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[173001_s_at] Histone deacetylase family

Description C35230_rc /REP_DB=TREMBL Accession /FEA=EST Transcript /REVCOMP /GB=C35230 /DEF=C.elegans cDNA clone yk426h1 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 81      6grp_high1_10_10 > 29      4grp_highest_8_8 > 50      4grp_high_8_8 > 33      6grp_highest_nonorm > 60      6grp_total > 28      4grp_total > 46      6grp_highest_sub > Cu      6grp_cgc > 03      6grp_high1_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 395
1 2 3 4 range
A 503
(3)
P 		301.1
(-0.9)
P 		192.2
(-3)
P 		230.8
(-2.3)
P 		311
B 559.3
(3)
P 		374.1
(-0)
P 		342.9
(-0.5)
P 		192.6
(-3)
P 		367
C 587.4
(3)
P 		303.6
(-3)
P 		305.4
(-3)
P 		311.3
(-2.8)
P 		284
avr 549.9
(3) 		326.3
(-1.4) 		280.2
(-2.3) 		244.9
(-3) 		305

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 206
1 2 3 4 5 6 range
A 498.2
(3)
P 		388.8
(-0.2)
P 		354.5
(-1.2)
P 		294.3
(-3)
P 		436
(1.2)
P 		348.4
(-1.4)
P 		204
B 500.5
(3)
P 		483.7
(2.5)
P 		306.7
(-3)
P 		398.9
(-0.1)
P 		403.7
(0)
P 		368.2
(-1.1)
P 		194
C 416.2
(3)
P 		392.8
(1.3)
P 		344.7
(-2.1)
P 		348.9
(-1.8)
P 		332.2
(-3)
P 		414.9
(2.9)
P 		84
avr 471.6
(3) 		421.8
(0.8) 		335.3
(-3) 		347.4
(-2.5) 		390.6
(-0.6) 		377.2
(-1.2) 		136
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 161
1 2 3 4 range
A 183.1
(3)
P 		65.4
(-1.7)
P 		50.3
(-2.3)
P 		33.8
(-3)
P 		149
B 178.4
(3)
P 		92.4
(-0.8)
P 		79.5
(-1.3)
P 		41
(-3)
P 		137
C 194.4
(3)
P 		87.3
(-1.5)
P 		106.4
(-0.7)
P 		52.5
(-3)
P 		142
avr 185.3
(3) 		81.7
(-1.3) 		78.7
(-1.5) 		42.4
(-3) 		143

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 104
1 2 3 4 5 6 range
A 91.8
(-1.4)
P 		138.3
(3)
P 		77.2
(-2.8)
P 		74.7
(-3)
P 		131.6
(2.4)
P 		84.8
(-2)
P 		64
B 174.1
(3)
P 		161
(2.2)
P 		74.5
(-3)
P 		105.7
(-1.1)
P 		164
(2.4)
P 		137.3
(0.8)
P 		100
C 154.3
(3)
P 		119.9
(0.5)
P 		87.7
(-1.8)
P 		70.2
(-3)
P 		107.5
(-0.3)
P 		138.9
(1.9)
P 		84
avr 140.1
(3) 		139.7
(3) 		79.8
(-3) 		83.5
(-2.6) 		134.4
(2.4) 		120.3
(1) 		60
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173001_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.26359
Sequence Type Exemplar sequence
Representative Public ID C35230 NCBI
Target Description C35230_rc /REP_DB=TREMBL Accession /FEA=EST Transcript /REVCOMP /GB=C35230 /DEF=C.elegans cDNA clone yk426h1 : 3prime end, single read.
Cluster Evidence This cluster is supported by a EST Transcript.
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_060625(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_060625 NCBI Caenorhabditis elegans Histone DeAcetylase family member (hda-3) (hda-3) mRNA, complete cds. 11/11 None
R06C1.1.1 ENSEMBL cdna:known chromosome:CEL140:I:11920920:11925834:-1 gene:R06C1.1 11/11 None
R06C1.1.2 ENSEMBL cdna:known chromosome:CEL140:I:11920920:11925836:-1 gene:R06C1.1 11/11 None
R06C1.1.3 ENSEMBL cdna:known chromosome:CEL140:I:11920920:11925841:-1 gene:R06C1.1 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
chrI:11920907-11921152(-) 81.67 81.67
Public Domain and Genome References
Gene Title Histone deacetylase family
Gene Symbol hda-3
Ensembl R06C1.1
Entrez Gene 173074 Entrez gene
SwissProt O62339 EMBL-EBI
WormBase CE18116 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:252982_AT histone deacetylase (RPD3A) at
CANINE:1599911_AT similar to histone deacetylase 1 cfa
CANINE_2:CFA.16801.1.S1_AT similar to histone deacetylase 1 cfa
CANINE_2:CFAAFFX.16598.1.S1_S_AT similar to histone deacetylase 1 cfa
HG-U133A:201209_AT histone deacetylase 1 hs
HG-U133_PLUS_2:201209_AT histone deacetylase 1 hs
HG-FOCUS:201209_AT histone deacetylase 1 hs
HG-U133A_2:201209_AT histone deacetylase 1 hs
HG-U95AV2:476_S_AT histone deacetylase 1 hs
HC-G110:476_S_AT histone deacetylase 1 hs
HUGENEFL:U50079_S_AT histone deacetylase 1 hs
HUGENEFL:D50405_AT histone deacetylase 1 hs
U133_X3P:G13128859_3P_AT histone deacetylase 1 hs
HG-U95AV2:38771_AT histone deacetylase 1 hs
MU11KSUBA:U80780_S_AT histone deacetylase 1 mm
MU11KSUBB:MSA.9756.0_F_AT histone deacetylase 1 mm
MU11KSUBB:MSA.41954.0_S_AT histone deacetylase 1 mm
MG-U74AV2:96046_AT histone deacetylase 1 mm
MG-U74CV2:129132_AT histone deacetylase 1 mm
MOE430A:1448246_AT histone deacetylase 1 mm
MOUSE430A_2:1448246_AT histone deacetylase 1 mm
MOUSE430_2:1448246_AT histone deacetylase 1 mm
RG-U34C:RC_AA818418_AT histone deacetylase 1 (predicted) rn
RAE230A:1388761_AT histone deacetylase 1 (predicted) rn
RAT230_2:1388761_AT histone deacetylase 1 (predicted) rn
RAE230B:1396820_AT histone deacetylase 1 (predicted) rn
RAT230_2:1396820_AT histone deacetylase 1 (predicted) rn
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 sequence similarity QuickGO AmiGO
122 negative regulation of transcription from RNA polymerase II promoter inferred from sequence similarity QuickGO AmiGO
16568 chromatin modification inferred from sequence similarity 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 sequence similarity 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 sequence similarity QuickGO AmiGO
3714 transcription corepressor activity inferred from sequence similarity QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB03240 Hypothetical protein R06C1.1 [Caenorhabditis elegans] emb|CAB03224.1| Hypothetical protein R06C1.1 [Caenorhabditis elegans] ref|NP_493026.1| Histone DeAcetylase family member (hda-3) [Caenorhabditis elegans] 0.0
blast CAE71712 Hypothetical protein CBG18689 [Caenorhabditis briggsae] 0.0
blast XP_394976 PREDICTED: similar to ENSANGP00000004321 [Apis mellifera] 1.0E-160
Protein Domains
Database ID Description E-Value
scop a.4.5.Replication initiation protein All alpha proteins; DNA/RNA-binding 3-helical bundle; "Winged helix" DNA-binding domain; Replication initiation protein 3.29999995231628
Pfam IPR000286 EMBL-EBI Histone deacetylase superfamily 1.0E-126
Sequence
Target Sequence 
>C. ELEGANS:173001_S_AT
aactttgtatttatatcgtctcttcaaactatttctttaatttatacgaatctcaacttc
tctaaacctctattgatcctcaaatctatttaaatctttcgttaaatcgacaattaaaaa
atttccgtcgtcaagtgtggtgccggtggtgcatacaccgccgcgcacaaatgcacagat
ttcggcgttttcga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AACTTTGTATTTATATCGTCTCTTC 255 139 74 Antisense
TTTATATCGTCTCTTCAAACTATTT 372 673 83 Antisense
ATTTATACGAATCTCAACTTCTCTA 460 13 113 Antisense
GAATCTCAACTTCTCTAAACCTCTA 218 329 121 Antisense
CTCTAAACCTCTATTGATCCTCAAA 161 231 133 Antisense
GATCCTCAAATCTATTTAAATCTTT 490 415 148 Antisense
TAAATCTTTCGTTAAATCGACAATT 563 641 164 Antisense
AATTTCCGTCGTCAAGTGTGGTGCC 170 173 193 Antisense
GTGTGGTGCCGGTGGTGCATACACC 514 487 208 Antisense
GCCGCGCACAAATGCACAGATTTCG 551 285 233 Antisense
AATGCACAGATTTCGGCGTTTTCGA 648 165 243 Antisense
Sequence Source Affymetrix Proprietary Database