[Home] | [Total List]

[193870_s_at] transcriptional regulatory protein (RPD3)

Description C08B11.2 /REP_DB=WormBase Gene ID /WP=CE01472 /GEN=hda-2 /TR=SW:Q09440 /GB=CAA86662.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=transcriptional regulatory protein (RPD3)
Cluster 6grp_highest_10_10 > 75      6grp_high1_10_10 > 57      4grp_highest_8_8 > 53      4grp_high_8_8 > 17      6grp_highest_nonorm > 83      6grp_total > 58      4grp_total > 31      6grp_highest_sub > Cu      6grp_cgc > 38      6grp_high1_sub > Cu      6grp_cgc_sub > Da      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 420
1 2 3 4 range
A 557.2
(3)
P 		345.6
(-0.7)
P 		212.4
(-3)
P 		456.8
(1.3)
P 		345
B 632.2
(3)
P 		242.6
(-3)
P 		278.4
(-2.4)
P 		443.3
(0.1)
P 		390
C 579.2
(3)
P 		290.4
(-3)
P 		316.6
(-2.5)
P 		415.5
(-0.4)
P 		289
avr 589.5
(3) 		292.9
(-2.6) 		269.1
(-3) 		438.5
(0.2) 		320

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 310
1 2 3 4 5 6 range
A 623.3
(3)
P 		412.4
(-2.3)
P 		465
(-0.9)
P 		382.5
(-3)
P 		463.4
(-1)
P 		603.2
(2.5)
P 		241
B 530.9
(0.9)
P 		357.4
(-3)
P 		417.5
(-1.6)
P 		412.5
(-1.8)
P 		392.5
(-2.2)
P 		622.9
(3)
P 		266
C 432.7
(-2.1)
P 		410
(-2.6)
P 		455.8
(-1.6)
P 		588.5
(1.3)
P 		391.5
(-3)
P 		667.4
(3)
P 		276
avr 529
(0.4) 		393.3
(-3) 		446.1
(-1.7) 		461.2
(-1.3) 		415.8
(-2.4) 		631.2
(3) 		238
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 147
1 2 3 4 range
A 202.9
(3)
P 		75
(-2.2)
P 		55.5
(-3)
P 		66.9
(-2.5)
P 		147
B 201.6
(3)
P 		59.9
(-3)
P 		64.5
(-2.8)
P 		94.5
(-1.5)
P 		142
C 191.7
(3)
P 		83.5
(-2.3)
P 		110.3
(-1)
P 		70.1
(-3)
P 		122
avr 198.7
(3) 		72.8
(-3) 		76.8
(-2.8) 		77.2
(-2.8) 		126

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 135
1 2 3 4 5 6 range
A 114.9
(-0.8)
P 		146.7
(3)
P 		101.3
(-2.5)
P 		97
(-3)
P 		139.8
(2.1)
P 		146.9
(3)
P 		50
B 184.7
(0.8)
P 		119
(-2.2)
P 		101.4
(-3)
P 		109.3
(-2.6)
P 		159.5
(-0.3)
P 		232.3
(3)
P 		131
C 160.4
(-0.5)
P 		125.1
(-2.5)
P 		116
(-3)
P 		118.3
(-2.9)
P 		126.7
(-2.4)
P 		223.4
(3)
P 		107
avr 153.3
(-0) 		130.3
(-1.5) 		106.2
(-3) 		108.2
(-2.9) 		142
(-0.7) 		200.9
(3) 		95
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 193870_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.2893
Sequence Type Exemplar sequence
Representative Public ID C08B11.2 NCBI
Target Description C08B11.2 /REP_DB=WormBase Gene ID /WP=CE01472 /GEN=hda-2 /TR=SW:Q09440 /GB=CAA86662.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=transcriptional regulatory protein (RPD3)
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_063277(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063277 NCBI Caenorhabditis elegans Histone DeAcetylase family member (hda-2) (hda-2) mRNA, complete cds. 11/11 None
SNAP00000039303 ENSEMBL cdna:SNAP chromosome:CEL140:II:8020840:8022528:-1 11/11 None
GENEFINDER00000039313 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:8020840:8022468:-1 11/11 None
C08B11.2 ENSEMBL cdna:known chromosome:CEL140:II:8020719:8022483:-1 gene:C08B11.2 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
chrII:8020836-8022465(-) 100.0 100.0
Public Domain and Genome References
Gene Title transcriptional regulatory protein (RPD3)
Gene Symbol hda-2
Ensembl C08B11.2
Entrez Gene 174285 Entrez gene
SwissProt Q09440 EMBL-EBI
WormBase CE01472 Wormbase
Functional Annotations
Ortholog
ID Title Organism
YEAST_2:1777548_AT Histone deacetylase required for gene activation via specific deacetylation of lysines in H3 and H4 histone tails; subunit of the Set3 complex, a meiotic-specific repressor of sporulation specific genes that contains deacetylase activity 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 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 CAA86662 Hypothetical protein C08B11.2 [Caenorhabditis elegans] ref|NP_495678.1| Histone DeAcetylase family member (hda-2) [Caenorhabditis elegans] sp|Q09440|HDA2_CAEEL Putative histone deacetylase 0.0
blast CAE67777 Hypothetical protein CBG13352 [Caenorhabditis briggsae] 0.0
blast XP_395811 PREDICTED: similar to ENSANGP00000012089 [Apis mellifera] 1.0E-115
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
Sequence
Target Sequence 
>C. ELEGANS:193870_S_AT
aatgcacatgcacgcgcagtcaaatacgtgaaaagtcttggaaaaccattgatggtcctt
ggtggtggtggatatacacttagaaatgttgcgagatgctgggcccttgaaactggagtc
attttaggtcttcgaatggacgatgaaatccctggaacatcattatactcgcactatttc
actccacgacttcttcgcccaaatttggttccaaaaatgaatgatgctaattctgcggca
tatttggcttctattgaaaaagaaacgctggcatgtttgagaatgattcgtggagcacca
tcagttcaaatgcaaaatattgttggaatcaggctcgacgaaattgagcaaatcgaagaa
aatgaacgactacaaaaatcatcaaaatcttcaattgaatatgaagttggaaaagtatca
gagaaaatggaagaagaatgctttgtagaagaagactcaaaacctccatcatttccaccg
ggtcaagatcctcgtcggattggtcagtactggggatatgacaggtctggattggctcca
cc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AATGCACATGCACGCGCAGTCAAAT 8 167 910 Antisense
AAATGTTGCGAGATGCTGGGCCCTT 614 117 993 Antisense
ATGCTGGGCCCTTGAAACTGGAGTC 368 39 1005 Antisense
AACTGGAGTCATTTTAGGTCTTCGA 384 143 1020 Antisense
TCCCTGGAACATCATTATACTCGCA 17 599 1058 Antisense
AATTCTGCGGCATATTTGGCTTCTA 524 177 1138 Antisense
GATTCGTGGAGCACCATCAGTTCAA 245 433 1194 Antisense
GAAGAAGACTCAAAACCTCCATCAT 519 339 1357 Antisense
TCATTTCCACCGGGTCAAGATCCTC 615 613 1378 Antisense
CCTCGTCGGATTGGTCAGTACTGGG 298 265 1399 Antisense
ATGACAGGTCTGGATTGGCTCCACC 38 45 1427 Antisense
Sequence Source Affymetrix Proprietary Database