[Home] | [Total List]

[188463_at] collagen

Description F22D6.10 /REP_DB=WormBase Gene ID /WP=CE05691 /TR=Q19725 /GB=CAA95812.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 98      4grp_total > 19      6grp_cgc > 79      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S5      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 102
1 2 3 4 range
A 73.3
(0.8)
A 		58.1
(-0.1)
A 		10.7
(-3)
A 		109.8
(3)
A 		99
B 15.2
(-2.1)
A 		11.4
(-2.6)
A 		57.4
(3)
A 		8.2
(-3)
A 		49
C 16.1
(-2.8)
A 		53.9
(-0.2)
A 		13.2
(-3)
A 		101.6
(3)
A 		88
avr 34.9
(-2) 		41.1
(-1.2) 		27.1
(-3) 		73.2
(3) 		46

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1678
1 2 3 4 5 6 range
A 14.5
(-3)
A 		35.9
(-2.9)
A 		69.6
(-2.8)
A 		340.3
(-1.6)
P 		1395
(3)
P 		1404.6
(3)
P 		1390
B 33.8
(-2.9)
A 		20.2
(-3)
A 		7
(-3)
A 		334
(-1.8)
P 		1655.2
(2.9)
P 		1684.6
(3)
P 		1678
C 23
(-3)
A 		76.8
(-2.8)
A 		63.3
(-2.8)
A 		400.9
(-1.6)
P 		1595.9
(3)
P 		1357.3
(2.1)
P 		1573
avr 23.8
(-3) 		44.3
(-2.9) 		46.6
(-2.9) 		358.4
(-1.7) 		1548.7
(3) 		1482.2
(2.7) 		1525
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 25
1 2 3 4 range
A 26.7
(3)
A 		12.6
(-0.5)
A 		2.8
(-3)
A 		16.1
(0.3)
A 		24
B 4.9
(-1.4)
A 		2.8
(-2.5)
A 		13.3
(3)
A 		1.8
(-3)
A 		12
C 5.3
(-2.7)
A 		15.5
(2.2)
A 		4.6
(-3)
A 		17.1
(3)
A 		13
avr 12.3
(3) 		10.3
(0.8) 		6.9
(-3) 		11.7
(2.3) 		5

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 671
1 2 3 4 5 6 range
A 2.7
(-3)
A 		12.8
(-2.9)
A 		15.1
(-2.8)
A 		86.3
(-1.8)
P 		420.9
(3)
P 		342
(1.9)
P 		418
B 11.7
(-2.9)
A 		6.7
(-3)
A 		1.7
(-3)
A 		88.5
(-2.2)
P 		672.5
(3)
P 		628.2
(2.6)
P 		671
C 8.5
(-3)
A 		23.4
(-2.8)
A 		16.1
(-2.9)
A 		80.6
(-2.1)
P 		516.4
(3)
P 		454.4
(2.3)
P 		508
avr 7.6
(-3) 		14.3
(-2.9) 		11
(-3) 		85.1
(-2.1) 		536.6
(3) 		474.9
(2.3) 		529
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188463_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.2375
Sequence Type Exemplar sequence
Representative Public ID F22D6.10 NCBI
Target Description F22D6.10 /REP_DB=WormBase Gene ID /WP=CE05691 /TR=Q19725 /GB=CAA95812.1 /SUBMIT=HINXTON /CHR=1 /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_059612(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059612 NCBI Caenorhabditis elegans F22D6.10 (collagen) mRNA, complete cds. 11/11 None
SNAP00000037655 ENSEMBL cdna:SNAP chromosome:CEL140:I:7113451:7114857:1 11/11 None
GENEFINDER00000037666 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:7113451:7114857:1 11/11 None
F22D6.10 ENSEMBL cdna:known chromosome:CEL140:I:7113451:7114857:1 gene:F22D6.10 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:7113381-7114788(+) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-60
Ensembl F22D6.10
Entrez Gene 172445 Entrez gene
SwissProt Q19725 EMBL-EBI
WormBase CE05691 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 CAA95812 Hypothetical protein F22D6.10 [Caenorhabditis elegans] ref|NP_492013.1| F22D6.10 [Caenorhabditis elegans] 1.0E-120
blast CAE73091 Hypothetical protein CBG20470 [Caenorhabditis briggsae] 2.0E-95
blast AAC71147 Collagen protein 88 [Caenorhabditis elegans] ref|NP_497131.1| COLlagen family member (col-88) [Caenorhabditis elegans] 2.0E-33
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.7E-21
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0017
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.5E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.5E-11
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_492013.1 1 7-29
F22D6.10 1 7-29
SNAP00000037655 1 7-29
GENEFINDER00000037666 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:188463_AT
gacaagccgggcaggatggacaagatggtaatactccatcggaagagtatggaaattctc
aggatggatcaacatctacgtgtccagcaggtcccccaggtgaacagggacctgatggtg
caccaggtgaagctggaagagatggacaaccaggtagtgacggacaatctggaaatgaag
gaccaactggaccacgtggatcaccaggaaacaaaggaagagatgggaatcctggaagag
acggaagtcctggaagaccaggaagggatggaactcgtggtgttggacagccaggttctc
cagggcaaccaggatcccgaggaccagaagggccaagaggccaaccaggaaatatgggaa
gacccggagaatatggagacgctggaccagctggacaacctggaaatgatggggaacagg
gaccggatggagtggtcggaatccctggtgagccaggtcttcctggatcagatgcttcgt
attgtcaatgtccagatcgtaccccaactgtggaaaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GACAAGCCGGGCAGGATGGACAAGA 633 363 350 Antisense
GGATCAACATCTACGTGTCCAGCAG 570 511 415 Antisense
GCAGGTCCCCCAGGTGAACAGGGAC 134 255 436 Antisense
GACAACCAGGTAGTGACGGACAATC 498 363 494 Antisense
TGGTGTTGGACAGCCAGGTTCTCCA 652 551 627 Antisense
TCCAGGGCAACCAGGATCCCGAGGA 456 587 648 Antisense
GACCCGGAGAATATGGAGACGCTGG 345 381 710 Antisense
TGGTCGGAATCCCTGGTGAGCCAGG 80 551 782 Antisense
GGTCTTCCTGGATCAGATGCTTCGT 562 503 805 Antisense
TATTGTCAATGTCCAGATCGTACCC 710 661 829 Antisense
CAGATCGTACCCCAACTGTGGAAAA 252 207 842 Antisense
Sequence Source Affymetrix Proprietary Database