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[193821_at] UBQ-2 ubiquitin; 60S Ribosomal protein L40

Description ZK1010.1 /REP_DB=WormBase Gene ID /WP=CE15495 /GEN=ubq-2 /TR=Q9U1P3 /GB=CAB04967.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=UBQ-2 ubiquitin; 60S Ribosomal protein L40
Cluster 6grp_highest_10_10 > 12      6grp_high1_10_10 > 20      4grp_highest_8_8 > 07      4grp_high_8_8 > 21      6grp_highest_nonorm > 29      6grp_total > 33      4grp_total > 18      6grp_cgc > 20      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 11945
1 2 3 4 range
A 16523.3
(-3)
P 		22072.1
(-0.1)
P 		20210.7
(-1)
P 		27838
(3)
P 		11315
B 18241
(-0.6)
P 		17492.5
(-1.5)
P 		16187.5
(-3)
P 		21317
(3)
P 		5130
C 15893.3
(-3)
P 		18028.4
(-1.6)
P 		16889
(-2.3)
P 		24909.7
(3)
P 		9016
avr 16885.9
(-3) 		19197.7
(-1.2) 		17762.4
(-2.3) 		24688.2
(3) 		7802

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 6388
1 2 3 4 5 6 range
A 16466.7
(2.2)
P 		11798.3
(-2.2)
P 		17311.2
(3)
P 		12608.4
(-1.4)
P 		10923.3
(-3)
P 		11414.5
(-2.5)
P 		6388
B 14254.4
(3)
P 		13805.6
(2.2)
P 		12987.3
(0.7)
P 		12804.3
(0.3)
P 		11011.4
(-3)
P 		12741.9
(0.2)
P 		3243
C 12744.9
(-1.4)
P 		14006.8
(0.7)
P 		11795
(-3)
P 		15426.2
(3)
P 		12520.1
(-1.8)
P 		12812.7
(-1.3)
P 		3631
avr 14488.7
(3) 		13203.6
(0.4) 		14031.2
(2.1) 		13613
(1.3) 		11484.9
(-3) 		12323
(-1.3) 		3004
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2265
1 2 3 4 range
A 6016.1
(3)
P 		4791.3
(-0.8)
P 		5283.5
(0.7)
P 		4074.9
(-3)
P 		1941
B 5816.9
(3)
P 		4320.3
(-1.3)
P 		3751
(-3)
P 		4542.7
(-0.7)
P 		2066
C 5261.1
(0.8)
P 		5183.3
(0.5)
P 		5886.4
(3)
P 		4200.2
(-3)
P 		1686
avr 5698
(3) 		4765
(-0.9) 		4973.6
(-0) 		4272.6
(-3) 		1425

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2181
1 2 3 4 5 6 range
A 3035.5
(-1.9)
P 		4196.1
(3)
P 		3770
(1.2)
P 		3197.8
(-1.2)
P 		3296.2
(-0.8)
P 		2779.1
(-3)
P 		1417
B 4959.8
(3)
P 		4595.3
(1.8)
P 		3153.7
(-3)
P 		3391.4
(-2.2)
P 		4473.8
(1.4)
P 		4751.4
(2.3)
P 		1806
C 4724
(3)
P 		4273.9
(1.4)
P 		3002
(-3)
P 		3102.2
(-2.7)
P 		4051.3
(0.7)
P 		4289.2
(1.5)
P 		1722
avr 4239.8
(2.4) 		4355.1
(3) 		3308.6
(-2.6) 		3230.5
(-3) 		3940.4
(0.8) 		3939.9
(0.8) 		1125
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193821_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6422
Sequence Type Exemplar sequence
Representative Public ID ZK1010.1 NCBI
Target Description ZK1010.1 /REP_DB=WormBase Gene ID /WP=CE15495 /GEN=ubq-2 /TR=Q9U1P3 /GB=CAB04967.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=UBQ-2 ubiquitin; 60S Ribosomal protein L40
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_067294(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067294 NCBI Caenorhabditis elegans UBiQuitin family member (ubq-2) (ubq-2) mRNA, complete cds. 11/11 None
SNAP00000035098 ENSEMBL cdna:SNAP chromosome:CEL140:III:12977525:12982711:-1 11/11 None
GENEFINDER00000035111 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:12977525:12978037:-1 11/11 None
ZK1010.1.1 ENSEMBL cdna:known chromosome:CEL140:III:12977426:12978045:-1 gene:ZK1010.1 11/11 None
ZK1010.1.3 ENSEMBL cdna:known chromosome:CEL140:III:12977427:12978045:-1 gene:ZK1010.1 11/11 None
ZK1010.1.2 ENSEMBL cdna:known chromosome:CEL140:III:12977428:12978039:-1 gene:ZK1010.1 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
chrIII:12977520-12978033(-) 100.0 100.0
Public Domain and Genome References
Gene Title UBQ-2 ubiquitin; 60S Ribosomal protein L40
Gene Symbol ubq-2
Ensembl ZK1010.1
Entrez Gene 176718 Entrez gene
SwissProt P49632 EMBL-EBI
P14792 EMBL-EBI
WormBase CE15495 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:13129_F_AT ubiquitin extension protein 1 (UBQ1) / 60S ribosomal protein L40 (RPL40B) at
ATH1-121501:252056_AT ubiquitin extension protein 1 (UBQ1) / 60S ribosomal protein L40 (RPL40B) at
CANINE:1583145_AT ubiquitin A-52 residue ribosomal protein fusion product 1 cfa
CANINE_2:CFA.3552.1.S1_S_AT ubiquitin A-52 residue ribosomal protein fusion product 1 cfa
DROSOPHILA_2:1633277_AT Ribosomal protein L40 dm
DROSGENOME1:143397_AT Ribosomal protein L40 dm
HG-U133_PLUS_2:221700_S_AT ubiquitin A-52 residue ribosomal protein fusion product 1 hs
HG-U133A_2:221700_S_AT ubiquitin A-52 residue ribosomal protein fusion product 1 hs
HG-U133A:221700_S_AT ubiquitin A-52 residue ribosomal protein fusion product 1 hs
HU35KSUBC:RC_C13999_F_AT ubiquitin A-52 residue ribosomal protein fusion product 1 hs
HUGENEFL:X56997_RNA1_AT ubiquitin A-52 residue ribosomal protein fusion product 1 hs
U133_X3P:G13569611_3P_S_AT ubiquitin A-52 residue ribosomal protein fusion product 1 hs
HG-U95C:57828_AT ubiquitin A-52 residue ribosomal protein fusion product 1 hs
HG-U95E:92101_S_AT Ubiquitin A-52 residue ribosomal protein fusion product 1 hs
MOE430A:1456365_AT ubiquitin A-52 residue ribosomal protein fusion product 1 mm
MOUSE430A_2:1456365_AT ubiquitin A-52 residue ribosomal protein fusion product 1 mm
MOUSE430_2:1456365_AT ubiquitin A-52 residue ribosomal protein fusion product 1 mm
MOE430A:1452701_X_AT ubiquitin A-52 residue ribosomal protein fusion product 1 mm
MOUSE430A_2:1452701_X_AT ubiquitin A-52 residue ribosomal protein fusion product 1 mm
MOUSE430_2:1452701_X_AT ubiquitin A-52 residue ribosomal protein fusion product 1 mm
MOE430A:1434623_AT ubiquitin A-52 residue ribosomal protein fusion product 1 mm
MOUSE430A_2:1434623_AT ubiquitin A-52 residue ribosomal protein fusion product 1 mm
MOUSE430_2:1434623_AT ubiquitin A-52 residue ribosomal protein fusion product 1 mm
MOE430A:1416624_A_AT ubiquitin A-52 residue ribosomal protein fusion product 1 mm
MOUSE430A_2:1416624_A_AT ubiquitin A-52 residue ribosomal protein fusion product 1 mm
MOUSE430_2:1416624_A_AT ubiquitin A-52 residue ribosomal protein fusion product 1 mm
MG-U74BV2:106149_AT Ubiquitin A-52 residue ribosomal protein fusion product 1, mRNA (cDNA clone MGC:6675 IMAGE:3500484) mm
MG-U74BV2:106553_AT Ubiquitin A-52 residue ribosomal protein fusion product 1, mRNA (cDNA clone MGC:6675 IMAGE:3500484) mm
MOUSE430_2:1435389_AT Ubiquitin A-52 residue ribosomal protein fusion product 1, mRNA (cDNA clone MGC:6675 IMAGE:3500484) mm
MOE430B:1435389_AT Ubiquitin A-52 residue ribosomal protein fusion product 1, mRNA (cDNA clone MGC:6675 IMAGE:3500484) mm
MOE430B:1446652_AT Ubiquitin A-52 residue ribosomal protein fusion product 1, mRNA (cDNA clone MGC:6675 IMAGE:3500484) mm
MOUSE430_2:1446652_AT Ubiquitin A-52 residue ribosomal protein fusion product 1, mRNA (cDNA clone MGC:6675 IMAGE:3500484) mm
MG-U74AV2:95907_AT Ubiquitin A-52 residue ribosomal protein fusion product 1, mRNA (cDNA clone MGC:103123 IMAGE:6477007) mm
MU11KSUBA:AA285406_S_AT Ubiquitin A-52 residue ribosomal protein fusion product 1, mRNA (cDNA clone MGC:103123 IMAGE:6477007) mm
MU19KSUBC:TC35990_AT Ubiquitin A-52 residue ribosomal protein fusion product 1, mRNA (cDNA clone MGC:6675 IMAGE:3500484) mm
RG-U34A:RC_AA818888_AT ubiquitin A-52 residue ribosomal protein fusion product 1 rn
RAE230A:1398754_AT ubiquitin A-52 residue ribosomal protein fusion product 1 rn
RAT230_2:1398754_AT ubiquitin A-52 residue ribosomal protein fusion product 1 rn
YEAST_2:1777035_AT Fusion protein, identical to Rpl40Bp, that is cleaved to yield ubiquitin and a ribosomal protein of the large (60S) ribosomal subunit with similarity to rat L40; ubiquitin may facilitate assembly of the ribosomal protein into ribosomes Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6412 protein biosynthesis inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5622 intracellular inferred from electronic annotation QuickGO AmiGO
5840 ribosome inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3735 structural constituent of ribosome inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB04967 Hypothetical protein ZK1010.1 [Caenorhabditis elegans] ref|NP_499695.1| UBiQuitin family member (ubq-2) [Caenorhabditis elegans] gb|AAC37252.1| ubiquitin/ribosomal fusion protein pir||T27638 ubiquitin/ribosomal protein ZK1010.1 - Caenorhabditis elegans 2.0E-68
blast CAB04967 Hypothetical protein ZK1010.1 [Caenorhabditis elegans] ref|NP_499695.1| UBiQuitin family member (ubq-2) [Caenorhabditis elegans] gb|AAC37252.1| ubiquitin/ribosomal fusion protein pir||T27638 ubiquitin/ribosomal protein ZK1010.1 - Caenorhabditis elegans 3.0E-68
blast CAE69561 Hypothetical protein CBG15773 [Caenorhabditis briggsae] 6.0E-67
Protein Domains
Database ID Description E-Value
Pfam IPR000626 EMBL-EBI Ubiquitin 1.3E-42
Pfam IPR001975 EMBL-EBI Ribosomal protein L40e 2.4E-33
Pfam IPR000626 EMBL-EBI Ubiquitin 1.3E-42
Pfam IPR001975 EMBL-EBI Ribosomal protein L40e 2.4E-33
Sequence
Target Sequence 
>C. ELEGANS:193821_AT
tcaagactctgacgggtaagactattaccctcgaagtcgaggcttccgataccattgaga
atgtcaaggccaagatccaagacaaggagggaatcccaccagatcagcaaagattgatct
tcgccggaaagcaactcgaggatggacgtactctctccgactacaacatccaaaaggagt
ctactctccacttggtgctccgtcttcgtggaggaatcatcgagccatctctccgtcagc
tcgcccagaagtacaactgcgacaagcagatctgcagaaagtgctatgctcgtctcccac
cacgtgccagcaactgcagaaagaagaagtgcggacactccagc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCAAGACTCTGACGGGTAAGACTAT 579 629 26 Antisense
TGACGGGTAAGACTATTACCCTCGA 612 567 35 Antisense
TTACCCTCGAAGTCGAGGCTTCCGA 101 683 50 Antisense
GGCTTCCGATACCATTGAGAATGTC 692 537 66 Antisense
GGTGCTCCGTCTTCGTGGAGGAATC 632 499 219 Antisense
GGAGGAATCATCGAGCCATCTCTCC 662 515 235 Antisense
GTCAGCTCGCCCAGAAGTACAACTG 509 463 260 Antisense
ACAACTGCGACAAGCAGATCTGCAG 216 111 278 Antisense
TGCAGAAAGTGCTATGCTCGTCTCC 152 579 298 Antisense
ACCACGTGCCAGCAACTGCAGAAAG 282 85 324 Antisense
AAAGAAGAAGTGCGGACACTCCAGC 58 121 345 Antisense
Sequence Source Affymetrix Proprietary Database