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[187879_at] Probable RNA binding protein

Description C07H6.4 /REP_DB=WormBase Gene ID /WP=CE00755 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=Probable RNA binding protein
Cluster 6grp_highest_10_10 > 56      6grp_high1_10_10 > 65      4grp_highest_8_8 > 45      4grp_high_8_8 > 08      6grp_highest_nonorm > 85      6grp_total > 55      4grp_total > 23      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 289
1 2 3 4 range
A 847.4
(3)
P 		645.4
(-3)
P 		653.1
(-2.8)
P 		722.7
(-0.7)
P 		202
B 722.5
(0.3)
P 		608.3
(-2.1)
P 		567.8
(-3)
P 		848.2
(3)
P 		280
C 856.4
(3)
P 		583.4
(-3)
P 		691.7
(-0.6)
P 		683
(-0.8)
P 		273
avr 808.8
(3) 		612.4
(-3) 		637.5
(-2.2) 		751.3
(1.2) 		196

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 678
1 2 3 4 5 6 range
A 746.6
(1.8)
P 		734.2
(1.4)
P 		700.2
(0.4)
P 		720.6
(1)
P 		590.6
(-3)
P 		786.6
(3)
P 		196
B 812.1
(-1.7)
P 		759.5
(-2.3)
P 		1268.1
(3)
P 		706.5
(-2.8)
P 		688.3
(-3)
P 		984.5
(0.1)
P 		580
C 670.2
(-2.7)
P 		761.6
(-1.6)
P 		779.1
(-1.3)
P 		776.1
(-1.4)
P 		649
(-3)
P 		1120.6
(3)
P 		472
avr 743
(-1.1) 		751.8
(-1) 		915.8
(2.1) 		734.4
(-1.3) 		642.6
(-3) 		963.9
(3) 		321
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 203
1 2 3 4 range
A 308.6
(3)
P 		140.1
(-2)
P 		170.7
(-1.1)
P 		105.8
(-3)
P 		203
B 230.4
(3)
P 		150.2
(-1.9)
P 		131.6
(-3)
P 		180.8
(-0)
P 		99
C 283.5
(3)
P 		167.7
(-1.1)
P 		241.1
(1.5)
P 		115.2
(-3)
P 		168
avr 274.2
(3) 		152.7
(-2.2) 		181.1
(-1) 		133.9
(-3) 		140

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 238
1 2 3 4 5 6 range
A 137.6
(-3)
P 		261.1
(3)
P 		152.5
(-2.3)
P 		182.8
(-0.8)
P 		178.2
(-1)
P 		191.5
(-0.4)
P 		124
B 282.6
(0.2)
P 		252.8
(-0.8)
P 		307.9
(1)
P 		187.1
(-3)
P 		279.6
(0.1)
P 		367.1
(3)
P 		180
C 248.4
(-0.5)
P 		232.4
(-0.9)
P 		198.3
(-1.8)
P 		156.1
(-3)
P 		210
(-1.5)
P 		375.1
(3)
P 		219
avr 222.9
(-0.9) 		248.8
(0.2) 		219.6
(-1) 		175.3
(-3) 		222.6
(-0.9) 		311.2
(3) 		136
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 187879_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7380
Sequence Type Exemplar sequence
Representative Public ID C07H6.4 NCBI
Target Description C07H6.4 /REP_DB=WormBase Gene ID /WP=CE00755 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=Probable 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_066247(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066247 NCBI Caenorhabditis elegans C07H6.4 (C07H6.4) mRNA, complete cds. 11/11 None
SNAP00000039489 ENSEMBL cdna:SNAP chromosome:CEL140:III:7499681:7503094:1 11/11 None
GENEFINDER00000039500 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:7499681:7503094:1 11/11 None
C07H6.4 ENSEMBL cdna:known chromosome:CEL140:III:7499648:7503149:1 gene:C07H6.4 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
chrIII:7499678-7503092(+) 94.75 100.0
Public Domain and Genome References
Gene Title Probable RNA binding protein
Ensembl C07H6.4
Entrez Gene 176063 Entrez gene
SwissProt Q95YF1 EMBL-EBI
WormBase CE00755 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:246924_AT RNA recognition motif (RRM)-containing protein at
CANINE:1595167_AT similar to U2-associated SR140 protein cfa
CANINE:1588962_AT similar to U2-associated SR140 protein cfa
CANINE_2:CFA.15101.1.A1_S_AT similar to U2-associated SR140 protein cfa
CANINE_2:CFAAFFX.12797.1.S1_S_AT similar to U2-associated SR140 protein cfa
DROSOPHILA_2:1639337_AT dm
DROSGENOME1:154204_AT dm
CHICKEN:GGA.4930.1.S1_AT similar to RIKEN cDNA 2610101N10 gga
CHICKEN:GGA.4930.2.S1_A_AT similar to RIKEN cDNA 2610101N10 gga
CHICKEN:GGA.4930.3.S1_A_AT similar to RIKEN cDNA 2610101N10 gga
HU35KSUBA:AB002330_AT U2-associated SR140 protein hs
HU35KSUBC:RC_AA262491_AT U2-associated SR140 protein hs
U133_X3P:HS.7976.0.A3_3P_AT U2-associated SR140 protein hs
U133_X3P:HS.7976.0.A2_3P_AT U2-associated SR140 protein hs
U133_X3P:HS.7976.0.A1_3P_S_AT U2-associated SR140 protein hs
U133_X3P:HS.7976.0.A1_3P_AT U2-associated SR140 protein hs
U133_X3P:HS.186572.0.A1_3P_AT U2-associated SR140 protein hs
U133_X3P:212058_3P_AT U2-associated SR140 protein hs
HG-U133A_2:212058_AT U2-associated SR140 protein hs
HG-U133_PLUS_2:212058_AT U2-associated SR140 protein hs
HG-U133A:212058_AT U2-associated SR140 protein hs
HG-U133A_2:212060_AT U2-associated SR140 protein hs
HG-U133_PLUS_2:212060_AT U2-associated SR140 protein hs
HG-U133A:212060_AT U2-associated SR140 protein hs
HG-U133A_2:212061_AT U2-associated SR140 protein hs
HG-U133_PLUS_2:212061_AT U2-associated SR140 protein hs
HG-U133A:212061_AT U2-associated SR140 protein hs
HG-U133_PLUS_2:236696_AT U2-associated SR140 protein hs
HG-U133B:236696_AT U2-associated SR140 protein hs
HG-U95AV2:38030_AT U2-associated SR140 protein hs
HG-U95B:43680_AT U2-associated SR140 protein hs
HG-U95B:52605_AT U2-associated SR140 protein hs
U133_X3P:HS.122571.0.A1_3P_AT U2-associated SR140 protein hs
U133_X3P:HS.114274.0.A1_3P_AT U2-associated SR140 protein hs
HG-U133_PLUS_2:229338_AT U2-associated SR140 protein hs
HG-U133B:229338_AT U2-associated SR140 protein hs
HG-U133_PLUS_2:236431_AT U2-associated SR140 protein hs
HG-U133B:236431_AT U2-associated SR140 protein hs
HG-U95E:80992_AT U2-associated SR140 protein hs
HG-U95E:89959_AT U2-associated SR140 protein hs
HU35KSUBD:RC_AA262952_AT U2-associated SR140 protein hs
MG-U74AV2:98134_AT RIKEN cDNA 2610101N10 gene mm
MG-U74BV2:164759_I_AT RIKEN cDNA 2610101N10 gene mm
MOE430A:1454914_AT RIKEN cDNA 2610101N10 gene mm
MOUSE430A_2:1454914_AT RIKEN cDNA 2610101N10 gene mm
MOUSE430_2:1454914_AT RIKEN cDNA 2610101N10 gene mm
MOE430A:1434300_AT RIKEN cDNA 2610101N10 gene mm
MOUSE430A_2:1434300_AT RIKEN cDNA 2610101N10 gene mm
MOUSE430_2:1434300_AT RIKEN cDNA 2610101N10 gene mm
MG-U74BV2:108994_AT RIKEN cDNA 2610101N10 gene (2610101N10Rik), mRNA mm
MOE430B:1444131_AT RIKEN cDNA 2610101N10 gene (2610101N10Rik), mRNA mm
MOUSE430_2:1444131_AT RIKEN cDNA 2610101N10 gene (2610101N10Rik), mRNA mm
MU19KSUBA:TC20976_AT RIKEN cDNA 2610101N10 gene (2610101N10Rik), mRNA mm
MU19KSUBA:TC20976_G_AT RIKEN cDNA 2610101N10 gene (2610101N10Rik), mRNA mm
RAE230A:1382135_AT similar to CG9346-PA (predicted) rn
RAT230_2:1382135_AT similar to CG9346-PA (predicted) rn
RAE230B:1379715_AT similar to CG9346-PA (predicted) rn
RAT230_2:1379715_AT similar to CG9346-PA (predicted) rn
RAE230A:1390335_AT Similar to CG9346-PA (predicted) rn
RAT230_2:1390335_AT Similar to CG9346-PA (predicted) rn
RAE230B:1394898_AT Similar to CG9346-PA (predicted) rn
RAT230_2:1394898_AT Similar to CG9346-PA (predicted) rn
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
Protein Similarities
Method ID Description E-Value
blast AAK85442 Hypothetical protein C07H6.4 [Caenorhabditis elegans] ref|NP_498648.1| C07H6.4 [Caenorhabditis elegans] 0.0
blast CAE64460 Hypothetical protein CBG09176 [Caenorhabditis briggsae] 0.0
blast XP_422593 PREDICTED: similar to RIKEN cDNA 2610101N10 [Gallus gallus] 7.0E-99
Protein Domains
Database ID Description E-Value
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 7.5E-9
Pfam IPR000061 EMBL-EBI SWAP/Surp 8.5E-12
Sequence
Target Sequence 
>C. ELEGANS:187879_AT
atcaacgtctacttattcaactgcaagtaaattcaaacctgttgagtctcgaaaacgtga
tggctcccctatattttcttcaaaatgggaccacgacggccgaaagtcgaatgaagaaga
ggatgaagacatcgatggagtcatgattacagacgacacgacttcagagaatctacaacg
agatagtctttctccaggagaaatcaaggacaaagaatcttcatttaccgtgctcacacc
ttctgatgaaaaacgaagaaagttgatacgagacgttgaagttcgtgccatcgccatgct
ggatgatttagaagctgacagagatcctgatgccaagagaaaagttgacgagtttagaag
gtgtgaaatggaaaaagtcgagaaagcattgcgaagtggagaatctaaaaagagtgatga
gaaaagtgaaagaaagagcgaaaagaaagaaaagaagcgtgataaagagaggaaaagaag
tcgttcgcgttctcgtgaccgtgacagagataggagccgccgtgatcgatcaagggatcg
ttccagagaccgagatagagatcgtgaccgggacagacgggaccgtgac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATCAACGTCTACTTATTCAACTGCA 176 27 2193 Antisense
GAGTCTCGAAAACGTGATGGCTCCC 519 399 2236 Antisense
ATGGGACCACGACGGCCGAAAGTCG 173 51 2277 Antisense
AAAGAATCTTCATTTACCGTGCTCA 635 123 2404 Antisense
GAGACGTTGAAGTTCGTGCCATCGC 662 393 2462 Antisense
GTGCCATCGCCATGCTGGATGATTT 459 477 2477 Antisense
GAAGCTGACAGAGATCCTGATGCCA 543 343 2503 Antisense
AAAAGAAGTCGTTCGCGTTCTCGTG 568 129 2665 Antisense
GACAGAGATAGGAGCCGCCGTGATC 338 367 2695 Antisense
AAGGGATCGTTCCAGAGACCGAGAT 480 157 2724 Antisense
TGACCGGGACAGACGGGACCGTGAC 64 567 2757 Antisense
Sequence Source Affymetrix Proprietary Database