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[171960_x_at] Core histone H2A/H2B/H3/H4

Description AV176858_rc /REP_DB=TREMBL Accession /GB=AV176858 /FEA=Transcript Cluster /DEF=Caenorhabditis elegans cDNA clone:yk519d8 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 73      6grp_high1_10_10 > 37      4grp_highest_8_8 > 59      4grp_high_8_8 > 25      6grp_highest_nonorm > 02      6grp_total > 27      4grp_total > 47      6grp_highest_sub > Cu      6grp_cgc > 06      6grp_cgc_sub > Cu      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2335
1 2 3 4 range
A 4381.8
(3)
P 		2778.2
(-1.7)
P 		2349.4
(-3)
P 		2487.1
(-2.6)
P 		2032
B 3905.5
(3)
P 		2297.4
(-3)
P 		2421.8
(-2.5)
P 		2992.1
(-0.4)
P 		1608
C 2938.4
(2.8)
P 		2972.3
(3)
P 		2047
(-3)
P 		2341.9
(-1.1)
P 		925
avr 3741.9
(3) 		2682.6
(-1.3) 		2272.7
(-3) 		2607
(-1.6) 		1469

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1817
1 2 3 4 5 6 range
A 2999.1
(3)
P 		2175.2
(0.1)
P 		2322.5
(0.6)
P 		1299.6
(-3)
P 		1422.4
(-2.6)
P 		2292.8
(0.5)
P 		1700
B 2945.9
(3)
P 		2537.3
(1.2)
P 		2211.8
(-0.2)
P 		1564
(-3)
P 		2057.2
(-0.9)
P 		2014.1
(-1)
P 		1382
C 3060.6
(2.8)
P 		2079.5
(-0.7)
P 		1449.2
(-3)
P 		1600.2
(-2.5)
P 		1894
(-1.4)
P 		3116.4
(3)
P 		1667
avr 3001.9
(3) 		2264
(0.1) 		1994.5
(-1) 		1487.9
(-3) 		1791.2
(-1.8) 		2474.4
(0.9) 		1514
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1231
1 2 3 4 range
A 1595.4
(3)
P 		603.1
(-1.8)
P 		614.2
(-1.8)
P 		364.1
(-3)
P 		1231
B 1245.4
(3)
P 		567.4
(-2.9)
P 		561.2
(-3)
P 		637.6
(-2.3)
P 		684
C 972.7
(3)
P 		854.5
(1.8)
P 		713.5
(0.3)
P 		394.9
(-3)
P 		578
avr 1271.2
(3) 		675
(-1.4) 		629.6
(-1.8) 		465.5
(-3) 		806

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 813
1 2 3 4 5 6 range
A 552.9
(0)
P 		773.6
(3)
P 		505.8
(-0.6)
P 		329.6
(-3)
P 		429.2
(-1.7)
P 		558.2
(0.1)
P 		444
B 1025
(3)
P 		844.6
(1.2)
P 		537.1
(-1.8)
P 		414.2
(-3)
P 		835.8
(1.1)
P 		751
(0.3)
P 		611
C 1134.4
(3)
P 		634.5
(-0.7)
P 		368.8
(-2.7)
P 		321.8
(-3)
P 		612.9
(-0.9)
P 		1043.3
(2.3)
P 		813
avr 904.1
(3) 		750.9
(1.3) 		470.6
(-1.7) 		355.2
(-3) 		626
(-0) 		784.2
(1.7) 		549
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 171960_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.27822
Sequence Type Exemplar sequence
Representative Public ID AV176858 NCBI
Target Description AV176858_rc /REP_DB=TREMBL Accession /GB=AV176858 /FEA=Transcript Cluster /DEF=Caenorhabditis elegans cDNA clone:yk519d8 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Transcript Cluster.
Annotation Method Description
Annotation Description This probe set was annotated using the Genome Target Overlap based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade B annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_067207
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
Y49E10.6.1 ENSEMBL cdna:known chromosome:CEL140:III:12367077:12368039:-1 gene:Y49E10.6 None
NM_067207 NCBI Caenorhabditis elegans HIStone family member (his-72) (his-72) mRNA, complete cds. A 
SNAP00000016068 ENSEMBL cdna:SNAP chromosome:CEL140:III:12367563:12368032:-1 None
Y49E10.6.2 ENSEMBL cdna:known chromosome:CEL140:III:12367077:12368041:-1 gene:Y49E10.6 None
GENEFINDER00000016112 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:12367563:12368032:-1 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
chrIII:12367412-12367775(-) 97.36 98.35
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:171960_X_AT
ggtgccatcggagtttccaggaggcatctgaagcataccttgtcggacttttcggaggac
accaacctgtgcgccatccacgccaagcgcgtcaccatcatgccaaaggacatgcaactc
gccagacgcatccgcggagaacgtgcttaagctccatcaccaattntcgaagcactttta
atattcattta

BLASTn GenBank NR
Note: "n"'s represent regions that are not probed by the probe sequences.
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGTGCCATCGGAGTTTCCAGGAGGC 687 501 20 Antisense
TCCAGGAGGCATCTGAAGCATACCT 436 589 35 Antisense
GAAGCATACCTTGTCGGACTTTTCG 462 339 49 Antisense
GCATACCTTGTCGGACTTTTCGGAG 514 307 52 Antisense
TTGTCGGACTTTTCGGAGGACACCA 557 669 59 Antisense
CTTTTCGGAGGACACCAACCTGTGC 134 187 67 Antisense
CGCGTCACCATCATGCCAAAGGACA 335 255 107 Antisense
CAAAGGACATGCAACTCGCCAGACG 175 193 123 Antisense
ACGCATCCGCGGAGAACGTGCTTAA 85 93 145 Antisense
GGAGAACGTGCTTAAGCTCCATCAC 665 519 155 Antisense
TCGAAGCACTTTTAATATTCATTTA 192 601 186 Antisense
Sequence Source Affymetrix Proprietary Database