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[172931_x_at] small nuclear ribonucleoprotein D2 like

Description C52E4.3 /REP_DB=WormBase Gene ID /WP=CE08945 /TR=SW:Q18786 /GB=CAB01413.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=small nuclear ribonucleoprotein D2 like
Cluster 6grp_highest_10_10 > 97      6grp_high1_10_10 > 78      4grp_highest_8_8 > 02      4grp_high_8_8 > 46      6grp_highest_nonorm > 77      6grp_total > 59      4grp_total > 49      6grp_highest_sub > Cu      6grp_cgc > 39      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1298
1 2 3 4 range
A 1199.8
(-3)
P 		2497.9
(3)
P 		2396.4
(2.5)
P 		1621.6
(-1.1)
P 		1298
B 1224.5
(-3)
P 		1990.3
(1.8)
P 		2178.7
(3)
P 		1556.3
(-0.9)
P 		954
C 1476.4
(-1.2)
P 		2126.7
(3)
P 		2040.2
(2.4)
P 		1206.5
(-3)
P 		920
avr 1300.2
(-3) 		2205
(3) 		2205.1
(3) 		1461.5
(-1.9) 		905

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 657
1 2 3 4 5 6 range
A 1463
(3)
P 		1162.9
(-3)
P 		1430.5
(2.4)
P 		1327.9
(0.3)
P 		1421.6
(2.2)
P 		1411.3
(2)
P 		300
B 1539.7
(0.8)
P 		1231.1
(-3)
P 		1482.6
(0.1)
P 		1318.1
(-1.9)
P 		1549.7
(0.9)
P 		1723.3
(3)
P 		492
C 1561.2
(0.4)
P 		1243.3
(-2.9)
P 		1230.6
(-3)
P 		1445
(-0.8)
P 		1357.7
(-1.7)
P 		1820.1
(3)
P 		590
avr 1521.3
(1.2) 		1212.4
(-3) 		1381.2
(-0.7) 		1363.7
(-0.9) 		1443
(0.2) 		1651.6
(3) 		439
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 508
1 2 3 4 range
A 436.8
(0.1)
P 		542.2
(1.7)
P 		626.5
(3)
P 		237.4
(-3)
P 		389
B 390.5
(-1)
P 		491.6
(2.5)
P 		504.8
(3)
P 		331.6
(-3)
P 		173
C 488.7
(0.4)
P 		611.4
(1.8)
P 		711.1
(3)
P 		203.4
(-3)
P 		508
avr 438.7
(0) 		548.4
(1.9) 		614.1
(3) 		257.5
(-3) 		357

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 373
1 2 3 4 5 6 range
A 269.7
(-3)
P 		413.6
(2.4)
P 		311.5
(-1.4)
P 		336.8
(-0.5)
P 		429
(3)
P 		343.6
(-0.2)
P 		159
B 535.8
(0.8)
P 		409.8
(-1.8)
P 		360
(-2.8)
P 		349.1
(-3)
P 		629.6
(2.7)
P 		642.6
(3)
P 		294
C 578.7
(2.4)
P 		379.4
(-1.3)
P 		313.2
(-2.6)
P 		290.6
(-3)
P 		439.3
(-0.2)
P 		609.3
(3)
P 		319
avr 461.4
(1) 		400.9
(-0.8) 		328.2
(-2.9) 		325.5
(-3) 		499.3
(2.1) 		531.8
(3) 		206
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172931_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.13070
Sequence Type Exemplar sequence
Representative Public ID C52E4.3 NCBI
Target Description C52E4.3 /REP_DB=WormBase Gene ID /WP=CE08945 /TR=SW:Q18786 /GB=CAB01413.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=small nuclear ribonucleoprotein D2 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_073603(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073603 NCBI Caenorhabditis elegans Small Nuclear Ribonucleoprotein family member (snr-4) (snr-4) mRNA, complete cds. 11/11 None
SNAP00000019785 ENSEMBL cdna:SNAP chromosome:CEL140:V:11981275:11982204:-1 9/11 None
GENEFINDER00000019792 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:11981275:11982204:-1 9/11 None
C52E4.3.2 ENSEMBL cdna:known chromosome:CEL140:V:11981104:11982311:-1 gene:C52E4.3 11/11 None
C52E4.3.1 ENSEMBL cdna:known chromosome:CEL140:V:11981105:11982322:-1 gene:C52E4.3 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
chrV:11981274-11982284(-) 100.0 100.0
Public Domain and Genome References
Gene Title small nuclear ribonucleoprotein D2 like
Gene Symbol snr-4
Ensembl C52E4.3
Entrez Gene 179639 Entrez gene
SwissProt Q18786 EMBL-EBI
WormBase CE08945 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:20614_S_AT small nuclear ribonucleoprotein D2, putative / snRNP core protein D2, putative / Sm protein D2, putative at
ATH1-121501:266482_AT small nuclear ribonucleoprotein D2, putative / snRNP core protein D2, putative / Sm protein D2, putative at
DROSGENOME1:141883_AT dm
DROSOPHILA_2:1635530_AT dm
DROSGENOME1:153483_AT dm
HG-U95AV2:35270_AT small nuclear ribonucleoprotein D2 polypeptide 16.5kDa hs
HG-U133A:200826_AT small nuclear ribonucleoprotein D2 polypeptide 16.5kDa hs
HG-U133_PLUS_2:200826_AT small nuclear ribonucleoprotein D2 polypeptide 16.5kDa hs
HG-FOCUS:200826_AT small nuclear ribonucleoprotein D2 polypeptide 16.5kDa hs
HG-U133A_2:200826_AT small nuclear ribonucleoprotein D2 polypeptide 16.5kDa hs
HUGENEFL:U15008_AT small nuclear ribonucleoprotein D2 polypeptide 16.5kDa hs
U133_X3P:G7242206_3P_AT small nuclear ribonucleoprotein D2 polypeptide 16.5kDa hs
MU11KSUBA:AA271024_S_AT small nuclear ribonucleoprotein D2 mm
MG-U74AV2:95049_AT small nuclear ribonucleoprotein D2 mm
MOE430A:1452680_AT small nuclear ribonucleoprotein D2 mm
MOUSE430A_2:1452680_AT small nuclear ribonucleoprotein D2 mm
MOUSE430_2:1452680_AT small nuclear ribonucleoprotein D2 mm
RG-U34A:RC_AA800946_F_AT small nuclear ribonucleoprotein D2 (predicted) rn
RG-U34B:RC_AI011181_F_AT small nuclear ribonucleoprotein D2 (predicted) rn
RG-U34C:RC_AI176294_AT small nuclear ribonucleoprotein D2 (predicted) rn
RAE230A:1371341_AT small nuclear ribonucleoprotein D2 (predicted) rn
RAT230_2:1371341_AT small nuclear ribonucleoprotein D2 (predicted) rn
YEAST_2:1770868_AT Core Sm protein Sm D2; part of heteroheptameric complex (with Smb1p, Smd1p, Smd3p, Sme1p, Smx3p, and Smx2p) that is part of the spliceosomal U1, U2, U4, and U5 snRNPs; homolog of human Sm D2 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 CAB01413 Hypothetical protein C52E4.3 [Caenorhabditis elegans] ref|NP_506004.1| Small Nuclear Ribonucleoprotein family member (snr-4) [Caenorhabditis elegans] sp|Q18786|SMD2_CAEEL Probable small nuclear ribonucleoprotein Sm D2 (snRNP core protein D2) (Sm-D2) 3.0E-52
blast CAE75361 Hypothetical protein CBG23345 [Caenorhabditis briggsae] 2.0E-50
blast CAB01413 Hypothetical protein C52E4.3 [Caenorhabditis elegans] ref|NP_506004.1| Small Nuclear Ribonucleoprotein family member (snr-4) [Caenorhabditis elegans] sp|Q18786|SMD2_CAEEL Probable small nuclear ribonucleoprotein Sm D2 (snRNP core protein D2) (Sm-D2) 1.0E-46
blast CAE75361 Hypothetical protein CBG23345 [Caenorhabditis briggsae] 6.0E-45
Protein Domains
Database ID Description E-Value
Pfam IPR001163 EMBL-EBI Small nuclear ribonucleoprotein (Sm protein) 1.5E-18
Pfam IPR001163 EMBL-EBI Small nuclear ribonucleoprotein (Sm protein) 1.5E-18
Sequence
Target Sequence 
>C. ELEGANS:172931_X_AT
ccaaaccccgttcagagatgactgctgaagaactcgctgcaaaggaggacgaggaattca
atgtcggaccactctccatcctcaccaactcagtcaaaaacaatcatcaagttctcatca
attgcagaaacaacaagaagcttctcggaagagttaaggcttttgacagacattgcaaca
tggtcctcgaaaatgtgaaggaaatgtggactgaagtgccaaagactggaaagggaaaga
agaaggcaaagtctgtcgccaaagatcgtttcatctcaaaaatgttcctccgcgg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CCAAACCCCGTTCAGAGATGACTGC 248 269 26 Antisense
AGATGACTGCTGAAGAACTCGCTGC 689 67 41 Antisense
GAACTCGCTGCAAAGGAGGACGAGG 218 347 55 Antisense
GGAATTCAATGTCGGACCACTCTCC 270 533 78 Antisense
CATCCTCACCAACTCAGTCAAAAAC 499 209 102 Antisense
CAAGTTCTCATCAATTGCAGAAACA 473 183 133 Antisense
GAAGCTTCTCGGAAGAGTTAAGGCT 635 341 162 Antisense
GTTAAGGCTTTTGACAGACATTGCA 428 439 178 Antisense
CAGACATTGCAACATGGTCCTCGAA 139 205 192 Antisense
GTCTGTCGCCAAAGATCGTTTCATC 612 471 276 Antisense
TCATCTCAAAAATGTTCCTCCGCGG 217 619 296 Antisense
Sequence Source Affymetrix Proprietary Database