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[176615_at]

Description R13A5.5 /REP_DB=WormBase Gene ID /WP=CE01377 /GEN=ceh-13 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 15      6grp_high1_10_10 > 40      4grp_highest_8_8 > 06      4grp_high_8_8 > 22      6grp_highest_nonorm > 71      6grp_total > 52      4grp_total > 16      6grp_highest_sub > 03      6grp_cgc > 93      6grp_high1_sub > 03      6grp_cgc_sub > 03      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 286
1 2 3 4 range
A 295.6
(1.3)
P 		166.6
(-3)
P 		345
(3)
P 		312.4
(1.9)
P 		178
B 275
(-3)
P 		431.2
(2.3)
P 		452.5
(3)
P 		392.1
(1)
P 		178
C 344.2
(2.1)
P 		373.6
(3)
P 		180.2
(-3)
P 		369.1
(2.9)
P 		193
avr 304.9
(-3) 		323.8
(-0.9) 		325.9
(-0.6) 		357.9
(3) 		53

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 537
1 2 3 4 5 6 range
A 252.9
(-3)
P 		259.9
(-2.8)
P 		444.4
(3)
P 		319.8
(-0.9)
P 		340.5
(-0.3)
P 		323.3
(-0.8)
P 		192
B 340.4
(0.1)
P 		300.6
(-0.7)
P 		483.9
(3)
P 		185.8
(-3)
P 		353.8
(0.4)
P 		399.8
(1.3)
P 		298
C 618.5
(1.8)
P 		390.8
(-0.9)
P 		518.4
(0.6)
P 		722.6
(3)
P 		275.2
(-2.2)
P 		210.9
(-3)
P 		512
avr 403.9
(0.3) 		317.1
(-2.8) 		482.2
(3) 		409.4
(0.4) 		323.2
(-2.6) 		311.3
(-3) 		171
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 78
1 2 3 4 range
A 107.6
(3)
P 		36.2
(-3)
P 		90.2
(1.5)
P 		45.7
(-2.2)
P 		71
B 87.7
(-1.9)
P 		106.5
(3)
P 		104.9
(2.6)
P 		83.6
(-3)
P 		23
C 113.9
(3)
P 		107.4
(2.2)
P 		62.8
(-2.9)
P 		62.2
(-3)
P 		52
avr 103.1
(3) 		83.4
(-0) 		86
(0.4) 		63.8
(-3) 		39

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 183
1 2 3 4 5 6 range
A 46.6
(-3)
P 		92.4
(1.9)
P 		96.8
(2.4)
P 		81.1
(0.7)
P 		102.7
(3)
P 		78.7
(0.4)
P 		56
B 118.5
(1.2)
P 		100
(0.1)
P 		117.5
(1.1)
P 		49.2
(-3)
P 		143.7
(2.7)
P 		149.1
(3)
P 		100
C 229.3
(3)
P 		119.2
(-1.2)
P 		131.9
(-0.7)
P 		145.3
(-0.2)
P 		89
(-2.3)
P 		70.6
(-3)
P 		159
avr 131.5
(3) 		103.9
(-1.2) 		115.4
(0.6) 		91.9
(-3) 		111.8
(0) 		99.5
(-1.8) 		40
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 176615_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6173
Sequence Type Exemplar sequence
Representative Public ID R13A5.5 NCBI
Target Description R13A5.5 /REP_DB=WormBase Gene ID /WP=CE01377 /GEN=ceh-13 /SUBMIT=ST.LOUIS /CHR=3 /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_066254(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066254 NCBI Caenorhabditis elegans C.Elegans Homeobox family member (ceh-13) (ceh-13) mRNA, complete cds. 11/11 None
GENEFINDER00000038267 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:7555580:7557649:1 11/11 None
SNAP00000038242 ENSEMBL cdna:SNAP chromosome:CEL140:III:7556762:7557649:1 9/11 None
R13A5.5 ENSEMBL cdna:known chromosome:CEL140:III:7555579:7558127:1 gene:R13A5.5 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
chrIII:7555859-7557647(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol ceh-13
Ensembl R13A5.5
Entrez Gene 176069 Entrez gene
SwissProt P17488 EMBL-EBI
WormBase CE28767 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFAAFFX.5332.1.S1_S_AT similar to homeobox A1 protein isoform a cfa
HG-U95AV2:502_S_AT homeo box A1 hs
HC-G110:502_S_AT homeo box A1 hs
HU35KSUBD:RC_AA173290_S_AT homeo box A1 hs
HUGENEFL:U37431_AT homeo box A1 hs
U133_X3P:HS.67397.1.S2_3P_A_AT homeo box A1 hs
HG-U133A_2:214639_S_AT homeo box A1 hs
HG-FOCUS:214639_S_AT homeo box A1 hs
HG-U133_PLUS_2:214639_S_AT homeo box A1 hs
HG-U133A:214639_S_AT homeo box A1 hs
MOUSE430_2:1420565_AT homeo box A1 mm
MOE430A:1420565_AT homeo box A1 mm
MOUSE430A_2:1420565_AT homeo box A1 mm
MU11KSUBA:M22115_S_AT homeo box A1 mm
MG-U74AV2:95297_AT homeo box A1 mm
RG-U34A:U93092_AT homeo box A1 rn
RAE230A:1369544_A_AT homeo box A1 rn
RAT230_2:1369544_A_AT homeo box A1 rn
RAE230A:1387612_AT homeo box A1 rn
RAT230_2:1387612_AT homeo box A1 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
5634 nucleus inferred from direct assay QuickGO AmiGO
5737 cytoplasm inferred from direct assay 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
3700 transcription factor activity inferred from sequence similarity QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAK84466 C.elegans homeobox protein 13 [Caenorhabditis elegans] emb|CAA34929.1| ceh-13 homeodomain protein [Caenorhabditis elegans] ref|NP_498655.1| C.Elegans Homeobox family member (ceh-13) [Caenorhabditis elegans] sp|P17488|HM13_CAEEL Homeobox protein ceh-13 1.0E-89
blast CAE64452 Hypothetical protein CBG09160 [Caenorhabditis briggsae] 6.0E-66
blast AAK84466 C.elegans homeobox protein 13 [Caenorhabditis elegans] emb|CAA34929.1| ceh-13 homeodomain protein [Caenorhabditis elegans] ref|NP_498655.1| C.Elegans Homeobox family member (ceh-13) [Caenorhabditis elegans] sp|P17488|HM13_CAEEL Homeobox protein ceh-13 7.0E-43
blast CAE64452 Hypothetical protein CBG09160 [Caenorhabditis briggsae] 5.0E-34
blast CAA07497 homeobox protein [Cupiennius salei] 1.0E-16
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-18
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 2.00000006274879E-22
Pfam IPR001356 EMBL-EBI Homeobox 2.9E-25
Pfam IPR001356 EMBL-EBI Homeobox 2.9E-25
Sequence
Target Sequence 
>C. ELEGANS:176615_AT
aacggtcacaaagaccagctgccccaaaaaagaaggtgatagacgaaaatggaacaaatc
gaaccaacttcacaacacatcaactgacagagcttgaaaaggaatttcacacagcaaaat
atgtcaatcgaacgagacgaactgaaattgcttcaaatctgaaactgcaggaggctcagg
tcaaaatctggtttcaaaatcgtcgaatgaaggagaaaaagcgtgaaaaagaaaaggcat
tcctggcccgtaacacatgggaatccaactcaccgacat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AACGGTCACAAAGACCAGCTGCCCC 585 143 23 Antisense
AGACCAGCTGCCCCAAAAAAGAAGG 632 51 34 Antisense
GGAACAAATCGAACCAACTTCACAA 366 529 73 Antisense
GAACCAACTTCACAACACATCAACT 629 345 83 Antisense
CACAACACATCAACTGACAGAGCTT 176 195 93 Antisense
GGAATTTCACACAGCAAAATATGTC 379 533 123 Antisense
GAACGAGACGAACTGAAATTGCTTC 370 347 152 Antisense
AATTGCTTCAAATCTGAAACTGCAG 15 179 168 Antisense
GAAACTGCAGGAGGCTCAGGTCAAA 424 357 183 Antisense
CATTCCTGGCCCGTAACACATGGGA 489 217 260 Antisense
ACATGGGAATCCAACTCACCGACAT 348 107 277 Antisense
Sequence Source Affymetrix Proprietary Database