[Home] | [Total List]

[175233_at]

Description AU114372_rc /REP_DB=TREMBL Accession /GB=AU114372 /CHR=5 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk718d5 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 87      6grp_high1_10_10 > 87      4grp_highest_8_8 > 41      4grp_high_8_8 > 49      6grp_highest_nonorm > 95      6grp_total > 87      4grp_total > 54      6grp_highest_sub > Da      6grp_cgc > 49      6grp_high1_sub > In      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 330
1 2 3 4 range
A 714.5
(3)
P 		651.9
(1.8)
P 		540.3
(-0.4)
P 		408.8
(-3)
P 		306
B 660
(3)
P 		545.2
(0.2)
P 		448.7
(-2.2)
P 		418.2
(-3)
P 		242
C 739
(3)
P 		518.8
(-2.1)
P 		713.3
(2.4)
P 		479.4
(-3)
P 		260
avr 704.5
(3) 		572
(0) 		567.4
(-0.1) 		435.5
(-3) 		269

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 535
1 2 3 4 5 6 range
A 864.7
(0.3)
P 		614.8
(-3)
P 		707.8
(-1.8)
P 		690.3
(-2)
P 		909.7
(0.8)
P 		1074.7
(3)
P 		460
B 539.5
(-3)
P 		560.9
(-2.8)
P 		557.8
(-2.8)
P 		578.9
(-2.5)
P 		743.9
(-0.6)
P 		1056.4
(3)
P 		517
C 566.8
(-3)
P 		598
(-2.3)
P 		668.1
(-0.7)
P 		746.1
(1.1)
P 		672.8
(-0.6)
P 		827.6
(3)
P 		261
avr 657
(-2) 		591.2
(-3) 		644.6
(-2.2) 		671.8
(-1.8) 		775.5
(-0.2) 		986.2
(3) 		395
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 200
1 2 3 4 range
A 260.2
(3)
P 		141.5
(-0.6)
P 		141.2
(-0.6)
P 		59.8
(-3)
P 		200
B 210.5
(3)
P 		134.7
(-0.7)
P 		104
(-2.3)
P 		89.1
(-3)
P 		121
C 244.6
(2.9)
P 		149.2
(-0.6)
P 		248.6
(3)
P 		80.8
(-3)
P 		168
avr 238.4
(3) 		141.8
(-0.6) 		164.6
(0.3) 		76.6
(-3) 		162

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 258
1 2 3 4 5 6 range
A 159.4
(-2.7)
P 		218.7
(0.2)
P 		154.1
(-3)
P 		175.1
(-2)
P 		274.5
(3)
P 		261.7
(2.4)
P 		120
B 187.7
(-1.8)
P 		186.7
(-1.8)
P 		135.5
(-3)
P 		153.3
(-2.6)
P 		302.2
(0.9)
P 		393.9
(3)
P 		258
C 210.1
(-0.2)
P 		182.5
(-1.5)
P 		170
(-2.1)
P 		150
(-3)
P 		217.7
(0.2)
P 		277
(3)
P 		127
avr 185.7
(-1.8) 		196
(-1.4) 		153.2
(-3) 		159.5
(-2.8) 		264.8
(1.2) 		310.9
(3) 		158
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 175233_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.21764
Sequence Type Exemplar sequence
Representative Public ID AU114372 NCBI
Target Description AU114372_rc /REP_DB=TREMBL Accession /GB=AU114372 /CHR=5 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk718d5 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_171515(11), NM_171514(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_171515 NCBI Caenorhabditis elegans Suppressor with Morphological effect on Genitalia family member (smg-4) (smg-4) mRNA, complete cds. 11/11 None
NM_171514 NCBI Caenorhabditis elegans Suppressor with Morphological effect on Genitalia family member (smg-4) (smg-4) mRNA, complete cds. 11/11 None
F46B6.3a ENSEMBL cdna:known chromosome:CEL140:V:9778578:9780325:-1 gene:F46B6.3 11/11 None
F46B6.3b ENSEMBL cdna:known chromosome:CEL140:V:9778585:9780324:-1 gene:F46B6.3 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000041196 3/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrV:9778587-9778878(-) 100.0 100.0
Public Domain and Genome References
Ensembl F46B6.3
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAD18872 Hypothetical protein F46B6.3b [Caenorhabditis elegans] ref|NP_741600.1| Suppressor with Morphological effect on Genitalia family member (smg-4) [Caenorhabditis elegans] 0.0
blast CAA94820 Hypothetical protein F46B6.3a [Caenorhabditis elegans] ref|NP_741601.1| Suppressor with Morphological effect on Genitalia family member (smg-4) [Caenorhabditis elegans] 1.0E-166
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-163
blast CAA94820 Hypothetical protein F46B6.3a [Caenorhabditis elegans] ref|NP_741601.1| Suppressor with Morphological effect on Genitalia family member (smg-4) [Caenorhabditis elegans] 1.0E-163
blast XP_624605 PREDICTED: similar to UPF3 regulator of nonsense transcripts homolog B isoform 1 [Apis mellifera] 4.0E-19
Protein Domains
Database ID Description E-Value
Pfam IPR005120 EMBL-EBI Smg-4/UPF3 4.2E-103
Sequence
Target Sequence 
>C. ELEGANS:175233_AT
acggcaccatcttctacaaaactcccaactcgtgcaactacgtccaatcatccaaaacgt
ccatccactgcaccgaatcattagcaattgttgttaaagattaatgttgattataagagg
agtaaatggattttttttgtttgattgtgaaaccgtcataatcgttttctatgtgctaca
tttctaatatgttcacttattccattctctgtattttcgattatcaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ACGGCACCATCTTCTACAAAACTCC 651 95 33 Antisense
AACTCGTGCAACTACGTCCAATCAT 164 141 59 Antisense
TGCAACTACGTCCAATCATCCAAAA 185 577 65 Antisense
CCATCCACTGCACCGAATCATTAGC 673 271 93 Antisense
GCACCGAATCATTAGCAATTGTTGT 48 315 102 Antisense
GTGAAACCGTCATAATCGTTTTCTA 367 481 179 Antisense
ATAATCGTTTTCTATGTGCTACATT 689 25 190 Antisense
GTGCTACATTTCTAATATGTTCACT 507 479 205 Antisense
TATGTTCACTTATTCCATTCTCTGT 615 655 220 Antisense
TATTCCATTCTCTGTATTTTCGATT 179 663 230 Antisense
CATTCTCTGTATTTTCGATTATCAA 304 217 235 Antisense
Sequence Source Affymetrix Proprietary Database