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[193161_at] centromere/microtubule binding protein

Description K01G5.5 /REP_DB=WormBase Gene ID /WP=CE16195 /TR=SW:O17919 /GB=CAB07244.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=centromere-microtubule binding protein
Cluster 6grp_highest_10_10 > 95      6grp_high1_10_10 > 58      4grp_highest_8_8 > 16      4grp_high_8_8 > 60      6grp_highest_nonorm > 58      6grp_total > 69      4grp_total > 59      6grp_highest_sub > Cu      6grp_high1_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 3423
1 2 3 4 range
A 4342.5
(1.1)
P 		5008.1
(2.5)
P 		5265
(3)
P 		2287.8
(-3)
P 		2977
B 4656.5
(1.5)
P 		4726.8
(1.7)
P 		5377
(3)
P 		2471.7
(-3)
P 		2905
C 4337.5
(1.3)
P 		5065.3
(2.6)
P 		5304.1
(3)
P 		1953.8
(-3)
P 		3350
avr 4445.5
(1.3) 		4933.4
(2.3) 		5315.4
(3) 		2237.8
(-3) 		3078

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1640
1 2 3 4 5 6 range
A 2470.4
(0.2)
P 		2499.4
(0.4)
P 		1692.8
(-3)
P 		1756.8
(-2.7)
P 		2163.3
(-1)
P 		3130.9
(3)
P 		1438
B 2998
(1.6)
P 		2517.8
(-0.5)
P 		2338.5
(-1.2)
P 		1922.1
(-3)
P 		2676
(0.2)
P 		3330.2
(3)
P 		1408
C 2679.5
(0.5)
P 		2459.2
(-0.4)
P 		1952.5
(-2.4)
P 		1792.8
(-3)
P 		2615.2
(0.2)
P 		3332.8
(3)
P 		1540
avr 2716
(0.7) 		2492.1
(-0.2) 		1994.6
(-2.3) 		1823.9
(-3) 		2484.8
(-0.2) 		3264.6
(3) 		1441
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1519
1 2 3 4 range
A 1581.1
(3)
P 		1087.1
(0.6)
P 		1376.4
(2)
P 		334.9
(-3)
P 		1246
B 1484.9
(3)
P 		1167.4
(1)
P 		1246
(1.5)
P 		526.7
(-3)
P 		958
C 1435.8
(1.4)
P 		1456.3
(1.5)
P 		1848.7
(3)
P 		329.4
(-3)
P 		1519
avr 1500.6
(3) 		1236.9
(1.6) 		1490.4
(2.9) 		397
(-3) 		1104

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 881
1 2 3 4 5 6 range
A 455.4
(-2)
P 		888.9
(3)
P 		368.7
(-3)
P 		445.6
(-2.1)
P 		652.8
(0.3)
P 		762.3
(1.5)
P 		520
B 1043.2
(1.4)
P 		838.1
(-0.3)
P 		567.9
(-2.5)
P 		509.1
(-3)
P 		1087.2
(1.7)
P 		1241.8
(3)
P 		733
C 993.2
(2)
P 		750.4
(0.1)
P 		497
(-1.9)
P 		360.5
(-3)
P 		846.2
(0.9)
P 		1115.7
(3)
P 		755
avr 830.6
(0.9) 		825.8
(0.9) 		477.9
(-2.6) 		438.4
(-3) 		862.1
(1.2) 		1039.9
(3) 		602
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193161_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7970
Sequence Type Exemplar sequence
Representative Public ID K01G5.5 NCBI
Target Description K01G5.5 /REP_DB=WormBase Gene ID /WP=CE16195 /TR=SW:O17919 /GB=CAB07244.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=centromere-microtubule binding protein
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_066969(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066969 NCBI Caenorhabditis elegans K01G5.5 (K01G5.5) mRNA, complete cds. 11/11 None
SNAP00000033489 ENSEMBL cdna:SNAP chromosome:CEL140:III:10748319:10749805:1 11/11 None
GENEFINDER00000033499 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:10748319:10749805:1 11/11 None
K01G5.5.3 ENSEMBL cdna:known chromosome:CEL140:III:10748301:10749957:1 gene:K01G5.5 11/11 None
K01G5.5.2 ENSEMBL cdna:known chromosome:CEL140:III:10748302:10749957:1 gene:K01G5.5 11/11 None
K01G5.5.1 ENSEMBL cdna:known chromosome:CEL140:III:10748306:10749957:1 gene:K01G5.5 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:10748314-10749801(+) 100.0 100.0
Public Domain and Genome References
Gene Title centromere/microtubule binding protein
Ensembl K01G5.5
Entrez Gene 176504 Entrez gene
SwissProt O17919 EMBL-EBI
WormBase CE16195 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:251667_AT dyskerin, putative / nucleolar protein NAP57, putative at
CANINE:1586804_AT similar to H/ACA ribonucleoprotein complex subunit 4 (Dyskerin) (Nucleolar protein family A member 4) (snoRNP protein DKC1) (Nopp140-associated protein of 57 kDa) (Nucleolar protein NAP57) (CBF5 homolog) cfa
CANINE_2:CFA.15181.1.A1_AT similar to H/ACA ribonucleoprotein complex subunit 4 (Dyskerin) (Nucleolar protein family A member 4) (snoRNP protein DKC1) (Nopp140-associated protein of 57 kDa) (Nucleolar protein NAP57) (CBF5 homolog) cfa
CANINE_2:CFA.15181.1.A1_S_AT similar to H/ACA ribonucleoprotein complex subunit 4 (Dyskerin) (Nucleolar protein family A member 4) (snoRNP protein DKC1) (Nopp140-associated protein of 57 kDa) (Nucleolar protein NAP57) (CBF5 homolog) cfa
CANINE_2:CFA.19618.1.S1_S_AT similar to H/ACA ribonucleoprotein complex subunit 4 (Dyskerin) (Nucleolar protein family A member 4) (snoRNP protein DKC1) (Nopp140-associated protein of 57 kDa) (Nucleolar protein NAP57) (CBF5 homolog) cfa
DROSOPHILA_2:1628188_AT Nucleolar protein at 60B dm
DROSGENOME1:153235_AT Nucleolar protein at 60B dm
DROSOPHILA_2:1639554_AT Nucleolar protein at 60B dm
CHICKEN:GGA.1015.1.S1_S_AT dyskeratosis congenita 1, dyskerin gga
HG-U133A:201478_S_AT dyskeratosis congenita 1, dyskerin hs
HG-U133_PLUS_2:201478_S_AT dyskeratosis congenita 1, dyskerin hs
HG-U133A_2:201478_S_AT dyskeratosis congenita 1, dyskerin hs
HG-U133A:201479_AT dyskeratosis congenita 1, dyskerin hs
HG-U133_PLUS_2:201479_AT dyskeratosis congenita 1, dyskerin hs
HG-FOCUS:201479_AT dyskeratosis congenita 1, dyskerin hs
HG-U133A_2:201479_AT dyskeratosis congenita 1, dyskerin hs
HG-U133_PLUS_2:216212_S_AT dyskeratosis congenita 1, dyskerin hs
HG-U133A_2:216212_S_AT dyskeratosis congenita 1, dyskerin hs
HG-U133A:216212_S_AT dyskeratosis congenita 1, dyskerin hs
HU35KSUBB:RC_T03313_AT dyskeratosis congenita 1, dyskerin hs
U133_X3P:G4503336_3P_AT dyskeratosis congenita 1, dyskerin hs
U133_X3P:G2737893_3P_A_AT dyskeratosis congenita 1, dyskerin hs
U133_X3P:HS.4747.1.S1_3P_A_AT dyskeratosis congenita 1, dyskerin hs
HG-U95AV2:34829_AT dyskeratosis congenita 1, dyskerin hs
MG-U74BV2:162627_AT cDNA sequence BC068171 mm
MOE430B:1438016_AT cDNA sequence BC068171 mm
MOUSE430_2:1438016_AT cDNA sequence BC068171 mm
MOE430B:1438015_AT cDNA sequence BC068171 mm
MOUSE430_2:1438015_AT cDNA sequence BC068171 mm
MOE430B:1441788_S_AT cDNA sequence BC068171 mm
MOUSE430_2:1441788_S_AT cDNA sequence BC068171 mm
MU19KSUBC:TC36174_AT CDNA sequence BC068171, mRNA (cDNA clone MGC:107501 IMAGE:6435181) mm
YEAST_2:1772442_AT Component of box H/ACA small nucleolar ribonucleoprotein particles (snoRNPs), probable rRNA pseudouridine synthase, binds to snoRNP Nop10p and also interacts with ribosomal biogenesis protein Nop53p Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6396 RNA processing inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3723 RNA binding inferred from electronic annotation QuickGO AmiGO
4730 pseudouridylate synthase activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB07244 Hypothetical protein K01G5.5 [Caenorhabditis elegans] ref|NP_499370.1| K01G5.5 [Caenorhabditis elegans] sp|O17919|DKC1_CAEEL Putative H/ACA ribonucleoprotein complex subunit 0.0
blast Q60YA8 Putative H/ACA ribonucleoprotein complex subunit 4 emb|CAE71406.1| Hypothetical protein CBG18316 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR002501 EMBL-EBI Pseudouridylate synthase TruB, N-terminal 4.0E-75
Pfam IPR002478 EMBL-EBI PUA domain 2.9E-25
Sequence
Target Sequence 
>C. ELEGANS:193161_AT
acaatgcacgacgttctcgatgctcagtatctcctagacacccagaaagacgagagctac
atgagacacatcgttcgtccacttgaggctcttctcacccagcacaagagagttgttgtc
aaggacagttgcatcaacgcgatctgctacggagccaagatccttattcccggaattctt
cgttacgacgatgacatcgaggttggcaaggagatcgtcatcatgtcgacgaagggagaa
gccatctgcatcgctattgctcagatgaacacatcaacgatcgcttcagtcgatcacgga
gtcgttgccaagtcgaagcgtgtcattatggagcgtgatgtgtacggaagaaagtgggga
cttggaccggttgcatccaagaagaagcaaatggtcaaggacggacttctagacaaattc
ggaaaaccaaatgacactactccaaaatcgtgggcca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ACAATGCACGACGTTCTCGATGCTC 599 113 760 Antisense
TCGATGCTCAGTATCTCCTAGACAC 543 603 776 Antisense
CATGAGACACATCGTTCGTCCACTT 668 209 819 Antisense
TTGCATCAACGCGATCTGCTACGGA 660 701 888 Antisense
TACGGAGCCAAGATCCTTATTCCCG 627 645 907 Antisense
TCCCGGAATTCTTCGTTACGACGAT 603 595 927 Antisense
AGAAGCCATCTGCATCGCTATTGCT 113 75 996 Antisense
GAACACATCAACGATCGCTTCAGTC 250 351 1026 Antisense
CGCTTCAGTCGATCACGGAGTCGTT 641 253 1041 Antisense
GGAGTCGTTGCCAAGTCGAAGCGTG 87 517 1057 Antisense
GACACTACTCCAAAATCGTGGGCCA 315 367 1192 Antisense
Sequence Source Affymetrix Proprietary Database