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[193023_at] small nuclear ribonucleoprotein (SNRNP)

Description W08E3.1 /REP_DB=WormBase Gene ID /WP=CE14704 /TR=P91918 /GB=CAB07132.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=small nuclear ribonucleoprotein (SNRNP)
Cluster 6grp_highest_10_10 > 62      6grp_high1_10_10 > 29      4grp_highest_8_8 > 10      4grp_high_8_8 > 62      6grp_highest_nonorm > 76      6grp_total > 27      4grp_total > 57      6grp_highest_sub > Cu      6grp_cgc > 05      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Decrease      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1336
1 2 3 4 range
A 1288.7
(-2.1)
P 		2005.3
(2.6)
P 		2059.2
(3)
P 		1146.3
(-3)
P 		913
B 1196.9
(-2.5)
P 		1697.6
(0.1)
P 		2253.8
(3)
P 		1092.3
(-3)
P 		1162
C 1333.9
(-1)
P 		1923.7
(1.7)
P 		2196.4
(3)
P 		917.4
(-3)
P 		1279
avr 1273.2
(-1.8) 		1875.5
(1.4) 		2169.8
(3) 		1052
(-3) 		1118

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 647
1 2 3 4 5 6 range
A 1193.8
(2)
P 		1236.7
(3)
P 		1122.7
(0.5)
P 		967
(-3)
P 		1154.9
(1.2)
P 		1203.8
(2.3)
P 		270
B 1496.3
(2)
P 		1411.6
(1.2)
P 		1606.9
(3)
P 		959.6
(-3)
P 		1329
(0.4)
P 		1362.5
(0.7)
P 		647
C 1522
(3)
P 		1384.5
(1.5)
P 		1012.4
(-2.6)
P 		974.1
(-3)
P 		1174
(-0.8)
P 		1140.1
(-1.2)
P 		548
avr 1404
(3) 		1344.3
(2.2) 		1247.3
(0.8) 		966.9
(-3) 		1219.3
(0.5) 		1235.5
(0.7) 		437
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 611
1 2 3 4 range
A 469.2
(1.9)
P 		435.3
(1.3)
P 		538.3
(3)
P 		167.8
(-3)
P 		371
B 381.7
(0.1)
P 		419.3
(0.9)
P 		522.3
(3)
P 		232.8
(-3)
P 		290
C 441.5
(-0.2)
P 		553.1
(0.9)
P 		765.5
(3)
P 		154.7
(-3)
P 		611
avr 430.8
(0.5) 		469.2
(1) 		608.7
(3) 		185.1
(-3) 		424

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 368
1 2 3 4 5 6 range
A 220.1
(-3)
P 		439.8
(3)
P 		244.5
(-2.3)
P 		245.2
(-2.3)
P 		348.5
(0.5)
P 		293.1
(-1)
P 		220
B 520.6
(2.6)
P 		469.9
(1.5)
P 		390.2
(-0.1)
P 		254.2
(-3)
P 		539.9
(3)
P 		508.1
(2.3)
P 		286
C 564.1
(3)
P 		422.5
(0.7)
P 		257.7
(-2)
P 		195.9
(-3)
P 		379.9
(-0)
P 		381.7
(0)
P 		368
avr 434.9
(2.7) 		444.1
(3) 		297.5
(-1.1) 		231.8
(-3) 		422.8
(2.4) 		394.3
(1.6) 		212
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193023_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.2379
Sequence Type Exemplar sequence
Representative Public ID W08E3.1 NCBI
Target Description W08E3.1 /REP_DB=WormBase Gene ID /WP=CE14704 /TR=P91918 /GB=CAB07132.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=small nuclear ribonucleoprotein (SNRNP)
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_060947(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_060947 NCBI Caenorhabditis elegans Small Nuclear Ribonucleoprotein family member (snr-2) (snr-2) mRNA, complete cds. 11/11 None
SNAP00000036233 ENSEMBL cdna:SNAP chromosome:CEL140:I:13347606:13348141:1 11/11 None
GENEFINDER00000036238 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:13347630:13348141:1 10/11 None
W08E3.1.1 ENSEMBL cdna:known chromosome:CEL140:I:13347515:13348334:1 gene:W08E3.1 11/11 None
W08E3.1.2 ENSEMBL cdna:known chromosome:CEL140:I:13347516:13348283:1 gene:W08E3.1 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
chrI:13347535-13348072(+) 99.59 99.59
Public Domain and Genome References
Gene Title small nuclear ribonucleoprotein (SNRNP)
Gene Symbol snr-2
Ensembl W08E3.1
Entrez Gene 173204 Entrez gene
SwissProt P91918 EMBL-EBI
WormBase CE14704 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6397 mRNA processing inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5634 nucleus inferred from electronic annotation QuickGO AmiGO
5732 small nucleolar ribonucleoprotein complex inferred from electronic annotation QuickGO AmiGO
30529 ribonucleoprotein complex inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB07132 Hypothetical protein W08E3.1 [Caenorhabditis elegans] ref|NP_493348.1| Small Nuclear Ribonucleoprotein family member (snr-2) [Caenorhabditis elegans] sp|P91918|RSMB_CAEEL Probable small nuclear ribonucleoprotein associated protein B (snRNP-B) (Sm protein B) (Sm-B) (SmB) 5.0E-49
blast CAB07132 Hypothetical protein W08E3.1 [Caenorhabditis elegans] ref|NP_493348.1| Small Nuclear Ribonucleoprotein family member (snr-2) [Caenorhabditis elegans] sp|P91918|RSMB_CAEEL Probable small nuclear ribonucleoprotein associated protein B (snRNP-B) (Sm protein B) (Sm-B) (SmB) 2.0E-48
blast CAE73012 Hypothetical protein CBG20368 [Caenorhabditis briggsae] 5.0E-48
blast CAE73012 Hypothetical protein CBG20368 [Caenorhabditis briggsae] 2.0E-47
blast CAB07132 Hypothetical protein W08E3.1 [Caenorhabditis elegans] ref|NP_493348.1| Small Nuclear Ribonucleoprotein family member (snr-2) [Caenorhabditis elegans] sp|P91918|RSMB_CAEEL Probable small nuclear ribonucleoprotein associated protein B (snRNP-B) (Sm protein B) (Sm-B) (SmB) 4.0E-44
blast CAE73012 Hypothetical protein CBG20368 [Caenorhabditis briggsae] 5.0E-43
Protein Domains
Database ID Description E-Value
Pfam IPR001163 EMBL-EBI Small nuclear ribonucleoprotein (Sm protein) 2.9E-20
Pfam IPR001163 EMBL-EBI Small nuclear ribonucleoprotein (Sm protein) 2.9E-20
Pfam IPR001163 EMBL-EBI Small nuclear ribonucleoprotein (Sm protein) 2.5E-18
Sequence
Target Sequence 
>C. ELEGANS:193023_AT
tgatggctcatctcaactacaggatgaagatcatccttcaggacggtagaaccttcatcg
gatttttcaaggctttcgacaagcatatgaacattttactcgcagagtgcgaggaacaca
gacaaatcaagccaaaggccggaaagaagaccgatggagaagaaaagcgaattctcggcc
tcgtactggtccgcggagaacatatcgtctcgatgaccgtcgacggaccaccaccaagag
atgacgattcagtgagactcgccaaggccggaggagctggaggtgtcggacaagccaagc
caggaggccgtggaatgccagctatgccaggaatgccgggaatgccacc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGATGGCTCATCTCAACTACAGGAT 343 567 38 Antisense
GAAGATCATCCTTCAGGACGGTAGA 401 337 63 Antisense
GACGGTAGAACCTTCATCGGATTTT 636 321 79 Antisense
GCATATGAACATTTTACTCGCAGAG 311 309 120 Antisense
CTGGTCCGCGGAGAACATATCGTCT 107 241 223 Antisense
ATCGTCTCGATGACCGTCGACGGAC 665 29 241 Antisense
CGATTCAGTGAGACTCGCCAAGGCC 196 249 282 Antisense
GAGCTGGAGGTGTCGGACAAGCCAA 312 387 311 Antisense
GACAAGCCAAGCCAGGAGGCCGTGG 238 365 326 Antisense
GAGGCCGTGGAATGCCAGCTATGCC 531 405 341 Antisense
TGCCAGGAATGCCGGGAATGCCACC 651 585 362 Antisense
Sequence Source Affymetrix Proprietary Database