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[186902_s_at]

Description Y116A8C.16 /REP_DB=WormBase Gene ID /WP=CE23325 /TR=Q9U2V5 /GB=CAB55122.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 72      6grp_high1_10_10 > 28      4grp_highest_8_8 > 53      4grp_high_8_8 > 18      6grp_highest_nonorm > 80      6grp_total > 27      4grp_total > 30      6grp_highest_sub > Cu      6grp_cgc > 05      6grp_high1_sub > De      6grp_cgc_sub > Cu      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 188
1 2 3 4 range
A 333.7
(3)
P 		146.2
(-3)
P 		207.8
(-1)
P 		268.1
(0.9)
P 		188
B 305.8
(3)
P 		228.8
(-0.4)
P 		173.3
(-2.8)
P 		169.9
(-3)
P 		136
C 214.5
(-1.5)
P 		248.5
(-0.2)
P 		175.5
(-3)
P 		334.6
(3)
P 		159
avr 284.7
(3) 		207.8
(-1.7) 		185.5
(-3) 		257.5
(1.4) 		99

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 139
1 2 3 4 5 6 range
A 309.4
(3)
P 		234.2
(-0.2)
P 		208.9
(-1.3)
P 		170.3
(-3)
P 		244.7
(0.2)
P 		233.3
(-0.3)
P 		139
B 306.5
(3)
P 		233
(-1.8)
P 		216.5
(-2.8)
P 		214
(-3)
P 		234.9
(-1.6)
P 		265.5
(0.3)
P 		93
C 273.9
(2.2)
P 		286.1
(3)
P 		231.3
(-0.5)
P 		199.8
(-2.6)
P 		193
(-3)
P 		207.6
(-2.1)
P 		93
avr 296.6
(3) 		251.1
(0.3) 		218.9
(-1.6) 		194.7
(-3) 		224.2
(-1.3) 		235.5
(-0.6) 		102
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 90
1 2 3 4 range
A 121.5
(3)
P 		31.7
(-3)
P 		54.3
(-1.5)
P 		39.2
(-2.5)
P 		90
B 97.5
(3)
P 		56.5
(-1)
P 		40.2
(-2.6)
P 		36.2
(-3)
P 		61
C 71
(2.8)
P 		71.4
(3)
P 		61.2
(-1.1)
P 		56.4
(-3)
P 		15
avr 96.7
(3) 		53.2
(-1.9) 		51.9
(-2.1) 		43.9
(-3) 		53

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 66
1 2 3 4 5 6 range
A 57
(-0.9)
P 		83.3
(3)
P 		45.5
(-2.7)
P 		43.2
(-3)
P 		73.8
(1.6)
P 		56.8
(-1)
P 		40
B 106.6
(3)
P 		77.5
(-0.2)
P 		52.6
(-3)
P 		56.7
(-2.5)
P 		95.4
(1.8)
P 		99
(2.2)
P 		54
C 101.5
(3)
P 		87.3
(1.6)
P 		58.9
(-1.2)
P 		40.2
(-3)
P 		62.5
(-0.8)
P 		69.5
(-0.1)
P 		61
avr 88.4
(3) 		82.7
(2.2) 		52.3
(-2.2) 		46.7
(-3) 		77.2
(1.4) 		75.1
(1.1) 		42
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 186902_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.9618
Sequence Type Exemplar sequence
Representative Public ID Y116A8C.16 NCBI
Target Description Y116A8C.16 /REP_DB=WormBase Gene ID /WP=CE23325 /TR=Q9U2V5 /GB=CAB55122.1 /SUBMIT=HINXTON /CHR=4 /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_070615(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_070615 NCBI Caenorhabditis elegans RhOMboid (Drosophila) related family member (rom-4) (rom-4) mRNA, complete cds. 11/11 None
GENEFINDER00000004199 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:17006820:17014543:1 11/11 None
Y116A8C.16 ENSEMBL cdna:known chromosome:CEL140:IV:17004811:17014841:1 gene:Y116A8C.16 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000004086 1/11 Cross Hyb Matching Probes None
SNAP00000004087 8/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIV:17008590-17014549(+) 67.51 67.51
Public Domain and Genome References
Gene Title
Gene Symbol rom-4
Ensembl Y116A8C.16
Entrez Gene 3565076 Entrez gene
SwissProt Q9U2V5 EMBL-EBI
WormBase CE29062 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1603518_AT similar to rhomboid family 1 cfa
CANINE:1587256_AT similar to rhomboid family 1 cfa
CANINE_2:CFA.14609.1.A1_AT similar to rhomboid family 1 cfa
CANINE_2:CFA.14643.1.A1_AT similar to rhomboid family 1 cfa
CANINE_2:CFAAFFX.30151.1.S1_AT similar to rhomboid family 1 cfa
CHICKEN:GGAAFFX.11292.1.S1_AT similar to rhomboid family 1; epidermal growth factor receptor, related sequence gga
CHICKEN:GGAAFFX.11292.2.S1_AT similar to rhomboid family 1; epidermal growth factor receptor, related sequence gga
CHICKEN:GGAAFFX.4637.1.S1_AT similar to rhomboid family 1; epidermal growth factor receptor, related sequence gga
HU35KSUBC:RC_AA443101_AT rhomboid family 1 (Drosophila) hs
HG-U133A:218686_S_AT rhomboid family 1 (Drosophila) hs
HG-U133_PLUS_2:218686_S_AT rhomboid family 1 (Drosophila) hs
HG-FOCUS:218686_S_AT rhomboid family 1 (Drosophila) hs
HG-U133A_2:218686_S_AT rhomboid family 1 (Drosophila) hs
U133_X3P:G11967982_3P_A_AT rhomboid family 1 (Drosophila) hs
U133_X3P:HS.57988.0.S1_3P_A_AT rhomboid family 1 (Drosophila) hs
HG-U133_PLUS_2:222711_S_AT rhomboid family 1 (Drosophila) hs
HG-U133B:222711_S_AT rhomboid family 1 (Drosophila) hs
HG-U95B:46138_AT rhomboid family 1 (Drosophila) hs
HG-U95E:80640_S_AT rhomboid family 1 (Drosophila) hs
HG-U95E:69807_AT Rhomboid family 1 (Drosophila) hs
MG-U74CV2:129023_AT rhomboid family 1 (Drosophila) mm
MOE430A:1424138_AT rhomboid family 1 (Drosophila) mm
MOUSE430A_2:1424138_AT rhomboid family 1 (Drosophila) mm
MOUSE430_2:1424138_AT rhomboid family 1 (Drosophila) mm
RG-U34B:RC_AI060130_AT rhomboid family 1 (Drosophila) (predicted) rn
RAE230A:1374191_AT rhomboid family 1 (Drosophila) (predicted) rn
RAT230_2:1374191_AT rhomboid family 1 (Drosophila) (predicted) rn
Protein Similarities
Method ID Description E-Value
blast CAB55122 Hypothetical protein Y116A8C.16 [Caenorhabditis elegans] ref|NP_503016.1| RhOMboid (Drosophila) related family member (rom-4) [Caenorhabditis elegans] 0.0
blast CAE57390 Hypothetical protein CBG00339 [Caenorhabditis briggsae] 0.0
blast CAB55154 Hypothetical protein Y116A8C.14 [Caenorhabditis elegans] ref|NP_503013.1| RhOMboid (Drosophila) related family member (rom-3) [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
scop a.4.1.Recombinase DNA-binding domain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Recombinase DNA-binding domain 9.99999968265523E-21
Pfam IPR002610 EMBL-EBI Peptidase S54, rhomboid-like protein 1.4E-52
Pfam IPR001584 EMBL-EBI Integrase, catalytic domain 4.3E-7
Pfam IPR002492 EMBL-EBI Transposase, Tc1/Tc3 4.0E-47
Pfam IPR002610 EMBL-EBI Peptidase S54, rhomboid-like protein 1.4E-52
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_503016.1 8 174-196,427-446,456-478,491-510,515-534,547-566,570-589,672-694
Y116A8C.16 8 174-196,427-446,456-478,491-510,515-534,547-566,570-589,672-694
GENEFINDER00000004199 8 393-415,646-665,675-697,710-729,734-753,766-785,789-808,891-913
Sequence
Target Sequence 
>C. ELEGANS:186902_S_AT
gattctggcggcggttattgtcgagtgttgtgataatagacgaatcataaaagagttcaa
gtgggctctcgttcaacatttaatcgttacactgcttgttttatgtattggatttattcc
atgggtcgataattgggcacatctttttggaacaatttttgggttattaactactataat
aatcttcccatatctcgactttggagatgacaataacaataatagggatccttctccaaa
cacagtacccaatacaccactgatgccacgtggctcaatgagcacaatgattaatattgc
ggaaacgccgacaatgacagctcaaggatacagtcaactggctaatggactcccatcgtc
tggagaacccgatggaacgactgtctccacggttcgatggatctggagaactctacgcga
aaaatttaaaaataaacgaacgttctacgtgctcatctcgacaattgtgctctctttcct
acttttcatcctattcgttgttt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GATTCTGGCGGCGGTTATTGTCGAG 130 433 2241 Antisense
GTGGGCTCTCGTTCAACATTTAATC 572 487 2301 Antisense
AATCTTCCCATATCTCGACTTTGGA 63 169 2421 Antisense
TAGGGATCCTTCTCCAAACACAGTA 503 605 2463 Antisense
TACACCACTGATGCCACGTGGCTCA 393 641 2493 Antisense
GCGGAAACGCCGACAATGACAGCTC 458 293 2539 Antisense
GTCAACTGGCTAATGGACTCCCATC 447 463 2573 Antisense
AACCCGATGGAACGACTGTCTCCAC 420 143 2606 Antisense
CTGTCTCCACGGTTCGATGGATCTG 458 239 2621 Antisense
TACGTGCTCATCTCGACAATTGTGC 157 649 2686 Antisense
CTACTTTTCATCCTATTCGTTGTTT 331 227 2719 Antisense
Sequence Source Affymetrix Proprietary Database