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[191777_at] Probable RNA binding protein

Description C27H5.3 /REP_DB=WormBase Gene ID /WP=CE27099 /TR=Q18265 /GB=AAC46657.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=Probable RNA binding protein
Cluster 6grp_highest_10_10 > 60      6grp_high1_10_10 > 06      4grp_highest_8_8 > 40      4grp_high_8_8 > 43      6grp_highest_nonorm > 70      6grp_total > 07      4grp_total > 53      6grp_highest_sub > De      6grp_high1_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 267
1 2 3 4 range
A 536
(3)
P 		524.6
(2.7)
P 		339.5
(-1.6)
P 		278.4
(-3)
P 		258
B 545
(3)
P 		415.6
(0.1)
P 		393.9
(-0.4)
P 		279.9
(-3)
P 		265
C 491.1
(1.5)
P 		536.1
(3)
P 		438.5
(-0.3)
P 		359.1
(-3)
P 		177
avr 524
(3) 		492.1
(2.1) 		390.6
(-0.7) 		305.8
(-3) 		218

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 278
1 2 3 4 5 6 range
A 347.2
(3)
P 		247.1
(-0.2)
P 		331
(2.5)
P 		273.2
(0.6)
P 		162.2
(-3)
P 		297.3
(1.4)
P 		185
B 385.8
(3)
P 		315.7
(0.9)
P 		187.9
(-3)
P 		188.7
(-3)
P 		198.5
(-2.7)
P 		210.6
(-2.3)
P 		198
C 439.7
(3)
P 		313.2
(-0.4)
P 		346.8
(0.5)
P 		233.3
(-2.6)
P 		300
(-0.8)
P 		218.5
(-3)
P 		221
avr 390.9
(3) 		292
(-0.5) 		288.6
(-0.6) 		231.7
(-2.6) 		220.2
(-3) 		242.1
(-2.2) 		171
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 154
1 2 3 4 range
A 195.1
(3)
P 		113.9
(-0.2)
P 		88.8
(-1.1)
P 		40.8
(-3)
P 		154
B 173.8
(3)
P 		102.6
(-0.7)
P 		91.3
(-1.3)
P 		59.7
(-3)
P 		114
C 162.6
(3)
P 		154.1
(2.5)
P 		152.8
(2.4)
P 		60.6
(-3)
P 		102
avr 177.2
(3) 		123.5
(0.4) 		111
(-0.2) 		53.7
(-3) 		124

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 117
1 2 3 4 5 6 range
A 64
(-0.7)
P 		87.9
(3)
P 		72.1
(0.6)
P 		69.3
(0.1)
P 		48.9
(-3)
P 		72.4
(0.6)
P 		39
B 134.3
(3)
P 		105.1
(1)
P 		45.6
(-3)
P 		50
(-2.7)
P 		80.7
(-0.6)
P 		78.5
(-0.8)
P 		89
C 163
(3)
P 		95.6
(-0.5)
P 		88.3
(-0.9)
P 		46.9
(-3)
P 		97.1
(-0.4)
P 		73.1
(-1.6)
P 		116
avr 120.4
(3) 		96.2
(0.8) 		68.7
(-1.8) 		55.4
(-3) 		75.6
(-1.1) 		74.7
(-1.2) 		65
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 191777_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.5309
Sequence Type Exemplar sequence
Representative Public ID C27H5.3 NCBI
Target Description C27H5.3 /REP_DB=WormBase Gene ID /WP=CE27099 /TR=Q18265 /GB=AAC46657.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=Probable RNA binding protein
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_063082(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063082 NCBI Caenorhabditis elegans C27H5.3 (C27H5.3) mRNA, complete cds. 11/11 A 
SNAP00000006110 ENSEMBL cdna:SNAP chromosome:CEL140:II:7154009:7155214:1 11/11 None
GENEFINDER00000006122 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:7152238:7155214:1 11/11 None
C27H5.3.1 ENSEMBL cdna:known chromosome:CEL140:II:7152497:7155405:1 gene:C27H5.3 11/11 A 
C27H5.3.2 ENSEMBL cdna:known chromosome:CEL140:II:7152560:7155655:1 gene:C27H5.3 11/11 A 
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
chrII:7152040-7155210(+) 82.66 100.0
Public Domain and Genome References
Gene Title Probable RNA binding protein
Ensembl C27H5.3
Entrez Gene 174175 Entrez gene
SwissProt Q18265 EMBL-EBI
WormBase CE27099 Wormbase
Functional Annotations
Ortholog
ID Title Organism
DROSOPHILA_2:1634362_A_AT cabeza dm
DROSGENOME1:142484_AT cabeza dm
HG-U133_PLUS_2:217370_X_AT fusion (involved in t(12;16) in malignant liposarcoma) hs
HG-U133A_2:217370_X_AT fusion (involved in t(12;16) in malignant liposarcoma) hs
HG-U133A:217370_X_AT fusion (involved in t(12;16) in malignant liposarcoma) hs
HG-U133_PLUS_2:200959_AT fusion (involved in t(12;16) in malignant liposarcoma) hs
HG-U133A:200959_AT fusion (involved in t(12;16) in malignant liposarcoma) hs
HG-FOCUS:200959_AT fusion (involved in t(12;16) in malignant liposarcoma) hs
HG-U133A_2:200959_AT fusion (involved in t(12;16) in malignant liposarcoma) hs
HU35KSUBB:RC_AA025166_S_AT fusion (involved in t(12;16) in malignant liposarcoma) hs
HU35KSUBB:RC_H93393_AT fusion (involved in t(12;16) in malignant liposarcoma) hs
HU35KSUBD:RC_AA299629_AT fusion (involved in t(12;16) in malignant liposarcoma) hs
HUGENEFL:X71428_AT fusion (involved in t(12;16) in malignant liposarcoma) hs
U133_X3P:G4826733_3P_X_AT fusion (involved in t(12;16) in malignant liposarcoma) hs
U133_X3P:G4826733_3P_S_AT fusion (involved in t(12;16) in malignant liposarcoma) hs
U133_X3P:G4826733_3P_AT fusion (involved in t(12;16) in malignant liposarcoma) hs
U133_X3P:HS2.392171.1.S1_3P_S_AT fusion (involved in t(12;16) in malignant liposarcoma) hs
U133_X3P:HS2.392171.1.S1_3P_AT fusion (involved in t(12;16) in malignant liposarcoma) hs
U133_X3P:HS.99969.3.S1_3P_AT fusion (involved in t(12;16) in malignant liposarcoma) hs
U133_X3P:HS.99969.2.S1_3P_S_AT fusion (involved in t(12;16) in malignant liposarcoma) hs
U133_X3P:HS.99969.2.S1_3P_A_AT fusion (involved in t(12;16) in malignant liposarcoma) hs
U133_X3P:217370_3P_X_AT fusion (involved in t(12;16) in malignant liposarcoma) hs
U133_X3P:200959_3P_AT fusion (involved in t(12;16) in malignant liposarcoma) hs
HG-U133_PLUS_2:1565716_AT fusion (involved in t(12;16) in malignant liposarcoma) hs
HG-U133_PLUS_2:1565717_S_AT fusion (involved in t(12;16) in malignant liposarcoma) hs
HG-U133A_2:215744_AT fusion (involved in t(12;16) in malignant liposarcoma) hs
HG-U133_PLUS_2:215744_AT fusion (involved in t(12;16) in malignant liposarcoma) hs
HG-U133A:215744_AT fusion (involved in t(12;16) in malignant liposarcoma) hs
HG-U95AV2:39180_AT fusion (involved in t(12;16) in malignant liposarcoma) hs
HG-U95B:43501_AT fusion (involved in t(12;16) in malignant liposarcoma) hs
HG-U95C:63941_AT fusion (involved in t(12;16) in malignant liposarcoma) hs
HG-U95E:73061_AT fusion (involved in t(12;16) in malignant liposarcoma) hs
HG-U133_PLUS_2:1565715_AT Fusion (involved in t(12;16) in malignant liposarcoma) hs
HG-U133_PLUS_2:231108_AT Fusion (involved in t(12;16) in malignant liposarcoma) hs
HG-U133B:231108_AT Fusion (involved in t(12;16) in malignant liposarcoma) hs
HG-U95C:59931_AT Fusion (involved in t(12;16) in malignant liposarcoma) hs
HG-U95C:61744_R_AT Fusion (involved in t(12;16) in malignant liposarcoma) hs
HU35KSUBC:RC_AA004533_AT Fusion (involved in t(12;16) in malignant liposarcoma) hs
MOE430A:1455831_AT fusion, derived from t(12;16) malignant liposarcoma (human) mm
MOUSE430A_2:1455831_AT fusion, derived from t(12;16) malignant liposarcoma (human) mm
MOUSE430_2:1455831_AT fusion, derived from t(12;16) malignant liposarcoma (human) mm
MU11KSUBB:MSA.3356.0_S_AT fusion, derived from t(12;16) malignant liposarcoma (human) mm
MU11KSUBB:MSA.10497.0_S_AT fusion, derived from t(12;16) malignant liposarcoma (human) mm
MU11KSUBB:MSA.17592.0_S_AT fusion, derived from t(12;16) malignant liposarcoma (human) mm
MG-U74BV2:107506_AT fusion, derived from t(12;16) malignant liposarcoma (human) mm
MOE430A:1451286_S_AT fusion, derived from t(12;16) malignant liposarcoma (human) mm
MOUSE430A_2:1451286_S_AT fusion, derived from t(12;16) malignant liposarcoma (human) mm
MOUSE430_2:1451286_S_AT fusion, derived from t(12;16) malignant liposarcoma (human) mm
MOE430A:1451285_AT fusion, derived from t(12;16) malignant liposarcoma (human) mm
MOUSE430A_2:1451285_AT fusion, derived from t(12;16) malignant liposarcoma (human) mm
MOUSE430_2:1451285_AT fusion, derived from t(12;16) malignant liposarcoma (human) mm
MU19KSUBA:TC15766_AT Fusion, derived from t(12;16) malignant liposarcoma (human) (Fus), mRNA mm
MU19KSUBC:TC41666_AT Fusion, derived from t(12;16) malignant liposarcoma (human) (Fus), mRNA mm
RAE230A:1373195_AT fusion (involved in t(12;16) in malignant liposarcoma) (predicted) rn
RAT230_2:1373195_AT fusion (involved in t(12;16) in malignant liposarcoma) (predicted) rn
RAE230A:1375689_AT Fusion (involved in t(12;16) in malignant liposarcoma) (predicted) rn
RAT230_2:1375689_AT Fusion (involved in t(12;16) in malignant liposarcoma) (predicted) rn
RAE230B:1393068_AT Fusion (involved in t(12;16) in malignant liposarcoma) (predicted) rn
RAT230_2:1393068_AT Fusion (involved in t(12;16) in malignant liposarcoma) (predicted) rn
RG-U34C:RC_AI227987_AT Fusion (involved in t(12;16) in malignant liposarcoma) (predicted) rn
Protein Similarities
Method ID Description E-Value
blast AAC46657 Hypothetical protein C27H5.3 [Caenorhabditis elegans] ref|NP_495483.1| C27H5.3 [Caenorhabditis elegans] 4.0E-54
blast AAC46657 Hypothetical protein C27H5.3 [Caenorhabditis elegans] ref|NP_495483.1| C27H5.3 [Caenorhabditis elegans] 2.0E-53
blast AAC46657 Hypothetical protein C27H5.3 [Caenorhabditis elegans] ref|NP_495483.1| C27H5.3 [Caenorhabditis elegans] 4.0E-53
blast CAE67550 Hypothetical protein CBG13075 [Caenorhabditis briggsae] 2.0E-50
blast CAE67550 Hypothetical protein CBG13075 [Caenorhabditis briggsae] 3.0E-50
blast CAE67550 Hypothetical protein CBG13075 [Caenorhabditis briggsae] 4.0E-50
Protein Domains
Database ID Description E-Value
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 1.3E-9
Pfam IPR001876 EMBL-EBI Zn-finger, Ran-binding 2.6E-7
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 1.3E-9
Pfam IPR001876 EMBL-EBI Zn-finger, Ran-binding 2.6E-7
Pfam IPR001876 EMBL-EBI Zn-finger, Ran-binding 2.6E-7
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 1.3E-9
Sequence
Target Sequence 
>C. ELEGANS:191777_AT
taacattcgtcgatgcttctgcagctcaacaagctataactatgtacaatgggcaaccat
tccctggcggctcaagcccgatgagtatttcactagccaagttccgcgctgatgcaggag
gtgaacgaggtggtcgtggtggacgaggcggtttcggaggtggtcgtggtggtcctatgg
gaggacgtggtggctttggcggtgatcgtggaggatatggcggcggcggtggtcgtggag
gattcgatggtggtcgcggtggtggcggtggattccgtggcggagaccgaggaggattcc
gaggtggtgatagaggaggcttccgcggaggagatcgtggaggattccgaggcggcgacc
gtggtggcgatcgtggaggattcagaggaggccgtggagtaggtggcggaaatgctaata
tggaacaaaggaagaatgactggccatgtgagcagtgcggaaatagcaacttcgctttca
gaagagaatgcaatcaatgccaagccccgagaccagatggagga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TAACATTCGTCGATGCTTCTGCAGC 231 639 1061 Antisense
GTACAATGGGCAACCATTCCCTGGC 556 461 1104 Antisense
GAGTATTTCACTAGCCAAGTTCCGC 311 397 1143 Antisense
CAAGTTCCGCGCTGATGCAGGAGGT 678 183 1158 Antisense
TGGTCGTGGTGGTCCTATGGGAGGA 59 551 1221 Antisense
TATGGGAGGACGTGGTGGCTTTGGC 598 551 1236 Antisense
TGGCTTTGGCGGTGATCGTGGAGGA 190 543 1251 Antisense
GGAGGATTCGATGGTGGTCGCGGTG 73 517 1297 Antisense
CGGTGGATTCCGTGGCGGAGACCGA 64 237 1326 Antisense
TAGAGGAGGCTTCCGCGGAGGAGAT 334 651 1371 Antisense
CCAAGCCCCGAGACCAGATGGAGGA 424 275 1560 Antisense
Sequence Source Affymetrix Proprietary Database