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[193767_s_at] RNA recognition motif. (aka RRM, RBD, or RNP domain)

Description F56A8.6 /REP_DB=WormBase Gene ID /WP=CE16126 /TR=O45577 /GB=CAB05746.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=RNA recognition motif. (aka RRM, RBD, or RNP domain)
Cluster 6grp_highest_10_10 > 87      6grp_high1_10_10 > 78      4grp_highest_8_8 > 55      4grp_high_8_8 > 19      6grp_highest_nonorm > 96      6grp_total > 68      4grp_total > 21      6grp_highest_sub > Da      6grp_cgc > 39      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Increase      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 271
1 2 3 4 range
A 806.2
(-2.5)
P 		987.8
(2.4)
P 		788.1
(-3)
P 		1011.2
(3)
P 		223
B 967.4
(3)
P 		869.7
(-0.2)
P 		783.1
(-3)
P 		898
(0.7)
P 		184
C 887.3
(2.9)
P 		740
(-3)
P 		786.5
(-1.1)
P 		889.5
(3)
P 		150
avr 887
(1.1) 		865.8
(0.3) 		785.9
(-3) 		932.9
(3) 		147

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 461
1 2 3 4 5 6 range
A 1005.6
(1.8)
P 		722
(-3)
P 		768.4
(-2.2)
P 		733.1
(-2.8)
P 		918.5
(0.3)
P 		1079
(3)
P 		357
B 874.6
(-0.6)
P 		696.5
(-3)
P 		914.8
(-0.1)
P 		768.7
(-2)
P 		883.6
(-0.5)
P 		1146.5
(3)
P 		450
C 760.4
(-2.2)
P 		699.5
(-3)
P 		771.2
(-2.1)
P 		798.1
(-1.7)
P 		782.8
(-1.9)
P 		1157.7
(3)
P 		458
avr 880.2
(-0.5) 		706
(-3) 		818.1
(-1.4) 		766.6
(-2.1) 		861.6
(-0.8) 		1127.7
(3) 		422
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 161
1 2 3 4 range
A 293.5
(3)
P 		214.4
(-0.3)
P 		206
(-0.6)
P 		148
(-3)
P 		146
B 308.5
(3)
P 		214.8
(-1.4)
P 		181.5
(-3)
P 		191.4
(-2.5)
P 		127
C 293.7
(3)
P 		212.7
(-0.4)
P 		274.1
(2.2)
P 		150
(-3)
P 		144
avr 298.6
(3) 		214
(-0.7) 		220.5
(-0.5) 		163.1
(-3) 		136

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 267
1 2 3 4 5 6 range
A 185.4
(-2)
P 		256.8
(1.9)
P 		167.3
(-3)
P 		185.9
(-2)
P 		277.2
(3)
P 		262.7
(2.2)
P 		110
B 304.3
(-0.3)
P 		231.8
(-2.2)
P 		222.1
(-2.5)
P 		203.6
(-3)
P 		359
(1.2)
P 		427.5
(3)
P 		224
C 281.8
(0.2)
P 		213.4
(-1.6)
P 		196.3
(-2.1)
P 		160.5
(-3)
P 		253.3
(-0.5)
P 		387.6
(3)
P 		227
avr 257.2
(-0.5) 		234
(-1.3) 		195.2
(-2.6) 		183.3
(-3) 		296.5
(0.9) 		359.3
(3) 		176
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 193767_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6895
Sequence Type Exemplar sequence
Representative Public ID F56A8.6 NCBI
Target Description F56A8.6 /REP_DB=WormBase Gene ID /WP=CE16126 /TR=O45577 /GB=CAB05746.1 /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_067333(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067333 NCBI Caenorhabditis elegans Cleavage and Polyadenylation Factor family member (cpf-2) (cpf-2) mRNA, complete cds. 11/11 None
SNAP00000043513 ENSEMBL cdna:SNAP chromosome:CEL140:III:13264714:13268391:-1 11/11 None
GENEFINDER00000043520 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:13266530:13268391:-1 11/11 None
F56A8.6.1 ENSEMBL cdna:known chromosome:CEL140:III:13266456:13268399:-1 gene:F56A8.6 11/11 None
F56A8.6.2 ENSEMBL cdna:known chromosome:CEL140:III:13266456:13268413:-1 gene:F56A8.6 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:13266525-13268387(-) 95.75 100.0
Public Domain and Genome References
Gene Title RNA recognition motif. (aka RRM, RBD, or RNP domain)
Gene Symbol cpf-2
Ensembl F56A8.6
Entrez Gene 176742 Entrez gene
SwissProt O45577 EMBL-EBI
WormBase CE16126 Wormbase
Functional Annotations
Ortholog
ID Title Organism
DROSOPHILA_2:1640568_AT Cleavage stimulation factor 64 kilodalton subunit dm
DROSGENOME1:144195_AT Cleavage stimulation factor 64 kilodalton subunit dm
HG-U133_PLUS_2:212901_S_AT cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant hs
HG-U133A_2:212901_S_AT cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant hs
HG-U133A:212901_S_AT cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant hs
HU35KSUBB:RC_N48963_AT cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant hs
HU35KSUBD:RC_AA422081_AT cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant hs
U133_X3P:HS.21992.1.S2_3P_AT cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant hs
U133_X3P:HS.21992.1.S1_3P_A_AT cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant hs
HG-U133A_2:212905_AT cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant hs
HG-U133_PLUS_2:212905_AT cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant hs
HG-U133A:212905_AT cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant hs
HG-U95AV2:41248_AT cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant hs
U133_X3P:HS2.407535.1.S1_3P_AT Cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant hs
HG-U133_PLUS_2:1561558_AT Cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant hs
HG-U95B:46540_R_AT Cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant hs
HG-U95C:50568_AT Cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant hs
HG-U95C:61156_I_AT Cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant hs
HG-U95C:61157_R_AT Cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant hs
HG-U95C:64961_R_AT Cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant hs
HU35KSUBB:RC_F09507_AT Cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant hs
HU35KSUBD:RC_H95817_AT Cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant hs
MU11KSUBA:AA415822_S_AT cleavage stimulation factor, 3' pre-RNA subunit 2, tau mm
MU11KSUBB:MSA.11941.0_AT cleavage stimulation factor, 3' pre-RNA subunit 2, tau mm
MG-U74AV2:104126_AT cleavage stimulation factor, 3' pre-RNA subunit 2, tau mm
MG-U74CV2:170665_AT cleavage stimulation factor, 3' pre-RNA subunit 2, tau mm
MG-U74CV2:170579_AT cleavage stimulation factor, 3' pre-RNA subunit 2, tau mm
MOE430A:1415920_AT cleavage stimulation factor, 3' pre-RNA subunit 2, tau mm
MOUSE430A_2:1415920_AT cleavage stimulation factor, 3' pre-RNA subunit 2, tau mm
MOUSE430_2:1415920_AT cleavage stimulation factor, 3' pre-RNA subunit 2, tau mm
MU19KSUBC:TC40941_AT Cleavage stimulation factor, 3' pre-RNA subunit 2, tau, mRNA (cDNA clone MGC:35607 IMAGE:5373155) mm
MU19KSUBC:TC40941_G_AT Cleavage stimulation factor, 3' pre-RNA subunit 2, tau, mRNA (cDNA clone MGC:35607 IMAGE:5373155) mm
Protein Similarities
Method ID Description E-Value
blast CAB05746 Hypothetical protein F56A8.6 [Caenorhabditis elegans] ref|NP_499734.1| Cleavage and Polyadenylation Factor family member (cpf-2) [Caenorhabditis elegans] 1.0E-133
blast CAE60055 Hypothetical protein CBG03568 [Caenorhabditis briggsae] 3.0E-92
Protein Domains
Database ID Description E-Value
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 4.1E-29
Sequence
Target Sequence 
>C. ELEGANS:193767_S_AT
ggagagaatctcccaaacagtcgcctccctggctccggagaaaatgttcgaactaatgaa
gcaactgcaagaatcgctgaagaacaatccatcggaactacacaaattcctggtcgagca
tccacaaatcgcctacgcggtgctccaagccgccgttgtcatgcgaatcgttgatccaca
gactgcacttggactccttcatcgtaataaggccgccacgctgacaccattccataatac
acctcaaggagcaccgccaatggttcagcaacaacagatgccgatgccaccgaagccaac
atttgctcatcctggcccatctatgggtcctccgatgggaccacctatgggtccacctat
gggacatccgcaagctcctcaatacggtcaaaattacgggcaaccagtggctccacagca
gtacaagccaccgccacagcagcagccaccagttcagatgagacctccagttcagcagcc
acaacaaaatcatcaagaagagcagcaaaatgcggagcttctgatgcaagtcatgcagct
cagcgagcac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGAGAGAATCTCCCAAACAGTCGCC 378 519 396 Antisense
ATTCCTGGTCGAGCATCCACAAATC 563 7 501 Antisense
TCGTAATAAGGCCGCCACGCTGACA 149 603 597 Antisense
TAATACACCTCAAGGAGCACCGCCA 632 633 630 Antisense
CGAAGCCAACATTTGCTCATCCTGG 238 253 686 Antisense
TATGGGTCCTCCGATGGGACCACCT 324 651 717 Antisense
TCCACCTATGGGACATCCGCAAGCT 424 589 747 Antisense
ATCCGCAAGCTCCTCAATACGGTCA 277 37 761 Antisense
AAATTACGGGCAACCAGTGGCTCCA 472 115 786 Antisense
CAGATGAGACCTCCAGTTCAGCAGC 132 207 850 Antisense
GCAAGTCATGCAGCTCAGCGAGCAC 306 321 921 Antisense
Sequence Source Affymetrix Proprietary Database