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Cluster Members
Consensus/Exemplar
Group Members

GeneChip Array Information

Probe Set ID

187252_s_at

GeneChip Array

C. elegans Genome Array

Organism Common Name

Nematode

Probe Design Information

Transcript ID(Array Design)

affy.Ce.7730

Sequence Type

Exemplar sequence

Representative Public ID

C28H8.3 NCBI

Target Description

C28H8.3 /REP_DB=WormBase Gene ID /WP=CE01825 /TR=SW:Q09475 /GB=AAA62291.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=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_065882(11)

Transcript Assignments

Representative Transcript	Description	Matching Probes	Related Probesets by Grade
NM_065882 NCBI	Caenorhabditis elegans C28H8.3 (C28H8.3) mRNA, complete cds.	11/11	None
SNAP00000005435 ENSEMBL	cdna:SNAP chromosome:CEL140:III:5908710:5914433:1	11/11	None
GENEFINDER00000005449 ENSEMBL	cdna:GeneFinder chromosome:CEL140:III:5908710:5914433:1	11/11	None
C28H8.3.3 ENSEMBL	cdna:known chromosome:CEL140:III:5908647:5914665:1 gene:C28H8.3	11/11	None
C28H8.3.1 ENSEMBL	cdna:known chromosome:CEL140:III:5908649:5915102:1 gene:C28H8.3	11/11	None
C28H8.3.2 ENSEMBL	cdna:known chromosome:CEL140:III:5908649:5914665:1 gene:C28H8.3	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
chrIII:5908730-5914432(+)	100.0	100.0

Public Domain and Genome References

Gene Title

Ensembl

C28H8.3

Entrez Gene

175834 Entrez gene

SwissProt

Q09475 EMBL-EBI

WormBase

CE29195 Wormbase

Functional Annotations

Ortholog

ID	Title	Organism
CANINE_2:CFAAFFX.14223.1.S1_AT	similar to C28H8.3	cfa
CANINE_2:CFAAFFX.14226.1.S1_S_AT	similar to C28H8.3	cfa
CHICKEN:GGAAFFX.22996.1.S1_AT	similar to hypothetical protein FLJ20035	gga
CHICKEN:GGAAFFX.6052.1.S1_S_AT	similar to hypothetical protein FLJ20035	gga
HG-U133_PLUS_2:218986_S_AT	hypothetical protein FLJ20035	hs
HG-U133A:218986_S_AT	hypothetical protein FLJ20035	hs
HG-U133A_2:218986_S_AT	hypothetical protein FLJ20035	hs
HU35KSUBA:RC_AA040062_S_AT	hypothetical protein FLJ20035	hs
U133_X3P:G8923037_3P_A_AT	hypothetical protein FLJ20035	hs
HG-U95C:59283_AT	hypothetical protein FLJ20035	hs
MG-U74BV2:104792_AT	cDNA sequence BC013672	mm
MOE430A:1451777_AT	cDNA sequence BC013672	mm
MOUSE430A_2:1451777_AT	cDNA sequence BC013672	mm
MOUSE430_2:1451777_AT	cDNA sequence BC013672	mm
MOE430B:1439114_AT	cDNA sequence BC013672	mm
MOUSE430_2:1439114_AT	cDNA sequence BC013672	mm
MG-U74BV2:105440_AT	CDNA sequence BC013672, mRNA (cDNA clone MGC:19297 IMAGE:4037887)	mm
MU19KSUBB:TC29635_AT	CDNA sequence BC013672, mRNA (cDNA clone MGC:19297 IMAGE:4037887)	mm
MU19KSUBB:TC29635_G_AT	CDNA sequence BC013672, mRNA (cDNA clone MGC:19297 IMAGE:4037887)	mm

Gene Ontology

GO Biological Process (view graph)
ID	Description	Evidence	Links
8152	metabolism	inferred from electronic annotation	QuickGO AmiGO
9307	DNA restriction-modification system	inferred from electronic annotation	QuickGO AmiGO
GO Cellular Component (view graph)
ID	Description	Evidence	Links
16020	membrane	inferred from electronic annotation	QuickGO AmiGO
GO Molecular Function (view graph)
ID	Description	Evidence	Links
3676	nucleic acid binding	inferred from electronic annotation	QuickGO AmiGO
4386	helicase activity	inferred from electronic annotation	QuickGO AmiGO
5524	ATP binding	inferred from electronic annotation	QuickGO AmiGO
8026	ATP-dependent helicase activity	inferred from electronic annotation	QuickGO AmiGO
15668	type III site-specific deoxyribonuclease activity	inferred from electronic annotation	QuickGO AmiGO
16462	pyrophosphatase activity	inferred from electronic annotation	QuickGO AmiGO

Protein Similarities

Method	ID	Description	E-Value
blast	NP_498283	C28H8.3 [Caenorhabditis elegans] gb\|AAA62291.2\| Hypothetical protein C28H8.3 [Caenorhabditis elegans] sp\|Q09475\|YP93_CAEEL Putative helicase C28H8.3	0.0
blast	A88470	protein C28H8.3 [imported] - Caenorhabditis elegans	0.0
blast	CAE64358	Hypothetical protein CBG09045 [Caenorhabditis briggsae]	0.0

Protein Domains

Database	ID	Description	E-Value
Pfam	IPR001650 EMBL-EBI	Helicase, C-terminal	1.1E-13
Pfam	IPR001410 EMBL-EBI	DEAD/DEAH box helicase	1.8E-14

Sequence

Target Sequence

>C. ELEGANS:187252_S_AT
ggaaaacgtgcaggtgactctccgcggattgccatcactgctaaaaccctatgtggaaga
gtacaatagcactgtcaccggactctacaagcgtttcatggctgcttcttcccaggatgg
aaatctttttgatccatctttcgccgtcagtggcaagcttgattctgaaagtgtttccct
cactgaagatttccttgttgctccacttttcgatcaatactcccacgatgaatctttcct
tccagtcattgatttcaataagaaagaccatcgtggacgcaagattcaacgcaatgcatt
tgcctacgatttctatgttcatggatcccgtaacatgctcatggatgtcaatggtttgca
tgtcagcgttgcttggttccttctgcacgactttgcggcgattcttgaacgtcttgcaat
tggagtgcacaatatggctcgccctcaagatccactcgttctggtgctcgaagag

BLASTn GenBank NR

Probe Info

Probe Sequence(5'-3')	Probe X	Probe Y	Probe Interrogation Position	Strandedness
GGAAAACGTGCAGGTGACTCTCCGC	617	527	4647	Antisense
GGATTGCCATCACTGCTAAAACCCT	233	507	4672	Antisense
CCGGACTCTACAAGCGTTTCATGGC	591	263	4724	Antisense
AAATCTTTTTGATCCATCTTTCGCC	333	117	4767	Antisense
ATCTTTCGCCGTCAGTGGCAAGCTT	393	21	4782	Antisense
GTGTTTCCCTCACTGAAGATTTCCT	119	487	4817	Antisense
ATACTCCCACGATGAATCTTTCCTT	522	23	4863	Antisense
TTGCATGTCAGCGTTGCTTGGTTCC	7	703	5002	Antisense
TTGCGGCGATTCTTGAACGTCTTGC	698	701	5039	Antisense
CACAATATGGCTCGCCCTCAAGATC	619	193	5074	Antisense
TCCACTCGTTCTGGTGCTCGAAGAG	317	589	5097	Antisense

Sequence Source

Affymetrix Proprietary Database

Description	C28H8.3 /REP_DB=WormBase Gene ID /WP=CE01825 /TR=SW:Q09475 /GB=AAA62291.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation
Cluster	6grp_highest_10_10 > 66 6grp_high1_10_10 > 66 4grp_highest_8_8 > 38 4grp_high_8_8 > 03 6grp_highest_nonorm > 58 6grp_total > 57 4grp_total > 14 6grp_highest_sub > Da 6grp_high1_sub > Da 6grp_total_sub > Cup