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[177840_at]

Description C53B4.2 /REP_DB=WormBase Gene ID /WP=CE03088 /TR=Q18796 /GB=CAA92451.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation
Cluster 6grp_total > 83      4grp_total > 27      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 65
1 2 3 4 range
A 13.9
(-3)
A 		76
(3)
A 		15.2
(-2.9)
A 		49.9
(0.5)
A 		62
B 21.9
(-1.9)
A 		18.9
(-2.2)
A 		11.7
(-3)
A 		68.4
(3)
A 		57
C 11.5
(-2.9)
A 		21.2
(-1.6)
A 		10.6
(-3)
A 		54.8
(3)
A 		44
avr 15.8
(-2.6) 		38.7
(0.5) 		12.5
(-3) 		57.7
(3) 		45

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 73
1 2 3 4 5 6 range
A 41.7
(-0.8)
A 		37.5
(-1.2)
A 		73.3
(2.2)
A 		22.4
(-2.5)
A 		82.5
(3)
A 		17.5
(-3)
A 		65
B 45.2
(-0.2)
A 		11.6
(-3)
A 		39.7
(-0.6)
A 		82.5
(3)
A 		28.8
(-1.5)
A 		36.3
(-0.9)
A 		71
C 21.8
(-1.7)
A 		66.1
(3)
A 		24.6
(-1.4)
A 		9.4
(-3)
A 		27.1
(-1.1)
A 		57.3
(2.1)
A 		57
avr 36.2
(-3) 		38.4
(-1.7) 		45.9
(2.9) 		38.1
(-1.8) 		46.1
(3) 		37
(-2.5) 		10
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 14
1 2 3 4 range
A 5.1
(-2.5)
A 		16.5
(3)
A 		4
(-3)
A 		7.3
(-1.4)
A 		13
B 7
(-0.8)
A 		4.7
(-2)
A 		2.7
(-3)
A 		14.6
(3)
A 		12
C 3.8
(-2.9)
A 		6.1
(-0.4)
A 		3.7
(-3)
A 		9.2
(3)
A 		6
avr 5.3
(-1.4) 		9.1
(1.9) 		3.5
(-3) 		10.4
(3) 		7

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 23
1 2 3 4 5 6 range
A 7.7
(-2)
A 		13.3
(-0.4)
A 		16
(0.4)
A 		5.7
(-2.6)
A 		24.9
(3)
A 		4.3
(-3)
A 		21
B 15.7
(1)
A 		3.8
(-3)
A 		9.6
(-1.1)
A 		21.8
(3)
A 		11.7
(-0.4)
A 		13.5
(0.2)
A 		18
C 8.1
(-1)
A 		20.2
(3)
A 		6.3
(-1.6)
A 		1.9
(-3)
A 		8.8
(-0.7)
A 		19.2
(2.7)
A 		18
avr 10.5
(-2.2) 		12.4
(-0.1) 		10.6
(-2.1) 		9.8
(-3) 		15.1
(3) 		12.3
(-0.2) 		5
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 177840_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.9390
Sequence Type Exemplar sequence
Representative Public ID C53B4.2 NCBI
Target Description C53B4.2 /REP_DB=WormBase Gene ID /WP=CE03088 /TR=Q18796 /GB=CAA92451.1 /SUBMIT=HINXTON /CHR=4 /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_069154(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069154 NCBI Caenorhabditis elegans C53B4.2 (C53B4.2) mRNA, complete cds. 11/11 None
SNAP00000003704 ENSEMBL cdna:SNAP chromosome:CEL140:IV:8966406:8967814:1 10/11 None
GENEFINDER00000003713 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:8966192:8970569:1 11/11 None
C53B4.2 ENSEMBL cdna:known chromosome:CEL140:IV:8966114:8967814:1 gene:C53B4.2 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
chrIV:8964878-8967820(+) 93.69 100.0
Public Domain and Genome References
Gene Title
Ensembl C53B4.2
Entrez Gene 353430 Entrez gene
SwissProt Q18796 EMBL-EBI
WormBase CE32836 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAA92450 Hypothetical protein C53B4.1 [Caenorhabditis elegans] ref|NP_501556.1| C53B4.1 [Caenorhabditis elegans] 0.0
blast CAE74077 Hypothetical protein CBG21731 [Caenorhabditis briggsae] 1.0E-178
blast CAA92451 Hypothetical protein C53B4.2 [Caenorhabditis elegans] ref|NP_501555.2| C53B4.2 [Caenorhabditis elegans] 1.0E-174
blast CAA92451 Hypothetical protein C53B4.2 [Caenorhabditis elegans] ref|NP_501555.2| C53B4.2 [Caenorhabditis elegans] 1.0E-151
blast CAA92451 Hypothetical protein C53B4.2 [Caenorhabditis elegans] ref|NP_501555.2| C53B4.2 [Caenorhabditis elegans] 1.0E-141
blast CAE63892 Hypothetical protein CBG08461 [Caenorhabditis briggsae] 4.0E-32
blast CAE63892 Hypothetical protein CBG08461 [Caenorhabditis briggsae] 9.0E-32
blast NP_498073 C45G9.8 [Caenorhabditis elegans] gb|AAA62551.1| Hypothetical protein C45G9.8 [Caenorhabditis elegans] sp|Q09280|YQI8_CAEEL Hypothetical protein C45G9.8 in chromosome III 2.0E-31
Protein Domains
Database ID Description E-Value
Pfam IPR005828 EMBL-EBI General substrate transporter 1.0E-7
Trans Membrane
ID Number Of Domains Domain Boundaries
GENEFINDER00000003713 7 467-489,591-610,615-637,677-699,750-767,779-798,813-835
Sequence
Target Sequence 
>C. ELEGANS:177840_AT
gttcctgtggaagactcgtatgattatgtgccaaaattgtcggttgtagagaagatgtcg
gatcagaatatctacataaagggagagactgattatgtcccattttgggcagcatatgtt
gaaccaaatgaagatgataccaaagacgtggaaccgcccatatcagttggaagtgatcat
gtcgaatcatttcatgaagggaaacttacactcaaaactatcaaatccgcgaaactggtg
cttgacgaatatcagccatcttgtcttttcatgaaacttgacgaaaagttctttcatcca
catctcgttttttcaaataccgttcgttcacttattaatgtgcaaggaccggctatggag
aaattgcaaccgataaaatctagctcaaaaaatgaagatgacgagggagaaagggaagag
gcaactcaattagaaggaaataatgtaacaatggccgaaaatatttctagaatttttagt
tacgagagatcccgtccaattctttctgctcgagaagcaaaagaacgtaatcagacattg
catgtatcttctccaaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTTCCTGTGGAAGACTCGTATGATT 618 441 979 Antisense
GAGACTGATTATGTCCCATTTTGGG 9 393 1063 Antisense
GATACCAAAGACGTGGAACCGCCCA 90 421 1114 Antisense
GGAACCGCCCATATCAGTTGGAAGT 255 529 1128 Antisense
ATCCGCGAAACTGGTGCTTGACGAA 102 37 1203 Antisense
AATATCAGCCATCTTGTCTTTTCAT 365 173 1226 Antisense
TTTCATCCACATCTCGTTTTTTCAA 240 673 1270 Antisense
TTTCAAATACCGTTCGTTCACTTAT 27 667 1289 Antisense
AATGTGCAAGGACCGGCTATGGAGA 701 163 1315 Antisense
AGTTACGAGAGATCCCGTCCAATTC 524 61 1456 Antisense
AGACATTGCATGTATCTTCTCCAAA 356 71 1511 Antisense
Sequence Source Affymetrix Proprietary Database