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[193586_at] Yeast nonsense-mediated mRNA decay protein like

Description T25G3.3 /REP_DB=WormBase Gene ID /WP=CE06512 /TR=Q22792 /GB=CAA96689.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=Yeast nonsense-mediated mRNA decay protein like
Cluster 6grp_highest_10_10 > 85      6grp_high1_10_10 > 67      4grp_highest_8_8 > 23      4grp_high_8_8 > 05      6grp_highest_nonorm > 78      6grp_total > 69      4grp_total > 02      6grp_highest_sub > Cu      6grp_high1_sub > Da      6grp_total_sub > Cup      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 7865
1 2 3 4 range
A 2434.3
(-2.2)
P 		1455.7
(-3)
P 		1505.9
(-3)
P 		8590.6
(3)
P 		7135
B 1919.3
(-2.8)
P 		1764.7
(-2.9)
P 		1674.5
(-3)
P 		9320.8
(3)
P 		7646
C 2578.4
(-2.2)
P 		1488
(-3)
P 		1938
(-2.7)
P 		9303.7
(3)
P 		7816
avr 2310.7
(-2.4) 		1569.5
(-3) 		1706.1
(-2.9) 		9071.7
(3) 		7502

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 801
1 2 3 4 5 6 range
A 1368.1
(-2.3)
P 		1374.1
(-2.3)
P 		1461.6
(-1.6)
P 		1703.1
(0.4)
P 		1288
(-3)
P 		2012.3
(3)
P 		724
B 1577
(0.3)
P 		1631.4
(0.8)
P 		1259.3
(-2.6)
P 		1211.5
(-3)
P 		1504.5
(-0.3)
P 		1873.1
(3)
P 		662
C 1713.8
(0.8)
P 		1448.2
(-1.5)
P 		1328
(-2.5)
P 		1266.6
(-3)
P 		1590.7
(-0.3)
P 		1980.5
(3)
P 		714
avr 1553
(-1) 		1484.6
(-1.7) 		1349.6
(-3) 		1393.7
(-2.6) 		1461.1
(-1.9) 		1955.3
(3) 		606
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1670
1 2 3 4 range
A 886.3
(0.6)
P 		316
(-3)
P 		393.7
(-2.5)
P 		1257.5
(3)
P 		942
B 612.1
(-2.2)
P 		435.8
(-2.8)
P 		388
(-3)
P 		1986.3
(3)
P 		1598
C 853.5
(-0.8)
P 		427.8
(-3)
P 		675.5
(-1.7)
P 		1568.8
(3)
P 		1141
avr 784
(-1.1) 		393.2
(-3) 		485.7
(-2.5) 		1604.2
(3) 		1211

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 446
1 2 3 4 5 6 range
A 252.2
(-3)
P 		488.7
(3)
P 		318.3
(-1.3)
P 		432
(1.5)
P 		388.7
(0.4)
P 		489.9
(3)
P 		238
B 548.7
(0.7)
P 		543
(0.6)
P 		305.8
(-3)
P 		320.9
(-2.8)
P 		611.3
(1.7)
P 		698.5
(3)
P 		393
C 635.2
(2.6)
P 		441.9
(-0.2)
P 		338
(-1.8)
P 		254.7
(-3)
P 		514.7
(0.8)
P 		663
(3)
P 		408
avr 478.7
(0.2) 		491.2
(0.5) 		320.7
(-3) 		335.9
(-2.7) 		504.9
(0.7) 		617.1
(3) 		296
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193586_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.1882
Sequence Type Exemplar sequence
Representative Public ID T25G3.3 NCBI
Target Description T25G3.3 /REP_DB=WormBase Gene ID /WP=CE06512 /TR=Q22792 /GB=CAA96689.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=Yeast nonsense-mediated mRNA decay protein 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_059713(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059713 NCBI Caenorhabditis elegans T25G3.3 (T25G3.3) mRNA, complete cds. 11/11 None
SNAP00000010744 ENSEMBL cdna:SNAP chromosome:CEL140:I:7567971:7570291:1 11/11 None
GENEFINDER00000010746 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:7567971:7570291:1 11/11 None
T25G3.3.2 ENSEMBL cdna:known chromosome:CEL140:I:7567964:7570469:1 gene:T25G3.3 11/11 None
T25G3.3.1 ENSEMBL cdna:known chromosome:CEL140:I:7567966:7570744:1 gene:T25G3.3 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
chrI:7567901-7570222(+) 100.0 100.0
Public Domain and Genome References
Gene Title Yeast nonsense-mediated mRNA decay protein like
Ensembl T25G3.3
Entrez Gene 3565801 Entrez gene
SwissProt Q22792 EMBL-EBI
WormBase CE30306 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:14568_S_AT nonsense-mediated mRNA decay NMD3 family protein at
ATH1-121501:263334_AT nonsense-mediated mRNA decay NMD3 family protein at
CANINE_2:CFAAFFX.22160.1.S1_AT similar to NMD3 homolog cfa
DROSOPHILA_2:1623733_AT Nonsense-mediated mRNA 3 dm
DROSGENOME1:153358_AT Nonsense-mediated mRNA 3 dm
CHICKEN:GGAAFFX.5992.1.S1_AT similar to Hypothetical protein MGC76205 gga
HG-U133_PLUS_2:218036_X_AT NMD3 homolog (S. cerevisiae) hs
HG-U133A:218036_X_AT NMD3 homolog (S. cerevisiae) hs
HG-FOCUS:218036_X_AT NMD3 homolog (S. cerevisiae) hs
HG-U133A_2:218036_X_AT NMD3 homolog (S. cerevisiae) hs
HU35KSUBA:RC_AA479922_AT NMD3 homolog (S. cerevisiae) hs
HU35KSUBC:RC_AA282197_AT NMD3 homolog (S. cerevisiae) hs
HU35KSUBD:RC_AA436679_AT NMD3 homolog (S. cerevisiae) hs
U133_X3P:G7705711_3P_X_AT NMD3 homolog (S. cerevisiae) hs
U133_X3P:G7705711_3P_A_AT NMD3 homolog (S. cerevisiae) hs
U133_X3P:HS.181022.0.A2_3P_AT NMD3 homolog (S. cerevisiae) hs
HG-U133_PLUS_2:222497_X_AT NMD3 homolog (S. cerevisiae) hs
HG-U133B:222497_X_AT NMD3 homolog (S. cerevisiae) hs
HG-U95B:44049_AT NMD3 homolog (S. cerevisiae) hs
HG-U95C:58858_S_AT NMD3 homolog (S. cerevisiae) hs
HG-U95C:63851_S_AT NMD3 homolog (S. cerevisiae) hs
HG-U95C:63852_R_AT NMD3 homolog (S. cerevisiae) hs
U133_X3P:HS.181022.1.S1_3P_A_AT NMD3 homolog (S. cerevisiae) hs
HG-U133_PLUS_2:231870_S_AT NMD3 homolog (S. cerevisiae) hs
HG-U133B:231870_S_AT NMD3 homolog (S. cerevisiae) hs
HG-U95E:73172_S_AT NMD3 homolog (S. cerevisiae) hs
HG-U95E:89304_AT NMD3 homolog (S. cerevisiae) hs
MU11KSUBA:AA175127_S_AT NMD3 homolog (S. cerevisiae) mm
MG-U74AV2:93741_AT NMD3 homolog (S. cerevisiae) mm
MOE430A:1437238_X_AT NMD3 homolog (S. cerevisiae) mm
MOUSE430A_2:1437238_X_AT NMD3 homolog (S. cerevisiae) mm
MOUSE430_2:1437238_X_AT NMD3 homolog (S. cerevisiae) mm
MOE430A:1448133_AT NMD3 homolog (S. cerevisiae) mm
MOUSE430A_2:1448133_AT NMD3 homolog (S. cerevisiae) mm
MOUSE430_2:1448133_AT NMD3 homolog (S. cerevisiae) mm
MOE430B:1438818_AT NMD3 homolog (S. cerevisiae) mm
MOUSE430_2:1438818_AT NMD3 homolog (S. cerevisiae) mm
MOUSE430_2:1447650_AT NMD3 homolog (S. cerevisiae) (Nmd3), mRNA mm
MOE430B:1447650_AT NMD3 homolog (S. cerevisiae) (Nmd3), mRNA mm
MG-U74CV2:167709_AT NMD3 homolog (S. cerevisiae) (Nmd3), mRNA mm
MU19KSUBA:TC17084_I_AT NMD3 homolog (S. cerevisiae) (Nmd3), mRNA mm
MU19KSUBB:TC34182_AT NMD3 homolog (S. cerevisiae) (Nmd3), mRNA mm
MU19KSUBB:TC34182_G_AT NMD3 homolog (S. cerevisiae) (Nmd3), mRNA mm
RAE230B:1393248_AT similar to expressed sequence C87860 (predicted) rn
RAT230_2:1393248_AT similar to expressed sequence C87860 (predicted) rn
YEAST_2:1770043_AT Protein involved in nuclear export of the large ribosomal subunit; acts as a Crm1p-dependent adapter protein for export of nascent ribosomal subunits through the nuclear pore complex Sc
Protein Similarities
Method ID Description E-Value
blast CAA96689 Hypothetical protein T25G3.3 [Caenorhabditis elegans] ref|NP_492114.2| T25G3.3 [Caenorhabditis elegans] 0.0
blast CAE66575 Hypothetical protein CBG11892 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR007064 EMBL-EBI NMD3 family 1.3E-125
Sequence
Target Sequence 
>C. ELEGANS:193586_AT
gaaaggcaggccacggatatgtgagtaagaaacacgaattggcagatgtatggttggtga
gaagtgatcaagttggaatgtctgatgctcaatctctatcagctagaactcacattggac
acttgttatcacctggagacttggttatggcattcgacatgaagaactgcaatgtgaata
atgcaactttcgatgccatgaacattgataatgttccggatgcaattattgtcagaaagg
tatttttacagtttttggaggaatactcaatattttatgaatttcaggtattcgatagaa
ctcgtcgtacagccaaacgtcaatggaagttgaagagattggttgttgatggtaatattg
ttggaaatgagacggcatcagttgctgatgaattccaaggatttatggaggatatcgaag
aagatgcactgatgagagagaagattaatatttataaagacgcagagaaaggaccaaatg
ttgatggagacgacgcagaagatcatccagatgctccaactcttgccgaaatgcttga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAAAGGCAGGCCACGGATATGTGAG 349 359 992 Antisense
GAATGTCTGATGCTCAATCTCTATC 567 331 1067 Antisense
CTATCAGCTAGAACTCACATTGGAC 388 223 1087 Antisense
GACACTTGTTATCACCTGGAGACTT 166 351 1109 Antisense
TGGAGACTTGGTTATGGCATTCGAC 501 547 1125 Antisense
GCAACTTTCGATGCCATGAACATTG 663 319 1174 Antisense
GGTATTCGATAGAACTCGTCGTACA 509 505 1278 Antisense
ACTCGTCGTACAGCCAAACGTCAAT 47 99 1291 Antisense
AAATGAGACGGCATCAGTTGCTGAT 157 119 1356 Antisense
GCAGAAGATCATCCAGATGCTCCAA 28 313 1486 Antisense
CTCCAACTCTTGCCGAAATGCTTGA 126 237 1505 Antisense
Sequence Source Affymetrix Proprietary Database