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[188245_at] collagen

Description F15A2.1 /REP_DB=WormBase Gene ID /WP=CE05630 /TR=Q19470 /GB=CAA94128.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 93      4grp_total > 50      6grp_cgc > 89      6grp_total_sub > Hat      6grp_rule_based > S5      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 292
1 2 3 4 range
A 16.9
(-3)
A 		228.2
(3)
A 		158.8
(1)
A 		36.8
(-2.4)
A 		211
B 17.3
(-3)
A 		190
(3)
A 		113.9
(0.4)
A 		80.2
(-0.8)
A 		173
C 78.1
(-2.1)
A 		309.1
(3)
A 		261.8
(1.9)
A 		39
(-3)
A 		270
avr 37.4
(-3) 		242.4
(3) 		178.2
(1.1) 		52
(-2.6) 		205

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 8634
1 2 3 4 5 6 range
A 180.4
(-3)
A 		293.7
(-2.9)
A 		201.7
(-3)
A 		488.8
(-2.7)
P 		6740.7
(3)
P 		1600.6
(-1.7)
P 		6560
B 172.3
(-3)
A 		181.6
(-3)
A 		222.8
(-3)
A 		470.9
(-2.7)
P 		7134.6
(3)
P 		1942.3
(-1.5)
P 		6962
C 296.6
(-2.9)
A 		198.4
(-3)
A 		322.4
(-2.9)
A 		422.9
(-2.8)
P 		8806.6
(3)
P 		1549.6
(-2.1)
P 		8608
avr 216.4
(-3) 		224.6
(-3) 		249
(-3) 		460.9
(-2.8) 		7560.6
(3) 		1697.5
(-1.8) 		7344
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 86
1 2 3 4 range
A 6.2
(-2.9)
A 		49.5
(3)
A 		41.5
(1.9)
A 		5.4
(-3)
A 		44
B 5.5
(-3)
A 		46.9
(3)
A 		26.4
(0)
A 		17.1
(-1.3)
A 		41
C 25.9
(-1.6)
A 		88.9
(2.8)
A 		91.2
(3)
A 		6.6
(-3)
A 		85
avr 12.5
(-2.7) 		61.8
(3) 		53
(2) 		9.7
(-3) 		52

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2866
1 2 3 4 5 6 range
A 33.2
(-3)
A 		104.5
(-2.8)
A 		43.9
(-3)
A 		124
(-2.7)
P 		2034.1
(3)
P 		389.7
(-1.9)
P 		2001
B 59.9
(-3)
A 		60.4
(-3)
A 		54.1
(-3)
A 		124.7
(-2.9)
P 		2898.7
(3)
P 		724.3
(-1.6)
P 		2845
C 109.9
(-2.9)
A 		60.5
(-3)
A 		82.1
(-3)
A 		85.1
(-2.9)
P 		2849.7
(3)
P 		518.7
(-2)
P 		2789
avr 67.7
(-3) 		75.1
(-3) 		60
(-3) 		111.3
(-2.9) 		2594.2
(3) 		544.2
(-1.9) 		2534
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188245_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17506
Sequence Type Exemplar sequence
Representative Public ID F15A2.1 NCBI
Target Description F15A2.1 /REP_DB=WormBase Gene ID /WP=CE05630 /TR=Q19470 /GB=CAA94128.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=collagen
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_077847(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_077847 NCBI Caenorhabditis elegans F15A2.1 (collagen) mRNA, complete cds. 11/11 None
SNAP00000028415 ENSEMBL cdna:SNAP chromosome:CEL140:X:13469391:13470297:1 11/11 None
GENEFINDER00000028425 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:13469391:13471844:1 11/11 None
F15A2.1 ENSEMBL cdna:known chromosome:CEL140:X:13469376:13470330:1 gene:F15A2.1 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:13469375-13470297(+) 91.1 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-184
Ensembl F15A2.1
Entrez Gene 181470 Entrez gene
SwissProt Q19470 EMBL-EBI
WormBase CE05630 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 CAA94128 Hypothetical protein F15A2.1 [Caenorhabditis elegans] ref|NP_510248.1| F15A2.1 [Caenorhabditis elegans] 4.0E-56
blast CAA94128 Hypothetical protein F15A2.1 [Caenorhabditis elegans] ref|NP_510248.1| F15A2.1 [Caenorhabditis elegans] 4.0E-53
blast CAE63145 Hypothetical protein CBG07447 [Caenorhabditis briggsae] 1.0E-47
blast CAE63145 Hypothetical protein CBG07447 [Caenorhabditis briggsae] 2.0E-47
blast NP_504525 COLlagen family member (col-140) [Caenorhabditis elegans] gb|AAC25888.1| Collagen protein 140 [Caenorhabditis elegans] 9.0E-18
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 3.8E-20
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.5E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.6E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.6E-11
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 3.8E-20
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.5E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.6E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.6E-11
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_510248.1 1 7-29
F15A2.1 1 7-29
SNAP00000028415 1 5-27
GENEFINDER00000028425 1 5-27
Sequence
Target Sequence 
>C. ELEGANS:188245_AT
tgacaacagccaatgccactgcggacttcagtctcaaggatgcccagacgggccaccagg
agctcgtggaccacaaggagcgccaggacttccaggagctccaggagttgatggaaagcc
aggagtcgacggaaaatctctcacatatgttcacgccgcagaggctgattgcattccatg
cccaggaggagaggctggaccacctggaccagatggagagccaggagtccgaggaccaaa
tggaccaccaggaccaaacggacatccaggacaaccaggaagaccaggaccagccggacc
agctgggccagaaggaaaagacggaccagttggaccacatggaccagccggaccagccgg
accacgcggaactcgccactccgccggagtaccaggaaaaccaggagatgtcggaccatg
cggaccagaaggaccaaagggagccccaggaactccaggaaagaacggagctccaggaga
tcgtggatttggtggacaaccaggagttccaggagagccaggagaggatggtactccagg
agaaccaggtgccgatggtgctccaggagacgatgccggatattgcgc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGACAACAGCCAATGCCACTGCGGA 640 571 270 Antisense
CCACTGCGGACTTCAGTCTCAAGGA 172 273 285 Antisense
TCAAGGATGCCCAGACGGGCCACCA 491 629 303 Antisense
CGACGGAAAATCTCTCACATATGTT 527 249 396 Antisense
CATATGTTCACGCCGCAGAGGCTGA 639 213 413 Antisense
CAGAGGCTGATTGCATTCCATGCCC 70 207 428 Antisense
TGGAGAGCCAGGAGTCCGAGGACCA 424 545 483 Antisense
GCCACTCCGCCGGAGTACCAGGAAA 523 279 644 Antisense
TCGGACCATGCGGACCAGAAGGACC 682 605 680 Antisense
GTACTCCAGGAGAACCAGGTGCCGA 684 457 800 Antisense
CAGGAGACGATGCCGGATATTGCGC 406 207 833 Antisense
Sequence Source Affymetrix Proprietary Database