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[172705_x_at] collagen

Description F57B1.3 /REP_DB=WormBase Gene ID /WP=CE11290 /TR=Q20922 /GB=CAB01509.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_highest_10_10 > 08      6grp_high1_10_10 > 42      6grp_highest_nonorm > 07      6grp_total > 20      4grp_total > 58      6grp_cgc > 74      6grp_high1_sub > 02_03      6grp_cgc_sub > 02_03_04_05      6grp_total_sub > Hat      6grp_rule_based > S2      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 19487
1 2 3 4 range
A 8095.4
(-0.5)
P 		17330.1
(2.3)
P 		19498.8
(3)
P 		22.2
(-3)
A 		19477
B 8228.6
(-0.3)
P 		14825.3
(1.9)
P 		18291.8
(3)
P 		11.9
(-3)
A 		18280
C 6747.5
(-0.5)
P 		13816.2
(2.2)
P 		16040.7
(3)
P 		86.8
(-3)
A 		15954
avr 7690.5
(-0.4) 		15323.9
(2.1) 		17943.8
(3) 		40.3
(-3) 		17904

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 13192
1 2 3 4 5 6 range
A 6734.2
(-3)
P 		16451.3
(2.3)
P 		17836
(3)
P 		17764.6
(3)
P 		12474.7
(0.1)
P 		6744.4
(-3)
P 		11102
B 8967.8
(-1.1)
P 		16527.2
(3)
P 		14209.8
(1.7)
P 		12516.5
(0.8)
P 		11815.3
(0.4)
P 		5574.3
(-3)
P 		10953
C 6930.8
(-1.9)
P 		17328
(3)
P 		17023
(2.9)
P 		9661
(-0.6)
P 		14289.3
(1.6)
P 		4643.6
(-3)
P 		12684
avr 7544.3
(-2) 		16768.8
(3) 		16356.3
(2.8) 		13314
(1.1) 		12859.8
(0.9) 		5654.1
(-3) 		11115
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 5588
1 2 3 4 range
A 2947.5
(0.5)
P 		3761.9
(1.4)
P 		5097.4
(3)
P 		3.2
(-3)
A 		5094
B 2624
(0.7)
P 		3661.5
(2.2)
P 		4238.6
(3)
P 		2.5
(-3)
A 		4236
C 2233.6
(-0.6)
P 		3972.2
(1.3)
P 		5590.7
(3)
P 		14.6
(-3)
A 		5576
avr 2601.7
(0.1) 		3798.5
(1.6) 		4975.6
(3) 		6.8
(-3) 		4969

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 4610
1 2 3 4 5 6 range
A 1241.4
(-3)
P 		5850.9
(3)
P 		3884.3
(0.4)
P 		4505.5
(1.2)
P 		3764.3
(0.3)
P 		1642
(-2.5)
P 		4610
B 3120.3
(-1.2)
P 		5501.2
(3)
P 		3450.6
(-0.6)
P 		3315.2
(-0.8)
P 		4800.4
(1.8)
P 		2078.6
(-3)
P 		3423
C 2568.9
(-1.4)
P 		5287.3
(3)
P 		4332.7
(1.5)
P 		1942.8
(-2.4)
P 		4623.8
(1.9)
P 		1554.5
(-3)
P 		3733
avr 2310.2
(-2.1) 		5546.5
(3) 		3889.2
(0.4) 		3254.5
(-0.6) 		4396.2
(1.2) 		1758.4
(-3) 		3788
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172705_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.14135
Sequence Type Exemplar sequence
Representative Public ID F57B1.3 NCBI
Target Description F57B1.3 /REP_DB=WormBase Gene ID /WP=CE11290 /TR=Q20922 /GB=CAB01509.1 /SUBMIT=HINXTON /CHR=5 /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_073882(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073882 NCBI Caenorhabditis elegans F57B1.3 (collagen) mRNA, complete cds. 11/11 None
SNAP00000007051 ENSEMBL cdna:SNAP chromosome:CEL140:V:13200917:13202022:-1 11/11 None
GENEFINDER00000007058 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:13200917:13201906:-1 11/11 None
F57B1.3 ENSEMBL cdna:known chromosome:CEL140:V:13200821:13201906:-1 gene:F57B1.3 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_073276 1/11 Cross Hyb Matching Probes A 
NM_073277 1/11 Cross Hyb Matching Probes A 
NM_059689 1/11 Cross Hyb Matching Probes A 
NM_059690 1/11 Cross Hyb Matching Probes A 
NM_070565 1/11 Cross Hyb Matching Probes A 
NM_073512 1/11 Cross Hyb Matching Probes A 
NM_075994 1/11 Cross Hyb Matching Probes None
NM_073883 7/11 Cross Hyb Matching Probes A 
NM_069714 1/11 Cross Hyb Matching Probes A 
NM_171361 1/11 Cross Hyb Matching Probes None
NM_073245 1/11 Cross Hyb Matching Probes A 
SNAP00000007970 1/11 Cross Hyb Matching Probes None
GENEFINDER00000007974 1/11 Cross Hyb Matching Probes None
SNAP00000007971 1/11 Cross Hyb Matching Probes None
GENEFINDER00000007980 1/11 Cross Hyb Matching Probes None
GENEFINDER00000044434 1/11 Cross Hyb Matching Probes None
SNAP00000044426 1/11 Cross Hyb Matching Probes None
SNAP00000000185 1/11 Cross Hyb Matching Probes None
GENEFINDER00000000214 1/11 Cross Hyb Matching Probes None
SNAP00000005950 1/11 Cross Hyb Matching Probes None
SNAP00000005951 1/11 Cross Hyb Matching Probes None
GENEFINDER00000005959 1/11 Cross Hyb Matching Probes None
GENEFINDER00000005960 1/11 Cross Hyb Matching Probes None
SNAP00000032051 1/11 Cross Hyb Matching Probes None
GENEFINDER00000032086 1/11 Cross Hyb Matching Probes None
SNAP00000002816 1/11 Cross Hyb Matching Probes None
SNAP00000002817 1/11 Cross Hyb Matching Probes None
GENEFINDER00000002822 1/11 Cross Hyb Matching Probes None
GENEFINDER00000002824 1/11 Cross Hyb Matching Probes None
SNAP00000007052 7/11 Cross Hyb Matching Probes None
GENEFINDER00000007063 7/11 Cross Hyb Matching Probes None
SNAP00000013927 1/11 Cross Hyb Matching Probes None
GENEFINDER00000013944 1/11 Cross Hyb Matching Probes None
SNAP00000027127 1/11 Cross Hyb Matching Probes None
GENEFINDER00000027152 1/11 Cross Hyb Matching Probes None
C15A11.5 1/11 Cross Hyb Matching Probes A 
C15A11.6 1/11 Cross Hyb Matching Probes A 
Y73B6BL.34 1/11 Cross Hyb Matching Probes None
F54D1.2 1/11 Cross Hyb Matching Probes R A 
Y51H4A.9 1/11 Cross Hyb Matching Probes A 
B0024.1 1/11 Cross Hyb Matching Probes R A 
F15H10.2 1/11 Cross Hyb Matching Probes A 
F15H10.1.2 1/11 Cross Hyb Matching Probes A 
F15H10.1.1 1/11 Cross Hyb Matching Probes A 
T11F9.9 1/11 Cross Hyb Matching Probes R A 
F57B1.4.1 7/11 Cross Hyb Matching Probes A 
F57B1.4.3 7/11 Cross Hyb Matching Probes None
F57B1.4.2 7/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrV:13200916-13201906(-) 87.15 100.0
chrV:13203688-13204690(-) 84.93 97.66
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-159
Ensembl F57B1.3
Entrez Gene 179803 Entrez gene
SwissProt Q20922 EMBL-EBI
WormBase CE11290 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 CAB01509 Hypothetical protein F57B1.3 [Caenorhabditis elegans] ref|NP_506283.1| F57B1.3 [Caenorhabditis elegans] 3.0E-61
blast CAB01508 Hypothetical protein F57B1.4 [Caenorhabditis elegans] ref|NP_506284.2| F57B1.4 [Caenorhabditis elegans] 9.0E-54
blast CAA98257 Hypothetical protein F15H10.1 [Caenorhabditis elegans] ref|NP_505678.1| F15H10.1 [Caenorhabditis elegans] sp|P20630|COL12_CAEEL Cuticle collagen 12 precursor emb|CAA35954.1| collagen [Caenorhabditis elegans] 7.0E-51
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 2.5E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.6E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.5E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.4E-7
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 2.5E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.6E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.5E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.4E-7
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_506283.1 1 20-42
F57B1.3 1 20-42
SNAP00000007051 1 26-48
GENEFINDER00000007058 1 20-42
Sequence
Target Sequence 
>C. ELEGANS:172705_X_AT
gacgccgcagtcggaggattcggaggatccgccggaggatcatgctgctcatgcggaacc
ggagctgctggaccagctggatccccaggacaagatggagccccaggaaacgacggagcc
ccaggagctccaggaaacccaggacaagatgcctctgaggaccaaaccgctggaccagac
agcttctgcttcgactgcccagctggaccaccagggccatcaggagccccaggacaaaag
ggaccttcaggagccccaggagtcccaggacaaaccggaggagcttcccttccaggacca
ccaggaccagccggaccaccaggaccatctggacaaccaggatccaacggaaacgccgga
gccccaggagccccaggacaagtcgtcgatgttccaggcaccccaggaccagctggacca
ccaggaccaccaggaccagccggagccccaggacagccaggacaatctggatccggtcaa
ccaggaggtccaggaccacaaggagatgccggagctccaggagccccaggacaaccagga
caagctggagccccaggacaagacggagacagcggatccgagggagcttgcg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GACGCCGCAGTCGGAGGATTCGGAG 260 381 325 Antisense
GATCCGCCGGAGGATCATGCTGCTC 235 417 350 Antisense
GCTGCTCATGCGGAACCGGAGCTGC 500 297 368 Antisense
GGAGCTGCTGGACCAGCTGGATCCC 166 521 385 Antisense
AACCGCTGGACCAGACAGCTTCTGC 349 147 489 Antisense
CAAAAGGGACCTTCAGGAGCCCCAG 44 191 559 Antisense
GAGTCCCAGGACAAACCGGAGGAGC 2 397 584 Antisense
GGACCACCAGGACCATCTGGACAAC 369 523 637 Antisense
GACAAGTCGTCGATGTTCCAGGCAC 131 365 701 Antisense
AGGACAATCTGGATCCGGTCAACCA 505 53 783 Antisense
GACAGCGGATCCGAGGGAGCTTGCG 692 367 892 Antisense
Sequence Source Affymetrix Proprietary Database