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[193791_s_at] small nuclear ribonuclearprotein SM D3

Description Y116A8C.42 /REP_DB=WormBase Gene ID /WP=CE23346 /GEN=snr-1 /TR=Q9U2U5 /GB=CAB55132.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=small nuclear ribonuclearprotein SM D3
Cluster 6grp_highest_10_10 > 79      6grp_high1_10_10 > 97      4grp_highest_8_8 > 01      4grp_high_8_8 > 53      6grp_highest_nonorm > 57      6grp_total > 79      4grp_total > 58      6grp_highest_sub > In      6grp_cgc > 78      6grp_high1_sub > In      6grp_cgc_sub > In      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2653
1 2 3 4 range
A 2212.5
(-1.5)
P 		3679.6
(2.5)
P 		3882.6
(3)
P 		1648.8
(-3)
P 		2234
B 2455.3
(-1.5)
P 		3942.8
(3)
P 		3674.6
(2.2)
P 		1974.9
(-3)
P 		1968
C 2549.3
(-1.3)
P 		4301.8
(3)
P 		3582.2
(1.2)
P 		1851.2
(-3)
P 		2451
avr 2405.7
(-1.4) 		3974.7
(3) 		3713.1
(2.3) 		1825
(-3) 		2150

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 956
1 2 3 4 5 6 range
A 1859.1
(-3)
P 		2393.6
(0.4)
P 		2276.2
(-0.4)
P 		2519.2
(1.1)
P 		2344.8
(0)
P 		2814.7
(3)
P 		956
B 2094.1
(-3)
P 		2681.3
(3)
P 		2167.8
(-2.3)
P 		2419.6
(0.3)
P 		2680.5
(3)
P 		2684
(3)
P 		590
C 2396.2
(-0.4)
P 		2377.5
(-0.6)
P 		2185.6
(-3)
P 		2208.4
(-2.7)
P 		2675.3
(3)
P 		2556.6
(1.5)
P 		490
avr 2116.5
(-3) 		2484.1
(0.9) 		2209.9
(-2) 		2382.4
(-0.2) 		2566.9
(1.8) 		2685.1
(3) 		569
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1007
1 2 3 4 range
A 805.6
(1.4)
P 		798.7
(1.3)
P 		1015
(3)
P 		241.3
(-3)
P 		774
B 783
(0.9)
P 		973.8
(3)
P 		851.5
(1.7)
P 		420.8
(-3)
P 		553
C 843.9
(0.4)
P 		1236.8
(2.9)
P 		1248.5
(3)
P 		312.1
(-3)
P 		936
avr 810.8
(1.1) 		1003.1
(2.7) 		1038.3
(3) 		324.7
(-3) 		714

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 746
1 2 3 4 5 6 range
A 342.7
(-3)
P 		851.3
(3)
P 		495.7
(-1.2)
P 		638.9
(0.5)
P 		707.6
(1.3)
P 		685.3
(1)
P 		509
B 728.6
(-0.8)
P 		892.5
(0.9)
P 		526.4
(-3)
P 		640.9
(-1.8)
P 		1089
(3)
P 		1000.8
(2.1)
P 		563
C 888.2
(3)
P 		725.4
(0.8)
P 		556.3
(-1.5)
P 		444.1
(-3)
P 		865.7
(2.7)
P 		855.9
(2.6)
P 		444
avr 653.2
(-0.9) 		823.1
(1.9) 		526.1
(-3) 		574.6
(-2.2) 		887.4
(3) 		847.3
(2.3) 		361
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 193791_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.10136
Sequence Type Exemplar sequence
Representative Public ID Y116A8C.42 NCBI
Target Description Y116A8C.42 /REP_DB=WormBase Gene ID /WP=CE23346 /GEN=snr-1 /TR=Q9U2U5 /GB=CAB55132.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=small nuclear ribonuclearprotein SM D3
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_070626(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_070626 NCBI Caenorhabditis elegans Small Nuclear Ribonucleoprotein family member (snr-1) (snr-1) mRNA, complete cds. 11/11 None
SNAP00000004099 ENSEMBL cdna:SNAP chromosome:CEL140:IV:17088016:17088527:1 11/11 None
GENEFINDER00000004163 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:17088016:17088527:1 11/11 None
Y116A8C.42 ENSEMBL cdna:known chromosome:CEL140:IV:17088010:17088791:1 gene:Y116A8C.42 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
U23937 5/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIV:17088021-17088533(+) 100.0 100.0
Public Domain and Genome References
Gene Title small nuclear ribonuclearprotein SM D3
Gene Symbol snr-1
Ensembl Y116A8C.42
Entrez Gene 178483 Entrez gene
SwissProt Q17348 EMBL-EBI
WormBase CE23346 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:261725_AT small nuclear ribonucleoprotein D3, putative / snRNP core protein D3, putative / Sm protein D3, putative at
CANINE:1584265_AT similar to small nuclear ribonucleoprotein D3 cfa
CANINE_2:CFA.11354.1.A1_AT similar to small nuclear ribonucleoprotein D3 cfa
CANINE_2:CFA.11354.1.A1_S_AT similar to small nuclear ribonucleoprotein D3 cfa
DROSOPHILA_2:1635915_AT Small ribonucleoprotein Sm D3 dm
DROSGENOME1:143973_AT Small ribonucleoprotein Sm D3 dm
CHICKEN:GGA.18895.1.S1_S_AT small nuclear ribonucleoprotein D3 polypeptide 18kDa gga
CHICKEN:GGA.8376.1.S1_S_AT small nuclear ribonucleoprotein D3 polypeptide 18kDa gga
HG-U133A:202567_AT small nuclear ribonucleoprotein D3 polypeptide 18kDa hs
HG-U133_PLUS_2:202567_AT small nuclear ribonucleoprotein D3 polypeptide 18kDa hs
HG-FOCUS:202567_AT small nuclear ribonucleoprotein D3 polypeptide 18kDa hs
HG-U133A_2:202567_AT small nuclear ribonucleoprotein D3 polypeptide 18kDa hs
HUGENEFL:U15009_AT small nuclear ribonucleoprotein D3 polypeptide 18kDa hs
U133_X3P:G4759159_3P_AT small nuclear ribonucleoprotein D3 polypeptide 18kDa hs
HG-U95AV2:40150_AT small nuclear ribonucleoprotein D3 polypeptide 18kDa hs
HG-U95E:77648_AT small nuclear ribonucleoprotein D3 polypeptide 18kDa hs
HU35KSUBC:RC_AA278320_AT Small nuclear ribonucleoprotein D3 polypeptide 18kDa hs
HG-U95B:44100_AT Small nuclear ribonucleoprotein D3 polypeptide 18kDa hs
HG-U95C:63879_AT Small nuclear ribonucleoprotein D3 polypeptide 18kDa hs
HU35KSUBA:RC_AA041276_AT Small nuclear ribonucleoprotein D3 polypeptide 18kDa hs
MG-U74AV2:98077_AT small nuclear ribonucleoprotein D3 mm
MG-U74CV2:167826_R_AT small nuclear ribonucleoprotein D3 mm
MOE430A:1422884_AT small nuclear ribonucleoprotein D3 mm
MOUSE430A_2:1422884_AT small nuclear ribonucleoprotein D3 mm
MOUSE430_2:1422884_AT small nuclear ribonucleoprotein D3 mm
MOE430A:1422885_AT small nuclear ribonucleoprotein D3 mm
MOUSE430A_2:1422885_AT small nuclear ribonucleoprotein D3 mm
MOUSE430_2:1422885_AT small nuclear ribonucleoprotein D3 mm
MG-U74CV2:139522_AT Small nuclear ribonucleoprotein D3, mRNA (cDNA clone MGC:7153 IMAGE:3256792) mm
MOE430A:1449629_S_AT Small nuclear ribonucleoprotein D3, mRNA (cDNA clone MGC:7153 IMAGE:3256792) mm
MOUSE430A_2:1449629_S_AT Small nuclear ribonucleoprotein D3, mRNA (cDNA clone MGC:7153 IMAGE:3256792) mm
MOUSE430_2:1449629_S_AT Small nuclear ribonucleoprotein D3, mRNA (cDNA clone MGC:7153 IMAGE:3256792) mm
MU19KSUBA:TC19943_AT Small nuclear ribonucleoprotein D3, mRNA (cDNA clone MGC:7153 IMAGE:3256792) mm
YEAST_2:1772092_AT Core Sm protein Sm D3; part of heteroheptameric complex (with Smb1p, Smd1p, Smd2p, Sme1p, Smx3p, and Smx2p) that is part of the spliceosomal U1, U2, U4, and U5 snRNPs; homolog of human Sm D3 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 CAB55132 Hypothetical protein Y116A8C.42 [Caenorhabditis elegans] ref|NP_503027.1| Small Nuclear Ribonucleoprotein family member (snr-1) [Caenorhabditis elegans] sp|Q17348|SMD3_CAEEL Small nuclear ribonucleoprotein Sm D3 (snRNP core protein D3) (Sm-D3) 5.0E-50
blast CAE57462 Hypothetical protein CBG00427 [Caenorhabditis briggsae] 6.0E-47
blast EAA00211 ENSANGP00000011800 [Anopheles gambiae str. PEST] ref|XP_320178.2| ENSANGP00000011800 [Anopheles gambiae str. PEST] 5.0E-33
Protein Domains
Database ID Description E-Value
Pfam IPR001163 EMBL-EBI Small nuclear ribonucleoprotein (Sm protein) 1.7E-16
Sequence
Target Sequence 
>C. ELEGANS:193791_S_AT
gacttcagttggtgtcccaatcaagattcttcatgaggccgaaggtcacatggtcacgct
cgaaaccgttacaggcgaagtttaccgaggaaaactttctgaagccgaagacaacatgaa
ctgtcagctggctgaaaccgttgtgactttccgcgacggaagaagtcatcaattggacaa
cgttttcattcgcggaaacaagatccgattcatgattctgccggatatgctcaaaaacgc
gccaatgttcaaaaatatcggaagagcccagaaaggagccattggaatgggtttgggagg
tctcgatcagcgtggaagaggacgtggaaccgctttccgtcgaccaatgggccgtggagg
acc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GACTTCAGTTGGTGTCCCAATCAAG 636 313 15 Antisense
TGAGGCCGAAGGTCACATGGTCACG 626 561 48 Antisense
CATGGTCACGCTCGAAACCGTTACA 229 209 63 Antisense
ACAACATGAACTGTCAGCTGGCTGA 429 111 125 Antisense
GGCTGAAACCGTTGTGACTTTCCGC 47 539 144 Antisense
ATTGGACAACGTTTTCATTCGCGGA 414 3 186 Antisense
CCGATTCATGATTCTGCCGGATATG 78 263 219 Antisense
GCCGGATATGCTCAAAAACGCGCCA 532 283 234 Antisense
TTGGGAGGTCTCGATCAGCGTGGAA 248 709 307 Antisense
GAAGAGGACGTGGAACCGCTTTCCG 89 337 329 Antisense
GTCGACCAATGGGCCGTGGAGGACC 49 475 353 Antisense
Sequence Source Affymetrix Proprietary Database