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[172899_x_at] Core histones H2A, H2B, H3 and H4

Description F08G2.3 /REP_DB=WormBase Gene ID /WP=CE03253 /TR=Q9TW44 /GB=CAB04057.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=Core histones H2A, H2B, H3 and H4
Cluster 6grp_highest_10_10 > 78      6grp_high1_10_10 > 96      4grp_highest_8_8 > 14      4grp_high_8_8 > 14      6grp_highest_nonorm > 79      6grp_total > 86      4grp_total > 09      6grp_highest_sub > In      6grp_cgc > 58      6grp_high1_sub > In      6grp_cgc_sub > In      6grp_total_sub > Increase      6grp_rule_based > S6      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 5112
1 2 3 4 range
A 946.3
(-3)
P 		2132.7
(-1.6)
P 		2018.4
(-1.7)
P 		5999.8
(3)
P 		5054
B 888.1
(-3)
P 		1533.2
(-2.1)
P 		1987.7
(-1.5)
P 		5414.6
(3)
P 		4527
C 992.1
(-3)
P 		1596.3
(-2.2)
P 		1727
(-2)
P 		5511
(3)
P 		4519
avr 942.2
(-3) 		1754.1
(-2) 		1911
(-1.8) 		5641.8
(3) 		4700

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2200
1 2 3 4 5 6 range
A 1078.5
(-2.6)
P 		966.8
(-3)
P 		1190.6
(-2.3)
P 		1629.5
(-0.8)
P 		1853.8
(-0.1)
P 		2798.3
(3)
P 		1832
B 761.8
(-3)
P 		964.7
(-2.4)
P 		1430.4
(-1.2)
P 		1462.7
(-1.1)
P 		1912.5
(0.2)
P 		2942.9
(3)
P 		2181
C 930.1
(-3)
P 		991.8
(-2.8)
P 		1283.5
(-2)
P 		1346.2
(-1.8)
P 		2001.9
(0.2)
P 		2961.7
(3)
P 		2032
avr 923.5
(-3) 		974.4
(-2.8) 		1301.5
(-1.9) 		1479.5
(-1.3) 		1922.7
(0) 		2901
(3) 		1978
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 871
1 2 3 4 range
A 344.5
(-3)
P 		463
(-1.7)
P 		527.6
(-0.9)
P 		878.2
(3)
P 		534
B 283.2
(-3)
P 		378.7
(-2.3)
P 		460.6
(-1.8)
P 		1153.8
(3)
P 		871
C 328.4
(-3)
P 		458.9
(-1.7)
P 		601.9
(-0.3)
P 		929.2
(3)
P 		601
avr 318.7
(-3) 		433.5
(-2) 		530
(-1.1) 		987.1
(3) 		668

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 899
1 2 3 4 5 6 range
A 198.8
(-3)
P 		343.8
(-1.2)
P 		259.3
(-2.2)
P 		413.3
(-0.3)
P 		559.4
(1.5)
P 		681.3
(3)
P 		483
B 265.1
(-3)
P 		321.1
(-2.6)
P 		347.3
(-2.4)
P 		387.4
(-2.1)
P 		777
(0.7)
P 		1097.4
(3)
P 		832
C 344.7
(-2.4)
P 		302.6
(-2.7)
P 		326.7
(-2.5)
P 		270.7
(-3)
P 		647.8
(0.1)
P 		991.5
(3)
P 		721
avr 269.5
(-3) 		322.5
(-2.5) 		311.1
(-2.6) 		357.1
(-2.2) 		661.4
(0.6) 		923.4
(3) 		654
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172899_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3448
Sequence Type Exemplar sequence
Representative Public ID F08G2.3 NCBI
Target Description F08G2.3 /REP_DB=WormBase Gene ID /WP=CE03253 /TR=Q9TW44 /GB=CAB04057.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=Core histones H2A, H2B, H3 and 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_064498(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_064498 NCBI Caenorhabditis elegans HIStone family member (his-42) (his-42) mRNA, complete cds. 11/11 None
SNAP00000034714 ENSEMBL cdna:SNAP chromosome:CEL140:II:13828184:13828594:-1 11/11 None
GENEFINDER00000034724 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:13828184:13828594:-1 11/11 None
F08G2.3 ENSEMBL cdna:known chromosome:CEL140:II:13828184:13828594:-1 gene:F08G2.3 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_068803 1/11 Cross Hyb Matching Probes A 
NM_065411 1/11 Cross Hyb Matching Probes A 
NM_064489 8/11 Cross Hyb Matching Probes A 
NM_064493 8/11 Cross Hyb Matching Probes A 
NM_064494 8/11 Cross Hyb Matching Probes A 
SNAP00000009815 8/11 Cross Hyb Matching Probes None
SNAP00000009819 8/11 Cross Hyb Matching Probes None
SNAP00000009820 8/11 Cross Hyb Matching Probes None
GENEFINDER00000009834 8/11 Cross Hyb Matching Probes None
GENEFINDER00000009837 8/11 Cross Hyb Matching Probes None
GENEFINDER00000009841 8/11 Cross Hyb Matching Probes None
GENEFINDER00000016650 1/11 Cross Hyb Matching Probes None
SNAP00000016641 1/11 Cross Hyb Matching Probes None
SNAP00000005174 1/11 Cross Hyb Matching Probes None
GENEFINDER00000005184 1/11 Cross Hyb Matching Probes None
ZK131.7 8/11 Cross Hyb Matching Probes A 
ZK131.3 8/11 Cross Hyb Matching Probes A 
ZK131.2 8/11 Cross Hyb Matching Probes A 
E03A3.4 1/11 Cross Hyb Matching Probes A 
F55G1.2 1/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:13823541-13823952(+) 97.81 97.81
chrII:13820103-13820514(+) 97.81 97.81
chrIV:11326564-11326975(+) 91.97 91.97
chrIV:8334292-8334703(+) 91.97 91.97
chrIV:7488238-7488649(+) 91.73 91.73
chrII:13828180-13828591(-) 100.0 100.0
chrII:13824742-13825153(-) 97.81 97.81
chrIV:11406427-11406838(-) 92.21 92.21
chrIV:11337829-11338240(-) 91.97 91.97
Public Domain and Genome References
Gene Title Core histones H2A, H2B, H3 and H4
Gene Symbol his-42
Ensembl F08G2.3
Entrez Gene 184200 Entrez gene
SwissProt P08898 EMBL-EBI
WormBase CE03253 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:257714_AT histone H3 at
CANINE_2:CFAAFFX.16507.1.S1_AT similar to histone 1, H2ai (predicted) cfa
CANINE_2:CFAAFFX.17046.1.S1_AT similar to histone 1, H2ai (predicted) cfa
CANINE_2:CFAAFFX.791.1.S1_S_AT similar to histone 1, H2ai (predicted) cfa
CANINE_2:CFAAFFX.945.1.S1_AT similar to histone 1, H2ai (predicted) cfa
CANINE_2:CFAAFFX.945.1.S1_S_AT similar to histone 1, H2ai (predicted) cfa
HG-U133_PLUS_2:208577_AT histone 1, H3c hs
HG-U133A:208577_AT histone 1, H3c hs
HG-FOCUS:208577_AT histone 1, H3c hs
HG-U133A_2:208577_AT histone 1, H3c hs
U133_X3P:G4504284_3P_AT histone 1, H3c hs
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 CAB05834 Hypothetical protein ZK131.7 [Caenorhabditis elegans] emb|CAB05833.1| Hypothetical protein ZK131.3 [Caenorhabditis elegans] emb|CAB05831.1| Hypothetical protein ZK131.2 [Caenorhabditis elegans] emb|CAA97411.1| Hypothetical protein B0035.10 [Caenorhabditis elegans] emb|CAA92733.1| Hypothetical protein F22B3.2 [Caenorhabditis elegans] emb|CAB07653.1| Hypothetical protein T10C6.13 [Caenorhabditis elegans] emb|CAB05209.1| Hypothetical protein F54E12.1 [Caenorhabditis elegans] emb|CAB04057.1| Hypothetical protein F08G2.3 [Caenorhabditis elegans] gb|AAC05102.1| Histone protein 32 [Caenorhabditis elegans] gb|AAK84514.1| Histone protein 49 [Caenorhabditis elegans] gb|AAF98226.1| Histone protein 17 [Caenorhabditis elegans] gb|AAF98231.1| Histone protein 27 [Caenorhabditis elegans] emb|CAA33644.1| Histone protein [Caenorhabditis elegans] gb|AAB00650.1| Histone protein 59 [Caenorhabditis elegans] gb|AAC48033.1| Histone protein 6 [Caenorhabditis elegans] ref|NP_505292.1| HIStone family member (his-27) [Caenorhabditis elegans] ref|NP_505297.1| HIStone family member (his-17) [Caenorhabditis elegans] ref|NP_496890.1| HIStone family member (his-13) [Caenorhabditis elegans] ref|NP_505199.1| HIStone family member (his-6) [Caenorhabditis elegans] ref|NP_501204.1| F55G1.2 [Caenorhabditis elegans] ref|NP_502138.1| HIStone family member (his-55) [Caenorhabditis elegans] ref|NP_502153.1| HIStone family member (his-63) [Caenorhabditis elegans] ref|NP_496899.1| HIStone family member (his-42) [Caenorhabditis elegans] ref|NP_505276.1| HIStone family member (his-49) [Caenorhabditis elegans] ref|NP_502134.1| HIStone family member (his-45) [Caenorhabditis elegans] ref|NP_507033.1| HIStone family member (his-2) [Caenorhabditis elegans] ref|NP_501407.1| HIStone family member (his-32) [Caenorhabditis elegans] ref|NP_496895.1| HIStone family member (his-25) [Caenorhabditis elegans] ref|NP_496894.1| HIStone family member (his-9) [Caenorhabditis elegans] gb|AAG50235.1| histone H3 [Caenorhabditis elegans] pir||HSKW3 histone H3 - Caenorhabditis elegans 5.0E-70
blast P08898 Histone H3 1.0E-69
blast AAH74969 H3/o protein [Homo sapiens] 2.0E-68
Protein Domains
Database ID Description E-Value
Pfam IPR007125 EMBL-EBI Histone core 1.6E-29
Sequence
Target Sequence 
>C. ELEGANS:172899_X_AT
tggctcgtactaagcaaaccgcccgtaaatcgaccggaggaaaggctccaagaaagcaat
tggccaccaaggctgcccgtaaatcggctccagcttccggaggtgtcaagaagccacatc
gttatcgtccaggaaccgtcgctctacgtgagatcagacgttaccagaaatccaccgagc
ttctcatccgcagagctccattccagcgtctcgtccgggagatcgcccaggatttcaaga
ccgatcttcgattccagtcttcagctgttatggctcttcaagaggccgccgaggcttacc
tcgttggacttttcgaggataccaacttgtgtgccatccat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGGCTCGTACTAAGCAAACCGCCCG 221 539 14 Antisense
CCACCAAGGCTGCCCGTAAATCGGC 305 273 77 Antisense
CAAGAAGCCACATCGTTATCGTCCA 334 183 120 Antisense
AACCGTCGCTCTACGTGAGATCAGA 269 147 147 Antisense
CAGACGTTACCAGAAATCCACCGAG 382 201 168 Antisense
GGAGATCGCCCAGGATTTCAAGACC 709 517 231 Antisense
TCAAGACCGATCTTCGATTCCAGTC 481 629 248 Antisense
GATTCCAGTCTTCAGCTGTTATGGC 29 435 263 Antisense
TCTTCAAGAGGCCGCCGAGGCTTAC 72 607 288 Antisense
GGCTTACCTCGTTGGACTTTTCGAG 359 371 306 Antisense
GGATACCAACTTGTGTGCCATCCAT 174 511 330 Antisense
Sequence Source Affymetrix Proprietary Database