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[173636_at]

Description CEK034AXR_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=C01B7.6 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D33642 /WB_GENE_ID=C01B7.6 /WP=CE06730 /CHR=5 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk34a10 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 33      6grp_high1_10_10 > 32      4grp_highest_8_8 > 54      4grp_high_8_8 > 09      6grp_highest_nonorm > 32      6grp_total > 31      4grp_total > 23      6grp_highest_sub > 02      6grp_cgc > 72      6grp_high1_sub > 02_03      6grp_cgc_sub > 02      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1275
1 2 3 4 range
A 1596.3
(3)
P 		544.3
(-2.7)
P 		485.8
(-3)
P 		1506.9
(2.5)
P 		1111
B 1558.7
(3)
P 		725.5
(-1.7)
P 		494.3
(-3)
P 		1370
(1.9)
P 		1064
C 1761.1
(3)
P 		690
(-2.7)
P 		634.3
(-3)
P 		1460.8
(1.4)
P 		1127
avr 1638.7
(3) 		653.3
(-2.4) 		538.1
(-3) 		1445.9
(1.9) 		1101

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1633
1 2 3 4 5 6 range
A 1318.9
(2.4)
P 		1404.2
(3)
P 		996.6
(-0.1)
P 		784.4
(-1.7)
P 		1161.9
(1.2)
P 		609.7
(-3)
P 		795
B 1531.8
(0.2)
P 		1402.2
(-0.3)
P 		2242.7
(3)
P 		1587
(0.4)
P 		736
(-3)
P 		995.4
(-2)
P 		1507
C 944.4
(-1.6)
P 		1842.7
(3)
P 		994.2
(-1.4)
P 		1395.3
(0.7)
P 		680
(-3)
P 		1040.8
(-1.1)
P 		1163
avr 1265
(0.5) 		1549.7
(3) 		1411.2
(1.8) 		1255.6
(0.4) 		859.3
(-3) 		882
(-2.8) 		690
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 469
1 2 3 4 range
A 581.2
(3)
P 		118.2
(-3)
P 		127
(-2.9)
P 		220.6
(-1.7)
P 		463
B 497.1
(3)
P 		179.2
(-2)
P 		114.5
(-3)
P 		292
(-0.2)
P 		383
C 583
(3)
P 		198.4
(-3)
P 		221.1
(-2.6)
P 		246.3
(-2.3)
P 		385
avr 553.8
(3) 		165.3
(-2.8) 		154.2
(-3) 		253
(-1.5) 		400

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 414
1 2 3 4 5 6 range
A 243.1
(-1.4)
P 		499.4
(3)
P 		217
(-1.8)
P 		198.9
(-2.1)
P 		350.6
(0.5)
P 		148.4
(-3)
P 		351
B 533
(2.7)
P 		466.7
(1.1)
P 		544.6
(3)
P 		420.3
(-0)
P 		299
(-3)
P 		371.2
(-1.2)
P 		246
C 350.1
(-0.7)
P 		562.3
(3)
P 		253
(-2.4)
P 		280.6
(-1.9)
P 		220
(-3)
P 		348.4
(-0.7)
P 		342
avr 375.4
(-0.7) 		509.5
(3) 		338.2
(-1.7) 		299.9
(-2.7) 		289.9
(-3) 		289.3
(-3) 		220
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173636_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.25240
Sequence Type Exemplar sequence
Representative Public ID CEK034AXR NCBI
Target Description CEK034AXR_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=C01B7.6 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D33642 /WB_GENE_ID=C01B7.6 /WP=CE06730 /CHR=5 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk34a10 : 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_072866(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_072866 NCBI Caenorhabditis elegans Regulator of Presynaptic Morphology family member (rpm-1) (rpm-1) mRNA, complete cds. 11/11 None
C01B7.6 ENSEMBL cdna:known chromosome:CEL140:V:8808003:8822542:-1 gene:C01B7.6 11/11 A 
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:8808014-8822544(-) 99.81 100.0
Public Domain and Genome References
Gene Title
Gene Symbol rpm-1
Ensembl C01B7.6
Entrez Gene 179259 Entrez gene
SwissProt Q17551 EMBL-EBI
WormBase CE06730 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1606157_AT similar to pam, highwire, rpm 1 cfa
CANINE:1603510_AT similar to pam, highwire, rpm 1 cfa
CANINE:1597969_AT similar to pam, highwire, rpm 1 cfa
CANINE:1591626_AT similar to pam, highwire, rpm 1 cfa
CANINE_2:CFA.16375.1.S1_AT similar to pam, highwire, rpm 1 cfa
CANINE_2:CFA.9716.1.A1_S_AT similar to pam, highwire, rpm 1 cfa
CANINE_2:CFAAFFX.8673.1.S1_S_AT similar to pam, highwire, rpm 1 cfa
CANINE_2:CFAAFFX.8688.1.S1_S_AT similar to pam, highwire, rpm 1 cfa
DROSOPHILA_2:1632637_AT highwire dm
DROSGENOME1:145096_AT highwire dm
DROSGENOME1:145093_AT highwire dm
CHICKEN:GGA.11563.1.S1_S_AT MYC binding protein 2 gga
CHICKEN:GGA.11616.1.S1_AT MYC binding protein 2 gga
CHICKEN:GGA.16723.1.S1_AT MYC binding protein 2 gga
CHICKEN:GGAAFFX.25128.1.S1_AT MYC binding protein 2 gga
HG-U133A:201960_S_AT MYC binding protein 2 hs
HG-U133_PLUS_2:201960_S_AT MYC binding protein 2 hs
HG-U133A_2:201960_S_AT MYC binding protein 2 hs
HU35KSUBA:RC_AA350690_AT MYC binding protein 2 hs
HU35KSUBC:RC_N49728_AT MYC binding protein 2 hs
HU35KSUBC:RC_H21386_AT MYC binding protein 2 hs
U133_X3P:G7662379_3P_A_AT MYC binding protein 2 hs
U133_X3P:HS2.396417.1.S1_3P_S_AT MYC binding protein 2 hs
U133_X3P:HS.151411.0.S1_3P_A_AT MYC binding protein 2 hs
HG-U133_PLUS_2:1557370_S_AT MYC binding protein 2 hs
HG-U133A_2:201959_S_AT MYC binding protein 2 hs
HG-U133_PLUS_2:201959_S_AT MYC binding protein 2 hs
HG-U133A:201959_S_AT MYC binding protein 2 hs
HG-U95AV2:39777_AT MYC binding protein 2 hs
HG-U95C:58721_I_AT MYC binding protein 2 hs
HG-U95C:58722_R_AT MYC binding protein 2 hs
HU35KSUBD:RC_Z40889_AT MYC binding protein 2 hs
MOE430A:1434937_AT pam, highwire, rpm 1 mm
MOUSE430A_2:1434937_AT pam, highwire, rpm 1 mm
MOUSE430_2:1434937_AT pam, highwire, rpm 1 mm
MU11KSUBA:AA189534_F_AT pam, highwire, rpm 1 mm
MG-U74AV2:93424_AT pam, highwire, rpm 1 mm
MG-U74BV2:114532_AT pam, highwire, rpm 1 mm
MG-U74BV2:109988_AT pam, highwire, rpm 1 mm
MOE430B:1454900_S_AT pam, highwire, rpm 1 mm
MOUSE430_2:1454900_S_AT pam, highwire, rpm 1 mm
MOE430B:1434274_AT pam, highwire, rpm 1 mm
MOUSE430_2:1434274_AT pam, highwire, rpm 1 mm
MOE430B:1458870_X_AT pam, highwire, rpm 1 mm
MOUSE430_2:1458870_X_AT pam, highwire, rpm 1 mm
MOE430B:1445340_AT pam, highwire, rpm 1 mm
MOUSE430_2:1445340_AT pam, highwire, rpm 1 mm
MOE430B:1447150_AT pam, highwire, rpm 1 mm
MOUSE430_2:1447150_AT pam, highwire, rpm 1 mm
MG-U74CV2:129117_AT Pam, highwire, rpm 1 (Phr1), mRNA mm
MOUSE430_2:1442858_AT Pam, highwire, rpm 1 (Phr1), mRNA mm
MOE430B:1442858_AT Pam, highwire, rpm 1 (Phr1), mRNA mm
MOE430B:1456715_AT Pam, highwire, rpm 1 (Phr1), mRNA mm
MOUSE430_2:1456715_AT Pam, highwire, rpm 1 (Phr1), mRNA mm
MOE430B:1457865_AT Pam, highwire, rpm 1 (Phr1), mRNA mm
MOUSE430_2:1457865_AT Pam, highwire, rpm 1 (Phr1), mRNA mm
MU19KSUBA:TC25060_AT Pam, highwire, rpm 1 (Phr1), mRNA mm
MU19KSUBA:TC25060_G_AT Pam, highwire, rpm 1 (Phr1), mRNA mm
MU19KSUBC:TC38522_AT Pam, highwire, rpm 1 (Phr1), mRNA mm
RG-U34A:RC_AA800029_AT pam, highwire, rpm 1 (predicted) rn
RAE230A:1390423_AT pam, highwire, rpm 1 (predicted) rn
RAT230_2:1390423_AT pam, highwire, rpm 1 (predicted) rn
RAE230A:1372863_AT pam, highwire, rpm 1 (predicted) rn
RAT230_2:1372863_AT pam, highwire, rpm 1 (predicted) rn
RAE230B:1397192_AT pam, highwire, rpm 1 (predicted) rn
RAT230_2:1397192_AT pam, highwire, rpm 1 (predicted) rn
Gene Ontology
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
8270 zinc ion binding inferred from electronic annotation QuickGO AmiGO
16787 hydrolase activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAA96117 Regulator of presynaptic morphology protein 1 [Caenorhabditis elegans] ref|NP_505267.1| Regulator of Presynaptic Morphology family member (rpm-1) [Caenorhabditis elegans] sp|Q17551|RPM1_CAEEL Ubiquitin ligase protein rpm-1 (Pam/highwire/rpm-1 protein) (Regulator of presynaptic morphology protein 1) (Synapse defective protein 3) 0.0
blast CAE57746 Hypothetical protein CBG00759 [Caenorhabditis briggsae] 0.0
blast AAK84508 Hypothetical protein F07B7.12 [Caenorhabditis elegans] ref|NP_505281.1| F07B7.12 [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
scop a.4.5.SCF ubiquitin ligase complex WHB domain All alpha proteins; DNA/RNA-binding 3-helical bundle; "Winged helix" DNA-binding domain; SCF ubiquitin ligase complex WHB domain 0.829999983310699
Pfam IPR000408 EMBL-EBI Regulator of chromosome condensation, RCC1 2.3E-7
Pfam IPR000315 EMBL-EBI Zn-finger, B-box 3.9E-11
Sequence
Target Sequence 
>C. ELEGANS:173636_AT
agtactttttgattcataattttatttttaaatctatccggtaaagcctcttatagcagt
cagtctttctgaattgtatcaaatgttcaaatagaaattattccctattgcctctgttca
gtacaaattgatctctctgtcttaccatttccaaaaatttattttttaaaaattgaccac
gggttgcttttagtgttgttttgattt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AGTACTTTTTGATTCATAATTTTAT 187 59 11303 Antisense
AAATCTATCCGGTAAAGCCTCTTAT 305 117 11332 Antisense
AGCCTCTTATAGCAGTCAGTCTTTC 666 83 11347 Antisense
GCAGTCAGTCTTTCTGAATTGTATC 525 311 11358 Antisense
AGAAATTATTCCCTATTGCCTCTGT 172 73 11395 Antisense
TCCCTATTGCCTCTGTTCAGTACAA 115 599 11404 Antisense
ATTGCCTCTGTTCAGTACAAATTGA 384 7 11409 Antisense
TACAAATTGATCTCTCTGTCTTACC 316 643 11424 Antisense
CTCTCTGTCTTACCATTTCCAAAAA 289 231 11435 Antisense
AATTGACCACGGGTTGCTTTTAGTG 248 175 11473 Antisense
GTTGCTTTTAGTGTTGTTTTGATTT 112 439 11485 Antisense
Sequence Source Affymetrix Proprietary Database