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[193949_s_at]

Description R04A9.5 /REP_DB=WormBase Gene ID /WP=CE04792 /TR=Q21694 /GB=AAA83287.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=homeobox; centromeric protein E; ribosomal protein S6 kinase
Cluster 6grp_highest_10_10 > 35      6grp_high1_10_10 > 53      4grp_highest_8_8 > 44      4grp_high_8_8 > 16      6grp_highest_nonorm > 80      6grp_total > 53      4grp_total > 31      6grp_highest_sub > 03      6grp_high1_sub > 03      6grp_total_sub > Hat      6grp_rule_based > S3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 105
1 2 3 4 range
A 163.2
(3)
P 		106.5
(-3)
P 		117
(-1.9)
P 		123.6
(-1.2)
P 		57
B 134.6
(2.2)
P 		99.1
(-0.6)
P 		67.3
(-3)
P 		145.3
(3)
P 		78
C 172.6
(3)
P 		117.1
(-3)
P 		151.1
(0.7)
P 		122.7
(-2.4)
P 		56
avr 156.8
(3) 		107.6
(-3) 		111.8
(-2.5) 		130.5
(-0.2) 		49

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 193
1 2 3 4 5 6 range
A 133.1
(-3)
P 		203.7
(1.7)
P 		222.9
(3)
P 		144.7
(-2.2)
P 		160.5
(-1.2)
P 		136.5
(-2.8)
P 		90
B 207
(0.1)
P 		195.6
(-0.3)
P 		301.6
(3)
P 		162
(-1.4)
P 		109.1
(-3)
P 		154.5
(-1.6)
P 		193
C 138.3
(-3)
P 		231.9
(1.8)
P 		254.5
(3)
P 		197.2
(0)
P 		152.5
(-2.3)
P 		154.2
(-2.2)
P 		116
avr 159.5
(-2.1) 		210.4
(0.5) 		259.7
(3) 		168
(-1.6) 		140.7
(-3) 		148.4
(-2.6) 		119
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 44
1 2 3 4 range
A 59.4
(3)
P 		23.1
(-2.3)
P 		30.6
(-1.2)
P 		18.1
(-3)
P 		41
B 42.9
(3)
P 		24.5
(-1)
P 		15.6
(-3)
P 		31
(0.4)
P 		27
C 57.1
(3)
P 		33.7
(-0.9)
P 		52.7
(2.3)
P 		20.7
(-3)
P 		36
avr 53.1
(3) 		27.1
(-2.2) 		33
(-1) 		23.3
(-3) 		30

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 49
1 2 3 4 5 6 range
A 24.5
(-3)
P 		72.5
(3)
P 		48.5
(0)
P 		36.7
(-1.5)
P 		48.4
(-0)
P 		33.2
(-1.9)
P 		48
B 72
(2.8)
P 		65.1
(1.4)
P 		73.2
(3)
P 		42.9
(-3)
P 		44.3
(-2.7)
P 		57.6
(-0.1)
P 		30
C 51.3
(-0.8)
P 		70.8
(3)
P 		64.8
(1.8)
P 		39.7
(-3)
P 		49.3
(-1.1)
P 		51.6
(-0.7)
P 		31
avr 49.3
(-1.1) 		69.5
(3) 		62.2
(1.5) 		39.8
(-3) 		47.3
(-1.5) 		47.5
(-1.4) 		30
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 193949_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.18607
Sequence Type Exemplar sequence
Representative Public ID R04A9.5 NCBI
Target Description R04A9.5 /REP_DB=WormBase Gene ID /WP=CE04792 /TR=Q21694 /GB=AAA83287.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=homeobox; centromeric protein E; ribosomal protein S6 kinase
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_075694(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_075694 NCBI Caenorhabditis elegans R04A9.5 (R04A9.5) mRNA, complete cds. 11/11 None
SNAP00000016337 ENSEMBL cdna:SNAP chromosome:CEL140:X:384523:387855:-1 11/11 None
GENEFINDER00000016354 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:384523:394782:-1 11/11 None
R04A9.5a ENSEMBL cdna:known chromosome:CEL140:X:384448:394538:-1 gene:R04A9.5 11/11 None
R04A9.5b ENSEMBL cdna:known chromosome:CEL140:X:384523:388797:-1 gene:R04A9.5 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
chrX:384522-394538(-) 97.99 97.99
Public Domain and Genome References
Gene Title
Ensembl R04A9.5
Entrez Gene 180394 Entrez gene
SwissProt Q86DC2 EMBL-EBI
WormBase CE33932 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 NP_508095 R04A9.5 [Caenorhabditis elegans] gb|AAP31434.1| Hypothetical protein R04A9.5 [Caenorhabditis elegans] 0.0
blast NP_001024829 R04A9.7 [Caenorhabditis elegans] gb|AAA83287.3| Hypothetical protein R04A9.7 [Caenorhabditis elegans] 0.0
blast NP_508095 R04A9.5 [Caenorhabditis elegans] gb|AAP31434.1| Hypothetical protein R04A9.5 [Caenorhabditis elegans] 1.0E-142
blast XP_781234 PREDICTED: similar to Ribosomal protein S6 kinase I (S6K) (p70-S6K) [Strongylocentrotus purpuratus] 5.0E-95
blast XP_781234 PREDICTED: similar to Ribosomal protein S6 kinase I (S6K) (p70-S6K) [Strongylocentrotus purpuratus] 2.0E-93
blast CAC70129 Hypothetical protein Y66D12A.5 [Caenorhabditis elegans] ref|NP_499497.2| Y66D12A.5 [Caenorhabditis elegans] 6.0E-10
Protein Families
Method ID Description E-Value
ec A2S7_HUMAN (Q96Q40) Serine/threonine-protein kinase ALS2CR7 (EC 2.7.1.37) (Amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 7) 2.0E-67
ec A2S7_HUMAN (Q96Q40) Serine/threonine-protein kinase ALS2CR7 (EC 2.7.1.37) (Amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 7) 4.0E-71
hanks 1.6.1 AGC group; AGC VI phosphorylate ribosomal protein S6; S6K 9.0E-77
hanks 1.6.1 AGC group; AGC VI phosphorylate ribosomal protein S6; S6K 4.0E-77
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 7.999999797903E-5
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 2.99999992421363E-5
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 9.99999974737875E-6
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 7.00000009601354E-6
Pfam IPR001356 EMBL-EBI Homeobox 27.0
Pfam IPR001356 EMBL-EBI Homeobox 3.1E-8
Pfam IPR000719 EMBL-EBI Protein kinase 1.6E-78
Pfam IPR000961 EMBL-EBI Protein kinase C-terminal domain 6.4E-10
Pfam IPR001356 EMBL-EBI Homeobox 27.0
Pfam IPR001356 EMBL-EBI Homeobox 3.1E-8
Pfam IPR001356 EMBL-EBI Homeobox 27.0
Pfam IPR001356 EMBL-EBI Homeobox 5.7E-9
Pfam IPR001356 EMBL-EBI Homeobox 27.0
Pfam IPR001356 EMBL-EBI Homeobox 3.1E-8
Pfam IPR000719 EMBL-EBI Protein kinase 1.6E-78
Pfam IPR000961 EMBL-EBI Protein kinase C-terminal domain 6.4E-10
Sequence
Target Sequence 
>C. ELEGANS:193949_S_AT
gacgcgtgttgtcgaattcgggagtttttgtctcgtgaaacggatactacttcctacata
gaaattacgaacgaagtgcaaactgtattggaggacgagattgaacttcaccttctctca
cggaaaaggttcactcttggatatgttcatgtgataatggagaaaactgacttagcacct
tcctacattcgtgcacaatatgaaaactggagaaggaagctttcgacaaaggatcgtgga
tcgtggaaaatcggggatagtgaagcagggttgaacaaatactttgcaaaaaacaacaag
cctggtgtgagacaacgagaaaaaatcgcaaagaaactagggctcagtgaacgtcaagtc
agaaactatttcaataagaagcggattaccgaaagaaaactgaaagtttggaaagatgcg
ccgaaggactttttaactctctctaagcaaacagttgatgaaatgatgaaaattgctgag
gaacgaagaaaaccgaatgatgaatatattcaaattgcaaatcgtcttggagtttcccac
atcaccctttgcagcttcatcgactggcaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GACGCGTGTTGTCGAATTCGGGAGT 372 379 1756 Antisense
TCGGGAGTTTTTGTCTCGTGAAACG 530 603 1773 Antisense
GAAACGGATACTACTTCCTACATAG 667 355 1792 Antisense
CGAGATTGAACTTCACCTTCTCTCA 251 251 1851 Antisense
CTTCTCTCACGGAAAAGGTTCACTC 233 221 1867 Antisense
GGTTCACTCTTGGATATGTTCATGT 436 507 1883 Antisense
GAAAACTGACTTAGCACCTTCCTAC 244 353 1917 Antisense
CACCTTCCTACATTCGTGCACAATA 631 201 1931 Antisense
ACTAGGGCTCAGTGAACGTCAAGTC 556 101 2091 Antisense
GCCGAAGGACTTTTTAACTCTCTCT 659 281 2175 Antisense
CCTTTGCAGCTTCATCGACTGGCAA 192 269 2301 Antisense
Sequence Source Affymetrix Proprietary Database