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[176049_at] small nuclear ribonucleoprotein Sm F (snRNP core protein F)

Description ZK652.1 /REP_DB=WormBase Gene ID /WP=CE00446 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 46      6grp_high1_10_10 > 64      4grp_highest_8_8 > 09      4grp_high_8_8 > 62      6grp_highest_nonorm > 57      6grp_total > 54      4grp_total > 58      6grp_cgc > 46      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2452
1 2 3 4 range
A 2447.3
(-1.4)
P 		3615.2
(3)
P 		3430
(2.3)
P 		2040.1
(-3)
P 		1575
B 2333.3
(-1.6)
P 		3161.5
(0.5)
P 		4142.9
(3)
P 		1788.7
(-3)
P 		2354
C 2704.6
(-0.1)
P 		3745.4
(2.9)
P 		3794.1
(3)
P 		1690.7
(-3)
P 		2103
avr 2495.1
(-1) 		3507.4
(2.1) 		3789
(3) 		1839.8
(-3) 		1949

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1423
1 2 3 4 5 6 range
A 2507.6
(-0.3)
P 		2132.1
(-2.6)
P 		3040.2
(3)
P 		2105.9
(-2.8)
P 		2073.8
(-3)
P 		2321.1
(-1.5)
P 		966
B 2657.6
(-0.8)
P 		2188.5
(-3)
P 		3467.8
(3)
P 		2251
(-2.7)
P 		2294
(-2.5)
P 		2754.1
(-0.3)
P 		1279
C 2421.4
(-0.5)
P 		2127.7
(-2.5)
P 		2456
(-0.3)
P 		2248.9
(-1.7)
P 		2045.2
(-3)
P 		2964.6
(3)
P 		919
avr 2528.9
(-0.2) 		2149.4
(-2.9) 		2988
(3) 		2201.9
(-2.5) 		2137.7
(-3) 		2679.9
(0.8) 		850
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1037
1 2 3 4 range
A 891.1
(2.9)
P 		784.8
(1.9)
P 		896.7
(3)
P 		298.6
(-3)
P 		598
B 744.1
(0.8)
P 		780.8
(1.1)
P 		960
(3)
P 		381.2
(-3)
P 		579
C 895.3
(0.5)
P 		1076.8
(1.6)
P 		1322.4
(3)
P 		285.1
(-3)
P 		1037
avr 843.5
(1.2) 		880.8
(1.5) 		1059.7
(3) 		321.6
(-3) 		738

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 575
1 2 3 4 5 6 range
A 462.3
(-3)
P 		758.3
(3)
P 		662.1
(1.1)
P 		534.1
(-1.5)
P 		625.8
(0.3)
P 		565.1
(-0.9)
P 		296
B 924.7
(1.6)
P 		728.5
(-1.2)
P 		842.1
(0.4)
P 		596.2
(-3)
P 		932
(1.7)
P 		1027
(3)
P 		431
C 897.5
(1.9)
P 		649.2
(-0.8)
P 		625.1
(-1.1)
P 		452.3
(-3)
P 		661.8
(-0.7)
P 		992.4
(3)
P 		540
avr 761.5
(1.2) 		712
(0.3) 		709.8
(0.3) 		527.5
(-3) 		739.9
(0.8) 		861.5
(3) 		334
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 176049_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.8068
Sequence Type Exemplar sequence
Representative Public ID ZK652.1 NCBI
Target Description ZK652.1 /REP_DB=WormBase Gene ID /WP=CE00446 /SUBMIT=ST.LOUIS /CHR=3 /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_066307(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066307 NCBI Caenorhabditis elegans Small Nuclear Ribonucleoprotein family member (snr-5) (snr-5) mRNA, complete cds. 11/11 None
ZK652.1.2 ENSEMBL cdna:known chromosome:CEL140:III:7861989:7862428:1 gene:ZK652.1 11/11 None
ZK652.1.1 ENSEMBL cdna:known chromosome:CEL140:III:7861991:7862538:1 gene:ZK652.1 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
chrIII:7861990-7862405(+) 100.0 100.0
Public Domain and Genome References
Gene Title small nuclear ribonucleoprotein Sm F (snRNP core protein F)
Gene Symbol snr-5
Ensembl ZK652.1
Entrez Gene 176103 Entrez gene
SwissProt P34659 EMBL-EBI
WormBase CE00446 Wormbase
Functional Annotations
Ortholog
ID Title Organism
DROSOPHILA_2:1628006_AT Developmental embryonic B dm
DROSGENOME1:143120_AT Developmental embryonic B dm
HG-U133A:203832_AT small nuclear ribonucleoprotein polypeptide F hs
HG-U133_PLUS_2:203832_AT small nuclear ribonucleoprotein polypeptide F hs
HG-FOCUS:203832_AT small nuclear ribonucleoprotein polypeptide F hs
HG-U133A_2:203832_AT small nuclear ribonucleoprotein polypeptide F hs
HU35KSUBD:RC_AA486737_AT small nuclear ribonucleoprotein polypeptide F hs
HUGENEFL:X85372_AT small nuclear ribonucleoprotein polypeptide F hs
U133_X3P:G4507130_3P_X_AT small nuclear ribonucleoprotein polypeptide F hs
U133_X3P:G4507130_3P_AT small nuclear ribonucleoprotein polypeptide F hs
HG-U95AV2:41403_AT small nuclear ribonucleoprotein polypeptide F hs
HG-U95C:57796_AT Small nuclear ribonucleoprotein polypeptide F hs
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 AAA28212 Small nuclear ribonucleoprotein protein 5 [Caenorhabditis elegans] ref|NP_498708.1| Small Nuclear Ribonucleoprotein family member (snr-5) [Caenorhabditis elegans] sp|P34659|RUXF_CAEEL Probable small nuclear ribonucleoprotein F (snRNP-F) (Sm protein F) (Sm-F) (SmF) 2.0E-43
blast CAE66872 Hypothetical protein CBG12250 [Caenorhabditis briggsae] 1.0E-37
blast BAD27986.1 putative small nuclear ribonucleoprotein polypeptide F [Oryza sativa (japonica cultivar-group)] 1.0E-28
Protein Domains
Database ID Description E-Value
Pfam IPR001163 EMBL-EBI Small nuclear ribonucleoprotein (Sm protein) 3.5E-25
Sequence
Target Sequence 
>C. ELEGANS:176049_AT
gtccgcagttcaaccagtgaacccaaaaccgttcctcaacagtctcaccggaaagtttgt
cgtttgcaaactgaagtggggaatggagtacaaaggtgtccttgttgctgtcgactccta
catgaatctgcagctggctcacgccgaggagtacattgacggaaacagtcaaggaaatct
cggagagattcttatccgatgcaacaacgttctctacgtgggaggc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTCCGCAGTTCAACCAGTGAACCCA 698 475 15 Antisense
GTTCCTCAACAGTCTCACCGGAAAG 193 439 45 Antisense
CTCACCGGAAAGTTTGTCGTTTGCA 335 229 58 Antisense
CAAAGGTGTCCTTGTTGCTGTCGAC 330 193 105 Antisense
TTGCTGTCGACTCCTACATGAATCT 220 701 119 Antisense
CTACATGAATCTGCAGCTGGCTCAC 17 227 132 Antisense
GGCTCACGCCGAGGAGTACATTGAC 227 539 150 Antisense
GAAACAGTCAAGGAAATCTCGGAGA 496 355 176 Antisense
GAGAGATTCTTATCCGATGCAACAA 393 395 197 Antisense
ATCCGATGCAACAACGTTCTCTACG 79 39 208 Antisense
CAACAACGTTCTCTACGTGGGAGGC 372 187 216 Antisense
Sequence Source Affymetrix Proprietary Database