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[171990_x_at] chromosome segregation protein (SMC-1)

Description AV198973_rc /REP_DB=TREMBL Accession /GB=AV198973 /FEA=Transcript Cluster /DEF=Caenorhabditis elegans cDNA clone:yk407c9 : 3prime end, single read.
Cluster 4grp_high_8_8 > 05      6grp_total > 43      4grp_total > 19      6grp_cgc > 80      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 130
1 2 3 4 range
A 119.5
(-0)
A 		118.8
(-0.1)
P 		164
(3)
P 		75.6
(-3)
M 		88
B 112.1
(0.4)
A 		121.1
(1.2)
M 		75.7
(-3)
P 		140.8
(3)
M 		65
C 128.6
(-1.4)
P 		129.1
(-1.4)
M 		101.7
(-3)
P 		205.1
(3)
P 		103
avr 120.1
(-1.6) 		123
(-0.9) 		113.8
(-3) 		140.5
(3) 		27

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 72
1 2 3 4 5 6 range
A 100.3
(0.7)
A 		83.8
(-1.1)
P 		121.9
(3)
P 		95.7
(0.2)
M 		98.6
(0.5)
M 		66.5
(-3)
A 		55
B 118.2
(3)
P 		115.3
(2.6)
P 		104.3
(1.2)
P 		70.6
(-3)
A 		79.9
(-1.8)
A 		89.9
(-0.6)
M 		48
C 123.1
(2)
M 		103.8
(0.4)
M 		127.3
(2.3)
P 		62.9
(-3)
A 		135.2
(3)
P 		91.6
(-0.6)
M 		72
avr 113.9
(2.4) 		101
(0.6) 		117.8
(3) 		76.4
(-3) 		104.6
(1.1) 		82.7
(-2.1) 		41
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 32
1 2 3 4 range
A 43.5
(3)
A 		25.8
(-0.3)
P 		42.9
(2.9)
P 		11.1
(-3)
M 		32
B 35.8
(3)
A 		29.9
(1.1)
M 		17.5
(-3)
P 		30
(1.1)
M 		18
C 42.6
(3)
P 		37.1
(-1.1)
M 		35.4
(-2.4)
P 		34.6
(-3)
P 		8
avr 40.6
(3) 		30.9
(-0.8) 		31.9
(-0.4) 		25.2
(-3) 		15

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 33
1 2 3 4 5 6 range
A 18.5
(-2)
A 		29.8
(3)
P 		26.6
(1.6)
P 		24.3
(0.6)
M 		29.8
(3)
M 		16.2
(-3)
A 		14
B 41.1
(3)
P 		38.4
(2.3)
P 		25.3
(-1.2)
P 		18.7
(-3)
A 		32.4
(0.7)
A 		33.5
(1)
M 		22
C 45.6
(3)
M 		31.7
(0.5)
M 		32.4
(0.6)
P 		12.7
(-3)
A 		43.8
(2.7)
P 		30.6
(0.3)
M 		33
avr 35.1
(2.9) 		33.3
(2.3) 		28.1
(0.4) 		18.6
(-3) 		35.3
(3) 		26.8
(-0.1) 		17
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 171990_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.27601
Sequence Type Exemplar sequence
Representative Public ID AV198973 NCBI
Target Description AV198973_rc /REP_DB=TREMBL Accession /GB=AV198973 /FEA=Transcript Cluster /DEF=Caenorhabditis elegans cDNA clone:yk407c9 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Transcript Cluster.
Annotation Method Description
Annotation Description This probe set was annotated using the Genome Target Overlap based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade B annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_065370
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
SNAP00000032874 ENSEMBL cdna:SNAP chromosome:CEL140:III:3813887:3819655:-1 None
GENEFINDER00000032879 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:3813887:3819655:-1 None
R13G10.1 ENSEMBL cdna:known chromosome:CEL140:III:3813531:3819655:-1 gene:R13G10.1 A 
NM_065370 NCBI Caenorhabditis elegans DumPY : shorter than wild-type family member (dpy-27) (dpy-27) mRNA, complete cds. 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
chrIII:3813676-3813949(-) 76.9 76.9
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:171990_X_AT
ggaggaagcaaatccatttccaccaccaattgttgtttaaccccgtgtgcggaggagcag
anattaaattgnagtaatanattttaaactaaattttggnnnnnnnnaagaaaactttgt
gnnnnntccaanaaatgagaccaactttctttccaagcttgtattttntaatattcgtct
agcttaannnnngccttgtgattttaattatttccct

BLASTn GenBank NR
Note: "n"'s represent regions that are not probed by the probe sequences.
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGAGGAAGCAAATCCATTTCCACCA 562 513 62 Antisense
AGGAAGCAAATCCATTTCCACCACC 95 55 64 Antisense
CATTTCCACCACCAATTGTTGTTTA 21 215 76 Antisense
CAATTGTTGTTTAACCCCGTGTGCG 641 179 88 Antisense
TGTTTAACCCCGTGTGCGGAGGAGC 485 1 95 Antisense
TTAACCCCGTGTGCGGAGGAGCAGA 647 683 98 Antisense
AATGAGACCAACTTTCTTTCCAAGC 346 165 195 Antisense
TGAGACCAACTTTCTTTCCAAGCTT 36 567 197 Antisense
ACCAACTTTCTTTCCAAGCTTGTAT 448 85 201 Antisense
CAACTTTCTTTCCAAGCTTGTATTT 366 189 203 Antisense
GCCTTGTGATTTTAATTATTTCCCT 343 281 254 Antisense
Sequence Source Affymetrix Proprietary Database