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[189624_at] procollagen alpha

Description T21D9.1 /REP_DB=WormBase Gene ID /WP=CE04989 /TR=Q22651 /GB=AAA81693.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=procollagen alpha
Cluster 6grp_total > 93      4grp_total > 56      6grp_cgc > 87      6grp_cgc_sub > 05      6grp_total_sub > Hat      6grp_rule_based > S5      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 46
1 2 3 4 range
A 10.5
(-2.2)
A 		13.2
(-1.8)
A 		48.6
(3)
A 		4.6
(-3)
A 		44
B 8.8
(-1.8)
A 		10.8
(-1.4)
A 		32.7
(3)
A 		3.1
(-3)
A 		30
C 10.6
(-1.6)
A 		11.7
(-1.3)
A 		33.6
(3)
A 		3.3
(-3)
A 		30
avr 10
(-1.9) 		11.9
(-1.6) 		38.3
(3) 		3.7
(-3) 		35

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2554
1 2 3 4 5 6 range
A 5.2
(-3)
A 		14.9
(-3)
A 		39.1
(-2.9)
A 		1439.6
(1.9)
P 		1754.8
(3)
P 		372.8
(-1.7)
P 		1750
B 7.8
(-3)
A 		7.9
(-3)
A 		71.2
(-2.8)
A 		1178.3
(0.3)
P 		2114.2
(3)
P 		431.1
(-1.8)
P 		2106
C 15.9
(-3)
A 		7.2
(-3)
A 		21.3
(-3)
A 		1013.8
(-0.6)
P 		2559.5
(3)
P 		307.4
(-2.3)
P 		2552
avr 9.6
(-3) 		10
(-3) 		43.9
(-2.9) 		1210.6
(0.4) 		2142.8
(3) 		370.4
(-2) 		2133
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 12
1 2 3 4 range
A 3.8
(-1.5)
A 		2.9
(-1.9)
A 		12.7
(3)
A 		0.7
(-3)
A 		12
B 2.8
(-1.2)
A 		2.7
(-1.3)
A 		7.6
(3)
A 		0.7
(-3)
A 		7
C 3.5
(-1.4)
A 		3.4
(-1.4)
A 		11.7
(3)
A 		0.5
(-3)
A 		11
avr 3.4
(-1.3) 		3
(-1.6) 		10.7
(3) 		0.6
(-3) 		10

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 858
1 2 3 4 5 6 range
A 1
(-3)
A 		5.3
(-3)
A 		8.5
(-2.9)
A 		365.1
(1.1)
P 		529.5
(3)
P 		90.8
(-2)
P 		529
B 2.7
(-3)
A 		2.6
(-3)
A 		17.3
(-2.9)
A 		312.1
(-0.8)
P 		859
(3)
P 		160.7
(-1.9)
P 		856
C 5.9
(-3)
A 		2.2
(-3)
A 		5.4
(-3)
A 		203.9
(-1.5)
P 		828.2
(3)
P 		102.9
(-2.3)
P 		826
avr 3.2
(-3) 		3.4
(-3) 		10.4
(-2.9) 		293.7
(-0.6) 		738.9
(3) 		118.1
(-2.1) 		736
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189624_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.18236
Sequence Type Exemplar sequence
Representative Public ID T21D9.1 NCBI
Target Description T21D9.1 /REP_DB=WormBase Gene ID /WP=CE04989 /TR=Q22651 /GB=AAA81693.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=procollagen alpha
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_075985(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_075985 NCBI Caenorhabditis elegans COLlagen family member (col-164) (col-164) mRNA, complete cds. 11/11 None
GENEFINDER00000000381 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:2093483:2094775:1 11/11 None
SNAP00000000379 ENSEMBL cdna:SNAP chromosome:CEL140:X:2093498:2094775:1 11/11 None
T21D9.1 ENSEMBL cdna:known chromosome:CEL140:X:2093469:2094775:1 gene:T21D9.1 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:2093482-2094775(+) 100.0 100.0
Public Domain and Genome References
Gene Title procollagen alpha
Gene Symbol col-164
Ensembl T21D9.1
Entrez Gene 180523 Entrez gene
SwissProt Q22651 EMBL-EBI
WormBase CE04989 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 AAA81693 Collagen protein 164 [Caenorhabditis elegans] ref|NP_508386.1| COLlagen family member (col-164) [Caenorhabditis elegans] 1.0E-134
blast AAA81693 Collagen protein 164 [Caenorhabditis elegans] ref|NP_508386.1| COLlagen family member (col-164) [Caenorhabditis elegans] 1.0E-131
blast CAE68355 Hypothetical protein CBG14092 [Caenorhabditis briggsae] 9.0E-94
blast CAE68355 Hypothetical protein CBG14092 [Caenorhabditis briggsae] 3.0E-91
Protein Domains
Database ID Description E-Value
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.4E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.8E-13
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.7E-14
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.4E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.8E-13
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.7E-14
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_508386.1 1 13-35
T21D9.1 1 13-35
GENEFINDER00000000381 1 13-35
SNAP00000000379 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:189624_AT
ggaccagaaggagaccatgggcatccaggaccaatgggaccagcaggagagaaaggaacc
agtggagctgacggaaaaggatttgctaaaggagcaccaggaccaaaaggaccgactgga
atggatggtcttgcaggagacgagggtcttccaggagagcgtggagaggatggttcagct
ggagcacagggagagactggaccacaaggaccacaaggagagaagggaccagatggattc
ccaggtcttccaggatccgccggagcttctggagaagatgctgcctattgcccatgccca
tcaagaaaaggagacatcgctggaggaggaggtggcggatacgctgcagccccaggaact
gaatttgaaggatccccagttgaatccgatccag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGACCAGAAGGAGACCATGGGCATC 408 523 577 Antisense
AGACCATGGGCATCCAGGACCAATG 511 69 588 Antisense
GGACCAATGGGACCAGCAGGAGAGA 209 523 604 Antisense
GACTGGAATGGATGGTCTTGCAGGA 591 375 690 Antisense
GCAGGAGACGAGGGTCTTCCAGGAG 379 311 709 Antisense
GAGAGGATGGTTCAGCTGGAGCACA 397 395 740 Antisense
GCTTCTGGAGAAGATGCTGCCTATT 689 305 841 Antisense
TGCCCATGCCCATCAAGAAAAGGAG 321 583 865 Antisense
AGGAGACATCGCTGGAGGAGGAGGT 387 55 885 Antisense
GAATTTGAAGGATCCCCAGTTGAAT 365 323 937 Antisense
GGATCCCCAGTTGAATCCGATCCAG 510 511 946 Antisense
Sequence Source Affymetrix Proprietary Database