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[193620_at] small nuclear ribonucleoprotein E (SNRNP-E) like

Description F28F8.3 /REP_DB=WormBase Gene ID /WP=CE09757 /TR=O18694 /GB=CAB03013.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=small nuclear ribonucleoprotein E (SNRNP-E) like
Cluster 6grp_highest_10_10 > 77      6grp_high1_10_10 > 86      4grp_highest_8_8 > 22      4grp_high_8_8 > 14      6grp_highest_nonorm > 97      6grp_total > 77      4grp_total > 09      6grp_highest_sub > Da      6grp_cgc > 49      6grp_high1_sub > In      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1416
1 2 3 4 range
A 808.1
(-3)
P 		1021.9
(-2)
P 		1095.8
(-1.7)
P 		2100.4
(3)
P 		1292
B 778.1
(-3)
P 		855.5
(-2.7)
P 		965.1
(-2.2)
P 		2183.2
(3)
P 		1405
C 767.2
(-3)
P 		785.7
(-2.9)
P 		900
(-2.4)
P 		2068.5
(3)
P 		1301
avr 784.5
(-3) 		887.7
(-2.5) 		987
(-2.1) 		2117.4
(3) 		1333

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 755
1 2 3 4 5 6 range
A 799.1
(-3)
P 		878.1
(-2.1)
P 		1037
(-0.4)
P 		1082.2
(0.1)
P 		825.7
(-2.7)
P 		1343.8
(3)
P 		545
B 903
(-2.2)
P 		822.2
(-2.9)
P 		896.6
(-2.3)
P 		811.4
(-3)
P 		1027
(-1.2)
P 		1516.5
(3)
P 		705
C 979.4
(-1.2)
P 		823
(-2.5)
P 		926.9
(-1.7)
P 		761.1
(-3)
P 		1246.9
(0.9)
P 		1500.4
(3)
P 		739
avr 893.8
(-2.5) 		841.1
(-3) 		953.5
(-1.9) 		884.9
(-2.6) 		1033.2
(-1.1) 		1453.6
(3) 		613
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 254
1 2 3 4 range
A 294.2
(2.1)
P 		221.8
(-3)
P 		286.5
(1.5)
P 		307.5
(3)
P 		86
B 248.1
(-2.1)
P 		211.3
(-3)
P 		223.6
(-2.7)
P 		465.2
(3)
P 		254
C 254
(-1.6)
P 		225.9
(-3)
P 		313.7
(1.3)
P 		348.8
(3)
P 		123
avr 265.4
(-1.2) 		219.7
(-3) 		274.6
(-0.9) 		373.8
(3) 		154

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 418
1 2 3 4 5 6 range
A 147.3
(-3)
P 		312.3
(2.5)
P 		225.8
(-0.4)
P 		274.5
(1.2)
P 		249.2
(0.4)
P 		327.2
(3)
P 		180
B 314.2
(-1.3)
P 		273.7
(-2)
P 		217.7
(-3)
P 		214.9
(-3)
P 		417.3
(0.5)
P 		565.5
(3)
P 		351
C 363
(0.6)
P 		251.1
(-1.3)
P 		235.9
(-1.6)
P 		153.1
(-3)
P 		403.5
(1.3)
P 		502.3
(3)
P 		349
avr 274.8
(-1.6) 		279
(-1.4) 		226.5
(-2.7) 		214.2
(-3) 		356.7
(0.4) 		465
(3) 		251
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193620_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.13896
Sequence Type Exemplar sequence
Representative Public ID F28F8.3 NCBI
Target Description F28F8.3 /REP_DB=WormBase Gene ID /WP=CE09757 /TR=O18694 /GB=CAB03013.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=small nuclear ribonucleoprotein E (SNRNP-E) like
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_074469(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_074469 NCBI Caenorhabditis elegans LSM Sm-like protein family member (lsm-5) (lsm-5) mRNA, complete cds. 11/11 None
SNAP00000036073 ENSEMBL cdna:SNAP chromosome:CEL140:V:15572964:15573239:1 11/11 None
GENEFINDER00000036083 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:15572964:15573239:1 11/11 None
F28F8.3.1 ENSEMBL cdna:known chromosome:CEL140:V:15572583:15573239:1 gene:F28F8.3 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
chrV:15572963-15573239(+) 100.0 100.0
Public Domain and Genome References
Gene Title small nuclear ribonucleoprotein E (SNRNP-E) like
Gene Symbol lsm-5
Ensembl F28F8.3
Entrez Gene 180047 Entrez gene
SwissProt O18694 EMBL-EBI
WormBase CE09757 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:248678_AT small nuclear ribonucleoprotein, putative / snRNP, putative / Sm protein, putative at
CANINE_2:CFAAFFX.875.1.S1_S_AT similar to LSM5 homolog, U6 small nuclear RNA associated cfa
DROSOPHILA_2:1631853_AT dm
DROSGENOME1:148261_AT dm
CHICKEN:GGA.1454.1.S1_AT LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) gga
HG-U133A:202904_S_AT LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-U133_PLUS_2:202904_S_AT LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-U133A_2:202904_S_AT LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-FOCUS:202904_S_AT LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-U133_PLUS_2:211747_S_AT LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-U133A:211747_S_AT LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-U133A_2:211747_S_AT LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HU35KSUBA:RC_AA027086_AT LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
U133_X3P:G6912487_3P_A_AT LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
U133_X3P:G13543564_3P_S_AT LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
U133_X3P:HS.227280.0.S2_3P_AT LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-U133A_2:202903_AT LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-U133_PLUS_2:202903_AT LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-U133A:202903_AT LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-U95AV2:34270_AT LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
MG-U74AV2:94389_AT LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MOUSE430_2:1418656_AT LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MOUSE430A_2:1418656_AT LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MOE430A:1418656_AT LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MU11KSUBA:AA245578_S_AT LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
RG-U34B:RC_AA956431_AT LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) (predicted) rn
RAE230A:1376483_AT LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) (predicted) rn
RAT230_2:1376483_AT LSM5 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 CAB03013 Hypothetical protein F28F8.3 [Caenorhabditis elegans] ref|NP_506870.1| LSM Sm-like protein family member (lsm-5) [Caenorhabditis elegans] 1.0E-46
blast CAE71635 Hypothetical protein CBG18602 [Caenorhabditis briggsae] 3.0E-46
blast XP_692400 PREDICTED: similar to LSM5 homolog, U6 small nuclear RNA associated [Danio rerio] 8.0E-35
Protein Domains
Database ID Description E-Value
Pfam IPR001163 EMBL-EBI Small nuclear ribonucleoprotein (Sm protein) 7.4E-23
Sequence
Target Sequence 
>C. ELEGANS:193620_AT
gctcattgacaagtgcatcggctcgaaaatctgggtgataatgaagaacgacaaggagat
cgtcggcactctgacaggcttcgatgactacgtgaacatggttctggaggacgtcgtcga
atacgagaacaccgccgacggcaagcgaatgaccaagttggacacgattcttctcaacgg
aaatcacatcacgatgctc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCTCATTGACAAGTGCATCGGCTCG 615 299 60 Antisense
GCATCGGCTCGAAAATCTGGGTGAT 446 309 74 Antisense
ACAAGGAGATCGTCGGCACTCTGAC 603 113 110 Antisense
GCACTCTGACAGGCTTCGATGACTA 681 315 125 Antisense
GGCTTCGATGACTACGTGAACATGG 349 537 136 Antisense
GAACATGGTTCTGGAGGACGTCGTC 59 351 153 Antisense
GTCGTCGAATACGAGAACACCGCCG 253 471 172 Antisense
CACCGCCGACGGCAAGCGAATGACC 428 201 189 Antisense
GACCAAGTTGGACACGATTCTTCTC 316 383 210 Antisense
GGACACGATTCTTCTCAACGGAAAT 19 527 219 Antisense
CAACGGAAATCACATCACGATGCTC 12 187 234 Antisense
Sequence Source Affymetrix Proprietary Database