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[188603_s_at] chromosome segregation protein (SMC-1)

Description R13G10.1 /REP_DB=WormBase Gene ID /WP=CE01052 /GEN=dpy-27 /TR=SW:P48996 /GB=CAA84669.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 64      6grp_high1_10_10 > 46      4grp_highest_8_8 > 62      4grp_high_8_8 > 18      6grp_highest_nonorm > 60      6grp_total > 45      4grp_total > 30      6grp_highest_sub > Cu      6grp_cgc > 35      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 383
1 2 3 4 range
A 542.1
(3)
P 		512.1
(2.4)
P 		257.1
(-3)
P 		460.5
(1.3)
P 		285
B 640.2
(3)
P 		349.4
(-3)
P 		403.6
(-1.9)
P 		538
(0.9)
P 		291
C 579.6
(2.8)
P 		346.7
(-1.7)
P 		279.7
(-3)
P 		588.8
(3)
P 		309
avr 587.3
(3) 		402.7
(-1) 		313.5
(-3) 		529.1
(1.7) 		274

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 404
1 2 3 4 5 6 range
A 485.1
(2.6)
P 		479.4
(2.5)
P 		399.3
(1)
P 		364.2
(0.4)
P 		181.6
(-3)
P 		504.9
(3)
P 		323
B 572.3
(3)
P 		392
(0.3)
P 		491.1
(1.8)
P 		312
(-0.9)
P 		168.2
(-3)
P 		394.5
(0.4)
P 		404
C 402.3
(1)
P 		423.6
(1.4)
P 		491.8
(2.7)
P 		347.6
(0)
P 		187.3
(-3)
P 		506.5
(3)
P 		319
avr 486.6
(3) 		431.7
(1.9) 		460.7
(2.5) 		341.3
(0.2) 		179
(-3) 		468.6
(2.6) 		308
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 137
1 2 3 4 range
A 197.4
(3)
P 		111.2
(-1)
P 		67.2
(-3)
P 		67.4
(-3)
P 		130
B 204.1
(3)
P 		86.3
(-3)
P 		93.5
(-2.6)
P 		114.6
(-1.6)
P 		118
C 191.9
(3)
P 		99.7
(-2.9)
P 		97.5
(-3)
P 		99.3
(-2.9)
P 		94
avr 197.8
(3) 		99.1
(-2.3) 		86.1
(-3) 		93.8
(-2.6) 		112

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 144
1 2 3 4 5 6 range
A 89.4
(-1.2)
P 		170.5
(3)
P 		87
(-1.3)
P 		92.4
(-1.1)
P 		54.8
(-3)
P 		122.9
(0.5)
P 		116
B 199.1
(3)
P 		130.5
(-0.1)
P 		119.3
(-0.7)
P 		82.6
(-2.3)
P 		68.3
(-3)
P 		147.1
(0.6)
P 		131
C 149.1
(1.9)
P 		129.3
(0.8)
P 		125.2
(0.6)
P 		69.9
(-2.5)
P 		60.6
(-3)
P 		169.6
(3)
P 		109
avr 145.9
(3) 		143.4
(2.8) 		110.5
(0.5) 		81.6
(-1.6) 		61.2
(-3) 		146.5
(3) 		85
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 188603_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7432
Sequence Type Exemplar sequence
Representative Public ID R13G10.1 NCBI
Target Description R13G10.1 /REP_DB=WormBase Gene ID /WP=CE01052 /GEN=dpy-27 /TR=SW:P48996 /GB=CAA84669.1 /SUBMIT=HINXTON /CHR=3 /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_065370(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065370 NCBI Caenorhabditis elegans DumPY : shorter than wild-type family member (dpy-27) (dpy-27) mRNA, complete cds. 11/11 None
SNAP00000032874 ENSEMBL cdna:SNAP chromosome:CEL140:III:3813887:3819655:-1 11/11 None
GENEFINDER00000032879 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:3813887:3819655:-1 11/11 None
R13G10.1 ENSEMBL cdna:known chromosome:CEL140:III:3813531:3819655:-1 gene:R13G10.1 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:3813886-3819655(-) 100.0 100.0
Public Domain and Genome References
Gene Title chromosome segregation protein (SMC-1)
Gene Symbol dpy-27
Ensembl R13G10.1
Entrez Gene 175492 Entrez gene
SwissProt P48996 EMBL-EBI
WormBase CE01052 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6810 transport inferred from electronic annotation QuickGO AmiGO
7059 chromosome segregation inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5634 nucleus inferred from electronic annotation QuickGO AmiGO
16020 membrane inferred from electronic annotation QuickGO AmiGO
5634 nucleus inferred from direct assay QuickGO AmiGO
228 nuclear chromosome inferred from direct assay 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 CAA84669 Hypothetical protein R13G10.1 [Caenorhabditis elegans] ref|NP_497771.1| DumPY : shorter than wild-type family member (dpy-27) [Caenorhabditis elegans] sp|P48996|DPY27_CAEEL Chromosome condensation protein dpy-27 (Dumpty-27 protein) gb|AAA62647.1| chromosome condensation protein 0.0
blast CAE72848 Hypothetical protein CBG20143 [Caenorhabditis briggsae] 0.0
blast CAA86336 Hypothetical protein F35G12.8 [Caenorhabditis elegans] ref|NP_497935.1| SMC (structural maintenance of chromosomes) family member (smc-4) [Caenorhabditis elegans] sp|Q20060|SMC4_CAEEL Structural maintenance of chromosome 4 (Protein smc-4) 1.0E-169
Protein Domains
Database ID Description E-Value
Pfam IPR003405 EMBL-EBI Structural maintenance of chromosome protein SMC, C-terminal 2.6E-110
Pfam IPR003395 EMBL-EBI SMC protein, N-terminal 6.7E-85
Pfam IPR010935 EMBL-EBI SMCs flexible hinge 1.5E-37
Sequence
Target Sequence 
>C. ELEGANS:188603_S_AT
caacacccctctacgtgatggatgaaatcgatgcggcactggacttgaacaatgtcagcc
tgattgcaaactatatcaagcattccgagcgaacacggaacgctcaatttatcataattt
cgcttcgaaatcaaatgttcgaggtcggaaatcgcttgcttggtatctataaaatcgatg
gaaaaacttataacattatggtggatccgatcgcggtggagatcaagaatcgtccgattt
tgaagattttcgaggaggagatcaaacggcgcgagaagctacgacgtgccgagattgaac
cggaaattgatttgagtaatgggctcagcaatgtcgttattgcaccaaaacgtaaacaac
gccggctggaaatgctgaaactctcggactttggtctcgatgatgacagtgatcttcctg
aatttaatagattcccacccgcaactcgtcgtgaattaagtgttgaggattcagatgaag
acgatgagccagtaagaagacgtccgcgtcgtcaagttgaagaggaagatgaagaggatg
aattgatcgaagaagcaactccatctccac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CAACACCCCTCTACGTGATGGATGA 708 187 3809 Antisense
TCGATGCGGCACTGGACTTGAACAA 433 601 3836 Antisense
AACACGGAACGCTCAATTTATCATA 7 137 3900 Antisense
GAGGTCGGAAATCGCTTGCTTGGTA 218 403 3949 Antisense
GTGGATCCGATCGCGGTGGAGATCA 611 489 4009 Antisense
ACGGCGCGAGAAGCTACGACGTGCC 283 95 4074 Antisense
AACAACGCCGGCTGGAAATGCTGAA 345 135 4163 Antisense
GAAACTCTCGGACTTTGGTCTCGAT 211 357 4185 Antisense
CACCCGCAACTCGTCGTGAATTAAG 330 199 4244 Antisense
GAGCCAGTAAGAAGACGTCCGCGTC 395 385 4294 Antisense
ATCGAAGAAGCAACTCCATCTCCAC 458 37 4354 Antisense
Sequence Source Affymetrix Proprietary Database