[Home] | [Total List]

[188659_at] collagen

Description Y38C1BA.3 /REP_DB=WormBase Gene ID /WP=CE21569 /TR=Q9N527 /GB=AAF60502.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_highest_10_10 > 19      6grp_high1_10_10 > 91      6grp_highest_nonorm > 55      6grp_total > 93      4grp_total > 49      6grp_highest_sub > 05      6grp_cgc > 98      6grp_high1_sub > 05      6grp_total_sub > Hat      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 3199
1 2 3 4 range
A 161.2
(-2.9)
A 		2828
(3)
P 		2617.5
(2.5)
P 		105.5
(-3)
A 		2723
B 114
(-2.9)
A 		2491.9
(1.5)
P 		3271
(3)
P 		80.2
(-3)
A 		3191
C 153.3
(-2.8)
A 		2871.5
(2.8)
P 		2956.1
(3)
P 		71.6
(-3)
A 		2885
avr 142.8
(-2.9) 		2730.5
(2.5) 		2948.2
(3) 		85.8
(-3) 		2862

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 4290
1 2 3 4 5 6 range
A 485.4
(-3)
P 		1234
(-1.1)
P 		923
(-1.9)
P 		2511.1
(2)
P 		2894.4
(3)
P 		918.8
(-1.9)
P 		2409
B 421.2
(-3)
P 		1208.7
(-1.4)
P 		1181.4
(-1.4)
P 		2169.5
(0.6)
P 		3335.8
(3)
P 		802
(-2.2)
P 		2915
C 535.6
(-3)
P 		1120.4
(-2.2)
P 		1098.4
(-2.2)
P 		1871.7
(-1.1)
P 		4711.5
(3)
P 		802
(-2.6)
P 		4176
avr 480.7
(-3) 		1187.7
(-1.7) 		1067.6
(-1.9) 		2184.1
(0.2) 		3647.2
(3) 		840.9
(-2.3) 		3167
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1018
1 2 3 4 range
A 58.7
(-2.6)
A 		613.9
(2.4)
P 		684.3
(3)
P 		15.4
(-3)
A 		669
B 36.3
(-2.8)
A 		615.4
(1.8)
P 		758
(3)
P 		17.1
(-3)
A 		741
C 50.8
(-2.8)
A 		825.6
(1.8)
P 		1030.3
(3)
P 		12.1
(-3)
A 		1018
avr 48.6
(-2.8) 		685
(2) 		824.2
(3) 		14.9
(-3) 		809

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1435
1 2 3 4 5 6 range
A 89.5
(-3)
P 		438.9
(-0.3)
P 		201
(-2.1)
P 		636.9
(1.2)
P 		873.4
(3)
P 		223.7
(-2)
P 		784
B 146.5
(-3)
P 		402.3
(-1.7)
P 		286.9
(-2.3)
P 		574.6
(-0.9)
P 		1355.3
(3)
P 		299.1
(-2.2)
P 		1209
C 198.5
(-3)
P 		341.9
(-2.4)
P 		279.6
(-2.6)
P 		376.4
(-2.2)
P 		1524.6
(3)
P 		268.5
(-2.7)
P 		1326
avr 144.8
(-3) 		394.4
(-1.6) 		255.8
(-2.4) 		529.3
(-0.9) 		1251.1
(3) 		263.8
(-2.4) 		1106
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188659_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11232
Sequence Type Exemplar sequence
Representative Public ID Y38C1BA.3 NCBI
Target Description Y38C1BA.3 /REP_DB=WormBase Gene ID /WP=CE21569 /TR=Q9N527 /GB=AAF60502.1 /SUBMIT=ST.LOUIS /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_067737(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067737 NCBI Caenorhabditis elegans Y38C1BA.3 (collagen) mRNA, complete cds. 11/11 None
SNAP00000017748 ENSEMBL cdna:SNAP chromosome:CEL140:IV:1818349:1820248:-1 11/11 None
GENEFINDER00000017752 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:1817656:1820248:-1 11/11 None
Y38C1BA.3 ENSEMBL cdna:known chromosome:CEL140:IV:1817309:1820251:-1 gene:Y38C1BA.3 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:1817661-1820254(-) 96.58 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-109
Ensembl Y38C1BA.3
Entrez Gene 176988 Entrez gene
SwissProt Q9N527 EMBL-EBI
WormBase CE21569 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 AAF60502 Collagen protein 109 [Caenorhabditis elegans] ref|NP_500138.1| Y38C1BA.3 [Caenorhabditis elegans] 2.0E-58
blast CAE63849 Hypothetical protein CBG08408 [Caenorhabditis briggsae] 1.0E-57
blast CAD66221 Hypothetical protein Y41C4A.19 [Caenorhabditis elegans] ref|NP_871711.1| Y41C4A.19 [Caenorhabditis elegans] 4.0E-18
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 4.8E-8
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.4E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 8.4E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.9E-9
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_500138.1 1 12-34
Y38C1BA.3 1 12-34
SNAP00000017748 1 12-34
GENEFINDER00000017752 1 12-34
Sequence
Target Sequence 
>C. ELEGANS:188659_AT
gccgggtgctgtaagccaggacacccagggcggcccggactcccaggacgtaacggaaag
cctggagttccaggagcaccaggacgaccaggaacccctggaagaccaccgattgtgtgc
gaagagcaagacgttccaccatgcaatccatgcccaccaggaccaccaggaccacaagga
ccaactggaaacagtggacaaccaggacggccaggtaatccaggacggccaggatcccca
ggaacaccgggacctgtcggaccaaatggagcatccggagactctggagcacctggaaac
gacggagagaagggagaaccaggacgaccggctcaatcgacaccatccacgccgggagag
ccaggaaatccgggagacgccggagcaaccgg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCCGGGTGCTGTAAGCCAGGACACC 514 283 280 Antisense
GTAACGGAAAGCCTGGAGTTCCAGG 162 457 329 Antisense
ACCCCTGGAAGACCACCGATTGTGT 652 87 373 Antisense
GACCACCGATTGTGTGCGAAGAGCA 324 383 383 Antisense
GAGCAAGACGTTCCACCATGCAATC 683 389 403 Antisense
GACAACCAGGACGGCCAGGTAATCC 501 365 476 Antisense
GGTAATCCAGGACGGCCAGGATCCC 349 503 493 Antisense
CGGGACCTGTCGGACCAAATGGAGC 67 245 527 Antisense
CAAATGGAGCATCCGGAGACTCTGG 284 193 542 Antisense
GAAGGGAGAACCAGGACGACCGGCT 675 321 588 Antisense
ATCCGGGAGACGCCGGAGCAACCGG 81 37 647 Antisense
Sequence Source Affymetrix Proprietary Database