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[193709_at] RNA recognition motif. (aka RRM, RBD, or RNP domain)

Description M18.7 /REP_DB=WormBase Gene ID /WP=CE06198 /TR=Q21559 /GB=CAA92829.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=RNA recognition motif. (aka RRM, RBD, or RNP domain)
Cluster 6grp_highest_10_10 > 84      6grp_high1_10_10 > 57      4grp_highest_8_8 > 16      4grp_high_8_8 > 52      6grp_highest_nonorm > 87      6grp_total > 58      4grp_total > 60      6grp_highest_sub > Cu      6grp_cgc > 27      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 855
1 2 3 4 range
A 1268.4
(1.2)
P 		1406.8
(3)
P 		1255.2
(1)
P 		943.8
(-3)
P 		463
B 1308
(1.2)
P 		1435.1
(2.9)
P 		1444.8
(3)
P 		981.3
(-3)
P 		464
C 1364.3
(1.4)
P 		1590.6
(3)
P 		1378.8
(1.5)
P 		735.2
(-3)
P 		855
avr 1313.6
(1.3) 		1477.5
(3) 		1359.6
(1.8) 		886.8
(-3) 		591

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 665
1 2 3 4 5 6 range
A 1082.9
(-0.7)
P 		1378
(1.9)
P 		830.8
(-3)
P 		1033.3
(-1.2)
P 		884.9
(-2.5)
P 		1495.6
(3)
P 		665
B 1094.3
(1)
P 		884.7
(-2.6)
P 		1009.9
(-0.5)
P 		860.7
(-3)
P 		913.9
(-2.1)
P 		1214.3
(3)
P 		354
C 1390.3
(2.9)
P 		907.7
(-3)
P 		1107.5
(-0.6)
P 		924.9
(-2.8)
P 		1041.4
(-1.4)
P 		1398.3
(3)
P 		491
avr 1189.2
(0.5) 		1056.8
(-1.4) 		982.7
(-2.4) 		939.6
(-3) 		946.7
(-2.9) 		1369.4
(3) 		430
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 357
1 2 3 4 range
A 461.8
(3)
P 		305.4
(0.1)
P 		328.1
(0.5)
P 		138.2
(-3)
P 		324
B 417.1
(3)
P 		354.4
(1.2)
P 		334.8
(0.6)
P 		209.1
(-3)
P 		208
C 451.6
(2.5)
P 		457.3
(2.6)
P 		480.5
(3)
P 		124
(-3)
P 		357
avr 443.5
(3) 		372.4
(1.5) 		381.1
(1.7) 		157.1
(-3) 		286

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 334
1 2 3 4 5 6 range
A 199.6
(-2.6)
P 		490.1
(3)
P 		180.9
(-3)
P 		262.1
(-1.4)
P 		267
(-1.3)
P 		364.1
(0.6)
P 		309
B 380.7
(1.1)
P 		294.5
(-1.2)
P 		245.2
(-2.5)
P 		228
(-3)
P 		371.3
(0.8)
P 		452.8
(3)
P 		225
C 515.3
(3)
P 		277
(-1.3)
P 		281.9
(-1.3)
P 		186
(-3)
P 		337
(-0.2)
P 		468.1
(2.1)
P 		329
avr 365.2
(1.1) 		353.9
(0.8) 		236
(-2.7) 		225.4
(-3) 		325.1
(-0.1) 		428.3
(3) 		203
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193709_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.8585
Sequence Type Exemplar sequence
Representative Public ID M18.7 NCBI
Target Description M18.7 /REP_DB=WormBase Gene ID /WP=CE06198 /TR=Q21559 /GB=CAA92829.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=RNA recognition motif. (aka RRM, RBD, or RNP domain)
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_069900(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069900 NCBI Caenorhabditis elegans Ref/ALY RNA export adaptor family member (aly-3) (aly-3) mRNA, complete cds. 11/11 None
GENEFINDER00000023295 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:12121331:12124568:1 11/11 None
M18.7.2 ENSEMBL cdna:known chromosome:CEL140:IV:12123124:12124778:1 gene:M18.7 11/11 None
M18.7.1 ENSEMBL cdna:known chromosome:CEL140:IV:12123258:12124778:1 gene:M18.7 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000023286 5/11 Cross Hyb Matching Probes None
SNAP00000023287 5/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIV:12123288-12124574(+) 100.0 100.0
Public Domain and Genome References
Gene Title RNA recognition motif. (aka RRM, RBD, or RNP domain)
Gene Symbol aly-3
Ensembl M18.7
Entrez Gene 178157 Entrez gene
SwissProt Q21559 EMBL-EBI
WormBase CE06198 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAA92828 Hypothetical protein M18.6 [Caenorhabditis elegans] ref|NP_502300.2| M18.6 [Caenorhabditis elegans] 0.0
blast CAE62186 Hypothetical protein CBG06233 [Caenorhabditis briggsae] 1.0E-144
blast CAA92829 Hypothetical protein M18.7 [Caenorhabditis elegans] ref|NP_502301.1| Ref/ALY RNA export adaptor family member (aly-3) [Caenorhabditis elegans] 3.0E-99
blast CAA92829 Hypothetical protein M18.7 [Caenorhabditis elegans] ref|NP_502301.1| Ref/ALY RNA export adaptor family member (aly-3) [Caenorhabditis elegans] 1.0E-98
blast CAE62187 Hypothetical protein CBG06234 [Caenorhabditis briggsae] 6.0E-83
blast CAB05180 Hypothetical protein F23B2.6 [Caenorhabditis elegans] ref|NP_501594.1| Ref/ALY RNA export adaptor family member (aly-2) [Caenorhabditis elegans] 7.0E-38
Protein Domains
Database ID Description E-Value
Pfam IPR003111 EMBL-EBI Peptidase S16, lon N-terminal 1.8E-92
Sequence
Target Sequence 
>C. ELEGANS:193709_AT
aaatacgagacccactggacttccacgccgctccggcggaagtggtggatggaaagactt
ggacgcggttcagaatcatggaatttcaagcagaggaaatgatagcaaggttattagagt
aaatatctctaatcttgccccaacagtcatttcaagcgatttggaggaactcttcggcga
ctacagactcagctcagtttcggtcaacttcaacgagcatggtgattcattgggtactgg
tgacatttcgctcaccaaacgtgatgctgagagacttgttcagaagtttagcggtgtcgc
tctagatggaaagatcatgaaattcgccgtcattgattcgagcaacatggctgggagagt
cgattttggaaacagatctcgtagttcaccgggaagatcatctcgtggattccaatcggg
tcctcgcagaaacaatggcaaaccagaagatttcctccgcgacggagtgcacgccggtga
catcaagagaggcggagctggtcgaggtggattccgcaagggaggccgtggtggagctcg
tgatgcaaaaccaaagaagaccgaagctgaactcgacgcgg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AAATACGAGACCCACTGGACTTCCA 644 113 120 Antisense
GACTTGGACGCGGTTCAGAATCATG 72 371 175 Antisense
TAATCTTGCCCCAACAGTCATTTCA 660 635 249 Antisense
GACTACAGACTCAGCTCAGTTTCGG 80 373 298 Antisense
ATTGGGTACTGGTGACATTTCGCTC 551 1 348 Antisense
AATTCGCCGTCATTGATTCGAGCAA 492 177 440 Antisense
ACAGATCTCGTAGTTCACCGGGAAG 463 107 491 Antisense
GAAGATCATCTCGTGGATTCCAATC 683 337 512 Antisense
TCCAATCGGGTCCTCGCAGAAACAA 710 523 530 Antisense
CGGAGTGCACGCCGGTGACATCAAG 297 243 582 Antisense
AAGACCGAAGCTGAACTCGACGCGG 325 151 676 Antisense
Sequence Source Affymetrix Proprietary Database