[Home] | [Total List]

[173816_at] SN-RNP U1

Description AV203635 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=K04G7.10 /5_PRIME_EXT_DB=WormBase Gene ID /GB=AV203635 /WB_GENE_ID=K04G7.10 /WP=CE01998 /CHR=3 /FEA=Genomic Cluster /DEF=SN-RNP U1; Caenorhabditis elegans cDNA clone:yk579a9 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 80      6grp_high1_10_10 > 18      4grp_highest_8_8 > 38      4grp_high_8_8 > 03      6grp_highest_nonorm > 20      6grp_total > 18      4grp_total > 05      6grp_cgc > 02      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1441
1 2 3 4 range
A 1311.6
(3)
P 		686.4
(-3)
P 		829.9
(-1.6)
P 		1313.7
(3)
P 		627
B 1169.9
(-1.1)
P 		827.3
(-3)
P 		826.1
(-3)
P 		1897.4
(3)
P 		1071
C 1321
(-0.5)
P 		746
(-3)
P 		735.8
(-3)
P 		2127.6
(3)
P 		1392
avr 1267.5
(0) 		753.2
(-3) 		797.3
(-2.7) 		1779.6
(3) 		1026

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 966
1 2 3 4 5 6 range
A 1297.6
(3)
P 		1018.5
(-0.6)
P 		892.1
(-2.2)
P 		985.5
(-1)
P 		972.2
(-1.1)
P 		826.6
(-3)
P 		471
B 1704.8
(3)
P 		1415.5
(1.2)
P 		739.8
(-3)
P 		1128
(-0.6)
P 		1094.4
(-0.8)
P 		1034.3
(-1.2)
P 		965
C 1706.1
(3)
P 		1135.1
(-1.6)
P 		962
(-3)
P 		1084.8
(-2)
P 		1295
(-0.3)
P 		980.7
(-2.8)
P 		744
avr 1569.5
(3) 		1189.7
(-0.2) 		864.6
(-3) 		1066.1
(-1.3) 		1120.5
(-0.8) 		947.2
(-2.3) 		705
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 329
1 2 3 4 range
A 477.5
(3)
P 		149
(-3)
P 		217
(-1.8)
P 		192.3
(-2.2)
P 		329
B 373.1
(2.1)
P 		204.3
(-2.6)
P 		191.4
(-3)
P 		404.3
(3)
P 		213
C 437.3
(3)
P 		214.5
(-3)
P 		256.5
(-1.9)
P 		358.7
(0.9)
P 		223
avr 429.3
(3) 		189.3
(-3) 		221.6
(-2.2) 		318.4
(0.2) 		240

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 453
1 2 3 4 5 6 range
A 239.2
(-1.4)
P 		362.2
(3)
P 		194.3
(-3)
P 		249.9
(-1)
P 		293.4
(0.5)
P 		201.3
(-2.7)
P 		168
B 593.2
(3)
P 		471.2
(1.2)
P 		179.7
(-3)
P 		298.8
(-1.3)
P 		444.7
(0.8)
P 		385.7
(-0)
P 		414
C 632.4
(3)
P 		346.4
(-1.1)
P 		244.9
(-2.6)
P 		218.2
(-3)
P 		419.1
(-0.1)
P 		328.3
(-1.4)
P 		414
avr 488.3
(3) 		393.3
(1) 		206.3
(-3) 		255.6
(-2) 		385.7
(0.8) 		305.1
(-0.9) 		282
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173816_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.23947
Sequence Type Exemplar sequence
Representative Public ID AV203635 NCBI
Target Description AV203635 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=K04G7.10 /5_PRIME_EXT_DB=WormBase Gene ID /GB=AV203635 /WB_GENE_ID=K04G7.10 /WP=CE01998 /CHR=3 /FEA=Genomic Cluster /DEF=SN-RNP U1; Caenorhabditis elegans cDNA clone:yk579a9 : 5prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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
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:7158906-7161073(-) 86.59 100.0
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 CAE70145 Hypothetical protein CBG16607 [Caenorhabditis briggsae] 1.0E-110
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
Sequence
Target Sequence 
>C. ELEGANS:173816_AT
ggtgatcgccgttgattctgaaaccaaaggccttgtggattttcctcgcttttatgtttg
ttttgtatccttcgatctgaaatttaccgatttttccttctgctttctatctcgtcctct
caaatcattttgtattcctaaacactt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGTGATCGCCGTTGATTCTGAAACC 510 499 986 Antisense
GATCGCCGTTGATTCTGAAACCAAA 456 417 989 Antisense
GTTGATTCTGAAACCAAAGGCCTTG 328 437 996 Antisense
CAAAGGCCTTGTGGATTTTCCTCGC 142 193 1010 Antisense
ATGTTTGTTTTGTATCCTTCGATCT 549 47 1039 Antisense
TTGTTTTGTATCCTTCGATCTGAAA 314 705 1043 Antisense
GTATCCTTCGATCTGAAATTTACCG 54 455 1050 Antisense
TCGATCTGAAATTTACCGATTTTTC 602 599 1057 Antisense
ATCTCGTCCTCTCAAATCATTTTGT 683 31 1094 Antisense
GTCCTCTCAAATCATTTTGTATTCC 671 475 1099 Antisense
AATCATTTTGTATTCCTAAACACTT 676 165 1108 Antisense
Sequence Source Affymetrix Proprietary Database