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[192890_s_at] DNA mismatch repair protein

Description T28A8.7 /REP_DB=WormBase Gene ID /WP=CE18978 /GEN=mlh-1 /TR=Q9XU10 /GB=CAB07283.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=DNA mismatch repair protein
Cluster 6grp_total > 88      4grp_total > 06      6grp_cgc > 69      6grp_cgc_sub > Da      6grp_total_sub > Increase      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 88
1 2 3 4 range
A 130.2
(2.9)
A 		52.9
(-3)
A 		90.6
(-0.1)
A 		131.2
(3)
A 		78
B 108.6
(1.8)
A 		103
(0.8)
A 		80
(-3)
A 		115.9
(3)
A 		36
C 99.9
(-3)
A 		104.5
(-2.3)
A 		116.9
(-0.5)
A 		141.3
(3)
A 		41
avr 112.9
(0.7) 		86.8
(-3) 		95.8
(-1.7) 		129.5
(3) 		43

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 202
1 2 3 4 5 6 range
A 143
(0.2)
A 		52.3
(-3)
A 		65
(-2.6)
A 		79.6
(-2)
A 		177.6
(1.4)
A 		224.1
(3)
A 		172
B 115.7
(-1.5)
A 		81.3
(-2.6)
A 		70.5
(-3)
A 		105.3
(-1.9)
A 		202.9
(1.3)
A 		253.9
(3)
A 		183
C 121.4
(-1.9)
A 		94.3
(-3)
A 		99.5
(-2.8)
A 		107.7
(-2.5)
A 		150.4
(-0.8)
A 		246.7
(3)
A 		152
avr 126.7
(-1.2) 		76
(-3) 		78.3
(-2.9) 		97.5
(-2.2) 		177
(0.7) 		241.6
(3) 		166
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 36
1 2 3 4 range
A 47.4
(3)
A 		11.5
(-3)
A 		23.7
(-1)
A 		19.2
(-1.7)
A 		36
B 34.6
(3)
A 		25.4
(-0.4)
A 		18.5
(-3)
A 		24.7
(-0.7)
A 		16
C 33.1
(0.3)
A 		30
(-0.8)
A 		40.7
(3)
A 		23.8
(-3)
A 		17
avr 38.4
(3) 		22.3
(-3) 		27.6
(-1) 		22.6
(-2.9) 		16

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 81
1 2 3 4 5 6 range
A 26.4
(-1.2)
A 		18.6
(-2.3)
A 		14.1
(-3)
A 		20.2
(-2.1)
A 		53.6
(2.9)
A 		54.6
(3)
A 		41
B 40.3
(-1.2)
A 		27
(-2.2)
A 		17.1
(-3)
A 		27.9
(-2.2)
A 		82.4
(2)
A 		94.7
(3)
A 		78
C 45
(-0.7)
A 		28.8
(-2.3)
A 		25.3
(-2.6)
A 		21.7
(-3)
A 		48.7
(-0.3)
A 		82.6
(3)
A 		61
avr 37.2
(-1.1) 		24.8
(-2.4) 		18.8
(-3) 		23.3
(-2.5) 		61.6
(1.4) 		77.3
(3) 		59
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 192890_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.8062
Sequence Type Exemplar sequence
Representative Public ID T28A8.7 NCBI
Target Description T28A8.7 /REP_DB=WormBase Gene ID /WP=CE18978 /GEN=mlh-1 /TR=Q9XU10 /GB=CAB07283.1 /SUBMIT=HINXTON /CHR=3 /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_067395(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067395 NCBI Caenorhabditis elegans MLH (MutL Homolog) family member (mlh-1) (mlh-1) mRNA, complete cds. 11/11 A 
SNAP00000022266 ENSEMBL cdna:SNAP chromosome:CEL140:III:13508863:13514075:-1 11/11 None
GENEFINDER00000022271 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:13508863:13514075:-1 11/11 None
T28A8.7.2 ENSEMBL cdna:known chromosome:CEL140:III:13508841:13514087:-1 gene:T28A8.7 11/11 None
T28A8.7.1 ENSEMBL cdna:known chromosome:CEL140:III:13508841:13514086:-1 gene:T28A8.7 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
chrIII:13508858-13514300(-) 100.0 100.0
Public Domain and Genome References
Gene Title DNA mismatch repair protein
Gene Symbol mlh-1
Ensembl T28A8.7
Entrez Gene 176783 Entrez gene
SwissProt Q9XU10 EMBL-EBI
WormBase CE35190 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6298 mismatch repair inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
5524 ATP binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB07283 Hypothetical protein T28A8.7 [Caenorhabditis elegans] ref|NP_499796.2| MLH (MutL Homolog) family member (mlh-1) [Caenorhabditis elegans] 0.0
blast CAE69257 Hypothetical protein CBG15306 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR002099 EMBL-EBI DNA mismatch repair protein 8.3E-13
Pfam IPR003594 EMBL-EBI ATP-binding region, ATPase-like 1.6E-7
Sequence
Target Sequence 
>C. ELEGANS:192890_S_AT
tgctccgagagtttttctaccagatttccgttttctcgttcggcaattacggatcctatc
gactcgacgaggagccgccggcaatcatcgaaattcttgaacttcttggagagctgagca
ctcgtgagccaaattacgcggctttcgaagtttttgcaaacgtggaaaatcgatttgcgg
cggagaagttgctcgccgagcacgctgacctgcttcacgactattttgccataaagttag
atcagctggagaatgggaggcttcatatcactgagattccatcactggtgcattattttg
tgccac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGCTCCGAGAGTTTTTCTACCAGAT 571 581 1736 Antisense
TCCGTTTTCTCGTTCGGCAATTACG 364 591 1762 Antisense
GGCAATTACGGATCCTATCGACTCG 637 519 1777 Antisense
CGAGGAGCCGCCGGCAATCATCGAA 578 249 1803 Antisense
TGGAGAGCTGAGCACTCGTGAGCCA 60 549 1842 Antisense
GCCAAATTACGCGGCTTTCGAAGTT 582 275 1863 Antisense
TGCGGCGGAGAAGTTGCTCGCCGAG 360 583 1911 Antisense
GCTTCACGACTATTTTGCCATAAAG 494 305 1947 Antisense
GAATGGGAGGCTTCATATCACTGAG 105 333 1986 Antisense
TATCACTGAGATTCCATCACTGGTG 55 659 2001 Antisense
TCACTGGTGCATTATTTTGTGCCAC 228 627 2017 Antisense
Sequence Source Affymetrix Proprietary Database