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[175419_at] homeobox

Description AV183820_rc /REP_DB=TREMBL Accession /GB=AV183820 /CHR=X /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk656e9 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 84      6grp_high1_10_10 > 47      4grp_highest_8_8 > 56      4grp_high_8_8 > 26      6grp_highest_nonorm > 91      6grp_total > 47      4grp_total > 37      6grp_highest_sub > Cu      6grp_cgc > 27      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 238
1 2 3 4 range
A 260.4
(3)
P 		170.3
(-2.3)
P 		158.4
(-3)
P 		176
(-2)
P 		102
B 289.8
(2.8)
P 		296.1
(3)
P 		137.1
(-3)
P 		265.7
(1.9)
P 		159
C 375
(3)
P 		290.6
(0.7)
P 		152.2
(-3)
P 		176.3
(-2.4)
P 		223
avr 308.4
(3) 		252.3
(0.9) 		149.2
(-3) 		206
(-0.9) 		159

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 262
1 2 3 4 5 6 range
A 325.4
(1.9)
P 		316.3
(1.7)
P 		110
(-3)
P 		129.8
(-2.5)
P 		204.8
(-0.8)
P 		372.3
(3)
P 		262
B 275.6
(2.3)
P 		248.9
(1)
P 		180.6
(-2.1)
P 		212.5
(-0.6)
P 		161.8
(-3)
P 		291.1
(3)
P 		129
C 249.9
(0.8)
P 		213
(-0.4)
P 		167.7
(-2)
P 		262.8
(1.3)
P 		139.1
(-3)
P 		312.2
(3)
P 		173
avr 283.6
(1.6) 		259.4
(0.7) 		152.8
(-3) 		201.7
(-1.3) 		168.6
(-2.5) 		325.2
(3) 		172
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 98
1 2 3 4 range
A 94.8
(3)
P 		37
(-2)
P 		41.4
(-1.6)
P 		25.8
(-3)
P 		69
B 92.4
(3)
P 		73.1
(1.1)
P 		31.8
(-3)
P 		56.6
(-0.5)
P 		61
C 124.1
(3)
P 		83.6
(0.4)
P 		53
(-1.5)
P 		29.7
(-3)
P 		94
avr 103.8
(3) 		64.6
(-0.5) 		42.1
(-2.6) 		37.4
(-3) 		66

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 89
1 2 3 4 5 6 range
A 60
(-0.6)
P 		112.5
(3)
P 		24
(-3)
P 		32.9
(-2.4)
P 		61.8
(-0.4)
P 		90.6
(1.5)
P 		89
B 95.9
(1.8)
P 		82.8
(0.6)
P 		43.8
(-3)
P 		56.3
(-1.8)
P 		65.7
(-1)
P 		108.6
(3)
P 		65
C 92.6
(1.8)
P 		65
(-0.8)
P 		42.7
(-3)
P 		52.8
(-2)
P 		45
(-2.8)
P 		104.5
(3)
P 		62
avr 82.8
(1.3) 		86.8
(1.7) 		36.8
(-3) 		47.3
(-2) 		57.5
(-1.1) 		101.2
(3) 		64
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 175419_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.22417
Sequence Type Exemplar sequence
Representative Public ID AV183820 NCBI
Target Description AV183820_rc /REP_DB=TREMBL Accession /GB=AV183820 /CHR=X /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk656e9 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_075941(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_075941 NCBI Caenorhabditis elegans T26C11.7 (homeobox) mRNA, complete cds. 11/11 None
T26C11.7 ENSEMBL cdna:known chromosome:CEL140:X:1853927:1856166:-1 gene:T26C11.7 11/11 A 
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:1853936-1854226(-) 100.0 100.0
Public Domain and Genome References
Gene Title homeobox
Gene Symbol ceh-39
Ensembl T26C11.7
Entrez Gene 180505 Entrez gene
SwissProt Q22812 EMBL-EBI
WormBase CE05026 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_508342 T26C11.7 [Caenorhabditis elegans] gb|AAC48215.1| C.elegans homeobox protein 39 [Caenorhabditis elegans] sp|Q22812|HM39_CAEEL Homeobox protein ceh-39 0.0
blast NP_508341 T26C11.6 [Caenorhabditis elegans] gb|AAC48216.2| C.elegans homeobox protein 21 [Caenorhabditis elegans] emb|CAD20808.1| CEH-21 protein [Caenorhabditis elegans] sp|Q22811|HM21_CAEEL Homeobox protein ceh-21 2.0E-67
blast T28912 probable homeobox protein - Caenorhabditis elegans 2.0E-67
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 9.99999974737875E-5
Pfam IPR001356 EMBL-EBI Homeobox 5.1E-5
Pfam IPR003350 EMBL-EBI Homeodomain protein CUT 1.1E-55
Sequence
Target Sequence 
>C. ELEGANS:175419_AT
aaaattgactactatcgttctgtttaatataaaatccttgattgttttaattgttaattg
tattaattccccatccaattcccatacctcttcattgccttatcaattttgtgaccgatc
ccaatccagccataacatttcagccataacacatt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AAAATTGACTACTATCGTTCTGTTT 609 131 118 Antisense
GACTACTATCGTTCTGTTTAATATA 245 373 124 Antisense
ATCCTTGATTGTTTTAATTGTTAAT 14 39 151 Antisense
GTTAATTGTATTAATTCCCCATCCA 691 445 170 Antisense
ATTGTATTAATTCCCCATCCAATTC 428 5 174 Antisense
CATACCTCTTCATTGCCTTATCAAT 71 215 200 Antisense
GCCTTATCAATTTTGTGACCGATCC 692 281 214 Antisense
CAATTTTGTGACCGATCCCAATCCA 240 181 221 Antisense
TCCCAATCCAGCCATAACATTTCAG 626 597 236 Antisense
TCCAGCCATAACATTTCAGCCATAA 421 587 242 Antisense
CATAACATTTCAGCCATAACACATT 39 215 248 Antisense
Sequence Source Affymetrix Proprietary Database