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[193295_at] DNA double-strand break repair

Description F10G7.4 /REP_DB=WormBase Gene ID /WP=CE02628 /GEN=coh-2 /TR=Q19325 /GB=AAA81127.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=DNA double-strand break repair
Cluster 6grp_highest_10_10 > 87      6grp_high1_10_10 > 87      6grp_highest_nonorm > 92      6grp_total > 87      4grp_total > 59      6grp_highest_sub > Da      6grp_cgc > 49      6grp_high1_sub > In      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 209
1 2 3 4 range
A 202.5
(1.5)
P 		224.2
(3)
P 		221.5
(2.8)
P 		138.2
(-3)
A 		86
B 199.2
(-0.2)
P 		240.8
(1.1)
P 		298.7
(3)
P 		111.1
(-3)
A 		188
C 207.9
(2.1)
P 		214.6
(2.4)
P 		227.5
(3)
P 		89.3
(-3)
A 		138
avr 203.2
(1) 		226.5
(2) 		249.2
(3) 		112.9
(-3) 		136

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 448
1 2 3 4 5 6 range
A 211.1
(-1.9)
P 		172.5
(-2.5)
P 		132.6
(-3)
P 		185.3
(-2.3)
P 		346.9
(-0.1)
P 		580.6
(3)
P 		448
B 205.4
(-2.5)
P 		192.9
(-2.7)
P 		178.3
(-3)
P 		235.2
(-2)
P 		319.3
(-0.5)
P 		513.2
(3)
P 		335
C 193.6
(-2.6)
P 		166.8
(-3)
P 		179.8
(-2.8)
P 		249
(-1.7)
P 		306.6
(-0.8)
P 		552.7
(3)
P 		386
avr 203.4
(-2.4) 		177.4
(-2.8) 		163.6
(-3) 		223.2
(-2.1) 		324.3
(-0.5) 		548.8
(3) 		385
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 64
1 2 3 4 range
A 73.7
(3)
P 		48.7
(0.2)
P 		57.9
(1.2)
P 		20.2
(-3)
A 		54
B 63.5
(2.2)
P 		59.5
(1.7)
P 		69.2
(3)
P 		23.7
(-3)
A 		46
C 68.8
(2)
P 		61.7
(1.4)
P 		79.3
(3)
P 		15.1
(-3)
A 		64
avr 68.7
(3) 		56.6
(1.5) 		68.8
(3) 		19.7
(-3) 		49

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 163
1 2 3 4 5 6 range
A 38.9
(-2.5)
P 		61.3
(-1.3)
P 		28.9
(-3)
P 		47
(-2)
P 		104.7
(1)
P 		141.4
(3)
P 		113
B 71.5
(-1.9)
P 		64.2
(-2.2)
P 		43.3
(-3)
P 		62.3
(-2.2)
P 		129.7
(0.5)
P 		191.4
(3)
P 		148
C 71.8
(-1.9)
P 		50.9
(-2.8)
P 		45.8
(-3)
P 		50.1
(-2.8)
P 		99.2
(-0.7)
P 		185
(3)
P 		139
avr 60.7
(-2) 		58.8
(-2.1) 		39.3
(-3) 		53.1
(-2.4) 		111.2
(0.2) 		172.6
(3) 		133
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193295_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.4102
Sequence Type Exemplar sequence
Representative Public ID F10G7.4 NCBI
Target Description F10G7.4 /REP_DB=WormBase Gene ID /WP=CE02628 /GEN=coh-2 /TR=Q19325 /GB=AAA81127.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=DNA double-strand break repair
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_062435(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_062435 NCBI Caenorhabditis elegans yeast SCC (mitotic condensin subunit) homolog family member (scc-1) (scc-1) mRNA, complete cds. 11/11 None
SNAP00000005194 ENSEMBL cdna:SNAP chromosome:CEL140:II:4698708:4700784:1 11/11 None
GENEFINDER00000005209 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:4698708:4700784:1 11/11 None
F10G7.4.2 ENSEMBL cdna:known chromosome:CEL140:II:4698706:4700977:1 gene:F10G7.4 11/11 None
F10G7.4.1 ENSEMBL cdna:known chromosome:CEL140:II:4698708:4700977:1 gene:F10G7.4 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:4698706-4700783(+) 100.0 100.0
Public Domain and Genome References
Gene Title DNA double-strand break repair
Gene Symbol scc-1
Ensembl F10G7.4
Entrez Gene 173808 Entrez gene
SwissProt Q19325 EMBL-EBI
WormBase CE02628 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:251485_AT cohesion family protein SYN3 (SYN3) at
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
7001 chromosome organization and biogenesis (sensu Eukaryota) inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
228 nuclear chromosome inferred from electronic annotation QuickGO AmiGO
5634 nucleus inferred from direct assay QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3684 damaged DNA binding inferred from sequence similarity QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast NP_494836 yeast SCC (mitotic condensin subunit) homolog family member (scc-1) [Caenorhabditis elegans] gb|AAA81127.1| Yeast scc (mitotic condensin subunit) homolog protein 1 [Caenorhabditis elegans] 0.0
blast CAE60649 Hypothetical protein CBG04295 [Caenorhabditis briggsae] 1.0E-171
Protein Domains
Database ID Description E-Value
Pfam IPR006910 EMBL-EBI Rad21/Rec8 like protein, N-terminal 3.9E-62
Pfam IPR006909 EMBL-EBI Rad21/Rec8 like protein, C-terminal 1.2E-25
Sequence
Target Sequence 
>C. ELEGANS:193295_AT
atattcaagcgcagggaccagccgttgatgaattctttaatgatgtgcgcatggatgatg
atgatgacagacaaccagctcaggaaatggactttggtgacaacttcgattttccacaag
aagtagaacatcaagagtgtgctccgatccctatccagagtggattcgctggagagaaca
aagagaacgaggacgcagaggattggtctgatccgttcggttcttcaaattccagcagac
gtggccagcttgaagcctatggattcggaaatacttcgacctacaaggaagacgatggca
aatgggcgaaacgcgccaagcacattctaaagaaagtctccgcggatattgagacttcgg
gacaagcggacttctcatctgtcacagcaactgccaagaatcgcaagcaagctgcagagc
aattttattcgttgcttaccctggccaagtctcaagcaataagtgttgatcaatcagagc
catacggagagatcgtaattcgtccaggagccaatttcaaagaagcatgtccactgagct
ctccgaaaccgatgggactt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATATTCAAGCGCAGGGACCAGCCGT 238 19 1340 Antisense
ACATCAAGAGTGTGCTCCGATCCCT 640 103 1467 Antisense
AGGATTGGTCTGATCCGTTCGGTTC 599 57 1538 Antisense
CGTTCGGTTCTTCAAATTCCAGCAG 318 245 1553 Antisense
TTCCAGCAGACGTGGCCAGCTTGAA 407 701 1569 Antisense
GAAACGCGCCAAGCACATTCTAAAG 538 357 1647 Antisense
TTCTCATCTGTCACAGCAACTGCCA 509 691 1711 Antisense
CAATTTTATTCGTTGCTTACCCTGG 234 181 1759 Antisense
AGAGATCGTAATTCGTCCAGGAGCC 285 67 1827 Antisense
AAGAAGCATGTCCACTGAGCTCTCC 227 153 1859 Antisense
GAGCTCTCCGAAACCGATGGGACTT 79 389 1875 Antisense
Sequence Source Affymetrix Proprietary Database