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[193784_at] RNA recognition motif. (aka RRM, RBD, or RNP domain)

Description K08F4.2 /REP_DB=WormBase Gene ID /WP=CE06150 /TR=Q21351 /GB=CAA93082.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=RNA recognition motif. (aka RRM, RBD, or RNP domain)
Cluster 6grp_highest_10_10 > 82      6grp_high1_10_10 > 38      4grp_highest_8_8 > 25      4grp_high_8_8 > 60      6grp_highest_nonorm > 86      6grp_total > 28      4grp_total > 60      6grp_highest_sub > Cu      6grp_high1_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 593
1 2 3 4 range
A 1626.9
(3)
P 		1424.1
(-0.3)
P 		1586.5
(2.3)
P 		1260.4
(-3)
P 		367
B 1680.2
(2.3)
P 		1621.5
(0)
P 		1699.4
(3)
P 		1542
(-3)
P 		157
C 1513.5
(0)
P 		1806.2
(3)
P 		1744.5
(2.4)
P 		1213.7
(-3)
P 		593
avr 1606.9
(1.8) 		1617.3
(1.9) 		1676.8
(3) 		1338.7
(-3) 		338

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 776
1 2 3 4 5 6 range
A 991.9
(0.6)
P 		1108.8
(2)
P 		689.5
(-3)
P 		1052.2
(1.3)
P 		868.2
(-0.9)
P 		1194.4
(3)
P 		505
B 1307.9
(3)
P 		1005.4
(-0.1)
P 		714.8
(-3)
P 		984
(-0.3)
P 		881.3
(-1.3)
P 		869.3
(-1.4)
P 		593
C 1343
(3)
P 		871.2
(-0.6)
P 		1152.9
(1.5)
P 		566.9
(-3)
P 		1077.6
(0.9)
P 		1002
(0.4)
P 		776
avr 1214.3
(3) 		995.1
(-0.6) 		852.4
(-3) 		867.7
(-2.7) 		942.4
(-1.5) 		1021.9
(-0.2) 		362
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 424
1 2 3 4 range
A 592.4
(3)
P 		309.1
(-1.2)
P 		414.7
(0.4)
P 		184.5
(-3)
P 		408
B 535.8
(3)
P 		400.5
(-0.9)
P 		393.8
(-1.1)
P 		328.6
(-3)
P 		207
C 501
(1.4)
P 		519.3
(1.7)
P 		608
(3)
P 		204.6
(-3)
P 		403
avr 543.1
(3) 		409.6
(0.4) 		472.2
(1.6) 		239.2
(-3) 		304

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 384
1 2 3 4 5 6 range
A 182.9
(-2.2)
P 		394.4
(3)
P 		150.2
(-3)
P 		266.9
(-0.1)
P 		262
(-0.3)
P 		290.8
(0.5)
P 		244
B 455.1
(3)
P 		334.6
(0.4)
P 		173.6
(-3)
P 		260.6
(-1.1)
P 		358
(0.9)
P 		324.2
(0.2)
P 		282
C 497.8
(3)
P 		265.8
(-0.6)
P 		293.4
(-0.2)
P 		114
(-3)
P 		348.7
(0.7)
P 		335.4
(0.5)
P 		384
avr 378.6
(3) 		331.6
(1.4) 		205.7
(-3) 		213.8
(-2.7) 		322.9
(1.1) 		316.8
(0.9) 		173
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193784_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.8816
Sequence Type Exemplar sequence
Representative Public ID K08F4.2 NCBI
Target Description K08F4.2 /REP_DB=WormBase Gene ID /WP=CE06150 /TR=Q21351 /GB=CAA93082.1 /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_069441(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069441 NCBI Caenorhabditis elegans K08F4.2 (K08F4.2) mRNA, complete cds. 11/11 None
SNAP00000005855 ENSEMBL cdna:SNAP chromosome:CEL140:IV:10127207:10128883:-1 11/11 None
GENEFINDER00000005872 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:10127207:10128916:-1 11/11 None
K08F4.2.1 ENSEMBL cdna:known chromosome:CEL140:IV:10126730:10128927:-1 gene:K08F4.2 11/11 None
K08F4.2.2 ENSEMBL cdna:known chromosome:CEL140:IV:10126733:10128929:-1 gene:K08F4.2 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:10127212-10129202(-) 100.0 100.0
Public Domain and Genome References
Gene Title RNA recognition motif. (aka RRM, RBD, or RNP domain)
Ensembl K08F4.2
Entrez Gene 177880 Entrez gene
SwissProt Q21351 EMBL-EBI
WormBase CE37535 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6606 protein import into nucleus inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5622 intracellular inferred from electronic annotation QuickGO AmiGO
5634 nucleus inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
8565 protein transporter activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA93082 Hypothetical protein K08F4.2 [Caenorhabditis elegans] ref|NP_501842.2| K08F4.2 [Caenorhabditis elegans] 1.0E-179
blast CAA93082 Hypothetical protein K08F4.2 [Caenorhabditis elegans] ref|NP_501842.2| K08F4.2 [Caenorhabditis elegans] 1.0E-173
blast CAE59930 Hypothetical protein CBG03416 [Caenorhabditis briggsae] 1.0E-121
blast CAE59930 Hypothetical protein CBG03416 [Caenorhabditis briggsae] 1.0E-115
Protein Domains
Database ID Description E-Value
Pfam IPR002075 EMBL-EBI Nuclear transport factor 2 (NTF2) 4.9E-28
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 2.9E-5
Pfam IPR002075 EMBL-EBI Nuclear transport factor 2 (NTF2) 4.9E-28
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 2.9E-5
Sequence
Target Sequence 
>C. ELEGANS:193784_AT
cacaaatgcaccacatgcagccttccatgcatcagcaacaacaaggatcgcatgctcctc
tttatcagcaacagagacagtcgcacccagctaatgaattgcgccaagctcaggaaagtt
cagatgccaacctaaatgagcgtaagatctatttgggaggaatcactcgagagattgtcc
ccagcaacacagctcaggctgaatcggaaatcaagcaggtgttctacaaatatggagaaa
tcgaggaggttcgcatgccgcgcaaggttcttgacagtccgaacgacacatcgaaacatg
cctttgcatttattaccatgcgtaacaaggccggagtaaaagccattttcgaagcggcta
caaaggatgagcaaggcgtgtggaagcttccactcaaactggatgcattcggatttgacg
gacatgctcaaattagtgagcaacgtgatcaaccacaaggcggcggattccgaggaggac
gtggaggtttccaaccacgcggtggacaattcttccgccgtggcggttc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CACAAATGCACCACATGCAGCCTTC 80 195 1040 Antisense
AACAAGGATCGCATGCTCCTCTTTA 374 135 1079 Antisense
GAATCACTCGAGAGATTGTCCCCAG 594 327 1199 Antisense
TCCCCAGCAACACAGCTCAGGCTGA 323 597 1217 Antisense
GAAATCGAGGAGGTTCGCATGCCGC 31 363 1276 Antisense
TGCCGCGCAAGGTTCTTGACAGTCC 592 583 1295 Antisense
GACACATCGAAACATGCCTTTGCAT 44 367 1324 Antisense
GGAAGCTTCCACTCAAACTGGATGC 231 531 1421 Antisense
TGATCAACCACAAGGCGGCGGATTC 700 563 1485 Antisense
GGTTTCCAACCACGCGGTGGACAAT 246 505 1525 Antisense
GACAATTCTTCCGCCGTGGCGGTTC 6 353 1544 Antisense
Sequence Source Affymetrix Proprietary Database