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[192630_at] Type I thrombospondin (TSP) repeats

Description F09F9.4 /REP_DB=WormBase Gene ID /WP=CE04349 /TR=Q19284 /GB=AAA81764.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=Type I thrombospondin (TSP) repeats
Cluster 6grp_highest_10_10 > 85      6grp_high1_10_10 > 58      4grp_high_8_8 > 27      6grp_highest_nonorm > 90      6grp_total > 57      4grp_total > 29      6grp_highest_sub > Cu      6grp_high1_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 88
1 2 3 4 range
A 166.8
(3)
P 		160.5
(1.9)
P 		133.4
(-3)
A 		134.9
(-2.7)
P 		33
B 127.9
(-2.6)
P 		166.3
(0.4)
P 		122.1
(-3)
P 		201
(3)
P 		79
C 198.5
(3)
P 		168.7
(0.9)
P 		113
(-3)
P 		155.7
(-0)
P 		86
avr 164.4
(2.9) 		165.2
(3) 		122.8
(-3) 		163.9
(2.8) 		42

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 228
1 2 3 4 5 6 range
A 205.4
(0.8)
P 		164.7
(-0.6)
P 		125.4
(-2)
P 		97
(-3)
P 		119
(-2.2)
P 		269.4
(3)
P 		172
B 217
(0.6)
P 		169.7
(-0.8)
P 		97.2
(-3)
P 		100.7
(-2.9)
P 		117.3
(-2.4)
P 		299.3
(3)
P 		202
C 154.7
(-1)
P 		205.2
(0.3)
P 		84.9
(-2.9)
P 		104.5
(-2.4)
P 		80.3
(-3)
P 		308.7
(3)
P 		228
avr 192.4
(-0.1) 		179.9
(-0.5) 		102.5
(-2.9) 		100.7
(-3) 		105.5
(-2.8) 		292.5
(3) 		192
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 46
1 2 3 4 range
A 60.7
(3)
P 		34.8
(-0.8)
P 		34.9
(-0.8)
A 		19.7
(-3)
P 		41
B 40.8
(2.2)
P 		41.1
(2.3)
P 		28.3
(-3)
P 		42.8
(3)
P 		15
C 65.7
(3)
P 		48.5
(0.4)
P 		39.4
(-1)
P 		26.3
(-3)
P 		39
avr 55.7
(3) 		41.5
(-0.3) 		34.2
(-1.9) 		29.6
(-3) 		26

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 91
1 2 3 4 5 6 range
A 37.9
(-1.1)
P 		58.6
(2)
P 		27.3
(-2.6)
P 		24.6
(-3)
P 		35.9
(-1.3)
P 		65.6
(3)
P 		41
B 75.5
(0.5)
P 		56.5
(-0.8)
P 		23.6
(-3)
P 		26.7
(-2.8)
P 		47.7
(-1.4)
P 		111.6
(3)
P 		88
C 57.3
(-0.4)
P 		62.6
(0)
P 		21.6
(-3)
P 		21
(-3)
P 		26
(-2.6)
P 		103.4
(3)
P 		82
avr 56.9
(-0.2) 		59.2
(0) 		24.2
(-3) 		24.1
(-3) 		36.5
(-1.9) 		93.5
(3) 		69
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192630_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.16612
Sequence Type Exemplar sequence
Representative Public ID F09F9.4 NCBI
Target Description F09F9.4 /REP_DB=WormBase Gene ID /WP=CE04349 /TR=Q19284 /GB=AAA81764.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=Type I thrombospondin (TSP) repeats
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_076300(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_076300 NCBI Caenorhabditis elegans F09F9.4 (F09F9.4) mRNA, complete cds. 11/11 None
SNAP00000015419 ENSEMBL cdna:SNAP chromosome:CEL140:X:4121871:4125314:-1 11/11 None
GENEFINDER00000015424 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:4121871:4128418:-1 11/11 None
F09F9.4 ENSEMBL cdna:known chromosome:CEL140:X:4121760:4128405:-1 gene:F09F9.4 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
chrX:4122392-4128363(-) 100.0 100.0
Public Domain and Genome References
Gene Title Type I thrombospondin (TSP) repeats
Ensembl F09F9.4
Entrez Gene 180688 Entrez gene
SwissProt Q19284 EMBL-EBI
WormBase CE04349 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAA81764 Hypothetical protein F09F9.4 [Caenorhabditis elegans] ref|NP_508701.1| F09F9.4 [Caenorhabditis elegans] 0.0
blast CAE68526 Hypothetical protein CBG14348 [Caenorhabditis briggsae] 0.0
blast CAE68526 Hypothetical protein CBG14348 [Caenorhabditis briggsae] 1.0E-167
blast AAA81764 Hypothetical protein F09F9.4 [Caenorhabditis elegans] ref|NP_508701.1| F09F9.4 [Caenorhabditis elegans] 1.0E-167
blast AAF49041 CG32227-PA [Drosophila melanogaster] gb|AAQ22451.1| RE53634p [Drosophila melanogaster] ref|NP_649200.2| CG32227-PA [Drosophila melanogaster] 6.0E-12
Protein Domains
Database ID Description E-Value
Pfam IPR000884 EMBL-EBI Thrombospondin, type I 6.4E-16
Pfam IPR000884 EMBL-EBI Thrombospondin, type I 6.4E-16
Pfam IPR000884 EMBL-EBI Thrombospondin, type I 6.4E-16
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_508701.1 2 7-26,518-540
F09F9.4 2 7-26,518-540
SNAP00000015419 1 232-254
GENEFINDER00000015424 2 20-42,535-557
Sequence
Target Sequence 
>C. ELEGANS:192630_AT
agtttggtcatctgattctcatcaagaatatcagttctctcttcccatgtctgctccgat
ttttgtcgtcctttggagcaaaagcaacgacactgctagattaaaacaaattgacgatgg
attcacagtttcgtactccgtgcgagatgctgattcttcaccaacagttgcaaaaatcga
ctcatgtcaaccattttgtccggaaacaatggctatagcgattatggctatcatcttcat
ctgcataatattcattccgccattagtatgtgcagcggtaacggcatccatgagaaggaa
tactagtccagaagtaccattgatggacaacaaatatgattcggaaatgattagaagtgg
caacacggagagcacacatgtaagctcaagaaattatgtagcgaagcggagcattgggat
tcagttgagtgtacaaagtacaccaagaacggctcgtgcttgcctatcccacgagtcacc
tgtaccaccccgtggacaatcttcactcagcgaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AGTTTGGTCATCTGATTCTCATCAA 513 63 1353 Antisense
CAAGAATATCAGTTCTCTCTTCCCA 305 185 1375 Antisense
TCCGATTTTTGTCGTCCTTTGGAGC 361 591 1407 Antisense
CAGTTTCGTACTCCGTGCGAGATGC 427 205 1478 Antisense
GATGCTGATTCTTCACCAACAGTTG 492 413 1498 Antisense
GACTCATGTCAACCATTTTGTCCGG 572 373 1531 Antisense
TTATGGCTATCATCTTCATCTGCAT 520 681 1574 Antisense
ATCTGCATAATATTCATTCCGCCAT 512 33 1591 Antisense
ATGTGCAGCGGTAACGGCATCCATG 96 45 1620 Antisense
AGTACACCAAGAACGGCTCGTGCTT 160 63 1789 Antisense
CCGTGGACAATCTTCACTCAGCGAA 418 265 1842 Antisense
Sequence Source Affymetrix Proprietary Database