[Home] | [Total List]

[173965_at] RNA recognition motif. (aka RRM, RBD, or RNP domain)

Description CEC2952 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=W09D10.1 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C09295 /WB_GENE_ID=W09D10.1 /WP=CE16562 /CHR=3 /FEA=Genomic Cluster /DEF=RNA recognition motif. (aka RRM, RBD, or RNP domain); C.elegans cDNA clone yk166e1 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 81      6grp_high1_10_10 > 29      4grp_highest_8_8 > 03      4grp_high_8_8 > 37      6grp_highest_nonorm > 60      6grp_total > 28      4grp_total > 42      6grp_highest_sub > Cu      6grp_high1_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 210
1 2 3 4 range
A 369
(-2.7)
P
566.7
(3)
P
416.6
(-1.3)
P
357.2
(-3)
P
210
B 357.3
(-3)
P
361.2
(-2.5)
P
393.7
(2)
P
401.4
(3)
P
44
C 420.9
(-3)
P
482.6
(3)
P
481.4
(2.9)
P
458.5
(0.7)
P
62
avr 382.4
(-3)
470.2
(3)
430.6
(0.3)
405.7
(-1.4)
88

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 391
1 2 3 4 5 6 range
A 611.3
(3)
P
320.6
(-1.5)
P
315.2
(-1.5)
P
220.1
(-3)
P
436.3
(0.3)
P
289.4
(-1.9)
P
391
B 539
(3)
P
483.4
(1.5)
P
355.3
(-2.1)
P
321.1
(-3)
P
351.9
(-2.2)
P
488.4
(1.6)
P
218
C 400.2
(2.4)
P
415
(3)
P
260.5
(-3)
P
314.2
(-0.9)
P
300.8
(-1.4)
P
361
(0.9)
P
155
avr 516.8
(3)
406.3
(0.1)
310.3
(-2.3)
285.1
(-3)
363
(-1)
379.6
(-0.6)
232
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 116
1 2 3 4 range
A 134.3
(3)
P
123
(2.2)
P
108.9
(1.1)
P
52.3
(-3)
P
82
B 113.9
(3)
P
89.2
(-2.2)
P
91.2
(-1.8)
P
85.5
(-3)
P
28
C 139.3
(1.1)
P
138.7
(1.1)
P
167.8
(3)
P
77.3
(-3)
P
91
avr 129.2
(3)
117
(1.7)
122.6
(2.3)
71.7
(-3)
58

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 132
1 2 3 4 5 6 range
A 112.7
(1.5)
P
114
(1.6)
P
68.6
(-2)
P
55.8
(-3)
P
131.7
(3)
P
70.5
(-1.8)
P
76
B 187.5
(3)
P
160.9
(1.4)
P
86.3
(-2.9)
P
85.1
(-3)
P
143
(0.4)
P
182.1
(2.7)
P
102
C 148.3
(3)
P
126.6
(1.5)
P
66.3
(-2.8)
P
63.2
(-3)
P
97.3
(-0.6)
P
120.9
(1.1)
P
85
avr 149.5
(3)
133.8
(1.8)
73.7
(-2.6)
68
(-3)
124
(1.1)
124.5
(1.2)
82
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173965_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.24301
Sequence Type Exemplar sequence
Representative Public ID CEC2952 NCBI
Target Description CEC2952 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=W09D10.1 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C09295 /WB_GENE_ID=W09D10.1 /WP=CE16562 /CHR=3 /FEA=Genomic Cluster /DEF=RNA recognition motif. (aka RRM, RBD, or RNP domain); C.elegans cDNA clone yk166e1 : 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_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
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:10736802-10739652(-) 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
blast AAX24661 SJCHGC04830 protein [Schistosoma japonicum] 2.0E-45
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:173965_AT
ctccttggactctgaaaaactagttttccacctaaaaaatgcataatttgacctgtgatt
ttatttttcttttctccctctctaaacactttctttcctaggaaactgcgcttctttttg
tgatttttttctagtaaattattattctcatcaacatttccccccgataaagttcggttg
tgtgagccccagaaattccagtcccttcagcatatccgaaatgtgtattaggaatactac
aacttttttttcagatttctatagcccctctctttttctttctccttcaacgtactaatt
ca


BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position
Strandedness
CTCCTTGGACTCTGAAAAACTAGTT 601 231 1487 Antisense
AATGCATAATTTGACCTGTGATTTT 433 165 1524 Antisense
TGACCTGTGATTTTATTTTTCTTTT 32 571 1535 Antisense
TCTCTAAACACTTTCTTTCCTAGGA 290 611 1565 Antisense
TTTCCTAGGAAACTGCGCTTCTTTT 143 669 1580 Antisense
ACTGCGCTTCTTTTTGTGATTTTTT 223 99 1591 Antisense
GTAAATTATTATTCTCATCAACATT 349 461 1620 Antisense
TAAAGTTCGGTTGTGTGAGCCCCAG 315 235 1654 Antisense
CAGTCCCTTCAGCATATCCGAAATG 497 207 1685 Antisense
TTTTTCAGATTTCTATAGCCCCTCT 490 675 1733 Antisense
CTTTCTCCTTCAACGTACTAATTCA 145 223 1764 Antisense
Sequence Source Affymetrix Proprietary Database