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[194027_s_at] Uncharacterized protein family UPF0034, Double-stranded RNA binding motif

Description Y54E5A.6 /REP_DB=WormBase Gene ID /WP=CE20317 /TR=Q9XWJ9 /GB=CAA21662.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=Uncharacterized protein family UPF0034, Double-stranded RNA binding motif
Cluster 6grp_high1_10_10 > 73      6grp_total > 74      4grp_total > 08      6grp_high1_sub > 03_04      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 252
1 2 3 4 range
A 183.6
(-3)
P 		259.8
(-0.1)
A 		197.5
(-2.5)
M 		343.4
(3)
P 		160
B 195.3
(-2.8)
P 		190.2
(-3)
A 		286.9
(0.5)
P 		353.9
(3)
P 		164
C 150.6
(-1.7)
P 		102.1
(-3)
A 		171.8
(-1.1)
P 		322.7
(3)
P 		221
avr 176.5
(-3) 		184
(-2.7) 		218.7
(-1.5) 		340
(3) 		164

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 205
1 2 3 4 5 6 range
A 162
(-0.6)
M 		126.7
(-2.7)
P 		224.1
(3)
P 		183.1
(0.6)
P 		120.9
(-3)
P 		155.1
(-1)
P 		103
B 163
(-3)
P 		169.4
(-2.4)
P 		207.3
(1.5)
M 		190.6
(-0.2)
P 		191.4
(-0.1)
P 		222.5
(3)
P 		60
C 76.5
(-3)
A 		136
(-1.3)
P 		168.3
(-0.3)
P 		281.5
(3)
P 		148.5
(-0.9)
P 		214.6
(1)
P 		205
avr 133.8
(-3) 		144
(-2.3) 		199.9
(1.7) 		218.4
(3) 		153.6
(-1.6) 		197.4
(1.5) 		85
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 46
1 2 3 4 range
A 66.8
(3)
P 		56.4
(-0.8)
A 		51.6
(-2.5)
M 		50.3
(-3)
P 		17
B 62.3
(0.2)
P 		47
(-3)
A 		66.5
(1.1)
P 		75.4
(3)
P 		28
C 49.9
(1)
P 		29.3
(-3)
A 		59.9
(3)
P 		54.4
(1.9)
P 		31
avr 59.7
(2.9) 		44.2
(-3) 		59.3
(2.7) 		60
(3) 		16

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 55
1 2 3 4 5 6 range
A 29.9
(-3)
M 		45.1
(1.8)
P 		48.8
(3)
P 		46.4
(2.2)
P 		36.5
(-0.9)
P 		37.8
(-0.5)
P 		19
B 56.7
(-1.8)
P 		56.4
(-1.9)
P 		50.3
(-3)
M 		50.5
(-3)
P 		77.8
(2)
P 		83
(3)
P 		33
C 28.3
(-3)
A 		41.5
(-1.2)
P 		42.8
(-1)
P 		56.6
(0.9)
P 		48
(-0.3)
P 		71.8
(3)
P 		44
avr 38.3
(-3) 		47.7
(-0.8) 		47.3
(-0.9) 		51.2
(-0) 		54.1
(0.7) 		64.2
(3) 		26
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 194027_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.1341
Sequence Type Exemplar sequence
Representative Public ID Y54E5A.6 NCBI
Target Description Y54E5A.6 /REP_DB=WormBase Gene ID /WP=CE20317 /TR=Q9XWJ9 /GB=CAA21662.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=Uncharacterized protein family UPF0034, Double-stranded RNA binding motif
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_061153(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_061153 NCBI Caenorhabditis elegans Y54E5A.6 (Y54E5A.6) mRNA, complete cds. 11/11 None
SNAP00000041549 ENSEMBL cdna:SNAP chromosome:CEL140:I:14716407:14723731:-1 11/11 None
GENEFINDER00000041552 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:14716407:14719047:-1 11/11 None
Y54E5A.6 ENSEMBL cdna:known chromosome:CEL140:I:14716407:14719047:-1 gene:Y54E5A.6 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:14716337-14718978(-) 100.0 100.0
Public Domain and Genome References
Gene Title Uncharacterized protein family UPF0034, Double-stranded RNA binding motif
Ensembl Y54E5A.6
Entrez Gene 173331 Entrez gene
SwissProt Q9XWJ9 EMBL-EBI
WormBase CE20317 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:252267_AT nitrogen regulation family protein at
CANINE_2:CFAAFFX.31122.1.S1_AT similar to dihydrouridine synthase 2-like (SMM1, S. cerevisiae) cfa
DROSOPHILA_2:1637823_AT dm
DROSGENOME1:141725_AT dm
CHICKEN:GGA.6313.1.S1_S_AT similar to hypothetical protein FLJ20399 gga
CHICKEN:GGAAFFX.25847.1.S1_AT similar to hypothetical protein FLJ20399 gga
HG-U133_PLUS_2:219486_AT dihydrouridine synthase 2-like (SMM1, S. cerevisiae) hs
HG-U133A:219486_AT dihydrouridine synthase 2-like (SMM1, S. cerevisiae) hs
HG-U133A_2:219486_AT dihydrouridine synthase 2-like (SMM1, S. cerevisiae) hs
HU35KSUBB:RC_T81075_AT dihydrouridine synthase 2-like (SMM1, S. cerevisiae) hs
U133_X3P:G8923373_3P_S_AT dihydrouridine synthase 2-like (SMM1, S. cerevisiae) hs
U133_X3P:G8923373_3P_AT dihydrouridine synthase 2-like (SMM1, S. cerevisiae) hs
HG-U133A_2:47105_AT dihydrouridine synthase 2-like (SMM1, S. cerevisiae) hs
HG-U133_PLUS_2:47105_AT dihydrouridine synthase 2-like (SMM1, S. cerevisiae) hs
HG-U133A:47105_AT dihydrouridine synthase 2-like (SMM1, S. cerevisiae) hs
HG-U95B:47105_AT dihydrouridine synthase 2-like (SMM1, S. cerevisiae) hs
HG-U95D:84056_AT Dipeptidase 2 hs
MOUSE430_2:1447751_X_AT dihydrouridine synthase 2-like (SMM1, S. cerevisiae) mm
MOE430B:1447751_X_AT dihydrouridine synthase 2-like (SMM1, S. cerevisiae) mm
MG-U74BV2:115097_AT dihydrouridine synthase 2-like (SMM1, S. cerevisiae) mm
MG-U74CV2:169392_AT dihydrouridine synthase 2-like (SMM1, S. cerevisiae) mm
MOE430B:1452687_AT dihydrouridine synthase 2-like (SMM1, S. cerevisiae) mm
MOUSE430_2:1452687_AT dihydrouridine synthase 2-like (SMM1, S. cerevisiae) mm
RG-U34B:RC_AI029709_AT similar to hypothetical protein FLJ20399 (predicted) rn
RAE230A:1389595_AT similar to hypothetical protein FLJ20399 (predicted) rn
RAT230_2:1389595_AT similar to hypothetical protein FLJ20399 (predicted) rn
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
8033 tRNA processing inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5622 intracellular inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3725 double-stranded RNA binding inferred from electronic annotation QuickGO AmiGO
16491 oxidoreductase activity inferred from electronic annotation QuickGO AmiGO
50660 FAD binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA21662 Hypothetical protein Y54E5A.6 [Caenorhabditis elegans] ref|NP_493554.1| Y54E5A.6 [Caenorhabditis elegans] 0.0
blast CAE72565 Hypothetical protein CBG19749 [Caenorhabditis briggsae] 0.0
blast NP_060273 dihydrouridine synthase 2-like (SMM1, S. cerevisiae) [Homo sapiens] gb|AAH06527.1| Dihydrouridine synthase 2-like (SMM1, S. cerevisiae) [Homo sapiens] dbj|BAE07219.1| up-regulated in lung cancer 8 [Homo sapiens] dbj|BAA91143.1| unnamed protein product [Homo sapiens] sp|Q9NX74|DUS2L_HUMAN tRNA-dihydrouridine synthase 2-like 3.0E-85
Protein Domains
Database ID Description E-Value
Pfam IPR001269 EMBL-EBI Protein of unknown function UPF0034 7.8E-41
Pfam IPR001159 EMBL-EBI Double-stranded RNA binding (DsRBD) domain 1.1E-7
Pfam IPR001269 EMBL-EBI Protein of unknown function UPF0034 7.8E-41
Pfam IPR001159 EMBL-EBI Double-stranded RNA binding (DsRBD) domain 1.1E-7
Sequence
Target Sequence 
>C. ELEGANS:194027_S_AT
tcaactccgtcaattttccgtcgggaaggatgtttagataaatacgaagatattcgaaat
tttctggaactcgcgtgccaatacgacgagtcttacactatgacaaaatacgttgttcaa
cggattctgggcgccgatcaggaatatgatccacgtggaaaggcgacggttgccgccgga
agtgtactgcagatttgtaaagcgtttggaatggaggatgtatatgataaatggcgagat
gaacgaaagaagaaacagagtaagaagcgagctcgtgttgacgatgacggtgtttataat
attgaagtctcatttccattaaaacgcctgaaaaactcggtcggcttctcgccaacgccc
aaaatggtgcttcacgactattgtgtggagacgaagatcccaaaagccacgtatgaggtc
gtaaaacgagatgataagcgattcgtggcgacggcgtgtattggtgacaagaaatatcga
tcaggaattggacaaccgaatttaagaatggctgagcaggtcgccgcgctcgcagcctta
catggaatgaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCAACTCCGTCAATTTTCCGTCGGG 439 629 733 Antisense
GAAATTTTCTGGAACTCGCGTGCCA 549 363 788 Antisense
TCGCGTGCCAATACGACGAGTCTTA 401 595 803 Antisense
CGTTGTTCAACGGATTCTGGGCGCC 440 247 843 Antisense
TGGAAAGGCGACGGTTGCCGCCGGA 110 545 888 Antisense
GCCGCCGGAAGTGTACTGCAGATTT 512 285 904 Antisense
TCTCGCCAACGCCCAAAATGGTGCT 297 611 1079 Antisense
GAAGATCCCAAAAGCCACGTATGAG 700 337 1125 Antisense
GATAAGCGATTCGTGGCGACGGCGT 171 423 1165 Antisense
AAGAATGGCTGAGCAGGTCGCCGCG 412 151 1236 Antisense
CGCTCGCAGCCTTACATGGAATGAA 457 255 1259 Antisense
Sequence Source Affymetrix Proprietary Database