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[172710_x_at] collagen

Description T06E4.6 /REP_DB=WormBase Gene ID /WP=CE06372 /TR=Q22260 /GB=CAA94792.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_highest_10_10 > 34      6grp_high1_10_10 > 42      4grp_high_8_8 > 61      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 > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 25440
1 2 3 4 range
A 12100.1
(-0.3)
P 		23799.4
(2.5)
P 		26014
(3)
P 		619.2
(-3)
P 		25395
B 12520
(-0.2)
P 		21581
(1.9)
P 		26059
(3)
P 		621.5
(-3)
P 		25438
C 11531.7
(-0)
P 		22420.2
(3)
P 		21236.2
(2.7)
P 		651.1
(-3)
M 		21769
avr 12050.6
(-0.1) 		22600.2
(2.5) 		24436.4
(3) 		630.6
(-3) 		23806

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 19897
1 2 3 4 5 6 range
A 14664.4
(-1)
P 		23630.4
(2.5)
P 		25031.2
(3)
P 		21741
(1.7)
P 		15522.5
(-0.7)
P 		9408.3
(-3)
P 		15623
B 14071.1
(-1)
P 		22357.4
(2)
P 		25010
(3)
P 		19340.5
(0.9)
P 		15042.1
(-0.7)
P 		8640.9
(-3)
P 		16369
C 15275.7
(-0.4)
P 		22444.8
(1.7)
P 		26646.1
(3)
P 		19773.1
(0.9)
P 		17610.3
(0.3)
P 		6748.8
(-3)
P 		19897
avr 14670.4
(-0.8) 		22810.9
(2) 		25562.4
(3) 		20284.9
(1.2) 		16058.3
(-0.3) 		8266
(-3) 		17296
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 7311
1 2 3 4 range
A 4405.7
(0.9)
P 		5166.2
(1.5)
P 		6800.6
(3)
P 		90.6
(-3)
P 		6710
B 3992.5
(0.9)
P 		5330
(2.3)
P 		6038.5
(3)
P 		132.4
(-3)
P 		5906
C 3817.3
(0.1)
P 		6445.9
(2.2)
P 		7401.5
(3)
P 		109.8
(-3)
M 		7292
avr 4071.8
(0.6) 		5647.4
(2) 		6746.9
(3) 		110.9
(-3) 		6636

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 6145
1 2 3 4 5 6 range
A 2703.3
(-2.6)
P 		8404.1
(3)
P 		5451.3
(0.1)
P 		5514
(0.2)
P 		4684
(-0.7)
P 		2290.6
(-3)
P 		6114
B 4896.1
(-0.6)
P 		7441.8
(3)
P 		6073.2
(1.1)
P 		5122.6
(-0.3)
P 		6111.4
(1.1)
P 		3222.1
(-3)
P 		4220
C 5662
(1.4)
P 		6848.6
(3)
P 		6781.9
(2.9)
P 		3976.4
(-0.8)
P 		5698.4
(1.5)
P 		2259.2
(-3)
P 		4589
avr 4420.5
(-0.8) 		7564.8
(3) 		6102.1
(1.2) 		4871
(-0.2) 		5497.9
(0.5) 		2590.6
(-3) 		4974
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172710_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11513
Sequence Type Exemplar sequence
Representative Public ID T06E4.6 NCBI
Target Description T06E4.6 /REP_DB=WormBase Gene ID /WP=CE06372 /TR=Q22260 /GB=CAA94792.1 /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_073083(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073083 NCBI Caenorhabditis elegans T06E4.6 (collagen) mRNA, complete cds. 11/11 None
SNAP00000007440 ENSEMBL cdna:SNAP chromosome:CEL140:V:9632514:9633544:1 11/11 None
GENEFINDER00000007452 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:9632541:9633544:1 11/11 None
T06E4.6 ENSEMBL cdna:known chromosome:CEL140:V:9632537:9633556:1 gene:T06E4.6 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_073276 1/11 Cross Hyb Matching Probes A 
NM_073277 1/11 Cross Hyb Matching Probes A 
NM_067556 1/11 Cross Hyb Matching Probes A 
NM_069466 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_069160 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_063358 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_073085 5/11 Cross Hyb Matching Probes A 
NM_073933 1/11 Cross Hyb Matching Probes A 
NM_069714 1/11 Cross Hyb Matching Probes A 
NM_066328 1/11 Cross Hyb Matching Probes None
NM_069715 1/11 Cross Hyb Matching Probes A 
NM_063908 1/11 Cross Hyb Matching Probes A 
NM_068206 1/11 Cross Hyb Matching Probes A 
NM_063181 1/11 Cross Hyb Matching Probes None
NM_182112 1/11 Cross Hyb Matching Probes B 
NM_062478 1/11 Cross Hyb Matching Probes None
SNAP00000004358 1/11 Cross Hyb Matching Probes None
GENEFINDER00000004367 1/11 Cross Hyb Matching Probes None
SNAP00000005485 1/11 Cross Hyb Matching Probes None
GENEFINDER00000005498 1/11 Cross Hyb Matching Probes None
SNAP00000014220 1/11 Cross Hyb Matching Probes None
GENEFINDER00000014231 1/11 Cross Hyb Matching Probes None
SNAP00000020588 1/11 Cross Hyb Matching Probes None
GENEFINDER00000020591 1/11 Cross Hyb Matching Probes None
SNAP00000003708 1/11 Cross Hyb Matching Probes None
GENEFINDER00000003712 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
SNAP00000034766 1/11 Cross Hyb Matching Probes None
GENEFINDER00000034774 1/11 Cross Hyb Matching Probes None
SNAP00000035582 1/11 Cross Hyb Matching Probes None
GENEFINDER00000035589 1/11 Cross Hyb Matching Probes None
SNAP00000042867 1/11 Cross Hyb Matching Probes None
GENEFINDER00000042874 1/11 Cross Hyb Matching Probes None
SNAP00000043526 1/11 Cross Hyb Matching Probes None
GENEFINDER00000043530 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
SNAP00000007442 5/11 Cross Hyb Matching Probes None
GENEFINDER00000007459 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
F11G11.11.2 1/11 Cross Hyb Matching Probes A 
F11G11.11.1 1/11 Cross Hyb Matching Probes A 
ZK1290.3a 1/11 Cross Hyb Matching Probes A B 
ZK1290.3b 1/11 Cross Hyb Matching Probes B 
M195.1 1/11 Cross Hyb Matching Probes A 
C09G5.4 1/11 Cross Hyb Matching Probes A 
C29E4.1 1/11 Cross Hyb Matching Probes None
C18H7.3 1/11 Cross Hyb Matching Probes A 
F58F6.1 1/11 Cross Hyb Matching Probes A 
F29B9.9 1/11 Cross Hyb Matching Probes A 
C53B4.5 1/11 Cross Hyb Matching Probes A 
C24F3.6 1/11 Cross Hyb Matching Probes None
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 
T06E4.4 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 
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:9632540-9633544(+) 96.56 100.0
chrV:9634942-9635903(-) 90.26 90.26
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-146
Ensembl T06E4.6
Entrez Gene 188178 Entrez gene
SwissProt Q22260 EMBL-EBI
WormBase CE06372 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 CAA94792 Hypothetical protein T06E4.6 [Caenorhabditis elegans] ref|NP_505484.1| T06E4.6 [Caenorhabditis elegans] 7.0E-50
blast CAA94788 Hypothetical protein T06E4.4 [Caenorhabditis elegans] ref|NP_505486.1| T06E4.4 [Caenorhabditis elegans] 2.0E-49
blast CAE72217 Hypothetical protein CBG19328 [Caenorhabditis briggsae] 1.0E-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 0.0010
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0014
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.7E-10
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 0.0010
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0014
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.7E-10
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_505484.1 1 5-27
T06E4.6 1 5-27
SNAP00000007440 1 13-35
GENEFINDER00000007452 1 5-27
Sequence
Target Sequence 
>C. ELEGANS:172710_X_AT
accaccaggacaaccaggagctcaaggagaggctggacacgctggagaggctggaaagcc
aggagccaacggagttaccatcggacttaccggaggaaatggaccatgtatcacttgccc
agctggagccccaggaccagccggagctcctggagcaccaggaccacaaggaccatctgg
agccccaggacaagacgctgttggagaaggaccaggaccagctggaccacaaggaccagc
cggagatgccggagctccaggacaagccggagcaccaggacatccaggagccccaggaca
aggaggacaacgcagccgtggaactccaggaccagctggagctccaggaccacaaggacc
agccggaggaccaggacaaccaggacaatccggaggagccggagcaccgggaccagctgg
agctccaggagcaccaggaggaccaggacagccgggacaagatggacagccaggagcccc
aggaaacgacggagctccaggaggagacgccgcttattgtccatgcccagctcgctctca
agttgtcaagcacc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ACCACCAGGACAACCAGGAGCTCAA 483 85 288 Antisense
AGCCAACGGAGTTACCATCGGACTT 509 81 351 Antisense
GAAATGGACCATGTATCACTTGCCC 459 361 383 Antisense
GGACCACAAGGACCATCTGGAGCCC 366 523 448 Antisense
GAAGGACCAGGACCAGCTGGACCAC 640 333 493 Antisense
GACCACAAGGACCAGCCGGAGATGC 91 385 512 Antisense
GCCGGAGGACCAGGACAACCAGGAC 573 283 649 Antisense
GGACCAGCTGGAGCTCCAGGAGCAC 313 523 697 Antisense
AGGACCAGGACAGCCGGGACAAGAT 349 55 726 Antisense
TCCAGGAGGAGACGCCGCTTATTGT 417 587 783 Antisense
GCTCGCTCTCAAGTTGTCAAGCACC 520 299 817 Antisense
Sequence Source Affymetrix Proprietary Database