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[188896_at] tRNA isopentenyltransferase

Description ZC395.6 /REP_DB=WormBase Gene ID /WP=CE26333 /GEN=gro-1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=tRNA isopentenyltransferase
Cluster 6grp_highest_10_10 > 57      6grp_high1_10_10 > 75      4grp_highest_8_8 > 59      4grp_high_8_8 > 25      6grp_highest_nonorm > 81      6grp_total > 65      4grp_total > 38      6grp_cgc > 57      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 222
1 2 3 4 range
A 318.8
(3)
P 		226.2
(-0.6)
P 		165.8
(-3)
P 		315.4
(2.9)
P 		153
B 288.7
(3)
P 		255.1
(0.9)
P 		192.2
(-3)
P 		251.1
(0.7)
P 		97
C 387.2
(3)
P 		215.1
(-1.7)
P 		242.6
(-0.9)
P 		165.7
(-3)
P 		222
avr 331.6
(3) 		232.1
(-1.5) 		200.2
(-3) 		244.1
(-1) 		131

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 190
1 2 3 4 5 6 range
A 255.6
(-1.8)
P 		256.7
(-1.7)
P 		357.2
(3)
P 		229.9
(-3)
P 		261.1
(-1.5)
P 		289.4
(-0.2)
P 		127
B 265.2
(-1.4)
P 		227.9
(-3)
P 		276.5
(-0.9)
P 		287
(-0.4)
P 		269.7
(-1.2)
P 		364.9
(3)
P 		137
C 241.2
(-3)
P 		259.6
(-2.4)
P 		294.6
(-1.2)
P 		366
(1.2)
P 		258.8
(-2.4)
P 		417.4
(3)
P 		176
avr 254
(-2.7) 		248.1
(-3) 		309.4
(0.4) 		294.3
(-0.5) 		263.2
(-2.2) 		357.2
(3) 		109
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 100
1 2 3 4 range
A 116.1
(3)
P 		49.1
(-2.5)
P 		43.3
(-3)
P 		46.2
(-2.8)
P 		73
B 92.1
(3)
P 		63
(-0.7)
P 		44.5
(-3)
P 		53.5
(-1.9)
P 		48
C 128.2
(3)
P 		61.8
(-1)
P 		84.5
(0.4)
P 		27.9
(-3)
P 		100
avr 112.1
(3) 		58
(-1.7) 		57.4
(-1.7) 		42.5
(-3) 		70

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 93
1 2 3 4 5 6 range
A 47.1
(-3)
P 		91.3
(3)
P 		77.8
(1.2)
P 		58.3
(-1.5)
P 		78.8
(1.3)
P 		70.5
(0.2)
P 		44
B 92.3
(-0.8)
P 		75.8
(-2.3)
P 		67.2
(-3)
P 		76
(-2.2)
P 		109.6
(0.7)
P 		136.1
(3)
P 		69
C 89.4
(-1.6)
P 		79.2
(-2.5)
P 		75
(-2.9)
P 		73.6
(-3)
P 		83.7
(-2.1)
P 		139.7
(3)
P 		66
avr 76.3
(-2.1) 		82.1
(-1.3) 		73.3
(-2.5) 		69.3
(-3) 		90.7
(-0.2) 		115.4
(3) 		46
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188896_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6910
Sequence Type Exemplar sequence
Representative Public ID ZC395.6 NCBI
Target Description ZC395.6 /REP_DB=WormBase Gene ID /WP=CE26333 /GEN=gro-1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=tRNA isopentenyltransferase
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_065721(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065721 NCBI Caenorhabditis elegans abnormal GROwth rate family member (gro-1) (gro-1) mRNA, complete cds. 11/11 None
SNAP00000016747 ENSEMBL cdna:SNAP chromosome:CEL140:III:5265135:5267087:1 11/11 None
GENEFINDER00000016762 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:5265135:5267087:1 11/11 None
ZC395.6 ENSEMBL cdna:known chromosome:CEL140:III:5265070:5267167:1 gene:ZC395.6 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
chrIII:5265091-5267086(+) 100.0 100.0
Public Domain and Genome References
Gene Title tRNA isopentenyltransferase
Gene Symbol gro-1
Ensembl ZC395.6
Entrez Gene 175725 Entrez gene
SwissProt Q9GYG3 EMBL-EBI
WormBase CE30119 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:17582_S_AT tRNA isopentenyltransferase 2 / IPP transferase 2 (IPT2) at
ATH1-121501:266208_AT tRNA isopentenyltransferase 2 / IPP transferase 2 (IPT2) at
CANINE:1604507_AT similar to tRNA isopentenyltransferase 1 cfa
CANINE_2:CFA.514.1.A1_AT similar to tRNA isopentenyltransferase 1 cfa
CANINE_2:CFAAFFX.5529.1.S1_S_AT similar to tRNA isopentenyltransferase 1 cfa
DROSOPHILA_2:1628813_AT dm
CHICKEN:GGA.7295.1.S1_AT similar to tRNA isopentenyltransferase 1; tRNA isopentenylpyrophosphate transferase gga
CHICKEN:GGAAFFX.26025.1.S1_AT similar to tRNA isopentenyltransferase 1; tRNA isopentenylpyrophosphate transferase gga
CHICKEN:GGAAFFX.26025.2.S1_S_AT similar to tRNA isopentenyltransferase 1; tRNA isopentenylpyrophosphate transferase gga
HG-U133_PLUS_2:218617_AT tRNA isopentenyltransferase 1 hs
HG-U133A:218617_AT tRNA isopentenyltransferase 1 hs
HG-FOCUS:218617_AT tRNA isopentenyltransferase 1 hs
HG-U133A_2:218617_AT tRNA isopentenyltransferase 1 hs
HU35KSUBA:RC_AA621762_AT tRNA isopentenyltransferase 1 hs
U133_X3P:G8923064_3P_AT tRNA isopentenyltransferase 1 hs
HG-U95B:54905_AT tRNA isopentenyltransferase 1 hs
MG-U74BV2:106008_AT tRNA isopentenyltransferase 1 mm
MG-U74CV2:167149_F_AT tRNA isopentenyltransferase 1 mm
MOE430A:1424489_A_AT tRNA isopentenyltransferase 1 mm
MOUSE430A_2:1424489_A_AT tRNA isopentenyltransferase 1 mm
MOUSE430_2:1424489_A_AT tRNA isopentenyltransferase 1 mm
MOUSE430_2:1460108_AT TRNA isopentenyltransferase 1 (Trit1), mRNA mm
MOE430B:1460108_AT TRNA isopentenyltransferase 1 (Trit1), mRNA mm
RG-U34B:RC_AA955962_AT tRNA isopentenyltransferase 1 (predicted) rn
RAE230A:1374133_AT tRNA isopentenyltransferase 1 (predicted) rn
RAT230_2:1374133_AT tRNA isopentenyltransferase 1 (predicted) rn
YEAST_2:1778245_AT Delta 2-isopentenyl pyrophosphate:tRNA isopentenyl transferase, required for biosynthesis of the modified base isopentenyladenosine in mitochondrial and cytoplasmic tRNAs; gene is nuclear and encodes two isozymic forms Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
8033 tRNA processing inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5634 nucleus inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3676 nucleic acid binding inferred from electronic annotation QuickGO AmiGO
4811 tRNA isopentenyltransferase activity inferred from electronic annotation QuickGO AmiGO
5524 ATP binding inferred from electronic annotation QuickGO AmiGO
8270 zinc ion binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAG00042 Abnormal growth rate protein 1 [Caenorhabditis elegans] ref|NP_498122.2| abnormal GROwth rate family member (gro-1) [Caenorhabditis elegans] gb|AAL14112.1| tRNA isopentenyl transferase [Caenorhabditis elegans] 0.0
blast T27538 hypothetical protein ZC395.6 - Caenorhabditis elegans 0.0
blast CAE73668 Hypothetical protein CBG21177 [Caenorhabditis briggsae] 1.0E-167
Protein Domains
Database ID Description E-Value
Pfam IPR002627 EMBL-EBI tRNA isopentenyltransferase 2.6E-22
Pfam IPR002627 EMBL-EBI tRNA isopentenyltransferase 1.6E-18
Pfam IPR002627 EMBL-EBI tRNA isopentenyltransferase 2.6E-22
Pfam IPR002627 EMBL-EBI tRNA isopentenyltransferase 1.6E-18
Sequence
Target Sequence 
>C. ELEGANS:188896_AT
atggatgcaacacctgaagttttagaagaaagacttgatggaagagttgataaaatgatt
aaattgggtttgaagaatgaattgatcgagttttataacgagcacgccgagtacataaat
cacagcaaatatggtgtcatgcaatgtattggtcttaaagaattcgttccatggctcaat
ttggacccatcagaaagagatacactcaatggggataaattgttcaagcaaggatgcgat
gatgtgaagcttcacactcgacaatatgcacggcgccagagacggtggtatcgatcgaga
cttttaaaacggtcggatggtgatcggaaaatggcaagtacaaaaatgctggatacatct
gacaagtaccgaataattagtgatggaatggacattgttgatcaatggatgaatggaatc
gatctatttgaagatatctccacagacaccaatccaattctaaaagggtccgatgcaaat
attctgctga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATGGATGCAACACCTGAAGTTTTAG 73 51 751 Antisense
GAGTTTTATAACGAGCACGCCGAGT 188 399 838 Antisense
GCACGCCGAGTACATAAATCACAGC 391 313 852 Antisense
TAAAGAATTCGTTCCATGGCTCAAT 198 639 906 Antisense
CATGGCTCAATTTGGACCCATCAGA 589 209 920 Antisense
GAAGCTTCACACTCGACAATATGCA 197 343 996 Antisense
CGACAATATGCACGGCGCCAGAGAC 293 253 1009 Antisense
AGAGACGGTGGTATCGATCGAGACT 198 69 1028 Antisense
GAAGATATCTCCACAGACACCAATC 627 337 1180 Antisense
CTCCACAGACACCAATCCAATTCTA 230 237 1188 Antisense
GGGTCCGATGCAAATATTCTGCTGA 661 497 1216 Antisense
Sequence Source Affymetrix Proprietary Database