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[193739_s_at] geranylgeranyl transferase beta subunit

Description Y48E1B.3 /REP_DB=WormBase Gene ID /WP=CE22159 /GEN=csp-1 /TR=O18197 /GB=CAB07699.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=geranylgeranyl transferase beta subunit
Cluster 6grp_highest_10_10 > 94      6grp_high1_10_10 > 59      4grp_highest_8_8 > 38      4grp_high_8_8 > 03      6grp_highest_nonorm > 91      6grp_total > 49      4grp_total > 05      6grp_highest_sub > Cu      6grp_high1_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 147
1 2 3 4 range
A 274.4
(-3)
P 		297
(-1.8)
P 		317.2
(-0.7)
P 		384.3
(3)
P 		110
B 354.7
(0.6)
P 		300.6
(-3)
P 		390.9
(3)
P 		326.6
(-1.3)
P 		90
C 421.3
(3)
P 		407.8
(2.3)
P 		306.5
(-3)
P 		379.3
(0.8)
P 		115
avr 350.1
(0.2) 		335.1
(-3) 		338.2
(-2.3) 		363.4
(3) 		28

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 257
1 2 3 4 5 6 range
A 241.9
(-0.9)
P 		310.3
(0.8)
P 		156.9
(-3)
P 		246.9
(-0.8)
P 		165.9
(-2.8)
P 		399.9
(3)
P 		243
B 158.3
(-3)
P 		167.7
(-1.8)
P 		171
(-1.4)
P 		193.1
(1.4)
P 		205.7
(3)
P 		169.4
(-1.6)
P 		47
C 341.2
(3)
P 		171.2
(-2.1)
P 		202.8
(-1.2)
P 		142.6
(-3)
P 		312.2
(2.1)
P 		238.1
(-0.1)
P 		199
avr 247.1
(1.6) 		216.4
(-0.4) 		176.9
(-3) 		194.2
(-1.9) 		227.9
(0.3) 		269.1
(3) 		92
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 83
1 2 3 4 range
A 99.9
(3)
P 		64.5
(-1.9)
P 		82.9
(0.7)
P 		56.3
(-3)
P 		44
B 113.1
(3)
P 		74.3
(-2.4)
P 		90.6
(-0.1)
P 		69.6
(-3)
P 		44
C 139.5
(3)
P 		117.3
(1.2)
P 		106.8
(0.4)
P 		64
(-3)
P 		76
avr 117.5
(3) 		85.4
(-0.6) 		93.4
(0.3) 		63.3
(-3) 		54

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 98
1 2 3 4 5 6 range
A 44.6
(-2.2)
P 		110.4
(3)
P 		34.2
(-3)
P 		62.6
(-0.8)
P 		50.1
(-1.7)
P 		97.4
(2)
P 		76
B 55.1
(-1.1)
P 		55.8
(-1)
P 		41.5
(-3)
P 		51.1
(-1.6)
P 		83.6
(3)
P 		63.2
(0.1)
P 		42
C 126.5
(3)
P 		52.2
(-1.6)
P 		51.6
(-1.6)
P 		28.7
(-3)
P 		101
(1.4)
P 		79.7
(0.1)
P 		98
avr 75.4
(2.3) 		72.8
(1.8) 		42.4
(-3) 		47.5
(-2.2) 		78.2
(2.7) 		80.1
(3) 		38
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 193739_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.2943
Sequence Type Exemplar sequence
Representative Public ID Y48E1B.3 NCBI
Target Description Y48E1B.3 /REP_DB=WormBase Gene ID /WP=CE22159 /GEN=csp-1 /TR=O18197 /GB=CAB07699.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=geranylgeranyl transferase beta subunit
Cluster Evidence This cluster is supported by a 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_064447(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_064447 NCBI Caenorhabditis elegans Y48E1B.3 (Y48E1B.3) mRNA, complete cds. 11/11 A 
SNAP00000010059 ENSEMBL cdna:SNAP chromosome:CEL140:II:13533528:13585325:-1 11/11 None
GENEFINDER00000010072 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:13547831:13553380:-1 11/11 None
Y48E1B.3 ENSEMBL cdna:known chromosome:CEL140:II:13547660:13567867:-1 gene:Y48E1B.3 11/11 A 
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
chrII:13547827-13567859(-) 100.0 100.0
Public Domain and Genome References
Gene Title geranylgeranyl transferase beta subunit
Ensembl Y48E1B.3
Entrez Gene 174999 Entrez gene
SwissProt O18197 EMBL-EBI
WormBase CE22159 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:19828_AT geranylgeranyl transferase type I beta subunit (GGT-IB) at
ATH1-121501:266985_AT geranylgeranyl transferase type I beta subunit (GGT-IB) at
CANINE_2:CFAAFFX.1287.1.S1_AT similar to protein geranylgeranyltransferase type I, beta subunit cfa
DROSOPHILA_2:1623853_AT subunit of type I geranylgeranyl transferase dm
DROSGENOME1:143774_AT subunit of type I geranylgeranyl transferase dm
HG-U95AV2:1275_AT protein geranylgeranyltransferase type I, beta subunit hs
HC-G110:1275_AT protein geranylgeranyltransferase type I, beta subunit hs
HG-U133_PLUS_2:206288_AT protein geranylgeranyltransferase type I, beta subunit hs
HG-U133A:206288_AT protein geranylgeranyltransferase type I, beta subunit hs
HG-FOCUS:206288_AT protein geranylgeranyltransferase type I, beta subunit hs
HG-U133A_2:206288_AT protein geranylgeranyltransferase type I, beta subunit hs
HUGENEFL:L25441_AT protein geranylgeranyltransferase type I, beta subunit hs
U133_X3P:G4826899_3P_AT protein geranylgeranyltransferase type I, beta subunit hs
MG-U74BV2:115249_AT protein geranylgeranyltransferase type I, beta subunit mm
MG-U74BV2:113270_AT protein geranylgeranyltransferase type I, beta subunit mm
MG-U74BV2:113271_AT protein geranylgeranyltransferase type I, beta subunit mm
MOE430B:1429770_AT protein geranylgeranyltransferase type I, beta subunit mm
MOUSE430_2:1429770_AT protein geranylgeranyltransferase type I, beta subunit mm
MOE430B:1429769_AT protein geranylgeranyltransferase type I, beta subunit mm
MOUSE430_2:1429769_AT protein geranylgeranyltransferase type I, beta subunit mm
MOE430B:1438229_AT protein geranylgeranyltransferase type I, beta subunit mm
MOUSE430_2:1438229_AT protein geranylgeranyltransferase type I, beta subunit mm
MOE430B:1438230_AT protein geranylgeranyltransferase type I, beta subunit mm
MOUSE430_2:1438230_AT protein geranylgeranyltransferase type I, beta subunit mm
MG-U74CV2:170736_AT protein geranylgeranyltransferase type I, beta subunit mm
MG-U74CV2:168952_I_AT Protein geranylgeranyltransferase type I, beta subunit (Pggt1b), mRNA mm
MU19KSUBC:TC38632_AT Protein geranylgeranyltransferase type I, beta subunit (Pggt1b), mRNA mm
RG-U34A:RC_AI235344_AT protein geranylgeranyltransferase type I, beta subunit rn
RAE230A:1369285_AT protein geranylgeranyltransferase type I, beta subunit rn
RAT230_2:1369285_AT protein geranylgeranyltransferase type I, beta subunit rn
Gene Ontology
GO Molecular Function (view graph)
ID Description Evidence Links
3824 catalytic activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB07699 Hypothetical protein Y48E1B.3 [Caenorhabditis elegans] ref|NP_496848.1| Y48E1B.3 [Caenorhabditis elegans] 0.0
blast CAB07689 Hypothetical protein Y48E1B.2a [Caenorhabditis elegans] ref|NP_496845.1| Y48E1B.2a [Caenorhabditis elegans] 0.0
blast CAE73333 Hypothetical protein CBG20762 [Caenorhabditis briggsae] 0.0
blast CAB07690 Hypothetical protein Y48E1B.4 [Caenorhabditis elegans] ref|NP_496849.1| Y48E1B.4 [Caenorhabditis elegans] 0.0
blast CAE73330 Hypothetical protein CBG20759 [Caenorhabditis briggsae] 1.0E-177
blast CAB07699 Hypothetical protein Y48E1B.3 [Caenorhabditis elegans] ref|NP_496848.1| Y48E1B.3 [Caenorhabditis elegans] 1.0E-150
blast CAE73330 Hypothetical protein CBG20759 [Caenorhabditis briggsae] 1.0E-132
blast XP_538560 PREDICTED: similar to protein geranylgeranyltransferase type I, beta subunit isoform 1 [Canis familiaris] 2.0E-66
Protein Domains
Database ID Description E-Value
Pfam IPR001330 EMBL-EBI Prenyltransferase/squalene oxidase 0.015
Pfam IPR001330 EMBL-EBI Prenyltransferase/squalene oxidase 0.011
Pfam IPR001330 EMBL-EBI Prenyltransferase/squalene oxidase 5.2E-9
Pfam IPR001330 EMBL-EBI Prenyltransferase/squalene oxidase 7.8E-4
Pfam IPR001330 EMBL-EBI Prenyltransferase/squalene oxidase 0.049
Pfam IPR001330 EMBL-EBI Prenyltransferase/squalene oxidase 0.015
Pfam IPR001330 EMBL-EBI Prenyltransferase/squalene oxidase 0.011
Pfam IPR001330 EMBL-EBI Prenyltransferase/squalene oxidase 5.2E-9
Pfam IPR001330 EMBL-EBI Prenyltransferase/squalene oxidase 7.8E-4
Pfam IPR001330 EMBL-EBI Prenyltransferase/squalene oxidase 0.0096
Pfam IPR001330 EMBL-EBI Prenyltransferase/squalene oxidase 0.0056
Pfam IPR001330 EMBL-EBI Prenyltransferase/squalene oxidase 0.011
Pfam IPR001330 EMBL-EBI Prenyltransferase/squalene oxidase 5.2E-9
Pfam IPR001330 EMBL-EBI Prenyltransferase/squalene oxidase 7.8E-4
Pfam IPR001330 EMBL-EBI Prenyltransferase/squalene oxidase 8.5E-8
Trans Membrane
ID Number Of Domains Domain Boundaries
SNAP00000010059 2 1554-1576,1588-1610
Sequence
Target Sequence 
>C. ELEGANS:193739_S_AT
atgtttctggagtcaaggcgtcggctcggaatcggacatgcgattcgtattctgtgcagt
agccatcagccatattctcgacggagacaaagagcaaacaatcgactggaccaagctcgc
cggctttctgcgtcaaagcctaaacatcgacggaggaatcggccaggctccgggagacga
gagccacggaggctctacattctgtgcaattgcctcgttggctctgtcgaacaggctttg
gactgaagaagtgctcacgcgacgggatatcgatcggcttattcgatgggctattcaaaa
acaggatatcggatttcacggaagggcccataagcctgatgatagttgctatgcattctg
gattggggccacgttga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATGTTTCTGGAGTCAAGGCGTCGGC 66 47 471 Antisense
GTCGGCTCGGAATCGGACATGCGAT 117 469 490 Antisense
GACATGCGATTCGTATTCTGTGCAG 386 369 505 Antisense
TGCAGTAGCCATCAGCCATATTCTC 236 579 525 Antisense
ATCGACGGAGGAATCGGCCAGGCTC 487 33 616 Antisense
CACGGAGGCTCTACATTCTGTGCAA 277 199 655 Antisense
CATTCTGTGCAATTGCCTCGTTGGC 181 217 668 Antisense
GCCTCGTTGGCTCTGTCGAACAGGC 179 281 682 Antisense
AGAAGTGCTCACGCGACGGGATATC 34 75 717 Antisense
GATTTCACGGAAGGGCCCATAAGCC 645 427 782 Antisense
GCATTCTGGATTGGGGCCACGTTGA 425 307 823 Antisense
Sequence Source Affymetrix Proprietary Database