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[191948_s_at] RNA binding protein (RNP like)

Description C17E4.5 /REP_DB=WormBase Gene ID /WP=CE08254 /TR=Q93233 /GB=CAB02750.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=RNA binding protein (RNP like)
Cluster 6grp_highest_10_10 > 83      6grp_high1_10_10 > 49      4grp_highest_8_8 > 63      4grp_high_8_8 > 28      6grp_highest_nonorm > 84      6grp_total > 09      4grp_total > 35      6grp_highest_sub > Cu      6grp_cgc > 0      6grp_high1_sub > Cu      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 302
1 2 3 4 range
A 545.5
(-0.2)
P 		650.6
(3)
P 		451.6
(-3)
P 		623.7
(2.2)
P 		199
B 506.3
(-0.8)
P 		626
(3)
P 		435.7
(-3)
P 		559.5
(0.9)
P 		190
C 592.3
(-3)
P 		737.9
(3)
P 		621.7
(-1.8)
P 		608.9
(-2.3)
P 		146
avr 548
(-1.4) 		671.5
(3) 		503
(-3) 		597.4
(0.4) 		169

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 342
1 2 3 4 5 6 range
A 663.5
(1.3)
P 		626.5
(0.3)
P 		563.2
(-1.5)
P 		721.7
(3)
P 		510.4
(-3)
P 		671.6
(1.6)
P 		211
B 561.3
(-0.5)
P 		508.3
(-3)
P 		595
(1.1)
P 		552.8
(-0.9)
P 		635.1
(3)
P 		577.8
(0.3)
P 		127
C 784
(3)
P 		442.2
(-3)
P 		600.7
(-0.2)
P 		627
(0.2)
P 		580.9
(-0.6)
P 		638
(0.4)
P 		342
avr 669.6
(3) 		525.7
(-3) 		586.3
(-0.5) 		633.8
(1.5) 		575.5
(-0.9) 		629.1
(1.3) 		144
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 125
1 2 3 4 range
A 198.6
(3)
P 		141.2
(-0.2)
P 		118.1
(-1.5)
P 		91.3
(-3)
P 		107
B 161.5
(3)
P 		154.6
(2.3)
P 		101
(-3)
P 		119.2
(-1.2)
P 		61
C 196.1
(1.9)
P 		212.1
(2.8)
P 		216.7
(3)
P 		102.7
(-3)
P 		114
avr 185.4
(3) 		169.3
(1.8) 		145.3
(0) 		104.4
(-3) 		81

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 168
1 2 3 4 5 6 range
A 122.3
(-3)
P 		222.8
(3)
P 		122.6
(-3)
P 		183
(0.6)
P 		154
(-1.1)
P 		163.5
(-0.5)
P 		101
B 195.3
(-0.3)
P 		169.2
(-1.7)
P 		144.5
(-3)
P 		146.4
(-2.9)
P 		258
(3)
P 		215.4
(0.7)
P 		114
C 290.6
(3)
P 		134.9
(-2.7)
P 		152.9
(-2)
P 		126.1
(-3)
P 		188
(-0.7)
P 		213.6
(0.2)
P 		165
avr 202.7
(3) 		175.6
(0.4) 		140
(-3) 		151.8
(-1.9) 		200
(2.7) 		197.5
(2.5) 		63
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 191948_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.1297
Sequence Type Exemplar sequence
Representative Public ID C17E4.5 NCBI
Target Description C17E4.5 /REP_DB=WormBase Gene ID /WP=CE08254 /TR=Q93233 /GB=CAB02750.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=RNA binding protein (RNP like)
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_060103(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_060103 NCBI Caenorhabditis elegans PolyA Binding protein family member (pab-3) (pab-3) mRNA, complete cds. 11/11 None
SNAP00000000952 ENSEMBL cdna:SNAP chromosome:CEL140:I:9429370:9430089:-1 11/11 None
GENEFINDER00000000965 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:9429370:9430486:-1 11/11 None
C17E4.5.1 ENSEMBL cdna:known chromosome:CEL140:I:9428965:9430122:-1 gene:C17E4.5 11/11 A 
C17E4.5.2 ENSEMBL cdna:known chromosome:CEL140:I:9428978:9430143:-1 gene:C17E4.5 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
chrI:9429300-9430020(-) 100.0 100.0
Public Domain and Genome References
Gene Title RNA binding protein (RNP like)
Gene Symbol pab-3
Ensembl C17E4.5
Entrez Gene 172768 Entrez gene
SwissProt Q93233 EMBL-EBI
WormBase CE08254 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:247173_AT polyadenylate-binding protein family protein / PABP family protein at
CANINE_2:CFAAFFX.17841.1.S1_AT poly(A) binding protein, nuclear 1 cfa
DROSOPHILA_2:1639719_AT dm
DROSGENOME1:143567_R_AT dm
DROSGENOME1:143566_I_AT dm
DROSOPHILA_2:1631244_A_AT dm
DROSOPHILA_2:1629694_AT dm
HG-U133_PLUS_2:213046_AT poly(A) binding protein, nuclear 1 hs
HG-U133A_2:213046_AT poly(A) binding protein, nuclear 1 hs
HG-FOCUS:213046_AT poly(A) binding protein, nuclear 1 hs
HG-U133A:213046_AT poly(A) binding protein, nuclear 1 hs
HG-U133_PLUS_2:201545_S_AT poly(A) binding protein, nuclear 1 hs
HG-U133A:201545_S_AT poly(A) binding protein, nuclear 1 hs
HG-U133A_2:201545_S_AT poly(A) binding protein, nuclear 1 hs
HG-U133A_2:201544_X_AT poly(A) binding protein, nuclear 1 hs
HG-U133_PLUS_2:201544_X_AT poly(A) binding protein, nuclear 1 hs
HG-U133A:201544_X_AT poly(A) binding protein, nuclear 1 hs
U133_X3P:G4758875_3P_A_AT poly(A) binding protein, nuclear 1 hs
U133_X3P:HS.117176.1.S1_3P_AT poly(A) binding protein, nuclear 1 hs
U133_X3P:HS.117176.0.S1_3P_X_AT poly(A) binding protein, nuclear 1 hs
U133_X3P:HS.117176.0.S1_3P_A_AT poly(A) binding protein, nuclear 1 hs
U133_X3P:201544_3P_X_AT poly(A) binding protein, nuclear 1 hs
HG-U95AV2:39050_AT poly(A) binding protein, nuclear 1 hs
MU11KSUBA:C78741_RC_S_AT poly(A) binding protein, nuclear 1 mm
MG-U74AV2:101476_AT poly(A) binding protein, nuclear 1 mm
MOE430A:1415728_AT poly(A) binding protein, nuclear 1 mm
MOE430B:1415728_AT poly(A) binding protein, nuclear 1 mm
MOUSE430A_2:1415728_AT poly(A) binding protein, nuclear 1 mm
MOUSE430_2:1415728_AT poly(A) binding protein, nuclear 1 mm
MOE430A:1422848_A_AT poly(A) binding protein, nuclear 1 mm
MOUSE430A_2:1422848_A_AT poly(A) binding protein, nuclear 1 mm
MOUSE430_2:1422848_A_AT poly(A) binding protein, nuclear 1 mm
MOE430A:1422850_AT poly(A) binding protein, nuclear 1 mm
MOUSE430A_2:1422850_AT poly(A) binding protein, nuclear 1 mm
MOUSE430_2:1422850_AT poly(A) binding protein, nuclear 1 mm
MOE430A:1422849_A_AT poly(A) binding protein, nuclear 1 mm
MOUSE430A_2:1422849_A_AT poly(A) binding protein, nuclear 1 mm
MOUSE430_2:1422849_A_AT poly(A) binding protein, nuclear 1 mm
MU19KSUBC:TC37067_AT Poly(A) binding protein, nuclear 1 (Pabpn1), mRNA mm
MU19KSUBC:TC37068_AT Poly(A) binding protein, nuclear 1 (Pabpn1), mRNA mm
MU19KSUBC:TC37069_AT Poly(A) binding protein, nuclear 1 (Pabpn1), mRNA mm
RG-U34B:RC_AA942947_AT poly(A) binding protein, nuclear 1 rn
RG-U34C:RC_AI236788_AT poly(A) binding protein, nuclear 1 rn
RAE230A:1371958_AT poly(A) binding protein, nuclear 1 rn
RAT230_2:1371958_AT poly(A) binding protein, nuclear 1 rn
RAE230B:1392480_AT poly(A) binding protein, nuclear 1 rn
RAT230_2:1392480_AT poly(A) binding protein, nuclear 1 rn
RAE230B:1379481_AT poly(A) binding protein, nuclear 1 rn
RAT230_2:1379481_AT poly(A) binding protein, nuclear 1 rn
RAE230B:1382922_AT Poly(A) binding protein, nuclear 1 rn
RAT230_2:1382922_AT Poly(A) binding protein, nuclear 1 rn
RG-U34C:RC_AI231070_AT Poly(A) binding protein, nuclear 1 rn
Protein Similarities
Method ID Description E-Value
blast CAB02750 Hypothetical protein C17E4.5 [Caenorhabditis elegans] ref|NP_492504.1| PolyA Binding protein family member (pab-3) [Caenorhabditis elegans] 1.0E-76
blast CAE60185 Hypothetical protein CBG03741 [Caenorhabditis briggsae] 9.0E-73
blast CAE60185 Hypothetical protein CBG03741 [Caenorhabditis briggsae] 1.0E-72
Protein Domains
Database ID Description E-Value
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 4.9E-19
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 4.9E-19
Trans Membrane
ID Number Of Domains Domain Boundaries
GENEFINDER00000000965 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:191948_S_AT
agatgatgcggatctctctgctatcgaaggagacttgaatgagatcgaggaggaacagaa
aaagttgaaagctattcaaaatgaaatggtcgggcacatgaacttgaacacaagcagtca
gagtaattcatcacaatcgctcttaacaccagaggagaaagcagaagctgatgctaaatc
agtgtacgtaggaaatgtagattatggtgcaactgccgaagaaatagagcaacattttca
tggatgcggatctgtatcccgcgtcactattcaatgtgacagattcagtggacatccgaa
aggattcgcatatgtcgaatttaccgagaaggaaggaatgcaaaacgcactagctatgac
agacagtcttcttagaggccgacaaatcaaagtagatccaaaacgaacaaacaagccggg
catgtcaacaactaacaggcctccattccgtgggcgtggaggacgtggacgcgggaacgt
cattgtcaaatacgtctatgcaggtggatttcgtccaagaggtcgtggggc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AGATGATGCGGATCTCTCTGCTATC 653 67 69 Antisense
GGTCGGGCACATGAACTTGAACACA 694 501 156 Antisense
AATTCATCACAATCGCTCTTAACAC 247 177 193 Antisense
TGGATGCGGATCTGTATCCCGCGTC 258 551 309 Antisense
TATCCCGCGTCACTATTCAATGTGA 605 657 323 Antisense
GACAGACAGTCTTCTTAGAGGCCGA 292 367 426 Antisense
AACAAGCCGGGCATGTCAACAACTA 336 133 478 Antisense
TGTCAACAACTAACAGGCCTCCATT 545 557 491 Antisense
CGTGGAGGACGTGGACGCGGGAACG 347 45 523 Antisense
ACGCGGGAACGTCATTGTCAAATAC 493 83 537 Antisense
GATTTCGTCCAAGAGGTCGTGGGGC 66 237 575 Antisense
Sequence Source Affymetrix Proprietary Database