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[190130_at] RNA-binding protein

Description C44E4.4 /REP_DB=WormBase Gene ID /WP=CE08718 /TR=O01806 /GB=AAB54169.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=RNA-binding protein
Cluster 6grp_highest_10_10 > 82      6grp_high1_10_10 > 29      4grp_highest_8_8 > 25      4grp_high_8_8 > 60      6grp_highest_nonorm > 75      6grp_total > 28      4grp_total > 59      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 1129
1 2 3 4 range
A 1573.7
(0.6)
P 		1735.9
(1.8)
P 		1905.7
(3)
P 		1066.9
(-3)
P 		839
B 1703.2
(1.5)
P 		1742.5
(1.7)
P 		1957.6
(3)
P 		966.5
(-3)
P 		991
C 1579.2
(1.5)
P 		1702
(2.3)
P 		1826.4
(3)
P 		828.5
(-3)
P 		998
avr 1618.7
(1.2) 		1726.8
(1.9) 		1896.6
(3) 		954
(-3) 		943

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 862
1 2 3 4 5 6 range
A 967.2
(0.9)
P 		1149.5
(3)
P 		625.4
(-3)
P 		812.6
(-0.9)
P 		751
(-1.6)
P 		1152.7
(3)
P 		527
B 1110.7
(3)
P 		886.3
(0.1)
P 		795.2
(-1.1)
P 		650.7
(-3)
P 		882
(0)
P 		947.7
(0.9)
P 		460
C 1487
(3)
P 		920.8
(-1.1)
P 		849.2
(-1.6)
P 		660.1
(-3)
P 		971.4
(-0.7)
P 		792.4
(-2)
P 		827
avr 1188.3
(3) 		985.5
(0.5) 		756.6
(-2.4) 		707.8
(-3) 		868.1
(-1) 		964.3
(0.2) 		481
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 497
1 2 3 4 range
A 573
(3)
P 		376.8
(0.2)
P 		498.2
(1.9)
P 		156.2
(-3)
P 		417
B 543.1
(3)
P 		430.3
(1)
P 		453.6
(1.4)
P 		206
(-3)
P 		337
C 522.7
(1.6)
P 		489.3
(1.2)
P 		636.6
(3)
P 		139.7
(-3)
P 		497
avr 546.3
(3) 		432.1
(1.2) 		529.5
(2.7) 		167.3
(-3) 		379

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 418
1 2 3 4 5 6 range
A 178.3
(-2.1)
P 		408.8
(3)
P 		136.2
(-3)
P 		206.1
(-1.5)
P 		226.6
(-1)
P 		280.6
(0.2)
P 		273
B 386.5
(3)
P 		295
(0.4)
P 		193.1
(-2.4)
P 		172.3
(-3)
P 		358.3
(2.2)
P 		353.4
(2.1)
P 		214
C 551.2
(3)
P 		281
(-0.9)
P 		216.1
(-1.8)
P 		132.8
(-3)
P 		314.3
(-0.4)
P 		265.3
(-1.1)
P 		418
avr 372
(3) 		328.3
(1.7) 		181.8
(-2.7) 		170.4
(-3) 		299.7
(0.8) 		299.8
(0.9) 		202
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190130_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.1179
Sequence Type Exemplar sequence
Representative Public ID C44E4.4 NCBI
Target Description C44E4.4 /REP_DB=WormBase Gene ID /WP=CE08718 /TR=O01806 /GB=AAB54169.1 /SUBMIT=ST.LOUIS /CHR=1 /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_059010(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059010 NCBI Caenorhabditis elegans C44E4.4 (C44E4.4) mRNA, complete cds. 11/11 None
SNAP00000019659 ENSEMBL cdna:SNAP chromosome:CEL140:I:4634111:4635403:1 11/11 None
GENEFINDER00000019664 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:4634111:4635403:1 11/11 None
C44E4.4 ENSEMBL cdna:known chromosome:CEL140:I:4634102:4635616:1 gene:C44E4.4 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
chrI:4634110-4635403(+) 93.28 100.0
Public Domain and Genome References
Gene Title RNA-binding protein
Ensembl C44E4.4
Entrez Gene 172070 Entrez gene
SwissProt O01806 EMBL-EBI
WormBase CE08718 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1592413_AT similar to autoantigen La cfa
CANINE:1586262_AT similar to autoantigen La cfa
CANINE_2:CFA.11068.1.A1_S_AT similar to autoantigen La cfa
CANINE_2:CFA.19683.1.S1_AT similar to autoantigen La cfa
CANINE_2:CFAAFFX.19266.1.S1_AT similar to autoantigen La cfa
DROSOPHILA_2:1631149_S_AT La autoantigen-like dm
DROSGENOME1:143668_AT La autoantigen-like dm
CHICKEN:GGA.1146.1.S1_S_AT Sjogren syndrome antigen B (autoantigen La) gga
CHICKEN:GGA.1146.2.S1_AT Sjogren syndrome antigen B (autoantigen La) gga
CHICKEN:GGAAFFX.12116.1.S1_AT Sjogren syndrome antigen B (autoantigen La) gga
HG-U133_PLUS_2:201138_S_AT Sjogren syndrome antigen B (autoantigen La) hs
HG-U133A:201138_S_AT Sjogren syndrome antigen B (autoantigen La) hs
HG-FOCUS:201138_S_AT Sjogren syndrome antigen B (autoantigen La) hs
HG-U133A_2:201138_S_AT Sjogren syndrome antigen B (autoantigen La) hs
HG-U133_PLUS_2:201139_S_AT Sjogren syndrome antigen B (autoantigen La) hs
HG-U133A:201139_S_AT Sjogren syndrome antigen B (autoantigen La) hs
HG-U133A_2:201139_S_AT Sjogren syndrome antigen B (autoantigen La) hs
HUGENEFL:X14684_S_AT Sjogren syndrome antigen B (autoantigen La) hs
U133_X3P:G10835066_3P_A_AT Sjogren syndrome antigen B (autoantigen La) hs
U133_X3P:HS.83715.0.S1_3P_A_AT Sjogren syndrome antigen B (autoantigen La) hs
U133_X3P:201139_3P_S_AT Sjogren syndrome antigen B (autoantigen La) hs
HG-U95AV2:38450_AT Sjogren syndrome antigen B (autoantigen La) hs
MOUSE430A_2:1416422_A_AT Sjogren syndrome antigen B mm
MOE430A:1416422_A_AT Sjogren syndrome antigen B mm
MOUSE430_2:1416422_A_AT Sjogren syndrome antigen B mm
MOUSE430A_2:1453928_A_AT Sjogren syndrome antigen B mm
MOE430A:1453928_A_AT Sjogren syndrome antigen B mm
MOUSE430_2:1453928_A_AT Sjogren syndrome antigen B mm
MU11KSUBA:L00993_S_AT Sjogren syndrome antigen B mm
MU11KSUBB:MSA.31087.0_F_AT Sjogren syndrome antigen B mm
MG-U74AV2:92579_AT Sjogren syndrome antigen B mm
MOE430A:1416423_X_AT Sjogren syndrome antigen B mm
MOUSE430A_2:1416423_X_AT Sjogren syndrome antigen B mm
MOUSE430_2:1416423_X_AT Sjogren syndrome antigen B mm
MOE430A:1416421_A_AT Sjogren syndrome antigen B mm
MOUSE430A_2:1416421_A_AT Sjogren syndrome antigen B mm
MOUSE430_2:1416421_A_AT Sjogren syndrome antigen B mm
MU19KSUBC:TC38011_AT Sjogren syndrome antigen B, mRNA (cDNA clone MGC:6189 IMAGE:3593742) mm
MU19KSUBC:TC40781_I_AT Sjogren syndrome antigen B, mRNA (cDNA clone MGC:6189 IMAGE:3593742) mm
RG-U34A:S59892_F_AT Sjogren syndrome antigen B rn
RG-U34A:X67859_AT Sjogren syndrome antigen B rn
RG-U34A:S59893_F_AT Sjogren syndrome antigen B rn
RAE230A:1387262_AT Sjogren syndrome antigen B rn
RAT230_2:1387262_AT Sjogren syndrome antigen B rn
RAE230B:1382649_AT Sjogren syndrome antigen B rn
RAT230_2:1382649_AT Sjogren syndrome antigen B rn
RG-U34B:RC_AI030649_AT Sjogren syndrome antigen B rn
RG-U34C:RC_AI073223_AT Sjogren syndrome antigen B rn
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6396 RNA processing inferred from electronic annotation QuickGO AmiGO
6405 RNA export from nucleus inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5634 nucleus inferred from electronic annotation QuickGO AmiGO
5737 cytoplasm inferred from electronic annotation QuickGO AmiGO
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 AAB54169 Hypothetical protein C44E4.4 [Caenorhabditis elegans] ref|NP_491411.1| C44E4.4 [Caenorhabditis elegans] 1.0E-178
blast CAE74489 Hypothetical protein CBG22240 [Caenorhabditis briggsae] 1.0E-136
blast NP_955841 Sjogren syndrome antigen B (autoantigen La) [Danio rerio] gb|AAH45392.1| Sjogren syndrome antigen B (autoantigen La) [Danio rerio] 2.0E-41
Protein Domains
Database ID Description E-Value
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 7.6E-9
Pfam IPR006630 EMBL-EBI RNA-binding protein Lupus Lal 1.1E-29
Sequence
Target Sequence 
>C. ELEGANS:190130_AT
gctcgtgctgcaaacaaggctgccaaatcagctaagaatacttctgaagcgattgaatca
gaaaaggctcagcacgctgtccgttacgagaaaggtctcattctggccgttgatggactt
ggacctgattcaactattgacagcatcaagactttcttcaaattgcacggatctgttgga
tacgttgcacatgaaaatggaggcaaaacagccgaaatccgcttcaacaatgacagcgaa
ggagcgcagaaggcctgggacaacgctgttgcagctggaactgatggaaaagtcattctt
caagaggctgagctctccgcacgagttttggatggagaagaggaggagaaatactggaca
gagttcaatgccagaaagaatcagaggcaaggaggtggacgtggaggacgcggtggtcgt
ggcggacgaggaggccgcggtggtcgtggaggtcgtggtggaagaggtggacgcggagac
cgccgaggtgataagcggtcagcaaacgatgaaggtgcagatggatctgatgagccaaag
gctaagcgtactgtgttcgctgag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCTCGTGCTGCAAACAAGGCTGCCA 601 299 607 Antisense
TCAGCACGCTGTCCGTTACGAGAAA 326 625 675 Antisense
CGAGAAAGGTCTCATTCTGGCCGTT 258 251 693 Antisense
CTGGCCGTTGATGGACTTGGACCTG 170 241 709 Antisense
GACTTTCTTCAAATTGCACGGATCT 157 371 756 Antisense
GGATCTGTTGGATACGTTGCACATG 187 513 775 Antisense
AACAGCCGAAATCCGCTTCAACAAT 413 135 813 Antisense
GCAGAAGGCCTGGGACAACGCTGTT 361 313 852 Antisense
AGCTCTCCGCACGAGTTTTGGATGG 480 79 917 Antisense
ACGCGGAGACCGCCGAGGTGATAAG 438 89 1077 Antisense
GGCTAAGCGTACTGTGTTCGCTGAG 125 539 1146 Antisense
Sequence Source Affymetrix Proprietary Database