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[193857_s_at] Yeast DNA mismatch repair protein MSH5 like

Description F09E8.3 /REP_DB=WormBase Gene ID /WP=CE26678 /GEN=msh-5 /TR=SW:Q19272 /GB=CAA98059.2 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=Yeast DNA mismatch repair protein MSH5 like
Cluster 6grp_total > 76      4grp_total > 01      6grp_cgc > 48      6grp_cgc_sub > Da      6grp_total_sub > Increase      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 204
1 2 3 4 range
A 128.7
(-2.6)
A 		126.5
(-3)
A 		143.4
(0)
A 		159.9
(3)
A 		33
B 152.5
(3)
A 		117.5
(-3)
A 		138.3
(0.6)
A 		150.7
(2.7)
A 		35
C 153.7
(-1.8)
A 		113.7
(-3)
A 		151
(-1.9)
A 		317.4
(3)
P 		204
avr 145
(-1.3) 		119.2
(-3) 		144.2
(-1.3) 		209.3
(3) 		90

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 343
1 2 3 4 5 6 range
A 149.3
(-3)
A 		159.6
(-2.8)
A 		158.8
(-2.8)
P 		279.3
(-0)
P 		219.5
(-1.4)
P 		412.4
(3)
P 		263
B 137.7
(-3)
A 		187.2
(-1.6)
A 		175.1
(-2)
M 		199.7
(-1.3)
P 		185.9
(-1.7)
P 		356.3
(3)
P 		219
C 105.1
(-3)
A 		166.7
(-1.9)
A 		187.7
(-1.6)
M 		241.9
(-0.6)
M 		150.2
(-2.2)
M 		448.5
(3)
P 		343
avr 130.7
(-3) 		171.2
(-2.1) 		173.9
(-2.1) 		240.3
(-0.6) 		185.2
(-1.8) 		405.7
(3) 		275
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 30
1 2 3 4 range
A 46.9
(3)
A 		27.5
(-2)
A 		37.5
(0.6)
A 		23.4
(-3)
A 		24
B 48.6
(3)
A 		29
(-3)
A 		32
(-2.1)
A 		32.1
(-2.1)
A 		20
C 50.9
(2.3)
A 		32.7
(-3)
A 		52.6
(2.7)
A 		53.5
(3)
P 		21
avr 48.8
(3) 		29.7
(-3) 		40.7
(0.5) 		36.3
(-0.9) 		19

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 123
1 2 3 4 5 6 range
A 27.5
(-3)
A 		56.8
(-0.6)
A 		34.6
(-2.4)
P 		70.8
(0.6)
P 		66.2
(0.2)
P 		100.4
(3)
P 		73
B 47.9
(-2.6)
A 		62.3
(-1.7)
A 		42.5
(-3)
M 		52.9
(-2.3)
P 		75.5
(-0.8)
P 		132.8
(3)
P 		90
C 39
(-3)
A 		50.9
(-2.4)
A 		47.8
(-2.5)
M 		48.6
(-2.5)
M 		48.6
(-2.5)
M 		150.2
(3)
P 		111
avr 38.1
(-3) 		56.7
(-1.8) 		41.6
(-2.8) 		57.4
(-1.7) 		63.4
(-1.3) 		127.8
(3) 		90
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 193857_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.9027
Sequence Type Exemplar sequence
Representative Public ID F09E8.3 NCBI
Target Description F09E8.3 /REP_DB=WormBase Gene ID /WP=CE26678 /GEN=msh-5 /TR=SW:Q19272 /GB=CAA98059.2 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=Yeast DNA mismatch repair protein MSH5 like
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_070130(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_070130 NCBI Caenorhabditis elegans MSH (MutS Homolog) family member (msh-5) (msh-5) mRNA, complete cds. 11/11 A 
SNAP00000017199 ENSEMBL cdna:SNAP chromosome:CEL140:IV:13155203:13164615:1 11/11 None
GENEFINDER00000017204 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:13155203:13166725:1 11/11 None
F09E8.3 ENSEMBL cdna:known chromosome:CEL140:IV:13155198:13163962:1 gene:F09E8.3 11/11 A 
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
chrIV:13155208-13161038(+) 91.08 100.0
Public Domain and Genome References
Gene Title Yeast DNA mismatch repair protein MSH5 like
Gene Symbol msh-5
Ensembl F09E8.3
Entrez Gene 178268 Entrez gene
SwissProt Q19272 EMBL-EBI
WormBase CE26678 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:257669_AT DNA mismatch repair MutS family protein at
CANINE:1592169_AT mutS homolog 5 (E. coli) cfa
CANINE_2:CFA.5530.1.A1_AT mutS homolog 5 (E. coli) cfa
CANINE_2:CFAAFFX.1863.1.S1_AT mutS homolog 5 (E. coli) cfa
HG-U133_PLUS_2:221406_S_AT mutS homolog 5 (E. coli) hs
HG-U133A_2:221406_S_AT mutS homolog 5 (E. coli) hs
HG-U133A:221406_S_AT mutS homolog 5 (E. coli) hs
HG-FOCUS:221406_S_AT mutS homolog 5 (E. coli) hs
HG-U133_PLUS_2:210410_S_AT mutS homolog 5 (E. coli) hs
HG-U133A:210410_S_AT mutS homolog 5 (E. coli) hs
HG-FOCUS:210410_S_AT mutS homolog 5 (E. coli) hs
HG-U133A_2:210410_S_AT mutS homolog 5 (E. coli) hs
HG-U95C:50183_AT mutS homolog 5 (E. coli) hs
HU35KSUBC:RC_AA459915_AT mutS homolog 5 (E. coli) hs
HU35KSUBD:RC_AA621155_AT mutS homolog 5 (E. coli) hs
U133_X3P:G2653648_3P_A_AT mutS homolog 5 (E. coli) hs
U133_X3P:G13376869_3P_S_AT mutS homolog 5 (E. coli) hs
U133_X3P:HS.112193.1.S2_3P_AT mutS homolog 5 (E. coli) hs
HG-U133A_2:212913_AT mutS homolog 5 (E. coli) hs
HG-U133_PLUS_2:212913_AT mutS homolog 5 (E. coli) hs
HG-U133A:212913_AT mutS homolog 5 (E. coli) hs
HG-U95AV2:41467_AT mutS homolog 5 (E. coli) hs
HG-U95C:59607_F_AT mutS homolog 5 (E. coli) hs
HG-U95C:63729_F_AT mutS homolog 5 (E. coli) hs
HG-U133_PLUS_2:230096_AT MutS homolog 5 (E. coli) hs
HG-U133B:230096_AT MutS homolog 5 (E. coli) hs
HG-U95C:50178_AT MutS homolog 5 (E. coli) hs
HG-U95C:50181_G_AT MutS homolog 5 (E. coli) hs
U133_X3P:HS.112193.2.A1_3P_AT MutS homolog 5 (E. coli) hs
MOUSE430_2:1449537_AT mutS homolog 5 (E. coli) mm
MOE430A:1449537_AT mutS homolog 5 (E. coli) mm
MOUSE430A_2:1449537_AT mutS homolog 5 (E. coli) mm
MG-U74AV2:103719_AT mutS homolog 5 (E. coli) mm
MOE430A:1430771_A_AT mutS homolog 5 (E. coli) mm
MOUSE430A_2:1430771_A_AT mutS homolog 5 (E. coli) mm
MOUSE430_2:1430771_A_AT mutS homolog 5 (E. coli) mm
RG-U34B:RC_AI059993_AT mutS homolog 5 rn
YEAST_2:1776554_AT Protein of the MutS family, forms a dimer with Msh4p that facilitates crossovers between homologs during meiosis; msh5-Y823H mutation confers tolerance to DNA alkylating agents; homologs present in C. elegans and humans Sc
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 CAA98059 Hypothetical protein F09E8.3 [Caenorhabditis elegans] ref|NP_502531.1| MSH (MutS Homolog) family member (msh-5) [Caenorhabditis elegans] gb|AAF76200.1| MSH-5 [Caenorhabditis elegans] sp|Q19272|MSH5_CAEEL MutS protein homolog 0.0
blast AAC70065 MutS homolog [Caenorhabditis elegans] 0.0
blast CAE58527 Hypothetical protein CBG01682 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR007696 EMBL-EBI MutS III 4.8E-8
Pfam IPR007861 EMBL-EBI MutS IV 3.2E-22
Pfam IPR000432 EMBL-EBI DNA mismatch repair protein MutS, C-terminal 3.9E-41
Pfam IPR007696 EMBL-EBI MutS III 1.1E-7
Pfam IPR007861 EMBL-EBI MutS IV 3.2E-22
Pfam IPR000432 EMBL-EBI DNA mismatch repair protein MutS, C-terminal 3.9E-41
Pfam IPR001283 EMBL-EBI Allergen V5/Tpx-1 related 9.0E-59
Sequence
Target Sequence 
>C. ELEGANS:193857_S_AT
aagatggtttcatggccgcagtagaatcatttgtgaaaagaaagaaaacatcattttgcg
aatcatcaatgcgaaatgtgagcgaggaaattgaaaaggagagatcagaagcttctactc
cggcatcgaaaagtcgcagtaccatcacagccagatcaaatagtgttctttcatcgcgat
cgatggcttcagtggatcaactttctgtgctcgatgccttgttaccaaaaaagaaaaaga
aaaaagtgacaggtagtagtatggaatcatcaatgtctcctgatccattccaagaagagg
atgaaggtactgaaggagaggaagatcaaataagtgcacctgtatctcgaccaacacttc
cgtctgtacagaaat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AAGATGGTTTCATGGCCGCAGTAGA 12 155 2888 Antisense
GAGAGATCAGAAGCTTCTACTCCGG 421 395 2986 Antisense
GCTTCTACTCCGGCATCGAAAAGTC 511 305 2998 Antisense
GAAAAGTCGCAGTACCATCACAGCC 66 355 3015 Antisense
CAAATAGTGTTCTTTCATCGCGATC 65 195 3044 Antisense
AGTGGATCAACTTTCTGTGCTCGAT 337 59 3078 Antisense
TGTGCTCGATGCCTTGTTACCAAAA 434 557 3093 Antisense
GGAATCATCAATGTCTCCTGATCCA 493 531 3150 Antisense
TGTCTCCTGATCCATTCCAAGAAGA 704 557 3161 Antisense
AAATAAGTGCACCTGTATCTCGACC 410 115 3215 Antisense
CCAACACTTCCGTCTGTACAGAAAT 507 275 3238 Antisense
Sequence Source Affymetrix Proprietary Database