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[176726_at]

Description Y39G8C.1 /REP_DB=WormBase Gene ID /WP=CE26838 /GB=CAC35856.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation
Cluster 6grp_total > 57      4grp_total > 23      6grp_cgc > 37      6grp_cgc_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 83
1 2 3 4 range
A 109.4
(2.4)
P 		67.3
(-2)
A 		58.3
(-3)
A 		114.6
(3)
P 		56
B 120
(3)
P 		55
(-1.7)
A 		37.4
(-3)
A 		106.6
(2)
P 		83
C 112.1
(3)
P 		55
(-2.4)
A 		48.5
(-3)
A 		71.2
(-0.9)
A 		64
avr 113.8
(3) 		59.1
(-2) 		48.1
(-3) 		97.5
(1.5) 		66

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 65
1 2 3 4 5 6 range
A 30.6
(-2.2)
A 		44.8
(-0)
A 		25.5
(-3)
A 		37.7
(-1.1)
A 		33.2
(-1.8)
A 		64.6
(3)
A 		39
B 68.9
(2.8)
A 		29.8
(-0.9)
A 		25.6
(-1.3)
A 		25.4
(-1.3)
A 		7
(-3)
A 		71.5
(3)
P 		65
C 19.7
(-3)
A 		43
(1.2)
A 		36.3
(-0)
A 		53.1
(3)
A 		32.4
(-0.7)
A 		52.1
(2.8)
A 		33
avr 39.7
(-0.6) 		39.2
(-0.7) 		29.1
(-2.2) 		38.7
(-0.7) 		24.2
(-3) 		62.7
(3) 		39
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 31
1 2 3 4 range
A 39.8
(3)
P 		14.6
(-3)
A 		15.2
(-2.9)
A 		16.8
(-2.5)
P 		25
B 38.3
(3)
P 		13.6
(-2)
A 		8.7
(-3)
A 		22.7
(-0.2)
P 		30
C 37.1
(3)
P 		15.8
(-2.1)
A 		16.9
(-1.8)
A 		12
(-3)
A 		25
avr 38.4
(3) 		14.7
(-2.7) 		13.6
(-3) 		17.2
(-2.1) 		25

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 24
1 2 3 4 5 6 range
A 5.6
(-3)
A 		15.9
(3)
A 		5.6
(-3)
A 		9.6
(-0.7)
A 		10
(-0.4)
A 		15.7
(2.9)
A 		10
B 24
(2.3)
A 		9.9
(-1.2)
A 		6.2
(-2.2)
A 		6.7
(-2)
A 		2.9
(-3)
A 		26.6
(3)
P 		24
C 7.3
(-3)
A 		13.1
(0.4)
A 		9.2
(-1.9)
A 		10.7
(-1)
A 		10.5
(-1.1)
A 		17.4
(3)
A 		10
avr 12.3
(-0.5) 		13
(-0.2) 		7
(-3) 		9
(-2.1) 		7.8
(-2.6) 		19.9
(3) 		13
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 176726_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3470
Sequence Type Exemplar sequence
Representative Public ID Y39G8C.1 NCBI
Target Description Y39G8C.1 /REP_DB=WormBase Gene ID /WP=CE26838 /GB=CAC35856.1 /SUBMIT=HINXTON /CHR=2 /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_064544(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_064544 NCBI Caenorhabditis elegans XRN (mouse/S. cerevisiae) ribonuclease related family member (xrn-1) (xrn-1) mRNA, complete cds. 11/11 None
SNAP00000006825 ENSEMBL cdna:SNAP chromosome:CEL140:II:14063800:14091200:1 11/11 None
GENEFINDER00000006831 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:14068888:14083915:1 11/11 None
Y39G8C.1 ENSEMBL cdna:known chromosome:CEL140:II:14068888:14083430:1 gene:Y39G8C.1 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
chrII:14068884-14083345(+) 99.48 100.0
Public Domain and Genome References
Gene Title
Gene Symbol xrn-1
Ensembl Y39G8C.1
Entrez Gene 175059 Entrez gene
SwissProt Q9BHK7 EMBL-EBI
WormBase CE32750 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1605514_AT similar to 5-3 exoribonuclease 1 cfa
CANINE_2:CFAAFFX.12559.1.S1_AT similar to 5-3 exoribonuclease 1 cfa
CANINE_2:CFAAFFX.12559.1.S1_S_AT similar to 5-3 exoribonuclease 1 cfa
CANINE_2:CFAAFFX.12579.1.S1_AT similar to 5-3 exoribonuclease 1 cfa
CANINE_2:CFAAFFX.12579.1.S1_S_AT similar to 5-3 exoribonuclease 1 cfa
DROSOPHILA_2:1624778_AT pacman dm
DROSGENOME1:154117_AT pacman dm
CHICKEN:GGAAFFX.1767.2.S1_S_AT similar to DNA strand-exchange protein SEP1 gga
CHICKEN:GGAAFFX.1767.4.S1_S_AT similar to DNA strand-exchange protein SEP1 gga
HG-U133_PLUS_2:233632_S_AT 5'-3' exoribonuclease 1 hs
HG-U133B:233632_S_AT 5'-3' exoribonuclease 1 hs
HG-U133_PLUS_2:225814_AT 5'-3' exoribonuclease 1 hs
HG-U133B:225814_AT 5'-3' exoribonuclease 1 hs
HU35KSUBB:RC_T66948_AT 5'-3' exoribonuclease 1 hs
HU35KSUBC:RC_N68610_AT 5'-3' exoribonuclease 1 hs
HU35KSUBC:RC_AA504116_AT 5'-3' exoribonuclease 1 hs
U133_X3P:HS2.82501.4.S1_3P_AT 5'-3' exoribonuclease 1 hs
U133_X3P:HS2.82501.1.S1_3P_S_AT 5'-3' exoribonuclease 1 hs
U133_X3P:HS.82501.1.S1_3P_A_AT 5'-3' exoribonuclease 1 hs
U133_X3P:HS.82501.0.S1_3P_X_AT 5'-3' exoribonuclease 1 hs
U133_X3P:HS.82501.0.S1_3P_AT 5'-3' exoribonuclease 1 hs
HG-U133_PLUS_2:1555785_A_AT 5'-3' exoribonuclease 1 hs
HG-U133_PLUS_2:1570394_AT 5'-3' exoribonuclease 1 hs
HG-U95B:42920_AT 5'-3' exoribonuclease 1 hs
HG-U95B:46550_AT 5'-3' exoribonuclease 1 hs
HG-U95B:47090_AT 5'-3' exoribonuclease 1 hs
HG-U95C:64909_AT 5'-3' exoribonuclease 1 hs
HG-U95D:86814_AT 5'-3' exoribonuclease 1 hs
HG-U133_PLUS_2:242995_AT 5'-3' exoribonuclease 1 hs
HG-U133B:242995_AT 5'-3' exoribonuclease 1 hs
HG-U95B:51954_R_AT 5'-3' exoribonuclease 1 hs
HG-U95D:75063_AT 5'-3' exoribonuclease 1 hs
HG-U95D:90008_AT 5'-3' exoribonuclease 1 hs
HU35KSUBC:RC_T71274_AT 5'-3' exoribonuclease 1 hs
U133_X3P:HS.76966.0.A1_3P_AT 5'-3' exoribonuclease 1 hs
MG-U74AV2:98283_AT 5'-3' exoribonuclease 1 mm
MOE430A:1450308_A_AT 5'-3' exoribonuclease 1 mm
MOUSE430A_2:1450308_A_AT 5'-3' exoribonuclease 1 mm
MOUSE430_2:1450308_A_AT 5'-3' exoribonuclease 1 mm
MOE430B:1446551_AT 5'-3' exoribonuclease 1 (Xrn1), mRNA mm
MOUSE430_2:1446551_AT 5'-3' exoribonuclease 1 (Xrn1), mRNA mm
MG-U74AV2:101231_AT 5'-3' exoribonuclease 1 (Xrn1), mRNA mm
MG-U74CV2:133241_AT 5'-3' exoribonuclease 1 (Xrn1), mRNA mm
MOE430B:1437475_AT 5'-3' exoribonuclease 1 (Xrn1), mRNA mm
MOUSE430_2:1437475_AT 5'-3' exoribonuclease 1 (Xrn1), mRNA mm
MOE430B:1442141_AT 5'-3' exoribonuclease 1 (Xrn1), mRNA mm
MOUSE430_2:1442141_AT 5'-3' exoribonuclease 1 (Xrn1), mRNA mm
MOE430B:1442399_AT 5'-3' exoribonuclease 1 (Xrn1), mRNA mm
MOUSE430_2:1442399_AT 5'-3' exoribonuclease 1 (Xrn1), mRNA mm
MOE430A:1446695_AT 5'-3' exoribonuclease 1 (Xrn1), mRNA mm
MOUSE430A_2:1446695_AT 5'-3' exoribonuclease 1 (Xrn1), mRNA mm
MOUSE430_2:1446695_AT 5'-3' exoribonuclease 1 (Xrn1), mRNA mm
MG-U74BV2:163560_AT 5'-3' exoribonuclease 1 (Xrn1), mRNA mm
MU19KSUBA:TC22118_AT 5'-3' exoribonuclease 1 (Xrn1), mRNA mm
MU19KSUBB:TC29109_AT 5'-3' exoribonuclease 1 (Xrn1), mRNA mm
MU11KSUBA:C78334_RC_AT 5'-3' exoribonuclease 1 (Xrn1), mRNA mm
RG-U34B:RC_AA998855_AT similar to 5-3 exonuclease (predicted) rn
RAE230B:1391107_AT similar to 5-3 exonuclease (predicted) rn
RAT230_2:1391107_AT similar to 5-3 exonuclease (predicted) rn
RAE230B:1385254_AT similar to 5-3 exonuclease (predicted) rn
RAT230_2:1385254_AT similar to 5-3 exonuclease (predicted) rn
RAE230B:1378759_AT Similar to 5-3 exonuclease (predicted) rn
RAT230_2:1378759_AT Similar to 5-3 exonuclease (predicted) rn
RAE230B:1381653_AT Similar to 5-3 exonuclease (predicted) rn
RAT230_2:1381653_AT Similar to 5-3 exonuclease (predicted) rn
YEAST_2:1774600_AT 5'-3' exonuclease involved in mRNA decay, evolutionarily conserved component of cytoplasmic processing (P) bodies, plays a role in microtubule-mediated processes, filamentous growth, and ribosomal RNA maturation Sc
Gene Ontology
GO Cellular Component (view graph)
ID Description Evidence Links
5634 nucleus inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
4527 exonuclease activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAC35856 Hypothetical protein Y39G8C.1 [Caenorhabditis elegans] ref|NP_496945.2| XRN (mouse/S. cerevisiae) ribonuclease related family member (xrn-1) [Caenorhabditis elegans] 0.0
blast T26774 hypothetical protein Y39G8C.b - Caenorhabditis elegans 0.0
blast CAE73396 Hypothetical protein CBG20837 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR004859 EMBL-EBI Putative 5-3 exonuclease domain 2.3E-78
Pfam IPR004859 EMBL-EBI Putative 5-3 exonuclease domain 1.6E-103
Pfam IPR004859 EMBL-EBI Putative 5-3 exonuclease domain 3.5E-40
Pfam IPR004859 EMBL-EBI Putative 5-3 exonuclease domain 1.0E-126
Trans Membrane
ID Number Of Domains Domain Boundaries
SNAP00000006825 2 193-215,242-264
Sequence
Target Sequence 
>C. ELEGANS:176726_AT
agggtcagcagatatcgtcgtcagactcgaaaatcaactgtggcctggcgttgaaatatt
ctcggagggatctatgtgtggcggattatacggatcgaacggagcacacgaatcagcgag
gcgtcacgaataaagtgtggttttacacgaatttggcgacccgtctagtgtcggaatata
ggcgaaagttcccggatgtctggaaatatttggaaacaatcgggcttacgcagcaagacg
atgtctactatacagaggacatttggagcaatgaaaagacgcgggagaagcgattcggcg
agctcagcgagtttctaggcggcctaccgagcctggaggccgagcagctcaagtgtggaa
cagtttacgcggatcgccagctgattacggagattgagatgattctcgcggagcctgatg
agaagaagccggtgatgaataagtatatgatggcgcctggtgcacttttccgttatgagc
ttta

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AGGGTCAGCAGATATCGTCGTCAGA 281 57 3120 Antisense
TGTGGCCTGGCGTTGAAATATTCTC 459 555 3158 Antisense
GGAGCACACGAATCAGCGAGGCGTC 319 519 3220 Antisense
TTTGGCGACCCGTCTAGTGTCGGAA 5 661 3271 Antisense
AGGCGAAAGTTCCCGGATGTCTGGA 476 53 3299 Antisense
GCCGAGCAGCTCAAGTGTGGAACAG 380 285 3458 Antisense
TGTGGAACAGTTTACGCGGATCGCC 149 555 3473 Antisense
CGGATCGCCAGCTGATTACGGAGAT 252 243 3489 Antisense
TGAGATGATTCTCGCGGAGCCTGAT 102 569 3514 Antisense
GTATATGATGGCGCCTGGTGCACTT 705 453 3562 Antisense
GTGCACTTTTCCGTTATGAGCTTTA 156 481 3579 Antisense
Sequence Source Affymetrix Proprietary Database