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[193792_s_at] ROP-1 ribonucleoprotein RO autoantigen

Description C12D8.11 /REP_DB=WormBase Gene ID /WP=CE15613 /GEN=rop-1 /TR=SW:Q27274 /GB=CAA16325.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=ROP-1 ribonucleoprotein RO autoantigen
Cluster 6grp_highest_10_10 > 11      6grp_high1_10_10 > 01      4grp_highest_8_8 > 34      4grp_high_8_8 > 57      6grp_highest_nonorm > 03      6grp_total > 14      4grp_total > 63      6grp_cgc > 30      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1845
1 2 3 4 range
A 2959
(3)
P 		1768.3
(-1.3)
P 		2291.6
(0.6)
P 		1285.7
(-3)
P 		1673
B 3042.5
(3)
P 		1859.4
(-0.9)
P 		2417.8
(0.9)
P 		1234.4
(-3)
P 		1808
C 2746.5
(3)
P 		1756.2
(-0.8)
P 		2263.1
(1.1)
P 		1197.1
(-3)
P 		1549
avr 2916
(3) 		1794.6
(-1) 		2324.2
(0.9) 		1239.1
(-3) 		1677

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2661
1 2 3 4 5 6 range
A 4347.9
(3)
P 		3453.2
(0.9)
P 		2780.5
(-0.7)
P 		3005.3
(-0.2)
P 		2093.6
(-2.3)
P 		1810.6
(-3)
P 		2537
B 3978.9
(3)
P 		3175.6
(0.9)
P 		2934.8
(0.2)
P 		2781.5
(-0.2)
P 		1913.8
(-2.5)
P 		1724.8
(-3)
P 		2254
C 3659.3
(3)
P 		3209.3
(1.6)
P 		3146.5
(1.4)
P 		3079.7
(1.2)
P 		2022.5
(-2)
P 		1687.3
(-3)
P 		1972
avr 3995.4
(3) 		3279.4
(1.1) 		2953.9
(0.2) 		2955.5
(0.2) 		2010
(-2.3) 		1740.9
(-3) 		2255
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 889
1 2 3 4 range
A 1077.4
(3)
P 		383.9
(-1.7)
P 		599.1
(-0.2)
P 		188.2
(-3)
P 		889
B 970.2
(3)
P 		459.2
(-1.3)
P 		560.3
(-0.5)
P 		263.1
(-3)
P 		707
C 909.2
(3)
P 		504.9
(-0.4)
P 		788.8
(2)
P 		201.9
(-3)
P 		707
avr 985.6
(3) 		449.3
(-1.2) 		649.4
(0.4) 		217.7
(-3) 		768

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 944
1 2 3 4 5 6 range
A 801.5
(-0.3)
P 		1228.1
(3)
P 		605.5
(-1.7)
P 		762.2
(-0.6)
P 		631.8
(-1.5)
P 		440.8
(-3)
P 		787
B 1384.5
(3)
P 		1057
(0.3)
P 		712.7
(-2.4)
P 		736.7
(-2.2)
P 		777.5
(-1.9)
P 		643.2
(-3)
P 		741
C 1356.4
(3)
P 		979.3
(0.1)
P 		800.8
(-1.2)
P 		619.3
(-2.6)
P 		654.5
(-2.3)
P 		564.8
(-3)
P 		792
avr 1180.8
(3) 		1088.1
(2.1) 		706.3
(-1.5) 		706.1
(-1.5) 		687.9
(-1.7) 		549.6
(-3) 		631
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 193792_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.12134
Sequence Type Exemplar sequence
Representative Public ID C12D8.11 NCBI
Target Description C12D8.11 /REP_DB=WormBase Gene ID /WP=CE15613 /GEN=rop-1 /TR=SW:Q27274 /GB=CAA16325.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=ROP-1 ribonucleoprotein RO autoantigen
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_073237(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073237 NCBI Caenorhabditis elegans RO (Ro) ribonucleoProtein family member (rop-1) (rop-1) mRNA, complete cds. 11/11 None
C12D8.11.2 ENSEMBL cdna:known chromosome:CEL140:V:10255415:10257638:-1 gene:C12D8.11 11/11 None
C12D8.11.1 ENSEMBL cdna:known chromosome:CEL140:V:10255415:10257636:-1 gene:C12D8.11 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
chrV:10255496-10257628(-) 100.0 100.0
Public Domain and Genome References
Gene Title ROP-1 ribonucleoprotein RO autoantigen
Gene Symbol rop-1
Ensembl C12D8.11
Entrez Gene 179425 Entrez gene
SwissProt Q27274 EMBL-EBI
WormBase CE15613 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFA.17405.1.S1_S_AT similar to 60kD Ro/SSA autoantigen cfa
CHICKEN:GGA.11917.1.S1_AT TROVE domain family, member 2 gga
HG-U133_PLUS_2:210438_X_AT TROVE domain family, member 2 hs
HG-U133A_2:210438_X_AT TROVE domain family, member 2 hs
HG-U133A:210438_X_AT TROVE domain family, member 2 hs
HG-U95AV2:35294_AT TROVE domain family, member 2 hs
HG-U95AV2:35295_G_AT TROVE domain family, member 2 hs
HG-U95AV2:35293_AT TROVE domain family, member 2 hs
HU35KSUBC:RC_AA075182_AT TROVE domain family, member 2 hs
HU35KSUBD:RC_N23197_AT TROVE domain family, member 2 hs
HUGENEFL:M25077_AT TROVE domain family, member 2 hs
U133_X3P:HS.554.2.A2_3P_A_AT TROVE domain family, member 2 hs
U133_X3P:HS.554.2.A1_3P_A_AT TROVE domain family, member 2 hs
HG-U133A_2:212852_S_AT TROVE domain family, member 2 hs
HG-FOCUS:212852_S_AT TROVE domain family, member 2 hs
HG-U133_PLUS_2:212852_S_AT TROVE domain family, member 2 hs
HG-U133A:212852_S_AT TROVE domain family, member 2 hs
HG-U95D:75421_AT TROVE domain family, member 2 hs
HG-U133A:212839_S_AT TROVE domain family, member 2 hs
HG-U133A_2:212839_S_AT TROVE domain family, member 2 hs
HG-U133_PLUS_2:212839_S_AT TROVE domain family, member 2 hs
HG-U133_PLUS_2:207520_AT TROVE domain family, member 2 hs
HG-U133A_2:207520_AT TROVE domain family, member 2 hs
HG-U133A:207520_AT TROVE domain family, member 2 hs
HU35KSUBA:AA058376_AT TROVE domain family, member 2 hs
HU35KSUBC:RC_AA056731_AT TROVE domain family, member 2 hs
HU35KSUBC:RC_AA010352_AT TROVE domain family, member 2 hs
U133_X3P:HS.554.0.A2_3P_AT TROVE domain family, member 2 hs
U133_X3P:HS.288178.0.A1_3P_AT TROVE domain family, member 2 hs
HG-U133A_2:213027_AT TROVE domain family, member 2 hs
HG-U133_PLUS_2:213027_AT TROVE domain family, member 2 hs
HG-U133A:213027_AT TROVE domain family, member 2 hs
HG-U95B:48240_AT TROVE domain family, member 2 hs
HG-U95C:63263_AT TROVE domain family, member 2 hs
HU35KSUBB:RC_AA001416_AT TROVE domain family, member 2 hs
HU35KSUBD:RC_H09086_AT TROVE domain family, member 2 hs
MU11KSUBA:U66843_S_AT TROVE domain family, member 2 mm
MU11KSUBB:MSA.27709.0_S_AT TROVE domain family, member 2 mm
MG-U74AV2:92265_F_AT TROVE domain family, member 2 mm
MG-U74BV2:110225_AT TROVE domain family, member 2 mm
MG-U74BV2:105859_AT TROVE domain family, member 2 mm
MG-U74AV2:161416_R_AT TROVE domain family, member 2 mm
MOE430A:1423433_AT TROVE domain family, member 2 mm
MOUSE430A_2:1423433_AT TROVE domain family, member 2 mm
MOUSE430_2:1423433_AT TROVE domain family, member 2 mm
MOE430B:1436533_AT TROVE domain family, member 2 mm
MOUSE430_2:1436533_AT TROVE domain family, member 2 mm
MOE430B:1436534_AT TROVE domain family, member 2 mm
MOUSE430_2:1436534_AT TROVE domain family, member 2 mm
MOE430B:1436535_AT TROVE domain family, member 2 mm
MOUSE430_2:1436535_AT TROVE domain family, member 2 mm
RAE230B:1395722_AT Sjogren syndrome antigen A2 (predicted) rn
RAT230_2:1395722_AT Sjogren syndrome antigen A2 (predicted) rn
RAE230B:1378242_AT Sjogren syndrome antigen A2 (predicted) rn
RAT230_2:1378242_AT Sjogren syndrome antigen A2 (predicted) rn
Gene Ontology
GO Cellular Component (view graph)
ID Description Evidence Links
30529 ribonucleoprotein complex inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3723 RNA binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA16325 Hypothetical protein C12D8.11 [Caenorhabditis elegans] emb|CAA98241.1| Hypothetical protein C12D8.11 [Caenorhabditis elegans] ref|NP_505638.1| RO (Ro) ribonucleoProtein family member (rop-1) [Caenorhabditis elegans] sp|Q27274|RO60_CAEEL 60-kDa SS-A/Ro ribonucleoprotein homolog gb|AAC41575.1| Ro ribonucleoprotein autoantigen gb|AAA96949.1| ribonucleoprotein Ro autoantigen homolog prf||2204248A 60kD Ro autoantigen 0.0
blast CAE64775 Hypothetical protein CBG09566 [Caenorhabditis briggsae] 0.0
blast XP_536115 PREDICTED: similar to 60kD Ro/SSA autoantigen [Canis familiaris] 1.0E-100
Protein Domains
Database ID Description E-Value
Pfam IPR008858 EMBL-EBI TROVE 1.0E-126
Sequence
Target Sequence 
>C. ELEGANS:193792_S_AT
ttgtgacgcccttgaagctggcttctacaaggcattcgtgaatgcaccaccaactggaaa
acgatactgcttggctctcgatgtttctggtagcatgacctctcgtgtcagttcgtcacc
actctcatgccgtgaagctgctaccggaatgtctttgatcaaccttcacaatgaagccga
agttagatgtgtcgccttctgtgataagctcactgagcttccgtttactaaggattggaa
gatcggacaagttaatgactacgttaacaaccttgatttcggcagaacagattgtggcct
tccaatgacttgggcaacagaaaataatctcaagtttgatgtcttcattatctacaccga
caacgatacctgggctggagagattcatccattcgaagccatcaaaaagtatcgtgaagc
ttctggtattcatgacgcgaaggtcattgtgatggcaatgcaggcatatgactactcgat
tgccgatccatctgatgctggtatgctcgacattaccggattcgattcggctgtaccaca
gat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTGTGACGCCCTTGAAGCTGGCTTC 499 703 1371 Antisense
GAAGCTGGCTTCTACAAGGCATTCG 574 343 1384 Antisense
AAACGATACTGCTTGGCTCTCGATG 226 127 1429 Antisense
GCTGCTACCGGAATGTCTTTGATCA 241 297 1507 Antisense
GTGTCGCCTTCTGTGATAAGCTCAC 368 487 1559 Antisense
CTCACTGAGCTTCCGTTTACTAAGG 597 227 1579 Antisense
GTGGCCTTCCAATGACTTGGGCAAC 76 489 1664 Antisense
TACACCGACAACGATACCTGGGCTG 490 641 1723 Antisense
TATGACTACTCGATTGCCGATCCAT 67 655 1837 Antisense
GATCCATCTGATGCTGGTATGCTCG 651 415 1855 Antisense
GATTCGATTCGGCTGTACCACAGAT 571 431 1889 Antisense
Sequence Source Affymetrix Proprietary Database