[Home] | [Total List]

[188469_at] collagen

Description T15B7.5 /REP_DB=WormBase Gene ID /WP=CE13656 /TR=O17035 /GB=AAB69960.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_highest_10_10 > 34      6grp_high1_10_10 > 33      6grp_highest_nonorm > 70      6grp_total > 10      4grp_total > 50      6grp_highest_sub > 02_03      6grp_cgc > 63      6grp_high1_sub > 02      6grp_cgc_sub > 02      6grp_total_sub > Hat      6grp_rule_based > S2      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 347
1 2 3 4 range
A 102
(-2)
P 		288.2
(1.3)
P 		378.7
(3)
P 		49.8
(-3)
A 		329
B 92.9
(-1.8)
A 		328.2
(3)
P 		211.9
(0.6)
P 		31.6
(-3)
A 		297
C 55.9
(-3)
P 		326.2
(3)
P 		156.5
(-0.8)
P 		72.7
(-2.6)
A 		270
avr 83.6
(-2.3) 		314.2
(3) 		249
(1.5) 		51.4
(-3) 		263

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 423
1 2 3 4 5 6 range
A 145.7
(-2.9)
P 		455.3
(3)
P 		235.3
(-1.2)
P 		332.2
(0.7)
P 		184
(-2.1)
P 		138.6
(-3)
P 		317
B 188.8
(-1.7)
P 		511.5
(3)
P 		318.3
(0.2)
P 		252.3
(-0.8)
P 		313
(0.1)
P 		101.4
(-3)
P 		410
C 145.7
(-2.1)
P 		471.2
(3)
P 		452.4
(2.7)
P 		295.3
(0.2)
P 		323.5
(0.7)
P 		88.8
(-3)
P 		382
avr 160.1
(-2.2) 		479.3
(3) 		335.3
(0.7) 		293.3
(-0) 		273.5
(-0.3) 		109.6
(-3) 		370
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 92
1 2 3 4 range
A 37.1
(-1.1)
P 		62.6
(0.6)
P 		99
(3)
P 		7.3
(-3)
A 		92
B 29.6
(-1.2)
A 		81.1
(3)
P 		49.1
(0.4)
P 		6.7
(-3)
A 		74
C 18.5
(-2.5)
P 		93.8
(3)
P 		54.5
(0.1)
P 		12.3
(-3)
A 		82
avr 28.4
(-1.3) 		79.2
(3) 		67.5
(2) 		8.8
(-3) 		70

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 143
1 2 3 4 5 6 range
A 26.9
(-3)
P 		161.9
(3)
P 		51.2
(-1.9)
P 		84.3
(-0.4)
P 		55.5
(-1.7)
P 		33.7
(-2.7)
P 		135
B 65.7
(-1.7)
P 		170.3
(3)
P 		77.3
(-1.2)
P 		66.8
(-1.7)
P 		127.2
(1)
P 		37.8
(-3)
P 		133
C 54
(-1.7)
P 		143.8
(3)
P 		115.1
(1.5)
P 		59.4
(-1.4)
P 		104.7
(0.9)
P 		29.7
(-3)
P 		114
avr 48.9
(-2.3) 		158.7
(3) 		81.2
(-0.7) 		70.2
(-1.2) 		95.8
(-0) 		33.7
(-3) 		125
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188469_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.12467
Sequence Type Exemplar sequence
Representative Public ID T15B7.5 NCBI
Target Description T15B7.5 /REP_DB=WormBase Gene ID /WP=CE13656 /TR=O17035 /GB=AAB69960.1 /SUBMIT=ST.LOUIS /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_072334(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_072334 NCBI Caenorhabditis elegans T15B7.5 (collagen) mRNA, complete cds. 11/11 None
SNAP00000035387 ENSEMBL cdna:SNAP chromosome:CEL140:V:6832298:6833287:1 11/11 None
GENEFINDER00000035400 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:6832298:6833287:1 11/11 None
T15B7.5 ENSEMBL cdna:known chromosome:CEL140:V:6832298:6833287:1 gene:T15B7.5 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
chrV:6832298-6833288(+) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-141
Ensembl T15B7.5
Entrez Gene 188515 Entrez gene
SwissProt O17035 EMBL-EBI
WormBase CE13656 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 AAB69960 Collagen protein 141 [Caenorhabditis elegans] ref|NP_504735.1| T15B7.5 [Caenorhabditis elegans] 5.0E-52
blast CAE71957 Hypothetical protein CBG19026 [Caenorhabditis briggsae] 3.0E-48
blast CAE71958 Hypothetical protein CBG19027 [Caenorhabditis briggsae] 1.0E-41
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.1E-28
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0015
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.6E-7
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.0E-12
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_504735.1 1 13-35
T15B7.5 1 13-35
SNAP00000035387 1 13-35
GENEFINDER00000035400 1 13-35
Sequence
Target Sequence 
>C. ELEGANS:188469_AT
caggatctggagctcgagtcaacccacaaaccggccgtgacagtttctgcatcacttgcc
cagccggaccaccaggacctgccggaactccaggagctccaggagccccaggaaacgctg
gagccccaggacaagattcctttggaggaggaccaggaccagctggaccaacaggaccta
ccggagacgccggagcaccaggacagccagggcatcccggatcccctggaaacccaggac
gtggagggcaacgcagccgtggacttccaggaccatcaggaagaccgggaccacaaggac
cggctggaggaccaggacagccaggacaatctggtggatcaggcacccccggacaacccg
gagcacctggagcaccagggcatccgggacaagcaggaactccaggaactccaggagcac
caggaaattctggagccccaggaggagatgccgcttattgcccatgcccagctcgttctg
ctgcaatggccgctcgcaagcgcgtcttcaaggttgctcgt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CAGGATCTGGAGCTCGAGTCAACCC 398 207 377 Antisense
GCCGTGACAGTTTCTGCATCACTTG 540 283 410 Antisense
GCCCCAGGACAAGATTCCTTTGGAG 573 277 499 Antisense
CAAGATTCCTTTGGAGGAGGACCAG 33 183 508 Antisense
CAGGACGTGGAGGGCAACGCAGCCG 551 207 611 Antisense
ACCTGGAGCACCAGGGCATCCGGGA 31 87 741 Antisense
GGCATCCGGGACAAGCAGGAACTCC 652 535 755 Antisense
ATCCGGGACAAGCAGGAACTCCAGG 80 37 758 Antisense
CAGGAAATTCTGGAGCCCCAGGAGG 159 207 797 Antisense
CTCGCAAGCGCGTCTTCAAGGTTGC 507 233 869 Antisense
CAAGCGCGTCTTCAAGGTTGCTCGT 670 185 873 Antisense
Sequence Source Affymetrix Proprietary Database