::: Dauer Metabolic Database :::

NetAffx Links

Cluster Members
Consensus/Exemplar
Group Members

GeneChip Array Information

Probe Set ID

172764_x_at

GeneChip Array

C. elegans Genome Array

Organism Common Name

Nematode

Probe Design Information

Transcript ID(Array Design)

affy.Ce.11905

Sequence Type

Exemplar sequence

Representative Public ID

F45F2.4 NCBI

Target Description

F45F2.4 /REP_DB=WormBase Gene ID /WP=CE04501 /GEN=his-7 /GB=AAC48024.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=histone H2A

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_072876(9), NM_072892(9), NM_072797(11), NM_072879(9), NM_072895(9)

Transcript Assignments

Representative Transcript	Description	Matching Probes	Related Probesets by Grade
NM_072876 NCBI	Caenorhabditis elegans HIStone family member (his-51) (his-51) mRNA, complete cds.	9/11	A
NM_072892 NCBI	Caenorhabditis elegans HIStone family member (his-21) (his-21) mRNA, complete cds.	9/11	A
NM_072797 NCBI	Caenorhabditis elegans HIStone family member (his-7) (his-7) mRNA, complete cds.	11/11	None
NM_072879 NCBI	Caenorhabditis elegans HIStone family member (his-53) (his-53) mRNA, complete cds.	9/11	A
NM_072895 NCBI	Caenorhabditis elegans HIStone family member (his-19) (his-19) mRNA, complete cds.	9/11	A
SNAP00000015093 ENSEMBL	cdna:SNAP chromosome:CEL140:V:8852375:8852758:-1	9/11	None
SNAP00000015096 ENSEMBL	cdna:SNAP chromosome:CEL140:V:8856257:8856640:1	9/11	None
GENEFINDER00000015145 ENSEMBL	cdna:GeneFinder chromosome:CEL140:V:8856257:8856640:1	9/11	None
GENEFINDER00000015151 ENSEMBL	cdna:GeneFinder chromosome:CEL140:V:8852375:8852758:-1	9/11	None
SNAP00000018184 ENSEMBL	cdna:SNAP chromosome:CEL140:V:8894470:8894853:-1	9/11	None
SNAP00000018187 ENSEMBL	cdna:SNAP chromosome:CEL140:V:8898352:8898735:1	9/11	None
GENEFINDER00000018197 ENSEMBL	cdna:GeneFinder chromosome:CEL140:V:8898352:8898735:1	9/11	None
GENEFINDER00000018200 ENSEMBL	cdna:GeneFinder chromosome:CEL140:V:8894470:8894853:-1	9/11	None
SNAP00000030772 ENSEMBL	cdna:SNAP chromosome:CEL140:V:8535968:8536351:1	11/11	None
GENEFINDER00000030788 ENSEMBL	cdna:GeneFinder chromosome:CEL140:V:8535968:8536351:1	11/11	None
F45F2.4 ENSEMBL	cdna:known chromosome:CEL140:V:8535968:8536351:1 gene:F45F2.4	11/11	None
F07B7.10 ENSEMBL	cdna:known chromosome:CEL140:V:8852375:8852758:-1 gene:F07B7.10	9/11	A
F07B7.3 ENSEMBL	cdna:known chromosome:CEL140:V:8856257:8856640:1 gene:F07B7.3	9/11	A
K06C4.3 ENSEMBL	cdna:known chromosome:CEL140:V:8894470:8894853:-1 gene:K06C4.3	9/11	A
K06C4.11 ENSEMBL	cdna:known chromosome:CEL140:V:8898352:8898735:1 gene:K06C4.11	9/11	A

Annotation Notes

Cross Hybridizing mRNA	Matched Probes	Nature of Assignment	Related Probesets by Grade
NM_069003	1/11	Cross Hyb Matching Probes	A B
NM_069007	1/11	Cross Hyb Matching Probes	A B
NM_069749	2/11	Cross Hyb Matching Probes	A B
NM_073062	1/11	Cross Hyb Matching Probes	A
NM_064486	2/11	Cross Hyb Matching Probes	A B
NM_064490	2/11	Cross Hyb Matching Probes	A B
NM_064497	2/11	Cross Hyb Matching Probes	A B
NM_074631	7/11	Cross Hyb Matching Probes	A B
NM_060241	1/11	Cross Hyb Matching Probes	A B
NM_069730	2/11	Cross Hyb Matching Probes	A B
NM_069740	2/11	Cross Hyb Matching Probes	A B
SNAP00000036752	1/11	Cross Hyb Matching Probes	None
GENEFINDER00000036755	1/11	Cross Hyb Matching Probes	None
SNAP00000009812	2/11	Cross Hyb Matching Probes	None
SNAP00000009816	2/11	Cross Hyb Matching Probes	None
GENEFINDER00000009836	2/11	Cross Hyb Matching Probes	None
GENEFINDER00000009839	2/11	Cross Hyb Matching Probes	None
SNAP00000034713	2/11	Cross Hyb Matching Probes	None
GENEFINDER00000034721	2/11	Cross Hyb Matching Probes	None
SNAP00000000481	1/11	Cross Hyb Matching Probes	None
GENEFINDER00000000494	1/11	Cross Hyb Matching Probes	None
SNAP00000002624	2/11	Cross Hyb Matching Probes	None
GENEFINDER00000002630	2/11	Cross Hyb Matching Probes	None
SNAP00000035837	2/11	Cross Hyb Matching Probes	None
GENEFINDER00000035847	2/11	Cross Hyb Matching Probes	None
SNAP00000036324	2/11	Cross Hyb Matching Probes	None
GENEFINDER00000036332	2/11	Cross Hyb Matching Probes	None
SNAP00000039431	1/11	Cross Hyb Matching Probes	None
GENEFINDER00000039433	1/11	Cross Hyb Matching Probes	None
SNAP00000009316	1/11	Cross Hyb Matching Probes	None
GENEFINDER00000009334	1/11	Cross Hyb Matching Probes	None
SNAP00000027915	7/11	Cross Hyb Matching Probes	None
GENEFINDER00000027922	7/11	Cross Hyb Matching Probes	None
T23D8.6	1/11	Cross Hyb Matching Probes	A B
ZK131.10	2/11	Cross Hyb Matching Probes	A B
ZK131.6	2/11	Cross Hyb Matching Probes	A B
F08G2.2	2/11	Cross Hyb Matching Probes	A B
F35H10.1	1/11	Cross Hyb Matching Probes	A B
F17E9.13	1/11	Cross Hyb Matching Probes	A B
B0035.7	2/11	Cross Hyb Matching Probes	A B
F54E12.5	2/11	Cross Hyb Matching Probes	A B
H02I12.7	2/11	Cross Hyb Matching Probes	A B
C50F4.13.1	1/11	Cross Hyb Matching Probes	A
C50F4.13.2	1/11	Cross Hyb Matching Probes	A
C50F4.13.3	1/11	Cross Hyb Matching Probes	A
T10C6.12	7/11	Cross Hyb Matching Probes	A B

Genomic Alignment of Consensus/Exemplar Sequence

Assembly

Wormbase March 2004

Alignment(s)

Position	Identity	Coverage	Cytoband
chrIV:8331653-8332036(+)	91.67	91.67
chrIV:11401068-11401448(+)	90.62	90.62
chrIV:11340388-11340768(+)	90.62	90.62
chrV:8535968-8536352(+)	100.0	100.0
chrV:8898352-8898736(+)	99.22	99.22
chrV:8856257-8856641(+)	99.22	99.22
chrV:16043390-16043774(+)	97.14	97.14
chrI:9997183-9997566(+)	90.36	90.36
chrII:13827219-13827603(+)	92.45	92.45
chrIV:8335323-8335706(-)	91.67	91.67
chrIV:7485824-7486207(-)	91.41	91.41
chrIV:11324036-11324416(-)	90.62	90.62
chrV:8894470-8894854(-)	99.22	99.22
chrV:8852375-8852759(-)	99.22	99.22
chrII:13821091-13821475(-)	92.45	92.45
chrII:13817654-13818037(-)	92.19	92.19

Public Domain and Genome References

Gene Title

histone H2A
histone H2A
histone H2A

Gene Symbol

his-51
his-53
his-7
his-19
his-21

Ensembl

F45F2.4
F07B7.10
F07B7.3
K06C4.3
K06C4.11

Entrez Gene

179261 Entrez gene
179265 Entrez gene
184112 Entrez gene
191669 Entrez gene
259800 Entrez gene

SwissProt

P09588 EMBL-EBI

WormBase

CE04501 Wormbase
CE04501 Wormbase
CE04501 Wormbase
CE04501 Wormbase
CE04501 Wormbase

Functional Annotations

Ortholog

ID	Title	Organism
ATGENOME1:17944_AT	histone H2A, putative	at
ATH1-121501:253920_AT	histone H2A, putative	at
ATGENOME1:17944_AT	histone H2A, putative	at
ATH1-121501:253920_AT	histone H2A, putative	at
CANINE_2:CFAAFFX.17024.1.S1_AT	similar to Histone H2A.1	cfa
CANINE_2:CFAAFFX.17664.1.S1_X_AT	similar to Histone H2A.1	cfa
CANINE_2:CFAAFFX.17680.1.S1_X_AT	similar to Histone H2A.1	cfa
CANINE_2:CFAAFFX.17024.1.S1_AT	similar to Histone H2A.1	cfa
CANINE_2:CFAAFFX.17664.1.S1_X_AT	similar to Histone H2A.1	cfa
CANINE_2:CFAAFFX.17680.1.S1_X_AT	similar to Histone H2A.1	cfa
CHICKEN:GGAAFFX.23665.1.A1_AT	similar to histone 2, H2ac	gga
CHICKEN:GGAAFFX.23666.1.S1_AT	similar to histone 2, H2ac	gga
CHICKEN:GGAAFFX.23665.1.A1_AT	similar to histone 2, H2ac	gga
CHICKEN:GGAAFFX.23666.1.S1_AT	similar to histone 2, H2ac	gga
U133_X3P:HS.134999.0.S1_3P_AT	Histone 1, H2am	hs
HG-U133A_2:214481_AT	Histone 1, H2am	hs
HG-FOCUS:214481_AT	Histone 1, H2am	hs
HG-U133_PLUS_2:214481_AT	Histone 1, H2am	hs
HG-U133A:214481_AT	Histone 1, H2am	hs
HG-U95AV2:33023_AT	Histone 1, H2am	hs
U133_X3P:HS.134999.0.S1_3P_AT	Histone 1, H2am	hs
HG-U133A_2:214481_AT	Histone 1, H2am	hs
HG-FOCUS:214481_AT	Histone 1, H2am	hs
HG-U133_PLUS_2:214481_AT	Histone 1, H2am	hs
HG-U133A:214481_AT	Histone 1, H2am	hs
HG-U95AV2:33023_AT	Histone 1, H2am	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	CAE60212	Hypothetical protein CBG03776 [Caenorhabditis briggsae]	9.0E-42

Protein Domains

Database	ID	Description	E-Value
Pfam	IPR007125 EMBL-EBI	Histone core	3.6E-55

Sequence

Target Sequence

>C. ELEGANS:172764_X_AT
aagtcccgctcatcaagagccggactccaattcccagttggtcgtcttcaccgtattctc
cgtaaaggaaactacgctcaacgtgttggagccggagccccagtttacctggctgctgtt
cttgagtacctcgctgctgaggttctcgagttggctggaaacgctgcccgtgacaacaag
aagaccagaattgccccaagacatctccaacttgccgtccgtaacgacgaggagttgaac
aaactgttggctggagtgaccatcgcacaa

BLASTn GenBank NR

Probe Info

Probe Sequence(5'-3')	Probe X	Probe Y	Probe Interrogation Position	Strandedness
AAGTCCCGCTCATCAAGAGCCGGAC	277	159	61	Antisense
TCCAATTCCCAGTTGGTCGTCTTCA	201	587	86	Antisense
TCTTCACCGTATTCTCCGTAAAGGA	165	617	105	Antisense
GCTCAACGTGTTGGAGCCGGAGCCC	59	301	136	Antisense
TTACCTGGCTGCTGTTCTTGAGTAC	186	683	165	Antisense
GAGTACCTCGCTGCTGAGGTTCTCG	312	399	184	Antisense
TCGAGTTGGCTGGAAACGCTGCCCG	380	595	206	Antisense
ACGCTGCCCGTGACAACAAGAAGAC	257	91	221	Antisense
AGACCAGAATTGCCCCAAGACATCT	129	71	242	Antisense
CCAACTTGCCGTCCGTAACGACGAG	375	275	267	Antisense
GTTGGCTGGAGTGACCATCGCACAA	635	435	306	Antisense

Sequence Source

Affymetrix Proprietary Database

Description	F45F2.4 /REP_DB=WormBase Gene ID /WP=CE04501 /GEN=his-7 /GB=AAC48024.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=histone H2A
Cluster	6grp_highest_10_10 > 58 6grp_high1_10_10 > 84 6grp_highest_nonorm > 68 6grp_total > 75 4grp_total > 57 6grp_cgc > 67 6grp_cgc_sub > In 4grp_rule_based > L3