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[185549_at] KH domain family of RNA binding proteins.

Description M7.6 /REP_DB=WormBase Gene ID /WP=CE03486 /CHR=4 /FEA=Sanger Annotation /DEF=(HINXTON) TR:Q21595 protein_id:CAA92748.1
Cluster 6grp_high1_10_10 > 61      6grp_total > 61      4grp_total > 0      6grp_cgc > 93      6grp_high1_sub > 04      6grp_cgc_sub > 03      6grp_total_sub > Hat      6grp_rule_based > S4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 193
1 2 3 4 range
A 125.3
(1.7)
P 		58.3
(-3)
A 		137.9
(2.6)
P 		143.7
(3)
P 		85
B 86.9
(-3)
P 		96.3
(-1.8)
A 		133.3
(3)
P 		133.3
(3)
P 		46
C 124.4
(-1.4)
P 		77.1
(-3)
M 		158.8
(-0.2)
P 		251.6
(3)
P 		175
avr 112.2
(-0.9) 		77.2
(-3) 		143.3
(1) 		176.2
(3) 		99

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 215
1 2 3 4 5 6 range
A 46.7
(-3)
A 		175.8
(1.2)
P 		210.4
(2.3)
P 		231
(3)
P 		108.1
(-1)
P 		131.7
(-0.2)
P 		184
B 145.4
(-1.3)
P 		124.7
(-2.1)
P 		261.5
(3)
P 		251.5
(2.6)
P 		168
(-0.5)
P 		99.4
(-3)
P 		162
C 131.3
(-1.9)
P 		147.9
(-1.1)
P 		190.7
(0.9)
P 		236.6
(3)
P 		108.2
(-3)
P 		114.6
(-2.7)
P 		128
avr 107.8
(-3) 		149.5
(-1.1) 		220.9
(2.1) 		239.7
(3) 		128.1
(-2.1) 		115.2
(-2.7) 		132
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 43
1 2 3 4 range
A 45.6
(3)
P 		12.7
(-3)
A 		36
(1.2)
P 		21
(-1.5)
P 		33
B 27.7
(0.3)
P 		23.8
(-3)
A 		30.9
(3)
P 		28.4
(0.9)
P 		7
C 41.2
(0.4)
P 		22.2
(-3)
M 		55.3
(3)
P 		42.4
(0.7)
P 		33
avr 38.2
(2.3) 		19.6
(-3) 		40.7
(3) 		30.6
(0.1) 		21

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 60
1 2 3 4 5 6 range
A 8.6
(-3)
A 		62.5
(3)
P 		45.8
(1.1)
P 		58.6
(2.6)
P 		32.6
(-0.3)
P 		32.1
(-0.4)
P 		54
B 50.6
(-0.4)
P 		41.5
(-2.2)
P 		63.5
(2.1)
P 		66.6
(2.7)
P 		68.3
(3)
P 		37.1
(-3)
P 		31
C 48.7
(3)
P 		45.1
(1.4)
P 		48.5
(2.9)
P 		47.6
(2.5)
P 		35
(-3)
P 		38.4
(-1.5)
P 		14
avr 36
(-3) 		49.7
(0.8) 		52.6
(1.6) 		57.6
(3) 		45.3
(-0.4) 		35.9
(-3) 		22
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 185549_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.9700
Sequence Type Exemplar sequence
Representative Public ID M7.6 NCBI
Target Description M7.6 /REP_DB=WormBase Gene ID /WP=CE03486 /CHR=4 /FEA=Sanger Annotation /DEF=(HINXTON) TR:Q21595 protein_id:CAA92748.1
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_069666(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069666 NCBI Caenorhabditis elegans BiCaudal C (Drosophila) homolog family member (bcc-1) (bcc-1) mRNA, complete cds. 11/11 A 
SNAP00000010384 ENSEMBL cdna:SNAP chromosome:CEL140:IV:11086256:11089355:-1 10/11 None
GENEFINDER00000010400 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:11086163:11089664:-1 10/11 None
M7.3 ENSEMBL cdna:known chromosome:CEL140:IV:11086062:11092524:-1 gene:M7.3 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
chrIV:11087631-11088866(-) 99.7 100.0
Public Domain and Genome References
Gene Title KH domain family of RNA binding proteins.
Gene Symbol bcc-1
Ensembl M7.3
Entrez Gene 178008 Entrez gene
SwissProt Q21593 EMBL-EBI
WormBase CE28064 Wormbase
Functional Annotations
Gene Ontology
GO Molecular Function (view graph)
ID Description Evidence Links
3676 nucleic acid binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA92750 Hypothetical protein M7.3 [Caenorhabditis elegans] ref|NP_502067.1| BiCaudal C (Drosophila) homolog family member (bcc-1) [Caenorhabditis elegans] 0.0
blast CAE61995 Hypothetical protein CBG06003 [Caenorhabditis briggsae] 0.0
blast CAE61995 Hypothetical protein CBG06003 [Caenorhabditis briggsae] 1.0E-179
blast T23821 hypothetical protein M7.4 - Caenorhabditis elegans 1.0E-103
blast T23821 hypothetical protein M7.4 - Caenorhabditis elegans 3.0E-98
Protein Domains
Database ID Description E-Value
Pfam IPR004087 EMBL-EBI KH 1.3E-12
Pfam IPR001660 EMBL-EBI Sterile alpha motif SAM 2.6E-9
Pfam IPR001660 EMBL-EBI Sterile alpha motif SAM 1.3E-6
Pfam IPR004087 EMBL-EBI KH 1.3E-12
Pfam IPR001660 EMBL-EBI Sterile alpha motif SAM 2.6E-9
Sequence
Target Sequence 
>C. ELEGANS:185549_AT
caggctccgagaagtgtgcaacaagaacaacgtgaccattcaaacatttccagaaacaca
atcaatttccattgttggtcctccatcgggagtattaaataaaattttgaagggtctttc
aagtgtgacagttcaatttgattgtaatatgatggatattcattatccagttcaacaatt
ggaacaagaaagaggaatacaagttacgtgtaaacgaaaaaacggggatattatgaccat
aacaatgaaatcaacagaatcaaaattagcagaagttcttcaatctcgtgaattactgtt
agctctaccaccaacaacatattcatctcctgatgattatgatccgaatcctgtgatgag
cagaccacctagtttaacacctttgcaaactgaaatggcatctggagtacgagtattttt
gactccgcccattgaatctccaaaatctccagatccagaggactctcc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CAGGCTCCGAGAAGTGTGCAACAAG 570 207 162 Antisense
ACGTGACCATTCAAACATTTCCAGA 436 95 191 Antisense
CATTGTTGGTCCTCCATCGGGAGTA 424 215 231 Antisense
GCAGAAGTTCTTCAATCTCGTGAAT 428 311 430 Antisense
GAATTACTGTTAGCTCTACCACCAA 695 323 451 Antisense
ACCACCAACAACATATTCATCTCCT 410 85 468 Antisense
GAATCCTGTGATGAGCAGACCACCT 273 329 507 Antisense
GACCACCTAGTTTAACACCTTTGCA 302 381 524 Antisense
GTACGAGTATTTTTGACTCCGCCCA 372 457 568 Antisense
TCCGCCCATTGAATCTCCAAAATCT 208 595 585 Antisense
AATCTCCAGATCCAGAGGACTCTCC 223 169 605 Antisense
Sequence Source Affymetrix Proprietary Database