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[178399_s_at]

Description F18E2.3 /REP_DB=WormBase Gene ID /WP=CE05664 /TR=Q19555 /GB=CAA99836.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 94      6grp_high1_10_10 > 58      4grp_highest_8_8 > 50      4grp_high_8_8 > 40      6grp_highest_nonorm > 86      6grp_total > 48      4grp_total > 55      6grp_highest_sub > Cu      6grp_cgc > 18      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 592
1 2 3 4 range
A 1219.3
(3)
P 		712.8
(-2.1)
P 		661.6
(-2.7)
P 		627.8
(-3)
P 		592
B 1174.4
(3)
P 		789.1
(-1.6)
P 		729.3
(-2.3)
P 		672.1
(-3)
P 		502
C 1167.9
(3)
P 		807.3
(-1.4)
P 		802.9
(-1.5)
P 		676.1
(-3)
P 		492
avr 1187.2
(3) 		769.7
(-1.7) 		731.3
(-2.2) 		658.7
(-3) 		529

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 789
1 2 3 4 5 6 range
A 1129.3
(0.5)
P 		1014.5
(-0.4)
P 		705.1
(-3)
P 		843.1
(-1.9)
P 		836.2
(-1.9)
P 		1427.6
(3)
P 		723
B 1263.4
(2.4)
P 		1049.7
(0.3)
P 		706.5
(-3)
P 		861.9
(-1.5)
P 		917.8
(-0.9)
P 		1321.3
(3)
P 		615
C 1127.1
(1.3)
P 		964.2
(-0.1)
P 		780.2
(-1.8)
P 		638.2
(-3)
P 		1020.7
(0.4)
P 		1321.1
(3)
P 		683
avr 1173.3
(1.2) 		1009.5
(-0.3) 		730.6
(-3) 		781.1
(-2.5) 		924.9
(-1.1) 		1356.7
(3) 		626
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 352
1 2 3 4 range
A 443.9
(3)
P 		154.7
(-1.9)
P 		172.9
(-1.6)
P 		91.9
(-3)
P 		352
B 374.5
(3)
P 		194.9
(-1.7)
P 		169
(-2.3)
P 		143.2
(-3)
P 		231
C 386.6
(3)
P 		232.1
(-0.4)
P 		279.8
(0.6)
P 		114
(-3)
P 		273
avr 401.7
(3) 		193.9
(-1.4) 		207.2
(-1.1) 		116.4
(-3) 		285

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 364
1 2 3 4 5 6 range
A 208.2
(-1.4)
P 		360.8
(3)
P 		153.6
(-3)
P 		213.8
(-1.3)
P 		252.3
(-0.1)
P 		347.6
(2.6)
P 		207
B 439.6
(2)
P 		349.4
(0.3)
P 		171.5
(-3)
P 		228.3
(-1.9)
P 		372.9
(0.8)
P 		492.7
(3)
P 		321
C 417.8
(2.5)
P 		294.2
(0.2)
P 		198.6
(-1.7)
P 		128.3
(-3)
P 		330.3
(0.9)
P 		442.3
(3)
P 		314
avr 355.2
(1.3) 		334.8
(0.8) 		174.6
(-3) 		190.1
(-2.6) 		318.5
(0.4) 		427.5
(3) 		253
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 178399_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.13139
Sequence Type Exemplar sequence
Representative Public ID F18E2.3 NCBI
Target Description F18E2.3 /REP_DB=WormBase Gene ID /WP=CE05664 /TR=Q19555 /GB=CAA99836.1 /SUBMIT=HINXTON /CHR=5 /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_073792(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073792 NCBI Caenorhabditis elegans yeast SCC (mitotic condensin subunit) homolog family member (scc-3) (scc-3) mRNA, complete cds. 11/11 None
SNAP00000032114 ENSEMBL cdna:SNAP chromosome:CEL140:V:12766535:12770261:1 11/11 None
GENEFINDER00000032121 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:12766535:12770261:1 11/11 None
F18E2.3 ENSEMBL cdna:known chromosome:CEL140:V:12766535:12770516:1 gene:F18E2.3 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
chrV:12766534-12770261(+) 99.18 100.0
Public Domain and Genome References
Gene Title
Gene Symbol scc-3
Ensembl F18E2.3
Entrez Gene 179749 Entrez gene
SwissProt Q19555 EMBL-EBI
WormBase CE05664 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFA.16649.1.S1_S_AT similar to stromal antigen 2 cfa
CANINE_2:CFA.18897.1.S1_S_AT similar to stromal antigen 2 cfa
CANINE_2:CFAAFFX.28426.1.S1_AT similar to stromal antigen 2 cfa
CANINE_2:CFAAFFX.28429.1.S1_S_AT similar to stromal antigen 2 cfa
CHICKEN:GGA.11155.1.S1_AT stromal antigen 2 gga
CHICKEN:GGA.11155.1.S1_S_AT stromal antigen 2 gga
CHICKEN:GGAAFFX.22599.1.S1_AT stromal antigen 2 gga
CHICKEN:GGAAFFX.22599.2.S1_S_AT stromal antigen 2 gga
HG-U133_PLUS_2:207983_S_AT stromal antigen 2 hs
HG-U133A:207983_S_AT stromal antigen 2 hs
HG-U133A_2:207983_S_AT stromal antigen 2 hs
HG-U133_PLUS_2:209023_S_AT stromal antigen 2 hs
HG-U133A_2:209023_S_AT stromal antigen 2 hs
HG-U133A:209023_S_AT stromal antigen 2 hs
HU35KSUBA:RC_AA428995_AT stromal antigen 2 hs
HU35KSUBC:RC_AA489057_AT stromal antigen 2 hs
HU35KSUBD:RC_AA504266_AT stromal antigen 2 hs
U133_X3P:G5730068_3P_A_AT stromal antigen 2 hs
U133_X3P:HS.8217.1.A2_3P_AT stromal antigen 2 hs
HG-U133A_2:209022_AT stromal antigen 2 hs
HG-FOCUS:209022_AT stromal antigen 2 hs
HG-U133_PLUS_2:209022_AT stromal antigen 2 hs
HG-U133A:209022_AT stromal antigen 2 hs
HG-U95AV2:34709_R_AT stromal antigen 2 hs
HG-U95C:48629_S_AT stromal antigen 2 hs
HG-U95C:48630_R_AT stromal antigen 2 hs
HG-U95C:64266_AT stromal antigen 2 hs
HG-U95D:84308_I_AT Stromal antigen 2 hs
HU35KSUBC:RC_H54694_AT Stromal antigen 2 hs
MU11KSUBA:AA461826_S_AT stromal antigen 2 mm
MG-U74AV2:92513_AT stromal antigen 2 mm
MG-U74AV2:104595_AT stromal antigen 2 mm
MOE430A:1421849_AT stromal antigen 2 mm
MOUSE430A_2:1421849_AT stromal antigen 2 mm
MOUSE430_2:1421849_AT stromal antigen 2 mm
MOE430A:1450396_AT stromal antigen 2 mm
MOUSE430A_2:1450396_AT stromal antigen 2 mm
MOUSE430_2:1450396_AT stromal antigen 2 mm
RAE230B:1382332_AT similar to stromal antigen 2 rn
RAT230_2:1382332_AT similar to stromal antigen 2 rn
RAE230B:1391404_AT similar to stromal antigen 2 rn
RAT230_2:1391404_AT similar to stromal antigen 2 rn
Gene Ontology
GO Cellular Component (view graph)
ID Description Evidence Links
785 chromatin inferred from direct assay QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3677 DNA binding inferred from sequence similarity QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA99836 Hypothetical protein F18E2.3 [Caenorhabditis elegans] ref|NP_506193.1| yeast SCC (mitotic condensin subunit) homolog family member (scc-3) [Caenorhabditis elegans] 0.0
blast CAE63991 Hypothetical protein CBG08584 [Caenorhabditis briggsae] 0.0
blast AAH84327 LOC495133 protein [Xenopus laevis] 1.0E-176
Protein Domains
Database ID Description E-Value
Pfam IPR005032 EMBL-EBI Stromal antigen (SA/STAG) protein 1.0E-126
Sequence
Target Sequence 
>C. ELEGANS:178399_S_AT
gcatctcatctcataaaacgctatcagtctcacttccaagacttcggagacattttcaaa
aatcttttatcaaagtgccgtgaaatttcatttgtcgaaactggcgtcatgatttgtgaa
actcttaaaaccctttattcacaattggacgaagatcaaggaacggatccactgtcagag
tcattcaattctattcgtgatcttgcaaaacgattaggacctgctttcggtgttgattat
gctaagaatcggtttgctatctcgtcattgcacaaaaaagccatcgattttgcattcgaa
gagtacgataaagaaaatcatcagatgccgaaaaacattttcttcttggaaattgctatc
gaatttagcgggaagttattggcacaggacaagatggctgtcgttcgttacttgaacaaa
atttacacaaaccgcgttggaacatcaacagtcgtttgggaaccatatcgattatacctc
ggatcactctcggatcgtaacgatgatgacaacatgtctgtgcgcagtggaatgaccgtt
acatcc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCATCTCATCTCATAAAACGCTATC 401 309 2674 Antisense
TAAAACGCTATCAGTCTCACTTCCA 365 639 2687 Antisense
CTCACTTCCAAGACTTCGGAGACAT 515 225 2702 Antisense
GTCGAAACTGGCGTCATGATTTGTG 165 475 2767 Antisense
GAACGGATCCACTGTCAGAGTCATT 607 347 2834 Antisense
GATTAGGACCTGCTTTCGGTGTTGA 60 431 2885 Antisense
TCGGTTTGCTATCTCGTCATTGCAC 618 605 2922 Antisense
ATCGATTATACCTCGGATCACTCTC 234 35 3140 Antisense
GGATCACTCTCGGATCGTAACGATG 340 511 3154 Antisense
TGACAACATGTCTGTGCGCAGTGGA 577 571 3180 Antisense
GCGCAGTGGAATGACCGTTACATCC 467 287 3195 Antisense
Sequence Source Affymetrix Proprietary Database