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[173650_s_at] collagen

Description CEK065D1R_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=ZK265.2 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D65641 /WB_GENE_ID=ZK265.2 /WP=CE15291 /CHR=1 /FEA=Genomic Cluster /DEF=collagen; C.elegans cDNA clone yk65d1 : 3prime end, single read.
Cluster 6grp_total > 94      4grp_total > 25      6grp_cgc > 88      6grp_total_sub > Hat      6grp_rule_based > S5      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 147
1 2 3 4 range
A 58.3
(-2.7)
A 		105.3
(3)
A 		102.8
(2.7)
A 		55.8
(-3)
A 		50
B 64.6
(-3)
A 		79.5
(-2.4)
A 		79.8
(-2.3)
A 		202.7
(3)
A 		138
C 61.2
(-3)
A 		66.9
(-0.8)
A 		67
(-0.8)
A 		76.9
(3)
A 		16
avr 61.4
(-3) 		83.9
(-0.3) 		83.2
(-0.4) 		111.8
(3) 		50

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2997
1 2 3 4 5 6 range
A 61.5
(-3)
A 		70.5
(-2.9)
A 		42.1
(-3)
A 		1181
(-0.2)
P 		2516.7
(3)
P 		1218.1
(-0.1)
P 		2475
B 55.8
(-3)
A 		65.9
(-3)
A 		64.6
(-3)
A 		1164.7
(0.1)
P 		2213.3
(3)
P 		1430.4
(0.8)
P 		2158
C 48.2
(-3)
A 		56.3
(-3)
A 		63.7
(-3)
A 		1142.6
(-0.8)
P 		3039.5
(3)
P 		1548.4
(0)
P 		2991
avr 55.2
(-3) 		64.2
(-3) 		56.8
(-3) 		1162.8
(-0.4) 		2589.8
(3) 		1399
(0.2) 		2535
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 35
1 2 3 4 range
A 21.2
(1.2)
A 		22.8
(1.7)
A 		26.9
(3)
A 		8.2
(-3)
A 		19
B 20.6
(-2.5)
A 		19.6
(-2.7)
A 		18.5
(-3)
A 		43.2
(3)
A 		25
C 20.2
(1.2)
A 		19.2
(0.6)
A 		23.4
(3)
A 		13
(-3)
A 		10
avr 20.7
(-2.5) 		20.5
(-3) 		22.9
(3) 		21.5
(-0.5) 		2

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 974
1 2 3 4 5 6 range
A 11.3
(-3)
A 		25.1
(-2.9)
A 		9.2
(-3)
A 		299.5
(-0.7)
P 		759.4
(3)
P 		296.6
(-0.7)
P 		750
B 19.4
(-3)
A 		21.9
(-3)
A 		15.7
(-3)
A 		308.5
(-1)
P 		899.3
(3)
P 		533.4
(0.5)
P 		884
C 17.9
(-3)
A 		17.2
(-3)
A 		16.2
(-3)
A 		229.8
(-1.7)
P 		983.6
(3)
P 		518.3
(0.1)
P 		967
avr 16.2
(-3) 		21.4
(-2.9) 		13.7
(-3) 		279.3
(-1.2) 		880.8
(3) 		449.4
(0) 		867
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173650_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.22689
Sequence Type Exemplar sequence
Representative Public ID CEK065D1R NCBI
Target Description CEK065D1R_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=ZK265.2 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D65641 /WB_GENE_ID=ZK265.2 /WP=CE15291 /CHR=1 /FEA=Genomic Cluster /DEF=collagen; C.elegans cDNA clone yk65d1 : 3prime 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_059844(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059844 NCBI Caenorhabditis elegans ZK265.2 (collagen) mRNA, complete cds. 11/11 None
SNAP00000032247 ENSEMBL cdna:SNAP chromosome:CEL140:I:8251879:8253109:-1 11/11 None
GENEFINDER00000032257 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:8251879:8253073:-1 11/11 None
ZK265.2 ENSEMBL cdna:known chromosome:CEL140:I:8251825:8253073:-1 gene:ZK265.2 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
chrI:8251771-8253005(-) 98.99 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-63
Ensembl ZK265.2
Entrez Gene 172607 Entrez gene
SwissProt Q94399 EMBL-EBI
WormBase CE15291 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6817 phosphate transport inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5737 cytoplasm inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
42302 structural constituent of cuticle inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB03513 Hypothetical protein ZK265.2 [Caenorhabditis elegans] ref|NP_492245.1| ZK265.2 [Caenorhabditis elegans] 8.0E-45
blast CAE56688 Hypothetical protein CBG24466 [Caenorhabditis briggsae] 8.0E-29
blast CAE56687 Hypothetical protein CBG24465 [Caenorhabditis briggsae] 1.0E-21
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 3.7E-22
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.2E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.8E-12
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 3.7E-22
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.2E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.8E-12
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_492245.1 1 7-29
ZK265.2 1 7-29
SNAP00000032247 1 20-42
GENEFINDER00000032257 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:173650_S_AT
aaccaggaccagttggtgcaccaggagctccaggaggaccaggaagagatggagaaccag
gagagaatggacaagatggacaacaaggaccagaagggccagctggagctgatggacaac
caggacatccaggaccagacggaccatcaggggatgttggagaggttggagctccaggag
ctgatgctgcctattgtccatgtccaccaagatccgctgagatggctgcaactggatcat
ccgactcccaaccagcgtcttatgaagctccagctccagcagcaacaaagggatatgatt
ctccagctccagcagcaccaaagggatatgatgctccagctccaactgctccacatccac
caccaccagctccagttgctccaccaaagcttcacgattatgaatcgccagctccagttg
ctgatgctcatgatgctgctccagctgcccagccatataagagaagaaaggtggccagag
ctcatatggttt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AACCAGGACCAGTTGGTGCACCAGG 1 147 666 Antisense
GACCAGACGGACCATCAGGGGATGT 455 383 798 Antisense
AAGATCCGCTGAGATGGCTGCAACT 607 153 874 Antisense
ACTCCCAACCAGCGTCTTATGAAGC 30 99 909 Antisense
AAGGGATATGATTCTCCAGCTCCAG 528 159 953 Antisense
CAAAGGGATATGATGCTCCAGCTCC 411 193 984 Antisense
TTGCTCCACCAAAGCTTCACGATTA 27 703 1041 Antisense
AGCTCCAGTTGCTGATGCTCATGAT 430 81 1075 Antisense
CTGATGCTCATGATGCTGCTCCAGC 251 237 1086 Antisense
CTCCAGCTGCCCAGCCATATAAGAG 624 235 1104 Antisense
AAGGTGGCCAGAGCTCATATGGTTT 400 159 1133 Antisense
Sequence Source Affymetrix Proprietary Database