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[173647_s_at] collagen

Description CEK065H3R_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=C53B4.5 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D65671 /WB_GENE_ID=C53B4.5 /WP=CE03091 /CHR=4 /FEA=Genomic Cluster /DEF=collagen; C.elegans cDNA clone yk65h3 : 3prime end, single read.
Cluster 6grp_high1_10_10 > 91      6grp_total > 93      4grp_total > 49      6grp_cgc > 99      6grp_high1_sub > 05      6grp_total_sub > Hat      6grp_rule_based > S5      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 272
1 2 3 4 range
A 42.4
(-2.5)
A 		291.3
(3)
P 		174.8
(0.4)
P 		19.8
(-3)
A 		272
B 32.6
(-3)
A 		159.4
(0.9)
P 		225.5
(3)
P 		37.3
(-2.9)
A 		193
C 28.3
(-3)
A 		270.4
(3)
P 		270.7
(3)
P 		41.3
(-2.7)
A 		242
avr 34.4
(-3) 		240.4
(3) 		223.7
(2.5) 		32.8
(-3) 		208

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 8770
1 2 3 4 5 6 range
A 21.2
(-3)
A 		148.6
(-2.9)
P 		173.1
(-2.9)
P 		131.6
(-2.9)
P 		6694
(3)
P 		1292.1
(-1.9)
P 		6673
B 82.4
(-3)
M 		137.2
(-2.9)
P 		124.1
(-3)
P 		231.8
(-2.9)
P 		6647.6
(3)
P 		1536.7
(-1.7)
P 		6565
C 43.5
(-3)
P 		140.4
(-2.9)
P 		134.4
(-2.9)
P 		94.7
(-3)
A 		8790.7
(3)
P 		1056.4
(-2.3)
P 		8747
avr 49
(-3) 		142.1
(-2.9) 		143.9
(-2.9) 		152.7
(-2.9) 		7377.4
(3) 		1295.1
(-2) 		7328
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 91
1 2 3 4 range
A 15.4
(-1.8)
A 		63.2
(3)
P 		45.7
(1.3)
P 		2.9
(-3)
A 		60
B 10.4
(-2.7)
A 		39.4
(1.3)
P 		52.3
(3)
P 		8
(-3)
A 		44
C 9.4
(-2.8)
A 		77.8
(1.9)
P 		94.3
(3)
P 		7
(-3)
A 		87
avr 11.7
(-2.4) 		60.1
(2.6) 		64.1
(3) 		6
(-3) 		58

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2841
1 2 3 4 5 6 range
A 3.9
(-3)
A 		52.8
(-2.9)
P 		37.7
(-2.9)
P 		33.4
(-2.9)
P 		2020
(3)
P 		314.6
(-2.1)
P 		2016
B 28.7
(-3)
M 		45.7
(-3)
P 		30.1
(-3)
P 		61.4
(-2.9)
P 		2700.8
(3)
P 		573
(-1.8)
P 		2672
C 16.1
(-3)
P 		42.8
(-2.9)
P 		34.2
(-3)
P 		19.1
(-3)
A 		2844.5
(3)
P 		353.6
(-2.3)
P 		2828
avr 16.2
(-3) 		47.1
(-2.9) 		34
(-3) 		38
(-2.9) 		2521.8
(3) 		413.7
(-2) 		2506
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173647_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.24567
Sequence Type Exemplar sequence
Representative Public ID CEK065H3R NCBI
Target Description CEK065H3R_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=C53B4.5 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D65671 /WB_GENE_ID=C53B4.5 /WP=CE03091 /CHR=4 /FEA=Genomic Cluster /DEF=collagen; C.elegans cDNA clone yk65h3 : 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_069160(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069160 NCBI Caenorhabditis elegans C53B4.5 (collagen) mRNA, complete cds. 11/11 A 
SNAP00000003708 ENSEMBL cdna:SNAP chromosome:CEL140:IV:8978906:8979775:-1 11/11 None
GENEFINDER00000003712 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:8978906:8979775:-1 11/11 None
C53B4.5 ENSEMBL cdna:known chromosome:CEL140:IV:8978803:8979775:-1 gene:C53B4.5 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:8978837-8979782(-) 91.64 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-119
Ensembl C53B4.5
Entrez Gene 177715 Entrez gene
SwissProt Q18799 EMBL-EBI
WormBase CE03091 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 CAA92453 Hypothetical protein C53B4.5 [Caenorhabditis elegans] ref|NP_501561.1| C53B4.5 [Caenorhabditis elegans] 9.0E-50
blast CAE74080 Hypothetical protein CBG21735 [Caenorhabditis briggsae] 3.0E-46
blast CAB97232 Hypothetical protein C24F3.6 [Caenorhabditis elegans] ref|NP_501867.1| COLlagen family member (col-124) [Caenorhabditis elegans] 4.0E-40
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.2E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 8.5E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 8.7E-13
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_501561.1 1 12-34
C53B4.5 1 12-34
SNAP00000003708 1 12-34
GENEFINDER00000003712 1 12-34
Sequence
Target Sequence 
>C. ELEGANS:173647_S_AT
gccaggagcaccaggtcttaacggaaatccaggacgcccaccaaaggagccatgtgagcc
aatcaccccaccaccatgcaagccatgcccagaaggaccaccaggaccagccggaccacc
aggaccacaaggaaacaagggaccactcggaccaccaggaccaccaggaccagaaggacc
aaatggaactgcaggaaacaagggaccagctggaccaccaggaccaggaggaaagccagg
accagctggaccaccaggagagaatggacgcaatggagagccacaaccaggatcaccagg
agagccaggacgtccaggacaaccaggatcccgcggaccagctggacaaccaggaaagga
tggagctcaaggaggaccaggagagaagggagccaacggagaaccaggacaaccaggaag
agacggacaaccaggacgtccaggacagccaggacgcgatggacatccaggagagaaggg
agtctgtccaaaatactgtgctctcgatggtggagtcttcttcgaggatggatcccgtcg
tt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCCAGGAGCACCAGGTCTTAACGGA 556 279 340 Antisense
GCACCAGGTCTTAACGGAAATCCAG 176 315 347 Antisense
GGACCAAATGGAACTGCAGGAAACA 363 523 515 Antisense
AATGGAACTGCAGGAAACAAGGGAC 330 161 521 Antisense
GAATGGACGCAATGGAGAGCCACAA 19 333 601 Antisense
GACGCAATGGAGAGCCACAACCAGG 478 377 606 Antisense
ATGGAGAGCCACAACCAGGATCACC 117 53 612 Antisense
GAGAAGGGAGCCAACGGAGAACCAG 132 391 722 Antisense
CAAAATACTGTGCTCTCGATGGTGG 647 189 828 Antisense
GTGCTCTCGATGGTGGAGTCTTCTT 609 479 837 Antisense
TTCTTCGAGGATGGATCCCGTCGTT 140 669 857 Antisense
Sequence Source Affymetrix Proprietary Database