[Home] | [Total List]

[193152_s_at] DNA mismatch repair protein

Description Y47G6A.11 /REP_DB=WormBase Gene ID /WP=CE24357 /GEN=msh-6 /TR=Q9N3T8 /GB=AAF60672.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=DNA mismatch repair protein
Cluster 6grp_highest_10_10 > 97      6grp_high1_10_10 > 78      4grp_high_8_8 > 61      6grp_highest_nonorm > 92      6grp_total > 78      4grp_total > 59      6grp_highest_sub > Cu      6grp_cgc > 49      6grp_high1_sub > Cu      6grp_cgc_sub > Da      6grp_total_sub > Increase      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 119
1 2 3 4 range
A 230
(-0.8)
P 		226.1
(-1)
P 		287.9
(3)
P 		195.7
(-3)
A 		92
B 241.2
(1.4)
P 		260
(3)
P 		245
(1.7)
P 		191.4
(-3)
P 		69
C 250.2
(0.3)
P 		303.9
(3)
P 		295.5
(2.6)
P 		184.8
(-3)
P 		119
avr 240.5
(0.5) 		263.3
(2.1) 		276.1
(3) 		190.6
(-3) 		86

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 492
1 2 3 4 5 6 range
A 330.7
(-0.5)
P 		202.1
(-2.2)
P 		144.2
(-3)
P 		228.3
(-1.9)
P 		407.2
(0.6)
P 		588
(3)
P 		444
B 227.8
(-2.2)
P 		180.3
(-2.9)
P 		177.1
(-3)
P 		218.1
(-2.3)
P 		377.5
(0.3)
P 		536.2
(3)
P 		359
C 244.4
(-2.3)
P 		194.5
(-3)
P 		205.1
(-2.9)
P 		248.9
(-2.3)
P 		361
(-0.7)
P 		635.7
(3)
P 		441
avr 267.6
(-1.7) 		192.3
(-2.8) 		175.5
(-3) 		231.8
(-2.2) 		381.9
(0) 		586.6
(3) 		411
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 74
1 2 3 4 range
A 83.7
(3)
P 		49.1
(-0.8)
P 		75.3
(2.1)
P 		28.6
(-3)
A 		55
B 76.9
(3)
P 		64.2
(0.9)
P 		56.8
(-0.3)
P 		40.8
(-3)
P 		36
C 82.8
(1.3)
P 		87.4
(1.7)
P 		103
(3)
P 		31.2
(-3)
P 		72
avr 81.1
(3) 		66.9
(1.2) 		78.4
(2.7) 		33.5
(-3) 		48

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 181
1 2 3 4 5 6 range
A 61
(-1.4)
P 		71.9
(-0.8)
P 		31.4
(-3)
P 		57.9
(-1.6)
P 		122.9
(1.9)
P 		143.2
(3)
P 		112
B 79.3
(-1.6)
P 		60
(-2.3)
P 		43
(-3)
P 		57.8
(-2.4)
P 		153.4
(1.2)
P 		199.9
(3)
P 		157
C 90.6
(-1.5)
P 		59.4
(-2.7)
P 		52.2
(-2.9)
P 		50.1
(-3)
P 		116.8
(-0.5)
P 		212.8
(3)
P 		163
avr 77
(-1.5) 		63.8
(-2.1) 		42.2
(-3) 		55.3
(-2.5) 		131
(0.7) 		185.3
(3) 		143
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 193152_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.54
Sequence Type Exemplar sequence
Representative Public ID Y47G6A.11 NCBI
Target Description Y47G6A.11 /REP_DB=WormBase Gene ID /WP=CE24357 /GEN=msh-6 /TR=Q9N3T8 /GB=AAF60672.1 /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_058762(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_058762 NCBI Caenorhabditis elegans MSH (MutS Homolog) family member (msh-6) (msh-6) mRNA, complete cds. 11/11 None
SNAP00000033972 ENSEMBL cdna:SNAP chromosome:CEL140:I:3449328:3462073:1 11/11 None
GENEFINDER00000034069 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:3451923:3462073:1 11/11 None
Y47G6A.11 ENSEMBL cdna:known chromosome:CEL140:I:3449328:3462168:1 gene:Y47G6A.11 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:3439108-3462073(+) 99.48 100.0
Public Domain and Genome References
Gene Title DNA mismatch repair protein
Gene Symbol msh-6
Ensembl Y47G6A.11
Entrez Gene 171914 Entrez gene
SwissProt Q9N3T8 EMBL-EBI
WormBase CE28985 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:17330_S_AT DNA mismatch repair protein MSH6-1 (MSH6-1) (AGAA.3) at
ATH1-121501:255562_AT DNA mismatch repair protein MSH6-1 (MSH6-1) (AGAA.3) at
CANINE:1591458_S_AT similar to mutS homolog 6 cfa
CANINE_2:CFAAFFX.4865.1.S1_S_AT similar to mutS homolog 6 cfa
DROSOPHILA_2:1637163_AT dm
DROSGENOME1:148795_AT dm
CHICKEN:GGA.18251.1.S1_AT mutS homolog 6 (E. coli) gga
CHICKEN:GGA.18251.1.S1_S_AT mutS homolog 6 (E. coli) gga
CHICKEN:GGAAFFX.22740.1.S1_AT mutS homolog 6 (E. coli) gga
HG-FOCUS:202911_AT mutS homolog 6 (E. coli) hs
HG-U133A:202911_AT mutS homolog 6 (E. coli) hs
HG-U133A_2:202911_AT mutS homolog 6 (E. coli) hs
HG-U133_PLUS_2:202911_AT mutS homolog 6 (E. coli) hs
HG-U133_PLUS_2:211450_S_AT mutS homolog 6 (E. coli) hs
HG-U133A:211450_S_AT mutS homolog 6 (E. coli) hs
HG-U133A_2:211450_S_AT mutS homolog 6 (E. coli) hs
HG-U133_PLUS_2:211449_AT mutS homolog 6 (E. coli) hs
HG-U133A:211449_AT mutS homolog 6 (E. coli) hs
HG-U133A_2:211449_AT mutS homolog 6 (E. coli) hs
HG-U95AV2:2003_S_AT mutS homolog 6 (E. coli) hs
HC-G110:2003_S_AT mutS homolog 6 (E. coli) hs
HUGENEFL:U73737_AT mutS homolog 6 (E. coli) hs
U133_X3P:G4504190_3P_AT mutS homolog 6 (E. coli) hs
U133_X3P:G2687868_3P_AT mutS homolog 6 (E. coli) hs
U133_X3P:G2687868_3P_A_AT mutS homolog 6 (E. coli) hs
HG-U133_PLUS_2:240148_AT MutS homolog 6 (E. coli) hs
HG-U133B:240148_AT MutS homolog 6 (E. coli) hs
HG-U95B:44762_AT MutS homolog 6 (E. coli) hs
HG-U95E:80342_AT MutS homolog 6 (E. coli) hs
HU35KSUBA:RC_AA476717_AT MutS homolog 6 (E. coli) hs
MU11KSUBA:U42190_S_AT mutS homolog 6 (E. coli) mm
MG-U74AV2:93299_AT mutS homolog 6 (E. coli) mm
MG-U74CV2:171535_R_AT mutS homolog 6 (E. coli) mm
MOE430A:1416915_AT mutS homolog 6 (E. coli) mm
MOUSE430A_2:1416915_AT mutS homolog 6 (E. coli) mm
MOUSE430_2:1416915_AT mutS homolog 6 (E. coli) mm
MU19KSUBA:TC25800_AT MutS homolog 6 (E. coli) (Msh6), mRNA mm
RG-U34B:RC_AI059688_S_AT mutS homolog 6 (E. coli) (predicted) rn
RG-U34C:RC_AA819391_AT mutS homolog 6 (E. coli) (predicted) rn
RAE230B:1377846_A_AT mutS homolog 6 (E. coli) (predicted) rn
RAT230_2:1377846_A_AT mutS homolog 6 (E. coli) (predicted) rn
RG-U34B:RC_AI059688_R_AT MutS homolog 6 (E. coli) (predicted) rn
YEAST_2:1775548_AT Protein required for mismatch repair in mitosis and meiosis, forms a complex with Msh2p to repair both single-base & insertion-deletion mispairs; potentially phosphorylated by Cdc28p Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
5975 carbohydrate metabolism inferred from electronic annotation QuickGO AmiGO
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
4553 hydrolase activity, hydrolyzing O-glycosyl compounds inferred from electronic annotation QuickGO AmiGO
5524 ATP binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast NP_491163 MSH (MutS Homolog) family member (msh-6) [Caenorhabditis elegans] gb|AAK95890.1| Msh (muts homolog) family protein 6 [Caenorhabditis elegans] 0.0
blast CAE68977 Hypothetical protein CBG14959 [Caenorhabditis briggsae] 0.0
blast AAH89270 Unknown (protein for MGC:85188) [Xenopus laevis] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR007695 EMBL-EBI DNA mismatch repair protein MutS, N-terminal 2.8E-53
Pfam IPR007861 EMBL-EBI MutS IV 1.4E-20
Pfam IPR007696 EMBL-EBI MutS III 4.0E-23
Pfam IPR007860 EMBL-EBI MutS II 1.3E-5
Pfam IPR000432 EMBL-EBI DNA mismatch repair protein MutS, C-terminal 1.1E-97
Pfam IPR007695 EMBL-EBI DNA mismatch repair protein MutS, N-terminal 2.8E-53
Pfam IPR007861 EMBL-EBI MutS IV 1.4E-20
Pfam IPR007696 EMBL-EBI MutS III 4.0E-23
Pfam IPR007860 EMBL-EBI MutS II 1.3E-5
Pfam IPR000432 EMBL-EBI DNA mismatch repair protein MutS, C-terminal 1.7E-80
Pfam IPR000432 EMBL-EBI DNA mismatch repair protein MutS, C-terminal 1.5E-9
Sequence
Target Sequence 
>C. ELEGANS:193152_S_AT
tggcgattctcgctcatattggttcaatggttcctgccttctcgatgcggctcactccaa
tcgatcgaattttcactcgtattggagccaacgataggattatgtgcggagaatcaacat
tcttcattgagctaaaagaaactgatattatgctcaaaaatgcgacaaagcattctctct
tgctcgtcgacgagctcggtcgtggcacaagtacattcgatggaactgccattgcttctg
ctgttttacaaaagatttctgatgatttggcgtgtcgaacattcttttctacacattatc
actcgatttgtgactcatttactaatcatccgaatgtcagattggcccatatgaaatgtg
tcgtggataaggagaacaatgaggatccaacaatggaagatgtcactttcttatacgaac
tcgaatctggaatttgcccaaaatcctacggtttctatgcagcaaaactggctggaattg
accatcaagtcgttcgaaatgcctatttggaaagcaataaattcgcatcaaatctcatca
ttgatcccaaaatccgacatcttgttg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGGCGATTCTCGCTCATATTGGTTC 393 543 4751 Antisense
TATTGGTTCAATGGTTCCTGCCTTC 321 665 4767 Antisense
GGCTCACTCCAATCGATCGAATTTT 695 535 4799 Antisense
CGACAAAGCATTCTCTCTTGCTCGT 240 253 4913 Antisense
GAGCTCGGTCGTGGCACAAGTACAT 56 389 4942 Antisense
TGCCATTGCTTCTGCTGTTTTACAA 586 585 4977 Antisense
GGCGTGTCGAACATTCTTTTCTACA 359 537 5019 Antisense
TCTTTTCTACACATTATCACTCGAT 682 615 5033 Antisense
GATGTCACTTTCTTATACGAACTCG 543 409 5149 Antisense
GCCCAAAATCCTACGGTTTCTATGC 94 285 5186 Antisense
GATCCCAAAATCCGACATCTTGTTG 433 417 5293 Antisense
Sequence Source Affymetrix Proprietary Database