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[189801_s_at] RNA binding protein

Description C50B8.1 /REP_DB=WormBase Gene ID /WP=CE08881 /TR=Q18724 /GB=CAB01127.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=RNA binding protein
Cluster 6grp_highest_10_10 > 87      6grp_high1_10_10 > 78      4grp_highest_8_8 > 15      4grp_high_8_8 > 14      6grp_highest_nonorm > 79      6grp_total > 78      4grp_total > 10      6grp_highest_sub > Da      6grp_high1_sub > Cu      6grp_total_sub > Increase      6grp_rule_based > S6      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 5991
1 2 3 4 range
A 1264.7
(-3)
P 		1656.4
(-2.6)
P 		1630.2
(-2.6)
P 		6981.2
(3)
P 		5717
B 1260.7
(-3)
P 		2056.3
(-2.2)
P 		1562.8
(-2.7)
P 		7083.5
(3)
P 		5823
C 1681.6
(-3)
P 		1953.5
(-2.7)
P 		1875.4
(-2.8)
P 		7251.6
(3)
P 		5570
avr 1402.3
(-3) 		1888.7
(-2.5) 		1689.5
(-2.7) 		7105.4
(3) 		5703

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2250
1 2 3 4 5 6 range
A 1126.7
(-3)
P 		1132
(-3)
P 		1269.6
(-2.6)
P 		1151.6
(-2.9)
P 		1972.5
(-0.5)
P 		3195.7
(3)
P 		2069
B 1656.4
(-1.8)
P 		1329.6
(-2.9)
P 		1302.3
(-3)
P 		1430.3
(-2.6)
P 		2444.9
(1)
P 		3023.9
(3)
P 		1722
C 1744.3
(-1.3)
P 		1246.2
(-2.7)
P 		1122.1
(-3)
P 		1262.6
(-2.6)
P 		1970.7
(-0.7)
P 		3372.5
(3)
P 		2250
avr 1509.1
(-2.2) 		1235.9
(-3) 		1231.3
(-3) 		1281.5
(-2.8) 		2129.4
(-0.3) 		3197.4
(3) 		1966
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1150
1 2 3 4 range
A 460.5
(-2.1)
P 		359.6
(-3)
P 		426.2
(-2.4)
P 		1021.9
(3)
P 		662
B 402
(-2.8)
P 		507.9
(-2.2)
P 		362.1
(-3)
P 		1509.5
(3)
P 		1147
C 556.7
(-3)
P 		561.7
(-3)
P 		653.6
(-2.1)
P 		1222.7
(3)
P 		666
avr 473.1
(-3) 		476.4
(-3) 		480.6
(-2.9) 		1251.4
(3) 		778

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 921
1 2 3 4 5 6 range
A 207.7
(-3)
P 		402.6
(-0.9)
P 		276.5
(-2.3)
P 		292.1
(-2.1)
P 		595.2
(1.1)
P 		778.1
(3)
P 		570
B 576.3
(-1.1)
P 		442.6
(-2.1)
P 		316.2
(-3)
P 		378.8
(-2.5)
P 		993.3
(2)
P 		1127.6
(3)
P 		811
C 646.5
(-0.3)
P 		380.2
(-2.1)
P 		285.6
(-2.8)
P 		253.9
(-3)
P 		637.7
(-0.4)
P 		1129
(3)
P 		875
avr 476.8
(-1.5) 		408.5
(-2) 		292.8
(-3) 		308.3
(-2.9) 		742.1
(0.8) 		1011.6
(3) 		719
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 189801_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.12559
Sequence Type Exemplar sequence
Representative Public ID C50B8.1 NCBI
Target Description C50B8.1 /REP_DB=WormBase Gene ID /WP=CE08881 /TR=Q18724 /GB=CAB01127.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=RNA binding protein
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_073959(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073959 NCBI Caenorhabditis elegans C50B8.1 (C50B8.1) mRNA, complete cds. 11/11 None
SNAP00000010250 ENSEMBL cdna:SNAP chromosome:CEL140:V:13568457:13568812:1 10/11 None
GENEFINDER00000010256 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:13568457:13569230:1 11/11 None
C50B8.1.2 ENSEMBL cdna:known chromosome:CEL140:V:13568453:13570065:1 gene:C50B8.1 11/11 None
C50B8.1.1 ENSEMBL cdna:known chromosome:CEL140:V:13568455:13570065:1 gene:C50B8.1 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
chrV:13568456-13569230(+) 100.0 100.0
Public Domain and Genome References
Gene Title RNA binding protein
Ensembl C50B8.1
Entrez Gene 179840 Entrez gene
SwissProt Q18724 EMBL-EBI
WormBase CE08881 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAB01127 Hypothetical protein C50B8.1 [Caenorhabditis elegans] ref|NP_506360.1| C50B8.1 [Caenorhabditis elegans] 6.0E-61
blast CAE66292 Hypothetical protein CBG11539 [Caenorhabditis briggsae] 5.0E-59
blast CAB01127 Hypothetical protein C50B8.1 [Caenorhabditis elegans] ref|NP_506360.1| C50B8.1 [Caenorhabditis elegans] 1.0E-49
blast CAE66292 Hypothetical protein CBG11539 [Caenorhabditis briggsae] 1.0E-47
Protein Domains
Database ID Description E-Value
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 4.6E-14
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 2.4E-14
Sequence
Target Sequence 
>C. ELEGANS:189801_S_AT
gaggagtcaccacgaatattagcaaactaatcgaagctagaccgaagaataccggtcaaa
ctgtctacttgacgcacgtcaaatgggttactggaaaatctcaattagaacactatttca
agcgatacgggtcaattcaaagtgttaacatgttctacgatcccgatacgggccttcatc
gtggatttgcatcgataaccttcgattcaaaagatggtgcgaataaggcgattgaacaac
gaccgcacgttatcgatggagatcgggtagacgtcgagccctata

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAGGAGTCACCACGAATATTAGCAA 679 403 29 Antisense
GAATACCGGTCAAACTGTCTACTTG 18 325 75 Antisense
CAAACTGTCTACTTGACGCACGTCA 487 191 85 Antisense
GACGCACGTCAAATGGGTTACTGGA 537 379 99 Antisense
AACACTATTTCAAGCGATACGGGTC 211 135 137 Antisense
GTTAACATGTTCTACGATCCCGATA 520 445 172 Antisense
TACGATCCCGATACGGGCCTTCATC 640 647 184 Antisense
GGCCTTCATCGTGGATTTGCATCGA 704 543 199 Antisense
AGGCGATTGAACAACGACCGCACGT 342 43 254 Antisense
ACGACCGCACGTTATCGATGGAGAT 551 91 267 Antisense
GATCGGGTAGACGTCGAGCCCTATA 145 417 289 Antisense
Sequence Source Affymetrix Proprietary Database