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[174001_s_at] RNA-binding protein

Description CEXT00227 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=K07H8.10 /5_PRIME_EXT_DB=WormBase Gene ID /GB=M79690 /WB_GENE_ID=K07H8.10 /WP=CE18030 /CHR=4 /FEA=Genomic Cluster /DEF=RNA-binding protein; wEST00227 Mixed stage, Stratagene (cat. no. 937006) Caenorhabditis elegans cDNA clone CEMSC38, mRNA sequence.
Cluster 6grp_highest_10_10 > 94      6grp_high1_10_10 > 59      4grp_highest_8_8 > 25      4grp_high_8_8 > 59      6grp_highest_nonorm > 67      6grp_total > 39      4grp_total > 60      6grp_highest_sub > Cu      6grp_high1_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2974
1 2 3 4 range
A 3604.2
(2.7)
P 		2870.2
(1.2)
P 		3742.7
(3)
P 		805.2
(-3)
P 		2938
B 3084.3
(1.7)
P 		3405.2
(2.4)
P 		3688.7
(3)
P 		992.9
(-3)
P 		2696
C 3130.2
(1.8)
P 		3353.7
(2.3)
P 		3710.9
(3)
P 		769.2
(-3)
P 		2942
avr 3272.9
(2.1) 		3209.7
(1.9) 		3714.1
(3) 		855.8
(-3) 		2858

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1092
1 2 3 4 5 6 range
A 1442.8
(-1.2)
P 		1872.5
(1.1)
P 		1122.9
(-3)
P 		1365.1
(-1.7)
P 		1760.5
(0.5)
P 		2214.4
(3)
P 		1092
B 1928
(3)
P 		1808.6
(2.1)
P 		1138
(-3)
P 		1577.2
(0.3)
P 		1527.2
(-0)
P 		1878.9
(2.6)
P 		790
C 2195.7
(3)
P 		1707.9
(-0.4)
P 		1595.7
(-1.2)
P 		1336.8
(-3)
P 		1860.8
(0.7)
P 		1534.5
(-1.6)
P 		859
avr 1855.5
(2.8) 		1796.3
(2.2) 		1285.5
(-3) 		1426.4
(-1.6) 		1716.2
(1.4) 		1875.9
(3) 		590
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1194
1 2 3 4 range
A 1312.3
(3)
P 		623
(-0.5)
P 		978.4
(1.3)
P 		117.9
(-3)
P 		1194
B 983.6
(3)
P 		841
(1.9)
P 		854.8
(2)
P 		211.6
(-3)
P 		772
C 1036.2
(1.7)
P 		964.2
(1.3)
P 		1293.4
(3)
P 		129.7
(-3)
P 		1164
avr 1110.7
(3) 		809.4
(1.1) 		1042.2
(2.6) 		153.1
(-3) 		958

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 569
1 2 3 4 5 6 range
A 266
(-2.7)
P 		666
(3)
P 		244.5
(-3)
P 		346.2
(-1.6)
P 		531.2
(1.1)
P 		539.1
(1.2)
P 		422
B 670.9
(2.6)
P 		602
(1.6)
P 		276.3
(-3)
P 		417.7
(-1)
P 		620.5
(1.9)
P 		700.6
(3)
P 		424
C 813.8
(3)
P 		521.1
(-0.2)
P 		406.1
(-1.5)
P 		268.8
(-3)
P 		602.1
(0.7)
P 		513.7
(-0.3)
P 		545
avr 583.6
(2.7) 		596.4
(3) 		309
(-3) 		344.2
(-2.3) 		584.6
(2.8) 		584.5
(2.8) 		287
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 174001_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.24605
Sequence Type Exemplar sequence
Representative Public ID CEXT00227 NCBI
Target Description CEXT00227 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=K07H8.10 /5_PRIME_EXT_DB=WormBase Gene ID /GB=M79690 /WB_GENE_ID=K07H8.10 /WP=CE18030 /CHR=4 /FEA=Genomic Cluster /DEF=RNA-binding protein; wEST00227 Mixed stage, Stratagene (cat. no. 937006) Caenorhabditis elegans cDNA clone CEMSC38, mRNA sequence.
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_068990(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_068990 NCBI Caenorhabditis elegans K07H8.10 (K07H8.10) mRNA, complete cds. 11/11 None
SNAP00000006919 ENSEMBL cdna:SNAP chromosome:CEL140:IV:8286853:8289500:-1 11/11 None
GENEFINDER00000006928 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:8286853:8289500:-1 11/11 None
K07H8.10.1 ENSEMBL cdna:known chromosome:CEL140:IV:8286569:8289511:-1 gene:K07H8.10 11/11 None
K07H8.10.2 ENSEMBL cdna:known chromosome:CEL140:IV:8286575:8289513:-1 gene:K07H8.10 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:8286859-8289507(-) 89.45 100.0
Public Domain and Genome References
Gene Title RNA-binding protein
Ensembl K07H8.10
Entrez Gene 177621 Entrez gene
SwissProt O45181 EMBL-EBI
WormBase CE18030 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:246623_AT nucleolin, putative at
CANINE:1585791_S_AT similar to nucleolin-related protein cfa
CANINE_2:CFA.4272.1.S1_AT similar to nucleolin-related protein cfa
CANINE_2:CFAAFFX.17297.1.S1_S_AT similar to nucleolin-related protein cfa
CHICKEN:GGA.3663.1.S1_A_AT nucleolin gga
CHICKEN:GGA.3663.2.S1_AT nucleolin gga
CHICKEN:GGA.3663.3.A1_AT Nucleolin gga
HG-U133A:200610_S_AT nucleolin hs
HG-U133_PLUS_2:200610_S_AT nucleolin hs
HG-FOCUS:200610_S_AT nucleolin hs
HG-U133A_2:200610_S_AT nucleolin hs
HUGENEFL:M60858_RNA1_AT nucleolin hs
U133_X3P:G4885510_3P_A_AT nucleolin hs
HG-U95AV2:32590_AT nucleolin hs
MOE430A:1415772_AT nucleolin mm
MOUSE430A_2:1415772_AT nucleolin mm
MOUSE430_2:1415772_AT nucleolin mm
MOUSE430A_2:1415773_AT nucleolin mm
MOUSE430_2:1415773_AT nucleolin mm
MOE430A:1415773_AT nucleolin mm
MOE430A:1415771_AT nucleolin mm
MOUSE430_2:1415771_AT nucleolin mm
MOUSE430A_2:1415771_AT nucleolin mm
MU11KSUBB:X07699_S_AT nucleolin mm
MG-U74AV2:100144_AT nucleolin mm
MG-U74CV2:137586_AT nucleolin mm
MOE430A:1456528_X_AT Nucleolin, mRNA (cDNA clone MGC:6363 IMAGE:3495665) mm
MOUSE430A_2:1456528_X_AT Nucleolin, mRNA (cDNA clone MGC:6363 IMAGE:3495665) mm
MOUSE430_2:1456528_X_AT Nucleolin, mRNA (cDNA clone MGC:6363 IMAGE:3495665) mm
MG-U74CV2:136117_AT Nucleolin, mRNA (cDNA clone MGC:6363 IMAGE:3495665) mm
MOE430B:1442404_AT Nucleolin, mRNA (cDNA clone MGC:6363 IMAGE:3495665) mm
MOUSE430_2:1442404_AT Nucleolin, mRNA (cDNA clone MGC:6363 IMAGE:3495665) mm
MU19KSUBA:TC16583_S_AT Nucleolin, mRNA (cDNA clone MGC:6363 IMAGE:3495665) mm
MU19KSUBB:TC28899_AT Nucleolin, mRNA (cDNA clone MGC:6363 IMAGE:3495665) mm
MU19KSUBB:TC31426_AT Nucleolin, mRNA (cDNA clone MGC:6363 IMAGE:3495665) mm
MU19KSUBB:TC31426_G_AT Nucleolin, mRNA (cDNA clone MGC:6363 IMAGE:3495665) mm
MU19KSUBC:TC35633_AT Nucleolin, mRNA (cDNA clone MGC:6363 IMAGE:3495665) mm
RG-U34A:M55017EXON_S_AT nucleolin rn
RG-U34A:M55015CDS_S_AT nucleolin rn
RAE230A:1398832_AT nucleolin rn
RAT230_2:1398832_AT nucleolin rn
YEAST_2:1772817_AT Nucleolar protein that binds nuclear localization sequences, required for pre-rRNA processing and ribosome biogenesis Sc
Protein Similarities
Method ID Description E-Value
blast AAC04430 Hypothetical protein K07H8.10 [Caenorhabditis elegans] ref|NP_501391.1| K07H8.10 [Caenorhabditis elegans] 0.0
blast CAE58447 Hypothetical protein CBG01584 [Caenorhabditis briggsae] 1.0E-125
Protein Domains
Database ID Description E-Value
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 6.9E-6
Sequence
Target Sequence 
>C. ELEGANS:174001_S_AT
gcttgtattcaacactgtcgcagattgcaagaaagctcacgatgttcttagcaaatctaa
gattcaaggaaaagctctttatgtagacttctgtctcagtgaaagcaaagctccaaaaga
agatggagttcgtccgattaatcctctccagctcttcatcaacgctctcccaggaacctg
caataacacagacttgaagaacatcttccgttcatccacagacattaagatccttcacgc
aagtggtcagccaaactcgaaaaagagagctttcatcacttttggaaccgtagaagacgc
tcaagctgcattcgcaaaatcaaatggattgaaggttaacaatcatctagtcgatgtgtt
ctatgcgagacatcaagagacgaaggttgacgtgaaaccaaagaaggcagctactccagc
ggttcaaaaaaaaattgttccgaaagttgctgctgattcgtcaggtgatgacagcgaaga
ggtggcgtcaagtgatgaaggaattcaggaagttgaagaagaacaaccaaaacaaaagaa
gctcgtgaaaaaggttgaaccgaagactattccacgtgtgc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCTTGTATTCAACACTGTCGCAGAT 580 305 1780 Antisense
AGCTCTTTATGTAGACTTCTGTCTC 536 79 1852 Antisense
GGAGTTCGTCCGATTAATCCTCTCC 673 515 1904 Antisense
CGCTCTCCCAGGAACCTGCAATAAC 508 255 1942 Antisense
TCTTCCGTTCATCCACAGACATTAA 647 617 1983 Antisense
AGATCCTTCACGCAAGTGGTCAGCC 337 67 2007 Antisense
GAGCTTTCATCACTTTTGGAACCGT 85 387 2046 Antisense
GAACCGTAGAAGACGCTCAAGCTGC 402 345 2064 Antisense
GCAGCTACTCCAGCGGTTCAAAAAA 56 315 2186 Antisense
AGTTGCTGCTGATTCGTCAGGTGAT 303 65 2224 Antisense
GAACCGAAGACTATTCCACGTGTGC 85 345 2336 Antisense
Sequence Source Affymetrix Proprietary Database