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[172613_x_at]

Description Y62E10A.12 /REP_DB=WormBase Gene ID /WP=CE28143 /TR=Q9U1W8 /GB=CAB60606.2 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 45      6grp_high1_10_10 > 53      4grp_highest_8_8 > 04      4grp_high_8_8 > 38      6grp_highest_nonorm > 76      6grp_total > 30      4grp_total > 34      6grp_cgc > 82      6grp_high1_sub > 03      6grp_cgc_sub > 03      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 501
1 2 3 4 range
A 903.5
(-3)
P 		1235.6
(2.3)
P 		1126.3
(0.5)
P 		1281.3
(3)
P 		378
B 1031
(-3)
P 		1361.8
(3)
P 		1335.2
(2.5)
P 		1136
(-1.1)
P 		331
C 1107.5
(-3)
P 		1404.5
(3)
P 		1155.2
(-2)
P 		1284.8
(0.6)
P 		297
avr 1014
(-3) 		1334
(3) 		1205.6
(0.6) 		1234
(1.1) 		320

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 518
1 2 3 4 5 6 range
A 1059.8
(-0.4)
P 		1109.1
(0.4)
P 		1253.7
(2.5)
P 		1285.4
(3)
P 		883.1
(-3)
P 		1124.5
(0.6)
P 		402
B 1027.8
(-2)
P 		1198.4
(0.3)
P 		1400.6
(3)
P 		973.9
(-2.7)
P 		954.1
(-3)
P 		1071.6
(-1.4)
P 		447
C 1078.4
(-0.8)
P 		1272.8
(2.8)
P 		963.3
(-3)
P 		1283.8
(3)
P 		1111
(-0.2)
P 		1140.1
(0.3)
P 		321
avr 1055.3
(-1) 		1193.4
(2.7) 		1205.9
(3) 		1181
(2.3) 		982.7
(-3) 		1112.1
(0.5) 		223
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 216
1 2 3 4 range
A 328.9
(3)
P 		268.2
(0.4)
P 		294.4
(1.5)
P 		187.6
(-3)
P 		141
B 328.8
(2.5)
P 		336.3
(3)
P 		309.4
(1.3)
P 		242.1
(-3)
P 		94
C 366.6
(1.8)
P 		403.8
(3)
P 		402.6
(3)
P 		216.6
(-3)
P 		187
avr 341.4
(3) 		336.1
(2.7) 		335.5
(2.7) 		215.4
(-3) 		126

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 204
1 2 3 4 5 6 range
A 195.4
(-3)
P 		394.4
(3)
P 		273
(-0.7)
P 		326
(0.9)
P 		266.5
(-0.9)
P 		273.8
(-0.6)
P 		199
B 357.6
(1.2)
P 		398.9
(3)
P 		340.1
(0.5)
P 		257.9
(-3)
P 		387.6
(2.5)
P 		399.6
(3)
P 		142
C 399.7
(3)
P 		388.4
(2.6)
P 		245.2
(-3)
P 		258.2
(-2.5)
P 		359.5
(1.4)
P 		381.6
(2.3)
P 		155
avr 317.6
(-1) 		393.9
(3) 		286.1
(-2.7) 		280.7
(-3) 		337.9
(0) 		351.7
(0.8) 		113
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172613_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.9402
Sequence Type Exemplar sequence
Representative Public ID Y62E10A.12 NCBI
Target Description Y62E10A.12 /REP_DB=WormBase Gene ID /WP=CE28143 /TR=Q9U1W8 /GB=CAB60606.2 /SUBMIT=HINXTON /CHR=4 /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_070178(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_070178 NCBI Caenorhabditis elegans LSM Sm-like protein family member (lsm-3) (lsm-3) mRNA, complete cds. 11/11 None
SNAP00000008081 ENSEMBL cdna:SNAP chromosome:CEL140:IV:13387438:13389004:1 11/11 None
GENEFINDER00000008093 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:13387438:13389004:1 11/11 None
Y62E10A.12.1 ENSEMBL cdna:known chromosome:CEL140:IV:13387172:13389086:1 gene:Y62E10A.12 11/11 None
Y62E10A.12.2 ENSEMBL cdna:known chromosome:CEL140:IV:13387438:13389199:1 gene:Y62E10A.12 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:13387443-13387682(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol lsm-3
Ensembl Y62E10A.12
Entrez Gene 178303 Entrez gene
SwissProt Q9U1W8 EMBL-EBI
WormBase CE28143 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:256333_AT small nuclear ribonucleoprotein, putative / snRNP, putative / Sm protein, putative at
CANINE:1583873_AT similar to LSM3 homolog, U6 small nuclear RNA associated cfa
CANINE_2:CFAAFFX.4877.1.S1_X_AT similar to LSM3 homolog, U6 small nuclear RNA associated cfa
CANINE_2:CFAAFFX.7588.1.S1_X_AT similar to LSM3 homolog, U6 small nuclear RNA associated cfa
CANINE_2:CFAAFFX.7654.1.S1_S_AT similar to LSM3 homolog, U6 small nuclear RNA associated cfa
DROSOPHILA_2:1639108_AT dm
DROSGENOME1:150476_AT dm
CHICKEN:GGA.1101.1.S1_A_AT similar to U6 snRNA-associated Sm-like protein LSm3 (MDS017) gga
CHICKEN:GGA.1101.2.S1_AT similar to U6 snRNA-associated Sm-like protein LSm3 (MDS017) gga
HG-U133_PLUS_2:202209_AT LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-U133A:202209_AT LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-FOCUS:202209_AT LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-U133A_2:202209_AT LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HU35KSUBA:RC_AA461098_S_AT LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HU35KSUBA:AA421213_AT LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
U133_X3P:G7657314_3P_AT LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-U95AV2:39009_AT LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
MU11KSUBA:AA462343_S_AT LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MG-U74AV2:94455_AT LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MOE430A:1448536_AT LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MOUSE430A_2:1448536_AT LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MOUSE430_2:1448536_AT LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
RG-U34B:RC_AA946082_AT LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) (predicted) rn
RAE230A:1388488_AT LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) (predicted) rn
RAT230_2:1388488_AT LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) (predicted) 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 CAB60606 Hypothetical protein Y62E10A.12 [Caenorhabditis elegans] ref|NP_502579.1| LSM Sm-like protein family member (lsm-3) [Caenorhabditis elegans] 6.0E-50
blast CAE58609 Hypothetical protein CBG01776 [Caenorhabditis briggsae] 3.0E-48
blast CAB60606 Hypothetical protein Y62E10A.12 [Caenorhabditis elegans] ref|NP_502579.1| LSM Sm-like protein family member (lsm-3) [Caenorhabditis elegans] 7.0E-44
blast CAE58609 Hypothetical protein CBG01776 [Caenorhabditis briggsae] 3.0E-42
Protein Domains
Database ID Description E-Value
Pfam IPR001163 EMBL-EBI Small nuclear ribonucleoprotein (Sm protein) 3.3E-25
Pfam IPR001163 EMBL-EBI Small nuclear ribonucleoprotein (Sm protein) 9.2E-14
Pfam IPR001163 EMBL-EBI Small nuclear ribonucleoprotein (Sm protein) 1.1E-4
Sequence
Target Sequence 
>C. ELEGANS:172613_X_AT
gaaagaagtgacactgtctgctacagtcgaagagccactcgatttgctccgtctcagttt
ggatgagagagtttatgtcaaaatgagaaacgacagagagttgcgcggtcgtctcagagc
tttcgatcaacatttgaac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAAAGAAGTGACACTGTCTGCTACA 369 359 27 Antisense
GAAGTGACACTGTCTGCTACAGTCG 656 335 31 Antisense
GTGACACTGTCTGCTACAGTCGAAG 68 483 34 Antisense
GTCTGCTACAGTCGAAGAGCCACTC 543 471 42 Antisense
GCTACAGTCGAAGAGCCACTCGATT 178 299 46 Antisense
GTCGAAGAGCCACTCGATTTGCTCC 481 473 52 Antisense
ATTTGCTCCGTCTCAGTTTGGATGA 327 17 68 Antisense
GAGAAACGACAGAGAGTTGCGCGGT 238 387 111 Antisense
ACGACAGAGAGTTGCGCGGTCGTCT 293 93 116 Antisense
GGTCGTCTCAGAGCTTTCGATCAAC 363 503 133 Antisense
CAGAGCTTTCGATCAACATTTGAAC 589 203 141 Antisense
Sequence Source Affymetrix Proprietary Database