AT hypothetical protein FLJ21616 hs
HU35KSUBA:RC_AA454840_S_AT Hypothetical protein FLJ21616 hs
U133_X3P:HS.308852.0.A1_3P_AT Hypothetical protein FLJ21616 hs
U133_X3P:HS.146278.0.A1_3P_AT Hypothetical protein FLJ21616 hs
HG-U133_PLUS_2:225504_AT Hypothetical protein FLJ21616 hs
HG-U133B:225504_AT Hypothetical protein FLJ21616 hs
HG-U133_PLUS_2:242850_AT Hypothetical protein FLJ21616 hs
HG-U133B:242850_AT Hypothetical protein FLJ21616 hs
HG-U95B:53850_AT Hypothetical protein FLJ21616 hs
HG-U95C:56300_S_AT Hypothetical protein FLJ21616 hs
HG-U95D:81399_AT Hypothetical protein FLJ21616 hs
HG-U133_PLUS_2:237893_AT Hypothetical protein FLJ21616 hs
HG-U133B:237893_AT Hypothetical protein FLJ21616 hs
HG-U95B:48217_AT Hypothetical protein FLJ21616 hs
HG-U95B:48409_AT Hypothetical protein FLJ21616 hs
HG-U95D:84221_R_AT Hypothetical protein FLJ21616 hs
HU35KSUBB:RC_N69469_AT Hypothetical protein FLJ21616 hs
HU35KSUBB:RC_T81305_AT Hypothetical protein FLJ21616 hs
U133_X3P:HS.194225.0.A1_3P_AT Hypothetical protein FLJ21616 hs
MOUSE430A_2:1436341_AT RIKEN cDNA F830020C16 gene mm
MOE430A:1436341_AT RIKEN cDNA F830020C16 gene mm
MOUSE430_2:1436341_AT RIKEN cDNA F830020C16 gene mm
MU11KSUBA:AA203803_S_AT RIKEN cDNA F830020C16 gene mm
MG-U74AV2:93693_AT RIKEN cDNA F830020C16 gene mm
MG-U74BV2:115477_AT RIKEN cDNA F830020C16 gene mm
MOE430A:1452449_AT RIKEN cDNA F830020C16 gene mm
MOUSE430A_2:1452449_AT RIKEN cDNA F830020C16 gene mm
MOUSE430_2:1452449_AT RIKEN cDNA F830020C16 gene mm
MOE430B:1443020_AT RIKEN cDNA F830020C16 gene, mRNA (cDNA clone IMAGE:3490304) mm
MOUSE430_2:1443020_AT RIKEN cDNA F830020C16 gene, mRNA (cDNA clone IMAGE:3490304) mm
MOE430B:1445428_AT RIKEN cDNA F830020C16 gene, mRNA (cDNA clone IMAGE:3490304) mm
MOUSE430_2:1445428_AT RIKEN cDNA F830020C16 gene, mRNA (cDNA clone IMAGE:3490304) mm
RAT230_2:1394626_AT similar to hypothetical protein FLJ21616 (predicted) rn
RAE230B:1394626_AT similar to hypothetical protein FLJ21616 (predicted) 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
Protein Similarities
Method ID Description E-Value
blast AAC78220 Hypothetical protein F54A5.1 [Caenorhabditis elegans] ref|NP_490803.1| F54A5.1 [Caenorhabditis elegans] 0.0
blast CAE74379 Hypothetical protein CBG22107 [Caenorhabditis briggsae] 1.0E-132
blast AAH77815 MGC80451 protein [Xenopus laevis] 3.0E-25
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 0.00300000002607703
Pfam IPR001356 EMBL-EBI Homeobox 5.0E-4
Pfam IPR001356 EMBL-EBI Homeobox 18.0
Sequence
Target Sequence 
>C. ELEGANS:180441_S_AT
gtcgagaacgctacgtgtttcgtccaattctgatccgaatgctcgaatcgttcttcacac
aaacgccattcccagatcttccacggcgagtcgaaatagcgaatgcttgcaatcacgttc
tgaagatggataagaaaggtgttgggttgatgccaaaggaggtggtcagccctcaagtcg
tttcgaattggtttgcaaataagcggaaggagttgagaagaagatccgctgaagcttcgg
ccgcctccacctcgtccgcttcgtcttctgcgtcatcgactgctaatcatgattctgtca
gtgtgtccagcatgagccctcgcgatgaagagacaagctcccgtaacacaaccccggaga
cagcaatctccccgtcaccagcagtgtccacttttgaagtgtcccgcccgtctgccatca
tctctgccacgtcatcaacaacctcgccaatctcaattccagcaacaatcattccatcag
tatcgccgtcagctctcgaacttttcgccatggcccaacagcttggagttcagcttccgg
ttccatttccaacattgccaacacactttttcccgtttcaaatggctccgttctacg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTCGAGAACGCTACGTGTTTCGTCC 630 473 659 Antisense
CGTGTTTCGTCCAATTCTGATCCGA 506 245 672 Antisense
AGATCTTCCACGGCGAGTCGAAATA 42 67 732 Antisense
GAATGCTTGCAATCACGTTCTGAAG 243 331 759 Antisense
TCAGCCCTCAAGTCGTTTCGAATTG 207 599 824 Antisense
TCTTCTGCGTCATCGACTGCTAATC 598 617 922 Antisense
TCTGTCAGTGTGTCCAGCATGAGCC 543 607 952 Antisense
TAACACAACCCCGGAGACAGCAATC 7 641 1002 Antisense
GTCACCAGCAGTGTCCACTTTTGAA 122 465 1032 Antisense
GTTCCATTTCCAACATTGCCAACAC 341 441 1198 Antisense
CCGTTTCAAATGGCTCCGTTCTACG 576 259 1231 Antisense
Sequence Source Affymetrix Proprietary Database