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[172863_x_at] Core histone H2A/H2B/H3/H4

Description Y49E10.6 /REP_DB=WormBase Gene ID /WP=CE22223 /TR=Q9U281 /GB=CAB11546.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Core histone H2A-H2B-H3-H4
Cluster 6grp_highest_10_10 > 62      6grp_high1_10_10 > 27      4grp_highest_8_8 > 56      4grp_high_8_8 > 34      6grp_highest_nonorm > 06      6grp_total > 26      4grp_total > 37      6grp_highest_sub > Cu      6grp_cgc > 24      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 3942
1 2 3 4 range
A 11725.7
(1.5)
P 		10941.8
(-0.5)
P 		9999.8
(-3)
P 		12298.5
(3)
P 		2299
B 12881.6
(3)
P 		11482.4
(-0.3)
P 		10682.5
(-2.2)
P 		10332.5
(-3)
P 		2549
C 11988.7
(3)
P 		11988.6
(3)
P 		8939.8
(-3)
P 		9197.1
(-2.5)
P 		3049
avr 12198.7
(3) 		11470.9
(1.1) 		9874
(-3) 		10609.4
(-1.1) 		2325

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 4813
1 2 3 4 5 6 range
A 10323.2
(3)
P 		9550.6
(1.6)
P 		8613
(-0.1)
P 		7073.4
(-2.9)
P 		7030.5
(-3)
P 		8335.5
(-0.6)
P 		3293
B 11440.5
(3)
P 		9215.4
(-0.1)
P 		8717.7
(-0.8)
P 		7844.5
(-2)
P 		7096.7
(-3)
P 		7735.4
(-2.1)
P 		4344
C 10073.9
(3)
P 		9164.1
(1.4)
P 		7399
(-1.7)
P 		6627.7
(-3)
P 		7019
(-2.3)
P 		8268.1
(-0.1)
P 		3446
avr 10612.5
(3) 		9310
(0.8) 		8243.2
(-1) 		7181.9
(-2.8) 		7048.7
(-3) 		8113
(-1.2) 		3564
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2719
1 2 3 4 range
A 4269.3
(3)
P 		2375.2
(-1.6)
P 		2614.1
(-1)
P 		1800.3
(-3)
P 		2469
B 4107.8
(3)
P 		2835.9
(-1)
P 		2475.4
(-2.1)
P 		2201.9
(-3)
P 		1906
C 3968.6
(3)
P 		3446.8
(1.7)
P 		3115.8
(0.9)
P 		1550.8
(-3)
P 		2418
avr 4115.2
(3) 		2886
(-0.3) 		2735.1
(-0.7) 		1851
(-3) 		2264

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2648
1 2 3 4 5 6 range
A 1903
(-2.6)
P 		3396.7
(3)
P 		1875.7
(-2.7)
P 		1794
(-3)
P 		2121.5
(-1.8)
P 		2029.4
(-2.1)
P 		1603
B 3980.7
(3)
P 		3067.4
(0.1)
P 		2116.9
(-2.9)
P 		2077.8
(-3)
P 		2883.3
(-0.5)
P 		2884.5
(-0.5)
P 		1903
C 3734
(3)
P 		2796.3
(0.7)
P 		1883.2
(-1.6)
P 		1332.8
(-3)
P 		2271.2
(-0.7)
P 		2767.8
(0.6)
P 		2401
avr 3205.9
(3) 		3086.8
(2.5) 		1958.6
(-2.1) 		1734.9
(-3) 		2425.3
(-0.2) 		2560.6
(0.4) 		1471
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172863_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6197
Sequence Type Exemplar sequence
Representative Public ID Y49E10.6 NCBI
Target Description Y49E10.6 /REP_DB=WormBase Gene ID /WP=CE22223 /TR=Q9U281 /GB=CAB11546.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Core histone H2A-H2B-H3-H4
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_067207(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067207 NCBI Caenorhabditis elegans HIStone family member (his-72) (his-72) mRNA, complete cds. 11/11 None
SNAP00000016068 ENSEMBL cdna:SNAP chromosome:CEL140:III:12367563:12368032:-1 11/11 None
GENEFINDER00000016112 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:12367563:12368032:-1 11/11 None
Y49E10.6.2 ENSEMBL cdna:known chromosome:CEL140:III:12367077:12368041:-1 gene:Y49E10.6 11/11 None
Y49E10.6.1 ENSEMBL cdna:known chromosome:CEL140:III:12367077:12368039:-1 gene:Y49E10.6 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_072798 2/11 Cross Hyb Matching Probes A B 
NM_072896 2/11 Cross Hyb Matching Probes A B 
NM_072875 2/11 Cross Hyb Matching Probes A B 
NM_074632 1/11 Cross Hyb Matching Probes A B 
NM_072891 2/11 Cross Hyb Matching Probes A B 
SNAP00000015092 2/11 Cross Hyb Matching Probes None
GENEFINDER00000015146 2/11 Cross Hyb Matching Probes None
SNAP00000018183 2/11 Cross Hyb Matching Probes None
SNAP00000018188 2/11 Cross Hyb Matching Probes None
GENEFINDER00000018196 2/11 Cross Hyb Matching Probes None
GENEFINDER00000018198 2/11 Cross Hyb Matching Probes None
SNAP00000027916 1/11 Cross Hyb Matching Probes None
GENEFINDER00000027930 1/11 Cross Hyb Matching Probes None
SNAP00000030773 2/11 Cross Hyb Matching Probes None
GENEFINDER00000030784 2/11 Cross Hyb Matching Probes None
F45F2.13 2/11 Cross Hyb Matching Probes A B 
F07B7.5 2/11 Cross Hyb Matching Probes A B 
K06C4.13 2/11 Cross Hyb Matching Probes A B 
K06C4.5 2/11 Cross Hyb Matching Probes A B 
T10C6.13 1/11 Cross Hyb Matching Probes A B 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIII:12367558-12368028(-) 100.0 100.0
Public Domain and Genome References
Gene Title Core histone H2A/H2B/H3/H4
Gene Symbol his-72
Ensembl Y49E10.6
Entrez Gene 176660 Entrez gene
SwissProt Q9U281 EMBL-EBI
WormBase CE22223 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:247180_AT histone H3 at
CANINE_2:CFAAFFX.17935.1.S1_S_AT similar to H3 histone, family 2 isoform 2 cfa
CANINE_2:CFAAFFX.945.1.S1_AT similar to H3 histone, family 2 isoform 2 cfa
CANINE_2:CFAAFFX.945.1.S1_S_AT similar to H3 histone, family 2 isoform 2 cfa
CHICKEN:GGA.6103.1.S1_AT similar to histone protein Hist2h3c1 gga
CHICKEN:GGA.6103.1.S1_X_AT similar to histone protein Hist2h3c1 gga
HG-U95AV2:34964_AT histone 1, H3d hs
HG-U133A:214472_AT histone 1, H3d hs
HG-U133_PLUS_2:214472_AT histone 1, H3d hs
HG-U133A_2:214472_AT histone 1, H3d hs
HG-FOCUS:214472_AT histone 1, H3d hs
HU35KSUBC:RC_T47071_F_AT histone 1, H3d hs
HUGENEFL:Z80776_AT histone 1, H3d hs
U133_X3P:HS.239458.0.S1_3P_S_AT histone 1, H3d hs
U133_X3P:HS.143042.0.S1_3P_AT histone 1, H3d hs
HG-U133A_2:214522_X_AT histone 1, H3d hs
HG-FOCUS:214522_X_AT histone 1, H3d hs
HG-U133_PLUS_2:214522_X_AT histone 1, H3d hs
HG-U133A:214522_X_AT histone 1, H3d hs
HG-U95AV2:31693_F_AT histone 1, H3d hs
RG-U34A:RC_AI045794_AT histone 1, H2ai (predicted) rn
RG-U34C:RC_AI179071_AT histone 1, H2ai (predicted) rn
RG-U34C:RC_AI137974_I_AT histone 1, H2ai (predicted) rn
RAE230A:1388276_AT histone 1, H2ai (predicted) rn
RAT230_2:1388276_AT histone 1, H2ai (predicted) rn
RG-U34C:RC_AI176481_AT Histone 1, H2ai (predicted) rn
YEAST_2:1775541_AT One of two identical histone H3 proteins (see also HHT1); core histone required for chromatin assembly, involved in heterochromatin-mediated telomeric and HM silencing; regulated by acetylation, methylation, and mitotic phosphorylation 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 CAB11546 Hypothetical protein Y49E10.6 [Caenorhabditis elegans] ref|NP_499608.1| HIStone family member (his-72) [Caenorhabditis elegans] emb|CAE66490.1| Hypothetical protein CBG11770 [Caenorhabditis briggsae] 2.0E-70
blast AAB04902 Histone protein 71 [Caenorhabditis elegans] ref|NP_509344.1| HIStone family member (his-71) [Caenorhabditis elegans] sp|Q10453|H33_CAEEL Histone H3.3 5.0E-70
Protein Domains
Database ID Description E-Value
Pfam IPR007125 EMBL-EBI Histone core 2.0E-29
Sequence
Target Sequence 
>C. ELEGANS:172863_X_AT
caaaccgctcgtaaatccaccggaggaaaggctccaagaaagcagttggccaccaaggcc
gcccgcaaatcggctccaaccaccggaggagtcaagaagccacatcgttaccgtccagga
actgtcgctctccgtgagattcgtcgttaccagaagtcgactgagcttctcatccgcaag
cttcctttccaacgtctcgttcgtgagattgcccaggacttcaagactgatctccgcttc
cagtcggctgccatcggagctctccaggaggcatctgaagcatacctcgtcggactcttc
gaggacaccaacctgtgcgccatccacgccaagcgcgtcaccatcatgccaaaggaca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CAAACCGCTCGTAAATCCACCGGAG 554 179 28 Antisense
GAAAGCAGTTGGCCACCAAGGCCGC 206 359 65 Antisense
GAGTCAAGAAGCCACATCGTTACCG 421 399 116 Antisense
ATCGTTACCGTCCAGGAACTGTCGC 279 35 131 Antisense
TCTCCGTGAGATTCGTCGTTACCAG 321 607 156 Antisense
AGAAGTCGACTGAGCTTCTCATCCG 286 75 179 Antisense
CCTTTCCAACGTCTCGTTCGTGAGA 35 261 211 Antisense
CAGGACTTCAAGACTGATCTCCGCT 380 209 241 Antisense
TGCCATCGGAGCTCTCCAGGAGGCA 438 585 276 Antisense
ATACCTCGTCGGACTCTTCGAGGAC 705 21 309 Antisense
CGCGTCACCATCATGCCAAAGGACA 334 255 361 Antisense
Sequence Source Affymetrix Proprietary Database