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[194239_x_at]

Description CEXT00688 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F59D8.A /5_PRIME_EXT_DB=WormBase Gene ID /GB=M80151 /WB_GENE_ID=F59D8.A /WP=CE20900 /CHR=X /FEA=Genomic Cluster /DEF=(ST.LOUIS) protein_id:AAF35966.1; wEST00688 Mixed stage, Stratagene (cat. no. 937006) Caenorhabditis elegans cDNA clone CEMSH78 similar to Vitellogenin 5, mRNA sequence.
Cluster 6grp_total > 99      4grp_total > 16      6grp_cgc > 79      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S5      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 177
1 2 3 4 range
A 106.9
(-3)
A 		158
(-0.4)
A 		174.6
(0.4)
A 		225.9
(3)
A 		119
B 96.9
(-3)
A 		100.8
(-2.7)
A 		181.2
(3)
A 		128.1
(-0.8)
A 		84
C 128.5
(-2.9)
A 		127.1
(-3)
A 		128.7
(-2.9)
A 		274.2
(3)
A 		147
avr 110.8
(-3) 		128.6
(-1.9) 		161.5
(0.1) 		209.4
(3) 		99

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 6082
1 2 3 4 5 6 range
A 111.3
(-2.9)
A 		73.5
(-2.9)
A 		19.4
(-3)
A 		69
(-2.9)
A 		5371
(3)
P 		4714.6
(2.3)
P 		5352
B 81.9
(-2.9)
A 		108.7
(-2.9)
A 		40.6
(-3)
A 		98.3
(-2.9)
A 		4318.3
(2.6)
P 		4611.7
(3)
P 		4571
C 40.9
(-3)
A 		91.5
(-2.9)
A 		117.8
(-2.9)
A 		120.1
(-2.9)
A 		6101.7
(3)
P 		4116
(1)
P 		6061
avr 78
(-3) 		91.2
(-3) 		59.3
(-3) 		95.8
(-3) 		5263.7
(3) 		4480.8
(2.1) 		5204
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 21
1 2 3 4 range
A 38.9
(-0.2)
A 		34.3
(-2.4)
A 		45.7
(3)
A 		33.1
(-3)
A 		13
B 30.9
(-0.9)
A 		24.9
(-3)
A 		42
(3)
A 		27.3
(-2.2)
A 		17
C 42.5
(0.7)
A 		36.6
(-3)
A 		44.9
(2.2)
A 		46.2
(3)
A 		10
avr 37.4
(-0.3) 		31.9
(-3) 		44.2
(3) 		35.5
(-1.2) 		12

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1970
1 2 3 4 5 6 range
A 20.5
(-2.9)
A 		26.1
(-2.9)
A 		4.2
(-3)
A 		17.5
(-3)
A 		1620.7
(3)
P 		1147.9
(1.2)
P 		1617
B 28.5
(-2.9)
A 		36.2
(-2.9)
A 		9.9
(-3)
A 		26
(-2.9)
A 		1754.5
(3)
P 		1719.7
(2.9)
P 		1745
C 15.1
(-3)
A 		27.9
(-3)
A 		30
(-3)
A 		24.2
(-3)
A 		1974.4
(3)
P 		1377.9
(1.2)
P 		1959
avr 21.4
(-3) 		30.1
(-2.9) 		14.7
(-3) 		22.6
(-3) 		1783.2
(3) 		1415.2
(1.8) 		1769
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 194239_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.26245
Sequence Type Exemplar sequence
Representative Public ID CEXT00688 NCBI
Target Description CEXT00688 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F59D8.A /5_PRIME_EXT_DB=WormBase Gene ID /GB=M80151 /WB_GENE_ID=F59D8.A /WP=CE20900 /CHR=X /FEA=Genomic Cluster /DEF=(ST.LOUIS) protein_id:AAF35966.1; wEST00688 Mixed stage, Stratagene (cat. no. 937006) Caenorhabditis elegans cDNA clone CEMSH78 similar to Vitellogenin 5, mRNA sequence.
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_076212(10)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_076212 NCBI Caenorhabditis elegans VITellogenin structural genes (yolk protein genes) family member (vit-3) (vit-3) mRNA, complete cds. 10/11 A 
SNAP00000016179 ENSEMBL cdna:SNAP chromosome:CEL140:X:3567445:3572527:-1 10/11 None
GENEFINDER00000016190 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:3567531:3572587:-1 9/11 None
F59D8.1.2 ENSEMBL cdna:known chromosome:CEL140:X:3567155:3572527:-1 gene:F59D8.1 10/11 A 
F59D8.1.1 ENSEMBL cdna:known chromosome:CEL140:X:3567155:3572527:-1 gene:F59D8.1 10/11 A 
F59D8.1.3 ENSEMBL cdna:known chromosome:CEL140:X:3567396:3572527:-1 gene:F59D8.1 10/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_076211 5/11 Cross Hyb Matching Probes A 
NM_076188 5/11 Cross Hyb Matching Probes A 
GENEFINDER00000029426 5/11 Cross Hyb Matching Probes None
SNAP00000029419 5/11 Cross Hyb Matching Probes None
SNAP00000036909 5/11 Cross Hyb Matching Probes None
GENEFINDER00000036913 5/11 Cross Hyb Matching Probes None
C04F6.1 5/11 Cross Hyb Matching Probes A 
F59D8.2 5/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrX:3403467-3408542(+) 97.65 97.65
chrX:3567446-3572529(-) 100.0 100.0
chrX:3558881-3563954(-) 98.92 98.92
Public Domain and Genome References
Gene Title
Gene Symbol vit-3
Ensembl F59D8.1
Entrez Gene 180647 Entrez gene
SwissProt Q9N4J2 EMBL-EBI
WormBase CE20900 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CHICKEN:GGA.4125.1.S1_AT vitellogenin I gga
HG-U133_PLUS_2:239061_AT tetra-peptide repeat homeobox-like hs
HG-U133B:239061_AT tetra-peptide repeat homeobox-like hs
U133_X3P:HS.216699.0.A1_3P_AT tetra-peptide repeat homeobox-like hs
HG-U95E:71466_AT tetra-peptide repeat homeobox-like hs
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6869 lipid transport inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
5319 lipid transporter activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAK09075 Vitellogenin structural genes (yolk protein genes) protein 3 [Caenorhabditis elegans] ref|NP_508613.1| VITellogenin structural genes (yolk protein genes) family member (vit-3) [Caenorhabditis elegans] sp|Q9N4J2|VIT3_CAEEL Vitellogenin 3 precursor 0.0
blast AAK09074 Vitellogenin structural genes (yolk protein genes) protein 4 [Caenorhabditis elegans] ref|NP_508612.1| VITellogenin structural genes (yolk protein genes) family member (vit-4) [Caenorhabditis elegans] sp|P18947|VIT4_CAEEL Vitellogenin 4 precursor 0.0
blast AAA83587 Vitellogenin structural genes (yolk protein genes) protein 5 [Caenorhabditis elegans] ref|NP_508589.1| VITellogenin structural genes (yolk protein genes) family member (vit-5) [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR001846 EMBL-EBI von Willebrand factor, type D 1.2E-40
Pfam IPR001747 EMBL-EBI Lipid transport protein, N-terminal 1.0E-126
Pfam IPR001846 EMBL-EBI von Willebrand factor, type D 1.2E-40
Pfam IPR001747 EMBL-EBI Lipid transport protein, N-terminal 1.0E-126
Trans Membrane
ID Number Of Domains Domain Boundaries
GENEFINDER00000016190 1 13-35
Sequence
Target Sequence 
>C. ELEGANS:194239_X_AT
accttattgttattcgtcttccacatggagaggttcgtttcgatggatacactgtcaaga
ccaacatgccatccgttgcttcacaaaaccaactttgcggactttgcggaaacaatgacg
gtgagagagacaatgagttcatgaccgctgacaactacgaaactgaggatgttgaggaat
tccaccgctcttaccttctcaagaacgaggaatgcgaagttgagaacgaccgcatctccg
agaagaagaactacagaaacaaatggaacagagaagagaagaagtccgactacgtgagca
gctccgactatgagaacaactacgatgaaaaggaaactgagaacgaacttttcaagaaga
ccctcatcaaggagttctccaaccgcgtctgcttctccatcgagccagtctctgagtgcc
gccgtggactcgaatccgagaagacttccaacgagaagatccgtttcacttgcatgccac
gccacagcaagaacgcccgccgtttcttgaaggaggctcgtgagcaaactgttgccgatt
tggtcgatttcccagtc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ACCTTATTGTTATTCGTCTTCCACA 563 87 4221 Antisense
AAGACCAACATGCCATCCGTTGCTT 688 153 4277 Antisense
GTTCATGACCGCTGACAACTACGAA 59 445 4357 Antisense
GGATGTTGAGGAATTCCACCGCTCT 301 513 4387 Antisense
CCGCTCTTACCTTCTCAAGAACGAG 316 263 4405 Antisense
TTGAGAACGACCGCATCTCCGAGAA 113 683 4440 Antisense
AGAAGTCCGACTACGTGAGCAGCTC 349 75 4500 Antisense
GACCCTCATCAAGGAGTTCTCCAAC 39 383 4579 Antisense
GAGAAGATCCGTTTCACTTGCATGC 38 393 4673 Antisense
GCCCGCCGTTTCTTGAAGGAGGCTC 143 285 4715 Antisense
TGCCGATTTGGTCGATTTCCCAGTC 397 585 4753 Antisense
Sequence Source Affymetrix Proprietary Database