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[173655_s_at]

Description CEK009BYR /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=T22D1.9 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D27396 /WB_GENE_ID=T22D1.9 /WP=CE17253 /CHR=4 /FEA=Genomic Cluster /GEN=rpn-1 /DEF=C.elegans cDNA clone yk9b11 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 71      6grp_high1_10_10 > 28      4grp_highest_8_8 > 02      4grp_high_8_8 > 46      6grp_highest_nonorm > 57      6grp_total > 18      4grp_total > 49      6grp_highest_sub > De      6grp_cgc > 13      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_total_sub > Decrease      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1452
1 2 3 4 range
A 2636.8
(-3)
P 		3573.5
(3)
P 		3571.6
(3)
P 		2704.8
(-2.6)
P 		937
B 3020.1
(-1.7)
P 		3663.3
(2.1)
P 		3819.6
(3)
P 		2801.6
(-3)
P 		1018
C 2367.7
(-3)
P 		3564.8
(3)
P 		3360.4
(2)
P 		2487.9
(-2.4)
P 		1197
avr 2674.9
(-2.9) 		3600.5
(3) 		3583.9
(2.9) 		2664.8
(-3) 		936

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1306
1 2 3 4 5 6 range
A 3426.4
(3)
P 		3030.3
(1.2)
P 		2120.7
(-3)
P 		2883.9
(0.5)
P 		2737.8
(-0.2)
P 		3089.8
(1.5)
P 		1306
B 2799.6
(3)
P 		2754.4
(2.3)
P 		2441
(-2.9)
P 		2762.9
(2.4)
P 		2432.5
(-3)
P 		2733.3
(1.9)
P 		367
C 2810.2
(0.7)
P 		2593.4
(-0.8)
P 		3138.4
(3)
P 		2341.7
(-2.6)
P 		2780
(0.5)
P 		2286
(-3)
P 		852
avr 3012.1
(3) 		2792.7
(0) 		2566.7
(-3) 		2662.8
(-1.7) 		2650.1
(-1.9) 		2703
(-1.2) 		445
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 775
1 2 3 4 range
A 960.1
(3)
P 		775.7
(1)
P 		933.7
(2.7)
P 		395.9
(-3)
P 		564
B 963.1
(3)
P 		904.7
(2)
P 		885.1
(1.7)
P 		597
(-3)
P 		366
C 783.8
(-0.1)
P 		1024.9
(1.8)
P 		1171.2
(3)
P 		419.5
(-3)
P 		752
avr 902.3
(1.9) 		901.8
(1.9) 		996.7
(3) 		470.8
(-3) 		526

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 616
1 2 3 4 5 6 range
A 631.6
(-1.3)
P 		1077.7
(3)
P 		461.8
(-3)
P 		731.4
(-0.4)
P 		826.2
(0.5)
P 		752.3
(-0.2)
P 		616
B 974.1
(2.4)
P 		916.8
(1.6)
P 		592.8
(-3)
P 		731.8
(-1)
P 		988.3
(2.6)
P 		1019.2
(3)
P 		426
C 1041.6
(3)
P 		791.3
(0.4)
P 		798.8
(0.4)
P 		470.9
(-3)
P 		899.6
(1.5)
P 		765.3
(0.1)
P 		571
avr 882.4
(2.1) 		928.6
(3) 		617.8
(-3) 		644.7
(-2.5) 		904.7
(2.5) 		845.6
(1.4) 		311
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173655_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.24701
Sequence Type Exemplar sequence
Representative Public ID CEK009BYR NCBI
Target Description CEK009BYR /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=T22D1.9 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D27396 /WB_GENE_ID=T22D1.9 /WP=CE17253 /CHR=4 /FEA=Genomic Cluster /GEN=rpn-1 /DEF=C.elegans cDNA clone yk9b11 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_068663(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_068663 NCBI Caenorhabditis elegans proteasome Regulatory Particle, Non-ATPase-like family member (rpn-1) (rpn-1) mRNA, complete cds. 11/11 None
SNAP00000024009 ENSEMBL cdna:SNAP chromosome:CEL140:IV:6906620:6909888:-1 11/11 None
GENEFINDER00000024028 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:6906620:6909888:-1 11/11 None
T22D1.9.1 ENSEMBL cdna:known chromosome:CEL140:IV:6906416:6909897:-1 gene:T22D1.9 11/11 None
T22D1.9.2 ENSEMBL cdna:known chromosome:CEL140:IV:6906416:6909904:-1 gene:T22D1.9 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
chrIV:6906626-6909895(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol rpn-1
Ensembl T22D1.9
Entrez Gene 177455 Entrez gene
SwissProt Q9GZH5 EMBL-EBI
WormBase CE17253 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1584518_AT similar to proteasome 26S non-ATPase subunit 2 cfa
CANINE_2:CFA.11834.1.A1_AT similar to proteasome 26S non-ATPase subunit 2 cfa
CANINE_2:CFA.18196.1.S1_S_AT similar to proteasome 26S non-ATPase subunit 2 cfa
CANINE_2:CFAAFFX.19624.1.S1_S_AT similar to proteasome 26S non-ATPase subunit 2 cfa
DROSOPHILA_2:1637349_AT dm
DROSGENOME1:154052_AT dm
CHICKEN:GGA.1351.1.S1_S_AT proteasome (prosome, macropain) 26S subunit, non-ATPase, 2 gga
CHICKEN:GGAAFFX.12863.1.S1_AT proteasome (prosome, macropain) 26S subunit, non-ATPase, 2 gga
HG-U133_PLUS_2:200830_AT proteasome (prosome, macropain) 26S subunit, non-ATPase, 2 hs
HG-U133A:200830_AT proteasome (prosome, macropain) 26S subunit, non-ATPase, 2 hs
HG-FOCUS:200830_AT proteasome (prosome, macropain) 26S subunit, non-ATPase, 2 hs
HG-U133A_2:200830_AT proteasome (prosome, macropain) 26S subunit, non-ATPase, 2 hs
HG-U95AV2:1166_AT proteasome (prosome, macropain) 26S subunit, non-ATPase, 2 hs
HC-G110:1166_AT proteasome (prosome, macropain) 26S subunit, non-ATPase, 2 hs
HUGENEFL:D78151_AT proteasome (prosome, macropain) 26S subunit, non-ATPase, 2 hs
U133_X3P:G4506226_3P_AT proteasome (prosome, macropain) 26S subunit, non-ATPase, 2 hs
HG-U95D:67421_AT proteasome (prosome, macropain) 26S subunit, non-ATPase, 2 hs
MOUSE430_2:1443477_AT proteasome (prosome, macropain) 26S subunit, non-ATPase, 2 mm
MOE430B:1443477_AT proteasome (prosome, macropain) 26S subunit, non-ATPase, 2 mm
MOUSE430_2:1415831_AT proteasome (prosome, macropain) 26S subunit, non-ATPase, 2 mm
MOUSE430A_2:1415831_AT proteasome (prosome, macropain) 26S subunit, non-ATPase, 2 mm
MOE430A:1415831_AT proteasome (prosome, macropain) 26S subunit, non-ATPase, 2 mm
MU11KSUBA:AA254158_S_AT proteasome (prosome, macropain) 26S subunit, non-ATPase, 2 mm
MU19KSUBB:TC28212_AT Proteasome (prosome, macropain) 26S subunit, non-ATPase, 2, mRNA (cDNA clone MGC:36563 IMAGE:4982313) mm
RG-U34A:D37934_G_AT proteasome (prosome, macropain) 26S subunit, non-ATPase, 2 (predicted) rn
RG-U34C:RC_AI172107_AT proteasome (prosome, macropain) 26S subunit, non-ATPase, 2 (predicted) rn
RAE230A:1398858_AT proteasome (prosome, macropain) 26S subunit, non-ATPase, 2 (predicted) rn
RAT230_2:1398858_AT proteasome (prosome, macropain) 26S subunit, non-ATPase, 2 (predicted) rn
YEAST_2:1776734_AT Non-ATPase base subunit of the 19S regulatory particle of the 26S proteasome; may participate in the recognition of several ligands of the proteasome; contains a leucine-rich repeat (LRR) domain, a site for protein?protein interactions Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
74 regulation of progression through cell cycle inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAF98630 Proteasome regulatory particle, non-atpase-like protein 1 [Caenorhabditis elegans] ref|NP_501064.1| proteasome Regulatory Particle, Non-ATPase-like family member (rpn-1) [Caenorhabditis elegans] 0.0
blast CAE61757 Hypothetical protein CBG05716 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR002015 EMBL-EBI Proteasome/cyclosome, regulatory subunit 21.0
Pfam IPR002015 EMBL-EBI Proteasome/cyclosome, regulatory subunit 0.026
Pfam IPR002015 EMBL-EBI Proteasome/cyclosome, regulatory subunit 0.059
Pfam IPR002015 EMBL-EBI Proteasome/cyclosome, regulatory subunit 0.0017
Pfam IPR002015 EMBL-EBI Proteasome/cyclosome, regulatory subunit 5.2
Pfam IPR002015 EMBL-EBI Proteasome/cyclosome, regulatory subunit 2.2
Pfam IPR002015 EMBL-EBI Proteasome/cyclosome, regulatory subunit 3.3E-5
Sequence
Target Sequence 
>C. ELEGANS:173655_S_AT
ctctcacgattctgacgctgataccgctcacaatgctattttcgcgatgggacttgttgg
agcaggaacaaacaatgctcgtcttgttgctatgctccgaaacctggcttcttatcacta
caaggatcaagtttctctaatgctggtcagaattgcacaaggacttactcatctcggaaa
aggaacaatgacgttgaacccatggcattctgataggcaattattgtctccaagtgcttt
ggcttctctcctttcaatttgcttctctttcctcgacgccaataacacgattctcaacaa
ccgtcagcattacttgctctacacgttggtgctcgcaatgcaaccaagaatgcttaccac
actggtagaagacgaaatgaagcctggaagcttgaaacagttgaacgtttctgttcgtgt
tggtcaagccgttgacgttgttgctcaagccggaaagccaaagacaatcactggattcca
aactcatactacgccagtcttgcttgcccatggtgaacgtgccgagttggcgaacgatga
agatctctctgtgactccacatcttgaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CTCTCACGATTCTGACGCTGATACC 268 229 2329 Antisense
TGATACCGCTCACAATGCTATTTTC 667 563 2347 Antisense
TCGTCTTGTTGCTATGCTCCGAAAC 340 605 2407 Antisense
GCACAAGGACTTACTCATCTCGGAA 603 317 2483 Antisense
GACGTTGAACCCATGGCATTCTGAT 534 377 2518 Antisense
TTGTCTCCAAGTGCTTTGGCTTCTC 49 703 2552 Antisense
GATTCTCAACAACCGTCAGCATTAC 42 433 2617 Antisense
ATTACTTGCTCTACACGTTGGTGCT 83 13 2637 Antisense
CAAACTCATACTACGCCAGTCTTGC 21 193 2807 Antisense
TCTTGCTTGCCCATGGTGAACGTGC 136 619 2826 Antisense
TCTCTCTGTGACTCCACATCTTGAA 448 611 2872 Antisense
Sequence Source Affymetrix Proprietary Database