[Home] | [Total List]

[189393_at] Yeast J0714 like

Description F40F8.9 /REP_DB=WormBase Gene ID /WP=CE05848 /TR=Q20229 /GB=CAA93263.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=Yeast J0714 like
Cluster 6grp_highest_10_10 > 76      6grp_high1_10_10 > 66      4grp_highest_8_8 > 06      4grp_high_8_8 > 22      6grp_highest_nonorm > 85      6grp_total > 68      4grp_total > 25      6grp_highest_sub > Da      6grp_cgc > 38      6grp_high1_sub > Da      6grp_cgc_sub > Da      6grp_total_sub > Increase      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 636
1 2 3 4 range
A 793.5
(-1.4)
P 		658.5
(-3)
P 		1154.2
(3)
P 		953.6
(0.6)
P 		496
B 657.7
(-3)
P 		1003.3
(1.1)
P 		753
(-1.9)
P 		1168.7
(3)
P 		511
C 868.8
(-2.1)
P 		1186
(1.7)
P 		797.8
(-3)
P 		1293.4
(3)
P 		496
avr 773.3
(-3) 		949.3
(-0.1) 		901.7
(-0.9) 		1138.6
(3) 		365

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 613
1 2 3 4 5 6 range
A 837.2
(2.1)
P 		839.9
(2.1)
P 		868.8
(3)
P 		814.9
(1.4)
P 		666.4
(-3)
P 		792.8
(0.7)
P 		202
B 782.3
(0)
P 		490.9
(-3)
P 		850.7
(0.7)
P 		639.4
(-1.5)
P 		744.3
(-0.4)
P 		1071.3
(3)
P 		580
C 762.9
(-0.8)
P 		597.4
(-2.7)
P 		567.1
(-3)
P 		715.4
(-1.3)
P 		782.3
(-0.6)
P 		1103.7
(3)
P 		537
avr 794.1
(-0.4) 		642.7
(-3) 		762.2
(-0.9) 		723.2
(-1.6) 		731
(-1.5) 		989.3
(3) 		347
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 201
1 2 3 4 range
A 288.9
(2.5)
P 		142.9
(-2.9)
P 		301.7
(3)
P 		139.6
(-3)
P 		162
B 209.7
(-0.2)
P 		247.8
(2.9)
P 		174.5
(-3)
P 		249.1
(3)
P 		75
C 287.6
(0.4)
P 		341
(3)
P 		278.1
(-0.1)
P 		218.1
(-3)
P 		123
avr 262.1
(3) 		243.9
(1.2) 		251.4
(1.9) 		202.3
(-3) 		60

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 256
1 2 3 4 5 6 range
A 154.3
(-3)
P 		298.7
(3)
P 		189.2
(-1.5)
P 		206.7
(-0.8)
P 		201.1
(-1.1)
P 		193
(-1.4)
P 		144
B 272.2
(-0.2)
P 		163.4
(-3)
P 		206.6
(-1.9)
P 		169.4
(-2.8)
P 		302.4
(0.5)
P 		399.5
(3)
P 		236
C 282.8
(0.7)
P 		182.3
(-2)
P 		144.3
(-3)
P 		143.9
(-3)
P 		253.2
(-0.1)
P 		369.5
(3)
P 		226
avr 236.4
(-0.4) 		214.8
(-1.3) 		180
(-2.7) 		173.3
(-3) 		252.2
(0.2) 		320.7
(3) 		147
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189393_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3069
Sequence Type Exemplar sequence
Representative Public ID F40F8.9 NCBI
Target Description F40F8.9 /REP_DB=WormBase Gene ID /WP=CE05848 /TR=Q20229 /GB=CAA93263.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=Yeast J0714 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_063984(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063984 NCBI Caenorhabditis elegans LSM Sm-like protein family member (lsm-1) (lsm-1) mRNA, complete cds. 11/11 None
SNAP00000001349 ENSEMBL cdna:SNAP chromosome:CEL140:II:11126866:11127294:1 11/11 None
GENEFINDER00000001358 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:11126866:11127294:1 11/11 None
F40F8.9.2 ENSEMBL cdna:known chromosome:CEL140:II:11126861:11127425:1 gene:F40F8.9 11/11 None
F40F8.9.1 ENSEMBL cdna:known chromosome:CEL140:II:11126863:11127443:1 gene:F40F8.9 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
chrII:11126862-11127291(+) 100.0 100.0
Public Domain and Genome References
Gene Title Yeast J0714 like
Gene Symbol lsm-1
Ensembl F40F8.9
Entrez Gene 174700 Entrez gene
SwissProt Q20229 EMBL-EBI
WormBase CE05848 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:259477_AT small nuclear ribonucleoprotein, putative / snRNP, putative / Sm protein, putative at
CANINE:1587933_AT similar to U6 snRNA-associated Sm-like protein LSm1 (Small nuclear ribonuclear CaSm) (Cancer-associated Sm-like) cfa
CANINE_2:CFA.14922.1.A1_AT similar to U6 snRNA-associated Sm-like protein LSm1 (Small nuclear ribonuclear CaSm) (Cancer-associated Sm-like) cfa
CANINE_2:CFAAFFX.10169.1.S1_AT similar to U6 snRNA-associated Sm-like protein LSm1 (Small nuclear ribonuclear CaSm) (Cancer-associated Sm-like) cfa
CANINE_2:CFAAFFX.10169.1.S1_S_AT similar to U6 snRNA-associated Sm-like protein LSm1 (Small nuclear ribonuclear CaSm) (Cancer-associated Sm-like) cfa
DROSOPHILA_2:1631263_AT dm
DROSGENOME1:147605_AT dm
HG-U133A:203534_AT LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-U133A_2:203534_AT LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-U133_PLUS_2:203534_AT LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-FOCUS:203534_AT LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HUGENEFL:AF000177_AT LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
U133_X3P:G7657312_3P_AT LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-U95AV2:39017_AT LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-U95D:75256_AT LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
MG-U74AV2:96946_AT LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MOE430A:1423873_AT LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MOUSE430A_2:1423873_AT LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MOUSE430_2:1423873_AT LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MOE430B:1441452_AT LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MOUSE430_2:1441452_AT LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MU19KSUBC:TC36736_AT LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae), mRNA (cDNA clone MGC:29255 IMAGE:5054997) mm
YEAST_2:1773172_AT Lsm (Like Sm) protein; forms heteroheptameric complex (with Lsm2p, Lsm3p, Lsm4p, Lsm5p, Lsm6p, and Lsm7p) involved in degradation of cytoplasmic mRNAs 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 CAA93263 Hypothetical protein F40F8.9 [Caenorhabditis elegans] ref|NP_496385.1| LSM Sm-like protein family member (lsm-1) [Caenorhabditis elegans] 6.0E-66
blast CAE59566 Hypothetical protein CBG02963 [Caenorhabditis briggsae] 2.0E-63
Protein Domains
Database ID Description E-Value
Pfam IPR001163 EMBL-EBI Small nuclear ribonucleoprotein (Sm protein) 6.7E-17
Sequence
Target Sequence 
>C. ELEGANS:189393_AT
atccctatttacccggagcaataagcttgttcgagcagcttgacaaaaaattattagttg
ttctccgcgacggacggaaattgattggcttcttgagatcgatagatcaatttgccaatc
ttatattggaagatgtcgtagaacgcacatttgttgagaaatacttctgtgaaacgggtc
aaggattcatgcttattcgcggagagaatgttgagcttgctggagaaatcgatgatacca
ttgagactggacttacgcaggtgtctcccgaagaatttcgtcggctggaggatgagtata
ttgccaaaaatccgccaaagttccta

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATCCCTATTTACCCGGAGCAATAAG 203 35 26 Antisense
AGCTTGTTCGAGCAGCTTGACAAAA 193 77 49 Antisense
AAATTATTAGTTGTTCTCCGCGACG 655 93 73 Antisense
GTTGTTCTCCGCGACGGACGGAAAT 368 435 82 Antisense
AATTGATTGGCTTCTTGAGATCGAT 167 179 104 Antisense
GGATTCATGCTTATTCGCGGAGAGA 226 509 208 Antisense
CGGAGAGAATGTTGAGCTTGCTGGA 583 243 225 Antisense
TTGAGACTGGACTTACGCAGGTGTC 389 705 266 Antisense
CGCAGGTGTCTCCCGAAGAATTTCG 599 251 281 Antisense
GAATTTCGTCGGCTGGAGGATGAGT 608 323 298 Antisense
TGCCAAAAATCCGCCAAAGTTCCTA 194 587 327 Antisense
Sequence Source Affymetrix Proprietary Database