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[192682_at] cuticle collagen ROL-6

Description T01B7.7 /REP_DB=WormBase Gene ID /WP=CE03591 /GEN=rol-6 /TR=SW:P20784 /GB=CAA91300.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=cuticle collagen ROL-6
Cluster 6grp_highest_10_10 > 44      6grp_high1_10_10 > 43      6grp_highest_nonorm > 34      6grp_total > 10      4grp_total > 49      6grp_highest_sub > 02      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 10035
1 2 3 4 range
A 81.1
(-3)
A 		10047.5
(3)
P 		9296.9
(2.6)
P 		14.8
(-3)
A 		10033
B 32.5
(-3)
A 		9123.2
(2.6)
P 		9751.6
(3)
P 		12.9
(-3)
A 		9739
C 23.4
(-3)
A 		8601.4
(3)
P 		8330.6
(2.8)
P 		48.6
(-3)
A 		8578
avr 45.7
(-3) 		9257.4
(3) 		9126.4
(2.9) 		25.4
(-3) 		9232

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 5766
1 2 3 4 5 6 range
A 767.8
(-2.7)
P 		6197.3
(3)
P 		2890.9
(-0.5)
P 		2635.9
(-0.7)
P 		1887.2
(-1.5)
P 		484.3
(-3)
P 		5713
B 650
(-2.7)
P 		4878.1
(3)
P 		3247
(0.8)
P 		2138.9
(-0.7)
P 		2002.3
(-0.9)
P 		431.7
(-3)
P 		4446
C 918.7
(-2.3)
P 		4779.5
(3)
P 		4012.7
(1.9)
P 		2211.2
(-0.5)
P 		2523.7
(-0.1)
P 		432.4
(-3)
P 		4347
avr 778.8
(-2.6) 		5285
(3) 		3383.5
(0.6) 		2328.7
(-0.7) 		2137.7
(-0.9) 		449.5
(-3) 		4836
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2901
1 2 3 4 range
A 29.5
(-2.9)
A 		2181
(2.4)
P 		2430.4
(3)
P 		2.2
(-3)
A 		2428
B 10.3
(-3)
A 		2253.2
(3)
P 		2259.7
(3)
P 		2.7
(-3)
A 		2257
C 7.7
(-3)
A 		2473
(2.1)
P 		2903.5
(3)
P 		8.2
(-3)
A 		2896
avr 15.8
(-3) 		2302.4
(2.5) 		2531.2
(3) 		4.4
(-3) 		2527

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2086
1 2 3 4 5 6 range
A 141.5
(-2.9)
P 		2204.1
(3)
P 		629.6
(-1.5)
P 		668.5
(-1.4)
P 		569.5
(-1.7)
P 		117.9
(-3)
P 		2086
B 226.2
(-2.7)
P 		1623.7
(3)
P 		788.5
(-0.4)
P 		566.5
(-1.3)
P 		813.5
(-0.3)
P 		161
(-3)
P 		1463
C 340.5
(-2.1)
P 		1458.4
(3)
P 		1021.3
(1)
P 		444.7
(-1.6)
P 		816.6
(0.1)
P 		144.8
(-3)
P 		1314
avr 236.1
(-2.6) 		1762.1
(3) 		813.1
(-0.5) 		559.9
(-1.5) 		733.2
(-0.8) 		141.2
(-3) 		1621
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192682_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3691
Sequence Type Exemplar sequence
Representative Public ID T01B7.7 NCBI
Target Description T01B7.7 /REP_DB=WormBase Gene ID /WP=CE03591 /GEN=rol-6 /TR=SW:P20784 /GB=CAA91300.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=cuticle collagen ROL-6
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_063457(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063457 NCBI Caenorhabditis elegans ROLler: helically twisted, animals roll when moving family member (rol-6) (rol-6) mRNA, complete cds. 11/11 None
SNAP00000025609 ENSEMBL cdna:SNAP chromosome:CEL140:II:8732973:8734120:1 11/11 None
GENEFINDER00000025627 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:8732973:8734120:1 11/11 None
T01B7.7 ENSEMBL cdna:known chromosome:CEL140:II:8732973:8734237:1 gene:T01B7.7 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
chrII:8732969-8734117(+) 100.0 100.0
Public Domain and Genome References
Gene Title cuticle collagen ROL-6
Gene Symbol rol-6
Ensembl T01B7.7
Entrez Gene 174397 Entrez gene
SwissProt P20784 EMBL-EBI
WormBase CE03591 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
5578 extracellular matrix (sensu Metazoa) inferred from sequence similarity QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
42302 structural constituent of cuticle inferred from electronic annotation QuickGO AmiGO
42329 structural constituent of cuticle (sensu Nematoda) inferred from sequence similarity QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA91300 Hypothetical protein T01B7.7 [Caenorhabditis elegans] ref|NP_495858.1| ROLler: helically twisted, animals roll when moving family member (rol-6) [Caenorhabditis elegans] sp|P20784|ROL6_CAEEL Cuticle collagen rol-6 gb|AAA28143.1| collagen (rol-6) 7.0E-79
blast CAE59721 Hypothetical protein CBG03154 [Caenorhabditis briggsae] 3.0E-78
blast CAB01588 Hypothetical protein ZK836.1 [Caenorhabditis elegans] ref|NP_506061.1| ZK836.1 [Caenorhabditis elegans] gb|AAL08218.1| cuticle collagen protein LON-3 [Caenorhabditis elegans] gb|AAL76993.1| cuticle collagen LON-3 [Caenorhabditis elegans] sp|Q23628|LON3_CAEEL Cuticle collagen lon-3 precursor 2.0E-40
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 7.4E-19
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 9.7E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.7E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.6E-7
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_495858.1 1 7-29
T01B7.7 1 7-29
SNAP00000025609 1 7-29
GENEFINDER00000025627 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:192682_AT
gcactgttgagaactcatgcccaccaggaccagctggaccagaaggagaggaaggaccag
atgggcacgatggacaagacggagtcccaggatttgacggaaaagatgccgaagatgttc
aaaacaccccaccaacaggatgcttcacctgtccacaaggaccacttggaccacaaggac
caaatggagctccaggactcagaggaatgcgcggagctcgtggacaaccaggacgtccag
gaagagacggaaacccaggaatgccaggagactgtggaccaccaggggccccaggatccg
atggaaagccaggatctccaggaggaaagggagacgatggagagagaccattgggccgcc
caggaccaagaggaccaccaggagaggctgggccagaaggaccacagggaccaactggaa
gagatgcttatccaggacagtctggaccacaaggagagccaggccttcaaggatat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCACTGTTGAGAACTCATGCCCACC 609 311 440 Antisense
GAAGGACCAGATGGGCACGATGGAC 694 333 490 Antisense
GACGGAGTCCCAGGATTTGACGGAA 518 375 517 Antisense
CGAAGATGTTCAAAACACCCCACCA 353 253 549 Antisense
CAACAGGATGCTTCACCTGTCCACA 9 189 572 Antisense
TGGAGCTCCAGGACTCAGAGGAATG 217 549 624 Antisense
CAGAGGAATGCGCGGAGCTCGTGGA 651 205 639 Antisense
ATGGAGAGAGACCATTGGGCCGCCC 40 51 776 Antisense
CCATTGGGCCGCCCAGGACCAAGAG 505 269 787 Antisense
GCTGGGCCAGAAGGACCACAGGGAC 431 293 826 Antisense
AGGAGAGCCAGGCCTTCAAGGATAT 436 53 891 Antisense
Sequence Source Affymetrix Proprietary Database