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[187230_at]

Description T28D9.4 /REP_DB=WormBase Gene ID /WP=CE02069 /TR=SW:Q10023 /GB=AAA68310.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 88      6grp_high1_10_10 > 88      4grp_highest_8_8 > 20      4grp_high_8_8 > 31      6grp_highest_nonorm > 95      6grp_total > 97      4grp_total > 24      6grp_highest_sub > Da      6grp_high1_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 279
1 2 3 4 range
A 230.8
(-1.9)
P 		191.1
(-3)
P 		403.5
(2.9)
P 		406.1
(3)
P 		215
B 143.5
(-3)
P 		280.3
(-0.1)
P 		348.2
(1.4)
P 		422.2
(3)
P 		279
C 194.9
(-3)
P 		280
(-0.2)
P 		346.1
(2)
P 		378.1
(3)
P 		183
avr 189.7
(-3) 		250.5
(-1.3) 		365.9
(2) 		402.1
(3) 		212

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1766
1 2 3 4 5 6 range
A 133.3
(-3)
P 		165.1
(-2.9)
P 		220
(-2.7)
P 		406.5
(-2)
P 		1190.8
(1)
P 		1729.3
(3)
P 		1596
B 187.6
(-3)
P 		187.9
(-3)
P 		244.9
(-2.8)
P 		487.8
(-1.9)
P 		1018.8
(-0.1)
P 		1898.9
(3)
P 		1711
C 140.4
(-3)
P 		225
(-2.7)
P 		286.6
(-2.5)
P 		510.2
(-1.6)
P 		955.4
(0)
P 		1748
(3)
P 		1608
avr 153.8
(-3) 		192.7
(-2.9) 		250.5
(-2.6) 		468.2
(-1.8) 		1055
(0.3) 		1792.1
(3) 		1638
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 79
1 2 3 4 range
A 84.1
(1)
P 		41.5
(-3)
P 		105.5
(3)
P 		59.4
(-1.3)
P 		64
B 45.8
(-3)
P 		69.2
(0.2)
P 		80.7
(1.7)
P 		90
(3)
P 		44
C 64.5
(-2.9)
P 		80.5
(-1.2)
P 		120.6
(3)
P 		63.8
(-3)
P 		57
avr 64.8
(-2.8) 		63.7
(-3) 		102.3
(3) 		71.1
(-1.8) 		39

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 684
1 2 3 4 5 6 range
A 24.6
(-3)
P 		58.7
(-2.5)
P 		47.9
(-2.6)
P 		103.1
(-1.8)
P 		359.3
(2.1)
P 		421
(3)
P 		396
B 65.3
(-2.9)
P 		62.5
(-3)
P 		59.5
(-3)
P 		129.2
(-2.4)
P 		413.9
(0.3)
P 		708.1
(3)
P 		649
C 52.1
(-3)
P 		68.7
(-2.8)
P 		72.9
(-2.8)
P 		102.6
(-2.4)
P 		309.2
(-0.1)
P 		585.2
(3)
P 		533
avr 47.3
(-3) 		63.3
(-2.8) 		60.1
(-2.9) 		111.6
(-2.3) 		360.8
(0.6) 		571.4
(3) 		524
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 187230_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.5431
Sequence Type Exemplar sequence
Representative Public ID T28D9.4 NCBI
Target Description T28D9.4 /REP_DB=WormBase Gene ID /WP=CE02069 /TR=SW:Q10023 /GB=AAA68310.1 /SUBMIT=ST.LOUIS /CHR=2 /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_062902(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_062902 NCBI Caenorhabditis elegans T28D9.4 (T28D9.4) mRNA, complete cds. 11/11 None
SNAP00000011376 ENSEMBL cdna:SNAP chromosome:CEL140:II:6475638:6477930:1 11/11 None
GENEFINDER00000011390 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:6475638:6477930:1 11/11 None
T28D9.4 ENSEMBL cdna:known chromosome:CEL140:II:6475638:6478020:1 gene:T28D9.4 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
chrII:6475634-6477927(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Ensembl T28D9.4
Entrez Gene 174070 Entrez gene
SwissProt Q10023 EMBL-EBI
WormBase CE36024 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAA68310 Hypothetical protein T28D9.4 [Caenorhabditis elegans] ref|NP_495303.2| T28D9.4 [Caenorhabditis elegans] sp|Q10023|YSX4_CAEEL Hypothetical protein T28D9.4 in chromosome II 0.0
blast CAE59317 Hypothetical protein CBG02657 [Caenorhabditis briggsae] 5.0E-43
blast CAE59317 Hypothetical protein CBG02657 [Caenorhabditis briggsae] 6.0E-43
blast CAE59317 Hypothetical protein CBG02657 [Caenorhabditis briggsae] 1.0E-39
Protein Domains
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_495303.2 6 57-79,133-155,160-182,216-238,349-371,386-408
T28D9.4 6 57-79,133-155,160-182,216-238,349-371,386-408
SNAP00000011376 4 57-79,133-155,298-320,335-357
GENEFINDER00000011390 6 57-79,133-155,160-182,216-238,386-408,423-445
Sequence
Target Sequence 
>C. ELEGANS:187230_AT
caaggtcacacactgttgcctcaatgtcttcgcatcttcggcgtttttcgtgctactaat
ggttctggtcgataaacaaggactcgataaaactcctaaatgtcttgccgctctctacgc
cttcgcaatgtggatgcagctggccactgtccgttaccgtcactttatcccgctgattct
cacagtagtcatcgaactggtcatcactggattggtttcctatcaaacgggagaattcat
cttctcgcacaccgctgaagtcaaggattacgtattcacagtgatgttcactattatcgc
tgtcttccgtttcgtcttcattattattcttttcaaagttctcatttacaaaaatccgcc
acactccctgacaactacagttcttctcaaaccaaccaatatccctgtcactttttcttc
tatcaaggcaccacaagagcttgacccaaccaacccatactacccccaaactgtctataa
ta

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CAAGGTCACACACTGTTGCCTCAAT 91 183 792 Antisense
GGCGTTTTTCGTGCTACTAATGGTT 274 537 831 Antisense
TAAAACTCCTAAATGTCTTGCCGCT 699 639 879 Antisense
TCTCTACGCCTTCGCAATGTGGATG 83 613 903 Antisense
TATCCCGCTGATTCTCACAGTAGTC 52 659 957 Antisense
TCTCGCACACCGCTGAAGTCAAGGA 301 609 1034 Antisense
ATGTTCACTATTATCGCTGTCTTCC 249 47 1075 Antisense
CTTCCGTTTCGTCTTCATTATTATT 668 219 1095 Antisense
TCAAACCAACCAATATCCCTGTCAC 460 629 1178 Antisense
GTCACTTTTTCTTCTATCAAGGCAC 526 465 1198 Antisense
TACTACCCCCAAACTGTCTATAATA 478 645 1249 Antisense
Sequence Source Affymetrix Proprietary Database