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[193119_s_at] small nuclear ribonucleoprotein Sm D1 (snRNP core protein D1)

Description T28D9.10 /REP_DB=WormBase Gene ID /WP=CE02065 /TR=SW:Q10013 /GB=AAA68313.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=Autoantigen small ribonucleoprotein
Cluster 6grp_highest_10_10 > 98      6grp_high1_10_10 > 89      4grp_highest_8_8 > 10      4grp_high_8_8 > 55      6grp_highest_nonorm > 58      6grp_total > 89      4grp_total > 48      6grp_highest_sub > Cu      6grp_cgc > 69      6grp_high1_sub > Cu      6grp_cgc_sub > Da      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1671
1 2 3 4 range
A 2828.8
(-2.2)
P 		2885.7
(-2)
P 		3923.1
(3)
P 		2667.5
(-3)
P 		1256
B 2391
(-3)
P 		3716.1
(1.8)
P 		4062.1
(3)
P 		2713.7
(-1.8)
P 		1671
C 2726
(-3)
P 		3974.3
(3)
P 		3852.5
(2.4)
P 		2732.9
(-3)
P 		1248
avr 2648.6
(-3) 		3525.4
(1.1) 		3945.9
(3) 		2704.7
(-2.7) 		1297

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1079
1 2 3 4 5 6 range
A 2254.6
(-3)
P 		2405.8
(-0.8)
P 		2374.6
(-1.2)
P 		2661
(3)
P 		2548.6
(1.3)
P 		2660.4
(3)
P 		406
B 2717
(-1.8)
P 		2700.3
(-1.9)
P 		2674.5
(-2.2)
P 		2593.2
(-3)
P 		3204.9
(3)
P 		2761.2
(-1.4)
P 		612
C 2925.2
(0.4)
P 		2674.6
(-1.2)
P 		2387.4
(-3)
P 		2534.1
(-2.1)
P 		2622.6
(-1.5)
P 		3333.9
(3)
P 		947
avr 2632.3
(-0.9) 		2593.6
(-1.4) 		2478.8
(-3) 		2596.1
(-1.4) 		2792
(1.3) 		2918.5
(3) 		440
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 952
1 2 3 4 range
A 1030
(3)
P 		626.4
(-0.8)
P 		1025.6
(3)
P 		390.5
(-3)
P 		640
B 762.5
(0)
P 		917.8
(2.6)
P 		941.3
(3)
P 		578.3
(-3)
P 		363
C 902.4
(0)
P 		1142.6
(1.6)
P 		1342.7
(3)
P 		460.8
(-3)
P 		882
avr 898.3
(1) 		895.6
(1) 		1103.2
(3) 		476.5
(-3) 		627

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 887
1 2 3 4 5 6 range
A 415.6
(-3)
P 		855.6
(3)
P 		517.1
(-1.6)
P 		674.9
(0.5)
P 		769.1
(1.8)
P 		647.7
(0.2)
P 		440
B 945.4
(-0.3)
P 		898.8
(-0.7)
P 		649.5
(-3)
P 		686.8
(-2.7)
P 		1302.1
(3)
P 		1029.6
(0.5)
P 		653
C 1084.3
(2.7)
P 		816.1
(0)
P 		607.6
(-2)
P 		509.6
(-3)
P 		848.6
(0.4)
P 		1116.1
(3)
P 		607
avr 815.1
(0.5) 		856.8
(1.2) 		591.4
(-3) 		623.8
(-2.5) 		973.3
(3) 		931.1
(2.3) 		382
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 193119_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.4434
Sequence Type Exemplar sequence
Representative Public ID T28D9.10 NCBI
Target Description T28D9.10 /REP_DB=WormBase Gene ID /WP=CE02065 /TR=SW:Q10013 /GB=AAA68313.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=Autoantigen small ribonucleoprotein
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_062905(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_062905 NCBI Caenorhabditis elegans Small Nuclear Ribonucleoprotein family member (snr-3) (snr-3) mRNA, complete cds. 11/11 None
SNAP00000011380 ENSEMBL cdna:SNAP chromosome:CEL140:II:6489014:6489700:-1 11/11 None
GENEFINDER00000011387 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:6489014:6489700:-1 11/11 None
T28D9.10.2 ENSEMBL cdna:known chromosome:CEL140:II:6488403:6489708:-1 gene:T28D9.10 11/11 None
T28D9.10.1 ENSEMBL cdna:known chromosome:CEL140:II:6488788:6489708:-1 gene:T28D9.10 11/11 None
T28D9.10.3 ENSEMBL cdna:known chromosome:CEL140:II:6488808:6489714:-1 gene:T28D9.10 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:6489010-6489697(-) 100.0 100.0
Public Domain and Genome References
Gene Title small nuclear ribonucleoprotein Sm D1 (snRNP core protein D1)
Gene Symbol snr-3
Ensembl T28D9.10
Entrez Gene 174072 Entrez gene
SwissProt Q10013 EMBL-EBI
WormBase CE02065 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:14551_AT small nuclear ribonucleoprotein D1, putative / snRNP core protein D1, putative / Sm protein D1, putative at
ATH1-121501:255458_AT small nuclear ribonucleoprotein D1, putative / snRNP core protein D1, putative / Sm protein D1, putative at
CANINE:1583377_S_AT small nuclear ribonucleoprotein D1 polypeptide 16kDa cfa
CANINE:1583376_AT small nuclear ribonucleoprotein D1 polypeptide 16kDa cfa
CANINE_2:CFA.6238.1.A1_AT small nuclear ribonucleoprotein D1 polypeptide 16kDa cfa
CANINE_2:CFA.6238.1.A1_S_AT small nuclear ribonucleoprotein D1 polypeptide 16kDa cfa
CANINE_2:CFAAFFX.27936.1.S1_AT small nuclear ribonucleoprotein D1 polypeptide 16kDa cfa
DROSOPHILA_2:1628088_AT small nuclear ribonucleoprotein at 69D dm
DROSGENOME1:148669_AT small nuclear ribonucleoprotein at 69D dm
HG-U133A:202690_S_AT small nuclear ribonucleoprotein D1 polypeptide 16kDa hs
HG-U133_PLUS_2:202690_S_AT small nuclear ribonucleoprotein D1 polypeptide 16kDa hs
HG-FOCUS:202690_S_AT small nuclear ribonucleoprotein D1 polypeptide 16kDa hs
HG-U133A_2:202690_S_AT small nuclear ribonucleoprotein D1 polypeptide 16kDa hs
HG-U133A:202691_AT small nuclear ribonucleoprotein D1 polypeptide 16kDa hs
HG-U133_PLUS_2:202691_AT small nuclear ribonucleoprotein D1 polypeptide 16kDa hs
HG-U133A_2:202691_AT small nuclear ribonucleoprotein D1 polypeptide 16kDa hs
HU35KSUBA:J03798_AT small nuclear ribonucleoprotein D1 polypeptide 16kDa hs
HUGENEFL:J03798_AT small nuclear ribonucleoprotein D1 polypeptide 16kDa hs
U133_X3P:G5902101_3P_AT small nuclear ribonucleoprotein D1 polypeptide 16kDa hs
U133_X3P:G12804598_3P_A_AT small nuclear ribonucleoprotein D1 polypeptide 16kDa hs
HG-U95AV2:37949_AT small nuclear ribonucleoprotein D1 polypeptide 16kDa hs
MU11KSUBA:M58558_S_AT small nuclear ribonucleoprotein D1 mm
MU11KSUBB:MSA.2008.0_S_AT small nuclear ribonucleoprotein D1 mm
MG-U74AV2:100577_AT small nuclear ribonucleoprotein D1 mm
MOE430A:1416336_S_AT small nuclear ribonucleoprotein D1 mm
MOUSE430A_2:1416336_S_AT small nuclear ribonucleoprotein D1 mm
MOUSE430_2:1416336_S_AT small nuclear ribonucleoprotein D1 mm
RAE230B:1383107_AT small nuclear ribonucleoprotein D1 (predicted) rn
RAT230_2:1383107_AT small nuclear ribonucleoprotein D1 (predicted) rn
RAE230B:1379320_AT Small nuclear ribonucleoprotein D1 (predicted) rn
RAT230_2:1379320_AT Small nuclear ribonucleoprotein D1 (predicted) rn
RG-U34C:RC_AI102591_AT Small nuclear ribonucleoprotein D1 (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 AAA68313 Small nuclear ribonucleoprotein protein 3 [Caenorhabditis elegans] ref|NP_495306.1| Small Nuclear Ribonucleoprotein family member (snr-3) [Caenorhabditis elegans] sp|Q10013|SMD1_CAEEL Probable small nuclear ribonucleoprotein Sm D1 (snRNP core protein D1) (Sm-D1) 9.0E-43
blast CAE59329 Hypothetical protein CBG02671 [Caenorhabditis briggsae] 2.0E-42
Protein Domains
Database ID Description E-Value
Pfam IPR001163 EMBL-EBI Small nuclear ribonucleoprotein (Sm protein) 1.4E-21
Sequence
Target Sequence 
>C. ELEGANS:193119_S_AT
gattcctgatgaagttgtctcacgagaccgtcaatattgaattgaagaacggtactcagg
tgtccggcactatcatgggagtcgatgttgcgatgaacacacatcttcgtgccgtctcaa
tgacagttaagaacaaggagccagtcaaactcgacacgctttcaatcagaggtaacaaca
tcagatacatcattttgccggatccactcgctcttgacacccttttaatcgacgatgaac
caagaaagaaggcccgtgccgctcgcgccggagcttcacgtggacgtggtcgtggtggaa
tgcgcggag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GATTCCTGATGAAGTTGTCTCACGA 633 433 26 Antisense
GTCTCACGAGACCGTCAATATTGAA 135 471 42 Antisense
AAGAACGGTACTCAGGTGTCCGGCA 95 153 70 Antisense
GTGTCCGGCACTATCATGGGAGTCG 57 487 85 Antisense
GATGAACACACATCTTCGTGCCGTC 627 411 117 Antisense
ATCTTCGTGCCGTCTCAATGACAGT 484 31 128 Antisense
AACTCGACACGCTTTCAATCAGAGG 633 141 173 Antisense
AGATACATCATTTTGCCGGATCCAC 600 65 208 Antisense
CTCTTGACACCCTTTTAATCGACGA 597 225 236 Antisense
CAAGAAAGAAGGCCCGTGCCGCTCG 645 183 266 Antisense
CGTGGTCGTGGTGGAATGCGCGGAG 122 245 310 Antisense
Sequence Source Affymetrix Proprietary Database