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[173396_s_at] RNA binding protein (RNP like)

Description AV178078_rc /REP_DB=TREMBL Accession /GB=AV178078 /FEA=Transcript Cluster /DEF=Caenorhabditis elegans cDNA clone:yk537g12 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 96      6grp_high1_10_10 > 79      4grp_highest_8_8 > 03      4grp_high_8_8 > 47      6grp_highest_nonorm > 78      6grp_total > 69      4grp_total > 41      6grp_highest_sub > Cu      6grp_cgc > 39      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 776
1 2 3 4 range
A 1400.2
(0.8)
P 		1145
(-3)
P 		1552.4
(3)
P 		1350.4
(0)
P 		407
B 1119.1
(-3)
P 		1511.5
(2.1)
P 		1244.3
(-1.4)
P 		1578.7
(3)
P 		460
C 1714.9
(0.5)
P 		1895.1
(3)
P 		1806.5
(1.8)
P 		1464
(-3)
P 		431
avr 1411.4
(-3) 		1517.2
(2.2) 		1534.4
(3) 		1464.4
(-0.4) 		123

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1237
1 2 3 4 5 6 range
A 1680.8
(-0)
P 		1533.6
(-2)
P 		1886.7
(2.7)
P 		1455.5
(-3)
P 		1912.2
(3)
P 		1835.2
(2)
P 		457
B 1617.5
(0.1)
P 		1512.1
(-0.6)
P 		1134.1
(-3)
P 		1697.3
(0.6)
P 		1970.2
(2.4)
P 		2062.4
(3)
P 		928
C 1964.1
(0.5)
P 		1605.2
(-1.6)
P 		1382.7
(-3)
P 		1385.4
(-3)
P 		1464.7
(-2.5)
P 		2371.3
(3)
P 		989
avr 1754.1
(-0.2) 		1550.3
(-2.2) 		1467.8
(-3) 		1512.7
(-2.6) 		1782.4
(0) 		2089.6
(3) 		622
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 432
1 2 3 4 range
A 509.8
(3)
P 		248.6
(-2)
P 		405.8
(1)
P 		197.7
(-3)
P 		312
B 356.9
(1.8)
P 		373.3
(3)
P 		288.3
(-3)
P 		336.4
(0.4)
P 		85
C 567.7
(2)
P 		544.9
(1.7)
P 		629.6
(3)
P 		246.9
(-3)
P 		383
avr 478.1
(3) 		388.9
(0.5) 		441.2
(2) 		260.3
(-3) 		218

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 525
1 2 3 4 5 6 range
A 309.9
(-3)
P 		545.4
(2.3)
P 		410.9
(-0.7)
P 		369.2
(-1.7)
P 		577
(3)
P 		446.8
(0.1)
P 		267
B 562.8
(0.3)
P 		503.3
(-0.4)
P 		275.4
(-3)
P 		449.5
(-1)
P 		800.5
(3)
P 		769
(2.6)
P 		525
C 728
(2.2)
P 		489.8
(-0.5)
P 		351.9
(-2.1)
P 		278.6
(-3)
P 		474
(-0.7)
P 		793.8
(3)
P 		515
avr 533.6
(0.5) 		512.8
(0.1) 		346.1
(-3) 		365.8
(-2.6) 		617.2
(2) 		669.9
(3) 		324
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173396_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.27671
Sequence Type Exemplar sequence
Representative Public ID AV178078 NCBI
Target Description AV178078_rc /REP_DB=TREMBL Accession /GB=AV178078 /FEA=Transcript Cluster /DEF=Caenorhabditis elegans cDNA clone:yk537g12 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Transcript 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_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
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:9428965-9429323(-) 96.99 96.99
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 NP_776994 poly(A) binding protein, nuclear 1 [Bos taurus] emb|CAA62006.1| polyA binding protein II [Bos taurus] sp|Q28165|PABP2_BOVIN Polyadenylate-binding protein 2 (Poly(A)-binding protein 2) (PolyA binding protein II) (PABII) (Polyadenylate-binding nuclear protein 1) (Nuclear poly(A)-binding protein 1) 1.0E-43
Protein Domains
Database ID Description E-Value
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 4.9E-19
Sequence
Target Sequence 
>C. ELEGANS:173396_S_AT
ttcgccccgtactaagaactcacgagaagacagattaaatcaaactcgnnnnnttatacc
tttatctgtacgttcggcgcaattcctgcccgcccattattccggaacttatccttttnc
ctttcttgagatcttctatgagtttcccttnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntcacaaannnnnnnnnnnnnnnnn
nnnnnnnnnntacaaccacgcattattcactgtctctcgttnnnccgatcggcttgtggc
ctacatgttttattgtctaccaa

BLASTn GenBank NR
Note: "n"'s represent regions that are not probed by the probe sequences.
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTCGCCCCGTACTAAGAACTCACGA 85 697 21 Antisense
GCCCCGTACTAAGAACTCACGAGAA 175 1 24 Antisense
GAACTCACGAGAAGACAGATTAAAT 405 349 36 Antisense
TATACCTTTATCTGTACGTTCGGCG 374 659 75 Antisense
CCTTTCTTGAGATCTTCTATGAGTT 356 269 140 Antisense
TTGAGATCTTCTATGAGTTTCCCTT 143 707 146 Antisense
ACAACCACGCATTATTCACTGTCTC 320 113 272 Antisense
CGATCGGCTTGTGGCCTACATGTTT 306 249 306 Antisense
TCGGCTTGTGGCCTACATGTTTTAT 235 607 309 Antisense
GTGGCCTACATGTTTTATTGTCTAC 577 491 316 Antisense
GCCTACATGTTTTATTGTCTACCAA 570 281 319 Antisense
Sequence Source Affymetrix Proprietary Database