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[175061_s_at] RNA binding protein

Description AV196982 /REP_DB=TREMBL Accession /GB=AV196982 /CHR=4 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk660g7 : 5prime end, single read.
Cluster 6grp_total > 68      4grp_total > 18      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 49
1 2 3 4 range
A 1.6
(-3)
A 		8.5
(-2.1)
A 		5
(-2.6)
A 		49.6
(3)
A 		48
B 4.4
(-2.3)
A 		26.1
(3)
A 		1.7
(-3)
A 		2.1
(-2.9)
A 		24
C 0.8
(-3)
A 		7.1
(-1.9)
A 		0.8
(-3)
A 		34
(3)
A 		33
avr 2.3
(-3) 		13.9
(-0.4) 		2.5
(-3) 		28.6
(3) 		26

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 103
1 2 3 4 5 6 range
A 5.4
(-2.7)
A 		1.1
(-3)
A 		2.3
(-2.9)
A 		3.8
(-2.8)
A 		20.8
(-1.8)
A 		101.1
(3)
P 		100
B 23.3
(-1.7)
A 		0.9
(-3)
A 		8.4
(-2.6)
A 		13.9
(-2.2)
A 		12.3
(-2.3)
A 		104
(3)
P 		103
C 0.9
(-3)
A 		1.5
(-3)
A 		1.3
(-3)
A 		9.9
(-2.3)
A 		24.3
(-1.3)
A 		83.2
(3)
P 		82
avr 9.9
(-2.4) 		1.2
(-3) 		4
(-2.8) 		9.2
(-2.5) 		19.1
(-1.9) 		96.1
(3) 		95
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 7
1 2 3 4 range
A 0.6
(-3)
A 		1.9
(-1.8)
A 		1.3
(-2.4)
A 		7.3
(3)
A 		7
B 1.4
(-2)
A 		6.4
(3)
A 		0.4
(-3)
A 		0.5
(-2.9)
A 		6
C 0.3
(-3)
A 		2.1
(-1)
A 		0.3
(-3)
A 		5.7
(3)
A 		5
avr 0.8
(-2.8) 		3.5
(1.4) 		0.7
(-3) 		4.5
(3) 		4

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 39
1 2 3 4 5 6 range
A 1
(-2.9)
A 		0.4
(-3)
A 		0.5
(-3)
A 		1
(-2.9)
A 		6.3
(-1.5)
A 		24.6
(3)
P 		24
B 8.1
(-1.8)
A 		0.3
(-3)
A 		2
(-2.7)
A 		3.7
(-2.5)
A 		5
(-2.3)
A 		38.8
(3)
P 		39
C 0.3
(-3)
A 		0.5
(-3)
A 		0.3
(-3)
A 		2
(-2.6)
A 		7.9
(-1.3)
A 		27.8
(3)
P 		28
avr 3.1
(-2.5) 		0.4
(-3) 		0.9
(-2.9) 		2.2
(-2.6) 		6.4
(-1.8) 		30.4
(3) 		30
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 175061_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.21524
Sequence Type Exemplar sequence
Representative Public ID AV196982 NCBI
Target Description AV196982 /REP_DB=TREMBL Accession /GB=AV196982 /CHR=4 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk660g7 : 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_068265(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_068265 NCBI Caenorhabditis elegans T08B6.5 (T08B6.5) mRNA, complete cds. 11/11 A 
SNAP00000024942 ENSEMBL cdna:SNAP chromosome:CEL140:IV:4889919:4890504:1 9/11 None
GENEFINDER00000024953 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:4889919:4890504:1 9/11 None
T08B6.5 ENSEMBL cdna:known chromosome:CEL140:IV:4889908:4890619:1 gene:T08B6.5 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
chrIV:4890335-4890615(+) 100.0 100.0
Public Domain and Genome References
Gene Title RNA binding protein
Ensembl T08B6.5
Entrez Gene 177260 Entrez gene
SwissProt O44530 EMBL-EBI
WormBase CE33690 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast NP_500666 T08B6.5 [Caenorhabditis elegans] gb|AAO91699.1| Hypothetical protein T08B6.5 [Caenorhabditis elegans] 1.0E-96
blast AAC46764 Hypothetical protein EEED8.4 [Caenorhabditis elegans] ref|NP_495022.1| EEED8.4 [Caenorhabditis elegans] sp|Q09295|YQO4_CAEEL Hypothetical RNA-binding protein EEED8.4 in chromosome II 4.0E-38
blast AAC46772 Hypothetical protein EEED8.12 [Caenorhabditis elegans] ref|NP_495021.1| EEED8.12 [Caenorhabditis elegans] sp|Q09301|YQOC_CAEEL Hypothetical RNA-binding protein EEED8.12 in chromosome II 4.0E-38
Protein Domains
Database ID Description E-Value
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 1.0E-18
Sequence
Target Sequence 
>C. ELEGANS:175061_S_AT
ggaatgggaagaactgctactgcacaaaaaccagctcattttgcaaagagctcacatggc
aaacccggctcacatcaaggagtcactgtagtcaagtacgtgtatgtgaatgctccgatc
aatggctcgcgttcaaagagattcgctccctattaataattttaggaacaatttcttgct
ttaaattttgattttcctgtgccttttctcctgtattttcattttcaaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGAATGGGAAGAACTGCTACTGCAC 145 533 32 Antisense
GAACTGCTACTGCACAAAAACCAGC 628 347 42 Antisense
AAAACCAGCTCATTTTGCAAAGAGC 189 129 58 Antisense
TCATTTTGCAAAGAGCTCACATGGC 624 619 67 Antisense
CAAAGAGCTCACATGGCAAACCCGG 272 193 75 Antisense
CCGGCTCACATCAAGGAGTCACTGT 270 265 96 Antisense
GGCTCACATCAAGGAGTCACTGTAG 472 537 98 Antisense
GGAGTCACTGTAGTCAAGTACGTGT 569 517 110 Antisense
GTCACTGTAGTCAAGTACGTGTATG 151 465 113 Antisense
TAAATTTTGATTTTCCTGTGCCTTT 704 641 213 Antisense
TTTCTCCTGTATTTTCATTTTCAAA 641 671 236 Antisense
Sequence Source Affymetrix Proprietary Database