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[175223_at] Putative membrane protein

Description AU115709_rc /REP_DB=TREMBL Accession /GB=AU115709 /CHR=3 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk735g9 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 12      6grp_high1_10_10 > 20      6grp_highest_nonorm > 61      6grp_total > 33      4grp_total > 14      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 403
1 2 3 4 range
A 445.2
(3)
P 		239.2
(-3)
A 		264.9
(-2.3)
A 		445.4
(3)
P 		206
B 465.4
(0.9)
P 		256.1
(-2.2)
A 		205.6
(-3)
A 		608.5
(3)
P 		403
C 475.2
(2)
P 		250.3
(-3)
A 		304.6
(-1.8)
P 		519.8
(3)
P 		270
avr 461.9
(1.6) 		248.5
(-3) 		258.4
(-2.8) 		524.6
(3) 		276

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 270
1 2 3 4 5 6 range
A 514.4
(3)
P 		369.9
(-1.2)
P 		336.9
(-2.1)
P 		375.2
(-1)
P 		311.8
(-2.8)
P 		305.8
(-3)
P 		209
B 489
(2.2)
P 		467.9
(1.6)
P 		518.9
(3)
P 		328.8
(-2.2)
P 		324.8
(-2.3)
P 		298
(-3)
P 		221
C 378.6
(0.5)
P 		366.8
(0.2)
P 		471.4
(3)
P 		471.9
(3)
P 		248.8
(-3)
P 		342.3
(-0.5)
P 		223
avr 460.7
(3) 		401.5
(0.9) 		442.4
(2.3) 		392
(0.5) 		295.1
(-3) 		315.4
(-2.3) 		166
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 115
1 2 3 4 range
A 162.1
(3)
P 		51.9
(-3)
A 		69.2
(-2.1)
A 		65.2
(-2.3)
P 		110
B 148.4
(3)
P 		63.3
(-2.1)
A 		47.6
(-3)
A 		129.7
(1.9)
P 		101
C 157.3
(3)
P 		72
(-3)
A 		106.2
(-0.6)
P 		87.6
(-1.9)
P 		85
avr 155.9
(3) 		62.4
(-3) 		74.3
(-2.2) 		94.2
(-1) 		94

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 97
1 2 3 4 5 6 range
A 94.8
(-0.8)
P 		131.6
(3)
P 		73.4
(-3)
P 		95.2
(-0.8)
P 		94.1
(-0.9)
P 		74.4
(-2.9)
P 		58
B 170.1
(3)
P 		155.7
(2)
P 		126
(-0.2)
P 		87.1
(-3)
P 		132
(0.2)
P 		111.1
(-1.3)
P 		83
C 140.3
(3)
P 		111.9
(0.2)
P 		120
(1)
P 		94.9
(-1.6)
P 		80.5
(-3)
P 		114.6
(0.4)
P 		60
avr 135.1
(3) 		133.1
(2.7) 		106.5
(-1) 		92.4
(-3) 		102.2
(-1.6) 		100
(-1.9) 		43
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 175223_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.21105
Sequence Type Exemplar sequence
Representative Public ID AU115709 NCBI
Target Description AU115709_rc /REP_DB=TREMBL Accession /GB=AU115709 /CHR=3 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk735g9 : 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_066862(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066862 NCBI Caenorhabditis elegans T20G5.4 (T20G5.4) mRNA, complete cds. 11/11 A 
SNAP00000033306 ENSEMBL cdna:SNAP chromosome:CEL140:III:10212432:10214635:1 11/11 None
GENEFINDER00000033350 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:10212432:10214635:1 11/11 None
T20G5.4 ENSEMBL cdna:known chromosome:CEL140:III:10212406:10214708:1 gene:T20G5.4 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
chrIII:10214062-10214639(+) 100.0 100.0
Public Domain and Genome References
Gene Title Putative membrane protein
Ensembl T20G5.4
Entrez Gene 176436 Entrez gene
SwissProt P34577 EMBL-EBI
WormBase CE28844 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAA83005 Hypothetical protein T20G5.4 [Caenorhabditis elegans] ref|NP_499263.1| T20G5.4 [Caenorhabditis elegans] sp|P34577|YNX4_CAEEL Hypothetical protein T20G5.4 in chromosome III 0.0
blast CAE64975 Hypothetical protein CBG09809 [Caenorhabditis briggsae] 0.0
blast CAE66881 Hypothetical protein CBG12260 [Caenorhabditis briggsae] 1.0E-135
Protein Domains
Database ID Description E-Value
Pfam IPR000615 EMBL-EBI Bestrophin 1.0E-126
Pfam IPR000615 EMBL-EBI Bestrophin 1.0E-126
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_499263.1 4 32-54,74-96,232-254,267-286
T20G5.4 4 32-54,74-96,232-254,267-286
SNAP00000033306 4 32-54,74-96,232-254,267-286
GENEFINDER00000033350 4 32-54,74-96,232-254,267-289
Sequence
Target Sequence 
>C. ELEGANS:175223_AT
gaatcggtgatattcttcgaccatcttcacttctcaacctaatgaaacacgcttcctcgt
cacgcagtttggagcggcagagaagtcccggaagcttcagaatggaaactctgacgcctg
gctcgccaacaaatacaccgattgaacccattga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAATCGGTGATATTCTTCGACCATC 332 329 101 Antisense
GTGATATTCTTCGACCATCTTCACT 384 485 107 Antisense
CCATCTTCACTTCTCAACCTAATGA 404 271 121 Antisense
ACCTAATGAAACACGCTTCCTCGTC 415 85 137 Antisense
CTTCCTCGTCACGCAGTTTGGAGCG 608 219 152 Antisense
TCGTCACGCAGTTTGGAGCGGCAGA 214 603 157 Antisense
GGAGCGGCAGAGAAGTCCCGGAAGC 117 521 171 Antisense
AAGTCCCGGAAGCTTCAGAATGGAA 688 121 183 Antisense
AGAATGGAAACTCTGACGCCTGGCT 479 73 199 Antisense
GGCTCGCCAACAAATACACCGATTG 208 539 220 Antisense
CAAATACACCGATTGAACCCATTGA 517 189 230 Antisense
Sequence Source Affymetrix Proprietary Database