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[190187_at] RNA-binding protein

Description H12I13.4 /REP_DB=WormBase Gene ID /WP=CE20960 /TR=Q9N5M6 /GB=AAF39879.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=RNA-binding protein
Cluster 6grp_total > 97      4grp_total > 24      6grp_cgc > 69      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 85
1 2 3 4 range
A 31.2
(-3)
A 		37
(-2.2)
A 		74.8
(3)
A 		74.1
(2.9)
A 		44
B 23.4
(-3)
A 		53.6
(1.9)
A 		42.6
(0.1)
A 		60.7
(3)
P 		37
C 8
(-3)
A 		64.2
(0.9)
A 		58.1
(0.5)
A 		93.4
(3)
A 		85
avr 20.9
(-3) 		51.6
(0.3) 		58.5
(1.1) 		76.1
(3) 		55

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 248
1 2 3 4 5 6 range
A 22
(-3)
A 		26.4
(-2.9)
A 		53.3
(-2.2)
A 		102.6
(-0.9)
A 		142.8
(0.2)
A 		251.3
(3)
P 		229
B 3.2
(-3)
A 		26.3
(-2.3)
A 		26.7
(-2.2)
A 		62.7
(-1.1)
A 		156.2
(1.9)
P 		189.5
(3)
P 		186
C 12.3
(-3)
A 		27.3
(-2.6)
A 		56.8
(-1.8)
A 		49
(-2)
A 		188.5
(1.8)
P 		234
(3)
P 		222
avr 12.5
(-3) 		26.7
(-2.6) 		45.6
(-2.1) 		71.4
(-1.3) 		162.5
(1.2) 		224.9
(3) 		212
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 18
1 2 3 4 range
A 11.3
(-1.3)
A 		8
(-3)
A 		19.5
(3)
A 		10.9
(-1.5)
A 		12
B 7.5
(-3)
A 		13.2
(3)
A 		9.9
(-0.5)
A 		12.9
(2.7)
P 		6
C 2.6
(-3)
A 		18.5
(2.4)
A 		20.2
(3)
A 		15.8
(1.5)
A 		18
avr 7.1
(-3) 		13.2
(0.9) 		16.5
(3) 		13.2
(0.9) 		9

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 77
1 2 3 4 5 6 range
A 4.1
(-3)
A 		9.4
(-2.4)
A 		11.6
(-2.2)
A 		26
(-0.7)
A 		43.1
(1.1)
A 		61.2
(3)
P 		57
B 1.1
(-3)
A 		8.7
(-2.3)
A 		6.5
(-2.5)
A 		16.6
(-1.7)
A 		63.5
(2.4)
P 		70.7
(3)
P 		70
C 4.6
(-3)
A 		8.3
(-2.7)
A 		14.5
(-2.2)
A 		9.9
(-2.6)
A 		61
(1.6)
P 		78.3
(3)
P 		74
avr 3.3
(-3) 		8.8
(-2.5) 		10.9
(-2.3) 		17.5
(-1.7) 		55.9
(1.7) 		70.1
(3) 		67
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190187_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.4533
Sequence Type Exemplar sequence
Representative Public ID H12I13.4 NCBI
Target Description H12I13.4 /REP_DB=WormBase Gene ID /WP=CE20960 /TR=Q9N5M6 /GB=AAF39879.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=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_062815(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_062815 NCBI Caenorhabditis elegans Fem-3 mRNA Binding Factor family member (fbf-1) (fbf-1) mRNA, complete cds. 11/11 A 
SNAP00000034376 ENSEMBL cdna:SNAP chromosome:CEL140:II:6078504:6080828:-1 11/11 None
GENEFINDER00000034380 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:6078504:6080674:-1 11/11 None
H12I13.4 ENSEMBL cdna:known chromosome:CEL140:II:6078504:6080745:-1 gene:H12I13.4 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:6078500-6080671(-) 100.0 100.0
Public Domain and Genome References
Gene Title RNA-binding protein
Gene Symbol fbf-1
Ensembl H12I13.4
Entrez Gene 174016 Entrez gene
SwissProt Q9N5M6 EMBL-EBI
WormBase CE20960 Wormbase
Functional Annotations
Gene Ontology
GO Molecular Function (view graph)
ID Description Evidence Links
3723 RNA binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAF39879 Fem-3 mrna binding factor protein 1 [Caenorhabditis elegans] ref|NP_495216.1| Fem-3 mRNA Binding Factor family member (fbf-1) [Caenorhabditis elegans] sp|Q9N5M6|FBF1_CAEEL Fem-3 mRNA binding factor 0.0
blast NP_495220 Fem-3 mRNA Binding Factor family member (fbf-2) [Caenorhabditis elegans] gb|AAC46716.1| Fem-3 mrna binding factor protein 2 [Caenorhabditis elegans] sp|Q09312|FBF2_CAEEL Fem-3 mRNA binding factor 0.0
blast CAE59353 Hypothetical protein CBG02702 [Caenorhabditis briggsae] 1.0E-110
Protein Domains
Database ID Description E-Value
Pfam IPR001313 EMBL-EBI Pumilio/Puf RNA-binding 7.3E-5
Pfam IPR001313 EMBL-EBI Pumilio/Puf RNA-binding 7.3E-5
Sequence
Target Sequence 
>C. ELEGANS:190187_AT
tcatgcgcaatcttctttcgttatcccaggaaaagtttgcgtctcatgttgtagagaaag
cattcctacatgcaccaatggaacttcttgctgaaatgatggacgagattttcgacggat
acatgccacacccgggcactggaaaagatgctctcgatatcatgatgttccatcaattcg
gaaactacgtcgttcaatgcatgctgactatttgctgtgatgctgtgtctggaagacgac
aaacgaaagaagggagctatgaccatgcaaactcattccaagtttggctcaaaaagttgc
actcgagagttacgaaagaaaggcatcgcttgtcaaggttctcatccggcaaaaagatga
tcgagacgcttgcccatctccgttcaactcatccgatttatggactccaatcttcgggac
atgaatcattcaagacggattgcttcagtactgcttccgaacacgatggtctagagttgg
aga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCATGCGCAATCTTCTTTCGTTATC 54 623 1322 Antisense
GAAAAGTTTGCGTCTCATGTTGTAG 102 355 1351 Antisense
TGCACCAATGGAACTTCTTGCTGAA 29 579 1392 Antisense
TTTCGACGGATACATGCCACACCCG 501 617 1431 Antisense
TGCCACACCCGGGCACTGGAAAAGA 473 585 1445 Antisense
GAAGGGAGCTATGACCATGCAAACT 232 335 1570 Antisense
TGACCATGCAAACTCATTCCAAGTT 109 571 1581 Antisense
AGTTTGGCTCAAAAAGTTGCACTCG 419 61 1602 Antisense
CCAATCTTCGGGACATGAATCATTC 419 277 1728 Antisense
ACTGCTTCCGAACACGATGGTCTAG 45 93 1771 Antisense
GAACACGATGGTCTAGAGTTGGAGA 269 351 1780 Antisense
Sequence Source Affymetrix Proprietary Database