[Home] | [Total List]

[172703_x_at] collagen

Description F57B1.4 /REP_DB=WormBase Gene ID /WP=CE11292 /TR=Q20921 /GB=CAB01508.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_highest_10_10 > 34      6grp_high1_10_10 > 42      4grp_highest_8_8 > 09      4grp_high_8_8 > 61      6grp_highest_nonorm > 08      6grp_total > 20      4grp_total > 58      6grp_highest_sub > 02_03      6grp_cgc > 73      6grp_high1_sub > 02_03      6grp_cgc_sub > 02_03      6grp_total_sub > Hat      6grp_rule_based > S3      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 30949
1 2 3 4 range
A 13698.7
(-0.4)
P 		28529.7
(2.5)
P 		31296.9
(3)
P 		467.2
(-3)
P 		30830
B 14428.5
(-0.1)
P 		23798.7
(1.9)
P 		29055.2
(3)
P 		348.4
(-3)
P 		28707
C 11900.9
(0.1)
P 		22391.1
(3)
P 		22277.7
(3)
P 		422.6
(-3)
P 		21969
avr 13342.7
(-0.1) 		24906.5
(2.4) 		27543.3
(3) 		412.7
(-3) 		27131

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 21851
1 2 3 4 5 6 range
A 14672.5
(-2.7)
P 		29392.6
(3)
P 		27691.1
(2.3)
P 		24089.1
(0.9)
P 		17472.5
(-1.6)
P 		13937.8
(-3)
P 		15455
B 14045.6
(-2.1)
P 		27132.1
(2.4)
P 		28779.8
(3)
P 		19823.7
(-0.1)
P 		17243.5
(-1)
P 		11587.8
(-3)
P 		17192
C 15616.1
(-1.5)
P 		28753.3
(2.1)
P 		31868
(3)
P 		19971.5
(-0.3)
P 		21836.9
(0.2)
P 		10017.4
(-3)
P 		21851
avr 14778.1
(-2) 		28426
(2.7) 		29446.3
(3) 		21294.8
(0.2) 		18851
(-0.6) 		11847.7
(-3) 		17599
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 8113
1 2 3 4 range
A 4987.7
(0.6)
P 		6193
(1.5)
P 		8181.6
(3)
P 		68.4
(-3)
P 		8113
B 4601.1
(1.1)
P 		5877.7
(2.2)
P 		6732.7
(3)
P 		74.2
(-3)
P 		6659
C 3939.5
(0)
P 		6437.6
(2)
P 		7764.5
(3)
P 		71.3
(-3)
P 		7693
avr 4509.4
(0.6) 		6169.4
(1.9) 		7559.6
(3) 		71.3
(-3) 		7488

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 7749
1 2 3 4 5 6 range
A 2704.8
(-3)
P 		10453.5
(3)
P 		6030.5
(-0.4)
P 		6109.6
(-0.4)
P 		5272.4
(-1)
P 		3393.4
(-2.5)
P 		7749
B 4887.2
(-2.3)
P 		9031.1
(3)
P 		6988.6
(0.4)
P 		5250.6
(-1.8)
P 		7005.8
(0.4)
P 		4321
(-3)
P 		4710
C 5788.2
(-0.3)
P 		8773.5
(3)
P 		8110.9
(2.3)
P 		4016.3
(-2.3)
P 		7066.1
(1.1)
P 		3353.4
(-3)
P 		5420
avr 4460.1
(-2.2) 		9419.4
(3) 		7043.3
(0.5) 		5125.5
(-1.5) 		6448.1
(-0.1) 		3689.3
(-3) 		5730
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172703_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.14244
Sequence Type Exemplar sequence
Representative Public ID F57B1.4 NCBI
Target Description F57B1.4 /REP_DB=WormBase Gene ID /WP=CE11292 /TR=Q20921 /GB=CAB01508.1 /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_073883(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073883 NCBI Caenorhabditis elegans F57B1.4 (collagen) mRNA, complete cds. 11/11 None
SNAP00000007051 ENSEMBL cdna:SNAP chromosome:CEL140:V:13200917:13202022:-1 9/11 None
SNAP00000007052 ENSEMBL cdna:SNAP chromosome:CEL140:V:13203689:13204690:-1 11/11 None
GENEFINDER00000007063 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:13203689:13204690:-1 11/11 None
F57B1.4.1 ENSEMBL cdna:known chromosome:CEL140:V:13203578:13204780:-1 gene:F57B1.4 11/11 A 
F57B1.4.3 ENSEMBL cdna:known chromosome:CEL140:V:13203578:13204690:-1 gene:F57B1.4 11/11 None
F57B1.4.2 ENSEMBL cdna:known chromosome:CEL140:V:13203578:13204780:-1 gene:F57B1.4 11/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_073276 3/11 Cross Hyb Matching Probes A 
NM_073277 3/11 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_073882 8/11 Cross Hyb Matching Probes A 
NM_069714 1/11 Cross Hyb Matching Probes A 
NM_171361 1/11 Cross Hyb Matching Probes None
NM_072673 1/11 Cross Hyb Matching Probes A 
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 3/11 Cross Hyb Matching Probes None
SNAP00000002817 3/11 Cross Hyb Matching Probes None
GENEFINDER00000002822 3/11 Cross Hyb Matching Probes None
GENEFINDER00000002824 3/11 Cross Hyb Matching Probes None
GENEFINDER00000007058 8/11 Cross Hyb Matching Probes None
SNAP00000013927 1/11 Cross Hyb Matching Probes None
GENEFINDER00000013944 1/11 Cross Hyb Matching Probes None
SNAP00000025313 1/11 Cross Hyb Matching Probes None
GENEFINDER00000025319 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 
ZC513.8 1/11 Cross Hyb Matching Probes A 
B0024.1 1/11 Cross Hyb Matching Probes R A 
F15H10.2 3/11 Cross Hyb Matching Probes A 
F15H10.1.2 3/11 Cross Hyb Matching Probes A 
F15H10.1.1 3/11 Cross Hyb Matching Probes A 
T11F9.9 1/11 Cross Hyb Matching Probes R A 
F57B1.3 8/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrV:13203688-13204940(-) 88.7 100.0
chrV:13200916-13201830(-) 67.79 78.99
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-160
Ensembl F57B1.4
Entrez Gene 179804 Entrez gene
SwissProt Q20921 EMBL-EBI
WormBase CE31962 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-59
blast CAB01509 Hypothetical protein F57B1.3 [Caenorhabditis elegans] ref|NP_506283.1| F57B1.3 [Caenorhabditis elegans] 9.0E-54
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 5.2E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 8.4E-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_506284.2 1 20-42
F57B1.4.1 1 20-42
F57B1.4.3 1 20-42
F57B1.4.2 1 20-42
SNAP00000007051 1 26-48
SNAP00000007052 1 20-42
GENEFINDER00000007063 1 20-42
Sequence
Target Sequence 
>C. ELEGANS:172703_X_AT
gatccgccggaggatcatgctgctcatgcggaaccggagctgctggaccagctggatccc
caggacaagacggagctccaggaaacgacggagccccaggagccccaggaaacccaggac
aagatgcctctgaggaccaaaccgctggaccagacagcttctgcttcgactgcccagctg
gaccaccaggaccatcaggagccccaggacaaaagggaccttcaggagccccaggagccc
caggacaatccggaggagcttcccttccaggaccaccaggaccagccggaccaccaggac
catctggacaaccaggatccaacggaaacgccggagccccaggagccccaggacaagtcg
tcgatgttccaggaaccccaggaccagctggaccaccaggaccaccaggaccagccggag
ccccaggacagccaggacaatctggatccgctcaaccaggaggcccaggaccacaaggag
atgccggagctccaggagccccaggacaaccaggacaagctggagccccaggacaagacg
gagacagcggatccgagggagcttgcg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GATCCGCCGGAGGATCATGCTGCTC 236 417 479 Antisense
GCTGCTCATGCGGAACCGGAGCTGC 501 297 497 Antisense
GGAGCTGCTGGACCAGCTGGATCCC 167 521 514 Antisense
GATCCCCAGGACAAGACGGAGCTCC 204 417 533 Antisense
AACCGCTGGACCAGACAGCTTCTGC 350 147 618 Antisense
CAAAAGGGACCTTCAGGAGCCCCAG 45 191 688 Antisense
AGCCCCAGGACAATCCGGAGGAGCT 442 83 714 Antisense
GGACCACCAGGACCATCTGGACAAC 370 523 766 Antisense
GCCCCAGGACAAGTCGTCGATGTTC 624 285 823 Antisense
GAGGCCCAGGACCACAAGGAGATGC 269 405 938 Antisense
GACAGCGGATCCGAGGGAGCTTGCG 693 367 1021 Antisense
Sequence Source Affymetrix Proprietary Database