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[189411_at] Yeast JTA107 like

Description ZK593.7 /REP_DB=WormBase Gene ID /WP=CE06628 /TR=Q23543 /GB=CAA93428.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=Yeast JTA107 like
Cluster 6grp_highest_10_10 > 67      6grp_high1_10_10 > 85      4grp_highest_8_8 > 14      4grp_high_8_8 > 22      6grp_highest_nonorm > 68      6grp_total > 76      4grp_total > 16      6grp_highest_sub > In      6grp_cgc > 57      6grp_total_sub > Increase      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2608
1 2 3 4 range
A 1853.9
(-3)
P 		2282.7
(-1.7)
P 		2623.4
(-0.7)
P 		3881.1
(3)
P 		2027
B 1668.6
(-3)
P 		2376.8
(-0.7)
P 		2553.3
(-0.2)
P 		3533.9
(3)
P 		1865
C 1838.2
(-3)
P 		2414.9
(-1.6)
P 		2274.7
(-1.9)
P 		4276.8
(3)
P 		2439
avr 1786.9
(-3) 		2358.1
(-1.4) 		2483.8
(-1) 		3897.3
(3) 		2110

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 950
1 2 3 4 5 6 range
A 2059.2
(-0.8)
P 		2085.3
(-0.4)
P 		2327.4
(3)
P 		2060.3
(-0.8)
P 		1902.5
(-3)
P 		1939.2
(-2.5)
P 		425
B 1856.6
(-0.8)
P 		1830
(-1.1)
P 		2044.3
(1.2)
P 		1655.3
(-3)
P 		2211.7
(3)
P 		2134
(2.2)
P 		556
C 1568.2
(-3)
P 		1712.4
(-2.1)
P 		1637.2
(-2.6)
P 		1965.2
(-0.5)
P 		1793.6
(-1.6)
P 		2518.5
(3)
P 		950
avr 1828
(-3) 		1875.9
(-2.2) 		2003
(-0.2) 		1893.6
(-1.9) 		1969.3
(-0.7) 		2197.2
(3) 		369
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 297
1 2 3 4 range
A 675
(2.7)
P 		495.5
(-3)
P 		685.8
(3)
P 		568.1
(-0.7)
P 		190
B 532.1
(-3)
P 		587
(-1.5)
P 		591.7
(-1.4)
P 		753.1
(3)
P 		221
C 608.5
(-3)
P 		694.3
(-0.2)
P 		792.8
(3)
P 		721.1
(0.7)
P 		184
avr 605.2
(-2.2) 		592.3
(-3) 		690.1
(3) 		680.8
(2.4) 		98

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 519
1 2 3 4 5 6 range
A 379.6
(-3)
P 		741.6
(3)
P 		506.9
(-0.9)
P 		522.5
(-0.6)
P 		574.1
(0.2)
P 		472.1
(-1.5)
P 		362
B 646
(-0.3)
P 		609.1
(-0.8)
P 		496.4
(-2.2)
P 		438.4
(-3)
P 		898.6
(3)
P 		795.8
(1.7)
P 		460
C 581.3
(-0.5)
P 		522.5
(-1.3)
P 		416.7
(-2.7)
P 		395.2
(-3)
P 		580.4
(-0.5)
P 		843.1
(3)
P 		448
avr 535.6
(-1) 		624.4
(1.1) 		473.3
(-2.5) 		452
(-3) 		684.4
(2.5) 		703.7
(3) 		252
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189411_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.9988
Sequence Type Exemplar sequence
Representative Public ID ZK593.7 NCBI
Target Description ZK593.7 /REP_DB=WormBase Gene ID /WP=CE06628 /TR=Q23543 /GB=CAA93428.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=Yeast JTA107 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_069633(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069633 NCBI Caenorhabditis elegans LSM Sm-like protein family member (lsm-7) (lsm-7) mRNA, complete cds. 11/11 None
SNAP00000042096 ENSEMBL cdna:SNAP chromosome:CEL140:IV:10933497:10934080:1 11/11 None
GENEFINDER00000042101 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:10933472:10934080:1 11/11 None
ZK593.7.1 ENSEMBL cdna:known chromosome:CEL140:IV:10933467:10934132:1 gene:ZK593.7 11/11 None
ZK593.7.2 ENSEMBL cdna:known chromosome:CEL140:IV:10933472:10934170:1 gene:ZK593.7 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:10933502-10934086(+) 100.0 100.0
Public Domain and Genome References
Gene Title Yeast JTA107 like
Gene Symbol lsm-7
Ensembl ZK593.7
Entrez Gene 177988 Entrez gene
SwissProt Q23543 EMBL-EBI
WormBase CE06628 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:263332_AT small nuclear ribonucleoprotein, putative / snRNP, putative / Sm protein, putative at
CANINE_2:CFA.8071.1.S1_AT similar to U6 snRNA-associated Sm-like protein LSm7 cfa
CANINE_2:CFA.8071.1.S1_X_AT similar to U6 snRNA-associated Sm-like protein LSm7 cfa
CANINE_2:CFA.8071.2.S1_A_AT similar to U6 snRNA-associated Sm-like protein LSm7 cfa
CANINE_2:CFA.8071.2.S1_S_AT similar to U6 snRNA-associated Sm-like protein LSm7 cfa
DROSOPHILA_2:1640520_AT dm
DROSGENOME1:146374_AT dm
CHICKEN:GGA.1788.1.S1_AT LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae) gga
CHICKEN:GGAAFFX.11985.1.S1_S_AT LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae) gga
CHICKEN:GGA.1788.2.S1_AT LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae) gga
HG-U95AV2:36848_R_AT LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-U133_PLUS_2:204559_S_AT LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-U133A:204559_S_AT LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-FOCUS:204559_S_AT LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-U133A_2:204559_S_AT LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HU35KSUBA:AA215299_I_AT LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HU35KSUBA:AA215299_S_AT LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
U133_X3P:G7706422_3P_A_AT LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-U95AV2:36846_S_AT LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
HG-U95AV2:36847_R_AT LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae) hs
MG-U74AV2:97907_AT LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MOE430A:1417313_AT LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MOUSE430A_2:1417313_AT LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MOUSE430_2:1417313_AT LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MOE430B:1452755_AT LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
MOUSE430_2:1452755_AT LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae) mm
RG-U34C:RC_AI232699_AT LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae) (predicted) rn
RAE230A:1376407_A_AT LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae) (predicted) rn
RAT230_2:1376407_A_AT LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae) (predicted) rn
RAE230B:1385121_AT LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae) (predicted) rn
RAT230_2:1385121_AT LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae) (predicted) rn
YEAST_2:1779078_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 CAA93428 Hypothetical protein ZK593.7 [Caenorhabditis elegans] ref|NP_502034.1| LSM Sm-like protein family member (lsm-7) [Caenorhabditis elegans] 1.0E-52
blast CAE61961 Hypothetical protein CBG05961 [Caenorhabditis briggsae] 4.0E-50
blast CAE61961 Hypothetical protein CBG05961 [Caenorhabditis briggsae] 5.0E-50
Protein Domains
Database ID Description E-Value
Pfam IPR001163 EMBL-EBI Small nuclear ribonucleoprotein (Sm protein) 2.7E-21
Pfam IPR001163 EMBL-EBI Small nuclear ribonucleoprotein (Sm protein) 2.7E-21
Sequence
Target Sequence 
>C. ELEGANS:189411_AT
gaaggagtctgtcgttgatctcaccagatttctcgacaaagagattcgcgtcaagttcca
aggaggacgtgaagcaagtggcgtgcttcgaggattcgatcagttgctcaatatggttct
tgatgactgccgcgagtatctccgtgatccacaaaatccttcggtcgtcggtgatgagac
aagacaactgggtcttattgtggctcgcggaacagcaattacagtagttagcccagcaga
tggactcgagc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAAGGAGTCTGTCGTTGATCTCACC 131 335 39 Antisense
GATCTCACCAGATTTCTCGACAAAG 520 419 55 Antisense
AGAGATTCGCGTCAAGTTCCAAGGA 469 57 78 Antisense
CAAGTGGCGTGCTTCGAGGATTCGA 278 181 113 Antisense
GAGGATTCGATCAGTTGCTCAATAT 525 403 128 Antisense
TCTTGATGACTGCCGCGAGTATCTC 464 617 156 Antisense
GAGTATCTCCGTGATCCACAAAATC 460 399 172 Antisense
TCCACAAAATCCTTCGGTCGTCGGT 234 385 186 Antisense
ACAACTGGGTCTTATTGTGGCTCGC 621 111 222 Antisense
GTGGCTCGCGGAACAGCAATTACAG 492 491 238 Antisense
GTTAGCCCAGCAGATGGACTCGAGC 108 447 265 Antisense
Sequence Source Affymetrix Proprietary Database