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[176316_at] U6 small nuclear RNA-associated Sm-like protein LSm6

Description Y71G12B.U /REP_DB=WormBase Gene ID /WP=CE22886 /CHR=1 /FEA=Sanger Annotation /DEF=(ST.LOUIS)
Cluster 6grp_highest_10_10 > 73      6grp_high1_10_10 > 37      4grp_highest_8_8 > 04      4grp_high_8_8 > 37      6grp_highest_nonorm > 85      6grp_total > 45      4grp_total > 42      6grp_highest_sub > Cu      6grp_cgc > 06      6grp_cgc_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 371
1 2 3 4 range
A 699.1
(-3)
P 		1032.6
(3)
P 		763.2
(-1.8)
P 		755.4
(-2)
P 		334
B 662.1
(-3)
P 		836.2
(0.9)
P 		930.4
(3)
P 		826.8
(0.7)
P 		268
C 837.7
(-0.1)
P 		925.6
(3)
P 		757.2
(-3)
P 		860.2
(0.7)
P 		168
avr 733
(-3) 		931.5
(3) 		816.9
(-0.5) 		814.1
(-0.5) 		199

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 490
1 2 3 4 5 6 range
A 819.3
(2.6)
P 		607.5
(-1.3)
P 		840.3
(3)
P 		518.4
(-3)
P 		662.7
(-0.3)
P 		700.2
(0.4)
P 		322
B 924.5
(1.6)
P 		727.1
(-1.8)
P 		1007.9
(3)
P 		657
(-2.9)
P 		653.6
(-3)
P 		828.1
(-0)
P 		354
C 825.7
(2)
P 		753.8
(0.4)
P 		594
(-3)
P 		872.9
(3)
P 		670.9
(-1.3)
P 		856
(2.6)
P 		279
avr 856.5
(3) 		696.1
(-2) 		814.1
(1.7) 		682.8
(-2.4) 		662.4
(-3) 		794.8
(1.1) 		194
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 167
1 2 3 4 range
A 254.5
(3)
P 		224.2
(1.7)
P 		199.5
(0.7)
P 		110.6
(-3)
P 		144
B 211.1
(2.3)
P 		206.5
(1.6)
P 		215.6
(3)
P 		176.2
(-3)
P 		39
C 277.3
(3)
P 		266.1
(2.5)
P 		263.9
(2.4)
P 		145
(-3)
P 		132
avr 247.6
(3) 		232.3
(2.1) 		226.3
(1.8) 		143.9
(-3) 		104

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 190
1 2 3 4 5 6 range
A 151
(-1.6)
P 		216.1
(3)
P 		183
(0.7)
P 		131.5
(-3)
P 		200
(1.9)
P 		170.5
(-0.2)
P 		85
B 321.7
(3)
P 		242
(-0.2)
P 		244.7
(-0.1)
P 		174
(-3)
P 		265.6
(0.7)
P 		308.8
(2.5)
P 		148
C 306
(3)
P 		230
(0.1)
P 		151.2
(-3)
P 		175.5
(-2.1)
P 		217.1
(-0.4)
P 		286.6
(2.2)
P 		155
avr 259.6
(3) 		229.4
(1.2) 		193
(-1) 		160.3
(-3) 		227.6
(1.1) 		255.3
(2.7) 		99
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 176316_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.18658
Sequence Type Exemplar sequence
Representative Public ID Y71G12B.U NCBI
Target Description Y71G12B.U /REP_DB=WormBase Gene ID /WP=CE22886 /CHR=1 /FEA=Sanger Annotation /DEF=(ST.LOUIS)
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_058482(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_058482 NCBI Caenorhabditis elegans LSM Sm-like protein family member (lsm-6) (lsm-6) mRNA, complete cds. 11/11 None
SNAP00000001784 ENSEMBL cdna:SNAP chromosome:CEL140:I:1701373:1701699:1 11/11 None
GENEFINDER00000001807 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:1701373:1701699:1 11/11 None
Y71G12B.14 ENSEMBL cdna:known chromosome:CEL140:I:1701359:1701739:1 gene:Y71G12B.14 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
chrI:1701372-1701699(+) 100.0 100.0
Public Domain and Genome References
Gene Title U6 small nuclear RNA-associated Sm-like protein LSm6
Gene Symbol lsm-6
Ensembl Y71G12B.14
Entrez Gene 190601 Entrez gene
SwissProt Q95XN6 EMBL-EBI
WormBase CE22886 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:251447_AT small nuclear ribonucleoprotein F, putative / U6 snRNA-associated Sm-like protein, putative / Sm protein F, putative at
CANINE:1600944_AT similar to U6 snRNA-associated Sm-like protein LSm6 cfa
CANINE_2:CFA.2820.1.S1_AT similar to U6 snRNA-associated Sm-like protein LSm6 cfa
CANINE_2:CFAAFFX.12446.1.S1_S_AT similar to U6 snRNA-associated Sm-like protein LSm6 cfa
DROSOPHILA_2:1628560_AT dm
DROSGENOME1:147588_AT dm
HG-U133_PLUS_2:205036_AT LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-U133A:205036_AT LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-FOCUS:205036_AT LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-U133A_2:205036_AT LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HU35KSUBA:W55958_AT LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HU35KSUBD:RC_AA446573_AT LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
U133_X3P:G5901997_3P_AT LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-U95AV2:35991_AT LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-U133_PLUS_2:241845_AT LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-U133B:241845_AT LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-U95D:87755_AT LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
U133_X3P:HS.190520.0.A1_3P_AT LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
MG-U74BV2:108576_AT LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MG-U74BV2:163790_AT LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MOE430B:1431054_AT LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MOUSE430_2:1431054_AT LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MOE430B:1437108_AT LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MOUSE430_2:1437108_AT LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MOE430B:1437109_S_AT LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MOUSE430_2:1437109_S_AT LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MOE430B:1455926_AT LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MOUSE430_2:1455926_AT LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MU19KSUBC:TC38367_AT LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MU19KSUBC:TC40236_AT LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae), mRNA (cDNA clone MGC:117708 IMAGE:30936207) mm
RG-U34C:RC_AA818406_AT similar to U6 snRNA-associated Sm-like protein LSm6 (Sm protein F) rn
RAE230B:1383202_AT similar to U6 snRNA-associated Sm-like protein LSm6 (Sm protein F) rn
RAT230_2:1383202_AT similar to U6 snRNA-associated Sm-like protein LSm6 (Sm protein F) rn
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 AAK73913 Lsm sm-like protein protein 6 [Caenorhabditis elegans] ref|NP_490883.1| LSM Sm-like protein family member (lsm-6) [Caenorhabditis elegans] 1.0E-37
blast CAE74418 Hypothetical protein CBG22150 [Caenorhabditis briggsae] 3.0E-37
blast NP_009011 Sm protein F [Homo sapiens] ref|XP_872946.1| PREDICTED: similar to U6 snRNA-associated Sm-like protein LSm6 [Bos taurus] gb|AAH78551.1| MGC85411 protein [Xenopus laevis] gb|AAH16026.1| Sm protein F [Homo sapiens] gb|AAH99484.1| Lsm6 protein [Mus musculus] gb|AAH30427.1| Lsm6 protein [Mus musculus] dbj|BAE24870.1| unnamed protein product [Mus musculus] gb|AAH98230.1| Lsm6 protein [Mus musculus] dbj|BAE34418.1| unnamed protein product [Mus musculus] dbj|BAE36530.1| unnamed protein product [Mus musculus] dbj|BAC37251.1| unnamed protein product [Mus musculus] dbj|BAB31555.1| unnamed protein product [Mus musculus] gb|AAY41032.1| unknown [Homo sapiens] emb|CAB45869.1| Lsm6 protein [Homo sapiens] sp|P62313|LSM6_MOUSE U6 snRNA-associated Sm-like protein LSm6 sp|P62312|LSM6_HUMAN U6 snRNA-associated Sm-like protein LSm6 (Sm protein F) gb|AAD56230.1| U6 snRNA-associated Sm-like protein LSm6 [Homo sapiens] 9.0E-31
Protein Domains
Database ID Description E-Value
Pfam IPR001163 EMBL-EBI Small nuclear ribonucleoprotein (Sm protein) 4.4E-22
Sequence
Target Sequence 
>C. ELEGANS:176316_AT
tgagcaaacgacagaatcccgccgaattcctgaagaaagtcatcggaaagccggttgtgg
tgaagctcaactctggcgtcgactaccgtggcattctcgcatgtctcgacggatatatga
acatcgcgctcgaacaaaccgaagaatacagcaacggacaacttcagaacaagtacggcg
atgcgttcatccg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGAGCAAACGACAGAATCCCGCCGA 127 569 14 Antisense
AATCCCGCCGAATTCCTGAAGAAAG 571 167 28 Antisense
GAAAGTCATCGGAAAGCCGGTTGTG 153 359 48 Antisense
AGCCGGTTGTGGTGAAGCTCAACTC 556 83 62 Antisense
CATTCTCGCATGTCTCGACGGATAT 250 217 105 Antisense
GACGGATATATGAACATCGCGCTCG 438 375 121 Antisense
GAACATCGCGCTCGAACAAACCGAA 376 351 132 Antisense
ATCGCGCTCGAACAAACCGAAGAAT 416 35 136 Antisense
ATACAGCAACGGACAACTTCAGAAC 621 23 159 Antisense
CTTCAGAACAAGTACGGCGATGCGT 697 219 175 Antisense
ACAAGTACGGCGATGCGTTCATCCG 522 113 182 Antisense
Sequence Source Affymetrix Proprietary Database