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[188684_s_at] SN-RNP U1

Description K04G7.10 /REP_DB=WormBase Gene ID /WP=CE01998 /TR=Q09584 /GB=AAA62536.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=SN-RNP U1
Cluster 6grp_highest_10_10 > 83      6grp_high1_10_10 > 48      4grp_highest_8_8 > 29      4grp_high_8_8 > 07      6grp_highest_nonorm > 90      6grp_total > 38      4grp_total > 0      6grp_highest_sub > Cu      6grp_cgc > 18      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 138
1 2 3 4 range
A 159.3
(1.8)
P 		109.5
(-3)
P 		126.9
(-1.3)
P 		172
(3)
P 		63
B 125.5
(-2.6)
P 		117.6
(-3)
P 		127
(-2.6)
P 		247.8
(3)
P 		130
C 174.6
(0.9)
P 		143.7
(-3)
P 		191.3
(3)
P 		187.9
(2.6)
P 		48
avr 153.1
(-0.8) 		123.6
(-3) 		148.4
(-1.1) 		202.6
(3) 		79

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 162
1 2 3 4 5 6 range
A 99.5
(-3)
P 		140
(-0.7)
P 		137.8
(-0.9)
P 		114.5
(-2.2)
P 		110.6
(-2.4)
P 		206.6
(3)
P 		107
B 227.9
(3)
P 		172.6
(0.5)
P 		93.1
(-3)
P 		93.1
(-3)
P 		151
(-0.4)
P 		177.5
(0.8)
P 		135
C 245.6
(3)
P 		127.6
(-1.4)
P 		83.4
(-3)
P 		89.5
(-2.8)
P 		121.3
(-1.6)
P 		176.8
(0.5)
P 		162
avr 191
(3) 		146.7
(0.1) 		104.8
(-2.6) 		99
(-3) 		127.6
(-1.1) 		187
(2.7) 		92
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 43
1 2 3 4 range
A 58
(3)
P 		23.8
(-3)
P 		33.2
(-1.4)
P 		25.2
(-2.8)
P 		34
B 40
(-0.2)
P 		29.1
(-3)
P 		29.4
(-2.9)
P 		52.8
(3)
P 		24
C 57.8
(1.5)
P 		41.3
(-1.4)
P 		66.7
(3)
P 		31.7
(-3)
P 		35
avr 51.9
(3) 		31.4
(-3) 		43.1
(0.4) 		36.6
(-1.5) 		21

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 73
1 2 3 4 5 6 range
A 18.3
(-3)
P 		49.8
(2.9)
P 		30
(-0.8)
P 		29
(-1)
P 		33.4
(-0.2)
P 		50.3
(3)
P 		32
B 79.3
(3)
P 		57.4
(0.7)
P 		22.6
(-3)
P 		24.6
(-2.8)
P 		61.4
(1.1)
P 		66.2
(1.6)
P 		57
C 91
(3)
P 		38.9
(-1.3)
P 		21.2
(-2.7)
P 		18
(-3)
P 		39.3
(-1.2)
P 		59.2
(0.4)
P 		73
avr 62.9
(3) 		48.7
(0.8) 		24.6
(-2.9) 		23.9
(-3) 		44.7
(0.2) 		58.6
(2.3) 		39
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 188684_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6052
Sequence Type Exemplar sequence
Representative Public ID K04G7.10 NCBI
Target Description K04G7.10 /REP_DB=WormBase Gene ID /WP=CE01998 /TR=Q09584 /GB=AAA62536.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=SN-RNP U1
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_066164(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066164 NCBI Caenorhabditis elegans RNP (RRM RNA binding domain) containing family member (rnp-7) (rnp-7) mRNA, complete cds. 11/11 None
SNAP00000036055 ENSEMBL cdna:SNAP chromosome:CEL140:III:7159077:7161074:-1 11/11 None
GENEFINDER00000036061 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:7159077:7161074:-1 11/11 None
K04G7.10 ENSEMBL cdna:known chromosome:CEL140:III:7158839:7161202:-1 gene:K04G7.10 11/11 A 
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
chrIII:7159074-7161072(-) 84.3 100.0
Public Domain and Genome References
Gene Title SN-RNP U1
Gene Symbol rnp-7
Ensembl K04G7.10
Entrez Gene 176002 Entrez gene
SwissProt Q09584 EMBL-EBI
WormBase CE30443 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:252182_AT U1 small nuclear ribonucleoprotein 70 (U1-70k) at
CANINE_2:CFA.17797.1.S1_AT similar to U1 small nuclear ribonucleoprotein 70 kDa cfa
CANINE_2:CFA.17797.2.S1_AT similar to U1 small nuclear ribonucleoprotein 70 kDa cfa
CANINE_2:CFAAFFX.6510.1.S1_S_AT similar to U1 small nuclear ribonucleoprotein 70 kDa cfa
DROSOPHILA_2:1635063_AT small nuclear ribonucleoprotein 70K dm
DROSGENOME1:155143_AT small nuclear ribonucleoprotein 70K dm
HG-U133_PLUS_2:201221_S_AT small nuclear ribonucleoprotein 70kDa polypeptide (RNP antigen) hs
HG-U133A:201221_S_AT small nuclear ribonucleoprotein 70kDa polypeptide (RNP antigen) hs
HG-U133A_2:201221_S_AT small nuclear ribonucleoprotein 70kDa polypeptide (RNP antigen) hs
HG-FOCUS:201221_S_AT small nuclear ribonucleoprotein 70kDa polypeptide (RNP antigen) hs
HG-U95AV2:40875_S_AT small nuclear ribonucleoprotein 70kDa polypeptide (RNP antigen) hs
HUGENEFL:X04654_S_AT small nuclear ribonucleoprotein 70kDa polypeptide (RNP antigen) hs
U133_X3P:G4507118_3P_S_AT small nuclear ribonucleoprotein 70kDa polypeptide (RNP antigen) hs
U133_X3P:G4507118_3P_A_AT small nuclear ribonucleoprotein 70kDa polypeptide (RNP antigen) hs
U133_X3P:HS.174051.1.S1_3P_AT small nuclear ribonucleoprotein 70kDa polypeptide (RNP antigen) hs
HG-U133A_2:213121_AT small nuclear ribonucleoprotein 70kDa polypeptide (RNP antigen) hs
HG-U133_PLUS_2:213121_AT small nuclear ribonucleoprotein 70kDa polypeptide (RNP antigen) hs
HG-U133A:213121_AT small nuclear ribonucleoprotein 70kDa polypeptide (RNP antigen) hs
HG-U95E:87370_AT small nuclear ribonucleoprotein 70kDa polypeptide (RNP antigen) hs
U133_X3P:HS2.287618.1.S1_3P_X_AT Small nuclear ribonucleoprotein 70kDa polypeptide (RNP antigen) hs
HG-U133_PLUS_2:1557683_AT Small nuclear ribonucleoprotein 70kDa polypeptide (RNP antigen) hs
HG-U133_PLUS_2:234047_AT Small nuclear ribonucleoprotein 70kDa polypeptide (RNP antigen) hs
HG-U133B:234047_AT Small nuclear ribonucleoprotein 70kDa polypeptide (RNP antigen) hs
HG-U95E:86145_AT Small nuclear ribonucleoprotein 70kDa polypeptide (RNP antigen) hs
MU11KSUBB:X15769_S_AT U1 small nuclear ribonucleoprotein polypeptide A mm
MU11KSUBB:MSA.2521.0_AT U1 small nuclear ribonucleoprotein polypeptide A mm
MOE430A:1451104_A_AT U1 small nuclear ribonucleoprotein polypeptide A mm
MOUSE430A_2:1451104_A_AT U1 small nuclear ribonucleoprotein polypeptide A mm
MOUSE430_2:1451104_A_AT U1 small nuclear ribonucleoprotein polypeptide A mm
MOE430B:1429010_AT U1 small nuclear ribonucleoprotein polypeptide A mm
MOUSE430_2:1429010_AT U1 small nuclear ribonucleoprotein polypeptide A mm
MOE430B:1429009_AT U1 small nuclear ribonucleoprotein polypeptide A mm
MOUSE430_2:1429009_AT U1 small nuclear ribonucleoprotein polypeptide A mm
MOE430B:1429011_X_AT U1 small nuclear ribonucleoprotein polypeptide A mm
MOUSE430_2:1429011_X_AT U1 small nuclear ribonucleoprotein polypeptide A mm
MU19KSUBA:TC20204_AT U1 small nuclear ribonucleoprotein polypeptide A, mRNA (cDNA clone IMAGE:3486572) mm
MU19KSUBA:TC20205_AT U1 small nuclear ribonucleoprotein polypeptide A, mRNA (cDNA clone IMAGE:3486572) mm
MU19KSUBC:TC37529_AT U1 small nuclear ribonucleoprotein polypeptide A, mRNA (cDNA clone IMAGE:3486572) mm
MU19KSUBC:TC37529_G_AT U1 small nuclear ribonucleoprotein polypeptide A, mRNA (cDNA clone IMAGE:3486572) mm
RG-U34A:RC_AA891322_G_AT U1 small nuclear ribonucleoprotein polypeptide A (predicted) rn
RG-U34B:RC_AA997283_AT U1 small nuclear ribonucleoprotein polypeptide A (predicted) rn
RAE230A:1371742_AT U1 small nuclear ribonucleoprotein polypeptide A (predicted) rn
RAT230_2:1371742_AT U1 small nuclear ribonucleoprotein polypeptide A (predicted) rn
RAE230B:1395261_AT U1 small nuclear ribonucleoprotein polypeptide A (predicted) rn
RAT230_2:1395261_AT U1 small nuclear ribonucleoprotein polypeptide A (predicted) rn
RAE230B:1384375_AT U1 small nuclear ribonucleoprotein polypeptide A (predicted) rn
RAT230_2:1384375_AT U1 small nuclear ribonucleoprotein polypeptide A (predicted) rn
RG-U34A:RC_AA891322_AT U1 small nuclear ribonucleoprotein polypeptide A (predicted) rn
RG-U34B:RC_AI044499_AT U1 small nuclear ribonucleoprotein polypeptide A (predicted) rn
RG-U34C:RC_AI233756_AT U1 small nuclear ribonucleoprotein polypeptide A (predicted) rn
Protein Similarities
Method ID Description E-Value
blast AAA62536 Rnp (rrm rna binding domain) containing protein 7 [Caenorhabditis elegans] ref|NP_498565.2| RNP (RRM RNA binding domain) containing family member (rnp-7) [Caenorhabditis elegans] 1.0E-119
blast AAA62536 Rnp (rrm rna binding domain) containing protein 7 [Caenorhabditis elegans] ref|NP_498565.2| RNP (RRM RNA binding domain) containing family member (rnp-7) [Caenorhabditis elegans] 1.0E-116
blast CAE70145 Hypothetical protein CBG16607 [Caenorhabditis briggsae] 1.0E-110
blast CAE70145 Hypothetical protein CBG16607 [Caenorhabditis briggsae] 1.0E-106
blast AAA62536 Rnp (rrm rna binding domain) containing protein 7 [Caenorhabditis elegans] ref|NP_498565.2| RNP (RRM RNA binding domain) containing family member (rnp-7) [Caenorhabditis elegans] 2.0E-80
blast CAE70145 Hypothetical protein CBG16607 [Caenorhabditis briggsae] 8.0E-75
blast AAF52471 CG8749-PA [Drosophila melanogaster] ref|NP_477205.1| CG8749-PA [Drosophila melanogaster] gb|AAL90360.1| RE35772p [Drosophila melanogaster] gb|AAL29049.1| LD46049p [Drosophila melanogaster] sp|P17133|RU17_DROME U1 small nuclear ribonucleoprotein 70 kDa (U1 snRNP 70 kDa) (snRNP70) 2.0E-58
Protein Domains
Database ID Description E-Value
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 5.2E-22
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 1.9E-17
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 5.7E-15
Sequence
Target Sequence 
>C. ELEGANS:188684_S_AT
aacaatggtccacgacgaggcaggaaaaccacgtggttacgcgtttatcgaatacagtga
caaggctgagatgcataccgcttacaaaaaagctgacggaatcaaagttgatggtaaacg
tctagttgtcgactatgaaagaggtcgtactcagaagacatggttgcctagaagacttgg
cggtggaaaaggagatactcgtaaaactcgcgaagctaaatcagtcattgaagaacgtga
aattgcgtctggatttggaggtgggtacgaggatcgagatagagaaagaagtggtagtcg
ggatagacgtcaagattcttaccgtaatggtggaggaaatgatcgtgatcgacgagaatc
atcgggcggatttagagataatcgcggtggaggtggcggattcggtggaggaggccgtga
tcgtttcaatgatcgaagtggtggtggtggatacggaggtgatcgtgatagaggaggtga
tagaggaggtgaccgtggaggaagccgat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AACAATGGTCCACGACGAGGCAGGA 148 135 399 Antisense
CCACGTGGTTACGCGTTTATCGAAT 329 273 427 Antisense
GGTAAACGTCTAGTTGTCGACTATG 546 503 511 Antisense
GGTTGCCTAGAAGACTTGGCGGTGG 677 507 560 Antisense
GGAGATACTCGTAAAACTCGCGAAG 578 517 589 Antisense
AACTCGCGAAGCTAAATCAGTCATT 165 141 603 Antisense
GAACGTGAAATTGCGTCTGGATTTG 550 347 631 Antisense
GGGATAGACGTCAAGATTCTTACCG 34 497 698 Antisense
GATCGACGAGAATCATCGGGCGGAT 388 415 745 Antisense
GTGGAGGAGGCCGTGATCGTTTCAA 644 489 803 Antisense
GGAGGTGACCGTGGAGGAAGCCGAT 263 517 883 Antisense
Sequence Source Affymetrix Proprietary Database