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[187400_s_at] U6 small nuclear RNA-associated Sm-like protein LSm4

Description F32A5.7 /REP_DB=WormBase Gene ID /WP=CE01277 /TR=SW:Q19952 /GB=AAC46661.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 68      6grp_high1_10_10 > 96      4grp_highest_8_8 > 11      4grp_high_8_8 > 47      6grp_highest_nonorm > 82      6grp_total > 87      4grp_total > 48      6grp_highest_sub > In      6grp_cgc > 57      6grp_high1_sub > In      6grp_total_sub > Increase      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 203
1 2 3 4 range
A 358.9
(-0)
P 		409.3
(2.2)
P 		427.8
(3)
P 		291
(-3)
P 		137
B 393
(-0.7)
P 		368.7
(-3)
P 		432.4
(3)
P 		387.7
(-1.2)
P 		64
C 290.7
(-3)
P 		450.7
(1.7)
P 		494.1
(3)
P 		443
(1.5)
P 		203
avr 347.5
(-3) 		409.6
(0.6) 		451.4
(3) 		373.9
(-1.5) 		104

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 245
1 2 3 4 5 6 range
A 295.9
(-2)
P 		263
(-3)
P 		457.2
(3)
P 		347.7
(-0.4)
P 		303.2
(-1.8)
P 		309
(-1.6)
P 		194
B 332.4
(-1.8)
P 		296.8
(-2.9)
P 		417.3
(0.7)
P 		292
(-3)
P 		402.1
(0.3)
P 		493
(3)
P 		201
C 382.2
(0.2)
P 		345.1
(-0.7)
P 		253.1
(-3)
P 		357.7
(-0.4)
P 		426.5
(1.2)
P 		498.4
(3)
P 		245
avr 336.8
(-1.4) 		301.6
(-3) 		375.9
(0.4) 		332.5
(-1.6) 		377.3
(0.4) 		433.5
(3) 		132
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 130
1 2 3 4 range
A 130.7
(3)
P 		88.8
(0.1)
P 		111.8
(1.7)
P 		42.6
(-3)
P 		88
B 125.3
(3)
P 		91.1
(-1.8)
P 		100.2
(-0.5)
P 		82.6
(-3)
P 		43
C 96.2
(-1.7)
P 		129.6
(0.4)
P 		172.2
(3)
P 		74.7
(-3)
P 		98
avr 117.4
(2) 		103.2
(0.6) 		128.1
(3) 		66.6
(-3) 		62

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 129
1 2 3 4 5 6 range
A 54.5
(-3)
P 		93.5
(2.2)
P 		99.6
(3)
P 		88.2
(1.5)
P 		91.5
(1.9)
P 		75.2
(-0.2)
P 		45
B 115.7
(-0.8)
P 		98.8
(-1.8)
P 		101.3
(-1.6)
P 		77.3
(-3)
P 		163.4
(1.9)
P 		183.8
(3)
P 		107
C 141.7
(1.5)
P 		105.3
(-0.6)
P 		64.4
(-3)
P 		71.9
(-2.6)
P 		138
(1.3)
P 		166.8
(3)
P 		102
avr 104
(-0.6) 		99.2
(-1.1) 		88.4
(-2.1) 		79.1
(-3) 		131
(2) 		141.9
(3) 		63
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 187400_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.5672
Sequence Type Exemplar sequence
Representative Public ID F32A5.7 NCBI
Target Description F32A5.7 /REP_DB=WormBase Gene ID /WP=CE01277 /TR=SW:Q19952 /GB=AAC46661.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=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_063113(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063113 NCBI Caenorhabditis elegans LSM Sm-like protein family member (lsm-4) (lsm-4) mRNA, complete cds. 11/11 None
SNAP00000015815 ENSEMBL cdna:SNAP chromosome:CEL140:II:7252338:7252945:-1 10/11 None
GENEFINDER00000015820 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:7252338:7252984:-1 11/11 None
F32A5.7 ENSEMBL cdna:known chromosome:CEL140:II:7252161:7253094:-1 gene:F32A5.7 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:7252333-7253028(-) 100.0 100.0
Public Domain and Genome References
Gene Title U6 small nuclear RNA-associated Sm-like protein LSm4
Gene Symbol lsm-4
Ensembl F32A5.7
Entrez Gene 174193 Entrez gene
SwissProt Q19952 EMBL-EBI
WormBase CE01277 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:246741_AT small nuclear ribonucleoprotein, putative / snRNP, putative / Sm protein, putative at
CANINE_2:CFA.17612.1.S1_S_AT similar to U6 snRNA-associated Sm-like protein LSm4 (Glycine-rich protein) (GRP) cfa
CANINE_2:CFA.17612.1.S1_AT similar to U6 snRNA-associated Sm-like protein LSm4 (Glycine-rich protein) (GRP) cfa
CHICKEN:GGA.6010.1.S1_AT LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) gga
HG-U133_PLUS_2:202737_S_AT LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-U133A_2:202737_S_AT LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-U133A:202737_S_AT LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
U133_X3P:G6912485_3P_A_AT LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
U133_X3P:HS.76719.0.S1_3P_A_AT LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-U133A_2:202736_S_AT LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-FOCUS:202736_S_AT LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-U133_PLUS_2:202736_S_AT LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-U133A:202736_S_AT LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-U95AV2:32559_S_AT LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HU35KSUBA:AA418341_AT LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HU35KSUBB:RC_H17486_AT LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
MU11KSUBB:MSA.8954.0_F_AT LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MU11KSUBB:MSA.3346.0_S_AT LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MG-U74AV2:93008_AT LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MOE430A:1448622_AT LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MOUSE430A_2:1448622_AT LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MOUSE430_2:1448622_AT LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MU19KSUBA:TC18925_AT LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae), mRNA (cDNA clone MGC:25600 IMAGE:4024321) mm
RAE230A:1371683_AT LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) (predicted) rn
RAT230_2:1371683_AT LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) (predicted) rn
RG-U34B:RC_AA964080_AT LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) (predicted) rn
YEAST_2:1776666_AT Lsm (Like Sm) protein; part of heteroheptameric complexes (Lsm2p-7p and either Lsm1p or 8p): cytoplasmic Lsm1p complex involved in mRNA decay; nuclear Lsm8p complex part of U6 snRNP and possibly involved in processing tRNA, snoRNA, and rRNA Sc
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 AAC46661 Lsm sm-like protein protein 4 [Caenorhabditis elegans] ref|NP_495514.1| LSM Sm-like protein family member (lsm-4) [Caenorhabditis elegans] sp|Q19952|LSM4_CAEEL Probable U6 snRNA-associated Sm-like protein LSm4 4.0E-44
blast CAE67582 Hypothetical protein CBG13115 [Caenorhabditis briggsae] 8.0E-44
blast AAC46661 Lsm sm-like protein protein 4 [Caenorhabditis elegans] ref|NP_495514.1| LSM Sm-like protein family member (lsm-4) [Caenorhabditis elegans] sp|Q19952|LSM4_CAEEL Probable U6 snRNA-associated Sm-like protein LSm4 4.0E-43
blast CAE67582 Hypothetical protein CBG13115 [Caenorhabditis briggsae] 9.0E-43
blast AAC46661 Lsm sm-like protein protein 4 [Caenorhabditis elegans] ref|NP_495514.1| LSM Sm-like protein family member (lsm-4) [Caenorhabditis elegans] sp|Q19952|LSM4_CAEEL Probable U6 snRNA-associated Sm-like protein LSm4 2.0E-35
blast CAE67582 Hypothetical protein CBG13115 [Caenorhabditis briggsae] 5.0E-35
blast NP_036453 U6 snRNA-associated Sm-like protein 4 [Homo sapiens] gb|AAI03244.1| Unknown (protein for MGC:128718) [Bos taurus] ref|XP_852362.1| PREDICTED: similar to U6 snRNA-associated Sm-like protein LSm4 (Glycine-rich protein) (GRP) [Canis familiaris] gb|AAH00387.1| U6 snRNA-associated Sm-like protein 4 [Homo sapiens] gb|AAH22198.1| U6 snRNA-associated Sm-like protein 4 [Homo sapiens] gb|AAH03652.1| U6 snRNA-associated Sm-like protein 4 [Homo sapiens] ref|XP_547854.1| PREDICTED: similar to U6 snRNA-associated Sm-like protein LSm4 (Glycine-rich protein) (GRP) [Canis familiaris] emb|CAB45867.1| Lsm4 protein [Homo sapiens] gb|AAF90055.1| LSm4 autoantigen [Homo sapiens] sp|Q9Y4Z0|LSM4_HUMAN U6 snRNA-associated Sm-like protein LSm4 (Glycine-rich protein) (GRP) gb|AAF17216.1| glycine-rich protein [Homo sapiens] gb|AAH23665.1| U6 snRNA-associated Sm-like protein 4 [Homo sapiens] gb|AAD56228.1| U6 snRNA-associated Sm-like protein LSm4 [Homo sapiens] 2.0E-32
Protein Domains
Database ID Description E-Value
Pfam IPR001163 EMBL-EBI Small nuclear ribonucleoprotein (Sm protein) 1.0E-15
Pfam IPR001163 EMBL-EBI Small nuclear ribonucleoprotein (Sm protein) 1.4E-20
Pfam IPR001163 EMBL-EBI Small nuclear ribonucleoprotein (Sm protein) 1.4E-20
Sequence
Target Sequence 
>C. ELEGANS:187400_S_AT
gctcaaaaccacccgatgcttgtggagttgaagaacggcgagacttataacggtcacctg
aaagcctgcgattcgtggatgaatattcatttggtggatgttattttcacatcaaaagac
ggtgacaagttcttcaaaatgtcagaagcgtatgtccggggatctactatcaagtatctc
agaattccagaaacagtggtcgatctcgtgaaaactgaagtcaacgaagttcgtcgtcaa
cagcagcgcgagcaatcccgtggtcgtggtggtggacgaggaggacgtggaggacaccgc
ggaggtggt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCTCAAAACCACCCGATGCTTGTGG 300 301 43 Antisense
GTGGAGTTGAAGAACGGCGAGACTT 246 491 64 Antisense
CGGCGAGACTTATAACGGTCACCTG 153 167 78 Antisense
TATAACGGTCACCTGAAAGCCTGCG 22 641 88 Antisense
GAAAGCCTGCGATTCGTGGATGAAT 574 359 102 Antisense
GTCAGAAGCGTATGTCCGGGGATCT 550 465 183 Antisense
ATGTCCGGGGATCTACTATCAAGTA 174 49 194 Antisense
GGTCGATCTCGTGAAAACTGAAGTC 431 501 240 Antisense
GAAGTCAACGAAGTTCGTCGTCAAC 191 337 259 Antisense
GTCGTCAACAGCAGCGCGAGCAATC 231 473 275 Antisense
ACGTGGAGGACACCGCGGAGGTGGT 187 95 327 Antisense
Sequence Source Affymetrix Proprietary Database