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[173104_at] small nuclear ribonucleoprotein (SNRNP)

Description AU116044_rc /REP_DB=TREMBL Accession /FEA=EST Transcript /REVCOMP /GB=AU116044 /DEF=Caenorhabditis elegans cDNA clone:yk740a1 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 85      6grp_high1_10_10 > 67      4grp_highest_8_8 > 18      4grp_high_8_8 > 63      6grp_highest_nonorm > 67      6grp_total > 58      4grp_total > 56      6grp_highest_sub > Cu      6grp_cgc > 27      6grp_high1_sub > Da      6grp_cgc_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1927
1 2 3 4 range
A 1706.2
(-2.1)
P 		1818.7
(-1.7)
P 		3207.2
(3)
P 		1448.9
(-3)
P 		1758
B 1524.7
(-3)
P 		2353.8
(2.3)
P 		2456.7
(3)
P 		1529.1
(-3)
P 		932
C 1667.7
(-1.1)
P 		2074.8
(0.8)
P 		2522.5
(3)
P 		1280
(-3)
P 		1243
avr 1632.9
(-2) 		2082.4
(0) 		2728.8
(3) 		1419.3
(-3) 		1310

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1035
1 2 3 4 5 6 range
A 1833.9
(0.7)
P 		1500.6
(-1.6)
P 		1517.3
(-1.5)
P 		1304.5
(-3)
P 		2160.5
(3)
P 		1873.8
(1)
P 		856
B 1970.9
(0.5)
P 		1829.1
(-0.4)
P 		1723.2
(-1.1)
P 		2105.2
(1.4)
P 		1444.2
(-3)
P 		2339.7
(3)
P 		896
C 1591.7
(-1.6)
P 		2080.7
(3)
P 		1530.6
(-2.2)
P 		2017.6
(2.4)
P 		1440.2
(-3)
P 		1945.3
(1.7)
P 		641
avr 1798.8
(-0.3) 		1803.5
(-0.2) 		1590.4
(-3) 		1809.1
(-0.2) 		1681.6
(-1.8) 		2052.9
(3) 		463
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 667
1 2 3 4 range
A 621.2
(0.9)
P 		394.8
(-1.2)
P 		838.4
(3)
P 		212.1
(-3)
P 		626
B 486.2
(0.8)
P 		581.3
(3)
P 		569.3
(2.7)
P 		325.9
(-3)
P 		255
C 552.1
(0)
P 		596.5
(0.4)
P 		879.2
(3)
P 		215.8
(-3)
P 		663
avr 553.2
(0.5) 		524.2
(0.2) 		762.3
(3) 		251.3
(-3) 		511

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 542
1 2 3 4 5 6 range
A 338.1
(-2.9)
P 		533.7
(0.8)
P 		330.4
(-3)
P 		330.8
(-3)
P 		651.9
(3)
P 		456.2
(-0.7)
P 		322
B 685.8
(0.5)
P 		608.8
(-0.5)
P 		418.4
(-3)
P 		557.6
(-1.2)
P 		586.8
(-0.8)
P 		872.5
(3)
P 		454
C 590
(1.6)
P 		634.9
(2.6)
P 		389.6
(-3)
P 		405.7
(-2.6)
P 		466
(-1.2)
P 		651.2
(3)
P 		262
avr 538
(0.4) 		592.5
(1.6) 		379.5
(-3) 		431.4
(-1.9) 		568.2
(1) 		660
(3) 		281
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173104_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.27571
Sequence Type Exemplar sequence
Representative Public ID AU116044 NCBI
Target Description AU116044_rc /REP_DB=TREMBL Accession /FEA=EST Transcript /REVCOMP /GB=AU116044 /DEF=Caenorhabditis elegans cDNA clone:yk740a1 : 3prime end, single read.
Cluster Evidence This cluster is supported by a EST Transcript.
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(10)
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. 10/11 None
W08E3.1.1 ENSEMBL cdna:known chromosome:CEL140:I:13347515:13348334:1 gene:W08E3.1 10/11 None
W08E3.1.2 ENSEMBL cdna:known chromosome:CEL140:I:13347516:13348283:1 gene:W08E3.1 10/11 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:13347951-13348205(+) 77.33 84.67
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 CAE73012 Hypothetical protein CBG20368 [Caenorhabditis briggsae] 5.0E-48
blast AAH03530 SNRPB protein [Homo sapiens] 1.0E-30
Protein Domains
Database ID Description E-Value
Pfam IPR001163 EMBL-EBI Small nuclear ribonucleoprotein (Sm protein) 2.9E-20
Sequence
Target Sequence 
>C. ELEGANS:173104_AT
atgtaggtaagggaatgccaccaggcggagcaccaggaggcctctctggagccatgcgcg
gacacggaggaccaggaatggcagccatgcagccaggatatggcggcccaccaggaggac
gtccattctaaaattttgctatccaaatccgcatgtttctatcatttttcccaccgatct
tgtatttttctctgttcttt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATGTAGGTAAGGGAATGCCACCAGG 127 41 49 Antisense
GGACGTCCATTCTAAAATTTTGCTA 76 525 165 Antisense
AATTTTGCTATCCAAATCCGCATGT 587 175 180 Antisense
GCTATCCAAATCCGCATGTTTCTAT 467 303 186 Antisense
ATCCAAATCCGCATGTTTCTATCAT 665 39 189 Antisense
AATCCGCATGTTTCTATCATTTTTC 687 167 194 Antisense
CGCATGTTTCTATCATTTTTCCCAC 705 253 198 Antisense
TTTCCCACCGATCTTGTATTTTTCT 703 669 215 Antisense
CCCACCGATCTTGTATTTTTCTCTG 366 259 218 Antisense
ACCGATCTTGTATTTTTCTCTGTTC 68 89 221 Antisense
GATCTTGTATTTTTCTCTGTTCTTT 109 421 224 Antisense
Sequence Source Affymetrix Proprietary Database