[Home] | [Total List]

[189762_at] cuticular collagen

Description K09H9.3 /REP_DB=WormBase Gene ID /WP=CE18038 /TR=O44989 /GB=AAB97570.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=cuticular collagen
Cluster 6grp_total > 94      4grp_total > 48      6grp_cgc > 89      6grp_total_sub > Hat      6grp_rule_based > S5      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 119
1 2 3 4 range
A 7
(-3)
A 		55
(-0.5)
A 		122.8
(3)
P 		30.3
(-1.8)
A 		116
B 24.8
(-1)
A 		53.4
(3)
A 		20.7
(-1.6)
A 		10.5
(-3)
A 		43
C 4.1
(-3)
A 		50
(1.5)
A 		65.1
(3)
P 		6.4
(-2.8)
A 		61
avr 12
(-3) 		52.8
(1.3) 		69.5
(3) 		15.7
(-2.6) 		58

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3050
1 2 3 4 5 6 range
A 21.5
(-3)
A 		45.2
(-2.9)
A 		64.7
(-2.9)
A 		653.4
(-1.4)
P 		2385.5
(3)
P 		1286.8
(0.2)
P 		2364
B 2.9
(-3)
A 		63.6
(-2.9)
P 		62.8
(-2.9)
A 		641.4
(-1.5)
P 		2574.2
(3)
P 		1703.5
(1)
P 		2571
C 38.7
(-3)
A 		53.1
(-3)
A 		73.1
(-2.9)
A 		620.3
(-1.8)
P 		3052.8
(3)
P 		1418.5
(-0.3)
P 		3014
avr 21
(-3) 		54
(-2.9) 		66.9
(-2.9) 		638.4
(-1.6) 		2670.8
(3) 		1469.6
(0.3) 		2650
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 31
1 2 3 4 range
A 2.5
(-3)
A 		11.9
(-1.1)
A 		32.1
(3)
P 		4.4
(-2.6)
A 		30
B 7.9
(0.1)
A 		13.2
(3)
A 		4.8
(-1.6)
A 		2.2
(-3)
A 		11
C 1.4
(-2.9)
A 		14.4
(0.7)
A 		22.7
(3)
P 		1.1
(-3)
A 		22
avr 3.9
(-2.5) 		13.2
(0.7) 		19.9
(3) 		2.6
(-3) 		17

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1045
1 2 3 4 5 6 range
A 4
(-3)
A 		16.1
(-2.9)
A 		14.1
(-2.9)
A 		165.7
(-1.6)
P 		719.8
(3)
P 		313.3
(-0.4)
P 		716
B 1
(-3)
A 		21.2
(-2.9)
P 		15.3
(-2.9)
A 		169.9
(-2)
P 		1045.9
(3)
P 		635.2
(0.6)
P 		1045
C 14.4
(-3)
A 		16.2
(-3)
A 		18.6
(-3)
A 		124.7
(-2.3)
P 		987.9
(3)
P 		474.8
(-0.2)
P 		974
avr 6.5
(-3) 		17.8
(-2.9) 		16
(-2.9) 		153.4
(-2) 		917.9
(3) 		474.4
(0.1) 		911
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189762_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.228
Sequence Type Exemplar sequence
Representative Public ID K09H9.3 NCBI
Target Description K09H9.3 /REP_DB=WormBase Gene ID /WP=CE18038 /TR=O44989 /GB=AAB97570.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=cuticular 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_058705(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_058705 NCBI Caenorhabditis elegans COLlagen family member (col-49) (col-49) mRNA, complete cds. 11/11 None
GENEFINDER00000035328 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:3137210:3138412:1 11/11 None
SNAP00000035323 ENSEMBL cdna:SNAP chromosome:CEL140:I:3137288:3138412:1 11/11 None
K09H9.3 ENSEMBL cdna:known chromosome:CEL140:I:3137210:3138412:1 gene:K09H9.3 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
chrI:3137209-3138412(+) 94.72 100.0
Public Domain and Genome References
Gene Title cuticular collagen
Gene Symbol col-49
Ensembl K09H9.3
Entrez Gene 187239 Entrez gene
SwissProt O44989 EMBL-EBI
WormBase CE18038 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 NP_491106 COLlagen family member (col-49) [Caenorhabditis elegans] gb|AAB97570.1| Collagen protein 49 [Caenorhabditis elegans] 1.0E-121
blast NP_491106 COLlagen family member (col-49) [Caenorhabditis elegans] gb|AAB97570.1| Collagen protein 49 [Caenorhabditis elegans] 1.0E-105
blast CAE60555 Hypothetical protein CBG04182 [Caenorhabditis briggsae] 1.0E-104
blast CAE60555 Hypothetical protein CBG04182 [Caenorhabditis briggsae] 2.0E-91
blast CAE66911 Hypothetical protein CBG12296 [Caenorhabditis briggsae] 4.0E-30
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 3.7E-16
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0016
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 8.3E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 8.7E-9
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 3.4E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0016
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 8.3E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 8.7E-9
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_491106.1 1 5-27
K09H9.3 1 5-27
GENEFINDER00000035328 1 5-27
Sequence
Target Sequence 
>C. ELEGANS:189762_AT
cagtgcaattgcgctgagccaacaaagaactgcccagcaggaccaccaggagagaaggga
tctctcggaaatccaggacaaccgggacccgatggagttgatggtgacaacggtgtggat
ggagacgtcgtgattcatgatatgccaaatcctaaagaatgcatcaagtgtccagcagga
ccaccaggaccaccaggaccacctggaccactcggaccacgtggtgacaagggaccgtcc
gggccacgtggagcacttggagatcaaggagaaactggtccagttggagaaattggagat
caaggaccaccaggatccgccggaagagctggaccaagaggtcaagccggacaaccagga
actatcgcaattgtcggattggctggaagaccaggaccacagggtccacttggagagcct
ggagcacaaggagagccaggagttgatggaaaagatggagctcttggagcacctggaaga
aaggcggagaacggaagaccaggaaaacgtggaaaggacggagttgcaggagtaccaggg
acacgtg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CAGTGCAATTGCGCTGAGCCAACAA 630 207 265 Antisense
AGGGATCTCTCGGAAATCCAGGACA 213 59 320 Antisense
GAGACGTCGTGATTCATGATATGCC 537 393 386 Antisense
GACCACTCGGACCACGTGGTGACAA 628 383 470 Antisense
CACGTGGTGACAAGGGACCGTCCGG 381 199 482 Antisense
GGCCACGTGGAGCACTTGGAGATCA 526 543 506 Antisense
ACCACCAGGATCCGCCGGAAGAGCT 481 85 570 Antisense
GACCAAGAGGTCAAGCCGGACAACC 319 383 596 Antisense
AACCAGGAACTATCGCAATTGTCGG 548 147 617 Antisense
GACCACAGGGTCCACTTGGAGAGCC 90 385 659 Antisense
GTTGCAGGAGTACCAGGGACACGTG 515 439 787 Antisense
Sequence Source Affymetrix Proprietary Database