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[190215_at] RNA-binding protein

Description H24K24.4 /REP_DB=WormBase Gene ID /WP=CE23823 /TR=Q9N5L0 /GB=AAF39900.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=RNA-binding protein
Cluster 6grp_total > 0      4grp_total > 01      6grp_total_sub > Hat      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 208
1 2 3 4 range
A 72
(-1.6)
A 		25.3
(-3)
A 		65.3
(-1.8)
A 		227.6
(3)
A 		202
B 63.7
(0.1)
A 		19.4
(-3)
A 		60.3
(-0.1)
A 		103.8
(3)
M 		84
C 19.8
(-3)
A 		74
(-1.1)
A 		70.5
(-1.2)
A 		189.2
(3)
P 		169
avr 51.8
(-2.5) 		39.6
(-3) 		65.4
(-1.8) 		173.5
(3) 		134

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 74
1 2 3 4 5 6 range
A 17.1
(-3)
A 		66.2
(3)
A 		17.1
(-3)
A 		19
(-2.8)
A 		20.6
(-2.6)
A 		65.2
(2.9)
A 		49
B 11.3
(-2.3)
A 		45.7
(3)
A 		23.4
(-0.5)
A 		7.1
(-3)
A 		38.9
(1.9)
A 		31.3
(0.8)
A 		39
C 15.9
(-2.8)
A 		68.9
(1.9)
A 		13.1
(-3)
A 		17.1
(-2.6)
A 		80.9
(3)
A 		17.5
(-2.6)
A 		68
avr 14.8
(-2.9) 		60.3
(3) 		17.9
(-2.5) 		14.4
(-3) 		46.8
(1.2) 		38
(0.1) 		46
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 29
1 2 3 4 range
A 26.2
(1.5)
A 		5.5
(-3)
A 		17.1
(-0.5)
A 		33.3
(3)
A 		28
B 20.3
(2.4)
A 		4.8
(-3)
A 		14
(0.2)
A 		22.1
(3)
M 		17
C 6.5
(-3)
A 		21.3
(0.5)
A 		24.6
(1.3)
A 		31.9
(3)
P 		25
avr 17.7
(-0.7) 		10.5
(-3) 		18.6
(-0.4) 		29.1
(3) 		19

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 24
1 2 3 4 5 6 range
A 3.2
(-3)
A 		23.5
(3)
A 		3.7
(-2.9)
A 		4.8
(-2.5)
A 		6.2
(-2.1)
A 		15.9
(0.8)
A 		20
B 3.9
(-2.1)
A 		15.2
(2.7)
A 		5.7
(-1.4)
A 		1.9
(-3)
A 		15.8
(3)
A 		11.7
(1.2)
A 		14
C 5.9
(-2.3)
A 		21
(1.6)
A 		3.3
(-3)
A 		3.4
(-3)
A 		26.2
(3)
A 		5.9
(-2.3)
A 		23
avr 4.3
(-2.7) 		19.9
(3) 		4.2
(-2.7) 		3.4
(-3) 		16.1
(1.6) 		11.2
(-0.2) 		17
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190215_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.15177
Sequence Type Exemplar sequence
Representative Public ID H24K24.4 NCBI
Target Description H24K24.4 /REP_DB=WormBase Gene ID /WP=CE23823 /TR=Q9N5L0 /GB=AAF39900.1 /SUBMIT=ST.LOUIS /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_070952(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_070952 NCBI Caenorhabditis elegans H24K24.4 (H24K24.4) mRNA, complete cds. 11/11 None
SNAP00000006370 ENSEMBL cdna:SNAP chromosome:CEL140:V:904798:910570:1 11/11 None
GENEFINDER00000006376 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:904798:915977:1 11/11 None
H24K24.4 ENSEMBL cdna:known chromosome:CEL140:V:904793:910836:1 gene:H24K24.4 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:904797-909102(+) 100.0 100.0
Public Domain and Genome References
Gene Title RNA-binding protein
Ensembl H24K24.4
Entrez Gene 186775 Entrez gene
SwissProt Q9N5L0 EMBL-EBI
WormBase CE36942 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6396 RNA processing inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3723 RNA binding inferred from electronic annotation QuickGO AmiGO
8173 RNA methyltransferase activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAF39900 Hypothetical protein H24K24.4 [Caenorhabditis elegans] ref|NP_503353.2| H24K24.4 [Caenorhabditis elegans] 0.0
blast CAE71051 Hypothetical protein CBG17893 [Caenorhabditis briggsae] 0.0
blast AAF39899 Hypothetical protein H24K24.3a [Caenorhabditis elegans] ref|NP_741507.1| H24K24.3a [Caenorhabditis elegans] sp|Q17335|ADHX_CAEEL Alcohol dehydrogenase class III (Glutathione-dependent formaldehyde dehydrogenase) (FDH) (FALDH) gb|AAB03374.1| alcohol dehydrogenase 1.0E-176
blast AAL32231 Hypothetical protein H24K24.3b [Caenorhabditis elegans] ref|NP_001024016.1| H24K24.3b [Caenorhabditis elegans] 1.0E-176
blast AAF39900 Hypothetical protein H24K24.4 [Caenorhabditis elegans] ref|NP_503353.2| H24K24.4 [Caenorhabditis elegans] 1.0E-171
blast XP_708195 PREDICTED: similar to HpaII tiny fragments locus 9c isoform 4 [Danio rerio] 2.0E-37
Protein Domains
Database ID Description E-Value
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 1.3E-9
Pfam IPR002085 EMBL-EBI Zinc-containing alcohol dehydrogenase superfamily 1.9E-96
Pfam IPR002085 EMBL-EBI Zinc-containing alcohol dehydrogenase superfamily 1.1E-23
Sequence
Target Sequence 
>C. ELEGANS:190215_AT
tctgttggactgccgattccgagtatcaccgccagcgtttttccagacgaatagccaggc
ggcggcggttctctactcgacgattggagagcattgtgggctcagtgaaaagaaaaccaa
cgaagatgttccagtggaaactgatgcatcggaaaaagccccagaagctccagcagcacc
ttcagagcccatccccgacgatccatccgatgctcctccggcaaagatcccgagaatcga
gccggagcccactgcagcagatgaagcacctgctccagaagatcccggaaccatccttct
tgacatttgctgtggaaccggaacgatcggtcaatgccttctgaaaaatattcaaaaatc
gcaaaaagtgtgctgcatcggaattgaaatgatcgccgaagcggtggaggacgccaaaca
aaatgcgaaacagaataaaatggaaacatgctgtaaatatattgctggaaaagccgagga
cacattccgatcgatgagatatcatctgccgaatggttttgatctacgaaaatcgagagt
ggtcggagtgctcgatccaccgagagccggaatgcacg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCTGTTGGACTGCCGATTCCGAGTA 646 605 1032 Antisense
TTCCAGACGAATAGCCAGGCGGCGG 631 699 1072 Antisense
AGATCCCGAGAATCGAGCCGGAGCC 613 65 1256 Antisense
CGGAGCCCACTGCAGCAGATGAAGC 166 243 1274 Antisense
GATGAAGCACCTGCTCCAGAAGATC 587 411 1291 Antisense
TCCAGAAGATCCCGGAACCATCCTT 652 587 1305 Antisense
AACCATCCTTCTTGACATTTGCTGT 704 147 1320 Antisense
AACGATCGGTCAATGCCTTCTGAAA 251 145 1353 Antisense
GATCGCCGAAGCGGTGGAGGACGCC 496 417 1422 Antisense
AGCCGAGGACACATTCCGATCGATG 282 83 1503 Antisense
GATCCACCGAGAGCCGGAATGCACG 413 415 1585 Antisense
Sequence Source Affymetrix Proprietary Database