[Home] | [Total List]

[171942_x_at]

Description AV182277_rc /REP_DB=TREMBL Accession /GB=AV182277 /FEA=Transcript Cluster /DEF=Caenorhabditis elegans cDNA clone:yk635e9 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 97      6grp_high1_10_10 > 79      6grp_highest_nonorm > 92      6grp_total > 79      4grp_total > 63      6grp_highest_sub > Cu      6grp_cgc > 59      6grp_high1_sub > Cu      6grp_cgc_sub > Da      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 148
1 2 3 4 range
A 229.5
(-3)
P 		247.8
(-1.6)
P 		239.7
(-2.2)
P 		310.7
(3)
A 		81
B 260
(2.8)
P 		188
(-3)
P 		262.4
(3)
P 		192.2
(-2.7)
A 		74
C 199.1
(0.6)
P 		204.8
(1.2)
P 		223.4
(3)
P 		162.3
(-3)
A 		61
avr 229.5
(0.4) 		213.5
(-3) 		241.8
(3) 		221.7
(-1.3) 		28

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 296
1 2 3 4 5 6 range
A 282.3
(-0.6)
P 		210.4
(-3)
P 		235.2
(-2.2)
P 		253.6
(-1.6)
P 		383.3
(2.7)
P 		391.5
(3)
P 		181
B 357.9
(0.6)
P 		277.6
(-1)
P 		387.4
(1.2)
P 		180.7
(-3)
P 		411.4
(1.7)
P 		476.7
(3)
P 		296
C 285
(0.5)
P 		291.6
(0.8)
P 		190.7
(-3)
P 		218.8
(-1.9)
P 		264.5
(-0.2)
P 		350.8
(3)
P 		160
avr 308.4
(-0.1) 		259.9
(-1.7) 		271.1
(-1.3) 		217.7
(-3) 		353.1
(1.3) 		406.3
(3) 		189
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 56
1 2 3 4 range
A 83.6
(3)
P 		53.8
(-1.7)
P 		62.7
(-0.3)
P 		45.5
(-3)
A 		38
B 82.9
(3)
P 		46.4
(-2.2)
P 		60.8
(-0.2)
P 		41
(-3)
A 		42
C 65.9
(1.6)
P 		58.9
(0.7)
P 		77.9
(3)
P 		27.4
(-3)
A 		51
avr 77.5
(3) 		53
(-0.7) 		67.1
(1.4) 		38
(-3) 		40

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 134
1 2 3 4 5 6 range
A 52
(-2.9)
P 		74.8
(-0.8)
P 		51.2
(-3)
P 		64.3
(-1.8)
P 		115.7
(3)
P 		95.3
(1.1)
P 		65
B 124.5
(0.5)
P 		92.4
(-0.9)
P 		94.1
(-0.9)
P 		47.9
(-3)
P 		167.2
(2.5)
P 		177.8
(3)
P 		130
C 105.6
(2)
P 		89
(0.7)
P 		48.5
(-2.6)
P 		44
(-3)
P 		85.6
(0.4)
P 		117.4
(3)
P 		73
avr 94
(0.2) 		85.4
(-0.4) 		64.6
(-2) 		52.1
(-3) 		122.8
(2.4) 		130.2
(3) 		78
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 171942_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.27889
Sequence Type Exemplar sequence
Representative Public ID AV182277 NCBI
Target Description AV182277_rc /REP_DB=TREMBL Accession /GB=AV182277 /FEA=Transcript Cluster /DEF=Caenorhabditis elegans cDNA clone:yk635e9 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Transcript 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_058776(9), NM_170843(9)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_058776 NCBI Caenorhabditis elegans RNP (RRM RNA binding domain) containing family member (rnp-6) (rnp-6) mRNA, complete cds. 9/11 A 
NM_170843 NCBI Caenorhabditis elegans RNP (RRM RNA binding domain) containing family member (rnp-6) (rnp-6) mRNA, complete cds. 9/11 A 
Y47G6A.20a ENSEMBL cdna:known chromosome:CEL140:I:3543515:3546896:-1 gene:Y47G6A.20 9/11 A 
Y47G6A.20c ENSEMBL cdna:known chromosome:CEL140:I:3543559:3546906:-1 gene:Y47G6A.20 9/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_058775 7/11 Cross Hyb Matching Probes A 
GENEFINDER00000034097 7/11 Cross Hyb Matching Probes None
SNAP00000033987 7/11 Cross Hyb Matching Probes None
Y47G6A.20b 7/11 Cross Hyb Matching Probes A 
Splice Variants
Entrez Total Refseq Isoforms Total Detected By This Probeset Refseq Probesets
171922 3 2 NM_058775 190513_at (11)
NM_058776 171942_x_at (9)
NM_170843 171942_x_at (9)
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrI:3543554-3544503(-) 69.67 69.67
Public Domain and Genome References
Ensembl Y47G6A.20
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast NP_740829 RNP (RRM RNA binding domain) containing family member (rnp-6) [Caenorhabditis elegans] gb|AAM81102.1| Rnp (rrm rna binding domain) containing protein 6, isoform c [Caenorhabditis elegans] 0.0
blast NP_491177 RNP (RRM RNA binding domain) containing family member (rnp-6) [Caenorhabditis elegans] gb|AAF60676.1| Rnp (rrm rna binding domain) containing protein 6, isoform a [Caenorhabditis elegans] 1.0E-166
blast NP_491176 RNP (RRM RNA binding domain) containing family member (rnp-6) [Caenorhabditis elegans] gb|AAF60666.1| Rnp (rrm rna binding domain) containing protein 6, isoform b [Caenorhabditis elegans] 1.0E-159
blast CAE68956 Hypothetical protein CBG14936 [Caenorhabditis briggsae] 1.0E-148
blast NP_491176 RNP (RRM RNA binding domain) containing family member (rnp-6) [Caenorhabditis elegans] gb|AAF60666.1| Rnp (rrm rna binding domain) containing protein 6, isoform b [Caenorhabditis elegans] 1.0E-143
blast NP_491177 RNP (RRM RNA binding domain) containing family member (rnp-6) [Caenorhabditis elegans] gb|AAF60676.1| Rnp (rrm rna binding domain) containing protein 6, isoform a [Caenorhabditis elegans] 1.0E-143
Protein Domains
Database ID Description E-Value
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 1.5E-24
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 2.5E-14
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 4.2E-12
Sequence
Target Sequence 
>C. ELEGANS:171942_X_AT
tcgtggatttggatacctcgaattcaataatttgacgtcgcaaagtgaggctatcgctgg
aatgaatatgttcgatttgggaggacaatatttgagagtcggcaaatgtgtagctccacc
ggatgctctcacccatcttccaccggcatccgtcagtgcaattccagccagngtatcanc
tnngtgtncacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncggttcctcac
cggtaggtgcaacaaacctgttctcta

BLASTn GenBank NR
Note: "n"'s represent regions that are not probed by the probe sequences.
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCGTGGATTTGGATACCTCGAATTC 364 593 15 Antisense
GGATTTGGATACCTCGAATTCAATA 82 509 19 Antisense
CGAATTCAATAATTTGACGTCGCAA 327 253 33 Antisense
GACGTCGCAAAGTGAGGCTATCGCT 334 377 48 Antisense
GAGGCTATCGCTGGAATGAATATGT 505 405 61 Antisense
GAATATGTTCGATTTGGGAGGACAA 263 323 78 Antisense
GGGAGGACAATATTTGAGAGTCGGC 451 495 93 Antisense
GAGTCGGCAAATGTGTAGCTCCACC 35 401 110 Antisense
CAAATGTGTAGCTCCACCGGATGCT 384 191 117 Antisense
CGGTTCCTCACCGGTAGGTGCAACA 203 243 244 Antisense
GTAGGTGCAACAAACCTGTTCTCTA 200 457 257 Antisense
Sequence Source Affymetrix Proprietary Database