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[193930_at] Low-density lipoprotein receptor domain class A (2 domains)

Description F09B12.5 /REP_DB=WormBase Gene ID /WP=CE17647 /TR=O62147 /GB=CAB05479.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=Low-density lipoprotein receptor domain class A (2 domains)
Cluster 6grp_total > 79      4grp_total > 10      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 122
1 2 3 4 range
A 5.8
(-2.9)
A 		5
(-3)
A 		12.9
(-2.3)
A 		75.3
(3)
A 		70
B 7.3
(-3)
A 		22
(1.9)
A 		10.8
(-1.8)
A 		25.4
(3)
A 		18
C 12
(-2.9)
A 		22.2
(-2.3)
A 		9.1
(-3)
A 		127.1
(3)
A 		118
avr 8.4
(-3) 		16.4
(-2.3) 		10.9
(-2.8) 		75.9
(3) 		68

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 22
1 2 3 4 5 6 range
A 13.1
(-0.7)
A 		12.2
(-1)
A 		5.1
(-3)
A 		7.3
(-2.4)
A 		7.6
(-2.3)
A 		25.9
(3)
A 		21
B 9.5
(-1.3)
A 		14
(0.2)
A 		4.3
(-3)
A 		5.6
(-2.6)
A 		22.3
(3)
A 		5.3
(-2.7)
A 		18
C 5.3
(-2.5)
A 		8.5
(-0.9)
A 		13.7
(1.7)
A 		16.2
(3)
A 		7.2
(-1.5)
A 		4.3
(-3)
A 		12
avr 9.3
(-1) 		11.6
(2) 		7.7
(-3) 		9.7
(-0.4) 		12.4
(3) 		11.8
(2.2) 		5
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 20
1 2 3 4 range
A 2.1
(-2.4)
A 		1.1
(-3)
A 		3.4
(-1.6)
A 		11
(3)
A 		10
B 2.3
(-3)
A 		5.4
(3)
A 		2.5
(-2.6)
A 		5.4
(3)
A 		3
C 4
(-2.7)
A 		6.4
(-1.9)
A 		3.2
(-3)
A 		21.4
(3)
A 		18
avr 2.8
(-3) 		4.3
(-2.1) 		3
(-2.9) 		12.6
(3) 		10

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 8
1 2 3 4 5 6 range
A 2.4
(-1.5)
A 		4.3
(0.7)
A 		1.1
(-3)
A 		1.8
(-2.2)
A 		2.3
(-1.6)
A 		6.3
(3)
A 		5
B 3.3
(-1.3)
A 		4.7
(-0.3)
A 		1
(-3)
A 		1.5
(-2.6)
A 		9.1
(3)
A 		2
(-2.3)
A 		8
C 2
(-1.3)
A 		2.6
(0.4)
A 		3.5
(3)
A 		3.3
(2.4)
A 		2.3
(-0.4)
A 		1.4
(-3)
A 		2
avr 2.6
(-1.4) 		3.9
(1.4) 		1.9
(-3) 		2.2
(-2.3) 		4.6
(3) 		3.2
(-0.1) 		3
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193930_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17443
Sequence Type Exemplar sequence
Representative Public ID F09B12.5 NCBI
Target Description F09B12.5 /REP_DB=WormBase Gene ID /WP=CE17647 /TR=O62147 /GB=CAB05479.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=Low-density lipoprotein receptor domain class A (2 domains)
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_078106(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_078106 NCBI Caenorhabditis elegans F09B12.5 (F09B12.5) mRNA, complete cds. 11/11 None
SNAP00000031081 ENSEMBL cdna:SNAP chromosome:CEL140:X:15084812:15088051:1 11/11 None
GENEFINDER00000031089 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:15084812:15093291:1 11/11 None
F09B12.5 ENSEMBL cdna:known chromosome:CEL140:X:15084784:15088051:1 gene:F09B12.5 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
chrX:15084783-15088051(+) 95.11 100.0
Public Domain and Genome References
Gene Title Low-density lipoprotein receptor domain class A (2 domains)
Ensembl F09B12.5
Entrez Gene 184225 Entrez gene
SwissProt O62147 EMBL-EBI
WormBase CE17647 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAC35810 Hypothetical protein F09B12.6 [Caenorhabditis elegans] ref|NP_510508.1| FLuoRide resistant family member (flr-4) [Caenorhabditis elegans] sp|Q9NLA1|FLR4_CAEEL Serine/threonine-protein kinase flr-4 (Fluoride resistant protein 4) dbj|BAA89795.1| FLR-4 [Caenorhabditis elegans] 0.0
blast CAE63261 Hypothetical protein CBG07634 [Caenorhabditis briggsae] 0.0
blast CAB05479 Hypothetical protein F09B12.5 [Caenorhabditis elegans] emb|CAB08563.1| Hypothetical protein F09B12.5 [Caenorhabditis elegans] ref|NP_510507.1| F09B12.5 [Caenorhabditis elegans] 1.0E-155
blast CAB05479 Hypothetical protein F09B12.5 [Caenorhabditis elegans] emb|CAB08563.1| Hypothetical protein F09B12.5 [Caenorhabditis elegans] ref|NP_510507.1| F09B12.5 [Caenorhabditis elegans] 1.0E-133
blast CAB05479 Hypothetical protein F09B12.5 [Caenorhabditis elegans] emb|CAB08563.1| Hypothetical protein F09B12.5 [Caenorhabditis elegans] ref|NP_510507.1| F09B12.5 [Caenorhabditis elegans] 1.0E-110
blast CAE63262 Hypothetical protein CBG07635 [Caenorhabditis briggsae] 2.0E-79
blast CAE63262 Hypothetical protein CBG07635 [Caenorhabditis briggsae] 5.0E-77
blast AAR83314 very low density lipoprotein receptor [Macaca mulatta] ref|NP_001028079.1| very low density lipoprotein receptor [Macaca mulatta] 3.0E-19
Protein Families
Method ID Description E-Value
hanks 3.1.5 CMCG Group; CMGC I Cyclin-dependent (CDKs) and close relatives; Cdk6 3.0E-17
Protein Domains
Database ID Description E-Value
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 7.0E-17
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 4.3E-5
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 7.0E-17
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 4.1E-9
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 4.3E-5
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 4.3E-5
Pfam IPR000719 EMBL-EBI Protein kinase 0.012
Pfam IPR000719 EMBL-EBI Protein kinase 3.6E-37
Trans Membrane
ID Number Of Domains Domain Boundaries
GENEFINDER00000031089 3 731-753,760-782,802-824
Sequence
Target Sequence 
>C. ELEGANS:193930_AT
gaatgcaacaaccaccacgataagtaattctttgtccaccacaactgtagtcaagtctac
cacgacgttacccatatcaacgacaactactacaaccacaacgattactccaaaacatac
gaatctgacgacaactgccacaacaactaaaaaagttacaacaactgaaagagcacattt
ggaaaacatcctgttgactattccattgaaatcaacaacgcaatctcctgcactaacatc
ttcttctgcaaaacctacaaaacctccaactacgagtgaaacatcaaaaccaacattccc
atcaactcttccagcatatgttctccccatgacaactacatcccatccatccacccacac
caccaccacccagaaagtgattgcccgcacatttgcgtcgcagccacacacaacgtcaca
gccgaaaattgtcgtaaaattgttaaatgacagtttttcaaattcaactactgataaagc
gaaaagcacagaaagtagtgcttctcgtgcttct

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAATGCAACAACCACCACGATAAGT 186 331 570 Antisense
AAGTAATTCTTTGTCCACCACAACT 317 157 591 Antisense
TAGTCAAGTCTACCACGACGTTACC 447 651 617 Antisense
TACGAATCTGACGACAACTGCCACA 84 649 687 Antisense
AACATCCTGTTGACTATTCCATTGA 633 137 754 Antisense
ATCAACAACGCAATCTCCTGCACTA 413 27 780 Antisense
TCCTGCACTAACATCTTCTTCTGCA 683 593 795 Antisense
TCAACTCTTCCAGCATATGTTCTCC 301 631 871 Antisense
GAAAGTGATTGCCCGCACATTTGCG 318 361 942 Antisense
CACACACAACGTCACAGCCGAAAAT 109 195 974 Antisense
AGAAAGTAGTGCTTCTCGTGCTTCT 33 73 1059 Antisense
Sequence Source Affymetrix Proprietary Database