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[173522_s_at]

Description CEC6802 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=W06H3.2 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C09680 /WB_GENE_ID=W06H3.2 /WP=CE20158 /CHR=5 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk174d5 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 77      6grp_high1_10_10 > 86      4grp_highest_8_8 > 22      4grp_high_8_8 > 14      6grp_highest_nonorm > 94      6grp_total > 77      4grp_total > 09      6grp_highest_sub > Da      6grp_cgc > 58      6grp_high1_sub > In      6grp_cgc_sub > In      6grp_total_sub > Increase      6grp_rule_based > S6      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 981
1 2 3 4 range
A 556
(-3)
P 		658.7
(-2.4)
P 		666.2
(-2.3)
P 		1512.5
(3)
P 		957
B 712.9
(-2.1)
P 		645.8
(-3)
P 		734.8
(-1.9)
P 		1115.4
(3)
P 		470
C 531.4
(-3)
P 		622.9
(-2.3)
P 		615.4
(-2.4)
P 		1334.3
(3)
P 		803
avr 600.1
(-3) 		642.5
(-2.6) 		672.1
(-2.4) 		1320.7
(3) 		721

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 668
1 2 3 4 5 6 range
A 422.5
(-3)
P 		418.7
(-3)
P 		430.3
(-2.9)
P 		485
(-2.3)
P 		586
(-1.1)
P 		951.6
(3)
P 		533
B 339.6
(-3)
P 		493.3
(-1.6)
P 		496.2
(-1.6)
P 		437.3
(-2.1)
P 		627.5
(-0.4)
P 		1007.4
(3)
P 		668
C 384.2
(-3)
P 		445.7
(-2.4)
P 		462.2
(-2.2)
P 		503.8
(-1.8)
P 		537.9
(-1.5)
P 		1007.8
(3)
P 		624
avr 382.1
(-3) 		452.6
(-2.3) 		462.9
(-2.2) 		475.4
(-2.1) 		583.8
(-1) 		988.9
(3) 		607
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 95
1 2 3 4 range
A 202.4
(1.5)
P 		143
(-3)
P 		174.2
(-0.6)
P 		221.4
(3)
P 		78
B 227.3
(2.2)
P 		159.5
(-3)
P 		170.3
(-2.2)
P 		237.7
(3)
P 		78
C 175.9
(-3)
P 		179.1
(-2.6)
P 		214.5
(1.7)
P 		225
(3)
P 		49
avr 201.9
(0.7) 		160.5
(-3) 		186.3
(-0.7) 		228
(3) 		68

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 298
1 2 3 4 5 6 range
A 77.9
(-3)
P 		148.9
(-0.2)
P 		93.7
(-2.4)
P 		123
(-1.2)
P 		176.8
(0.9)
P 		231.7
(3)
P 		154
B 118.2
(-2.9)
P 		164.2
(-1.9)
P 		120.5
(-2.9)
P 		115.8
(-3)
P 		254.9
(0.2)
P 		375.7
(3)
P 		260
C 142.4
(-2)
P 		136
(-2.1)
P 		117.6
(-2.6)
P 		101.3
(-3)
P 		174.1
(-1.1)
P 		337.4
(3)
P 		236
avr 112.8
(-2.9) 		149.7
(-1.9) 		110.6
(-3) 		113.4
(-2.9) 		201.9
(-0.3) 		314.9
(3) 		204
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173522_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.25598
Sequence Type Exemplar sequence
Representative Public ID CEC6802 NCBI
Target Description CEC6802 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=W06H3.2 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C09680 /WB_GENE_ID=W06H3.2 /WP=CE20158 /CHR=5 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk174d5 : 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_074841(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_074841 NCBI Caenorhabditis elegans PseudoUridine Synthase family member (pus-1) (pus-1) mRNA, complete cds. 11/11 None
SNAP00000017339 ENSEMBL cdna:SNAP chromosome:CEL140:V:16792032:16797588:-1 10/11 None
GENEFINDER00000017342 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:16795424:16795837:-1 11/11 None
W06H3.2 ENSEMBL cdna:known chromosome:CEL140:V:16795347:16797588:-1 gene:W06H3.2 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
chrV:16795366-16797534(-) 99.39 100.0
Public Domain and Genome References
Gene Title
Gene Symbol pus-1
Ensembl W06H3.2
Entrez Gene 180123 Entrez gene
SwissProt Q9XXN0 EMBL-EBI
WormBase CE20158 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:255887_AT tRNA pseudouridine synthase family protein at
CANINE:1592206_AT similar to tRNA pseudouridine synthase A (tRNA-uridine isomerase I) (tRNA pseudouridylate synthase I) cfa
CANINE_2:CFA.6493.1.A1_AT similar to tRNA pseudouridine synthase A (tRNA-uridine isomerase I) (tRNA pseudouridylate synthase I) cfa
CANINE_2:CFAAFFX.10600.1.S1_AT similar to tRNA pseudouridine synthase A (tRNA-uridine isomerase I) (tRNA pseudouridylate synthase I) cfa
DROSOPHILA_2:1639514_AT dm
DROSGENOME1:150267_AT dm
HG-U133_PLUS_2:218670_AT pseudouridylate synthase 1 hs
HG-U133A:218670_AT pseudouridylate synthase 1 hs
HG-FOCUS:218670_AT pseudouridylate synthase 1 hs
HG-U133A_2:218670_AT pseudouridylate synthase 1 hs
HU35KSUBA:RC_AA598712_AT pseudouridylate synthase 1 hs
HU35KSUBC:RC_AA098793_S_AT pseudouridylate synthase 1 hs
U133_X3P:G13376819_3P_X_AT pseudouridylate synthase 1 hs
U133_X3P:G13376819_3P_AT pseudouridylate synthase 1 hs
HG-U95C:59607_F_AT pseudouridylate synthase 1 hs
HG-U95C:65572_AT pseudouridylate synthase 1 hs
HG-U95D:89512_AT pseudouridylate synthase 1 hs
HG-U95B:44280_I_AT Pseudouridylate synthase 1 hs
HG-U95B:44281_R_AT Pseudouridylate synthase 1 hs
MG-U74AV2:103544_AT pseudouridine synthase 1 mm
MOUSE430_2:1418869_A_AT pseudouridine synthase 1 mm
MOE430A:1418869_A_AT pseudouridine synthase 1 mm
MOUSE430A_2:1418869_A_AT pseudouridine synthase 1 mm
MG-U74BV2:114206_AT pseudouridine synthase 1 mm
MU11KSUBA:AA207755_AT Pseudouridine synthase 1, mRNA (cDNA clone MGC:11791 IMAGE:3595162) mm
MU19KSUBA:TC24192_AT Pseudouridine synthase 1, mRNA (cDNA clone MGC:11791 IMAGE:3595162) mm
MU19KSUBA:TC24192_G_AT Pseudouridine synthase 1, mRNA (cDNA clone MGC:11791 IMAGE:3595162) mm
MU19KSUBB:TC32944_AT Pseudouridine synthase 1, mRNA (cDNA clone MGC:11791 IMAGE:3595162) mm
RG-U34C:RC_AI146005_AT pseudouridine synthase 1 (predicted) rn
RAE230A:1373741_AT pseudouridine synthase 1 (predicted) rn
RAT230_2:1373741_AT pseudouridine synthase 1 (predicted) rn
RAE230B:1396122_AT Pseudouridine synthase 1 (predicted) rn
RAT230_2:1396122_AT Pseudouridine synthase 1 (predicted) rn
YEAST_2:1772225_AT tRNA:pseudouridine synthase, introduces pseudouridines at positions 26-28, 34-36, 65, and 67 of tRNA; nuclear protein that appears to be involved in tRNA export; also acts on U2 snRNA Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
8033 tRNA processing inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
4730 pseudouridylate synthase activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA16518 Hypothetical protein W06H3.2 [Caenorhabditis elegans] ref|NP_507242.1| PseudoUridine Synthase family member (pus-1) [Caenorhabditis elegans] 0.0
blast CAE56256 Hypothetical protein CBG23897 [Caenorhabditis briggsae] 0.0
blast AAF55785 CG4159-PA [Drosophila melanogaster] ref|NP_650899.1| CG4159-PA [Drosophila melanogaster] 4.0E-65
blast AAF55785 CG4159-PA [Drosophila melanogaster] ref|NP_650899.1| CG4159-PA [Drosophila melanogaster] 5.0E-65
blast CAA16518 Hypothetical protein W06H3.2 [Caenorhabditis elegans] ref|NP_507242.1| PseudoUridine Synthase family member (pus-1) [Caenorhabditis elegans] 7.0E-52
Protein Domains
Database ID Description E-Value
Pfam IPR001406 EMBL-EBI tRNA pseudouridine synthase 4.9E-13
Pfam IPR001406 EMBL-EBI tRNA pseudouridine synthase 4.9E-13
Sequence
Target Sequence 
>C. ELEGANS:173522_S_AT
tggatatcccaatggctccaggactgggtctcctcctcgagcggactcattacgattcct
acgatcgaaagaattcaaaatcccacgaaccactgaccgattggggagagatcatcgaaa
aagaaatcgagcggaccaagttcgagctcatcaccaaggatatgatcgagacggagctgc
tcactcagggaatgctcaaatggcttgcggatcttgttcatcacgacttcacggctaatg
cggaagctgaggagcccgagaagaagacttttgtgacgatggcggcggcttgtgcgagca
aggcggccaaggagcaggatggtgttgctccagaggctcaagatgctccgaaggaagccg
aggctccagcagaagtcactcctgagccagtagcagcgacgtc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGGATATCCCAATGGCTCCAGGACT 353 551 849 Antisense
GAGCGGACTCATTACGATTCCTACG 217 379 887 Antisense
CCACGAACCACTGACCGATTGGGGA 317 255 931 Antisense
AGCGGACCAAGTTCGAGCTCATCAC 17 83 978 Antisense
ATGATCGAGACGGAGCTGCTCACTC 268 47 1010 Antisense
CTGCTCACTCAGGGAATGCTCAAAT 700 237 1025 Antisense
AAATGGCTTGCGGATCTTGTTCATC 196 121 1046 Antisense
AGACTTTTGTGACGATGGCGGCGGC 697 69 1113 Antisense
GCTCCAGAGGCTCAAGATGCTCCGA 539 297 1175 Antisense
GATGCTCCGAAGGAAGCCGAGGCTC 141 415 1190 Antisense
CTCCTGAGCCAGTAGCAGCGACGTC 34 235 1227 Antisense
Sequence Source Affymetrix Proprietary Database