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[189464_at] homeobox protein

Description T13C5.4 /REP_DB=WormBase Gene ID /WP=CE04945 /TR=Q22459 /GB=AAK39290.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=homeobox protein
Cluster 6grp_total > 02      4grp_total > 12      6grp_rule_based > S2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 335
1 2 3 4 range
A 129.2
(-0.1)
P 		104.3
(-0.9)
A 		38
(-3)
A 		228.3
(3)
A 		190
B 115.3
(0.4)
A 		63.4
(-1.2)
A 		4.8
(-3)
A 		200
(3)
P 		195
C 112.1
(-1.9)
P 		77.1
(-2.7)
A 		62.3
(-3)
A 		340.2
(3)
P 		278
avr 118.9
(-0.7) 		81.6
(-1.7) 		35
(-3) 		256.2
(3) 		221

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 99
1 2 3 4 5 6 range
A 129.3
(3)
A 		115.1
(1.7)
A 		92.4
(-0.3)
A 		62.3
(-3)
A 		88.8
(-0.6)
A 		71.2
(-2.2)
A 		67
B 89.8
(-1.5)
A 		161.6
(3)
P 		66.5
(-3)
A 		69.2
(-2.8)
A 		83.7
(-1.9)
A 		91.9
(-1.4)
A 		95
C 103
(-0.2)
A 		126.8
(3)
A 		93.2
(-1.5)
A 		91.1
(-1.8)
A 		82.2
(-3)
A 		90.8
(-1.8)
A 		45
avr 107.4
(0.3) 		134.5
(3) 		84
(-2) 		74.2
(-3) 		84.9
(-1.9) 		84.6
(-2) 		60
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 56
1 2 3 4 range
A 47.1
(3)
P 		22.6
(-1)
A 		9.9
(-3)
A 		33.4
(0.8)
A 		37
B 36.8
(2.2)
A 		15.7
(-0.9)
A 		1.1
(-3)
A 		42.6
(3)
P 		42
C 37.1
(-0.4)
P 		22.2
(-2.9)
A 		21.7
(-3)
A 		57.4
(3)
P 		36
avr 40.3
(2.3) 		20.2
(-1.3) 		10.9
(-3) 		44.5
(3) 		34

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 38
1 2 3 4 5 6 range
A 23.8
(-1.1)
A 		40.9
(3)
A 		20.1
(-2)
A 		15.8
(-3)
A 		26.8
(-0.4)
A 		17.3
(-2.6)
A 		25
B 31.2
(-0.6)
A 		53.8
(3)
P 		16.2
(-3)
A 		18.3
(-2.7)
A 		34
(-0.2)
A 		34.3
(-0.1)
A 		38
C 38.2
(2.9)
A 		38.7
(3)
A 		23.7
(-1.4)
A 		18.3
(-3)
A 		26.6
(-0.6)
A 		30.4
(0.6)
A 		20
avr 31.1
(0) 		44.5
(3) 		20
(-2.4) 		17.5
(-3) 		29.1
(-0.4) 		27.3
(-0.8) 		27
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189464_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17129
Sequence Type Exemplar sequence
Representative Public ID T13C5.4 NCBI
Target Description T13C5.4 /REP_DB=WormBase Gene ID /WP=CE04945 /TR=Q22459 /GB=AAK39290.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=homeobox protein
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_076636(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_076636 NCBI Caenorhabditis elegans T13C5.4 (T13C5.4) mRNA, complete cds. 11/11 None
SNAP00000030094 ENSEMBL cdna:SNAP chromosome:CEL140:X:6191563:6192114:-1 9/11 None
GENEFINDER00000030099 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:6191563:6192153:-1 10/11 None
T13C5.4 ENSEMBL cdna:known chromosome:CEL140:X:6191563:6192906:-1 gene:T13C5.4 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:6191562-6192318(-) 98.64 98.64
Public Domain and Genome References
Gene Title homeobox protein
Ensembl T13C5.4
Entrez Gene 188474 Entrez gene
SwissProt Q22459 EMBL-EBI
WormBase CE04945 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 AAK39290 Hypothetical protein T13C5.4 [Caenorhabditis elegans] ref|NP_509037.1| T13C5.4 [Caenorhabditis elegans] 1.0E-115
blast AAK39290 Hypothetical protein T13C5.4 [Caenorhabditis elegans] ref|NP_509037.1| T13C5.4 [Caenorhabditis elegans] 2.0E-81
blast AAK39290 Hypothetical protein T13C5.4 [Caenorhabditis elegans] ref|NP_509037.1| T13C5.4 [Caenorhabditis elegans] 1.0E-73
blast CAE68888 Hypothetical protein CBG14858 [Caenorhabditis briggsae] 1.0E-32
blast CAE68888 Hypothetical protein CBG14858 [Caenorhabditis briggsae] 5.0E-19
blast CAA92001 Hypothetical protein R08B4.2 [Caenorhabditis elegans] ref|NP_509860.1| R08B4.2 [Caenorhabditis elegans] 8.0E-19
blast CAA92001 Hypothetical protein R08B4.2 [Caenorhabditis elegans] ref|NP_509860.1| R08B4.2 [Caenorhabditis elegans] 3.0E-14
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 8.00000002901995E-15
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 2.99999990479657E-20
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 1.99999994343614E-9
Pfam IPR001356 EMBL-EBI Homeobox 8.9E-28
Pfam IPR001356 EMBL-EBI Homeobox 8.7E-12
Pfam IPR001356 EMBL-EBI Homeobox 1.7E-19
Sequence
Target Sequence 
>C. ELEGANS:189464_AT
gatcgaataacttcaatcctgacagaaagaaacggaaccgaataacgtttgatgcaaatc
aaatcgatgagatggaaaaggtgtttgcagaaaatcagtatccggacactatgagccgag
aaaaattggcaaacaaaattcaacttcacgaggagcgagttcaaatttggtttcaaaatc
gtcgtgcaaagtatcgtcgagagcagaaacaaactggccatccatacgagccaccttcaa
tcactaaaaatcctacaggtgaaaaagaaaaaactcaggattgcactactttgacaagtg
catcatctccaggcccttcaaacctatctaatgatactcttgtttcaattgaaatggcac
ctaaaattggaactaaaagcgtcaatttgttcccagatcaggctctttcaaacactctga
acatgatcatcaatgctaacaaaaatgcttcggaaaacaattatgaatccgaggatcaat
tcaatgcggaaagtgcgaaacttttaatgctaactctttccaatttattc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GATCGAATAACTTCAATCCTGACAG 470 415 116 Antisense
GTATCCGGACACTATGAGCCGAGAA 134 455 213 Antisense
ATCGTCGTGCAAAGTATCGTCGAGA 551 35 293 Antisense
CAAACTGGCCATCCATACGAGCCAC 12 193 325 Antisense
TACGAGCCACCTTCAATCACTAAAA 647 647 340 Antisense
AACTCAGGATTGCACTACTTTGACA 189 103 387 Antisense
TTTGACAAGTGCATCATCTCCAGGC 1 667 405 Antisense
CCAGGCCCTTCAAACCTATCTAATG 58 273 424 Antisense
GCGTCAATTTGTTCCCAGATCAGGC 710 289 494 Antisense
CAGGCTCTTTCAAACACTCTGAACA 334 209 514 Antisense
AATGCTAACTCTTTCCAATTTATTC 433 163 621 Antisense
Sequence Source Affymetrix Proprietary Database