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[190742_at] collagen alpha chain

Description K03H9.2 /REP_DB=WormBase Gene ID /WP=CE01996 /TR=SW:Q09578 /GB=AAC46668.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=collagen alpha chain
Cluster 6grp_total > 92      4grp_total > 16      6grp_cgc > 97      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 107
1 2 3 4 range
A 5.4
(-3)
A 		25.8
(-1.9)
A 		44.1
(-0.8)
A 		112
(3)
A 		107
B 4.9
(-3)
A 		8.2
(-0.1)
A 		7.7
(-0.6)
A 		11.8
(3)
A 		7
C 21.9
(-3)
A 		29.3
(-1.9)
A 		30.7
(-1.7)
A 		61.9
(3)
A 		40
avr 10.7
(-3) 		21.1
(-1.8) 		27.5
(-1) 		61.9
(3) 		51

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 74
1 2 3 4 5 6 range
A 41.1
(-0.9)
A 		29.2
(-2.9)
A 		64.3
(3)
A 		39.7
(-1.1)
A 		43.3
(-0.5)
A 		28.6
(-3)
A 		36
B 36
(-0.5)
A 		24.9
(-1.4)
A 		6.2
(-3)
A 		77.8
(3)
A 		63.9
(1.8)
A 		13.5
(-2.4)
A 		72
C 3.8
(-3)
A 		76.8
(3)
A 		8.6
(-2.6)
A 		16.8
(-1.9)
A 		50
(0.8)
A 		6.6
(-2.8)
A 		73
avr 27
(-1.2) 		43.6
(1.5) 		26.4
(-1.3) 		44.8
(1.7) 		52.4
(3) 		16.2
(-3) 		36
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 15
1 2 3 4 range
A 2
(-3)
A 		5.6
(-1.5)
A 		11.5
(1)
A 		16.4
(3)
A 		14
B 1.6
(-3)
A 		2
(-0.3)
A 		1.8
(-1.7)
A 		2.5
(3)
A 		1
C 7.3
(-3)
A 		8.4
(-1.1)
A 		10.7
(3)
A 		10.4
(2.5)
A 		3
avr 3.6
(-3) 		5.3
(-1.4) 		8
(1.3) 		9.8
(3) 		6

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 25
1 2 3 4 5 6 range
A 7.6
(-2.5)
A 		10.4
(-0.1)
A 		14
(3)
A 		10.1
(-0.3)
A 		13.1
(2.2)
A 		7
(-3)
A 		7
B 12.5
(-0.3)
A 		8.3
(-1.3)
A 		1.5
(-3)
A 		20.6
(1.7)
A 		26
(3)
A 		5
(-2.1)
A 		25
C 1.4
(-3)
A 		23.4
(3)
A 		2.2
(-2.8)
A 		3.4
(-2.5)
A 		16.2
(1)
A 		2.2
(-2.8)
A 		22
avr 7.2
(-1.9) 		14
(1.1) 		5.9
(-2.5) 		11.4
(-0.1) 		18.4
(3) 		4.7
(-3) 		14
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190742_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.5124
Sequence Type Exemplar sequence
Representative Public ID K03H9.2 NCBI
Target Description K03H9.2 /REP_DB=WormBase Gene ID /WP=CE01996 /TR=SW:Q09578 /GB=AAC46668.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=collagen alpha chain
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_062893(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_062893 NCBI Caenorhabditis elegans COLlagen family member (col-75) (col-75) mRNA, complete cds. 11/11 None
SNAP00000017294 ENSEMBL cdna:SNAP chromosome:CEL140:II:6426240:6427370:1 11/11 None
GENEFINDER00000017298 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:6426240:6432779:1 10/11 None
K03H9.2 ENSEMBL cdna:known chromosome:CEL140:II:6426240:6427370:1 gene:K03H9.2 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
chrII:6426236-6427367(+) 100.0 100.0
Public Domain and Genome References
Gene Title collagen alpha chain
Gene Symbol col-75
Ensembl K03H9.2
Entrez Gene 186968 Entrez gene
SwissProt Q09578 EMBL-EBI
WormBase CE01996 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 AAC46668 Collagen protein 75 [Caenorhabditis elegans] ref|NP_495294.1| COLlagen family member (col-75) [Caenorhabditis elegans] sp|Q09578|YRF2_CAEEL Putative cuticle collagen K03H9.2 1.0E-111
blast AAC46668 Collagen protein 75 [Caenorhabditis elegans] ref|NP_495294.1| COLlagen family member (col-75) [Caenorhabditis elegans] sp|Q09578|YRF2_CAEEL Putative cuticle collagen K03H9.2 1.0E-102
blast CAE59325 Hypothetical protein CBG02667 [Caenorhabditis briggsae] 9.0E-87
blast AAC46667 Hypothetical protein K03H9.1 [Caenorhabditis elegans] ref|NP_495295.1| K03H9.1 [Caenorhabditis elegans] 4.0E-81
blast CAE59325 Hypothetical protein CBG02667 [Caenorhabditis briggsae] 5.0E-79
blast CAE73812 Hypothetical protein CBG21362 [Caenorhabditis briggsae] 6.0E-16
Protein Domains
Database ID Description E-Value
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.3E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.1E-13
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.0E-8
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_495294.1 1 7-29
K03H9.2 1 7-29
SNAP00000017294 1 7-29
GENEFINDER00000017298 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:190742_AT
taaatacatgcccgcctggacggattggaattacaggacctgatggacaaccaggcaaag
atggccttcctggaatgcctggatctcccggaatacccggagaacttccaaatattttat
atcagcaagtttttggatgccgaatctgtccttatggaccaaaaggaaaatctggatata
agggaatcgatggtcctccgggtattcccggttggcctggagaacctggtgttcgcggaa
tgaatggagaacgaggatcaacaggtctggatggagcacctggtgaaccagggtcacctg
gtctcccaggatttgcgggattacctggtagcattggcataactggaatcaaaggagtca
tgggtgaagttggagagccgggagcccctggaattcctggagaagagggactttctggac
ccactggtcaacctggatcgcctgggtcgattggggcgatggggtatgagggtgcctatg
gagatcgtggagaacctggcccaccgggaccaattggaagacgcggaggacctggtcttg
actctcattactgtccctgtccatctcggaaaatgt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TAAATACATGCCCGCCTGGACGGAT 7 643 254 Antisense
CCTGGATCTCCCGGAATACCCGGAG 61 263 331 Antisense
GATGCCGAATCTGTCCTTATGGACC 70 415 389 Antisense
TAAGGGAATCGATGGTCCTCCGGGT 583 627 432 Antisense
TATTCCCGGTTGGCCTGGAGAACCT 624 661 456 Antisense
GTCACCTGGTCTCCCAGGATTTGCG 26 467 546 Antisense
GAGCCCCTGGAATTCCTGGAGAAGA 429 385 635 Antisense
GAAGAGGGACTTTCTGGACCCACTG 332 337 655 Antisense
GACGCGGAGGACCTGGTCTTGACTC 55 381 773 Antisense
CTGGTCTTGACTCTCATTACTGTCC 103 241 785 Antisense
TGTCCCTGTCCATCTCGGAAAATGT 704 555 805 Antisense
Sequence Source Affymetrix Proprietary Database