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[192776_at] Yeast RPD3 protein like

Description C53A5.3 /REP_DB=WormBase Gene ID /WP=CE08952 /GEN=hda-1 /TR=SW:O17695 /GB=CAB03984.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Yeast RPD3 protein like
Cluster 6grp_highest_10_10 > 83      6grp_high1_10_10 > 38      4grp_highest_8_8 > 24      4grp_high_8_8 > 52      6grp_highest_nonorm > 76      6grp_total > 37      4grp_total > 52      6grp_highest_sub > Cu      6grp_cgc > 16      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 736
1 2 3 4 range
A 1144.7
(1)
P 		1338.3
(3)
P 		1116.6
(0.7)
P 		750.3
(-3)
P 		588
B 1090.4
(1.5)
P 		1222.2
(3)
P 		1186.3
(2.6)
P 		704.2
(-3)
P 		518
C 1099.8
(2.2)
P 		1175.6
(3)
P 		966.8
(0.8)
P 		602.3
(-3)
P 		573
avr 1111.6
(1.6) 		1245.4
(3) 		1089.9
(1.3) 		685.6
(-3) 		560

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 293
1 2 3 4 5 6 range
A 1137.3
(2)
P 		993.7
(-0.9)
P 		891.9
(-3)
P 		898.2
(-2.9)
P 		1004.3
(-0.7)
P 		1184.4
(3)
P 		293
B 1175.3
(3)
P 		1059.3
(0.3)
P 		921.6
(-3)
P 		1001.1
(-1.1)
P 		944.2
(-2.5)
P 		1108.3
(1.4)
P 		254
C 1143.1
(3)
P 		1030.9
(-0.4)
P 		1021.9
(-0.6)
P 		1048.7
(0.2)
P 		943.3
(-3)
P 		978.3
(-1.9)
P 		200
avr 1151.9
(3) 		1028
(-0.6) 		945.1
(-3) 		982.7
(-1.9) 		963.9
(-2.5) 		1090.3
(1.2) 		207
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 315
1 2 3 4 range
A 416.8
(3)
P 		290.5
(0.5)
P 		291.9
(0.6)
P 		109.8
(-3)
P 		307
B 347.7
(3)
P 		301.8
(1.6)
P 		274.9
(0.8)
P 		150.1
(-3)
P 		198
C 364.1
(3)
P 		338
(2.4)
P 		337
(2.4)
P 		101.6
(-3)
P 		263
avr 376.2
(3) 		310.1
(1.4) 		301.3
(1.2) 		120.5
(-3) 		256

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 230
1 2 3 4 5 6 range
A 209.7
(-2.4)
P 		353.4
(3)
P 		194.2
(-3)
P 		227.8
(-1.7)
P 		303.1
(1.1)
P 		288.4
(0.6)
P 		159
B 408.9
(2.9)
P 		352.6
(1.1)
P 		223.8
(-3)
P 		265.2
(-1.7)
P 		383.6
(2.1)
P 		413.3
(3)
P 		190
C 423.7
(3)
P 		314.5
(-0.1)
P 		260.1
(-1.6)
P 		210.9
(-3)
P 		305.2
(-0.3)
P 		327.5
(0.3)
P 		213
avr 347.4
(3) 		340.2
(2.6) 		226
(-3) 		234.6
(-2.6) 		330.6
(2.2) 		343.1
(2.8) 		121
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192776_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.13058
Sequence Type Exemplar sequence
Representative Public ID C53A5.3 NCBI
Target Description C53A5.3 /REP_DB=WormBase Gene ID /WP=CE08952 /GEN=hda-1 /TR=SW:O17695 /GB=CAB03984.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Yeast RPD3 protein like
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_074198(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_074198 NCBI Caenorhabditis elegans Histone DeAcetylase family member (hda-1) (hda-1) mRNA, complete cds. 11/11 None
SNAP00000009284 ENSEMBL cdna:SNAP chromosome:CEL140:V:14528018:14529566:1 11/11 None
GENEFINDER00000009301 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:14527306:14529566:1 11/11 None
C53A5.3.2 ENSEMBL cdna:known chromosome:CEL140:V:14527972:14529988:1 gene:C53A5.3 11/11 None
C53A5.3.1 ENSEMBL cdna:known chromosome:CEL140:V:14527978:14529988:1 gene:C53A5.3 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:14527996-14529566(+) 100.0 100.0
Public Domain and Genome References
Gene Title Yeast RPD3 protein like
Gene Symbol hda-1
Ensembl C53A5.3
Entrez Gene 179959 Entrez gene
SwissProt O17695 EMBL-EBI
WormBase CE08952 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:247371_AT histone deacetylase, putative at
CANINE:1598926_S_AT similar to Histone deacetylase 2 (HD2) cfa
CANINE_2:CFA.2864.1.A1_S_AT similar to Histone deacetylase 2 (HD2) cfa
DROSOPHILA_2:1633700_AT dm
DROSGENOME1:153325_AT dm
CHICKEN:GGA.2951.1.S1_AT histone deacetylase 2 gga
HG-U133_PLUS_2:201833_AT histone deacetylase 2 hs
HG-U133A_2:201833_AT histone deacetylase 2 hs
HG-U133A:201833_AT histone deacetylase 2 hs
HG-FOCUS:201833_AT histone deacetylase 2 hs
HG-U95AV2:34368_AT histone deacetylase 2 hs
HUGENEFL:U31814_AT histone deacetylase 2 hs
U133_X3P:G4557640_3P_AT histone deacetylase 2 hs
HG-U133_PLUS_2:242141_AT Histone deacetylase 2 hs
HG-U133B:242141_AT Histone deacetylase 2 hs
U133_X3P:HS.232662.0.A1_3P_AT Histone deacetylase 2 hs
U133_X3P:HS.232662.0.A1_3P_X_AT Histone deacetylase 2 hs
MOUSE430_2:1439704_AT histone deacetylase 2 mm
MOE430B:1439704_AT histone deacetylase 2 mm
MU11KSUBA:U31758_S_AT histone deacetylase 2 mm
MG-U74AV2:160643_AT histone deacetylase 2 mm
MOE430A:1449080_AT histone deacetylase 2 mm
MOUSE430A_2:1449080_AT histone deacetylase 2 mm
MOUSE430_2:1449080_AT histone deacetylase 2 mm
MOE430B:1445684_S_AT histone deacetylase 2 mm
MOUSE430_2:1445684_S_AT histone deacetylase 2 mm
RG-U34A:RC_AA892297_AT histone deacetylase 2 rn
RAE230A:1390308_AT histone deacetylase 2 rn
RAT230_2:1390308_AT histone deacetylase 2 rn
RAE230A:1370908_AT histone deacetylase 2 rn
RAT230_2:1370908_AT histone deacetylase 2 rn
YEAST_2:1774173_AT Histone deacetylase; regulates transcription and silencing Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
16575 histone deacetylation inferred from electronic annotation QuickGO AmiGO
16575 histone deacetylation inferred from direct assay QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5634 nucleus inferred from electronic annotation QuickGO AmiGO
118 histone deacetylase complex inferred from physical interaction QuickGO AmiGO
16581 NuRD complex inferred from physical interaction QuickGO AmiGO
5634 nucleus inferred from direct assay QuickGO AmiGO
1674 female germ cell nucleus inferred from direct assay QuickGO AmiGO
5737 cytoplasm inferred from direct assay QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
4407 histone deacetylase activity inferred from electronic annotation QuickGO AmiGO
4407 histone deacetylase activity inferred from direct assay QuickGO AmiGO
3714 transcription corepressor activity inferred from physical interaction QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB03984 Hypothetical protein C53A5.3 [Caenorhabditis elegans] ref|NP_506599.1| Histone DeAcetylase family member (hda-1) [Caenorhabditis elegans] sp|O17695|HDA1_CAEEL Histone deacetylase 0.0
blast CAE60876 Hypothetical protein CBG04588 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000286 EMBL-EBI Histone deacetylase superfamily 1.0E-126
Pfam IPR000286 EMBL-EBI Histone deacetylase superfamily 1.0E-126
Pfam IPR000286 EMBL-EBI Histone deacetylase superfamily 1.0E-126
Sequence
Target Sequence 
>C. ELEGANS:192776_AT
ccctgtgctgttgttcttcaatgtggagctgattctctcaacggagatagacttggacca
ttcaatctgaccttgaaaggccacggagaatgtgctcgtttcttccgaagctacaacgtt
ccacttatgatggtcggtggaggtggatacactccaagaaatgtggcacgttgttggacg
tacgaaacctcgattgccgtcgataaggaagttccaaatgagttgccatacaatgactac
ttcgaatactttggaccaaactaccgacttcacatcgagtcgtcgaatgcagcaaatgaa
aatagctccgatatgctggctaaattgcaaactgacgtcatcgccaatctcgagcagctc
acttttgttccaagtgttcaaatgagaccgatcccagaagacgccctctctgcattgaat
gatgactcattgatcgccgaccaagctaatcccgacaaacgactaccaccacaaattacc
gatg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CCCTGTGCTGTTGTTCTTCAATGTG 608 259 784 Antisense
GACTTGGACCATTCAATCTGACCTT 137 369 833 Antisense
ACGGAGAATGTGCTCGTTTCTTCCG 26 97 866 Antisense
TTCTTCCGAAGCTACAACGTTCCAC 406 687 883 Antisense
CGTACGAAACCTCGATTGCCGTCGA 247 245 962 Antisense
TCTCGAGCAGCTCACTTTTGTTCCA 185 611 1131 Antisense
AATGAGACCGATCCCAGAAGACGCC 131 163 1164 Antisense
ACGCCCTCTCTGCATTGAATGATGA 455 91 1184 Antisense
ACTCATTGATCGCCGACCAAGCTAA 261 101 1208 Antisense
GCTAATCCCGACAAACGACTACCAC 246 301 1228 Antisense
CGACTACCACCACAAATTACCGATG 75 253 1243 Antisense
Sequence Source Affymetrix Proprietary Database