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[191659_at] Prokaryotic ribonuclease PH

Description C14A4.5 /REP_DB=WormBase Gene ID /WP=CE02146 /TR=Q17952 /GB=CAA90109.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=Prokaryotic ribonuclease PH
Cluster 6grp_highest_10_10 > 59      6grp_high1_10_10 > 95      4grp_highest_8_8 > 37      4grp_high_8_8 > 02      6grp_highest_nonorm > 82      6grp_total > 85      4grp_total > 06      6grp_highest_sub > In      6grp_cgc > 67      6grp_high1_sub > In      6grp_cgc_sub > In      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 359
1 2 3 4 range
A 381.1
(1)
P 		207.1
(-3)
P 		236.5
(-2.3)
P 		467.6
(3)
P 		261
B 432.7
(1.6)
P 		202.8
(-3)
P 		279.4
(-1.5)
P 		499.8
(3)
P 		297
C 367.2
(-0)
P 		188.7
(-3)
P 		252
(-1.9)
P 		547.8
(3)
P 		359
avr 393.7
(0.8) 		199.5
(-3) 		256
(-1.9) 		505.1
(3) 		306

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 319
1 2 3 4 5 6 range
A 337
(0)
P 		246
(-3)
P 		304.5
(-1.1)
P 		356.2
(0.7)
P 		383
(1.6)
P 		426.5
(3)
P 		181
B 236.1
(-3)
P 		361.7
(0.3)
P 		299.5
(-1.3)
P 		453.1
(2.7)
P 		420.3
(1.8)
P 		466.2
(3)
P 		230
C 182.7
(-3)
P 		333.5
(-0.2)
P 		354.4
(0.2)
P 		380.9
(0.7)
P 		319.8
(-0.4)
P 		502
(3)
P 		319
avr 251.9
(-3) 		313.7
(-1.3) 		319.5
(-1.1) 		396.7
(1.1) 		374.4
(0.5) 		464.9
(3) 		213
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 94
1 2 3 4 range
A 138.8
(3)
P 		45
(-3)
P 		61.8
(-1.9)
P 		68.4
(-1.5)
P 		94
B 138
(3)
P 		50.1
(-3)
P 		64.8
(-2)
P 		106.5
(0.8)
P 		88
C 121.5
(3)
P 		54.3
(-3)
P 		87.8
(-0)
P 		92.4
(0.4)
P 		67
avr 132.8
(3) 		49.8
(-3) 		71.5
(-1.4) 		89.1
(-0.2) 		83

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 112
1 2 3 4 5 6 range
A 62.1
(-3)
P 		87.5
(-0.2)
P 		66.3
(-2.5)
P 		90.3
(0.2)
P 		115.6
(3)
P 		103.8
(1.7)
P 		54
B 82.2
(-2.4)
P 		120.4
(-0.2)
P 		72.7
(-3)
P 		120
(-0.2)
P 		170.8
(2.8)
P 		173.9
(3)
P 		101
C 67.7
(-3)
P 		101.7
(-1)
P 		90.2
(-1.7)
P 		76.6
(-2.5)
P 		103.5
(-0.9)
P 		168
(3)
P 		100
avr 70.7
(-3) 		103.2
(-0.5) 		76.4
(-2.6) 		95.6
(-1.1) 		130
(1.6) 		148.6
(3) 		78
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 191659_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3002
Sequence Type Exemplar sequence
Representative Public ID C14A4.5 NCBI
Target Description C14A4.5 /REP_DB=WormBase Gene ID /WP=CE02146 /TR=Q17952 /GB=CAA90109.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=Prokaryotic ribonuclease PH
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_063883(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063883 NCBI Caenorhabditis elegans Cell-death-Related Nuclease family member (crn-5) (crn-5) mRNA, complete cds. 11/11 None
SNAP00000002487 ENSEMBL cdna:SNAP chromosome:CEL140:II:10592673:10593410:1 11/11 None
GENEFINDER00000002509 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:10592673:10593410:1 11/11 None
C14A4.5 ENSEMBL cdna:known chromosome:CEL140:II:10592668:10593441:1 gene:C14A4.5 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
chrII:10592669-10593407(+) 100.0 100.0
Public Domain and Genome References
Gene Title Prokaryotic ribonuclease PH
Gene Symbol crn-5
Ensembl C14A4.5
Entrez Gene 174634 Entrez gene
SwissProt Q17952 EMBL-EBI
WormBase CE02146 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:252508_AT 3' exoribonuclease family domain 1-containing protein at
CANINE_2:CFAAFFX.8435.1.S1_AT similar to Exosome complex exonuclease RRP46 (Ribosomal RNA processing protein 46) (Exosome component 5) (p12B) (Chronic myelogenous leukemia tumor antigen 28) cfa
DROSOPHILA_2:1638292_AT dm
DROSGENOME1:153132_AT dm
HG-U133_PLUS_2:218481_AT exosome component 5 hs
HG-U133A:218481_AT exosome component 5 hs
HG-FOCUS:218481_AT exosome component 5 hs
HG-U133A_2:218481_AT exosome component 5 hs
U133_X3P:G9910359_3P_AT exosome component 5 hs
HG-U95B:53133_AT exosome component 5 hs
HU35KSUBC:RC_AA449450_AT Exosome component 5 hs
MU11KSUBA:AA409134_RC_S_AT exosome component 5 mm
MG-U74AV2:97249_AT exosome component 5 mm
MG-U74AV2:162153_I_AT exosome component 5 mm
MOE430A:1417167_AT exosome component 5 mm
MOUSE430A_2:1417167_AT exosome component 5 mm
MOUSE430_2:1417167_AT exosome component 5 mm
MG-U74CV2:168975_I_AT Exosome component 5, mRNA (cDNA clone MGC:27748 IMAGE:2651418) mm
MU19KSUBA:TC19167_S_AT Exosome component 5, mRNA (cDNA clone MGC:27748 IMAGE:2651418) mm
MU19KSUBC:TC39434_S_AT Exosome component 5, mRNA (cDNA clone MGC:27748 IMAGE:2651418) mm
RG-U34B:RC_AA943578_AT exosome component 5 (predicted) rn
RAE230A:1372942_AT exosome component 5 (predicted) rn
RAT230_2:1372942_AT exosome component 5 (predicted) rn
YEAST_2:1775054_AT Protein involved in rRNA processing; component of the exosome 3->5 exonuclease complex 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
175 3'-5'-exoribonuclease activity inferred from electronic annotation QuickGO AmiGO
3723 RNA binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA90109 Hypothetical protein C14A4.5 [Caenorhabditis elegans] ref|NP_496284.1| Cell-death-Related Nuclease family member (crn-5) [Caenorhabditis elegans] gb|AAP57301.1| cell death-related nuclease 5 [Caenorhabditis elegans] 1.0E-121
blast CAE59645 Hypothetical protein CBG03059 [Caenorhabditis briggsae] 1.0E-108
blast XP_686045 PREDICTED: similar to Exosome complex exonuclease RRP46 (Ribosomal RNA processing protein 46) (Exosome component 5) (p12B) (Chronic myelogenous leukemia tumor antigen 28) isoform 1 [Danio rerio] ref|XP_682789.1| PREDICTED: similar to Exosome complex exonuclease RRP46 (Ribosomal RNA processing protein 46) (Exosome component 5) (p12B) (Chronic myelogenous leukemia tumor antigen 28) isoform 1 [Danio rerio] 6.0E-22
Protein Domains
Database ID Description E-Value
Pfam IPR001247 EMBL-EBI 3 exoribonuclease 1.2E-7
Sequence
Target Sequence 
>C. ELEGANS:191659_AT
gaaatgcgttgtgagctctcgttcctcaaaaacgcggatggctcggcatgcttctcccag
ggtgccacgtgtatttgggcttcatgcagtggtcctggagatgttcacgcttcgaaagca
agtgatgaggctatgactctggatattagttatagagcaaattgtggagataacaagttc
aatgtgctgaacaatatcattcattctactctatccaatgcaatcaatctcgaattgttt
ccccacacaacaatttctgtcacagtacatggaattcaggatgatggaagtatgggagct
gtagcgataaatggagcttgttttgctctacttgacaatggaatgccattcgaaacagtc
ttctgtggtgtccttattgttcgtgtcaaagatgagctgattattgatccgacagcaaaa
caagaagctgcatcgactggaagagtgctcttttcagtgtgcaaaggatccgatggacat
ccagaagtgtgtgcgatggacgctataggacattgggattttattcagctggaagccgcg
tggtcattggcacaaccatctgccagtgctatt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAAATGCGTTGTGAGCTCTCGTTCC 41 363 31 Antisense
CAAAAACGCGGATGGCTCGGCATGC 400 191 57 Antisense
TATTTGGGCTTCATGCAGTGGTCCT 491 661 102 Antisense
AGTGGTCCTGGAGATGTTCACGCTT 514 59 118 Antisense
ATATCATTCATTCTACTCTATCCAA 292 19 224 Antisense
ATCAATCTCGAATTGTTTCCCCACA 172 27 253 Antisense
TTCCCCACACAACAATTTCTGTCAC 439 697 269 Antisense
GAGCTTGTTTTGCTCTACTTGACAA 408 389 344 Antisense
GTCTTCTGTGGTGTCCTTATTGTTC 56 469 388 Antisense
TGGAAGCCGCGTGGTCATTGGCACA 235 547 560 Antisense
GGCACAACCATCTGCCAGTGCTATT 418 535 579 Antisense
Sequence Source Affymetrix Proprietary Database