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[193798_s_at] RNA recognition motif. (aka RRM, RBD, or RNP domain)

Description W09D10.1 /REP_DB=WormBase Gene ID /WP=CE16562 /TR=O18181 /GB=CAB07858.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=RNA recognition motif. (aka RRM, RBD, or RNP domain)
Cluster 6grp_highest_10_10 > 40      6grp_high1_10_10 > 03      4grp_highest_8_8 > 02      4grp_high_8_8 > 54      6grp_highest_nonorm > 40      6grp_total > 06      4grp_total > 50      6grp_highest_sub > De      6grp_high1_sub > De      6grp_total_sub > Decrease      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 353
1 2 3 4 range
A 452.2
(-3)
P 		736.9
(3)
P 		688.2
(2)
P 		485.8
(-2.3)
P 		285
B 612.3
(-2.9)
P 		684.3
(0.4)
P 		742.5
(3)
P 		610
(-3)
P 		133
C 622.9
(-0.8)
P 		805.3
(3)
P 		767.6
(2.2)
P 		514.7
(-3)
P 		291
avr 562.5
(-2.2) 		742.2
(3) 		732.8
(2.7) 		536.8
(-3) 		205

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 580
1 2 3 4 5 6 range
A 865.1
(3)
P 		591.4
(-0.5)
P 		690.3
(0.8)
P 		396.8
(-3)
P 		512.4
(-1.5)
P 		513.8
(-1.5)
P 		468
B 976.9
(3)
P 		778.1
(0.6)
P 		800.2
(0.9)
P 		619.5
(-1.3)
P 		504
(-2.6)
P 		473.4
(-3)
P 		504
C 865.7
(3)
P 		696.3
(0.8)
P 		631
(-0)
P 		498.5
(-1.7)
P 		527.5
(-1.4)
P 		400.3
(-3)
P 		465
avr 902.6
(3) 		688.6
(0.1) 		707.2
(0.3) 		504.9
(-2.4) 		514.6
(-2.3) 		462.5
(-3) 		440
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 196
1 2 3 4 range
A 164.6
(2.2)
P 		160
(1.9)
P 		179.9
(3)
P 		71.1
(-3)
P 		109
B 195.3
(3)
P 		169
(0.6)
P 		172.1
(0.9)
P 		130
(-3)
P 		65
C 206.2
(1)
P 		231.5
(1.8)
P 		267.5
(3)
P 		86.8
(-3)
P 		181
avr 188.7
(2) 		186.8
(1.9) 		206.5
(3) 		96
(-3) 		111

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 240
1 2 3 4 5 6 range
A 159.5
(0.2)
P 		210.3
(3)
P 		150.3
(-0.3)
P 		100.6
(-3)
P 		154.6
(-0)
P 		125.1
(-1.7)
P 		110
B 339.9
(3)
P 		259
(0.2)
P 		194.3
(-2)
P 		164.1
(-3)
P 		204.8
(-1.6)
P 		176.5
(-2.6)
P 		176
C 320.9
(3)
P 		212.5
(0.1)
P 		160.6
(-1.4)
P 		100.3
(-3)
P 		170.7
(-1.1)
P 		134
(-2.1)
P 		221
avr 273.4
(3) 		227.3
(1.2) 		168.4
(-1.2) 		121.7
(-3) 		176.7
(-0.8) 		145.2
(-2.1) 		152
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 193798_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7471
Sequence Type Exemplar sequence
Representative Public ID W09D10.1 NCBI
Target Description W09D10.1 /REP_DB=WormBase Gene ID /WP=CE16562 /TR=O18181 /GB=CAB07858.1 /SUBMIT=HINXTON /CHR=3 /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_066963(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066963 NCBI Caenorhabditis elegans W09D10.1 (W09D10.1) mRNA, complete cds. 11/11 None
SNAP00000014516 ENSEMBL cdna:SNAP chromosome:CEL140:III:10737128:10739655:-1 11/11 None
GENEFINDER00000014532 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:10737128:10739655:-1 11/11 None
W09D10.1.2 ENSEMBL cdna:known chromosome:CEL140:III:10736770:10739663:-1 gene:W09D10.1 11/11 None
W09D10.1.1 ENSEMBL cdna:known chromosome:CEL140:III:10736770:10739669:-1 gene:W09D10.1 11/11 None
W09D10.1.3 ENSEMBL cdna:known chromosome:CEL140:III:10736770:10739670:-1 gene:W09D10.1 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
chrIII:10737123-10739651(-) 100.0 100.0
Public Domain and Genome References
Gene Title RNA recognition motif. (aka RRM, RBD, or RNP domain)
Ensembl W09D10.1
Entrez Gene 176499 Entrez gene
SwissProt O18181 EMBL-EBI
WormBase CE16562 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CHICKEN:GGAAFFX.10174.1.S1_S_AT similar to stromal membrane-associated protein SMAP1A gga
HG-U133_PLUS_2:218137_S_AT stromal membrane-associated protein 1 hs
HG-U133A:218137_S_AT stromal membrane-associated protein 1 hs
HG-U133A_2:218137_S_AT stromal membrane-associated protein 1 hs
HU35KSUBA:AA054109_AT stromal membrane-associated protein 1 hs
HU35KSUBA:R16442_AT stromal membrane-associated protein 1 hs
HU35KSUBB:RC_F01551_AT stromal membrane-associated protein 1 hs
U133_X3P:G11345477_3P_A_AT stromal membrane-associated protein 1 hs
HG-U95AV2:38878_AT stromal membrane-associated protein 1 hs
HG-U95C:49151_S_AT stromal membrane-associated protein 1 hs
HG-U95C:49152_R_AT stromal membrane-associated protein 1 hs
HG-U95B:57182_AT stromal membrane-associated protein 1 hs
HG-U95E:75574_AT stromal membrane-associated protein 1 hs
HG-U95E:78765_AT stromal membrane-associated protein 1 hs
HU35KSUBA:RC_AA017515_AT Stromal membrane-associated protein 1 hs
HU35KSUBC:RC_H50834_AT Stromal membrane-associated protein 1 hs
MOUSE430_2:1431744_A_AT stromal membrane-associated protein 1 mm
MOE430A:1431744_A_AT stromal membrane-associated protein 1 mm
MOUSE430A_2:1431744_A_AT stromal membrane-associated protein 1 mm
MG-U74AV2:160196_AT stromal membrane-associated protein 1 mm
MG-U74BV2:164195_AT stromal membrane-associated protein 1 mm
MOE430A:1453998_AT stromal membrane-associated protein 1 mm
MOUSE430A_2:1453998_AT stromal membrane-associated protein 1 mm
MOUSE430_2:1453998_AT stromal membrane-associated protein 1 mm
MOE430A:1423956_AT stromal membrane-associated protein 1 mm
MOUSE430A_2:1423956_AT stromal membrane-associated protein 1 mm
MOUSE430_2:1423956_AT stromal membrane-associated protein 1 mm
MOE430A:1432029_A_AT stromal membrane-associated protein 1 mm
MOUSE430A_2:1432029_A_AT stromal membrane-associated protein 1 mm
MOUSE430_2:1432029_A_AT stromal membrane-associated protein 1 mm
MG-U74CV2:134707_AT Stromal membrane-associated protein 1, mRNA (cDNA clone MGC:6912 IMAGE:2810817) mm
MU19KSUBA:TC20470_AT Stromal membrane-associated protein 1, mRNA (cDNA clone MGC:6912 IMAGE:2810817) mm
MU19KSUBA:TC20470_G_AT Stromal membrane-associated protein 1, mRNA (cDNA clone MGC:6912 IMAGE:2810817) mm
MU19KSUBB:TC34946_AT Stromal membrane-associated protein 1, mRNA (cDNA clone MGC:6912 IMAGE:2810817) mm
YEAST_2:1770740_AT ADP-ribosylation factor (ARF) GTPase activating protein (GAP) effector, involved in Trans-Golgi-Network (TGN) transport; contains C2C2H2 cysteine/histidine motif Sc
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
3677 DNA binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB07858 Hypothetical protein W09D10.1 [Caenorhabditis elegans] ref|NP_499364.1| W09D10.1 [Caenorhabditis elegans] 0.0
blast CAE71411 Hypothetical protein CBG18321 [Caenorhabditis briggsae] 1.0E-166
Protein Domains
Database ID Description E-Value
Pfam IPR001164 EMBL-EBI Human Rev interacting-like protein (hRIP) 1.0E-66
Sequence
Target Sequence 
>C. ELEGANS:193798_S_AT
aacgcagatattctttcgcttttcggcccatctggtggcatatcggctccgaatgtagtt
gctcccggaggatttgccggatttggactgcaagctgctccggctcaaatcccgcaacaa
gcttcttcgttccaccaattcggggctccagctccagctccacaacaaaatgatatgttt
ggaggactgtcgggtatcaattttggagcaccaccaccatcggctcaaatgtctcaaatc
ccaccaatggctccaccacaatactttggagctgctcaatttggagcaatgtcttccagt
ggattcggtggaatgagtatgcagtctaaaccaacgcctacttcaccaactggatcacaa
ggattcaatattccgaataaatcgaatgctttcgctgatttggcacttggaaaggtaatg
aagacaaactacggacaaagtgcaattcatcaccaagcggcaccaatttcctctaataga
gcgtcaccgatgccggcacaatccaacactgccgccaacaatgatcttttcgatatgttc
gcctcggcaccgccaccggttacagtcaattcgtc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AACGCAGATATTCTTTCGCTTTTCG 373 145 892 Antisense
TTTTCGGCCCATCTGGTGGCATATC 452 673 911 Antisense
GTTGCTCCCGGAGGATTTGCCGGAT 630 437 949 Antisense
CCGGATTTGGACTGCAAGCTGCTCC 218 263 968 Antisense
TCAAATCCCGCAACAAGCTTCTTCG 421 629 996 Antisense
ATCGGCTCAAATGTCTCAAATCCCA 100 35 1110 Antisense
GTATGCAGTCTAAACCAACGCCTAC 164 453 1208 Antisense
TCTAATAGAGCGTCACCGATGCCGG 710 613 1363 Antisense
CCAACACTGCCGCCAACAATGATCT 69 277 1394 Antisense
GATCTTTTCGATATGTTCGCCTCGG 331 417 1414 Antisense
CGCCACCGGTTACAGTCAATTCGTC 671 199 1442 Antisense
Sequence Source Affymetrix Proprietary Database