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[192941_at] U1 small nuclear ribonucleoprotein A

Description K08D10.4 /REP_DB=WormBase Gene ID /WP=CE07356 /TR=Q21322 /GB=AAA98032.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=U1 small nuclear ribonucleoprotein A
Cluster 6grp_highest_10_10 > 78      6grp_high1_10_10 > 87      4grp_highest_8_8 > 25      4grp_high_8_8 > 51      6grp_highest_nonorm > 86      6grp_total > 87      4grp_total > 60      6grp_highest_sub > In      6grp_cgc > 58      6grp_high1_sub > In      6grp_cgc_sub > In      6grp_total_sub > Increase      6grp_rule_based > S6      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 456
1 2 3 4 range
A 950.4
(-1.5)
P 		1159.4
(3)
P 		1016.4
(-0.1)
P 		882.4
(-3)
P 		277
B 1121.2
(3)
P 		970.8
(0.2)
P 		1046.1
(1.6)
P 		803.7
(-3)
P 		318
C 999.4
(2.3)
P 		930.9
(1.1)
P 		1037.7
(3)
P 		703.3
(-3)
P 		334
avr 1023.7
(2.8) 		1020.4
(2.7) 		1033.4
(3) 		796.5
(-3) 		237

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 544
1 2 3 4 5 6 range
A 905.6
(-2.3)
P 		874.7
(-3)
P 		921.1
(-1.9)
P 		1011.8
(0.2)
P 		953
(-1.2)
P 		1131.9
(3)
P 		257
B 825.8
(-2.8)
P 		807.8
(-3)
P 		884.1
(-2)
P 		857.6
(-2.4)
P 		1087.6
(0.5)
P 		1283.4
(3)
P 		476
C 889.5
(-2.4)
P 		841.8
(-3)
P 		909.5
(-2.2)
P 		940.2
(-1.8)
P 		1070.3
(-0.3)
P 		1351.6
(3)
P 		510
avr 873.6
(-2.5) 		841.4
(-3) 		904.9
(-2.1) 		936.5
(-1.6) 		1037
(-0.2) 		1255.6
(3) 		414
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 243
1 2 3 4 range
A 346
(3)
P 		251.7
(0.4)
P 		265.7
(0.8)
P 		129.2
(-3)
P 		217
B 357.5
(3)
P 		239.8
(-0.8)
P 		242.4
(-0.7)
P 		171.3
(-3)
P 		186
C 330.8
(2.2)
P 		267.6
(0.7)
P 		361.7
(3)
P 		118.6
(-3)
P 		243
avr 344.8
(3) 		253
(0.3) 		289.9
(1.4) 		139.7
(-3) 		205

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 312
1 2 3 4 5 6 range
A 166.9
(-3)
P 		311.1
(3)
P 		200.6
(-1.6)
P 		256.6
(0.7)
P 		287.6
(2)
P 		275.6
(1.5)
P 		144
B 287.3
(-1.3)
P 		268.9
(-1.8)
P 		214.7
(-3)
P 		227.1
(-2.7)
P 		441.9
(2.2)
P 		478.6
(3)
P 		264
C 329.7
(0.2)
P 		256.8
(-1.5)
P 		231.5
(-2)
P 		189.1
(-3)
P 		346.3
(0.6)
P 		452.5
(3)
P 		263
avr 261.3
(-1.5) 		278.9
(-1) 		215.6
(-3) 		224.3
(-2.7) 		358.6
(1.6) 		402.2
(3) 		187
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192941_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11129
Sequence Type Exemplar sequence
Representative Public ID K08D10.4 NCBI
Target Description K08D10.4 /REP_DB=WormBase Gene ID /WP=CE07356 /TR=Q21322 /GB=AAA98032.1 /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_068103(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_068103 NCBI Caenorhabditis elegans RNP (RRM RNA binding domain) containing family member (rnp-2) (rnp-2) mRNA, complete cds. 11/11 None
SNAP00000009685 ENSEMBL cdna:SNAP chromosome:CEL140:IV:4172101:4173891:1 11/11 None
GENEFINDER00000009697 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:4172101:4173891:1 11/11 None
K08D10.4 ENSEMBL cdna:known chromosome:CEL140:IV:4172095:4173981:1 gene:K08D10.4 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:4172106-4173897(+) 100.0 100.0
Public Domain and Genome References
Gene Title U1 small nuclear ribonucleoprotein A
Gene Symbol rnp-2
Ensembl K08D10.4
Entrez Gene 177181 Entrez gene
SwissProt Q21322 EMBL-EBI
WormBase CE28597 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:12410_G_AT small nuclear ribonucleoprotein U1A / spliceosomal protein U1A / U1snRNP-specific protein at
ATGENOME1:12409_AT small nuclear ribonucleoprotein U1A / spliceosomal protein U1A / U1snRNP-specific protein at
ATH1-121501:245124_AT small nuclear ribonucleoprotein U1A / spliceosomal protein U1A / U1snRNP-specific protein at
CANINE:1600320_S_AT similar to U1 small nuclear ribonucleoprotein A (U1 snRNP protein A) (U1A protein) (U1-A) cfa
CANINE_2:CFAAFFX.359.1.S1_S_AT similar to U1 small nuclear ribonucleoprotein A (U1 snRNP protein A) (U1A protein) (U1-A) cfa
CANINE_2:CFAAFFX.8568.1.S1_AT similar to U1 small nuclear ribonucleoprotein A (U1 snRNP protein A) (U1A protein) (U1-A) cfa
HG-U133_PLUS_2:201770_AT small nuclear ribonucleoprotein polypeptide A hs
HG-U133A_2:201770_AT small nuclear ribonucleoprotein polypeptide A hs
HG-U133A:201770_AT small nuclear ribonucleoprotein polypeptide A hs
HG-FOCUS:201770_AT small nuclear ribonucleoprotein polypeptide A hs
HU35KSUBA:R36775_AT small nuclear ribonucleoprotein polypeptide A hs
HUGENEFL:M60784_S_AT small nuclear ribonucleoprotein polypeptide A hs
U133_X3P:G4759155_3P_AT small nuclear ribonucleoprotein polypeptide A hs
HG-U95AV2:40842_AT small nuclear ribonucleoprotein polypeptide A hs
HG-U95D:85973_AT small nuclear ribonucleoprotein polypeptide A hs
MU11KSUBA:L15447_F_AT small nuclear ribonucleoprotein polypeptide A mm
MU11KSUBB:MSA.78.0_F_AT small nuclear ribonucleoprotein polypeptide A mm
MG-U74AV2:100101_AT small nuclear ribonucleoprotein polypeptide A mm
MOE430A:1417274_AT small nuclear ribonucleoprotein polypeptide A mm
MOUSE430A_2:1417274_AT small nuclear ribonucleoprotein polypeptide A mm
MOUSE430_2:1417274_AT small nuclear ribonucleoprotein polypeptide A mm
MU19KSUBA:TC23016_AT Small nuclear ribonucleoprotein polypeptide A, mRNA (cDNA clone MGC:6132 IMAGE:3483391) mm
MU19KSUBA:TC23017_AT Small nuclear ribonucleoprotein polypeptide A, mRNA (cDNA clone MGC:6132 IMAGE:3483391) mm
MU19KSUBA:TC23017_G_AT Small nuclear ribonucleoprotein polypeptide A, mRNA (cDNA clone MGC:6132 IMAGE:3483391) mm
MU19KSUBC:TC37707_F_AT Small nuclear ribonucleoprotein polypeptide A, mRNA (cDNA clone MGC:6132 IMAGE:3483391) mm
RG-U34C:RC_AI230728_AT small nuclear ribonucleoprotein polypeptide A (predicted) rn
RAE230A:1388436_AT small nuclear ribonucleoprotein polypeptide A (predicted) rn
RAT230_2:1388436_AT small nuclear ribonucleoprotein polypeptide A (predicted) rn
Protein Similarities
Method ID Description E-Value
blast AAA98032 Rnp (rrm rna binding domain) containing protein 2 [Caenorhabditis elegans] ref|NP_500504.1| RNP (RRM RNA binding domain) containing family member (rnp-2) [Caenorhabditis elegans] 1.0E-113
blast AAA98032 Rnp (rrm rna binding domain) containing protein 2 [Caenorhabditis elegans] ref|NP_500504.1| RNP (RRM RNA binding domain) containing family member (rnp-2) [Caenorhabditis elegans] 1.0E-109
blast CAE68286 Hypothetical protein CBG13971 [Caenorhabditis briggsae] 1.0E-99
blast CAE68286 Hypothetical protein CBG13971 [Caenorhabditis briggsae] 7.0E-96
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] 9.0E-57
Protein Domains
Database ID Description E-Value
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 3.5E-12
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 2.8E-10
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 7.7E-6
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 2.8E-10
Sequence
Target Sequence 
>C. ELEGANS:192941_AT
gcagaagttgcgccgaacagcactctgtacatcaacaatctcaacgagaagatcaaaatc
gatgagctgcgaaaatcgctcgtcgccgtcttcaaacaattcggcgaaattgtcagtgtg
atgtgtttcaggacgctgaagatgcgcgggcaggctcatctccccgccgcatctgccgcc
cgagaagcgttgaatggttttccattttacgaaaagccaatgagaattcaattcgcaagg
gaggattctgacgtcgtcgcccaggaaaaggggacatatatcaagcgggagcccaaatat
ctatcggagaagattctgaagaagccaaagagccgaaagaaggaaaatggaggcgatgga
ccagcgccgcccaacaaaatcctattttgcacgaatcttccagattcggcgaccgctgaa
atgcttgagattatgttcaatcaattcgcgggtctcaaagacattcgaatggttccaaat
cgtccaggaatcgcttttgtcgaatttgacacagattctttggcaattccagcacgtaca
acactcaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCAGAAGTTGCGCCGAACAGCACTC 426 311 16 Antisense
TGAGCTGCGAAAATCGCTCGTCGCC 675 569 78 Antisense
TCGTCGCCGTCTTCAAACAATTCGG 576 603 95 Antisense
ATCTGCCGCCCGAGAAGCGTTGAAT 209 23 186 Antisense
GCAAGGGAGGATTCTGACGTCGTCG 273 321 250 Antisense
AGCGGGAGCCCAAATATCTATCGGA 580 79 299 Antisense
ATCCTATTTTGCACGAATCTTCCAG 10 39 394 Antisense
CTTCCAGATTCGGCGACCGCTGAAA 153 219 412 Antisense
TTCAATCAATTCGCGGGTCTCAAAG 453 685 451 Antisense
AATCGTCCAGGAATCGCTTTTGTCG 336 169 493 Antisense
CAATTCCAGCACGTACAACACTCAA 2 181 539 Antisense
Sequence Source Affymetrix Proprietary Database