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[171735_x_at] collagen

Description CEK072GXR_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=T06E4.4 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D66041 /WB_GENE_ID=T06E4.4 /WP=CE06370 /CHR=5 /FEA=Genomic Cluster /DEF=collagen; C.elegans cDNA clone yk72g10 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 34      6grp_high1_10_10 > 42      6grp_highest_nonorm > 08      6grp_total > 31      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 > L2      

Scale

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G range Absolute graph Relative graph Expression Table Dauer Comp.
4 31071
1 2 3 4 range
A 14279.9
(-0.3)
P
31348
(3)
P
29387
(2.6)
P
276.8
(-3)
A
31071
B 15017.1
(-0.1)
P
27790.4
(2.4)
P
30802.4
(3)
P
309.6
(-3)
A
30493
C 14573.5
(-0)
P
29025.3
(3)
P
23764.6
(1.9)
P
379.4
(-3)
M
28646
avr 14623.5
(-0)
29387.9
(3)
27984.7
(2.7)
321.9
(-3)
29066

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1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 27954
1 2 3 4 5 6 range
A 15969.9
(-0.8)
P
31927.5
(3)
P
30205.1
(2.6)
P
24657.9
(1.3)
P
14019.6
(-1.2)
P
6591.5
(-3)
P
25336
B 13812.6
(-0.9)
P
27440
(2.7)
P
28747.1
(3)
P
20110.7
(0.8)
P
13794.2
(-0.9)
P
5601.3
(-3)
P
23146
C 15658.8
(-0.5)
P
27642.4
(2.1)
P
31558.5
(3)
P
20599.1
(0.6)
P
16799.7
(-0.2)
P
3973.3
(-3)
P
27585
avr 15147.1
(-0.6)
29003.3
(2.7)
30170.2
(3)
21789.2
(1)
14871.2
(-0.7)
5388.7
(-3)
24782
No Scale

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G range Absolute graph Relative graph Expression Table Dauer Comp.
4 8304
1 2 3 4 range
A 5199.3
(1.1)
P
6804.8
(2.3)
P
7682.3
(3)
P
40.5
(-3)
A
7642
B 4788.8
(1)
P
6863.6
(2.8)
P
7137.6
(3)
P
66
(-3)
A
7072
C 4824.2
(0.4)
P
8344.9
(3)
P
8282.7
(3)
P
64
(-3)
M
8281
avr 4937.4
(0.8)
7337.8
(2.7)
7700.9
(3)
56.8
(-3)
7644

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1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 10025
1 2 3 4 5 6 range
A 2943.9
(-2.2)
P
11355
(3)
P
6578
(0.1)
P
6253.8
(-0.1)
P
4230.5
(-1.4)
P
1604.8
(-3)
P
9750
B 4806.1
(-0.7)
P
9133.6
(3)
P
6980.6
(1.2)
P
5326.6
(-0.2)
P
5604.4
(-0)
P
2088.7
(-3)
P
7045
C 5804
(0.8)
P
8434.5
(3)
P
8032.2
(2.7)
P
4142.5
(-0.6)
P
5436.1
(0.5)
P
1330.1
(-3)
P
7104
avr 4518
(-0.9)
9641
(3)
7196.9
(1.2)
5241
(-0.3)
5090.3
(-0.4)
1674.5
(-3)
7967
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 171735_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.25233
Sequence Type Exemplar sequence
Representative Public ID CEK072GXR NCBI
Target Description CEK072GXR_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=T06E4.4 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D66041 /WB_GENE_ID=T06E4.4 /WP=CE06370 /CHR=5 /FEA=Genomic Cluster /DEF=collagen; C.elegans cDNA clone yk72g10 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_073085(11)
Transcript Assignments
Representative
Transcript
Description Matching Probes Related Probesets by Grade
NM_073085 NCBI Caenorhabditis elegans T06E4.4 (collagen) mRNA, complete cds. 11/11 A 
SNAP00000007442 ENSEMBL cdna:SNAP chromosome:CEL140:V:9634906:9635910:-1 11/11 None
GENEFINDER00000007459 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:9634906:9635910:-1 11/11 None
T06E4.4 ENSEMBL cdna:known chromosome:CEL140:V:9634855:9635921:-1 gene:T06E4.4 11/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_067008 1/11 Cross Hyb Matching Probes A 
NM_067009 1/11 Cross Hyb Matching Probes A 
NM_073276 1/11 Cross Hyb Matching Probes A 
NM_073277 1/11 Cross Hyb Matching Probes A 
NM_069896 1/11 Cross Hyb Matching Probes A 
NM_071851 1/11 Cross Hyb Matching Probes A 
NM_073512 1/11 Cross Hyb Matching Probes A 
NM_070299 1/11 Cross Hyb Matching Probes A 
NM_069971 1/11 Cross Hyb Matching Probes A 
NM_073083 5/11 Cross Hyb Matching Probes A 
NM_063358 1/11 Cross Hyb Matching Probes A 
NM_073882 1/11 Cross Hyb Matching Probes A 
NM_073883 1/11 Cross Hyb Matching Probes A 
NM_067669 1/11 Cross Hyb Matching Probes A 
NM_073899 1/11 Cross Hyb Matching Probes A 
NM_073933 1/11 Cross Hyb Matching Probes A 
NM_072334 1/11 Cross Hyb Matching Probes A 
NM_067007 1/11 Cross Hyb Matching Probes A 
NM_069714 1/11 Cross Hyb Matching Probes A 
NM_069715 1/11 Cross Hyb Matching Probes A 
NM_063908 1/11 Cross Hyb Matching Probes A 
SNAP00000004358 1/11 Cross Hyb Matching Probes None
GENEFINDER00000004367 1/11 Cross Hyb Matching Probes None
SNAP00000014220 1/11 Cross Hyb Matching Probes None
GENEFINDER00000014231 1/11 Cross Hyb Matching Probes None
SNAP00000036390 1/11 Cross Hyb Matching Probes None
GENEFINDER00000036401 1/11 Cross Hyb Matching Probes None
SNAP00000036391 1/11 Cross Hyb Matching Probes None
GENEFINDER00000036400 1/11 Cross Hyb Matching Probes None
SNAP00000036392 1/11 Cross Hyb Matching Probes None
GENEFINDER00000036395 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
SNAP00000017981 1/11 Cross Hyb Matching Probes None
GENEFINDER00000017990 1/11 Cross Hyb Matching Probes None
SNAP00000023282 1/11 Cross Hyb Matching Probes None
GENEFINDER00000023293 1/11 Cross Hyb Matching Probes None
SNAP00000035582 1/11 Cross Hyb Matching Probes None
GENEFINDER00000035589 1/11 Cross Hyb Matching Probes None
SNAP00000043808 1/11 Cross Hyb Matching Probes None
GENEFINDER00000043818 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
SNAP00000007051 1/11 Cross Hyb Matching Probes None
SNAP00000007052 1/11 Cross Hyb Matching Probes None
GENEFINDER00000007058 1/11 Cross Hyb Matching Probes None
GENEFINDER00000007063 1/11 Cross Hyb Matching Probes None
SNAP00000007440 5/11 Cross Hyb Matching Probes None
GENEFINDER00000007452 5/11 Cross Hyb Matching Probes None
SNAP00000011265 1/11 Cross Hyb Matching Probes None
GENEFINDER00000011290 1/11 Cross Hyb Matching Probes None
SNAP00000011428 1/11 Cross Hyb Matching Probes None
GENEFINDER00000011431 1/11 Cross Hyb Matching Probes None
SNAP00000013927 1/11 Cross Hyb Matching Probes None
GENEFINDER00000013944 1/11 Cross Hyb Matching Probes None
SNAP00000020011 1/11 Cross Hyb Matching Probes None
GENEFINDER00000020025 1/11 Cross Hyb Matching Probes None
SNAP00000023063 1/11 Cross Hyb Matching Probes None
GENEFINDER00000023069 1/11 Cross Hyb Matching Probes None
SNAP00000035387 1/11 Cross Hyb Matching Probes None
GENEFINDER00000035400 1/11 Cross Hyb Matching Probes None
M195.1 1/11 Cross Hyb Matching Probes A 
C09G5.4 1/11 Cross Hyb Matching Probes A 
W05B2.6 1/11 Cross Hyb Matching Probes A 
W05B2.5 1/11 Cross Hyb Matching Probes A 
W05B2.1 1/11 Cross Hyb Matching Probes A 
F58F6.1 1/11 Cross Hyb Matching Probes A 
F54D1.2 1/11 Cross Hyb Matching Probes R A 
F54D1.3 1/11 Cross Hyb Matching Probes R A 
M18.1 1/11 Cross Hyb Matching Probes A 
F08G5.4 1/11 Cross Hyb Matching Probes A 
F52B11.4 1/11 Cross Hyb Matching Probes A 
F41F3.4 1/11 Cross Hyb Matching Probes A 
T15B7.5 1/11 Cross Hyb Matching Probes A 
T06E4.6 5/11 Cross Hyb Matching Probes 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 
F57B1.3 1/11 Cross Hyb Matching Probes A 
F57B1.4.1 1/11 Cross Hyb Matching Probes A 
F57B1.4.3 1/11 Cross Hyb Matching Probes None
F57B1.4.2 1/11 Cross Hyb Matching Probes A 
C50B6.4 1/11 Cross Hyb Matching Probes A 
Y2H9A.3 1/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrV:9634876-9635911(-) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-147
Ensembl T06E4.4
Entrez Gene 179351 Entrez gene
SwissProt Q22256 EMBL-EBI
WormBase CE06370 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 CAA94788 Hypothetical protein T06E4.4 [Caenorhabditis elegans] ref|NP_505486.1| T06E4.4 [Caenorhabditis elegans] 7.0E-50
blast CAA94792 Hypothetical protein T06E4.6 [Caenorhabditis elegans] ref|NP_505484.1| T06E4.6 [Caenorhabditis elegans] 2.0E-49
blast CAE72217 Hypothetical protein CBG19328 [Caenorhabditis briggsae] 4.0E-47
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.1E-25
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.7E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.4E-7
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.9E-10
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_505486.1 1 5-27
T06E4.4 1 5-27
SNAP00000007442 1 5-27
GENEFINDER00000007459 1 5-27
Sequence
Target Sequence
>C. ELEGANS:171735_X_AT
ccaggccaaccaggagctcaaggagaggctggacacgctggagaggctggaaagccagga
gccaacggagttaccatcggacttaccggaggaaatggaccatgtatcacttgcccagct
ggagccccaggaccagccggagctcctggagcaccaggaccacaaggaccatctggagcc
ccaggacaagacgctgttggaggaggaccagggccagctggaccacagggaccagccgga
gatgccggagctccaggacaagccggagcaccaggacatccaggagccccaggacaagga
ggacaacgcagccgtggaactccaggaccatctggagctccaggaccacaaggaccagcc
ggaggaccaggacagccaggacaatccggaggagccggagccccaggaccagctggagct
ccaggagcaccaggaggaccaggaaacgcgggaaccccaggaaccccaggagcaccagga
aacgctggagcaccaggaggagacgccgcatattgtccatgcccagctcgtgccagcgct
gttcgcaagcaccgcaaggtcttccgtagacgtcacgccaaggtttc


BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position
Strandedness
CCAGGCCAACCAGGAGCTCAAGGAG 500 271 293 Antisense
AGCCAACGGAGTTACCATCGGACTT 508 81 352 Antisense
GAAATGGACCATGTATCACTTGCCC 458 361 384 Antisense
GGACCACAAGGACCATCTGGAGCCC 365 523 449 Antisense
GGACCAGCCGGAGATGCCGGAGCTC 406 523 521 Antisense
GCCGTGGAACTCCAGGACCATCTGG 151 283 603 Antisense
TCTGGAGCTCCAGGACCACAAGGAC 591 607 623 Antisense
GAGGACCAGGACAGCCAGGACAATC 528 403 654 Antisense
GGACCAGCTGGAGCTCCAGGAGCAC 312 523 698 Antisense
AGGAGGAGACGCCGCATATTGTCCA 301 57 787 Antisense
TCCGTAGACGTCACGCCAAGGTTTC 10 263 855 Antisense
Sequence Source Affymetrix Proprietary Database