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[179987_at]

Description Y39E4B.5 /REP_DB=WormBase Gene ID /WP=CE21717 /TR=Q9U2K5 /GB=CAB54427.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 88      6grp_high1_10_10 > 88      4grp_high_8_8 > 35      6grp_highest_nonorm > 92      6grp_total > 88      4grp_total > 44      6grp_highest_sub > Da      6grp_high1_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 82
1 2 3 4 range
A 129.8
(3)
P 		119.2
(0.7)
P 		102.7
(-3)
P 		126.9
(2.4)
A 		27
B 133
(1.6)
P 		145.7
(3)
P 		122.7
(0.4)
P 		91.8
(-3)
P 		54
C 147.1
(0.7)
P 		174.1
(3)
P 		103.8
(-3)
P 		116
(-2)
P 		70
avr 136.6
(1.4) 		146.3
(3) 		109.7
(-3) 		111.6
(-2.7) 		37

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 493
1 2 3 4 5 6 range
A 156.6
(-2.2)
P 		114
(-2.8)
P 		102.2
(-3)
P 		104.7
(-3)
P 		390.4
(1.3)
P 		499.9
(3)
P 		398
B 115
(-2.7)
P 		95.3
(-2.9)
P 		87.4
(-3)
P 		140.5
(-2.4)
P 		349.9
(0.2)
P 		580.7
(3)
P 		493
C 103.4
(-3)
P 		151.1
(-2.4)
P 		103.5
(-3)
P 		155.4
(-2.3)
P 		303.4
(-0.5)
P 		580.5
(3)
P 		477
avr 125
(-2.6) 		120.1
(-2.7) 		97.7
(-3) 		133.5
(-2.5) 		347.9
(0.3) 		553.7
(3) 		456
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 32
1 2 3 4 range
A 47.2
(3)
P 		25.9
(-1.5)
P 		26.8
(-1.3)
P 		18.6
(-3)
A 		29
B 42.4
(3)
P 		36
(1.3)
P 		28.4
(-0.7)
P 		19.6
(-3)
P 		23
C 48.7
(2.7)
P 		50.1
(3)
P 		36.2
(0.3)
P 		19.6
(-3)
P 		31
avr 46.1
(3) 		37.3
(1) 		30.5
(-0.5) 		19.3
(-3) 		27

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 195
1 2 3 4 5 6 range
A 28.9
(-2.6)
P 		40.6
(-1.9)
P 		22.3
(-3)
P 		26.5
(-2.7)
P 		117.8
(2.8)
P 		121.7
(3)
P 		99
B 40
(-2.4)
P 		31.7
(-2.7)
P 		21.2
(-3)
P 		37.2
(-2.5)
P 		142.2
(0.7)
P 		216.5
(3)
P 		195
C 38.3
(-2.6)
P 		46.1
(-2.3)
P 		26.3
(-3)
P 		31.2
(-2.8)
P 		98.2
(-0.4)
P 		194.3
(3)
P 		168
avr 35.7
(-2.5) 		39.5
(-2.4) 		23.3
(-3) 		31.6
(-2.7) 		119.4
(0.7) 		177.5
(3) 		154
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 179987_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7271
Sequence Type Exemplar sequence
Representative Public ID Y39E4B.5 NCBI
Target Description Y39E4B.5 /REP_DB=WormBase Gene ID /WP=CE21717 /TR=Q9U2K5 /GB=CAB54427.1 /SUBMIT=HINXTON /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_067319(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067319 NCBI Caenorhabditis elegans Y39E4B.5 (Y39E4B.5) mRNA, complete cds. 11/11 None
SNAP00000012016 ENSEMBL cdna:SNAP chromosome:CEL140:III:13165363:13172443:1 11/11 None
GENEFINDER00000012034 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:13169434:13172443:1 11/11 None
Y39E4B.5 ENSEMBL cdna:known chromosome:CEL140:III:13169434:13172586:1 gene:Y39E4B.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:13169429-13172439(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Ensembl Y39E4B.5
Entrez Gene 176735 Entrez gene
SwissProt Q9U2K5 EMBL-EBI
WormBase CE21717 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
6810 transport inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5622 intracellular inferred from electronic annotation QuickGO AmiGO
16021 integral to membrane inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3700 transcription factor activity inferred from electronic annotation QuickGO AmiGO
5215 transporter activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB54427 Hypothetical protein Y39E4B.5 [Caenorhabditis elegans] ref|NP_499720.1| Y39E4B.5 [Caenorhabditis elegans] 0.0
blast CAE59000 Hypothetical protein CBG02274 [Caenorhabditis briggsae] 0.0
blast CAA98077 Hypothetical protein ZK829.9 [Caenorhabditis elegans] ref|NP_502272.1| ZK829.9 [Caenorhabditis elegans] 1.0E-82
Protein Domains
Database ID Description E-Value
Pfam IPR005828 EMBL-EBI General substrate transporter 6.3E-13
Pfam IPR005828 EMBL-EBI General substrate transporter 6.3E-13
Pfam IPR005828 EMBL-EBI General substrate transporter 6.7E-14
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_499720.1 10 91-113,118-140,153-170,180-202,269-291,301-323,330-352,367-389,402-424,429-451
Y39E4B.5 10 91-113,118-140,153-170,180-202,269-291,301-323,330-352,367-389,402-424,429-451
SNAP00000012016 12 12-31,63-85,98-120,124-146,159-176,186-208,275-297,307-329,336-358,373-395,408-430,435-457
GENEFINDER00000012034 10 114-136,141-163,176-193,203-225,292-314,324-346,353-375,390-412,425-447,452-474
Sequence
Target Sequence 
>C. ELEGANS:179987_AT
ggctcaagtcgttctgacgttgtcctcaatctgtggagcatctatcattgatcgattttc
gagacggaagctgctcatcacttttggaattttatccaacgtgttgctcgtggcattctc
attcttctctcatctatccgccacagtagtctcaccatattcgtggcccaaatacgcgtg
tctggcgtctcttcttgcctactgcatctcttttggaatggttcttggcccgttgtcatg
gtttgtggcgccagaacttgtcagtcaacgtcatcgctgtacaattttctcggcttgttt
cgctattcacaatcttctcatcgcgctcacggatttcgctacgattccacttttccgtat
cttcggcagcatgtgtttcgtgttcctgttcgttgtaccgtcgttcttctgtctctgcta
catctacctgttcatgccggaaacgctcggaaaatccacgttggacatcattcacgagat
gattgatcgtggactgcacggatcggagcatcatctcgtcaatt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGCTCAAGTCGTTCTGACGTTGTCC 369 537 933 Antisense
GACGTTGTCCTCAATCTGTGGAGCA 580 377 948 Antisense
GAGACGGAAGCTGCTCATCACTTTT 560 393 993 Antisense
ATCCAACGTGTTGCTCGTGGCATTC 229 41 1026 Antisense
TTGCCTACTGCATCTCTTTTGGAAT 368 699 1127 Antisense
GGCCCGTTGTCATGGTTTGTGGCGC 298 543 1159 Antisense
GTCATCGCTGTACAATTTTCTCGGC 270 467 1202 Antisense
GCGCTCACGGATTTCGCTACGATTC 349 287 1255 Antisense
CACTTTTCCGTATCTTCGGCAGCAT 252 197 1280 Antisense
CGGCAGCATGTGTTTCGTGTTCCTG 606 241 1296 Antisense
GGATCGGAGCATCATCTCGTCAATT 129 513 1432 Antisense
Sequence Source Affymetrix Proprietary Database