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[172701_x_at] collagen

Description C29F4.1 /REP_DB=WormBase Gene ID /WP=CE03038 /TR=Q18302 /GB=CAA92729.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_highest_10_10 > 05      6grp_high1_10_10 > 50      4grp_highest_8_8 > 16      4grp_high_8_8 > 52      6grp_highest_nonorm > 09      6grp_total > 41      4grp_total > 59      6grp_highest_sub > 03_04      6grp_cgc > 60      6grp_high1_sub > 03_04      6grp_total_sub > Hat      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 43466
1 2 3 4 range
A 31173.2
(0.6)
P 		48015.8
(3)
P 		44802.6
(2.5)
P 		5251.7
(-3)
P 		42764
B 34125.8
(1.4)
P 		39941.1
(2.3)
P 		44826.5
(3)
P 		5282.8
(-3)
P 		39544
C 29895.3
(1.9)
P 		35615
(3)
P 		32847.4
(2.5)
P 		4549.5
(-3)
P 		31066
avr 31731.4
(1.4) 		41190.6
(3) 		40825.5
(2.9) 		5028
(-3) 		36163

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 26019
1 2 3 4 5 6 range
A 43727.2
(2.5)
P 		35032.2
(-0.5)
P 		45055.4
(3)
P 		39966.1
(1.2)
P 		30127.6
(-2.3)
P 		28042.4
(-3)
P 		17013
B 34049.6
(1.2)
P 		34238.3
(1.2)
P 		39857.9
(3)
P 		36804.3
(2)
P 		24541.4
(-1.8)
P 		20884
(-3)
P 		18974
C 33119.6
(0.7)
P 		35020
(1.2)
P 		41935.8
(3)
P 		37449.7
(1.8)
P 		31589.2
(0.3)
P 		19036.7
(-3)
P 		22899
avr 36965.5
(1.4) 		34763.5
(0.7) 		42283
(3) 		38073.4
(1.7) 		28752.7
(-1.1) 		22654.4
(-3) 		19629
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 10945
1 2 3 4 range
A 11350.2
(2.8)
P 		10422.9
(2.3)
P 		11712.3
(3)
P 		768.7
(-3)
P 		10944
B 10882.4
(3)
P 		9864.5
(2.4)
P 		10387.3
(2.7)
P 		1125.8
(-3)
P 		9757
C 9896.2
(2.1)
P 		10239.5
(2.3)
P 		11448.3
(3)
P 		767.1
(-3)
P 		10681
avr 10709.6
(2.7) 		10175.6
(2.4) 		11182.6
(3) 		887.2
(-3) 		10295

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 6087
1 2 3 4 5 6 range
A 8060.8
(-1.7)
P 		12459.2
(3)
P 		9812.1
(0.2)
P 		10136.3
(0.5)
P 		9091.2
(-0.6)
P 		6827.5
(-3)
P 		5632
B 11847.6
(3)
P 		11396.5
(2.3)
P 		9678.7
(-0.2)
P 		9748.2
(-0.1)
P 		9970.9
(0.2)
P 		7787.5
(-3)
P 		4060
C 12276
(3)
P 		10685.7
(1.4)
P 		10673.4
(1.4)
P 		7531.2
(-1.8)
P 		10221.8
(0.9)
P 		6372.7
(-3)
P 		5903
avr 10728.1
(2) 		11513.8
(3) 		10054.7
(1.1) 		9138.6
(-0.2) 		9761.3
(0.7) 		6995.9
(-3) 		4518
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172701_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.8778
Sequence Type Exemplar sequence
Representative Public ID C29F4.1 NCBI
Target Description C29F4.1 /REP_DB=WormBase Gene ID /WP=CE03038 /TR=Q18302 /GB=CAA92729.1 /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_069706(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069706 NCBI Caenorhabditis elegans C29F4.1 (collagen) mRNA, complete cds. 11/11 None
SNAP00000037122 ENSEMBL cdna:SNAP chromosome:CEL140:IV:11225487:11226456:1 11/11 None
GENEFINDER00000037126 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:11225487:11226456:1 11/11 None
C29F4.1.2 ENSEMBL cdna:known chromosome:CEL140:IV:11225476:11226485:1 gene:C29F4.1 11/11 None
C29F4.1.1 ENSEMBL cdna:known chromosome:CEL140:IV:11225476:11226650:1 gene:C29F4.1 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_067008 1/11 Cross Hyb Matching Probes A 
NM_067009 1/11 Cross Hyb Matching Probes A 
NM_073485 1/11 Cross Hyb Matching Probes A 
NM_073487 1/11 Cross Hyb Matching Probes A 
NM_069125 3/11 Cross Hyb Matching Probes A 
NM_069126 3/11 Cross Hyb Matching Probes A 
NM_001028312 1/11 Cross Hyb Matching Probes None
NM_072974 1/11 Cross Hyb Matching Probes A 
NM_073512 1/11 Cross Hyb Matching Probes A 
NM_182455 1/11 Cross Hyb Matching Probes A 
NM_062479 2/11 Cross Hyb Matching Probes A 
NM_067007 1/11 Cross Hyb Matching Probes A 
NM_068118 1/11 Cross Hyb Matching Probes A 
NM_063909 1/11 Cross Hyb Matching Probes A 
NM_062477 1/11 Cross Hyb Matching Probes A 
SNAP00000005484 1/11 Cross Hyb Matching Probes None
SNAP00000005486 2/11 Cross Hyb Matching Probes None
GENEFINDER00000005492 1/11 Cross Hyb Matching Probes None
GENEFINDER00000005502 2/11 Cross Hyb Matching Probes None
SNAP00000014221 1/11 Cross Hyb Matching Probes None
GENEFINDER00000014237 1/11 Cross Hyb Matching Probes None
SNAP00000036390 1/11 Cross Hyb Matching Probes None
GENEFINDER00000036401 1/11 Cross Hyb Matching Probes None
SNAP00000036391 1/11 Cross Hyb Matching Probes None
GENEFINDER00000036400 1/11 Cross Hyb Matching Probes None
SNAP00000036392 1/11 Cross Hyb Matching Probes None
GENEFINDER00000036395 1/11 Cross Hyb Matching Probes None
SNAP00000000181 1/11 Cross Hyb Matching Probes None
GENEFINDER00000000222 1/11 Cross Hyb Matching Probes None
SNAP00000005654 3/11 Cross Hyb Matching Probes None
SNAP00000005655 3/11 Cross Hyb Matching Probes None
GENEFINDER00000005663 3/11 Cross Hyb Matching Probes None
GENEFINDER00000005664 3/11 Cross Hyb Matching Probes None
SNAP00000023158 1/11 Cross Hyb Matching Probes None
GENEFINDER00000023159 1/11 Cross Hyb Matching Probes None
SNAP00000033943 1/11 Cross Hyb Matching Probes None
GENEFINDER00000033946 1/11 Cross Hyb Matching Probes None
SNAP00000043808 1/11 Cross Hyb Matching Probes None
GENEFINDER00000043818 1/11 Cross Hyb Matching Probes None
SNAP00000013927 1/11 Cross Hyb Matching Probes None
GENEFINDER00000013944 1/11 Cross Hyb Matching Probes None
SNAP00000017929 1/11 Cross Hyb Matching Probes None
SNAP00000017931 1/11 Cross Hyb Matching Probes None
GENEFINDER00000017933 1/11 Cross Hyb Matching Probes None
SNAP00000023009 1/11 Cross Hyb Matching Probes None
GENEFINDER00000023017 1/11 Cross Hyb Matching Probes None
SNAP00000029185 1/11 Cross Hyb Matching Probes None
GENEFINDER00000029188 1/11 Cross Hyb Matching Probes None
SNAP00000031753 1/11 Cross Hyb Matching Probes None
GENEFINDER00000031755 1/11 Cross Hyb Matching Probes None
F11G11.10 1/11 Cross Hyb Matching Probes A 
F11G11.12 2/11 Cross Hyb Matching Probes A 
C09G5.5 1/11 Cross Hyb Matching Probes A 
W05B2.6 1/11 Cross Hyb Matching Probes A 
W05B2.5 1/11 Cross Hyb Matching Probes A 
W05B2.1 1/11 Cross Hyb Matching Probes A 
F30B5.1 1/11 Cross Hyb Matching Probes A 
T28C6.4 3/11 Cross Hyb Matching Probes A 
T28C6.6 3/11 Cross Hyb Matching Probes A 
Y51H4A.28 1/11 Cross Hyb Matching Probes None
B0222.7 1/11 Cross Hyb Matching Probes A 
F55C10.2 1/11 Cross Hyb Matching Probes A 
F55C10.3 1/11 Cross Hyb Matching Probes A 
T11F9.9 1/11 Cross Hyb Matching Probes R A 
T10E10.5 1/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIV:11225492-11226462(+) 97.22 100.0
chrIV:8824801-8825960(+) 82.56 96.33
chrIV:8822993-8824152(-) 96.33 96.33
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-125
Ensembl C29F4.1
Entrez Gene 178029 Entrez gene
SwissProt Q18302 EMBL-EBI
WormBase CE03038 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 CAA92729 Hypothetical protein C29F4.1 [Caenorhabditis elegans] ref|NP_502107.1| C29F4.1 [Caenorhabditis elegans] 5.0E-30
blast CAE62024 Hypothetical protein CBG06035 [Caenorhabditis briggsae] 1.0E-29
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.4E-13
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.9E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.6E-13
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_502107.1 1 12-34
C29F4.1.2 1 12-34
C29F4.1.1 1 12-34
SNAP00000037122 1 12-34
GENEFINDER00000037126 1 12-34
Sequence
Target Sequence 
>C. ELEGANS:172701_X_AT
ggaggatgtgatgcttgctgccttccaggagccgctggaccagccggaaccccaggaaaa
ccaggacgcccaggaaagccaggagcaccaggacttccaggaaacccaggacgcccacca
cagcagccatgtgagccaatcaccccaccaccatgcaagccatgcccagccggaccagct
ggagccccaggaccagctggaccagccggagatgccggagccaacggaaacccaggagcc
ccaggacaagacggacagccaggagccccaggaaacaagggaccatctggaccaaacgga
aacccaggagccccaggagccccaggacagccaggacaagatgctccatccgagccaatc
accccaggagcaccaggaccagctggaccagccggaccacaaggacaaccaggagcccca
ggacagccaggacacgatggacaaccaggagccccaggaccaaagggaccaaatggaaac
ccaggagccccaggagccgacggaaacccaggagccccaggacaagctggaactgccgga
ggtgccggagagaagggaatctgtccaaagtactgcgcc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGAGGATGTGATGCTTGCTGCCTTC 29 517 292 Antisense
GAAAGCCAGGAGCACCAGGACTTCC 321 359 365 Antisense
CCACCACAGCAGCCATGTGAGCCAA 408 273 406 Antisense
TGGACCAGCCGGAGATGCCGGAGCC 708 547 489 Antisense
TGCCGGAGCCAACGGAAACCCAGGA 545 575 504 Antisense
CAGCCAGGAGCCCCAGGAAACAAGG 247 203 547 Antisense
GCCCCAGGACAGCCAGGACAAGATG 627 285 610 Antisense
ACAAGATGCTCCATCCGAGCCAATC 536 113 627 Antisense
GGACCACAAGGACAACCAGGAGCCC 6 523 685 Antisense
GACAAGCTGGAACTGCCGGAGGTGC 180 365 812 Antisense
GGGAATCTGTCCAAAGTACTGCGCC 624 493 846 Antisense
Sequence Source Affymetrix Proprietary Database