[Home] | [Total List]

[175143_s_at] RNA recognition motif. (aka RRM, RBD, or RNP domain)

Description AV202487 /REP_DB=TREMBL Accession /GB=AV202487 /CHR=1 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk551b3 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 33      6grp_high1_10_10 > 23      4grp_highest_8_8 > 24      4grp_high_8_8 > 51      6grp_highest_nonorm > 16      6grp_total > 12      4grp_total > 60      6grp_highest_sub > 02      6grp_high1_sub > 02      6grp_total_sub > Hat      6grp_rule_based > S2      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 6868
1 2 3 4 range
A 15475
(1.5)
P 		17163.8
(3)
P 		16072.9
(2)
P 		10311.4
(-3)
P 		6852
B 15968.4
(2.9)
P 		15870.1
(2.8)
P 		16050.1
(3)
P 		10832.2
(-3)
P 		5218
C 14557
(3)
P 		13184.4
(1.1)
P 		14234
(2.5)
P 		10295.7
(-3)
P 		4261
avr 15333.5
(2.9) 		15406.1
(2.9) 		15452.3
(3) 		10479.8
(-3) 		4973

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 5537
1 2 3 4 5 6 range
A 7522.2
(1.2)
P 		8749.4
(3)
P 		7033.4
(0.5)
P 		8675.9
(2.9)
P 		5060
(-2.4)
P 		4635.6
(-3)
P 		4114
B 8710.3
(1.9)
P 		9688.7
(3)
P 		9432.8
(2.7)
P 		6874.6
(-0)
P 		6269.6
(-0.7)
P 		4151.6
(-3)
P 		5537
C 7409.7
(0.8)
P 		9065.3
(3)
P 		6299.1
(-0.7)
P 		5081.3
(-2.3)
P 		6211
(-0.8)
P 		4532.2
(-3)
P 		4533
avr 7880.7
(1.4) 		9167.8
(3) 		7588.4
(1) 		6877.3
(0.1) 		5846.9
(-1.2) 		4439.8
(-3) 		4728
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 4125
1 2 3 4 range
A 5634.4
(3)
P 		3725.8
(0.2)
P 		4201.8
(0.9)
P 		1509.4
(-3)
P 		4125
B 5092.2
(3)
P 		3919.5
(0.5)
P 		3719.2
(0)
P 		2308.3
(-3)
P 		2784
C 4818.8
(2.7)
P 		3790.6
(0.8)
P 		4961
(3)
P 		1736
(-3)
P 		3225
avr 5181.8
(3) 		3812
(0.5) 		4294
(1.4) 		1851.2
(-3) 		3331

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2203
1 2 3 4 5 6 range
A 1386.7
(-2.2)
P 		3111.7
(3)
P 		1531.7
(-1.8)
P 		2200.4
(0.2)
P 		1526.9
(-1.8)
P 		1128.6
(-3)
P 		1983
B 3030.7
(2.3)
P 		3225
(3)
P 		2290.6
(-0.3)
P 		1820.8
(-2)
P 		2547.3
(0.6)
P 		1548.1
(-3)
P 		1677
C 2746.5
(2.9)
P 		2766.1
(3)
P 		1603.2
(-1)
P 		1021.9
(-3)
P 		2009.8
(0.4)
P 		1517.2
(-1.3)
P 		1744
avr 2388
(0.6) 		3034.3
(3) 		1808.5
(-1.5) 		1681
(-2) 		2028
(-0.7) 		1398
(-3) 		1636
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 175143_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.20268
Sequence Type Exemplar sequence
Representative Public ID AV202487 NCBI
Target Description AV202487 /REP_DB=TREMBL Accession /GB=AV202487 /CHR=1 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk551b3 : 5prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_060628(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_060628 NCBI Caenorhabditis elegans R06C1.4 (R06C1.4) mRNA, complete cds. 11/11 None
SNAP00000025115 ENSEMBL cdna:SNAP chromosome:CEL140:I:11921804:11939757:1 11/11 None
GENEFINDER00000025122 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:11938929:11939757:1 11/11 None
R06C1.4.1 ENSEMBL cdna:known chromosome:CEL140:I:11938847:11939989:1 gene:R06C1.4 11/11 None
R06C1.4.2 ENSEMBL cdna:known chromosome:CEL140:I:11938876:11939989:1 gene:R06C1.4 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
chrI:11939383-11939742(+) 100.0 100.0
Public Domain and Genome References
Gene Title RNA recognition motif. (aka RRM, RBD, or RNP domain)
Ensembl R06C1.4
Entrez Gene 173076 Entrez gene
SwissProt O62337 EMBL-EBI
WormBase CE18119 Wormbase
Functional Annotations
Gene Ontology
GO Molecular Function (view graph)
ID Description Evidence Links
3676 nucleic acid binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB03222 Hypothetical protein R06C1.4 [Caenorhabditis elegans] ref|NP_493029.1| R06C1.4 [Caenorhabditis elegans] 2.0E-42
blast CAB03222 Hypothetical protein R06C1.4 [Caenorhabditis elegans] ref|NP_493029.1| R06C1.4 [Caenorhabditis elegans] 1.0E-36
blast CAE71709 Hypothetical protein CBG18686 [Caenorhabditis briggsae] 3.0E-35
blast CAE71709 Hypothetical protein CBG18686 [Caenorhabditis briggsae] 7.0E-30
Protein Domains
Database ID Description E-Value
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 1.2E-27
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 1.8E-24
Sequence
Target Sequence 
>C. ELEGANS:175143_S_AT
ggaaacgttccataccaaggaactgaggaggagatcggaaactacttcgccgccgtcgga
catgttaacaacgtcagaatcgtgtacgatcgtgaaaccggacgcccacgcggtttcgca
ttcgtcgagttctccgaggaagccggagctcaaagagccgtcgaacaacttaacggagtt
gccttcaatggacgcaaccttcgtgtcaactacgccaacaagt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGAAACGTTCCATACCAAGGAACTG 391 519 18 Antisense
GGAGATCGGAAACTACTTCGCCGCC 560 511 47 Antisense
TCGCCGCCGTCGGACATGTTAACAA 702 597 64 Antisense
CAACGTCAGAATCGTGTACGATCGT 290 187 86 Antisense
TGTACGATCGTGAAACCGGACGCCC 149 557 100 Antisense
GCATTCGTCGAGTTCTCCGAGGAAG 25 307 135 Antisense
GAGGAAGCCGGAGCTCAAAGAGCCG 413 401 153 Antisense
GAGCCGTCGAACAACTTAACGGAGT 647 385 172 Antisense
AACGGAGTTGCCTTCAATGGACGCA 290 133 189 Antisense
AATGGACGCAACCTTCGTGTCAACT 703 161 204 Antisense
CTTCGTGTCAACTACGCCAACAAGT 216 221 216 Antisense
Sequence Source Affymetrix Proprietary Database