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[173889_s_at] Polyprenyl synthetases

Description AV190643 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=R06C1.2 /5_PRIME_EXT_DB=WormBase Gene ID /GB=AV190643 /WB_GENE_ID=R06C1.2 /WP=CE23901 /CHR=1 /FEA=Genomic Cluster /DEF=Polyprenyl synthetases; Caenorhabditis elegans cDNA clone:yk573d7 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 48      6grp_high1_10_10 > 83      4grp_highest_8_8 > 33      4grp_high_8_8 > 58      6grp_highest_nonorm > 73      6grp_total > 74      4grp_total > 61      6grp_high1_sub > 04      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 197
1 2 3 4 range
A 396.3
(2.4)
P 		366.3
(1.1)
P 		409.9
(3)
P 		272.6
(-3)
P 		137
B 469.4
(3)
P 		395.2
(0.7)
P 		439.3
(2.1)
P 		275.3
(-3)
P 		194
C 396.7
(2.4)
P 		393.9
(2.2)
P 		404.7
(3)
P 		328.4
(-3)
P 		76
avr 420.8
(3) 		385.1
(1.3) 		418
(2.9) 		292.1
(-3) 		129

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 276
1 2 3 4 5 6 range
A 523.5
(-0.2)
P 		470.9
(-2.2)
P 		488.5
(-1.5)
P 		607
(3)
P 		450
(-3)
P 		511
(-0.7)
P 		157
B 479.3
(-1.2)
P 		399.2
(-3)
P 		665.8
(3)
P 		607.4
(1.7)
P 		472
(-1.4)
P 		542.4
(0.2)
P 		267
C 389.6
(-3)
P 		395.4
(-2.9)
P 		498.8
(-0.4)
P 		635.3
(2.9)
P 		501.1
(-0.3)
P 		639.1
(3)
P 		250
avr 464.1
(-1.7) 		421.8
(-3) 		551
(1) 		616.6
(3) 		474.4
(-1.4) 		564.2
(1.4) 		195
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 110
1 2 3 4 range
A 144.3
(3)
P 		79.5
(-0.7)
P 		107.2
(0.9)
P 		39.9
(-3)
P 		104
B 149.7
(3)
P 		97.6
(-0.4)
P 		101.8
(-0.2)
P 		58.7
(-3)
P 		91
C 131.3
(2.3)
P 		113.2
(1)
P 		141.1
(3)
P 		55.4
(-3)
P 		86
avr 141.8
(3) 		96.8
(0) 		116.7
(1.3) 		51.3
(-3) 		91

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 117
1 2 3 4 5 6 range
A 96.5
(-3)
P 		167.5
(3)
P 		106.4
(-2.2)
P 		153.9
(1.9)
P 		135.8
(0.3)
P 		124.4
(-0.6)
P 		71
B 166.8
(-0.1)
P 		132.9
(-3)
P 		161.7
(-0.5)
P 		160.9
(-0.6)
P 		191.8
(2.1)
P 		202.2
(3)
P 		69
C 144.4
(-1.5)
P 		120.7
(-3)
P 		127
(-2.6)
P 		127.8
(-2.5)
P 		162.1
(-0.3)
P 		213.9
(3)
P 		93
avr 135.9
(-2.5) 		140.4
(-1.9) 		131.7
(-3) 		147.5
(-1) 		163.2
(0.9) 		180.2
(3) 		49
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173889_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.23051
Sequence Type Exemplar sequence
Representative Public ID AV190643 NCBI
Target Description AV190643 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=R06C1.2 /5_PRIME_EXT_DB=WormBase Gene ID /GB=AV190643 /WB_GENE_ID=R06C1.2 /WP=CE23901 /CHR=1 /FEA=Genomic Cluster /DEF=Polyprenyl synthetases; Caenorhabditis elegans cDNA clone:yk573d7 : 5prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_060626(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_060626 NCBI Caenorhabditis elegans R06C1.2 (R06C1.2) mRNA, complete cds. 11/11 None
SNAP00000025114 ENSEMBL cdna:SNAP chromosome:CEL140:I:11921780:11937629:-1 9/11 None
GENEFINDER00000025123 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:11926148:11932030:-1 11/11 None
R06C1.2 ENSEMBL cdna:known chromosome:CEL140:I:11926008:11932030:-1 gene:R06C1.2 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:11926079-11931962(-) 100.0 100.0
Public Domain and Genome References
Gene Title Polyprenyl synthetases
Ensembl R06C1.2
Entrez Gene 173075 Entrez gene
SwissProt O62336 EMBL-EBI
WormBase CE23901 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
7186 G-protein coupled receptor protein signaling pathway inferred from electronic annotation QuickGO AmiGO
8299 isoprenoid biosynthesis inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
16021 integral to membrane inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
1584 rhodopsin-like receptor activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB03221 Hypothetical protein R06C1.2 [Caenorhabditis elegans] ref|NP_493027.1| R06C1.2 [Caenorhabditis elegans] 0.0
blast CAB03220 Hypothetical protein R06C1.3 [Caenorhabditis elegans] ref|NP_493028.2| WAVE (actin cytoskeleton modulator) homolog family member (wve-1) [Caenorhabditis elegans] 0.0
blast CAE71711 Hypothetical protein CBG18688 [Caenorhabditis briggsae] 1.0E-179
blast CAB03240 Hypothetical protein R06C1.1 [Caenorhabditis elegans] emb|CAB03224.1| Hypothetical protein R06C1.1 [Caenorhabditis elegans] ref|NP_493026.1| Histone DeAcetylase family member (hda-3) [Caenorhabditis elegans] 1.0E-179
blast CAB03221 Hypothetical protein R06C1.2 [Caenorhabditis elegans] ref|NP_493027.1| R06C1.2 [Caenorhabditis elegans] 1.0E-177
blast CAB03221 Hypothetical protein R06C1.2 [Caenorhabditis elegans] ref|NP_493027.1| R06C1.2 [Caenorhabditis elegans] 1.0E-176
blast CAE71711 Hypothetical protein CBG18688 [Caenorhabditis briggsae] 1.0E-164
blast AAI06511 Unknown (protein for MGC:131256) [Xenopus laevis] 5.0E-50
Protein Domains
Database ID Description E-Value
scop a.4.5.Replication initiation protein All alpha proteins; DNA/RNA-binding 3-helical bundle; "Winged helix" DNA-binding domain; Replication initiation protein 3.29999995231628
Pfam IPR000092 EMBL-EBI Polyprenyl synthetase 2.7E-37
Pfam IPR000092 EMBL-EBI Polyprenyl synthetase 2.7E-37
Pfam IPR000286 EMBL-EBI Histone deacetylase superfamily 1.0E-126
Pfam IPR003124 EMBL-EBI Actin-binding WH2 1.5E-7
Sequence
Target Sequence 
>C. ELEGANS:173889_S_AT
gcctggacacgtgaatcttgatcggctttgcgaggcttatcgcaagtccaaacagaagac
gttgattggacagttcctggacacatcatcagtgaatcaaatctcgtctttcacatggga
tcgttatgaattaatggttgaaaataaaacatcacattatacagtatttcatccaattca
aatggctcttatcatatcagacgtcttagcttatcatggatctgtgaaaaaagttgctta
tcaaattggattcctatttcaatcacaagatgattttttggatgtttatggagatcctaa
aattaccggaaaaattggaactgatattcaagatggaaaatgtacttggcttgccgtacg
agctcttcagaaaatgcacaaaacgccggaaaaatggggggccaagcttattgaggaatt
taagacgagttttggatcggtggaccccgagaaagtggagaaaattaagcggatttatga
tgagctgcagttgaaacaagaattccggcgatttgagaagcatttttcgggagagataaa
aaagagcatatccgagattcctgacgtcatcaacccactgcgaccggttctagatgga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCCTGGACACGTGAATCTTGATCGG 662 281 442 Antisense
CTTGATCGGCTTTGCGAGGCTTATC 359 215 458 Antisense
GAGGCTTATCGCAAGTCCAAACAGA 502 405 473 Antisense
GGACAGTTCCTGGACACATCATCAG 381 525 509 Antisense
AATCTCGTCTTTCACATGGGATCGT 454 169 541 Antisense
ATGGCTCTTATCATATCAGACGTCT 397 53 623 Antisense
GACGTCTTAGCTTATCATGGATCTG 251 375 641 Antisense
ATGTACTTGGCTTGCCGTACGAGCT 479 47 781 Antisense
GAGTTTTGGATCGGTGGACCCCGAG 497 395 868 Antisense
GCATATCCGAGATTCCTGACGTCAT 232 307 987 Antisense
CCCACTGCGACCGGTTCTAGATGGA 302 259 1015 Antisense
Sequence Source Affymetrix Proprietary Database