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[193072_s_at] DNA mismatch repair protein

Description H26D21.2 /REP_DB=WormBase Gene ID /WP=CE21000 /GEN=msh-2 /TR=Q9TXR4 /GB=AAC78226.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=DNA mismatch repair protein
Cluster 6grp_highest_10_10 > 88      6grp_high1_10_10 > 88      4grp_highest_8_8 > 17      4grp_high_8_8 > 61      6grp_highest_nonorm > 93      6grp_total > 97      4grp_total > 59      6grp_highest_sub > Da      6grp_cgc > 69      6grp_high1_sub > Da      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 203
1 2 3 4 range
A 364.3
(1.2)
P 		342.5
(0.2)
P 		405.1
(3)
P 		272.6
(-3)
P 		133
B 351
(0.3)
P 		400.8
(3)
P 		359.2
(0.8)
P 		289.1
(-3)
P 		112
C 285.7
(-0.7)
P 		358.7
(1.4)
P 		412.6
(3)
P 		209.4
(-3)
P 		203
avr 333.7
(0.4) 		367.3
(1.9) 		392.3
(3) 		257
(-3) 		135

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 543
1 2 3 4 5 6 range
A 313.3
(-2.5)
P 		320.5
(-2.3)
P 		283.2
(-3)
P 		468.6
(0.3)
P 		566.1
(2)
P 		623
(3)
P 		340
B 343.8
(-2)
P 		250
(-3)
P 		259.2
(-2.9)
P 		358.3
(-1.8)
P 		508.1
(-0.1)
P 		792.7
(3)
P 		543
C 350.8
(-1.9)
P 		254.4
(-3)
P 		389.4
(-1.5)
P 		385.9
(-1.5)
P 		573.8
(0.6)
P 		792.1
(3)
P 		538
avr 336
(-2.2) 		275
(-3) 		310.6
(-2.5) 		404.3
(-1.3) 		549.3
(0.6) 		735.9
(3) 		461
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 109
1 2 3 4 range
A 132.6
(3)
P 		74.3
(-0.8)
P 		105.9
(1.3)
P 		39.9
(-3)
P 		93
B 111.9
(3)
P 		99
(1.5)
P 		83.2
(-0.4)
P 		61.6
(-3)
P 		50
C 94.6
(0.3)
P 		103.1
(0.7)
P 		143.8
(3)
P 		35.3
(-3)
P 		109
avr 113
(3) 		92.1
(1.1) 		111
(2.8) 		45.6
(-3) 		67

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 238
1 2 3 4 5 6 range
A 57.7
(-3)
P 		114
(-0)
P 		61.7
(-2.8)
P 		118.8
(0.2)
P 		170.8
(3)
P 		151.7
(2)
P 		113
B 119.6
(-1.5)
P 		83.2
(-2.5)
P 		62.9
(-3)
P 		94.9
(-2.2)
P 		206.5
(0.7)
P 		295.6
(3)
P 		233
C 130
(-1.3)
P 		77.6
(-3)
P 		99.1
(-2.3)
P 		77.6
(-3)
P 		185.7
(0.5)
P 		265.2
(3)
P 		188
avr 102.4
(-2) 		91.6
(-2.4) 		74.6
(-3) 		97.1
(-2.2) 		187.7
(1.2) 		237.5
(3) 		163
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 193072_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.161
Sequence Type Exemplar sequence
Representative Public ID H26D21.2 NCBI
Target Description H26D21.2 /REP_DB=WormBase Gene ID /WP=CE21000 /GEN=msh-2 /TR=Q9TXR4 /GB=AAC78226.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=DNA mismatch repair protein
Cluster Evidence This cluster is supported by a 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_058801(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_058801 NCBI Caenorhabditis elegans MSH (MutS Homolog) family member (msh-2) (msh-2) mRNA, complete cds. 11/11 None
SNAP00000020759 ENSEMBL cdna:SNAP chromosome:CEL140:I:3694373:3697537:-1 11/11 None
GENEFINDER00000020762 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:3694373:3697537:-1 11/11 None
H26D21.2 ENSEMBL cdna:known chromosome:CEL140:I:3694316:3697553:-1 gene:H26D21.2 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
chrI:3694372-3697537(-) 100.0 100.0
Public Domain and Genome References
Gene Title DNA mismatch repair protein
Gene Symbol msh-2
Ensembl H26D21.2
Entrez Gene 171938 Entrez gene
SwissProt Q9TXR4 EMBL-EBI
WormBase CE21000 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6259 DNA metabolism inferred from electronic annotation QuickGO AmiGO
6298 mismatch repair inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3684 damaged DNA binding inferred from electronic annotation QuickGO AmiGO
5524 ATP binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAC78226 Msh (muts homolog) family protein 2 [Caenorhabditis elegans] ref|NP_491202.1| MSH (MutS Homolog) family member (msh-2) [Caenorhabditis elegans] 0.0
blast CAE66683 Hypothetical protein CBG12022 [Caenorhabditis briggsae] 0.0
blast XP_702697 PREDICTED: hypothetical protein XP_697605 [Danio rerio] 1.0E-119
Protein Domains
Database ID Description E-Value
Pfam IPR007861 EMBL-EBI MutS IV 3.3E-24
Pfam IPR007696 EMBL-EBI MutS III 6.9E-25
Pfam IPR007696 EMBL-EBI MutS III 1.1E-8
Pfam IPR000432 EMBL-EBI DNA mismatch repair protein MutS, C-terminal 6.8E-116
Sequence
Target Sequence 
>C. ELEGANS:193072_S_AT
gtggaaagagcacttacctccgatcagcagctctttccattcttctcgcccaaatcggat
cgttcgttccatgctcctccgctacaatttcggtcgttgatgggattttcacacgagttg
gtgcatccgacaagcaatcgcaaggaatttccacatttatggctgaaatgctcgattgct
ctgcgattcttcaaagagccactaagaattcattcgtggtaattgatgaacttggaagag
gaacttcgacgtttgatggatttggaatagcatcggctattgcacaggacattttgaatc
gtatccaatgtctatccatcttcgccacacatttccatgagatgggaaaactcgctgaac
agccgggagctgttgcccttcaaatgggagttcaaatcgagaataatgaaattcacatgc
tctacaaggttttcgagggagttgcacagtgctccttcggcctccaagttgccaaaatgg
ttggaatcgatgaaaatgtcattaataaagcggcccaacttctggaaggcctc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTGGAAAGAGCACTTACCTCCGATC 207 491 1940 Antisense
AAATCGGATCGTTCGTTCCATGCTC 679 117 1991 Antisense
GTTGGTGCATCCGACAAGCAATCGC 694 435 2056 Antisense
AATGCTCGATTGCTCTGCGATTCTT 13 167 2106 Antisense
CATCGGCTATTGCACAGGACATTTT 529 211 2210 Antisense
TGAATCGTATCCAATGTCTATCCAT 530 575 2234 Antisense
GGAGCTGTTGCCCTTCAAATGGGAG 655 521 2305 Antisense
TTCACATGCTCTACAAGGTTTTCGA 685 681 2351 Antisense
GAGGGAGTTGCACAGTGCTCCTTCG 604 401 2374 Antisense
CTTCGGCCTCCAAGTTGCCAAAATG 654 219 2394 Antisense
AGCGGCCCAACTTCTGGAAGGCCTC 190 75 2448 Antisense
Sequence Source Affymetrix Proprietary Database