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[193972_at] S. pombe double-strand-break repair protein, RAD21

Description K08A8.3 /REP_DB=WormBase Gene ID /WP=CE04726 /GEN=coh-1 /TR=Q21306 /GB=AAA79748.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=S. pombe double-strand-break repair protein, RAD21
Cluster 6grp_highest_10_10 > 51      6grp_high1_10_10 > 16      4grp_highest_8_8 > 58      4grp_high_8_8 > 33      6grp_highest_nonorm > 90      6grp_total > 25      4grp_total > 46      6grp_highest_sub > De      6grp_cgc > 24      6grp_high1_sub > De      6grp_cgc_sub > Cu      6grp_total_sub > Decrease      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 141
1 2 3 4 range
A 195.5
(3)
P 		163.9
(-0.1)
P 		133.8
(-3)
P 		144.1
(-2)
P 		62
B 239.5
(3)
P 		140.2
(-1.3)
P 		115.8
(-2.3)
P 		99.8
(-3)
P 		140
C 172.1
(3)
P 		117.8
(-1.5)
P 		99
(-3)
P 		132.3
(-0.3)
P 		73
avr 202.4
(3) 		140.6
(-1.3) 		116.2
(-3) 		125.4
(-2.4) 		86

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 110
1 2 3 4 5 6 range
A 157.4
(3)
P 		138.4
(1.9)
P 		98.5
(-0.4)
P 		78.5
(-1.5)
P 		52
(-3)
P 		119.4
(0.8)
P 		105
B 127.4
(3)
P 		95.5
(0.6)
P 		55
(-2.4)
P 		88.1
(0.1)
P 		68.8
(-1.4)
P 		47.3
(-3)
P 		80
C 146.8
(3)
P 		135.7
(2)
P 		120.4
(0.7)
P 		98.4
(-1.2)
P 		78.3
(-3)
P 		81.5
(-2.7)
P 		69
avr 143.9
(3) 		123.2
(1.4) 		91.3
(-1.1) 		88.3
(-1.3) 		66.4
(-3) 		82.7
(-1.7) 		78
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 55
1 2 3 4 range
A 71.2
(3)
P 		35.6
(-1.3)
P 		35
(-1.3)
P 		21.1
(-3)
P 		50
B 76.4
(3)
P 		34.6
(-1.6)
P 		26.8
(-2.4)
P 		21.3
(-3)
P 		55
C 57
(3)
P 		33.9
(-1)
P 		34.5
(-0.9)
P 		22.3
(-3)
P 		35
avr 68.2
(3) 		34.7
(-1.3) 		32.1
(-1.6) 		21.6
(-3) 		47

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 41
1 2 3 4 5 6 range
A 29
(-0.6)
P 		49.2
(3)
P 		21.5
(-2)
P 		19.9
(-2.2)
P 		15.7
(-3)
P 		29.1
(-0.6)
P 		34
B 44.3
(3)
P 		31.8
(0.6)
P 		13.4
(-3)
P 		23.3
(-1.1)
P 		27.9
(-0.2)
P 		17.6
(-2.2)
P 		31
C 54.4
(3)
P 		41.4
(0.7)
P 		30.7
(-1.1)
P 		19.8
(-3)
P 		25.3
(-2)
P 		27.3
(-1.7)
P 		35
avr 42.6
(3) 		40.8
(2.5) 		21.9
(-2.8) 		21
(-3) 		23
(-2.4) 		24.7
(-2) 		22
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193972_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.16508
Sequence Type Exemplar sequence
Representative Public ID K08A8.3 NCBI
Target Description K08A8.3 /REP_DB=WormBase Gene ID /WP=CE04726 /GEN=coh-1 /TR=Q21306 /GB=AAA79748.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=S. pombe double-strand-break repair protein, RAD21
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_076861(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_076861 NCBI Caenorhabditis elegans COHesin family member (coh-1) (coh-1) mRNA, complete cds. 11/11 None
GENEFINDER00000011628 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:7466266:7474956:-1 11/11 None
K08A8.3 ENSEMBL cdna:known chromosome:CEL140:X:7465199:7475239:-1 gene:K08A8.3 11/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000011621 2/11 Cross Hyb Matching Probes None
SNAP00000011622 5/11 Cross Hyb Matching Probes None
SNAP00000011623 1/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrX:7466264-7475238(-) 100.0 100.0
Public Domain and Genome References
Gene Title S. pombe double-strand-break repair protein, RAD21
Gene Symbol coh-1
Ensembl K08A8.3
Entrez Gene 181003 Entrez gene
SwissProt Q21306 EMBL-EBI
WormBase CE04726 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1604145_AT similar to Double-strand-break repair protein rad21 homolog (hHR21) (Nuclear matrix protein 1) (NXP-1) (SCC1 homolog) cfa
CANINE_2:CFA.1703.1.A1_AT similar to Double-strand-break repair protein rad21 homolog (hHR21) (Nuclear matrix protein 1) (NXP-1) (SCC1 homolog) cfa
CANINE_2:CFA.19873.1.S1_AT similar to Double-strand-break repair protein rad21 homolog (hHR21) (Nuclear matrix protein 1) (NXP-1) (SCC1 homolog) cfa
CANINE_2:CFA.20666.1.S1_S_AT similar to Double-strand-break repair protein rad21 homolog (hHR21) (Nuclear matrix protein 1) (NXP-1) (SCC1 homolog) cfa
CANINE_2:CFA.21550.1.S1_S_AT similar to Double-strand-break repair protein rad21 homolog (hHR21) (Nuclear matrix protein 1) (NXP-1) (SCC1 homolog) cfa
CANINE_2:CFAAFFX.2157.1.S1_AT similar to Double-strand-break repair protein rad21 homolog (hHR21) (Nuclear matrix protein 1) (NXP-1) (SCC1 homolog) cfa
CHICKEN:GGA.4474.1.S1_S_AT RAD21 homolog (S. pombe) gga
CHICKEN:GGA.20047.1.S1_AT Similar to Double-strand-break repair protein rad21 homolog (hHR21) (Nuclear matrix protein 1) (NXP-1) (SCC1 homolog) gga
HG-U133_PLUS_2:200608_S_AT RAD21 homolog (S. pombe) hs
HG-U133A:200608_S_AT RAD21 homolog (S. pombe) hs
HG-FOCUS:200608_S_AT RAD21 homolog (S. pombe) hs
HG-U133A_2:200608_S_AT RAD21 homolog (S. pombe) hs
HG-U133_PLUS_2:200607_S_AT RAD21 homolog (S. pombe) hs
HG-U133A_2:200607_S_AT RAD21 homolog (S. pombe) hs
HG-U133A:200607_S_AT RAD21 homolog (S. pombe) hs
HU35KSUBD:RC_AA287642_S_AT RAD21 homolog (S. pombe) hs
HUGENEFL:D38551_AT RAD21 homolog (S. pombe) hs
U133_X3P:G5453993_3P_A_AT RAD21 homolog (S. pombe) hs
U133_X3P:HS.81848.0.S1_3P_A_AT RAD21 homolog (S. pombe) hs
HG-U95AV2:38114_AT RAD21 homolog (S. pombe) hs
U133_X3P:HS2.424244.1.S1_3P_AT RAD21 homolog (S. pombe) hs
HG-U133_PLUS_2:1560207_AT RAD21 homolog (S. pombe) hs
MOE430A:1416162_AT RAD21 homolog (S. pombe) mm
MOUSE430_2:1416162_AT RAD21 homolog (S. pombe) mm
MOUSE430A_2:1416162_AT RAD21 homolog (S. pombe) mm
MOUSE430_2:1416161_AT RAD21 homolog (S. pombe) mm
MOE430A:1416161_AT RAD21 homolog (S. pombe) mm
MOUSE430A_2:1416161_AT RAD21 homolog (S. pombe) mm
MG-U74AV2:94768_AT RAD21 homolog (S. pombe) mm
MOUSE430_2:1455938_X_AT RAD21 homolog (S. pombe) mm
MOUSE430A_2:1455938_X_AT RAD21 homolog (S. pombe) mm
MOE430A:1455938_X_AT RAD21 homolog (S. pombe) mm
MU11KSUBA:D37790_S_AT RAD21 homolog (S. pombe) mm
MU11KSUBB:MSA.1791.0_I_AT RAD21 homolog (S. pombe) mm
MU19KSUBB:TC33672_AT RAD21 homolog (S. pombe) (Rad21), mRNA mm
RG-U34C:RC_AI231313_AT similar to HR21spA rn
RAE230A:1388504_AT similar to HR21spA rn
RAT230_2:1388504_AT similar to HR21spA rn
RAE230B:1382823_AT Similar to HR21spA rn
RAT230_2:1382823_AT Similar to HR21spA rn
RG-U34B:RC_AI070008_AT Similar to HR21spA rn
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 AAA79748 Cohesin family protein 1 [Caenorhabditis elegans] ref|NP_509262.1| COHesin family member (coh-1) [Caenorhabditis elegans] 0.0
blast CAE70217 Hypothetical protein CBG16697 [Caenorhabditis briggsae] 0.0
blast XP_861017 PREDICTED: similar to Double-strand-break repair protein rad21 homolog (hHR21) (Nuclear matrix protein 1) (NXP-1) (SCC1 homolog) isoform 3 [Canis familiaris] 1.0E-55
Protein Domains
Database ID Description E-Value
Pfam IPR006910 EMBL-EBI Rad21/Rec8 like protein, N-terminal 1.3E-59
Pfam IPR006909 EMBL-EBI Rad21/Rec8 like protein, C-terminal 8.4E-26
Pfam IPR006910 EMBL-EBI Rad21/Rec8 like protein, N-terminal 1.3E-59
Pfam IPR006909 EMBL-EBI Rad21/Rec8 like protein, C-terminal 8.4E-26
Sequence
Target Sequence 
>C. ELEGANS:193972_AT
tggtagttaccaagcacgacgacgttgacgagaaaaacgagtggatcaaaaacgctttgg
gtcttcgtgagattggagaagaagagctgcaacagcagcaacaagaaatggatatgcatg
ttcaggacgattcatcgtatgtcgacgactttgacgaggttccaccactcgactttgatc
aactggatatgatggatatgccacaatcgatggatgatatcaacatggtcgacgatgatg
taccacagcgtaacccattgtcaccgtttgccccgatggtcgaagatgaggagatgtctc
caagtgagaagcgcaagaagcgtgatgaagagaaagaagagccagagactgacgaggata
accgctggtcaaagagaactcacgcgttgttgcagaacattgcgactaaattggaaaatc
aaaatggacaggttgaactggatgaaatgttgaagaagggaacaagtcgaaaggtggctg
ccgccaagttctactctcttctgtgtctgaaaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGGTAGTTACCAAGCACGACGACGT 692 551 1370 Antisense
GGATATGCATGTTCAGGACGATTCA 54 511 1479 Antisense
GGACGATTCATCGTATGTCGACGAC 223 523 1494 Antisense
GTCGACGACTTTGACGAGGTTCCAC 488 473 1510 Antisense
CCACCACTCGACTTTGATCAACTGG 410 273 1531 Antisense
TGTACCACAGCGTAACCCATTGTCA 439 559 1608 Antisense
CGTTTGCCCCGATGGTCGAAGATGA 205 245 1634 Antisense
GAGACTGACGAGGATAACCGCTGGT 311 393 1714 Antisense
ACCGCTGGTCAAAGAGAACTCACGC 661 89 1730 Antisense
TCGAAAGGTGGCTGCCGCCAAGTTC 556 599 1836 Antisense
TTCTACTCTCTTCTGTGTCTGAAAA 310 691 1858 Antisense
Sequence Source Affymetrix Proprietary Database