[Home] | [Total List]

[192875_s_at] U1 small nuclear ribonucleoprotein C

Description F08B4.7 /REP_DB=WormBase Gene ID /WP=CE09232 /TR=P90815 /GB=AAB37732.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=U1 small nuclear ribonucleoprotein C
Cluster 6grp_highest_10_10 > 91      6grp_high1_10_10 > 29      4grp_highest_8_8 > 11      4grp_high_8_8 > 47      6grp_highest_nonorm > 74      6grp_total > 39      4grp_total > 48      6grp_high1_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 330
1 2 3 4 range
A 509.8
(-3)
P 		692.9
(1.1)
P 		781
(3)
P 		600
(-1)
P 		271
B 505.4
(-3)
P 		689.1
(1)
P 		777.7
(3)
P 		619.5
(-0.5)
P 		272
C 574.1
(-3)
P 		624.6
(-1.8)
P 		835.4
(3)
P 		586.5
(-2.7)
P 		261
avr 529.8
(-3) 		668.9
(0.1) 		798
(3) 		602
(-1.4) 		268

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 290
1 2 3 4 5 6 range
A 730.6
(0.2)
P 		672.8
(-1.8)
P 		673.9
(-1.8)
P 		805.5
(2.7)
P 		638.5
(-3)
P 		813.8
(3)
P 		175
B 729.6
(-1.4)
P 		861.6
(2.3)
P 		745.3
(-1)
P 		675.5
(-3)
P 		884.9
(3)
P 		827
(1.3)
P 		209
C 928.2
(3)
P 		844.4
(1.1)
P 		686.7
(-2.4)
P 		660.4
(-3)
P 		812.1
(0.4)
P 		668.3
(-2.8)
P 		268
avr 796.1
(3) 		792.9
(2.8) 		702
(-3) 		713.8
(-2.2) 		778.5
(1.9) 		769.7
(1.3) 		94
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 203
1 2 3 4 range
A 185.6
(2)
P 		150.4
(0.2)
P 		204.2
(3)
P 		87.8
(-3)
P 		116
B 161.2
(0.6)
P 		170.2
(1.8)
P 		180.2
(3)
P 		132
(-3)
P 		48
C 190
(-0.2)
P 		179.6
(-0.5)
P 		291.2
(3)
P 		98.9
(-3)
P 		192
avr 178.9
(0.7) 		166.7
(0.1) 		225.2
(3) 		106.2
(-3) 		119

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 227
1 2 3 4 5 6 range
A 134.7
(-3)
P 		239.3
(3)
P 		146.8
(-2.3)
P 		204.3
(1)
P 		192.7
(0.3)
P 		198.1
(0.6)
P 		105
B 253.9
(-0.5)
P 		286.8
(0.6)
P 		181
(-2.9)
P 		178.9
(-3)
P 		359.5
(3)
P 		308.4
(1.3)
P 		181
C 344
(3)
P 		257.7
(0.5)
P 		174.8
(-1.8)
P 		132.8
(-3)
P 		262.8
(0.7)
P 		223.7
(-0.4)
P 		211
avr 244.2
(1.4) 		261.3
(2.4) 		167.5
(-3) 		172
(-2.7) 		271.7
(3) 		243.4
(1.4) 		104
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 192875_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.9803
Sequence Type Exemplar sequence
Representative Public ID F08B4.7 NCBI
Target Description F08B4.7 /REP_DB=WormBase Gene ID /WP=CE09232 /TR=P90815 /GB=AAB37732.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=U1 small nuclear ribonucleoprotein C
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_069089(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069089 NCBI Caenorhabditis elegans F08B4.7 (F08B4.7) mRNA, complete cds. 11/11 None
SNAP00000041286 ENSEMBL cdna:SNAP chromosome:CEL140:IV:8682554:8687791:-1 11/11 None
GENEFINDER00000041290 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:8686957:8687791:-1 11/11 None
F08B4.7.1 ENSEMBL cdna:known chromosome:CEL140:IV:8686698:8687948:-1 gene:F08B4.7 11/11 None
F08B4.7.3 ENSEMBL cdna:known chromosome:CEL140:IV:8686751:8687797:-1 gene:F08B4.7 11/11 None
F08B4.7.2 ENSEMBL cdna:known chromosome:CEL140:IV:8686751:8687792:-1 gene:F08B4.7 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:8686962-8687797(-) 100.0 100.0
Public Domain and Genome References
Gene Title U1 small nuclear ribonucleoprotein C
Ensembl F08B4.7
Entrez Gene 177674 Entrez gene
SwissProt P90815 EMBL-EBI
WormBase CE09232 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:255431_AT proline-rich family protein at
CANINE:1601007_X_AT similar to U1 small nuclear ribonucleoprotein C (U1 snRNP protein C) (U1C protein) (U1-C) cfa
CANINE:1586113_X_AT similar to U1 small nuclear ribonucleoprotein C (U1 snRNP protein C) (U1C protein) (U1-C) cfa
CANINE_2:CFA.14421.1.S1_AT similar to U1 small nuclear ribonucleoprotein C (U1 snRNP protein C) (U1C protein) (U1-C) cfa
CANINE_2:CFA.4615.1.A1_AT similar to U1 small nuclear ribonucleoprotein C (U1 snRNP protein C) (U1C protein) (U1-C) cfa
CANINE_2:CFAAFFX.20593.1.S1_AT similar to U1 small nuclear ribonucleoprotein C (U1 snRNP protein C) (U1C protein) (U1-C) cfa
CANINE_2:CFAAFFX.660.1.S1_S_AT similar to U1 small nuclear ribonucleoprotein C (U1 snRNP protein C) (U1C protein) (U1-C) cfa
DROSOPHILA_2:1639046_AT dm
DROSGENOME1:150171_AT dm
CHICKEN:GGAAFFX.25617.1.S1_AT similar to U1 snRNP-specific protein C gga
HG-FOCUS:201342_AT small nuclear ribonucleoprotein polypeptide C hs
HG-U133A:201342_AT small nuclear ribonucleoprotein polypeptide C hs
HG-U133_PLUS_2:201342_AT small nuclear ribonucleoprotein polypeptide C hs
HG-U133A_2:201342_AT small nuclear ribonucleoprotein polypeptide C hs
HUGENEFL:X12517_AT small nuclear ribonucleoprotein polypeptide C hs
U133_X3P:G4507126_3P_AT small nuclear ribonucleoprotein polypeptide C hs
HG-U95AV2:38675_AT small nuclear ribonucleoprotein polypeptide C hs
MU11KSUBA:U70315_S_AT similar to U1 snRNP-specific protein C mm
MG-U74AV2:94313_AT similar to U1 snRNP-specific protein C mm
RG-U34C:RC_AI169361_AT U1 small nuclear ribonucleoprotein 1C (predicted) rn
RG-U34C:RC_AI231355_AT U1 small nuclear ribonucleoprotein 1C (predicted) rn
RAE230A:1371486_AT U1 small nuclear ribonucleoprotein 1C (predicted) rn
RAT230_2:1371486_AT U1 small nuclear ribonucleoprotein 1C (predicted) rn
Gene Ontology
GO Cellular Component (view graph)
ID Description Evidence Links
5634 nucleus inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3676 nucleic acid binding inferred from electronic annotation QuickGO AmiGO
8270 zinc ion binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAB37729 Hypothetical protein F08B4.5 [Caenorhabditis elegans] ref|NP_501489.2| F08B4.5 [Caenorhabditis elegans] sp|Q19196|DPOE2_CAEEL Putative DNA polymerase epsilon subunit B (DNA polymerase II subunit B) 0.0
blast T29484 hypothetical protein F08B4.5 - Caenorhabditis elegans 0.0
blast CAE72481 Hypothetical protein CBG19657 [Caenorhabditis briggsae] 0.0
blast AAB37732 Hypothetical protein F08B4.7 [Caenorhabditis elegans] ref|NP_501490.1| F08B4.7 [Caenorhabditis elegans] 1.0E-37
blast CAE72480 Hypothetical protein CBG19656 [Caenorhabditis briggsae] 5.0E-37
Protein Domains
Database ID Description E-Value
Pfam IPR003604 EMBL-EBI Zn-finger, U1-like 2.0E-28
Pfam IPR007185 EMBL-EBI DNA polymerase epsilon subunit B 1.3E-84
Sequence
Target Sequence 
>C. ELEGANS:192875_S_AT
gattactgcgacacatttttgacacatgactcgccatcagtgagaaaaacgcacaatgga
ggaagaaaacacaaggataacgtcagaatgttttatcagaaatggatggaagaccaagca
cagaagcttgttgatcaaactgcacgggcatttgccacaaatagaatgcaaggagccgta
ccacgtacaacaatgggaatggcccctgtaccaccagtgggtcatcatccgatgatggga
ggtcccccaggaatgccaatgatggctcctcgacc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GATTACTGCGACACATTTTTGACAC 90 431 31 Antisense
GACACATGACTCGCCATCAGTGAGA 146 367 51 Antisense
GGATGGAAGACCAAGCACAGAAGCT 599 513 134 Antisense
GAAGCTTGTTGATCAAACTGCACGG 498 341 153 Antisense
TCAAACTGCACGGGCATTTGCCACA 228 629 165 Antisense
ATGCAAGGAGCCGTACCACGTACAA 57 43 196 Antisense
GAGCCGTACCACGTACAACAATGGG 697 385 203 Antisense
ACAATGGGAATGGCCCCTGTACCAC 690 111 220 Antisense
TGTACCACCAGTGGGTCATCATCCG 42 561 237 Antisense
TCATCCGATGATGGGAGGTCCCCCA 271 619 255 Antisense
GAATGCCAATGATGGCTCCTCGACC 247 331 281 Antisense
Sequence Source Affymetrix Proprietary Database