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[192965_at] U1 small nuclear ribonucleoprotein A

Description K08D10.3 /REP_DB=WormBase Gene ID /WP=CE07355 /TR=Q21323 /GB=AAA98033.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=U1 small nuclear ribonucleoprotein A
Cluster 6grp_highest_10_10 > 73      6grp_high1_10_10 > 37      4grp_highest_8_8 > 01      4grp_high_8_8 > 45      6grp_highest_nonorm > 74      6grp_total > 45      4grp_total > 50      6grp_highest_sub > Cu      6grp_cgc > 45      6grp_total_sub > Cup      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 472
1 2 3 4 range
A 605.9
(-1.6)
P 		702.4
(0.4)
P 		830.1
(3)
P 		536.7
(-3)
P 		293
B 513.6
(-3)
P 		868.4
(3)
P 		654.3
(-0.6)
P 		536.8
(-2.6)
P 		355
C 651.5
(-0.5)
P 		924.8
(3)
P 		701.4
(0.2)
P 		452.6
(-3)
P 		472
avr 590.3
(-1.5) 		831.9
(3) 		728.6
(1.1) 		508.7
(-3) 		323

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 379
1 2 3 4 5 6 range
A 675.6
(-0)
P 		756.8
(1.4)
P 		702.4
(0.4)
P 		647.6
(-0.5)
P 		504.3
(-3)
P 		849.9
(3)
P 		346
B 662.6
(1.1)
P 		605.3
(-0.8)
P 		721.7
(3)
P 		539.4
(-3)
P 		602.1
(-0.9)
P 		631.9
(0)
P 		182
C 883.3
(3)
P 		642.8
(-1.2)
P 		729
(0.3)
P 		540.4
(-3)
P 		672.2
(-0.7)
P 		686.2
(-0.4)
P 		343
avr 740.5
(3) 		668.3
(0.4) 		717.7
(2.2) 		575.8
(-3) 		592.9
(-2.4) 		722.7
(2.4) 		165
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 190
1 2 3 4 range
A 220.6
(3)
P 		152.5
(0.1)
P 		217
(2.8)
P 		78.6
(-3)
P 		142
B 163.8
(-0)
P 		214.5
(3)
P 		151.6
(-0.8)
P 		114.4
(-3)
P 		100
C 215.7
(1.4)
P 		265.9
(3)
P 		244.5
(2.3)
P 		76.3
(-3)
P 		190
avr 200
(2.5) 		211
(3) 		204.4
(2.7) 		89.8
(-3) 		121

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 219
1 2 3 4 5 6 range
A 124.5
(-3)
P 		269.2
(3)
P 		153
(-1.8)
P 		164.3
(-1.3)
P 		152.2
(-1.9)
P 		206.9
(0.4)
P 		145
B 230.5
(2.2)
P 		201.5
(0.5)
P 		175.2
(-1.1)
P 		142.9
(-3)
P 		244.6
(3)
P 		235.6
(2.5)
P 		102
C 327.4
(3)
P 		196.1
(-0.6)
P 		185.6
(-0.9)
P 		108.7
(-3)
P 		217.5
(-0)
P 		229.7
(0.3)
P 		219
avr 227.5
(3) 		222.3
(2.6) 		171.3
(-0.8) 		138.6
(-3) 		204.8
(1.5) 		224.1
(2.8) 		89
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192965_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.10407
Sequence Type Exemplar sequence
Representative Public ID K08D10.3 NCBI
Target Description K08D10.3 /REP_DB=WormBase Gene ID /WP=CE07355 /TR=Q21323 /GB=AAA98033.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=U1 small nuclear ribonucleoprotein A
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_068104(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_068104 NCBI Caenorhabditis elegans RNP (RRM RNA binding domain) containing family member (rnp-3) (rnp-3) mRNA, complete cds. 11/11 None
SNAP00000009686 ENSEMBL cdna:SNAP chromosome:CEL140:IV:4174088:4176155:1 11/11 None
GENEFINDER00000009698 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:4174088:4176155:1 11/11 None
K08D10.3 ENSEMBL cdna:known chromosome:CEL140:IV:4174080:4176257:1 gene:K08D10.3 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
chrIV:4174093-4176161(+) 100.0 100.0
Public Domain and Genome References
Gene Title U1 small nuclear ribonucleoprotein A
Gene Symbol rnp-3
Ensembl K08D10.3
Entrez Gene 177182 Entrez gene
SwissProt Q21323 EMBL-EBI
WormBase CE07355 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:14128_AT small nuclear ribonucleoprotein U2B, putative / spliceosomal protein, putative at
ATH1-121501:255871_AT small nuclear ribonucleoprotein U2B, putative / spliceosomal protein, putative at
CANINE_2:CFA.10214.2.A1_S_AT similar to U2 small nuclear ribonucleoprotein B cfa
CANINE_2:CFAAFFX.9232.1.S1_S_AT similar to U2 small nuclear ribonucleoprotein B cfa
CHICKEN:GGA.4634.1.S1_AT small nuclear ribonucleoprotein polypeptide B'' gga
HG-U133A_2:202505_AT small nuclear ribonucleoprotein polypeptide B'' hs
HG-U133A:202505_AT small nuclear ribonucleoprotein polypeptide B'' hs
HG-U133_PLUS_2:202505_AT small nuclear ribonucleoprotein polypeptide B'' hs
HG-FOCUS:202505_AT small nuclear ribonucleoprotein polypeptide B'' hs
HU35KSUBD:RC_T40439_S_AT small nuclear ribonucleoprotein polypeptide B'' hs
HUGENEFL:M15841_AT small nuclear ribonucleoprotein polypeptide B'' hs
U133_X3P:G4507122_3P_AT small nuclear ribonucleoprotein polypeptide B'' hs
HG-U95AV2:38399_AT small nuclear ribonucleoprotein polypeptide B'' hs
HG-U95D:74555_AT small nuclear ribonucleoprotein polypeptide B'' hs
U133_X3P:HS2.280378.1.A1_3P_AT Small nuclear ribonucleoprotein polypeptide B'' hs
HG-U133_PLUS_2:1561965_AT Small nuclear ribonucleoprotein polypeptide B'' hs
HG-U95B:44293_AT Small nuclear ribonucleoprotein polypeptide B'' hs
HU35KSUBB:RC_AA224340_AT Small nuclear ribonucleoprotein polypeptide B'' hs
MOUSE430A_2:1452422_A_AT U2 small nuclear ribonucleoprotein B mm
MOE430A:1452422_A_AT U2 small nuclear ribonucleoprotein B mm
MOUSE430_2:1452422_A_AT U2 small nuclear ribonucleoprotein B mm
MU11KSUBB:X63019_S_AT U2 small nuclear ribonucleoprotein B mm
MU11KSUBB:MSA.1939.0_AT U2 small nuclear ribonucleoprotein B mm
MU11KSUBB:MSA.1939.0_G_AT U2 small nuclear ribonucleoprotein B mm
MG-U74AV2:92839_F_AT U2 small nuclear ribonucleoprotein B mm
MOE430A:1426613_A_AT U2 small nuclear ribonucleoprotein B mm
MOUSE430A_2:1426613_A_AT U2 small nuclear ribonucleoprotein B mm
MOUSE430_2:1426613_A_AT U2 small nuclear ribonucleoprotein B mm
MU19KSUBC:TC35648_I_AT U2 small nuclear ribonucleoprotein B (Snrpb2), mRNA mm
RG-U34B:RC_AI012309_AT U2 small nuclear ribonucleoprotein B (predicted) rn
RG-U34B:RC_AA944322_AT U2 small nuclear ribonucleoprotein B (predicted) rn
RAE230A:1389576_AT U2 small nuclear ribonucleoprotein B (predicted) rn
RAT230_2:1389576_AT U2 small nuclear ribonucleoprotein B (predicted) rn
RG-U34B:RC_AA900468_AT U2 small nuclear ribonucleoprotein B (predicted) rn
Protein Similarities
Method ID Description E-Value
blast AAA98033 Rnp (rrm rna binding domain) containing protein 3 [Caenorhabditis elegans] ref|NP_500505.1| RNP (RRM RNA binding domain) containing family member (rnp-3) [Caenorhabditis elegans] 1.0E-121
blast CAE68287 Hypothetical protein CBG13972 [Caenorhabditis briggsae] 1.0E-100
blast XP_857793 PREDICTED: similar to U2 small nuclear ribonucleoprotein B isoform 9 [Canis familiaris] 3.0E-57
Protein Domains
Database ID Description E-Value
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 4.7E-13
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 1.4E-10
Sequence
Target Sequence 
>C. ELEGANS:192965_AT
ctctcttcacatggttttcacacaattcggtgaaataattcagctaatgtcatttcgaaa
ggaaaaaatgcgcggacaagcacatatcgtcttcaaagaggtctcatcagcgtcaaatgc
tcttcgagccctgcaaggattcccattttatggaaaaccaatgagaattcaatatgcaag
agaggattctgatgtgatttctcgtgccaaaggaacttttgtcgaaaaacgacaaaaatc
cacgaaaatcgccaaaaaaccatatgaaaaaccggcgaaaaatggaaaatcggcagcgga
gccgactcaaaaggagccgcaggagactgacggaccaggattgccgaataatattctttt
ctgctcgaatattccagaaggaaccgagccagaacagattcagaccattttcagccaatt
cccaggacttcgtgaggttcgctggatgccaaacaccaaggattttgcatttatcgaata
cgaatccgaagatctttcagagccagcacgtcaagctctcgacaatttc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CTCTCTTCACATGGTTTTCACACAA 217 231 90 Antisense
GCGCGGACAAGCACATATCGTCTTC 340 287 159 Antisense
GAGGTCTCATCAGCGTCAAATGCTC 250 403 187 Antisense
AATGCTCTTCGAGCCCTGCAAGGAT 693 165 205 Antisense
GATTCTGATGTGATTTCTCGTGCCA 590 431 274 Antisense
GGAGCCGACTCAAAAGGAGCCGCAG 383 521 387 Antisense
GAGCCGCAGGAGACTGACGGACCAG 544 385 403 Antisense
GATTCAGACCATTTTCAGCCAATTC 177 431 486 Antisense
CTTCGTGAGGTTCGCTGGATGCCAA 199 219 517 Antisense
GAAGATCTTTCAGAGCCAGCACGTC 413 337 577 Antisense
AGCACGTCAAGCTCTCGACAATTTC 353 77 594 Antisense
Sequence Source Affymetrix Proprietary Database