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[190588_s_at] nidogen like

Description F54F3.1 /REP_DB=WormBase Gene ID /WP=CE18731 /GEN=nid-1 /TR=Q93791 /GB=CAB01972.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=nidogen like
Cluster 6grp_highest_10_10 > 15      6grp_high1_10_10 > 40      4grp_highest_8_8 > 17      4grp_high_8_8 > 60      6grp_highest_nonorm > 42      6grp_total > 52      4grp_total > 59      6grp_highest_sub > 03      6grp_cgc > 82      6grp_high1_sub > 03      6grp_cgc_sub > 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 1352
1 2 3 4 range
A 917.2
(0.5)
P 		803.4
(0)
P 		1474.2
(3)
P 		121.8
(-3)
P 		1352
B 934.6
(0.9)
P 		1127
(1.9)
P 		1353.2
(3)
P 		152.9
(-3)
P 		1200
C 850.5
(0.7)
P 		913.6
(1)
P 		1303.5
(3)
P 		123.6
(-3)
P 		1180
avr 900.8
(0.7) 		948
(0.9) 		1377
(3) 		132.8
(-3) 		1244

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 619
1 2 3 4 5 6 range
A 913.6
(-0.1)
P 		804.9
(-1.2)
P 		1216.4
(3)
P 		874
(-0.5)
P 		691.5
(-2.3)
P 		622.9
(-3)
P 		594
B 927.6
(0.3)
P 		992.5
(1)
P 		1185.3
(3)
P 		882.9
(-0.2)
P 		669.4
(-2.4)
P 		612.4
(-3)
P 		573
C 745
(-1.5)
P 		1001.1
(1.2)
P 		1171.3
(3)
P 		1131.3
(2.6)
P 		597
(-3)
P 		688.5
(-2)
P 		574
avr 862.1
(-0.6) 		932.8
(0.2) 		1191
(3) 		962.7
(0.5) 		652.6
(-2.9) 		641.3
(-3) 		550
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 437
1 2 3 4 range
A 333.9
(2.2)
P 		174.4
(-0.4)
P 		385.4
(3)
P 		17.8
(-3)
P 		368
B 298
(2.7)
P 		278.3
(2.2)
P 		313.6
(3)
P 		32.6
(-3)
P 		281
C 281.5
(0.6)
P 		262.7
(0.3)
P 		454.3
(3)
P 		20.8
(-3)
P 		434
avr 304.5
(1.7) 		238.5
(0.6) 		384.4
(3) 		23.7
(-3) 		361

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 179
1 2 3 4 5 6 range
A 168.4
(-2.3)
P 		286.3
(3)
P 		264.9
(2)
P 		221.7
(0.1)
P 		208.7
(-0.5)
P 		151.6
(-3)
P 		135
B 322.8
(2.6)
P 		330.4
(3)
P 		287.8
(0.5)
P 		233.8
(-2.7)
P 		272
(-0.4)
P 		228.4
(-3)
P 		102
C 276.1
(1.4)
P 		305.5
(3)
P 		298.1
(2.6)
P 		227.5
(-1.2)
P 		193.2
(-3)
P 		230.5
(-1)
P 		112
avr 255.8
(0) 		307.4
(3) 		283.6
(1.6) 		227.7
(-1.6) 		224.6
(-1.8) 		203.5
(-3) 		104
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 190588_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.14041
Sequence Type Exemplar sequence
Representative Public ID F54F3.1 NCBI
Target Description F54F3.1 /REP_DB=WormBase Gene ID /WP=CE18731 /GEN=nid-1 /TR=Q93791 /GB=CAB01972.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=nidogen like
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_073827(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073827 NCBI Caenorhabditis elegans NIDogen (basement membrane protein family member (nid-1) (nid-1) mRNA, complete cds. 11/11 None
SNAP00000002933 ENSEMBL cdna:SNAP chromosome:CEL140:V:12912708:12919551:1 11/11 None
GENEFINDER00000002939 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:12912708:12919551:1 11/11 None
F54F3.1 ENSEMBL cdna:known chromosome:CEL140:V:12912703:12919780:1 gene:F54F3.1 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
chrV:12912707-12919551(+) 100.0 100.0
Public Domain and Genome References
Gene Title nidogen like
Gene Symbol nid-1
Ensembl F54F3.1
Entrez Gene 179770 Entrez gene
SwissProt Q93791 EMBL-EBI
WormBase CE18731 Wormbase
Functional Annotations
Ortholog
ID Title Organism
DROSOPHILA_2:1632082_AT Nidogen/entactin dm
DROSGENOME1:154737_AT Nidogen/entactin dm
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
7160 cell-matrix adhesion inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
16020 membrane inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
5509 calcium ion binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB01972 Hypothetical protein F54F3.1 [Caenorhabditis elegans] ref|NP_506228.1| NIDogen (basement membrane protein family member (nid-1) [Caenorhabditis elegans] 0.0
blast CAE64719 Hypothetical protein CBG09505 [Caenorhabditis briggsae] 0.0
blast AAF58809 CG12908-PA, isoform A [Drosophila melanogaster] ref|NP_610575.1| CG12908-PA, isoform A [Drosophila melanogaster] 1.0E-130
Protein Domains
Database ID Description E-Value
Pfam IPR006209 EMBL-EBI EGF-like domain 1.8E-9
Pfam IPR006209 EMBL-EBI EGF-like domain 1.5E-4
Pfam IPR006209 EMBL-EBI EGF-like domain 4.2E-4
Pfam IPR006209 EMBL-EBI EGF-like domain 1.2E-5
Pfam IPR006209 EMBL-EBI EGF-like domain 2.0E-4
Pfam IPR000033 EMBL-EBI Low-density lipoprotein receptor, YWTD repeat 1.0E-9
Pfam IPR000033 EMBL-EBI Low-density lipoprotein receptor, YWTD repeat 1.2E-6
Pfam IPR000033 EMBL-EBI Low-density lipoprotein receptor, YWTD repeat 5.2E-7
Pfam IPR000033 EMBL-EBI Low-density lipoprotein receptor, YWTD repeat 6.1E-5
Pfam IPR010362 EMBL-EBI Nid 2.2E-35
Pfam IPR000033 EMBL-EBI Low-density lipoprotein receptor, YWTD repeat 1.0E-9
Pfam IPR000033 EMBL-EBI Low-density lipoprotein receptor, YWTD repeat 1.2E-6
Pfam IPR000033 EMBL-EBI Low-density lipoprotein receptor, YWTD repeat 5.2E-7
Pfam IPR000033 EMBL-EBI Low-density lipoprotein receptor, YWTD repeat 6.1E-5
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_506228.1 1 7-29
F54F3.1 1 7-29
SNAP00000002933 1 7-29
GENEFINDER00000002939 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:190588_S_AT
ctgaaggtcttgtcaatccacgttcagtggttttggatctatacggacgacacttgtact
actcggattggcatcgtgagaatccatacatcggaagagttgacatggatggaaagaaca
atcgagtattcttaaatgaagatgtccatcttccaaatggtctcactattcttccaaaca
gacgcgaactctgttgggtggacgctggaaatcacagactttcatgtattcagtacaatg
gagctggtagaagaactgtgttcagtagtcttcagtatccgtttggtttgactcatgatg
aagaacaaaaattctattggactgattggaaagacaaccgcattcattcagttggtgtct
atggagaaggataccgtagcttccaaatttcccttggtggatcaggaaaagtatttggaa
tccttgccgttccaaaatcatgcgtcggtccatcaactccatgttctgaagacaacggtg
gctgccaacatctttgccttccaggacagaat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CTGAAGGTCTTGTCAATCCACGTTC 658 235 4208 Antisense
ACGGACGACACTTGTACTACTCGGA 156 97 4250 Antisense
GGCATCGTGAGAATCCATACATCGG 306 537 4277 Antisense
AACTCTGTTGGGTGGACGCTGGAAA 534 139 4394 Antisense
GTAGTCTTCAGTATCCGTTTGGTTT 407 455 4472 Antisense
CCGCATTCATTCAGTTGGTGTCTAT 122 263 4545 Antisense
GCTTCCAAATTTCCCTTGGTGGATC 429 217 4586 Antisense
AATCCTTGCCGTTCCAAAATCATGC 183 167 4626 Antisense
GTCCATCAACTCCATGTTCTGAAGA 414 477 4655 Antisense
AACGGTGGCTGCCAACATCTTTGCC 501 143 4681 Antisense
ACATCTTTGCCTTCCAGGACAGAAT 100 107 4695 Antisense
Sequence Source Affymetrix Proprietary Database