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[177219_at]

Description M28.8 /REP_DB=WormBase Gene ID /WP=CE02286 /TR=Q21574 /GB=CAA90132.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 39      6grp_high1_10_10 > 92      4grp_high_8_8 > 31      6grp_highest_nonorm > 81      6grp_total > 84      4grp_total > 60      6grp_highest_sub > 04      6grp_high1_sub > 04_05      6grp_total_sub > Hat      6grp_rule_based > S4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 214
1 2 3 4 range
A 161.4
(-1.9)
P 		139.4
(-3)
P 		254.2
(3)
P 		160.9
(-1.9)
P 		115
B 153
(3)
P 		142.3
(2.4)
P 		78.1
(-1)
P 		40.2
(-3)
A 		113
C 124
(0.4)
P 		76.7
(-1.8)
P 		181
(3)
P 		50.9
(-3)
A 		130
avr 146.1
(1.3) 		119.5
(-0.6) 		171.1
(3) 		84
(-3) 		87

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 307
1 2 3 4 5 6 range
A 337.9
(0.1)
P 		197.6
(-3)
P 		341.9
(0.2)
P 		385.7
(1.2)
P 		467.4
(3)
P 		411.6
(1.8)
P 		270
B 160.8
(-3)
P 		194.9
(-2.1)
P 		325.3
(1.4)
P 		382.9
(3)
P 		340.7
(1.9)
P 		276.6
(0.1)
P 		222
C 171.4
(-3)
P 		216.5
(-2)
P 		238
(-1.6)
P 		450.4
(3)
P 		402.9
(2)
P 		325.4
(0.3)
P 		279
avr 223.4
(-2.4) 		203
(-3) 		301.7
(-0.1) 		406.3
(3) 		403.7
(2.9) 		337.9
(1) 		203
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 58
1 2 3 4 range
A 58.8
(1.9)
P 		30.3
(-2)
P 		66.4
(3)
P 		23.5
(-3)
P 		43
B 48.8
(3)
P 		35.1
(1)
P 		18.1
(-1.6)
P 		8.6
(-3)
A 		40
C 41.1
(0.6)
P 		22.1
(-1.5)
P 		63.1
(3)
P 		8.6
(-3)
A 		55
avr 49.6
(3) 		29.2
(-0.4) 		49.2
(2.9) 		13.6
(-3) 		36

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 85
1 2 3 4 5 6 range
A 62.3
(-3)
P 		70.3
(-2.4)
P 		74.5
(-2.1)
P 		97.8
(-0.3)
P 		141.1
(3)
P 		100.2
(-0.1)
P 		79
B 56
(-3)
P 		64.9
(-2.4)
P 		79
(-1.3)
P 		101.4
(0.3)
P 		138.4
(3)
P 		103.2
(0.4)
P 		82
C 63.5
(-2.8)
P 		66.1
(-2.5)
P 		60.6
(-3)
P 		90.6
(-0.4)
P 		130.4
(3)
P 		108.9
(1.2)
P 		70
avr 60.6
(-3) 		67.1
(-2.5) 		71.4
(-2.1) 		96.6
(-0.2) 		136.6
(3) 		104.1
(0.4) 		76
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 177219_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3232
Sequence Type Exemplar sequence
Representative Public ID M28.8 NCBI
Target Description M28.8 /REP_DB=WormBase Gene ID /WP=CE02286 /TR=Q21574 /GB=CAA90132.1 /SUBMIT=HINXTON /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_063893(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063893 NCBI Caenorhabditis elegans M28.8 (M28.8) mRNA, complete cds. 11/11 None
SNAP00000007400 ENSEMBL cdna:SNAP chromosome:CEL140:II:10628180:10632980:1 11/11 None
GENEFINDER00000007416 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:10628180:10637866:1 11/11 None
M28.8 ENSEMBL cdna:known chromosome:CEL140:II:10628180:10633114:1 gene:M28.8 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:10628176-10632977(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Ensembl M28.8
Entrez Gene 174641 Entrez gene
SwissProt Q21574 EMBL-EBI
WormBase CE02286 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
8152 metabolism inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA90132 Hypothetical protein M28.8 [Caenorhabditis elegans] ref|NP_496294.1| M28.8 [Caenorhabditis elegans] 0.0
blast CAE59633 Hypothetical protein CBG03046 [Caenorhabditis briggsae] 0.0
blast CAA90130 Hypothetical protein M28.2 [Caenorhabditis elegans] ref|NP_496295.1| M28.2 [Caenorhabditis elegans] 0.0
blast CAA90129 Hypothetical protein M28.9 [Caenorhabditis elegans] ref|NP_496296.1| M28.9 [Caenorhabditis elegans] 1.0E-148
Protein Domains
Database ID Description E-Value
Pfam IPR005135 EMBL-EBI Endonuclease/exonuclease/phosphatase 4.6E-15
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 3.1E-20
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_496294.1 5 96-118,139-161,386-408,415-437,667-689
M28.8 5 96-118,139-161,386-408,415-437,667-689
SNAP00000007400 5 96-118,139-161,386-408,415-437,640-662
GENEFINDER00000007416 10 96-118,139-161,386-408,415-437,667-689,826-848,929-951,972-994,1218-1240,1252-1274
Sequence
Target Sequence 
>C. ELEGANS:177219_AT
gttcatgtgccgtccatttgtagatgtatacaataatggaggtttcgtaatgtgtgaaca
atttggaaagcctattcaaggactgtgggctgctgttggattaactggactctttctgtt
tttccagtcaattcttttgcttctagtctatcgctggttgaggacaaatagtgatgattt
ggcaatgtataactacagagataagaatgactcaacgtcaaaatacagtggcacccgaaa
actcggtggcaaaaaggaccaagttcgtccaactgaggaattgtgggcaacaccaatatt
gagctcaacttcaaatacggaaacacgacagcttccaagagttcgaccatatgatatgga
tattgttcagccatcagagtatgactattcctacggcactggatcgcaatcacattatcc
acgtgttcaagttcttcc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTTCATGTGCCGTCCATTTGTAGAT 202 445 1932 Antisense
AAGGACTGTGGGCTGCTGTTGGATT 505 159 2009 Antisense
TGGACTCTTTCTGTTTTTCCAGTCA 496 547 2037 Antisense
TTTCCAGTCAATTCTTTTGCTTCTA 490 669 2052 Antisense
TTGCTTCTAGTCTATCGCTGGTTGA 676 703 2068 Antisense
GTGGCACCCGAAAACTCGGTGGCAA 201 487 2159 Antisense
GGGCAACACCAATATTGAGCTCAAC 233 493 2216 Antisense
ACAGCTTCCAAGAGTTCGACCATAT 592 107 2259 Antisense
AGAGTATGACTATTCCTACGGCACT 206 67 2307 Antisense
TACGGCACTGGATCGCAATCACATT 591 647 2323 Antisense
ATTATCCACGTGTTCAAGTTCTTCC 676 13 2345 Antisense
Sequence Source Affymetrix Proprietary Database