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Cluster Members
Consensus/Exemplar
Group Members

GeneChip Array Information

Probe Set ID

180099_s_at

GeneChip Array

C. elegans Genome Array

Organism Common Name

Nematode

Probe Design Information

Transcript ID(Array Design)

affy.Ce.1237

Sequence Type

Exemplar sequence

Representative Public ID

Y54E5A.5 NCBI

Target Description

Y54E5A.5 /REP_DB=WormBase Gene ID /WP=CE20316 /TR=Q9XWK2 /GB=CAA21658.1 /SUBMIT=HINXTON /CHR=1 /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_061152(11)

Transcript Assignments

Representative Transcript	Description	Matching Probes	Related Probesets by Grade
NM_061152 NCBI	Caenorhabditis elegans Y54E5A.5 (Y54E5A.5) mRNA, complete cds.	11/11	None
SNAP00000041548 ENSEMBL	cdna:SNAP chromosome:CEL140:I:14707364:14715985:-1	11/11	None
GENEFINDER00000041553 ENSEMBL	cdna:GeneFinder chromosome:CEL140:I:14715284:14715985:-1	11/11	None
Y54E5A.5.1 ENSEMBL	cdna:known chromosome:CEL140:I:14714776:14715993:-1 gene:Y54E5A.5	11/11	None
Y54E5A.5.2 ENSEMBL	cdna:known chromosome:CEL140:I:14715169:14715995:-1 gene:Y54E5A.5	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
chrI:14715214-14715916(-)	100.0	100.0

Public Domain and Genome References

Gene Title

Ensembl

Y54E5A.5

Entrez Gene

173330 Entrez gene

SwissProt

Q9XWK2 EMBL-EBI

WormBase

CE20316 Wormbase

Functional Annotations

Ortholog

ID	Title	Organism
CANINE:1603229_X_AT	similar to CG7519-PA	cfa
CANINE:1603871_X_AT	similar to CG7519-PA	cfa
CANINE:1599340_X_AT	similar to CG7519-PA	cfa
CANINE:1599016_X_AT	similar to CG7519-PA	cfa
CANINE:1594965_X_AT	similar to CG7519-PA	cfa
CANINE:1583770_X_AT	similar to CG7519-PA	cfa
CANINE_2:CFA.12181.1.A1_S_AT	similar to CG7519-PA	cfa
DROSOPHILA_2:1633822_AT		dm
DROSGENOME1:149182_AT		dm
HG-U133_PLUS_2:224177_S_AT	chromosome X open reading frame 26	hs
HG-U133B:224177_S_AT	chromosome X open reading frame 26	hs
HG-U133_PLUS_2:223294_AT	chromosome X open reading frame 26	hs
HG-U133B:223294_AT	chromosome X open reading frame 26	hs
U133_X3P:G7106879_3P_A_AT	chromosome X open reading frame 26	hs
U133_X3P:G12654754_3P_AT	chromosome X open reading frame 26	hs
HG-U95E:71756_AT	chromosome X open reading frame 26	hs
HG-U95E:84523_AT	chromosome X open reading frame 26	hs
HG-U95E:90144_AT	chromosome X open reading frame 26	hs
MU11KSUBA:AA050541_S_AT	RIKEN cDNA 2610029G23 gene	mm
MG-U74AV2:161520_AT	RIKEN cDNA 2610029G23 gene	mm
MOE430A:1417921_AT	RIKEN cDNA 2610029G23 gene	mm
MOUSE430A_2:1417921_AT	RIKEN cDNA 2610029G23 gene	mm
MOUSE430_2:1417921_AT	RIKEN cDNA 2610029G23 gene	mm
MU19KSUBC:TC36647_AT	RIKEN cDNA 2610029G23 gene (2610029G23Rik), mRNA	mm
MU19KSUBC:TC36647_G_AT	RIKEN cDNA 2610029G23 gene (2610029G23Rik), mRNA	mm
RG-U34B:RC_AA965113_AT	similar to RIKEN cDNA 2610029G23	rn
RAE230A:1372543_AT	similar to RIKEN cDNA 2610029G23	rn
RAT230_2:1372543_AT	similar to RIKEN cDNA 2610029G23	rn

Protein Similarities

Method	ID	Description	E-Value
blast	CAA21657	Hypothetical protein Y54E5A.4 [Caenorhabditis elegans] ref\|NP_493552.1\| Nuclear Pore complex Protein family member (npp-4) [Caenorhabditis elegans]	1.0E-123
blast	CAA21658	Hypothetical protein Y54E5A.5 [Caenorhabditis elegans] ref\|NP_493553.1\| Y54E5A.5 [Caenorhabditis elegans]	2.0E-83
blast	CAA21658	Hypothetical protein Y54E5A.5 [Caenorhabditis elegans] ref\|NP_493553.1\| Y54E5A.5 [Caenorhabditis elegans]	6.0E-80
blast	CAE72566	Hypothetical protein CBG19750 [Caenorhabditis briggsae]	1.0E-70

Protein Domains

Database	ID	Description	E-Value
Pfam	IPR008476 EMBL-EBI	Protein of unknown function DUF757	5.7E-104

Sequence

Target Sequence

>C. ELEGANS:180099_S_AT
ggcgatcaaagccggcgaacggtccgaagttcacatgaatctgataatgcggtgtgacac
tcgggttcttcggctcaacaagcatcaggatgcgattctcgccgcatttcgaagctcatt
ccccgatttgaatgtggaggaggtgacgacgagtttgctgaaagacggcggagccaagga
gacatggcgcgagttttgtgagcaattcaaggatatcgtcgacgattattcaatgggaac
actgatgagaattcatgcttcgaaggcttacagtccggaaaatactgtggttgttccaag
aatcatctacctggcaatcgagatggcacgcaacgtggagggtgtcaac

BLASTn GenBank NR

Probe Info

Probe Sequence(5'-3')	Probe X	Probe Y	Probe Interrogation Position	Strandedness
GGCGATCAAAGCCGGCGAACGGTCC	434	539	72	Antisense
AACGGTCCGAAGTTCACATGAATCT	525	143	89	Antisense
AATGCGGTGTGACACTCGGGTTCTT	276	167	117	Antisense
GGTTCTTCGGCTCAACAAGCATCAG	219	507	135	Antisense
ATCAGGATGCGATTCTCGCCGCATT	640	27	155	Antisense
GAAGCTCATTCCCCGATTTGAATGT	280	343	182	Antisense
GAGGAGGTGACGACGAGTTTGCTGA	634	403	208	Antisense
GAGACATGGCGCGAGTTTTGTGAGC	473	393	250	Antisense
CATGCTTCGAAGGCTTACAGTCCGG	499	203	325	Antisense
TACCTGGCAATCGAGATGGCACGCA	692	645	379	Antisense
GGCACGCAACGTGGAGGGTGTCAAC	706	535	396	Antisense

Sequence Source

Affymetrix Proprietary Database

Description	Y54E5A.5 /REP_DB=WormBase Gene ID /WP=CE20316 /TR=Q9XWK2 /GB=CAA21658.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation
Cluster	6grp_highest_10_10 > 74 6grp_high1_10_10 > 57 4grp_highest_8_8 > 23 4grp_high_8_8 > 06 6grp_highest_nonorm > 86 6grp_total > 58 4grp_total > 02 6grp_highest_sub > Cu 6grp_high1_sub > Cu 6grp_total_sub > Cup 4grp_rule_based > L4