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[188857_at] Snf5 (yeast)

Description R07E5.3 /REP_DB=WormBase Gene ID /WP=CE01045 /TR=Q21831 /GB=CAA83625.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Snf5 (yeast)
Cluster 6grp_highest_10_10 > 96      6grp_high1_10_10 > 79      4grp_highest_8_8 > 35      4grp_high_8_8 > 56      6grp_highest_nonorm > 73      6grp_total > 69      4grp_total > 63      6grp_highest_sub > Cu      6grp_high1_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 223
1 2 3 4 range
A 626.1
(3)
P 		420.2
(-3)
P 		532.1
(0.3)
P 		434.4
(-2.6)
P 		206
B 594.2
(1.1)
P 		507.2
(-2.4)
P 		643.1
(3)
P 		491.8
(-3)
P 		151
C 614.2
(2.8)
P 		557.8
(-1.8)
P 		616.7
(3)
P 		542.7
(-3)
P 		74
avr 611.5
(3) 		495.1
(-2.7) 		597.3
(2.3) 		489.6
(-3) 		122

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 300
1 2 3 4 5 6 range
A 498.5
(0)
P 		535.2
(1.1)
P 		391.7
(-3)
P 		505.9
(0.2)
P 		499.7
(0.1)
P 		602.7
(3)
P 		211
B 532.7
(-0.8)
P 		474.3
(-2.6)
P 		500.2
(-1.8)
P 		463.4
(-3)
P 		648.8
(3)
P 		586.1
(1)
P 		185
C 639.8
(1.6)
P 		536.2
(-1.2)
P 		591.1
(0.3)
P 		470.7
(-3)
P 		512.5
(-1.9)
P 		692
(3)
P 		221
avr 557
(0.1) 		515.2
(-1.6) 		494.3
(-2.4) 		480
(-3) 		553.7
(0) 		626.9
(3) 		147
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 164
1 2 3 4 range
A 228
(3)
P 		91.2
(-2)
P 		139.1
(-0.2)
P 		63.6
(-3)
P 		164
B 189.5
(3)
P 		125.3
(-1.5)
P 		149
(0.1)
P 		104.8
(-3)
P 		85
C 203.3
(2.4)
P 		160.4
(0.4)
P 		214.9
(3)
P 		91.5
(-3)
P 		123
avr 206.9
(3) 		125.6
(-1.1) 		167.7
(1) 		86.6
(-3) 		120

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 178
1 2 3 4 5 6 range
A 91.9
(-2.6)
P 		190.3
(3)
P 		85.3
(-3)
P 		128.3
(-0.5)
P 		150.8
(0.7)
P 		146.7
(0.5)
P 		105
B 185.4
(-0.3)
P 		157.9
(-1.5)
P 		121.5
(-3)
P 		122.7
(-2.9)
P 		263.6
(3)
P 		218.6
(1.1)
P 		142
C 237.1
(3)
P 		163.6
(-0.1)
P 		150.4
(-0.7)
P 		94.7
(-3)
P 		165.8
(-0)
P 		231.7
(2.8)
P 		142
avr 171.5
(1) 		170.6
(1) 		119.1
(-2.7) 		115.2
(-3) 		193.4
(2.6) 		199
(3) 		84
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188857_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6992
Sequence Type Exemplar sequence
Representative Public ID R07E5.3 NCBI
Target Description R07E5.3 /REP_DB=WormBase Gene ID /WP=CE01045 /TR=Q21831 /GB=CAA83625.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Snf5 (yeast)
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_065489(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065489 NCBI Caenorhabditis elegans R07E5.3 (R07E5.3) mRNA, complete cds. 11/11 None
SNAP00000012848 ENSEMBL cdna:SNAP chromosome:CEL140:III:4404758:4406045:1 11/11 None
GENEFINDER00000012865 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:4404758:4407072:1 11/11 None
R07E5.3 ENSEMBL cdna:known chromosome:CEL140:III:4404755:4407231:1 gene:R07E5.3 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
chrIII:4404757-4406045(+) 100.0 100.0
Public Domain and Genome References
Gene Title Snf5 (yeast)
Ensembl R07E5.3
Entrez Gene 175571 Entrez gene
SwissProt Q21831 EMBL-EBI
WormBase CE01045 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1590853_AT similar to SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 cfa
CANINE_2:CFA.9379.1.S1_AT similar to SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 cfa
CANINE_2:CFAAFFX.21777.1.S1_AT similar to SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 cfa
DROSOPHILA_2:1625112_AT Snf5-related 1 dm
DROSGENOME1:152195_AT Snf5-related 1 dm
CHICKEN:GGA.4349.1.S1_S_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 gga
CHICKEN:GGA.4349.2.S1_S_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 gga
CHICKEN:GGA.8558.1.S1_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 gga
HG-U133_PLUS_2:228898_S_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 hs
HG-U133B:228898_S_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 hs
HU35KSUBC:RC_T64349_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 hs
U133_X3P:HS.159971.2.A1_3P_A_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 hs
U133_X3P:HS.14587.2.S1_3P_A_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 hs
HG-U133A_2:212167_S_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 hs
HG-FOCUS:212167_S_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 hs
HG-U133_PLUS_2:212167_S_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 hs
HG-U133A:212167_S_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 hs
HG-U95AV2:40416_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 hs
HG-U133_PLUS_2:231324_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 hs
HG-U133B:231324_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 hs
HG-U95E:86416_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 hs
U133_X3P:HS.198671.0.A1_3P_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 hs
MG-U74AV2:96050_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 mm
MOE430A:1416045_A_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 mm
MOUSE430A_2:1416045_A_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 mm
MOUSE430_2:1416045_A_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 mm
MOE430A:1435856_X_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1, mRNA (cDNA clone MGC:36040 IMAGE:3154501) mm
MOUSE430A_2:1435856_X_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1, mRNA (cDNA clone MGC:36040 IMAGE:3154501) mm
MOUSE430_2:1435856_X_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1, mRNA (cDNA clone MGC:36040 IMAGE:3154501) mm
MOUSE430_2:1456938_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1, mRNA (cDNA clone MGC:36040 IMAGE:3154501) mm
MOE430B:1456938_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1, mRNA (cDNA clone MGC:36040 IMAGE:3154501) mm
MU19KSUBA:TC24709_S_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1, mRNA (cDNA clone MGC:36040 IMAGE:3154501) mm
MU19KSUBB:TC33273_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1, mRNA (cDNA clone MGC:36040 IMAGE:3154501) mm
RN-U34:RC_H33459_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 (predicted) rn
RG-U34A:RC_H33459_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 (predicted) rn
RN-U34:RC_H33459_G_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 (predicted) rn
RG-U34A:RC_H33459_G_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 (predicted) rn
RAE230A:1371914_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 (predicted) rn
RAT230_2:1371914_AT SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 (predicted) rn
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6338 chromatin remodeling inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
228 nuclear chromosome inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA83625 Hypothetical protein R07E5.3 [Caenorhabditis elegans] ref|NP_497890.1| R07E5.3 [Caenorhabditis elegans] 0.0
blast CAE71212 Hypothetical protein CBG18075 [Caenorhabditis briggsae] 0.0
blast XP_781133 PREDICTED: similar to SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 isoform b [Strongylocentrotus purpuratus] 3.0E-96
Protein Domains
Database ID Description E-Value
Pfam IPR006939 EMBL-EBI SNF5/SMARCB1/INI1 1.0E-126
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 4.5E-17
Sequence
Target Sequence 
>C. ELEGANS:188857_AT
gagaagatcttgtgccaattcgattggatatggagttggatggaatcaaacttcgcgata
cgttcactttcaataaaaacgagaaaatgatcactcccgagatgattgccgaaattatgt
gtgaagatcttgatctaccattggcagttttccagcctgctattactgcagcaattaatc
agcagctcgaagcttctacagaagcgccaccattggatgtgaacatttgtgatcagagag
ccgttctcaagttgaatattaatgttggaaaccagagtttggttgatcaattcgagtggg
atatgtcggatcctaataacagcccggaagagttttcacgaaacatctgcaaagagcttg
gcctcggtggtgaatttatgtcaggaattgcatattcaattcgcggacagttacaatgga
atcaaagaacatatgcgttttcagaaagcccactggccactgttgattgcccgttcagaa
ca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAGAAGATCTTGTGCCAATTCGATT 7 393 545 Antisense
ACTTCGCGATACGTTCACTTTCAAT 493 103 594 Antisense
AGATCTTGATCTACCATTGGCAGTT 256 67 669 Antisense
GCAGTTTTCCAGCCTGCTATTACTG 661 311 688 Antisense
ATCAGCAGCTCGAAGCTTCTACAGA 85 29 722 Antisense
TTCTACAGAAGCGCCACCATTGGAT 415 689 738 Antisense
GTCGGATCCTAATAACAGCCCGGAA 145 473 849 Antisense
AAGAGCTTGGCCTCGGTGGTGAATT 448 153 896 Antisense
GCATATTCAATTCGCGGACAGTTAC 158 307 934 Antisense
TTTCAGAAAGCCCACTGGCCACTGT 328 669 983 Antisense
CACTGTTGATTGCCCGTTCAGAACA 240 197 1002 Antisense
Sequence Source Affymetrix Proprietary Database