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[187937_s_at]

Description F46B6.3 /REP_DB=WormBase Gene ID /WP=CE26973 /GEN=smg-4 /TR=Q20445 /GB=CAA94820.2 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 67      6grp_high1_10_10 > 75      4grp_highest_8_8 > 15      4grp_high_8_8 > 14      6grp_highest_nonorm > 85      6grp_total > 66      4grp_total > 09      6grp_highest_sub > In      6grp_cgc > 57      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 764
1 2 3 4 range
A 667.6
(-3)
P 		787.4
(-1.8)
P 		811.4
(-1.6)
P 		1266.3
(3)
P 		599
B 735.9
(-3)
P 		823.1
(-2.2)
P 		863.6
(-1.9)
P 		1431.7
(3)
P 		696
C 865.9
(-1.8)
P 		816.7
(-2.2)
P 		738.8
(-3)
P 		1361.6
(3)
P 		623
avr 756.5
(-3) 		809.1
(-2.5) 		804.6
(-2.5) 		1353.2
(3) 		597

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 565
1 2 3 4 5 6 range
A 617.7
(-2.9)
P 		652.2
(-2.5)
P 		825
(-0.3)
P 		931.2
(1)
P 		610.2
(-3)
P 		1088.5
(3)
P 		478
B 587.8
(-2.6)
P 		562
(-3)
P 		909.2
(2.1)
P 		665.2
(-1.5)
P 		657.2
(-1.6)
P 		967.9
(3)
P 		406
C 660.4
(-1.4)
P 		523.2
(-3)
P 		648.9
(-1.5)
P 		569.5
(-2.5)
P 		697.2
(-0.9)
P 		1031.9
(3)
P 		509
avr 622
(-2.4) 		579.1
(-3) 		794.4
(-0.1) 		722
(-1.1) 		654.9
(-2) 		1029.4
(3) 		450
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 134
1 2 3 4 range
A 243.1
(3)
P 		170.9
(-3)
P 		212.1
(0.4)
P 		185.4
(-1.8)
P 		72
B 234.7
(-1)
P 		203.3
(-2.8)
P 		200.1
(-3)
P 		305.1
(3)
P 		105
C 286.6
(3)
P 		234.8
(-2.5)
P 		257.5
(-0.1)
P 		229.6
(-3)
P 		57
avr 254.8
(3) 		203
(-3) 		223.2
(-0.7) 		240
(1.3) 		52

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 247
1 2 3 4 5 6 range
A 113.9
(-3)
P 		232
(1.7)
P 		179.7
(-0.4)
P 		236.2
(1.9)
P 		184.1
(-0.2)
P 		265
(3)
P 		151
B 204.5
(-2.1)
P 		187.1
(-2.6)
P 		220.8
(-1.6)
P 		176.2
(-3)
P 		267
(-0.1)
P 		360.9
(3)
P 		185
C 244.8
(0.4)
P 		159.7
(-1.8)
P 		165.1
(-1.7)
P 		114.5
(-3)
P 		225.6
(-0.1)
P 		345.4
(3)
P 		231
avr 187.7
(-2.5) 		192.9
(-2.3) 		188.5
(-2.5) 		175.6
(-3) 		225.6
(-1) 		323.8
(3) 		148
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 187937_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11269
Sequence Type Exemplar sequence
Representative Public ID F46B6.3 NCBI
Target Description F46B6.3 /REP_DB=WormBase Gene ID /WP=CE26973 /GEN=smg-4 /TR=Q20445 /GB=CAA94820.2 /SUBMIT=HINXTON /CHR=5 /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_073120(9)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073120 NCBI Caenorhabditis elegans F46B6.12 (F46B6.12) mRNA, complete cds. 9/11 None
GENEFINDER00000041207 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:9777576:9782099:-1 11/11 None
F46B6.12.1 ENSEMBL cdna:known chromosome:CEL140:V:9777495:9778416:-1 gene:F46B6.12 9/11 None
F46B6.12.2 ENSEMBL cdna:known chromosome:CEL140:V:9777519:9778418:-1 gene:F46B6.12 9/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_171515 2/11 Cross Hyb Matching Probes None
NM_171514 2/11 Cross Hyb Matching Probes None
SNAP00000041195 5/11 Cross Hyb Matching Probes None
SNAP00000041196 2/11 Cross Hyb Matching Probes None
F46B6.3a 2/11 Cross Hyb Matching Probes A 
F46B6.3b 2/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrV:9777575-9780324(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Ensembl F46B6.12
Entrez Gene 179370 Entrez gene
SwissProt Q9BI88 EMBL-EBI
WormBase CE26972 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:13540_AT expressed protein at
ATH1-121501:253385_AT expressed protein at
CANINE:1584985_S_AT similar to CG4646-PA cfa
CANINE:1604865_AT similar to CG4646-PA cfa
CANINE_2:CFA.4366.3.A1_AT similar to CG4646-PA cfa
CANINE_2:CFAAFFX.29250.1.S1_AT similar to CG4646-PA cfa
CANINE_2:CFAAFFX.29250.1.S1_S_AT similar to CG4646-PA cfa
DROSOPHILA_2:1638233_AT dm
DROSGENOME1:142934_AT dm
CHICKEN:GGA.5905.1.S1_AT similar to hypothetical protein FLJ20580 gga
CHICKEN:GGA.5905.2.S1_A_AT similar to hypothetical protein FLJ20580 gga
U133_X3P:HS.146861.0.S1_3P_A_AT chromosome 1 open reading frame 123 hs
HG-U133A_2:203197_S_AT chromosome 1 open reading frame 123 hs
HG-U133_PLUS_2:203197_S_AT chromosome 1 open reading frame 123 hs
HG-U133A:203197_S_AT chromosome 1 open reading frame 123 hs
HG-U95AV2:39743_AT chromosome 1 open reading frame 123 hs
MOUSE430_2:1426467_S_AT RIKEN cDNA 0610037L13 gene mm
MOE430A:1426467_S_AT RIKEN cDNA 0610037L13 gene mm
MOUSE430A_2:1426467_S_AT RIKEN cDNA 0610037L13 gene mm
MG-U74BV2:109535_AT RIKEN cDNA 0610037L13 gene mm
MG-U74BV2:112780_AT RIKEN cDNA 0610037L13 gene mm
MG-U74CV2:169658_AT RIKEN cDNA 0610037L13 gene mm
MOE430A:1426468_AT RIKEN cDNA 0610037L13 gene mm
MOUSE430A_2:1426468_AT RIKEN cDNA 0610037L13 gene mm
MOUSE430_2:1426468_AT RIKEN cDNA 0610037L13 gene mm
MOE430A:1456370_S_AT RIKEN cDNA 0610037L13 gene mm
MOUSE430A_2:1456370_S_AT RIKEN cDNA 0610037L13 gene mm
MOUSE430_2:1456370_S_AT RIKEN cDNA 0610037L13 gene mm
MOE430B:1429879_AT RIKEN cDNA 0610037L13 gene mm
MOUSE430_2:1429879_AT RIKEN cDNA 0610037L13 gene mm
MOE430A:1438343_AT RIKEN cDNA 0610037L13 gene (0610037L13Rik), mRNA mm
MOUSE430A_2:1438343_AT RIKEN cDNA 0610037L13 gene (0610037L13Rik), mRNA mm
MOUSE430_2:1438343_AT RIKEN cDNA 0610037L13 gene (0610037L13Rik), mRNA mm
MU19KSUBA:TC17115_AT RIKEN cDNA 0610037L13 gene (0610037L13Rik), mRNA mm
MU19KSUBA:TC19293_AT RIKEN cDNA 0610037L13 gene (0610037L13Rik), mRNA mm
RG-U34B:RC_AA848824_AT Similar to RIKEN cDNA 0610037L13 rn
RG-U34C:RC_AI176734_AT Similar to RIKEN cDNA 0610037L13 rn
RAE230A:1373009_AT Similar to RIKEN cDNA 0610037L13 rn
RAT230_2:1373009_AT Similar to RIKEN cDNA 0610037L13 rn
RAE230B:1379288_AT Similar to RIKEN cDNA 0610037L13 rn
RAT230_2:1379288_AT Similar to RIKEN cDNA 0610037L13 rn
Protein Similarities
Method ID Description E-Value
blast CAA94821 Hypothetical protein F46B6.4 [Caenorhabditis elegans] ref|NP_505523.1| F46B6.4 [Caenorhabditis elegans] 0.0
blast CAE72253 Hypothetical protein CBG19372 [Caenorhabditis briggsae] 0.0
blast CAD18872 Hypothetical protein F46B6.3b [Caenorhabditis elegans] ref|NP_741600.1| Suppressor with Morphological effect on Genitalia family member (smg-4) [Caenorhabditis elegans] 1.0E-164
blast CAC35815 Hypothetical protein F46B6.12 [Caenorhabditis elegans] ref|NP_505521.1| F46B6.12 [Caenorhabditis elegans] 2.0E-78
blast CAE72252 Hypothetical protein CBG19371 [Caenorhabditis briggsae] 7.0E-71
blast XP_536703 PREDICTED: similar to CG4646-PA [Canis familiaris] 2.0E-34
Protein Domains
Database ID Description E-Value
Pfam IPR008584 EMBL-EBI Eukaryotic protein of unknown function DUF866 1.7E-53
Pfam IPR005120 EMBL-EBI Smg-4/UPF3 4.2E-103
Pfam IPR008584 EMBL-EBI Eukaryotic protein of unknown function DUF866 1.1E-58
Trans Membrane
ID Number Of Domains Domain Boundaries
GENEFINDER00000041207 1 478-500
Sequence
Target Sequence 
>C. ELEGANS:187937_S_AT
ccgtccatctccagctaaaactgttggcgagcaacaaggcgaggattggattaagaaatt
aactgatccgaagtcagctccaatgaaaaagaaacacgatccttttcttgctctcgaact
gaagtgtcaattgaaaggtatcactgatcttcgtccggatgacactgattcgtttcattg
gcacatgaaacttaagtgtactaattgtggtgaagctccagatcactggcagtatgtagt
gctcaatgagatgcttgatgttccaggaagtcgtggtgaggcaaatcttgtggaaaaatg
caagctgtgtggaagagtcaacactttgaccattgtcgaggatatgttcaaaagctacaa
catcgaacaaaacgagaaatggcaacagattgcagtgttcgattgccgtggacttgaacc
gtttgattttgatccgagagacgaatggattgccaaaagcgttgaaactggaaacgcatt
ccacgagattgatttgagtgagaaggaatgggtggactttgatgataaagcaatggaagc
cgttgagattagcgagatgtcctcccaattc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CCGTCCATCTCCAGCTAAAACTGTT 470 265 888 Antisense
AACTGATCCGAAGTCAGCTCCAATG 404 141 948 Antisense
CCTTTTCTTGCTCTCGAACTGAAGT 393 269 988 Antisense
GAAAGGTATCACTGATCTTCGTCCG 232 359 1020 Antisense
ATCTTCGTCCGGATGACACTGATTC 480 31 1034 Antisense
GACACTGATTCGTTTCATTGGCACA 342 367 1048 Antisense
GGTGAAGCTCCAGATCACTGGCAGT 452 501 1096 Antisense
GATTGCAGTGTTCGATTGCCGTGGA 558 433 1275 Antisense
ATTGCCGTGGACTTGAACCGTTTGA 219 3 1289 Antisense
GAAACGCATTCCACGAGATTGATTT 117 359 1358 Antisense
GATTAGCGAGATGTCCTCCCAATTC 280 429 1434 Antisense
Sequence Source Affymetrix Proprietary Database