[Home] | [Total List]

[173767_s_at] collagen /// collagen

Description CEK058GZF /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=C15A11.6 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D68997 /WB_GENE_ID=C15A11.6 /WP=CE08174 /CHR=1 /FEA=Genomic Cluster /GEN=col-7 /DEF=collagen; C.elegans cDNA clone yk58g12 : 5prime end, single read.
Cluster 4grp_high_8_8 > 54      6grp_total > 94      4grp_total > 57      6grp_cgc > 89      6grp_total_sub > Hat      6grp_rule_based > S5      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 222
1 2 3 4 range
A 114.8
(-2.5)
A 		142.5
(-1.6)
P 		282.7
(3)
P 		99.5
(-3)
A 		183
B 73.3
(-2.6)
A 		273.6
(3)
P 		261
(2.6)
P 		60.5
(-3)
P 		213
C 92.2
(-3)
P 		274.2
(3)
P 		204.2
(0.7)
P 		109.7
(-2.4)
M 		182
avr 93.4
(-2.9) 		230.1
(2.3) 		249.3
(3) 		89.9
(-3) 		159

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3213
1 2 3 4 5 6 range
A 79
(-3)
A 		315
(-2.5)
P 		81.7
(-3)
P 		503.9
(-2.1)
P 		2884.5
(3)
P 		1861.9
(0.8)
P 		2806
B 83.6
(-3)
A 		255.4
(-2.6)
P 		59.3
(-3)
P 		458.1
(-2.3)
P 		3266.5
(3)
P 		1717.9
(0.1)
P 		3207
C 83.6
(-3)
A 		354.5
(-2.5)
P 		193.4
(-2.8)
P 		561.9
(-2.1)
P 		3272.5
(3)
P 		1511.4
(-0.3)
P 		3189
avr 82.1
(-3) 		308.3
(-2.6) 		111.5
(-2.9) 		508
(-2.2) 		3141.2
(3) 		1697.1
(0.2) 		3059
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 66
1 2 3 4 range
A 41.8
(-0.2)
A 		30.9
(-1.4)
P 		73.9
(3)
P 		14.6
(-3)
A 		59
B 23.4
(-1.8)
A 		67.6
(3)
P 		60.5
(2.2)
P 		12.9
(-3)
P 		55
C 30.5
(-1.8)
P 		78.8
(3)
P 		71.2
(2.2)
P 		18.5
(-3)
M 		60
avr 31.9
(-1.1) 		59.1
(1.9) 		68.5
(3) 		15.3
(-3) 		53

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1313
1 2 3 4 5 6 range
A 14.6
(-3)
A 		112
(-2.3)
P 		17.8
(-3)
P 		127.8
(-2.2)
P 		870.4
(3)
P 		453.3
(0.1)
P 		856
B 29.1
(-2.9)
A 		85
(-2.7)
P 		14.4
(-3)
P 		121.3
(-2.5)
P 		1327.1
(3)
P 		640.6
(-0.1)
P 		1313
C 31
(-3)
A 		108.2
(-2.5)
P 		49.2
(-2.9)
P 		113
(-2.5)
P 		1058.9
(3)
P 		506
(-0.2)
P 		1028
avr 24.9
(-3) 		101.7
(-2.6) 		27.1
(-3) 		120.7
(-2.5) 		1085.5
(3) 		533.3
(-0.1) 		1061
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173767_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.22644
Sequence Type Exemplar sequence
Representative Public ID CEK058GZF NCBI
Target Description CEK058GZF /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=C15A11.6 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D68997 /WB_GENE_ID=C15A11.6 /WP=CE08174 /CHR=1 /FEA=Genomic Cluster /GEN=col-7 /DEF=collagen; C.elegans cDNA clone yk58g12 : 5prime 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_059689(11), NM_059690(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059689 NCBI Caenorhabditis elegans C15A11.5 (collagen) mRNA, complete cds. 11/11 None
NM_059690 NCBI Caenorhabditis elegans C15A11.6 (collagen) mRNA, complete cds. 11/11 None
SNAP00000007970 ENSEMBL cdna:SNAP chromosome:CEL140:I:7409826:7410837:1 11/11 None
GENEFINDER00000007974 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:7409826:7410837:1 11/11 None
SNAP00000007971 ENSEMBL cdna:SNAP chromosome:CEL140:I:7411470:7412481:-1 11/11 None
GENEFINDER00000007980 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:7411470:7412481:-1 11/11 None
C15A11.5 ENSEMBL cdna:known chromosome:CEL140:I:7409826:7410837:1 gene:C15A11.5 11/11 None
C15A11.6 ENSEMBL cdna:known chromosome:CEL140:I:7411470:7412481:-1 gene:C15A11.6 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
chrI:7409755-7410789(+) 99.69 99.69
chrI:7411379-7412413(-) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
collagen
Gene Symbol col-7
col-62
Ensembl C15A11.5
C15A11.6
Entrez Gene 172494 Entrez gene
172495 Entrez gene
SwissProt P18832 EMBL-EBI
Q93207 EMBL-EBI
WormBase CE08173 Wormbase
CE08174 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 CAB01961 Hypothetical protein C15A11.5 [Caenorhabditis elegans] ref|NP_492090.1| C15A11.5 [Caenorhabditis elegans] sp|P18832|COL7_CAEEL Cuticle collagen 7 precursor 2.0E-54
blast CAB01958 Hypothetical protein C15A11.6 [Caenorhabditis elegans] ref|NP_492091.1| C15A11.6 [Caenorhabditis elegans] 2.0E-54
blast CAB01958 Hypothetical protein C15A11.6 [Caenorhabditis elegans] ref|NP_492091.1| C15A11.6 [Caenorhabditis elegans] 1.0E-53
blast CAB01961 Hypothetical protein C15A11.5 [Caenorhabditis elegans] ref|NP_492090.1| C15A11.5 [Caenorhabditis elegans] sp|P18832|COL7_CAEEL Cuticle collagen 7 precursor 1.0E-53
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.3E-25
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.3E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.8E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.2E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 9.3E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.5E-9
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_492090.1 1 7-29
NP_492091.1 1 7-29
C15A11.5 1 7-29
C15A11.6 1 7-29
SNAP00000007970 1 7-29
GENEFINDER00000007974 1 7-29
SNAP00000007971 1 7-29
GENEFINDER00000007980 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:173767_S_AT
caggacagcctggtgttgctgggccatctcatcatcagaaacaagaatgcatcaaatgtc
cacaaggacttccaggaccagctggagctccaggacaacctggaccaaagggaccaaatg
gaaatccaggagccccagcacaaggtggaggtcagggaccaccaggacctccagggccag
ctggaagtgctggatcaccaggacaggccggagctccaggaaatcctggtagcccaggaa
aatctggacaacgtggacgcggtcttccaggaccatcgggtgcaccaggatcacaaggac
caccaggagccccaggtcaaccaggaagcgggaatgctccaggaccagctggaccaccag
ggccagcaggaccaaatggacaaccaggacatccaggacaagatggacagccaggagcac
caggaaatgatggaacaccaggatccgatgctgcttattgtccttgcccaactcgtagtt
ctgttcttcgtcatcgtaatgtcaaccgtcatcgtgcagctgcttcaaagaagcgtgttg
ttgccaagaagcgtgttgcaaagaagcgtgtggttgcagctagacgtcatgt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CAGGACAGCCTGGTGTTGCTGGGCC 206 209 363 Antisense
CTGGGCCATCTCATCATCAGAAACA 43 241 381 Antisense
GGAGCCCCAGCACAAGGTGGAGGTC 301 521 491 Antisense
TCTGGACAACGTGGACGCGGTCTTC 708 607 605 Antisense
AGGAAGCGGGAATGCTCCAGGACCA 355 55 685 Antisense
CACCAGGGCCAGCAGGACCAAATGG 20 201 717 Antisense
ATGATGGAACACCAGGATCCGATGC 659 45 789 Antisense
TAGTTCTGTTCTTCGTCATCGTAAT 514 653 838 Antisense
TAATGTCAACCGTCATCGTGCAGCT 218 637 859 Antisense
CATCGTGCAGCTGCTTCAAAGAAGC 445 211 872 Antisense
GTGTGGTTGCAGCTAGACGTCATGT 697 487 930 Antisense
Sequence Source Affymetrix Proprietary Database