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[192223_at] homeobox protein (otd subfamily)

Description R08B4.2 /REP_DB=WormBase Gene ID /WP=CE03536 /TR=Q21836 /GB=CAA92001.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=homeobox protein (otd subfamily)
Cluster 6grp_highest_10_10 > 52      6grp_high1_10_10 > 35      4grp_highest_8_8 > 59      4grp_high_8_8 > 25      6grp_highest_nonorm > 80      6grp_total > 26      4grp_total > 38      6grp_highest_sub > 01_02      6grp_cgc > 14      6grp_high1_sub > 02      6grp_cgc_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 323
1 2 3 4 range
A 431.7
(3)
P 		285.4
(-0.2)
P 		160.4
(-3)
P 		263.1
(-0.7)
P 		271
B 447
(3)
P 		235.5
(-0.9)
P 		123.8
(-3)
P 		261.8
(-0.4)
P 		323
C 423.7
(3)
P 		158.8
(-3)
P 		160.4
(-2.9)
P 		157.9
(-3)
P 		266
avr 434.1
(3) 		226.6
(-1.4) 		148.2
(-3) 		227.6
(-1.3) 		286

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 209
1 2 3 4 5 6 range
A 316.5
(3)
P 		287.6
(2)
P 		160.6
(-2.3)
P 		153.7
(-2.5)
P 		140.3
(-3)
P 		193.7
(-1.2)
P 		176
B 339.6
(3)
P 		270.5
(0.8)
P 		216.2
(-0.9)
P 		196.3
(-1.5)
P 		150
(-3)
P 		198.9
(-1.5)
P 		190
C 208.6
(-1.2)
P 		349.6
(3)
P 		184
(-2)
P 		149.8
(-3)
P 		152.1
(-2.9)
P 		207.3
(-1.3)
P 		200
avr 288.2
(2.4) 		302.6
(3) 		186.9
(-1.5) 		166.6
(-2.3) 		147.5
(-3) 		200
(-1) 		155
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 131
1 2 3 4 range
A 157.2
(3)
P 		61.9
(-1.8)
P 		41.9
(-2.8)
P 		38.5
(-3)
P 		119
B 142.5
(3)
P 		58.2
(-1.4)
P 		28.7
(-3)
P 		55.8
(-1.6)
P 		114
C 140.3
(3)
P 		45.7
(-2)
P 		55.9
(-1.5)
P 		26.6
(-3)
P 		114
avr 146.7
(3) 		55.3
(-2.2) 		42.2
(-2.9) 		40.3
(-3) 		106

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 88
1 2 3 4 5 6 range
A 58.4
(-0.9)
P 		102.3
(3)
P 		35
(-3)
P 		39
(-2.6)
P 		42.3
(-2.3)
P 		47.2
(-1.9)
P 		67
B 118.2
(3)
P 		90
(0.4)
P 		52.5
(-3)
P 		52
(-3)
P 		61
(-2.2)
P 		74.2
(-1)
P 		66
C 77.3
(0.7)
P 		106.7
(3)
P 		46.8
(-1.7)
P 		30.1
(-3)
P 		49.2
(-1.5)
P 		69.4
(0.1)
P 		77
avr 84.6
(1.5) 		99.7
(3) 		44.8
(-2.6) 		40.4
(-3) 		50.8
(-1.9) 		63.6
(-0.7) 		59
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192223_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.16653
Sequence Type Exemplar sequence
Representative Public ID R08B4.2 NCBI
Target Description R08B4.2 /REP_DB=WormBase Gene ID /WP=CE03536 /TR=Q21836 /GB=CAA92001.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=homeobox protein (otd subfamily)
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_077459(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_077459 NCBI Caenorhabditis elegans R08B4.2 (R08B4.2) mRNA, complete cds. 11/11 None
SNAP00000019868 ENSEMBL cdna:SNAP chromosome:CEL140:X:11122519:11124049:-1 11/11 None
GENEFINDER00000019871 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:11122519:11125540:-1 11/11 None
R08B4.2 ENSEMBL cdna:known chromosome:CEL140:X:11121866:11125537:-1 gene:R08B4.2 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:11122518-11125480(-) 100.0 100.0
Public Domain and Genome References
Gene Title homeobox protein (otd subfamily)
Gene Symbol alr-1
Ensembl R08B4.2
Entrez Gene 181302 Entrez gene
SwissProt Q21836 EMBL-EBI
WormBase CE03536 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFAAFFX.20923.1.S1_S_AT similar to aristaless related homeobox cfa
HU35KSUBD:RC_AA496211_AT aristaless related homeobox hs
U133_X3P:HS.103538.0.S1_3P_AT aristaless related homeobox hs
HG-U133_PLUS_2:238878_AT aristaless related homeobox hs
HG-U133B:238878_AT aristaless related homeobox hs
HG-U95B:58068_AT aristaless related homeobox hs
HG-U133_PLUS_2:231020_AT Aristaless related homeobox hs
HG-U133B:231020_AT Aristaless related homeobox hs
HG-U95E:77307_AT Aristaless related homeobox hs
U133_X3P:HS.157208.0.A1_3P_AT Aristaless related homeobox hs
MG-U74AV2:92186_AT aristaless related homeobox gene (Drosophila) mm
MOUSE430_2:1420926_AT aristaless related homeobox gene (Drosophila) mm
MOE430A:1420926_AT aristaless related homeobox gene (Drosophila) mm
MOUSE430A_2:1420926_AT aristaless related homeobox gene (Drosophila) mm
MU11KSUBA:AB006103_AT aristaless related homeobox gene (Drosophila) mm
MG-U74CV2:166042_F_AT aristaless related homeobox gene (Drosophila) mm
MOE430A:1450042_AT aristaless related homeobox gene (Drosophila) mm
MOUSE430A_2:1450042_AT aristaless related homeobox gene (Drosophila) mm
MOUSE430_2:1450042_AT aristaless related homeobox gene (Drosophila) mm
MOUSE430_2:1441175_AT Aristaless related homeobox gene (Drosophila) (Arx), mRNA mm
MOE430B:1441175_AT Aristaless related homeobox gene (Drosophila) (Arx), mRNA mm
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 CAA92001 Hypothetical protein R08B4.2 [Caenorhabditis elegans] ref|NP_509860.1| R08B4.2 [Caenorhabditis elegans] 1.0E-161
blast CAE70698 Hypothetical protein CBG17430 [Caenorhabditis briggsae] 1.0E-130
blast CAA92001 Hypothetical protein R08B4.2 [Caenorhabditis elegans] ref|NP_509860.1| R08B4.2 [Caenorhabditis elegans] 3.0E-84
blast CAE70698 Hypothetical protein CBG17430 [Caenorhabditis briggsae] 5.0E-66
blast AAF51505 CG3935-PA [Drosophila melanogaster] gb|AAM52023.1| RE68460p [Drosophila melanogaster] ref|NP_722629.1| CG3935-PA [Drosophila melanogaster] sp|Q06453|AL_DROME Homeobox protein aristaless 1.0E-26
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 9.99999988726602E-27
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 4.0000001089808E-27
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 3.99999992980668E-13
Pfam IPR001356 EMBL-EBI Homeobox 4.5E-32
Pfam IPR001356 EMBL-EBI Homeobox 4.5E-13
Pfam IPR001356 EMBL-EBI Homeobox 4.5E-32
Sequence
Target Sequence 
>C. ELEGANS:192223_AT
caagaacgcagcagtactcatcacccttatcaagctccaatgagtattccaaattcaaat
ggagataatccgtaccagatgatgctcagccaagaagctatttttgcagctatcaatcag
caagccgcggctcatcttttaaatgaacaagtacggattgcaacatctgatcgtcggtct
cagtccccgtctgtaccagtgaccacatcttctccaatcttgccaacttctgtgacacct
acgttccaaaacgcagatgcattaaatatgttgttcggtggaattactcctgttacgcag
cagttgctttatgttcaacaattcagcagagctatggatgctttccgcactcagcttctg
ggatcagtcccagcaggagctacggctgaagtcaccgatgttgtagcattaaaaactgaa
gactcgaaatcgaatagtagagcgggaagctcatcacccactccaactgaaagttccgga
gctgctgcaacatccacgagtcctacgaattttgc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CAAGAACGCAGCAGTACTCATCACC 431 185 535 Antisense
ATCACCCTTATCAAGCTCCAATGAG 43 29 554 Antisense
AGCAAGCCGCGGCTCATCTTTTAAA 151 75 653 Antisense
TTGCAACATCTGATCGTCGGTCTCA 706 701 692 Antisense
TTCTGTGACACCTACGTTCCAAAAC 351 693 762 Antisense
GAATTACTCCTGTTACGCAGCAGTT 244 323 815 Antisense
GCAGAGCTATGGATGCTTTCCGCAC 599 311 860 Antisense
GGAGCTACGGCTGAAGTCACCGATG 5 521 910 Antisense
TAGAGCGGGAAGCTCATCACCCACT 288 653 972 Antisense
AAAGTTCCGGAGCTGCTGCAACATC 155 123 1004 Antisense
CATCCACGAGTCCTACGAATTTTGC 369 209 1025 Antisense
Sequence Source Affymetrix Proprietary Database