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[172698_x_at] collagen

Description C53B4.5 /REP_DB=WormBase Gene ID /WP=CE03091 /TR=Q18799 /GB=CAA92453.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_highest_10_10 > 09      6grp_high1_10_10 > 90      4grp_highest_8_8 > 09      4grp_high_8_8 > 53      6grp_highest_nonorm > 19      6grp_total > 82      4grp_total > 58      6grp_cgc > 98      6grp_rule_based > S5      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 29725
1 2 3 4 range
A 10179.8
(-1.1)
P 		30629.3
(3)
P 		28069.3
(2.5)
P 		904
(-3)
P 		29725
B 10577.8
(-1)
P 		24423.6
(2)
P 		28936.4
(3)
P 		1061.2
(-3)
P 		27875
C 10301.4
(-0.5)
P 		23400.8
(3)
P 		22408.5
(2.7)
P 		956.2
(-3)
P 		22445
avr 10353
(-0.8) 		26151.2
(2.9) 		26471.4
(3) 		973.8
(-3) 		25498

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 19880
1 2 3 4 5 6 range
A 13413.3
(-3)
P 		21666.3
(0.5)
P 		21764.2
(0.6)
P 		26472.9
(2.6)
P 		27423.9
(3)
P 		15407
(-2.1)
P 		14011
B 13998.4
(-2.5)
P 		22719.2
(1.8)
P 		21012.3
(1)
P 		23981.3
(2.5)
P 		25081.1
(3)
P 		12895.5
(-3)
P 		12186
C 13504.8
(-2.5)
P 		19360.6
(-0.7)
P 		20488.5
(-0.4)
P 		20605.1
(-0.4)
P 		31756.8
(3)
P 		11877.2
(-3)
P 		19880
avr 13638.8
(-2.9) 		21248.7
(0.2) 		21088.3
(0.1) 		23686.4
(1.2) 		28087.3
(3) 		13393.2
(-3) 		14694
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 7678
1 2 3 4 range
A 3706.5
(-0)
P 		6648.8
(2.4)
P 		7337.9
(3)
P 		132.3
(-3)
P 		7206
B 3373.2
(-0.1)
P 		6032.1
(2.4)
P 		6705.2
(3)
P 		226.1
(-3)
P 		6479
C 3410.1
(-0.5)
P 		6727.9
(2.2)
P 		7810.1
(3)
P 		161.2
(-3)
P 		7649
avr 3496.6
(-0.2) 		6469.6
(2.3) 		7284.4
(3) 		173.2
(-3) 		7111

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 7803
1 2 3 4 5 6 range
A 2472.6
(-3)
P 		7705.6
(2.4)
P 		4739.8
(-0.7)
P 		6714.1
(1.4)
P 		8275.3
(3)
P 		3751.1
(-1.7)
P 		5803
B 4870.8
(-2.9)
P 		7562.3
(0.1)
P 		5102.4
(-2.7)
P 		6351.8
(-1.3)
P 		10190.1
(3)
P 		4808.7
(-3)
P 		5381
C 5005.6
(-2)
P 		5907.5
(-1.2)
P 		5214.7
(-1.8)
P 		4143.7
(-2.8)
P 		10276
(3)
P 		3976
(-3)
P 		6300
avr 4116.3
(-3) 		7058.5
(0.2) 		5019
(-2) 		5736.5
(-1.2) 		9580.5
(3) 		4178.6
(-2.9) 		5464
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172698_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.10161
Sequence Type Exemplar sequence
Representative Public ID C53B4.5 NCBI
Target Description C53B4.5 /REP_DB=WormBase Gene ID /WP=CE03091 /TR=Q18799 /GB=CAA92453.1 /SUBMIT=HINXTON /CHR=4 /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_069160(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069160 NCBI Caenorhabditis elegans C53B4.5 (collagen) mRNA, complete cds. 11/11 A 
SNAP00000003708 ENSEMBL cdna:SNAP chromosome:CEL140:IV:8978906:8979775:-1 11/11 None
GENEFINDER00000003712 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:8978906:8979775:-1 11/11 None
C53B4.5 ENSEMBL cdna:known chromosome:CEL140:IV:8978803:8979775:-1 gene:C53B4.5 11/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_067556 1/11 Cross Hyb Matching Probes A 
NM_069466 4/11 Cross Hyb Matching Probes A 
NM_077847 1/11 Cross Hyb Matching Probes A 
NM_062965 1/11 Cross Hyb Matching Probes A 
NM_001029563 1/11 Cross Hyb Matching Probes None
NM_182248 1/11 Cross Hyb Matching Probes A 
NM_073083 1/11 Cross Hyb Matching Probes None
NM_075994 1/11 Cross Hyb Matching Probes A 
NM_077846 2/11 Cross Hyb Matching Probes A 
NM_073085 1/11 Cross Hyb Matching Probes A 
NM_063409 1/11 Cross Hyb Matching Probes A 
NM_077154 1/11 Cross Hyb Matching Probes None
NM_066328 1/11 Cross Hyb Matching Probes A 
NM_072673 1/11 Cross Hyb Matching Probes A 
NM_068206 1/11 Cross Hyb Matching Probes A 
NM_063181 1/11 Cross Hyb Matching Probes None
SNAP00000000073 1/11 Cross Hyb Matching Probes None
GENEFINDER00000000088 1/11 Cross Hyb Matching Probes None
SNAP00000013421 1/11 Cross Hyb Matching Probes None
GENEFINDER00000013453 1/11 Cross Hyb Matching Probes None
SNAP00000010839 1/11 Cross Hyb Matching Probes None
GENEFINDER00000010850 1/11 Cross Hyb Matching Probes None
SNAP00000034766 1/11 Cross Hyb Matching Probes None
GENEFINDER00000034774 1/11 Cross Hyb Matching Probes None
SNAP00000042867 1/11 Cross Hyb Matching Probes None
GENEFINDER00000042874 1/11 Cross Hyb Matching Probes None
SNAP00000043526 4/11 Cross Hyb Matching Probes None
GENEFINDER00000043530 4/11 Cross Hyb Matching Probes None
SNAP00000007440 1/11 Cross Hyb Matching Probes None
SNAP00000007442 1/11 Cross Hyb Matching Probes None
GENEFINDER00000007459 1/11 Cross Hyb Matching Probes None
SNAP00000025313 1/11 Cross Hyb Matching Probes None
GENEFINDER00000025319 1/11 Cross Hyb Matching Probes None
SNAP00000028415 1/11 Cross Hyb Matching Probes None
GENEFINDER00000028425 1/11 Cross Hyb Matching Probes None
SNAP00000008502 1/11 Cross Hyb Matching Probes None
GENEFINDER00000008503 1/11 Cross Hyb Matching Probes None
SNAP00000039146 2/11 Cross Hyb Matching Probes None
GENEFINDER00000039152 2/11 Cross Hyb Matching Probes None
SNAP00000033176 1/11 Cross Hyb Matching Probes None
GENEFINDER00000033181 1/11 Cross Hyb Matching Probes None
T14B4.7a.2 1/11 Cross Hyb Matching Probes A 
T14B4.7a.1 1/11 Cross Hyb Matching Probes A 
T14B4.7b.1 1/11 Cross Hyb Matching Probes None
T14B4.7b.2 1/11 Cross Hyb Matching Probes None
ZK1290.3a 1/11 Cross Hyb Matching Probes A B 
F54C9.4 1/11 Cross Hyb Matching Probes A 
C29E4.1 1/11 Cross Hyb Matching Probes A 
C18H7.3 1/11 Cross Hyb Matching Probes A 
F29B9.9 1/11 Cross Hyb Matching Probes A 
C24F3.6 4/11 Cross Hyb Matching Probes None
ZC513.8 1/11 Cross Hyb Matching Probes A 
T06E4.6 1/11 Cross Hyb Matching Probes A 
T06E4.4 1/11 Cross Hyb Matching Probes A 
EGAP7.1.2 1/11 Cross Hyb Matching Probes None
C35B8.1 1/11 Cross Hyb Matching Probes A 
F02D10.1 2/11 Cross Hyb Matching Probes A 
F15A2.1 1/11 Cross Hyb Matching Probes A 
H06A10.2 1/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIV:8978911-8979781(-) 90.92 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-119
Ensembl C53B4.5
Entrez Gene 177715 Entrez gene
SwissProt Q18799 EMBL-EBI
WormBase CE03091 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 CAA92453 Hypothetical protein C53B4.5 [Caenorhabditis elegans] ref|NP_501561.1| C53B4.5 [Caenorhabditis elegans] 9.0E-50
blast CAE74080 Hypothetical protein CBG21735 [Caenorhabditis briggsae] 3.0E-46
blast CAB97232 Hypothetical protein C24F3.6 [Caenorhabditis elegans] ref|NP_501867.1| COLlagen family member (col-124) [Caenorhabditis elegans] 4.0E-40
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.2E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 8.5E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 8.7E-13
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_501561.1 1 12-34
C53B4.5 1 12-34
SNAP00000003708 1 12-34
GENEFINDER00000003712 1 12-34
Sequence
Target Sequence 
>C. ELEGANS:172698_X_AT
aatgcgagggatgctgtcttccaggagcacaaggaccaccaggaaccccaggacgtgctg
gacgaccaggaaagccaggagcaccaggtcttaacggaaatccaggacgcccaccaaagg
agccatgtgagccaatcaccccaccaccatgcaagccatgcccagaaggaccaccaggac
cagccggaccaccaggaccacaaggaaacaagggaccactcggaccaccaggaccaccag
gaccagaaggaccaaatggaactgcaggaaacaagggaccagctggaccaccaggaccag
gaggaaagccaggaccagctggaccaccaggagagaatggacgcaatggagagccacaac
caggatcaccaggagagccaggacgtccaggacaaccaggatcccgcggaccagctggac
aaccaggaaaggatggagctcaaggaggaccaggagagaagggagccaacggagaaccag
gacaaccaggaagagacggacaaccaggacgtccaggacagccaggacgcgatggacatc
caggagagaagggagtctgtccaaaatactgtgctctcg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AATGCGAGGGATGCTGTCTTCCAGG 54 167 266 Antisense
ACCAGGAACCCCAGGACGTGCTGGA 120 87 303 Antisense
GCCAGGAGCACCAGGTCTTAACGGA 555 279 339 Antisense
ATGCAAGCCATGCCCAGAAGGACCA 356 43 414 Antisense
GGACCACCAGGACCAGAAGGACCAA 405 523 496 Antisense
GAAACAAGGGACCAGCTGGACCACC 414 355 533 Antisense
GGAAAGCCAGGACCAGCTGGACCAC 122 527 568 Antisense
TGGAGAGCCACAACCAGGATCACCA 413 549 612 Antisense
GGATCACCAGGAGAGCCAGGACGTC 685 507 628 Antisense
GACAGCCAGGACGCGATGGACATCC 114 369 782 Antisense
GTCTGTCCAAAATACTGTGCTCTCG 656 471 820 Antisense
Sequence Source Affymetrix Proprietary Database