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[187227_at]

Description Y54E10A.14 /REP_DB=WormBase Gene ID /WP=CE24443 /TR=Q9N3E5 /GB=AAF60768.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation
Cluster 6grp_total > 52      4grp_total > 12      6grp_cgc > 90      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 100
1 2 3 4 range
A 39.5
(-3)
A 		62.9
(-1.1)
A 		49.8
(-2.1)
A 		112
(3)
A 		73
B 35.6
(-1.6)
A 		62.1
(3)
A 		44.1
(-0.1)
A 		27.4
(-3)
A 		35
C 76.8
(1.3)
A 		14.8
(-2.8)
A 		12.2
(-3)
A 		103.2
(3)
A 		91
avr 50.6
(-1) 		46.6
(-1.5) 		35.4
(-3) 		80.9
(3) 		46

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 80
1 2 3 4 5 6 range
A 86.2
(3)
A 		15.7
(-2.5)
A 		37
(-0.8)
A 		46.2
(-0.1)
A 		55.5
(0.6)
A 		9.2
(-3)
A 		77
B 49.3
(-2.9)
A 		49.3
(-2.9)
A 		87.5
(3)
A 		68.6
(0.1)
A 		70.8
(0.4)
A 		48.7
(-3)
A 		39
C 7.6
(-3)
A 		36.4
(-0.4)
A 		73.8
(3)
A 		27.4
(-1.2)
A 		11.3
(-2.7)
A 		42
(0.1)
A 		66
avr 47.7
(-0.4) 		33.8
(-2.9) 		66.1
(3) 		47.4
(-0.4) 		45.9
(-0.7) 		33.3
(-3) 		33
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 21
1 2 3 4 range
A 14.4
(-0.5)
A 		13.6
(-1.9)
A 		13
(-3)
A 		16.4
(3)
A 		3
B 11.3
(0.5)
A 		15.3
(3)
A 		10.2
(-0.2)
A 		5.8
(-3)
A 		10
C 25.4
(3)
A 		4.2
(-3)
A 		4.2
(-3)
A 		17.4
(0.7)
A 		21
avr 17
(3) 		11
(-1.6) 		9.1
(-3) 		13.2
(0.1) 		8

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 27
1 2 3 4 5 6 range
A 15.9
(2.6)
A 		5.6
(-1.6)
A 		8
(-0.6)
A 		11.7
(0.9)
A 		16.8
(3)
A 		2.2
(-3)
A 		15
B 17.1
(-2.7)
A 		16.4
(-3)
A 		21.2
(-0.7)
A 		18.2
(-2.1)
A 		28.8
(3)
A 		18.1
(-2.2)
A 		12
C 2.8
(-3)
A 		11.1
(0.1)
A 		18.8
(3)
A 		5.5
(-2)
A 		3.7
(-2.7)
A 		14.1
(1.2)
A 		16
avr 11.9
(-2) 		11
(-3) 		16
(2.6) 		11.8
(-2.1) 		16.4
(3) 		11.5
(-2.4) 		5
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 187227_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.40
Sequence Type Exemplar sequence
Representative Public ID Y54E10A.14 NCBI
Target Description Y54E10A.14 /REP_DB=WormBase Gene ID /WP=CE24443 /TR=Q9N3E5 /GB=AAF60768.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation
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_058724
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
Y54E10A.14 ENSEMBL cdna:known chromosome:CEL140:I:3217365:3220157:-1 gene:Y54E10A.14 None
NM_058724 NCBI Caenorhabditis elegans RhOMboid (Drosophila) related family member (rom-5) (rom-5) mRNA, complete cds. None
SNAP00000033833 ENSEMBL cdna:SNAP chromosome:CEL140:I:3217421:3222951:-1 None
GENEFINDER00000033838 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:3217421:3222951:-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
chrI:3218431-3220078(-) 54.59 58.14
Public Domain and Genome References
Gene Title
Gene Symbol rom-5
Ensembl Y54E10A.14
Entrez Gene 190260 Entrez gene
SwissProt Q9N3E5 EMBL-EBI
WormBase CE30043 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFA.20151.1.S1_AT similar to presenilin associated, rhomboid-like cfa
CANINE_2:CFAAFFX.18610.1.S1_AT similar to presenilin associated, rhomboid-like cfa
CANINE_2:CFAAFFX.18610.1.S1_S_AT similar to presenilin associated, rhomboid-like cfa
CANINE_2:CFAAFFX.18618.1.S1_S_AT similar to presenilin associated, rhomboid-like cfa
DROSOPHILA_2:1627697_AT rhomboid-7 dm
DROSGENOME1:147049_AT rhomboid-7 dm
CHICKEN:GGA.3498.2.S1_A_AT presenilin associated, rhomboid-like gga
CHICKEN:GGA.8898.1.S1_AT presenilin associated, rhomboid-like gga
CHICKEN:GGAAFFX.21421.1.S1_S_AT presenilin associated, rhomboid-like gga
HG-U133_PLUS_2:228881_AT presenilin associated, rhomboid-like hs
HG-U133B:228881_AT presenilin associated, rhomboid-like hs
HU35KSUBA:AA248589_AT presenilin associated, rhomboid-like hs
HU35KSUBA:RC_AA075311_F_AT presenilin associated, rhomboid-like hs
HU35KSUBD:RC_H95566_F_AT presenilin associated, rhomboid-like hs
HU35KSUBD:RC_H93412_AT presenilin associated, rhomboid-like hs
HG-U133A:218271_S_AT presenilin associated, rhomboid-like hs
HG-U133_PLUS_2:218271_S_AT presenilin associated, rhomboid-like hs
HG-U133A_2:218271_S_AT presenilin associated, rhomboid-like hs
U133_X3P:G8924133_3P_S_AT presenilin associated, rhomboid-like hs
U133_X3P:HS.13094.1.A1_3P_AT presenilin associated, rhomboid-like hs
HG-U95B:57809_AT presenilin associated, rhomboid-like hs
HG-U95E:91862_S_AT presenilin associated, rhomboid-like hs
MG-U74AV2:96641_AT presenilin associated, rhomboid-like mm
MOE430A:1433478_AT presenilin associated, rhomboid-like mm
MOUSE430A_2:1433478_AT presenilin associated, rhomboid-like mm
MOUSE430_2:1433478_AT presenilin associated, rhomboid-like mm
MU19KSUBA:TC14792_AT Presenilin associated, rhomboid-like (Psarl), mRNA mm
RG-U34C:RC_AI104250_AT presenilin associated, rhomboid-like (predicted) rn
RAE230A:1372645_AT presenilin associated, rhomboid-like (predicted) rn
RAT230_2:1372645_AT presenilin associated, rhomboid-like (predicted) rn
Protein Similarities
Method ID Description E-Value
blast CAE68990 Hypothetical protein CBG14977 [Caenorhabditis briggsae] 1.0E-138
blast CAE68990 Hypothetical protein CBG14977 [Caenorhabditis briggsae] 1.0E-134
blast AAF60768 Rhomboid (drosophila) related protein 5 [Caenorhabditis elegans] ref|NP_491125.2| RhOMboid (Drosophila) related family member (rom-5) [Caenorhabditis elegans] 2.0E-72
blast AAF60768 Rhomboid (drosophila) related protein 5 [Caenorhabditis elegans] ref|NP_491125.2| RhOMboid (Drosophila) related family member (rom-5) [Caenorhabditis elegans] 8.0E-72
blast AAF60768 Rhomboid (drosophila) related protein 5 [Caenorhabditis elegans] ref|NP_491125.2| RhOMboid (Drosophila) related family member (rom-5) [Caenorhabditis elegans] 4.0E-68
blast CAE68990 Hypothetical protein CBG14977 [Caenorhabditis briggsae] 2.0E-61
blast NP_061092 presenilin associated, rhomboid-like [Homo sapiens] gb|AAH14058.1| Presenilin associated, rhomboid-like [Homo sapiens] 2.0E-35
blast NP_061092 presenilin associated, rhomboid-like [Homo sapiens] gb|AAH14058.1| Presenilin associated, rhomboid-like [Homo sapiens] 1.0E-31
Protein Domains
Database ID Description E-Value
Pfam IPR002610 EMBL-EBI Peptidase S54, rhomboid-like protein 6.1E-14
Pfam IPR002610 EMBL-EBI Peptidase S54, rhomboid-like protein 1.5E-13
Pfam IPR002610 EMBL-EBI Peptidase S54, rhomboid-like protein 3.4E-13
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_491125.2 5 7-29,33-55,62-84,99-118,125-147
Y54E10A.14 5 7-29,33-55,62-84,99-118,125-147
SNAP00000033833 4 206-223,230-252,267-286,293-315
GENEFINDER00000033838 4 206-223,230-252,288-307,314-336
Sequence
Target Sequence 
>C. ELEGANS:187227_AT
cagttgtctcctcatttgttagtattgttgataaggcagttgtacgatcaccgattagag
ctctcggagcaagtggagccattttggcagctcttacatatacttgcatgcagattcctg
atgaatcaaaaaattttcgatttttttccgaaaaaatttcagaaaaatcaaattttgatg
atttcggtgagaaaaatgtttttttcaaaaaaaatgcaaatttttcgaattttttggaaa
aaactgacatacctattttatttaaattttttttaaaaatcgaaaaatcatcaaatttgt
tccggcaaattcttattttcggcacattgccggtttgccggtttgccagaaattttaaat
tcccgcaatttgctaatttgctagaaattttcattttcggcaatttgccagttttccgat
ttgccggaatttttcaatttccggcaattaaattttcaattccgccaatttgccggttta
ccgatttaccggaaattttcaattccgccaatttgccggtttcccgattgtccggaaact
ctccattctggcaaattgc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CAGTTGTCTCCTCATTTGTTAGTAT 169 207 149 Antisense
ATAAGGCAGTTGTACGATCACCGAT 598 25 179 Antisense
GATCACCGATTAGAGCTCTCGGAGC 233 421 194 Antisense
GTGGAGCCATTTTGGCAGCTCTTAC 60 491 221 Antisense
GCAGCTCTTACATATACTTGCATGC 664 313 235 Antisense
AAATCATCAAATTTGTTCCGGCAAA 708 117 433 Antisense
AAATTCTTATTTTCGGCACATTGCC 293 115 455 Antisense
TTTTAAATTCCCGCAATTTGCTAAT 131 655 501 Antisense
TTTCGGCAATTTGCCAGTTTTCCGA 319 671 543 Antisense
TCCCGATTGTCCGGAAACTCTCCAT 596 595 670 Antisense
GAAACTCTCCATTCTGGCAAATTGC 514 357 683 Antisense
Sequence Source Affymetrix Proprietary Database