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[189914_s_at] histone H2A variant

Description R08C7.3 /REP_DB=WormBase Gene ID /WP=CE07426 /TR=Q27511 /GB=AAC48074.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=histone H2A variant
Cluster 6grp_highest_10_10 > 96      6grp_high1_10_10 > 68      4grp_highest_8_8 > 32      4grp_high_8_8 > 51      6grp_highest_nonorm > 58      6grp_total > 59      4grp_total > 52      6grp_highest_sub > Cu      6grp_high1_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2825
1 2 3 4 range
A 3716.8
(3)
P 		3536.6
(2.5)
P 		3248.4
(1.7)
P 		1627.4
(-3)
P 		2089
B 3747.4
(2)
P 		4162.3
(3)
P 		3358.5
(1.1)
P 		1572
(-3)
P 		2590
C 3496.5
(2.2)
P 		3835.9
(3)
P 		3010.3
(1)
P 		1336.9
(-3)
P 		2499
avr 3653.6
(2.5) 		3844.9
(3) 		3205.7
(1.4) 		1512.1
(-3) 		2333

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3602
1 2 3 4 5 6 range
A 2926.7
(-0.8)
P 		2332.9
(-2)
P 		1814.1
(-2.9)
P 		1775.1
(-3)
P 		2710.7
(-1.2)
P 		4967.8
(3)
P 		3193
B 3458.7
(0.7)
P 		2087.2
(-2.1)
P 		1672.1
(-3)
P 		1683.7
(-3)
P 		2927.8
(-0.4)
P 		4577.5
(3)
P 		2905
C 3202.1
(-0.5)
P 		2106.8
(-2.3)
P 		1702.1
(-3)
P 		1927.4
(-2.6)
P 		2837.3
(-1.1)
P 		5273.7
(3)
P 		3572
avr 3195.8
(-0.3) 		2175.6
(-2.2) 		1729.4
(-3) 		1795.4
(-2.9) 		2825.3
(-1) 		4939.7
(3) 		3210
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1128
1 2 3 4 range
A 1353.3
(3)
P 		767.7
(-0.2)
P 		849.2
(0.3)
P 		238.2
(-3)
P 		1115
B 1195
(3)
P 		1028
(1.8)
P 		778.3
(0.1)
P 		335
(-3)
P 		860
C 1157.4
(3)
P 		1102.9
(2.6)
P 		1049.2
(2.3)
P 		225.4
(-3)
P 		932
avr 1235.2
(3) 		966.2
(1.3) 		892.2
(0.9) 		266.2
(-3) 		969

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1378
1 2 3 4 5 6 range
A 539.5
(-1.9)
P 		829.7
(0.2)
P 		395.1
(-3)
P 		450.2
(-2.6)
P 		818
(0.1)
P 		1209.5
(3)
P 		814
B 1203.5
(0.7)
P 		694.7
(-1.7)
P 		406
(-3)
P 		446
(-2.8)
P 		1189.5
(0.6)
P 		1706.9
(3)
P 		1301
C 1186.9
(0.5)
P 		642.9
(-1.9)
P 		433.2
(-2.8)
P 		387.6
(-3)
P 		918.1
(-0.7)
P 		1765.4
(3)
P 		1378
avr 976.6
(-0) 		722.4
(-1.4) 		411.4
(-3) 		427.9
(-2.9) 		975.2
(-0.1) 		1560.6
(3) 		1149
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 189914_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11252
Sequence Type Exemplar sequence
Representative Public ID R08C7.3 NCBI
Target Description R08C7.3 /REP_DB=WormBase Gene ID /WP=CE07426 /TR=Q27511 /GB=AAC48074.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=histone H2A variant
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_068168(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_068168 NCBI Caenorhabditis elegans R08C7.3 (R08C7.3) mRNA, complete cds. 11/11 None
SNAP00000031361 ENSEMBL cdna:SNAP chromosome:CEL140:IV:4446229:4446701:1 11/11 None
GENEFINDER00000031371 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:4446229:4446701:1 11/11 None
R08C7.3.2 ENSEMBL cdna:known chromosome:CEL140:IV:4446109:4446963:1 gene:R08C7.3 11/11 None
R08C7.3.1 ENSEMBL cdna:known chromosome:CEL140:IV:4446204:4446989:1 gene:R08C7.3 11/11 None
R08C7.3.3 ENSEMBL cdna:known chromosome:CEL140:IV:4446209:4446928:1 gene:R08C7.3 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
chrIV:4446234-4446707(+) 100.0 100.0
Public Domain and Genome References
Gene Title histone H2A variant
Ensembl R08C7.3
Entrez Gene 177212 Entrez gene
SwissProt Q27511 EMBL-EBI
WormBase CE07426 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:12398_AT histone H2A, putative at
ATH1-121501:263264_AT histone H2A, putative at
CANINE:1587456_AT similar to H2A histone family, member V isoform 5 cfa
CANINE_2:CFA.14197.1.A1_AT similar to H2A histone family, member V isoform 5 cfa
CANINE_2:CFA.20820.1.S1_AT similar to H2A histone family, member V isoform 5 cfa
CANINE_2:CFA.9499.1.A1_AT similar to H2A histone family, member V isoform 5 cfa
CANINE_2:CFAAFFX.5646.1.S1_S_AT similar to H2A histone family, member V isoform 5 cfa
DROSOPHILA_2:1639087_AT Histone H2A variant dm
DROSGENOME1:154022_AT Histone H2A variant dm
CHICKEN:GGAAFFX.11551.1.S1_S_AT H2A histone family, member V gga
HG-U133_PLUS_2:202487_S_AT H2A histone family, member V hs
HG-U133A:202487_S_AT H2A histone family, member V hs
HG-U133A_2:202487_S_AT H2A histone family, member V hs
HU35KSUBA:AA236820_AT H2A histone family, member V hs
HU35KSUBA:AA091752_AT H2A histone family, member V hs
HU35KSUBA:W07195_AT H2A histone family, member V hs
HU35KSUBA:D31550_AT H2A histone family, member V hs
HU35KSUBA:HUM_ALU_AT H2A histone family, member V hs
HU35KSUBB:HUM_ALU_AT H2A histone family, member V hs
HU35KSUBC:HUM_ALU_AT H2A histone family, member V hs
HU35KSUBD:HUM_ALU_AT H2A histone family, member V hs
HUGENEFL:HUM_ALU_AT H2A histone family, member V hs
HC-G110:HUM_ALU_AT H2A histone family, member V hs
HU35KSUBA:RC_AA489459_AT H2A histone family, member V hs
HU35KSUBA:RC_AA282343_AT H2A histone family, member V hs
HU35KSUBD:RC_AA456097_AT H2A histone family, member V hs
U133_X3P:G6912615_3P_X_AT H2A histone family, member V hs
U133_X3P:G6912615_3P_A_AT H2A histone family, member V hs
U133_X3P:HS.301005.1.S2_3P_AT H2A histone family, member V hs
U133_X3P:HS.301005.1.S1_3P_A_AT H2A histone family, member V hs
U133_X3P:HS.118236.0.S1_3P_AT H2A histone family, member V hs
HG-U133A_2:212205_AT H2A histone family, member V hs
HG-FOCUS:212205_AT H2A histone family, member V hs
HG-U133_PLUS_2:212205_AT H2A histone family, member V hs
HG-U133A:212205_AT H2A histone family, member V hs
HG-U133A_2:212206_S_AT H2A histone family, member V hs
HG-U133_PLUS_2:212206_S_AT H2A histone family, member V hs
HG-U133A:212206_S_AT H2A histone family, member V hs
HG-U133_PLUS_2:227085_AT H2A histone family, member V hs
HG-U133B:227085_AT H2A histone family, member V hs
HG-U95AV2:39046_AT H2A histone family, member V hs
HG-U95AV2:39092_AT H2A histone family, member V hs
HG-U95B:44821_AT H2A histone family, member V hs
HG-U95B:47250_AT H2A histone family, member V hs
HG-U95C:65132_AT H2A histone family, member V hs
HG-U95E:77491_AT H2A histone family, member V hs
MU11KSUBA:AA285607_S_AT H2A histone family, member V mm
MG-U74AV2:96710_AT H2A histone family, member V mm
MOE430A:1428029_A_AT H2A histone family, member V mm
MOUSE430A_2:1428029_A_AT H2A histone family, member V mm
MOUSE430_2:1428029_A_AT H2A histone family, member V mm
MG-U74BV2:115201_AT H2A histone family, member V, mRNA (cDNA clone MGC:41420 IMAGE:3369668) mm
MOE430B:1436596_AT H2A histone family, member V, mRNA (cDNA clone MGC:41420 IMAGE:3369668) mm
MOUSE430_2:1436596_AT H2A histone family, member V, mRNA (cDNA clone MGC:41420 IMAGE:3369668) mm
RG-U34A:RC_AA892470_AT H2A histone family, member V (predicted) rn
RAE230A:1388827_AT H2A histone family, member V (predicted) rn
RAT230_2:1388827_AT H2A histone family, member V (predicted) rn
YEAST_2:1776021_AT Histone variant H2AZ, exchanged for histone H2A in nucleosomes by the SWR1 complex; involved in transcriptional regulation through prevention of the spread of silent heterochromatin Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6334 nucleosome assembly inferred from electronic annotation QuickGO AmiGO
7001 chromosome organization and biogenesis (sensu Eukaryota) inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
786 nucleosome inferred from electronic annotation QuickGO AmiGO
5634 nucleus inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3677 DNA binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAC48074 Hypothetical protein R08C7.3 [Caenorhabditis elegans] ref|NP_500569.1| R08C7.3 [Caenorhabditis elegans] 8.0E-48
blast CAE58534 Hypothetical protein CBG01691 [Caenorhabditis briggsae] 8.0E-48
Protein Domains
Database ID Description E-Value
Pfam IPR007125 EMBL-EBI Histone core 7.2E-46
Sequence
Target Sequence 
>C. ELEGANS:189914_S_AT
ggaaagtccaaatcgaaggtcgtatcgagaagtgctcgcgctggactccaattccctgtc
ggacgtatccatcgtttcttgaagcagagaaccacttccagcggacgtgtcggagctact
gccgcagtatacagcgctgccatcctcgaatatctcaccgccgaagtcctcgagttggcc
ggtaacgcctccaaggatcttaaggtgaagcgtatcaccccaagacatcttcatcttgct
atcagaggagacgaagagctcgacactctcatcaaggccaccatcgccggaggaggagtc
atcccacacatccatcgttatttga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGAAAGTCCAAATCGAAGGTCGTAT 484 525 49 Antisense
GTCGTATCGAGAAGTGCTCGCGCTG 329 473 67 Antisense
ATCGAGAAGTGCTCGCGCTGGACTC 564 33 72 Antisense
GTCGGACGTATCCATCGTTTCTTGA 504 471 106 Antisense
GTATCCATCGTTTCTTGAAGCAGAG 557 455 113 Antisense
TGAAGCAGAGAACCACTTCCAGCGG 348 575 128 Antisense
GTCGGAGCTACTGCCGCAGTATACA 552 471 157 Antisense
CGGTAACGCCTCCAAGGATCTTAAG 634 241 228 Antisense
AAGGTGAAGCGTATCACCCCAAGAC 218 159 250 Antisense
GACATCTTCATCTTGCTATCAGAGG 202 371 272 Antisense
ATCCCACACATCCATCGTTATTTGA 686 37 349 Antisense
Sequence Source Affymetrix Proprietary Database