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[193296_at] Leucine Rich Repeat (2 copies)

Description C15H11.3 /REP_DB=WormBase Gene ID /WP=CE08180 /GEN=nxf-1 /TR=Q9XVS7 /GB=CAB02734.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Leucine Rich Repeat (2 copies)
Cluster 6grp_total > 59      4grp_total > 03      6grp_cgc > 28      6grp_cgc_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 80
1 2 3 4 range
A 45.1
(-3)
A 		50.8
(-2.6)
A 		60.9
(-1.8)
A 		121.7
(3)
A 		77
B 59.1
(-3)
A 		67.5
(-0.8)
A 		59.7
(-2.8)
A 		81.6
(3)
A 		23
C 75.9
(3)
A 		48.3
(-1.8)
A 		41.3
(-3)
A 		53.9
(-0.8)
A 		35
avr 60
(-1.9) 		55.5
(-2.7) 		54
(-3) 		85.7
(3) 		32

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 90
1 2 3 4 5 6 range
A 84.6
(3)
A 		43.5
(-2)
A 		34.9
(-3)
A 		48.6
(-1.3)
A 		46.8
(-1.6)
A 		60.1
(0)
M 		50
B 79.9
(2.5)
A 		34.1
(-3)
A 		50.4
(-1.1)
A 		40.5
(-2.2)
A 		61.1
(0.2)
A 		84.5
(3)
P 		50
C 45.4
(-1.4)
M 		59.4
(-0.4)
A 		21
(-3)
A 		61.3
(-0.3)
A 		40.6
(-1.7)
A 		110.8
(3)
P 		90
avr 70
(1.2) 		45.7
(-1.8) 		35.4
(-3) 		50.1
(-1.2) 		49.5
(-1.3) 		85.1
(3) 		50
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 16
1 2 3 4 range
A 16.4
(1.8)
A 		11
(-3)
A 		15.9
(1.3)
A 		17.8
(3)
A 		7
B 18.9
(3)
A 		16.7
(0.4)
A 		13.8
(-3)
A 		17.4
(1.2)
A 		5
C 25.1
(3)
A 		13.9
(-1.2)
A 		14.4
(-1)
A 		9.1
(-3)
A 		16
avr 20.1
(3) 		13.9
(-3) 		14.7
(-2.2) 		14.8
(-2.1) 		6

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 32
1 2 3 4 5 6 range
A 15.6
(3)
A 		15.5
(2.9)
A 		7.6
(-3)
A 		12.3
(0.5)
A 		14.1
(1.9)
A 		14.6
(2.3)
M 		8
B 27.8
(1.9)
A 		11.4
(-2.8)
A 		12.2
(-2.6)
A 		10.7
(-3)
A 		24.8
(1.1)
A 		31.5
(3)
P 		21
C 16.8
(-0.8)
M 		18.1
(-0.6)
A 		5.3
(-3)
A 		12.3
(-1.7)
A 		13.1
(-1.5)
A 		37.1
(3)
P 		32
avr 20.1
(0.6) 		15
(-0.9) 		8.4
(-3) 		11.8
(-1.9) 		17.3
(-0.2) 		27.7
(3) 		19
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193296_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.13536
Sequence Type Exemplar sequence
Representative Public ID C15H11.3 NCBI
Target Description C15H11.3 /REP_DB=WormBase Gene ID /WP=CE08180 /GEN=nxf-1 /TR=Q9XVS7 /GB=CAB02734.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Leucine Rich Repeat (2 copies)
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_074166(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_074166 NCBI Caenorhabditis elegans Nuclear eXport Factor family member (nxf-1) (nxf-1) mRNA, complete cds. 11/11 None
SNAP00000026575 ENSEMBL cdna:SNAP chromosome:CEL140:V:14415209:14417600:-1 11/11 None
GENEFINDER00000026589 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:14415209:14417600:-1 11/11 None
C15H11.3 ENSEMBL cdna:known chromosome:CEL140:V:14415209:14418380:-1 gene:C15H11.3 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
chrV:14415208-14418380(-) 100.0 100.0
Public Domain and Genome References
Gene Title Leucine Rich Repeat (2 copies)
Gene Symbol nxf-1
Ensembl C15H11.3
Entrez Gene 191736 Entrez gene
SwissProt Q9XVS7 EMBL-EBI
WormBase CE08180 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1592008_AT similar to nuclear RNA export factor 1 cfa
CANINE_2:CFA.21557.1.A1_AT similar to nuclear RNA export factor 1 cfa
CANINE_2:CFAAFFX.23934.1.S1_S_AT similar to nuclear RNA export factor 1 cfa
DROSOPHILA_2:1627673_AT small bristles dm
DROSGENOME1:144830_AT small bristles dm
DROSGENOME1:144828_AT small bristles dm
HG-U133A:208922_S_AT nuclear RNA export factor 1 hs
HG-U133A_2:208922_S_AT nuclear RNA export factor 1 hs
HG-U133_PLUS_2:208922_S_AT nuclear RNA export factor 1 hs
HG-FOCUS:208922_S_AT nuclear RNA export factor 1 hs
HU35KSUBA:RC_AA465212_I_AT nuclear RNA export factor 1 hs
HU35KSUBA:D83883_S_AT nuclear RNA export factor 1 hs
HU35KSUBA:AA370960_AT nuclear RNA export factor 1 hs
HU35KSUBB:RC_R86957_AT nuclear RNA export factor 1 hs
HUGENEFL:U80073_AT nuclear RNA export factor 1 hs
U133_X3P:G13436184_3P_S_AT nuclear RNA export factor 1 hs
HG-U95AV2:35302_AT nuclear RNA export factor 1 hs
MU11KSUBA:AA270881_AT nuclear RNA export factor 1 homolog (S. cerevisiae) mm
MU11KSUBA:AA270881_G_AT nuclear RNA export factor 1 homolog (S. cerevisiae) mm
MU11KSUBA:AA104830_G_AT nuclear RNA export factor 1 homolog (S. cerevisiae) mm
MU11KSUBA:AA104830_AT nuclear RNA export factor 1 homolog (S. cerevisiae) mm
MG-U74AV2:101079_AT nuclear RNA export factor 1 homolog (S. cerevisiae) mm
MOE430A:1416791_A_AT nuclear RNA export factor 1 homolog (S. cerevisiae) mm
MOUSE430A_2:1416791_A_AT nuclear RNA export factor 1 homolog (S. cerevisiae) mm
MOUSE430_2:1416791_A_AT nuclear RNA export factor 1 homolog (S. cerevisiae) mm
MOE430B:1439092_AT Nuclear RNA export factor 1 homolog (S. cerevisiae), mRNA (cDNA clone MGC:11583 IMAGE:3710546) mm
MOUSE430_2:1439092_AT Nuclear RNA export factor 1 homolog (S. cerevisiae), mRNA (cDNA clone MGC:11583 IMAGE:3710546) mm
MU19KSUBB:TC26287_AT Nuclear RNA export factor 1 homolog (S. cerevisiae), mRNA (cDNA clone MGC:11583 IMAGE:3710546) mm
MU19KSUBB:TC34000_AT Nuclear RNA export factor 1 homolog (S. cerevisiae), mRNA (cDNA clone MGC:11583 IMAGE:3710546) mm
RAT230_2:1398861_AT hypothetical gene supported by NM_021579 rn
RAE230A:1398861_AT hypothetical gene supported by NM_021579 rn
RG-U34A:AF093139_S_AT hypothetical gene supported by NM_021579 rn
RG-U34B:RC_AA900348_S_AT hypothetical gene supported by NM_021579 rn
RG-U34C:RC_AI104946_G_AT hypothetical gene supported by NM_021579 rn
RG-U34C:RC_AI104946_AT hypothetical gene supported by NM_021579 rn
RG-U34C:AA848482_S_AT hypothetical gene supported by NM_021579 rn
YEAST_2:1776732_AT Poly(A)RNA binding protein involved in nuclear mRNA export, component of the nuclear pore; ortholog of human TAP Sc
Protein Similarities
Method ID Description E-Value
blast CAB02734 Hypothetical protein C15H11.3 [Caenorhabditis elegans] ref|NP_506567.1| Nuclear eXport Factor family member (nxf-1) [Caenorhabditis elegans] sp|Q9XVS7|NXF1_CAEEL Nuclear RNA export factor 0.0
blast CAE60907 Hypothetical protein CBG04623 [Caenorhabditis briggsae] 0.0
blast CAE60905 Hypothetical protein CBG04621 [Caenorhabditis briggsae] 6.0E-83
Protein Domains
Database ID Description E-Value
Pfam IPR005637 EMBL-EBI TAP C-terminal domain 2.0E-31
Pfam IPR005637 EMBL-EBI TAP C-terminal domain 2.0E-31
Sequence
Target Sequence 
>C. ELEGANS:193296_AT
cgtcatagagcttctcgttcagcgcgtggagccatggatattgcagttgctctctcaaaa
ctgccaacatctagccatatgagggacacatttattgtcgacgtttttctccaatcaaat
gatcttctcggattcacagttcaaggactattctgcgatggtgatcttacacagacccct
tcacccagtttcttcagcagatcatttttggtgtctccgagagagaatgactcagttgca
gtaatctctgatcagctttttatcacagttgcctcgttggatcgattagaaaagttcaag
aagctgtacgatcaatctattgcaaatggtgcggccgtggaacaagttagcgccgttcaa
attgcacaaatcggagttaacggaatgggattcgacggagcacctgcactaccgattcgt
gaggaaatgatcaaagcgatgtgccagttcagtggaatgattccaccattcagtgagaaa
tgtcttgcagactgcgcttggaactttgact

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CGTCATAGAGCTTCTCGTTCAGCGC 217 247 1327 Antisense
TCGTTCAGCGCGTGGAGCCATGGAT 79 605 1341 Antisense
TTGTCGACGTTTTTCTCCAATCAAA 5 709 1421 Antisense
ATGATCTTCTCGGATTCACAGTTCA 201 47 1445 Antisense
GATGGTGATCTTACACAGACCCCTT 636 407 1483 Antisense
CACCCAGTTTCTTCAGCAGATCATT 292 201 1508 Antisense
CAGCTTTTTATCACAGTTGCCTCGT 358 197 1579 Antisense
AGTTAGCGCCGTTCAAATTGCACAA 210 63 1671 Antisense
GAATGGGATTCGACGGAGCACCTGC 259 333 1709 Antisense
CACCTGCACTACCGATTCGTGAGGA 518 201 1727 Antisense
GCAGACTGCGCTTGGAACTTTGACT 349 313 1813 Antisense
Sequence Source Affymetrix Proprietary Database