[Home] | [Total List]

[188313_s_at] collagen

Description F56D5.1 /REP_DB=WormBase Gene ID /WP=CE05967 /TR=Q20880 /GB=CAA93499.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 68      4grp_total > 50      6grp_cgc > 39      6grp_cgc_sub > Cu      6grp_total_sub > Increase      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 136
1 2 3 4 range
A 25.4
(-2.1)
A 		140.4
(3)
A 		62.1
(-0.5)
A 		4.6
(-3)
A 		136
B 48.9
(0.3)
A 		62.2
(1.5)
A 		77.2
(3)
A 		15.3
(-3)
A 		62
C 36.8
(-1.6)
A 		59.8
(2.4)
A 		28.7
(-3)
A 		63.5
(3)
A 		35
avr 37
(-2.1) 		87.5
(3) 		56
(-0.2) 		27.8
(-3) 		60

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 260
1 2 3 4 5 6 range
A 73.6
(-1.7)
A 		72.9
(-1.8)
A 		18.8
(-3)
A 		134.4
(-0.3)
A 		45.2
(-2.4)
A 		278.7
(3)
A 		260
B 96
(-0.9)
A 		72.8
(-1.8)
A 		51.9
(-2.7)
A 		44.7
(-3)
A 		174.5
(2.4)
A 		188.9
(3)
A 		144
C 101.3
(-0.5)
A 		69.1
(-1.9)
A 		83.3
(-1.3)
A 		45.8
(-3)
A 		98.7
(-0.6)
A 		177.5
(3)
A 		132
avr 90.3
(-1.6) 		71.6
(-2.3) 		51.3
(-3) 		75
(-2.1) 		106.1
(-1) 		215
(3) 		164
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 30
1 2 3 4 range
A 9.2
(-1.3)
A 		30.5
(3)
A 		16.2
(0.1)
A 		0.7
(-3)
A 		30
B 15.6
(2.1)
A 		15.4
(2)
A 		17.9
(3)
A 		3.3
(-3)
A 		15
C 12.2
(-1.2)
A 		17.2
(3)
A 		10
(-3)
A 		10.7
(-2.4)
A 		7
avr 12.3
(-0.2) 		21
(3) 		14.7
(0.7) 		4.9
(-3) 		16

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 67
1 2 3 4 5 6 range
A 13.6
(-2.1)
A 		25.9
(-0.9)
A 		4.1
(-3)
A 		34.1
(-0.2)
A 		13.6
(-2.1)
A 		67.9
(3)
A 		64
B 33.4
(-0.8)
A 		24.2
(-1.7)
A 		12.6
(-2.9)
A 		11.8
(-3)
A 		70.9
(3)
A 		70.4
(2.9)
A 		59
C 37.5
(0.4)
A 		21.1
(-1.6)
A 		21.2
(-1.6)
A 		9.2
(-3)
A 		31.9
(-0.3)
A 		59.4
(3)
A 		50
avr 28.2
(-1.2) 		23.7
(-1.8) 		12.6
(-3) 		18.4
(-2.3) 		38.8
(-0.1) 		65.9
(3) 		53
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 188313_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.9675
Sequence Type Exemplar sequence
Representative Public ID F56D5.1 NCBI
Target Description F56D5.1 /REP_DB=WormBase Gene ID /WP=CE05967 /TR=Q20880 /GB=CAA93499.1 /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_069254(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069254 NCBI Caenorhabditis elegans F56D5.1 (collagen) mRNA, complete cds. 11/11 A 
SNAP00000006176 ENSEMBL cdna:SNAP chromosome:CEL140:IV:9394958:9396187:-1 11/11 None
GENEFINDER00000006190 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:9394958:9396187:-1 11/11 None
F56D5.1 ENSEMBL cdna:known chromosome:CEL140:IV:9394911:9396195:-1 gene:F56D5.1 11/11 A 
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
chrIV:9394963-9396193(-) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-121
Ensembl F56D5.1
Entrez Gene 177771 Entrez gene
SwissProt Q20880 EMBL-EBI
WormBase CE05967 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 CAA93499 Hypothetical protein F56D5.1 [Caenorhabditis elegans] ref|NP_501655.1| F56D5.1 [Caenorhabditis elegans] 1.0E-163
blast CAA93499 Hypothetical protein F56D5.1 [Caenorhabditis elegans] ref|NP_501655.1| F56D5.1 [Caenorhabditis elegans] 1.0E-142
blast CAE58642 Hypothetical protein CBG01810 [Caenorhabditis briggsae] 1.0E-134
blast CAE58642 Hypothetical protein CBG01810 [Caenorhabditis briggsae] 1.0E-117
blast AAA83336 Dumpy : shorter than wild-type protein 8 [Caenorhabditis elegans] ref|NP_508873.1| DumPY : shorter than wild-type family member (dpy-8) [Caenorhabditis elegans] 6.0E-47
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 2.1E-6
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.8E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.4E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.8E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.4E-10
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_501655.1 1 12-31
F56D5.1 1 12-31
GENEFINDER00000006190 1 12-31
Sequence
Target Sequence 
>C. ELEGANS:188313_S_AT
gtggattgccaggaaatgcgggacgaaaaggaaaatctggaaagtcgggacatccaggac
aaccaggaggaatcggagcaagtggagcaaaaggaccaactggtacacgtggaacacctg
gaatgaagggaccaccaggagatactattattgccggagaaggaattaaaggacctccag
ggctacaaggatcacaaggacctaaaggaccaccaggaaattccggtagatcatctaata
ttagaggtccatcaggtaaacctggacaacagggtggaattggaggaactggaaagttcg
gaaaatacggagagcagggtggaatcggtgcaccgggagaaccaggactgccagcaacat
attgtccatccgattgtggagttaacacgattctctcacaatttggaagtcgtgctcaac
atccagaatcgatcaacggagaggacaatggagcacctgcagcaaatacagaagagtaca
attctgaagaacgaattgaatcgccagctccacctgctccacagccaactaccaatcagc
aacaggaaaccgttgcagctgctgc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTGGATTGCCAGGAAATGCGGGACG 581 489 473 Antisense
TGGAAAGTCGGGACATCCAGGACAA 530 547 510 Antisense
GACAACCAGGAGGAATCGGAGCAAG 86 365 530 Antisense
GGACCAACTGGTACACGTGGAACAC 403 521 565 Antisense
GTACACGTGGAACACCTGGAATGAA 679 457 575 Antisense
GACCACCAGGAGATACTATTATTGC 7 385 602 Antisense
GAATTAAAGGACCTCCAGGGCTACA 89 321 635 Antisense
GGACCTCCAGGGCTACAAGGATCAC 559 523 643 Antisense
GGACCACCAGGAAATTCCGGTAGAT 638 521 679 Antisense
GAGGTCCATCAGGTAAACCTGGACA 103 403 716 Antisense
AACAGGAAACCGTTGCAGCTGCTGC 213 133 1013 Antisense
Sequence Source Affymetrix Proprietary Database