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[192069_s_at] chromosome segregation protein

Description F35G12.8 /REP_DB=WormBase Gene ID /WP=CE03287 /TR=Q20060 /GB=CAA86336.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=chromosome segregation protein
Cluster 6grp_highest_10_10 > 85      6grp_high1_10_10 > 57      4grp_highest_8_8 > 41      4grp_high_8_8 > 49      6grp_highest_nonorm > 84      6grp_total > 58      4grp_total > 62      6grp_highest_sub > Cu      6grp_cgc > 28      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 556
1 2 3 4 range
A 816.8
(3)
P 		496.6
(-1.1)
P 		555.3
(-0.3)
P 		345.4
(-3)
P 		471
B 569.3
(3)
P 		464.8
(0.7)
P 		456.3
(0.5)
P 		294.1
(-3)
P 		275
C 694.5
(3)
P 		522.2
(0.6)
P 		567.3
(1.2)
P 		260.7
(-3)
P 		434
avr 693.5
(3) 		494.5
(-0) 		526.3
(0.4) 		300.1
(-3) 		393

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 686
1 2 3 4 5 6 range
A 634
(-0.3)
P 		599.4
(-0.6)
P 		328.6
(-3)
P 		488.7
(-1.6)
P 		551.4
(-1.1)
P 		1014.7
(3)
P 		686
B 753.3
(1.2)
P 		512.4
(-2.2)
P 		461.5
(-3)
P 		459.7
(-3)
P 		511.2
(-2.3)
P 		879.8
(3)
P 		420
C 806.5
(1.4)
P 		496.5
(-2.6)
P 		469.4
(-3)
P 		534.1
(-2.2)
P 		582.6
(-1.5)
P 		933.8
(3)
P 		464
avr 731.3
(0.6) 		536.1
(-1.7) 		419.8
(-3) 		494.2
(-2.1) 		548.4
(-1.5) 		942.8
(3) 		523
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 253
1 2 3 4 range
A 297.4
(3)
P 		107.8
(-1.6)
P 		145.2
(-0.7)
P 		50.6
(-3)
P 		247
B 181.6
(3)
P 		114.8
(-0.4)
P 		105.7
(-0.8)
P 		62.7
(-3)
P 		119
C 229.9
(3)
P 		150.1
(0.4)
P 		197.7
(2)
P 		44
(-3)
P 		186
avr 236.3
(3) 		124.2
(-0.7) 		149.5
(0.2) 		52.4
(-3) 		184

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 257
1 2 3 4 5 6 range
A 116.9
(-1.5)
P 		213.2
(1.8)
P 		71.6
(-3)
P 		123.9
(-1.2)
P 		166.4
(0.2)
P 		247
(3)
P 		175
B 262.1
(1.2)
P 		170.6
(-1.4)
P 		112.1
(-3)
P 		121.8
(-2.7)
P 		207.7
(-0.3)
P 		328.1
(3)
P 		216
C 298.9
(2.6)
P 		151.5
(-1.7)
P 		119.5
(-2.6)
P 		107.4
(-3)
P 		188.5
(-0.6)
P 		312.6
(3)
P 		205
avr 226
(0.8) 		178.4
(-0.6) 		101.1
(-3) 		117.7
(-2.5) 		187.5
(-0.3) 		295.9
(3) 		195
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 192069_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7761
Sequence Type Exemplar sequence
Representative Public ID F35G12.8 NCBI
Target Description F35G12.8 /REP_DB=WormBase Gene ID /WP=CE03287 /TR=Q20060 /GB=CAA86336.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=chromosome segregation 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_065534(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065534 NCBI Caenorhabditis elegans SMC (structural maintenance of chromosomes) family member (smc-4) (smc-4) mRNA, complete cds. 11/11 None
SNAP00000042243 ENSEMBL cdna:SNAP chromosome:CEL140:III:4587471:4592785:1 11/11 None
GENEFINDER00000042258 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:4587471:4592785:1 11/11 None
F35G12.8 ENSEMBL cdna:known chromosome:CEL140:III:4587471:4593074:1 gene:F35G12.8 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:4587470-4592785(+) 100.0 100.0
Public Domain and Genome References
Gene Title chromosome segregation protein
Gene Symbol smc-4
Ensembl F35G12.8
Entrez Gene 175603 Entrez gene
SwissProt Q20060 EMBL-EBI
WormBase CE03287 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
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 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) 0.0
blast CAE71177 Hypothetical protein CBG18034 [Caenorhabditis briggsae] 0.0
blast P50532 Structural maintenance of chromosome 4 (Chromosome-associated protein C) (Chromosome assembly protein XCAP-C) gb|AAA64679.1| XCAP-C 1.0E-169
Protein Domains
Database ID Description E-Value
Pfam IPR003405 EMBL-EBI Structural maintenance of chromosome protein SMC, C-terminal 3.5E-122
Pfam IPR003395 EMBL-EBI SMC protein, N-terminal 2.9E-84
Pfam IPR010935 EMBL-EBI SMCs flexible hinge 9.8E-38
Pfam IPR003405 EMBL-EBI Structural maintenance of chromosome protein SMC, C-terminal 3.5E-122
Pfam IPR010935 EMBL-EBI SMCs flexible hinge 6.2E-21
Sequence
Target Sequence 
>C. ELEGANS:192069_S_AT
atatgtttgaactcgccaatcgtctcgttggtatctataaagttgatgggtgtactcgta
atgtagccattgatccattgagagtttgtgagatggcgaagcaaattacggacagtttgg
ggcaggccacgtgtactcttcctgatgaagtaactcaacgattcaatgagacaatgagtc
ggcagaataaggaaatgattgcacaagaaaaacaatatccgaacttcccatcatcaaatg
agatttcaaaggccgaaaagattgttaacgttgaaggacgtgtcaggaaagaattgattc
aaactacccgagatgtcacttcaagaccacaatccaaagcaacgacaagtggcgatggaa
ctgaaagaccggctagtcggtcagcaagtcgacccgaatctcgtataaatcaaatgaaat
atcctgctccacgccttgtcgaaagatcgtcgtcacagaatgttcgtagcccgagaaagg
cacgaaacatagaggccgatgagactactccaccttcaaagcgttcaaattccgcaagta
caccaaaacgatctccaatgaaaccgttgacaccgtcgagta

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATATGTTTGAACTCGCCAATCGTCT 387 21 4034 Antisense
GGACAGTTTGGGGCAGGCCACGTGT 12 527 4143 Antisense
CCACGTGTACTCTTCCTGATGAAGT 543 273 4160 Antisense
ATATCCGAACTTCCCATCATCAAAT 460 21 4248 Antisense
ATTGATTCAAACTACCCGAGATGTC 9 5 4326 Antisense
GATGTCACTTCAAGACCACAATCCA 650 409 4345 Antisense
TCAGCAAGTCGACCCGAATCTCGTA 46 625 4414 Antisense
GCTCCACGCCTTGTCGAAAGATCGT 351 297 4459 Antisense
GTCGTCACAGAATGTTCGTAGCCCG 181 473 4482 Antisense
CGTTCAAATTCCGCAAGTACACCAA 609 245 4555 Antisense
ATGAAACCGTTGACACCGTCGAGTA 316 43 4591 Antisense
Sequence Source Affymetrix Proprietary Database