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[173071_s_at] collagen

Description AV177885_rc /REP_DB=TREMBL Accession /FEA=EST Transcript /REVCOMP /GB=AV177885 /DEF=Caenorhabditis elegans cDNA clone:yk535b9 : 3prime end, single read.
Cluster 6grp_total > 58      4grp_total > 18      6grp_cgc > 17      6grp_cgc_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 103
1 2 3 4 range
A 6.6
(-3)
A 		39.1
(-1)
A 		13.5
(-2.6)
A 		106.1
(3)
A 		100
B 21.2
(3)
A 		4.9
(-3)
A 		15.9
(1)
A 		20.2
(2.6)
A 		16
C 3.3
(-3)
A 		39
(2)
A 		6.4
(-2.6)
A 		46.3
(3)
A 		43
avr 10.4
(-3) 		27.7
(-0.8) 		11.9
(-2.8) 		57.5
(3) 		47

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 191
1 2 3 4 5 6 range
A 110.6
(1.3)
A 		5.5
(-3)
A 		52.2
(-1.1)
A 		6.8
(-2.9)
A 		6.1
(-3)
A 		153.1
(3)
P 		148
B 123.6
(2.7)
P 		37.4
(-1.5)
A 		5.4
(-3)
A 		6.6
(-2.9)
A 		7.7
(-2.9)
A 		129.7
(3)
P 		124
C 139.9
(1.2)
P 		26.8
(-2.4)
A 		79.6
(-0.7)
A 		11.9
(-2.9)
A 		7.7
(-3)
A 		196.1
(3)
P 		188
avr 124.7
(1.6) 		23.2
(-2.4) 		45.7
(-1.5) 		8.4
(-3) 		7.2
(-3) 		159.6
(3) 		152
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 14
1 2 3 4 range
A 2.4
(-3)
A 		8.5
(-0.2)
A 		3.5
(-2.5)
A 		15.5
(3)
A 		13
B 6.8
(3)
A 		1.2
(-3)
A 		3.7
(-0.3)
A 		4.3
(0.3)
A 		6
C 1.1
(-3)
A 		11.2
(3)
A 		2.2
(-2.3)
A 		7.8
(1)
A 		10
avr 3.4
(-2.7) 		7
(0.8) 		3.1
(-3) 		9.2
(3) 		6

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 64
1 2 3 4 5 6 range
A 20.4
(0.2)
A 		2
(-2.9)
A 		11.4
(-1.4)
A 		1.7
(-3)
A 		1.8
(-3)
A 		37.3
(3)
P 		36
B 43
(2.3)
P 		12.5
(-1.6)
A 		1.3
(-3)
A 		1.7
(-2.9)
A 		3.1
(-2.8)
A 		48.4
(3)
P 		47
C 51.8
(1.7)
P 		8.2
(-2.5)
A 		20.3
(-1.3)
A 		2.4
(-3)
A 		2.5
(-3)
A 		65.7
(3)
P 		63
avr 38.4
(1.5) 		7.6
(-2.3) 		11
(-1.9) 		1.9
(-3) 		2.5
(-2.9) 		50.5
(3) 		49
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173071_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.27066
Sequence Type Exemplar sequence
Representative Public ID AV177885 NCBI
Target Description AV177885_rc /REP_DB=TREMBL Accession /FEA=EST Transcript /REVCOMP /GB=AV177885 /DEF=Caenorhabditis elegans cDNA clone:yk535b9 : 3prime end, single read.
Cluster Evidence This cluster is supported by a EST Transcript.
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_069254(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069254 NCBI Caenorhabditis elegans F56D5.1 (collagen) mRNA, complete cds. 11/11 A 
SNAP00000006176 ENSEMBL cdna:SNAP chromosome:CEL140:IV:9394958:9396187:-1 11/11 None
GENEFINDER00000006190 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:9394958:9396187:-1 11/11 None
F56D5.1 ENSEMBL cdna:known chromosome:CEL140:IV:9394911:9396195:-1 gene:F56D5.1 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:9395026-9395289(-) 87.0 87.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-121
Ensembl F56D5.1
Entrez Gene 177771 Entrez gene
SwissProt Q20880 EMBL-EBI
WormBase CE05967 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 CAA93499 Hypothetical protein F56D5.1 [Caenorhabditis elegans] ref|NP_501655.1| F56D5.1 [Caenorhabditis elegans] 1.0E-163
blast CAA93499 Hypothetical protein F56D5.1 [Caenorhabditis elegans] ref|NP_501655.1| F56D5.1 [Caenorhabditis elegans] 1.0E-142
blast CAE58642 Hypothetical protein CBG01810 [Caenorhabditis briggsae] 1.0E-134
blast CAE58642 Hypothetical protein CBG01810 [Caenorhabditis briggsae] 1.0E-117
blast AAA83336 Dumpy : shorter than wild-type protein 8 [Caenorhabditis elegans] ref|NP_508873.1| DumPY : shorter than wild-type family member (dpy-8) [Caenorhabditis elegans] 6.0E-47
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 2.1E-6
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.8E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.4E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.8E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.4E-10
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_501655.1 1 12-31
F56D5.1 1 12-31
GENEFINDER00000006190 1 12-31
Sequence
Target Sequence 
>C. ELEGANS:173071_S_AT
ggagagcagggtggaatcggtgcaccgggagaaccaggactgccagcaacatattgtcca
tccgattgtggagttaacacgattctctcacaatttggaagtcgtgctcaacatccagaa
tcgatcaacggagaggacaatggagcacctgcagcaaatacagaagagtacaattctgaa
gaacgaattgaatcgccagctccacctgctccacagccaactaccaatcagcaaca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGAGAGCAGGGTGGAATCGGTGCAC 478 519 27 Antisense
GAACCAGGACTGCCAGCAACATATT 2 347 57 Antisense
TGCCAGCAACATATTGTCCATCCGA 633 585 67 Antisense
TTGTCCATCCGATTGTGGAGTTAAC 615 699 80 Antisense
GTGGAGTTAACACGATTCTCTCACA 210 491 94 Antisense
GATTCTCTCACAATTTGGAAGTCGT 618 431 107 Antisense
CTCAACATCCAGAATCGATCAACGG 577 227 133 Antisense
GGACAATGGAGCACCTGCAGCAAAT 652 525 161 Antisense
GGAGCACCTGCAGCAAATACAGAAG 300 519 168 Antisense
TGAAGAACGAATTGAATCGCCAGCT 300 573 203 Antisense
CACAGCCAACTACCAATCAGCAACA 482 195 238 Antisense
Sequence Source Affymetrix Proprietary Database