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[188079_s_at] --- /// recombiation protein

Description T02G5.6 /REP_DB=WormBase Gene ID /WP=CE04858 /GEN=msh-4 /TR=Q22103 /GB=AAA82400.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation
Cluster 6grp_high1_10_10 > 98      6grp_total > 96      4grp_total > 09      6grp_cgc > 78      6grp_high1_sub > In      6grp_cgc_sub > In      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 67
1 2 3 4 range
A 20
(-2.2)
P 		16.1
(-3)
A 		47
(3)
A 		39.7
(1.6)
M 		31
B 35.7
(-0.1)
A 		47.8
(1.4)
A 		12
(-3)
A 		60.8
(3)
P 		49
C 18.8
(-3)
A 		20.4
(-2.8)
A 		24.5
(-2.4)
P 		79.3
(3)
P 		61
avr 24.8
(-3) 		28.1
(-2.4) 		27.8
(-2.5) 		59.9
(3) 		35

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 180
1 2 3 4 5 6 range
A 7.3
(-3)
A 		27.7
(-2.1)
P 		77.9
(-0)
P 		52.3
(-1.1)
P 		120.6
(1.7)
P 		150.6
(3)
P 		143
B 18.4
(-3)
P 		43.9
(-2.1)
A 		45.4
(-2)
A 		73.1
(-1.1)
P 		155.5
(1.9)
P 		187.3
(3)
P 		169
C 18.4
(-3)
A 		52.6
(-1.6)
P 		56.7
(-1.5)
M 		87.6
(-0.2)
P 		169
(3)
P 		143
(2)
P 		151
avr 14.7
(-3) 		41.4
(-1.9) 		60
(-1.1) 		71
(-0.7) 		148.4
(2.5) 		160.3
(3) 		146
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 11
1 2 3 4 range
A 7.3
(-0.4)
P 		3.5
(-3)
A 		12.3
(3)
A 		5.8
(-1.4)
M 		9
B 11.4
(2.1)
A 		11.8
(2.3)
A 		2.8
(-3)
A 		13
(3)
P 		10
C 6.2
(-2.8)
A 		5.9
(-3)
A 		8.5
(-0.9)
P 		13.4
(3)
P 		8
avr 8.3
(-1) 		7.1
(-3) 		7.9
(-1.7) 		10.7
(3) 		4

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 69
1 2 3 4 5 6 range
A 1.4
(-3)
A 		9.8
(-1.6)
P 		17
(-0.3)
P 		13.3
(-1)
P 		36.4
(2.9)
P 		36.7
(3)
P 		35
B 6.4
(-3)
P 		14.6
(-2.2)
A 		11
(-2.6)
A 		19.4
(-1.8)
P 		63.2
(2.4)
P 		69.9
(3)
P 		64
C 6.8
(-3)
A 		16.1
(-1.8)
P 		14.4
(-2)
M 		17.6
(-1.6)
P 		54.7
(3)
P 		47.9
(2.1)
P 		48
avr 4.9
(-3) 		13.5
(-1.9) 		14.1
(-1.8) 		16.8
(-1.5) 		51.4
(3) 		51.5
(3) 		47
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 188079_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.5890
Sequence Type Exemplar sequence
Representative Public ID T02G5.6 NCBI
Target Description T02G5.6 /REP_DB=WormBase Gene ID /WP=CE04858 /GEN=msh-4 /TR=Q22103 /GB=AAA82400.1 /SUBMIT=ST.LOUIS /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_063057(11), NM_063050(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063057 NCBI Caenorhabditis elegans MSH (MutS Homolog) family member (msh-4) (msh-4) mRNA, complete cds. 11/11 None
NM_063050 NCBI Caenorhabditis elegans High Incidence of Males (increased X chromosome loss) family member (him-14) (him-14) mRNA, complete cds. 11/11 A 
SNAP00000014285 ENSEMBL cdna:SNAP chromosome:CEL140:II:7078080:7078388:1 11/11 None
GENEFINDER00000014301 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:7078080:7078388:1 11/11 None
ZK1127.11 ENSEMBL cdna:known chromosome:CEL140:II:7064985:7069896:-1 gene:ZK1127.11 11/11 A 
T02G5.6 ENSEMBL cdna:known chromosome:CEL140:II:7078080:7078497:1 gene:T02G5.6 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:7078075-7078493(+) 100.0 100.0
chrII:7066771-7067186(-) 97.22 97.22
Public Domain and Genome References
Gene Title
recombiation protein
Gene Symbol msh-4
him-14
Ensembl ZK1127.11
T02G5.6
Entrez Gene 174157 Entrez gene
191708 Entrez gene
SwissProt Q22103 EMBL-EBI
Q23405 EMBL-EBI
WormBase CE04858 Wormbase
CE24714 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:17491_AT DNA mismatch repair MutS family protein at
ATH1-121501:245419_AT DNA mismatch repair MutS family protein at
CANINE_2:CFAAFFX.31219.1.S1_AT similar to MutS protein homolog 4 cfa
HG-U133_PLUS_2:210533_AT mutS homolog 4 (E. coli) hs
HG-U133A:210533_AT mutS homolog 4 (E. coli) hs
HG-FOCUS:210533_AT mutS homolog 4 (E. coli) hs
HG-U133A_2:210533_AT mutS homolog 4 (E. coli) hs
HG-U95AV2:31714_AT mutS homolog 4 (E. coli) hs
U133_X3P:G4336727_3P_AT mutS homolog 4 (E. coli) hs
MOUSE430_2:1419511_AT mutS homolog 4 (E. coli) mm
MOE430A:1419511_AT mutS homolog 4 (E. coli) mm
MOUSE430A_2:1419511_AT mutS homolog 4 (E. coli) mm
MG-U74CV2:165550_AT mutS homolog 4 (E. coli) mm
YEAST_2:1776312_AT Protein involved in meiotic recombination, required for normal levels of crossing over, colocalizes with Zip2p to discrete foci on meiotic chromosomes, has homology to bacterial MutS protein Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6298 mismatch repair inferred from electronic annotation QuickGO AmiGO
6259 DNA metabolism 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 AAB93433 High incidence of males (increased x chromosome loss) protein 14 [Caenorhabditis elegans] ref|NP_495451.1| High Incidence of Males (increased X chromosome loss) family member (him-14) [Caenorhabditis elegans] gb|AAD52669.1| HIM-14 protein [Caenorhabditis elegans] sp|Q23405|HIM14_CAEEL MUTS protein homolog him-14 0.0
blast E88197 protein him-14 [imported] - Caenorhabditis elegans 0.0
blast CAE56902 Hypothetical protein CBG24743 [Caenorhabditis briggsae] 0.0
blast NP_495458 MSH (MutS Homolog) family member (msh-4) [Caenorhabditis elegans] gb|AAA82400.1| Msh (muts homolog) family protein 4 [Caenorhabditis elegans] 1.0E-54
blast AAB93433 High incidence of males (increased x chromosome loss) protein 14 [Caenorhabditis elegans] ref|NP_495451.1| High Incidence of Males (increased X chromosome loss) family member (him-14) [Caenorhabditis elegans] gb|AAD52669.1| HIM-14 protein [Caenorhabditis elegans] sp|Q23405|HIM14_CAEEL MUTS protein homolog him-14 1.0E-52
blast E88197 protein him-14 [imported] - Caenorhabditis elegans 1.0E-52
Protein Domains
Database ID Description E-Value
Pfam IPR000432 EMBL-EBI DNA mismatch repair protein MutS, C-terminal 3.6E-18
Pfam IPR000432 EMBL-EBI DNA mismatch repair protein MutS, C-terminal 2.4E-20
Pfam IPR000432 EMBL-EBI DNA mismatch repair protein MutS, C-terminal 2.9E-21
Pfam IPR007861 EMBL-EBI MutS IV 6.0E-16
Pfam IPR007696 EMBL-EBI MutS III 1.6E-16
Pfam IPR000432 EMBL-EBI DNA mismatch repair protein MutS, C-terminal 1.7E-70
Sequence
Target Sequence 
>C. ELEGANS:188079_S_AT
gggtcataacgacgagttgatcagaaataagtctgcatttgcatctgaaatgtcagatgc
agctgcaatcgtacagtatgccgataaaaactcacttgtagttcttgatgagctagcacg
aagcacatcgactgaagaaggaatcgccatcacctatgcgatttgtgagaaggttctaaa
gttacatagctataccttcctggctacacattttctcgatattgcagctctcgccaacta
ttcaaatgcaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGGTCATAACGACGAGTTGATCAGA 120 497 15 Antisense
GAAATAAGTCTGCATTTGCATCTGA 125 363 38 Antisense
TGAAATGTCAGATGCAGCTGCAATC 397 571 60 Antisense
GCAGCTGCAATCGTACAGTATGCCG 270 313 73 Antisense
GTATGCCGATAAAAACTCACTTGTA 144 455 90 Antisense
AAAACTCACTTGTAGTTCTTGATGA 442 129 101 Antisense
GTAGTTCTTGATGAGCTAGCACGAA 398 455 112 Antisense
ATCGCCATCACCTATGCGATTTGTG 608 37 157 Antisense
TTCCTGGCTACACATTTTCTCGATA 471 699 211 Antisense
TGGCTACACATTTTCTCGATATTGC 386 545 215 Antisense
GCTCTCGCCAACTATTCAAATGCAA 644 299 241 Antisense
Sequence Source Affymetrix Proprietary Database