[Home] | [Total List]

[179040_at]

Description F28D9.4 /REP_DB=WormBase Gene ID /WP=CE23687 /TR=Q9U3H6 /GB=CAB54229.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation
Cluster 6grp_high1_10_10 > 46      4grp_highest_8_8 > 61      4grp_high_8_8 > 17      6grp_total > 07      4grp_total > 31      6grp_high1_sub > Cu      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 88
1 2 3 4 range
A 158.8
(3)
P 		139
(1.5)
P 		82.1
(-3)
P 		90.1
(-2.4)
P 		77
B 130.4
(3)
P 		70.7
(-3)
P 		119
(1.9)
P 		115.6
(1.5)
P 		60
C 123.9
(-0.4)
P 		112.1
(-1.7)
P 		100
(-3)
P 		155.9
(3)
P 		56
avr 137.7
(3) 		107.3
(-1.9) 		100.4
(-3) 		120.5
(0.2) 		37

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 128
1 2 3 4 5 6 range
A 133
(3)
P 		66.2
(-1.6)
P 		84.2
(-0.3)
P 		45
(-3)
A 		60.3
(-2)
A 		57.4
(-2.2)
A 		88
B 113.2
(3)
P 		76.7
(0.5)
P 		58.9
(-0.7)
P 		99.5
(2.1)
P 		25.3
(-3)
P 		85.7
(1.1)
P 		88
C 74.7
(1.6)
P 		90.5
(2.6)
P 		53
(0.1)
P 		96.8
(3)
P 		5
(-3)
A 		73.6
(1.5)
P 		92
avr 107
(3) 		77.8
(0.7) 		65.4
(-0.3) 		80.4
(0.9) 		30.2
(-3) 		72.2
(0.3) 		77
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 45
1 2 3 4 range
A 57.8
(3)
P 		30.2
(-0.7)
P 		21.5
(-1.9)
P 		13.2
(-3)
P 		45
B 41.6
(3)
P 		17.5
(-3)
P 		27.6
(-0.5)
P 		24.6
(-1.2)
P 		24
C 41
(3)
P 		32.2
(-0.6)
P 		34.9
(0.5)
P 		26.3
(-3)
P 		15
avr 46.8
(3) 		26.6
(-1.8) 		28
(-1.4) 		21.4
(-3) 		25

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 38
1 2 3 4 5 6 range
A 24.5
(3)
P 		23.5
(2.5)
P 		18.3
(0.2)
P 		11.4
(-3)
A 		18.2
(0.1)
A 		14
(-1.8)
A 		13
B 39.4
(3)
P 		25.5
(0.1)
P 		14.3
(-2.2)
P 		26.4
(0.3)
P 		10.3
(-3)
P 		32
(1.5)
P 		29
C 27.7
(3)
P 		27.6
(3)
P 		13.5
(-0.3)
P 		19.5
(1.1)
P 		1.6
(-3)
A 		24.7
(2.3)
P 		26
avr 30.5
(3) 		25.5
(1.5) 		15.4
(-1.4) 		19.1
(-0.3) 		10
(-3) 		23.6
(1) 		21
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 179040_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.1292
Sequence Type Exemplar sequence
Representative Public ID F28D9.4 NCBI
Target Description F28D9.4 /REP_DB=WormBase Gene ID /WP=CE23687 /TR=Q9U3H6 /GB=CAB54229.1 /SUBMIT=HINXTON /CHR=1 /FEA=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_060473(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_060473 NCBI Caenorhabditis elegans F28D9.4 (F28D9.4) mRNA, complete cds. 11/11 None
GENEFINDER00000044709 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:11183152:11190186:-1 11/11 None
F28D9.4 ENSEMBL cdna:known chromosome:CEL140:I:11175669:11185850:-1 gene:F28D9.4 11/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000044706 8/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrI:11183082-11185777(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Ensembl F28D9.4
Entrez Gene 173012 Entrez gene
SwissProt Q9U3H6 EMBL-EBI
WormBase CE23687 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAB54229 Hypothetical protein F28D9.4 [Caenorhabditis elegans] ref|NP_492874.1| F28D9.4 [Caenorhabditis elegans] 3.0E-63
blast CAB54229 Hypothetical protein F28D9.4 [Caenorhabditis elegans] ref|NP_492874.1| F28D9.4 [Caenorhabditis elegans] 6.0E-62
blast CAB04214 Hypothetical protein F28D9.1 [Caenorhabditis elegans] ref|NP_492875.2| SR protein related family member (rsr-1) [Caenorhabditis elegans] 5.0E-52
blast CAE63487 Hypothetical protein CBG07955 [Caenorhabditis briggsae] 7.0E-52
blast CAE63487 Hypothetical protein CBG07955 [Caenorhabditis briggsae] 1.0E-50
Protein Domains
Database ID Description E-Value
Pfam IPR002483 EMBL-EBI Splicing factor PWI 1.4E-24
Pfam IPR002483 EMBL-EBI Splicing factor PWI 1.4E-15
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_492874.1 1 85-107
F28D9.4 1 85-107
GENEFINDER00000044709 2 169-191,857-879
Sequence
Target Sequence 
>C. ELEGANS:179040_AT
gacgtgacgtcattgagcagcagcccagcagcaacaccgtcctctctgtcgggacacgca
cttgtcgcacttgacagaattgatacgagcaatacggctggatatattaaatctgtaatc
ggtggaacatctctcgtaactcttcttctcggaattcgaagtgcctggaaacattccagg
cagcctgaagctgcggatcttgcggctgcacagctcttctcgggagccgcattcgctgga
aaagccctcggagtggctacagtaatcaccgtatccggcttcacactattcattgtcggt
gtctcagcaattcttcaagtcaattcaccacgccaatttggctcggcgatgaaaactgcg
tttggcgattcgattcgattgccgcagagtgccaagtcgc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GACGTGACGTCATTGAGCAGCAGCC 345 377 19 Antisense
ACGCACTTGTCGCACTTGACAGAAT 709 91 74 Antisense
GGCAGCCTGAAGCTGCGGATCTTGC 78 537 197 Antisense
CATTCGCTGGAAAAGCCCTCGGAGT 167 217 248 Antisense
GTGGCTACAGTAATCACCGTATCCG 365 489 271 Antisense
CGGCTTCACACTATTCATTGTCGGT 201 243 294 Antisense
TGTCGGTGTCTCAGCAATTCTTCAA 232 557 312 Antisense
TTCTTCAAGTCAATTCACCACGCCA 147 691 329 Antisense
TCACCACGCCAATTTGGCTCGGCGA 476 625 343 Antisense
AAACTGCGTTTGGCGATTCGATTCG 567 125 371 Antisense
CGATTGCCGCAGAGTGCCAAGTCGC 195 249 394 Antisense
Sequence Source Affymetrix Proprietary Database