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[188637_at] collagen

Description M01A12.1 /REP_DB=WormBase Gene ID /WP=CE12238 /TR=P91396 /GB=AAB42221.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 93      4grp_total > 43      6grp_cgc > 98      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 155
1 2 3 4 range
A 95.3
(-3)
A 		170.7
(1.9)
A 		187.5
(3)
A 		97.3
(-2.9)
A 		92
B 127.1
(0.1)
P 		200.9
(3)
A 		46.4
(-3)
A 		53.2
(-2.7)
A 		155
C 106.2
(2.4)
A 		110.3
(3)
A 		66.8
(-3)
A 		98.5
(1.4)
P 		44
avr 109.5
(-1) 		160.6
(3) 		100.2
(-1.7) 		83
(-3) 		78

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 315
1 2 3 4 5 6 range
A 145.6
(2.1)
A 		141.1
(1.9)
M 		127.6
(1.1)
A 		129.9
(1.3)
A 		161.4
(3)
A 		53.1
(-3)
A 		108
B 143.6
(-2.1)
A 		154.5
(-1.8)
A 		103.1
(-3)
A 		142.4
(-2.1)
A 		367.7
(3)
A 		136.4
(-2.2)
A 		265
C 170
(-0.6)
P 		149.4
(-1.2)
A 		127.1
(-1.8)
A 		162.4
(-0.8)
A 		288.8
(3)
A 		88.5
(-3)
A 		200
avr 153.1
(-1) 		148.3
(-1.1) 		119.3
(-2.1) 		144.9
(-1.3) 		272.6
(3) 		92.7
(-3) 		180
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 39
1 2 3 4 range
A 34.7
(0.5)
A 		37
(0.9)
A 		49
(3)
A 		14.2
(-3)
A 		35
B 40.5
(1.6)
P 		49.6
(3)
A 		10.7
(-3)
A 		11.3
(-2.9)
A 		39
C 35.1
(3)
A 		31.7
(1.9)
A 		23.3
(-0.8)
A 		16.6
(-3)
P 		19
avr 36.8
(2.4) 		39.4
(3) 		27.7
(0.2) 		14
(-3) 		25

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 137
1 2 3 4 5 6 range
A 26.8
(-0.8)
A 		50.2
(3)
M 		27.8
(-0.6)
A 		32.9
(0.2)
A 		48.7
(2.8)
A 		12.9
(-3)
A 		37
B 50
(-1.8)
A 		51.4
(-1.7)
A 		25
(-3)
A 		37.7
(-2.4)
A 		149.4
(3)
A 		50.9
(-1.8)
A 		124
C 63
(0.1)
P 		45.6
(-1.5)
A 		32.3
(-2.7)
A 		32.7
(-2.7)
A 		93.5
(3)
A 		29.6
(-3)
A 		64
avr 46.6
(-1.4) 		49.1
(-1.2) 		28.4
(-3) 		34.4
(-2.5) 		97.2
(3) 		31.1
(-2.8) 		69
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188637_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.1197
Sequence Type Exemplar sequence
Representative Public ID M01A12.1 NCBI
Target Description M01A12.1 /REP_DB=WormBase Gene ID /WP=CE12238 /TR=P91396 /GB=AAB42221.1 /SUBMIT=ST.LOUIS /CHR=1 /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_059250(9)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059250 NCBI Caenorhabditis elegans M01A12.1 (collagen) mRNA, complete cds. 9/11 None
SNAP00000024465 ENSEMBL cdna:SNAP chromosome:CEL140:I:5645230:5646317:1 11/11 None
GENEFINDER00000024484 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:5645253:5646317:1 10/11 None
M01A12.1 ENSEMBL cdna:known chromosome:CEL140:I:5645397:5646317:1 gene:M01A12.1 9/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_182090 1/11 Cross Hyb Matching Probes None
M01A12.3 1/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrI:5643156-5646317(+) 98.0 98.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-53
Ensembl M01A12.1
Entrez Gene 172222 Entrez gene
SwissProt P91396 EMBL-EBI
WormBase CE33533 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
Protein Similarities
Method ID Description E-Value
blast CAE68931 Hypothetical protein CBG14911 [Caenorhabditis briggsae] 1.0E-106
blast CAE68931 Hypothetical protein CBG14911 [Caenorhabditis briggsae] 1.0E-101
blast AAO44910 Collagen protein 53 [Caenorhabditis elegans] ref|NP_491651.2| M01A12.1 [Caenorhabditis elegans] 4.0E-85
blast AAO44910 Collagen protein 53 [Caenorhabditis elegans] ref|NP_491651.2| M01A12.1 [Caenorhabditis elegans] 6.0E-85
blast AAO44910 Collagen protein 53 [Caenorhabditis elegans] ref|NP_491651.2| M01A12.1 [Caenorhabditis elegans] 7.0E-85
blast CAE68931 Hypothetical protein CBG14911 [Caenorhabditis briggsae] 2.0E-80
blast CAA63070 collagen [Brugia pahangi] 9.0E-35
blast CAA63070 collagen [Brugia pahangi] 5.0E-32
Protein Domains
Database ID Description E-Value
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 9.1E-8
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.6E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 9.1E-8
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.6E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 9.1E-8
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.6E-12
Sequence
Target Sequence 
>C. ELEGANS:188637_AT
catgctgcattggaccacctggaatgaaaggatttccaggaaagaattcaagagatggat
atgacggagaaccaggtcgagatggccaacctggacgtccagcagatggtgatagtcgaa
tggtatgtatacgtgaatgcccaacaggacgacctggacgtgaaggtggagatggaccaa
aaggatcaaaaggacaaagaggacgtactggtcagcaaggagattcagcgccaccgtcaa
tacgtggtgaacctggagaaagaggagataagggattccctggagttgcaggaccagccg
gagaaccaggtgaaccaggacatatctatgtgtctgatggaccacctggaaaagatggag
aaacagggccacgtgggccaccaggtgagaaaggaagaactggaagagacggagaagatg
gattacctggtgaacgaggtgaacgtggatatcaaggattaaaaggagaaattggaaaaa
gaggacctgtgggaacttttgggccaattggtccaaaaggagaaccatggccatgtgaat
catgtccaccgcc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CATGCTGCATTGGACCACCTGGAAT 556 209 1211 Antisense
AGGTCGAGATGGCCAACCTGGACGT 491 57 1284 Antisense
CGTGAATGCCCAACAGGACGACCTG 518 245 1342 Antisense
GTCAGCAAGGAGATTCAGCGCCACC 280 467 1421 Antisense
TCAGCGCCACCGTCAATACGTGGTG 440 625 1435 Antisense
GATTCCCTGGAGTTGCAGGACCAGC 437 433 1484 Antisense
GGACCAGCCGGAGAACCAGGTGAAC 392 523 1501 Antisense
CTATGTGTCTGATGGACCACCTGGA 159 225 1536 Antisense
GAGAAACAGGGCCACGTGGGCCACC 79 393 1568 Antisense
GACCTGTGGGAACTTTTGGGCCAAT 328 383 1694 Antisense
GGCCATGTGAATCATGTCCACCGCC 37 545 1739 Antisense
Sequence Source Affymetrix Proprietary Database