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[193951_at] RNA recognition motif. (aka RRM, RBD, or RNP domain) (6 domains)

Description T23F6.4 /REP_DB=WormBase Gene ID /WP=CE18963 /TR=Q9XU67 /GB=CAB05631.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=RNA recognition motif. (aka RRM, RBD, or RNP domain) (6 domains)
Cluster 6grp_highest_10_10 > 55      6grp_high1_10_10 > 55      4grp_highest_8_8 > 42      4grp_high_8_8 > 48      6grp_highest_nonorm > 72      6grp_total > 55      4grp_total > 54      6grp_cgc > 55      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 323
1 2 3 4 range
A 590.1
(3)
P 		397.2
(-2)
P 		436
(-1)
P 		356.4
(-3)
P 		234
B 503.1
(3)
P 		373.4
(-1.1)
P 		381.5
(-0.8)
P 		311.2
(-3)
P 		192
C 455.7
(3)
P 		334.5
(-0.9)
P 		398.6
(1.2)
P 		267.4
(-3)
P 		188
avr 516.3
(3) 		368.4
(-1.3) 		405.4
(-0.3) 		311.7
(-3) 		205

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 203
1 2 3 4 5 6 range
A 349
(-3)
P 		393.5
(-0.6)
P 		414.4
(0.5)
P 		368.9
(-1.9)
P 		380.9
(-1.3)
P 		461
(3)
P 		112
B 401.8
(0.1)
P 		407.8
(0.4)
P 		445.1
(2.2)
P 		335.5
(-3)
P 		427.3
(1.3)
P 		463
(3)
P 		128
C 361.5
(-0.9)
P 		493.1
(3)
P 		406.5
(0.4)
P 		439.7
(1.4)
P 		290.1
(-3)
P 		439.1
(1.4)
P 		203
avr 370.8
(-2.7) 		431.5
(1.4) 		422
(0.8) 		381.4
(-2) 		366.1
(-3) 		454.4
(3) 		88
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 170
1 2 3 4 range
A 214.8
(3)
P 		86.2
(-1.7)
P 		114
(-0.7)
P 		52.2
(-3)
P 		163
B 160.4
(3)
P 		92.2
(-1.3)
P 		88.4
(-1.6)
P 		66.3
(-3)
P 		94
C 150.9
(3)
P 		96.2
(-0.1)
P 		138.9
(2.3)
P 		45.1
(-3)
P 		106
avr 175.4
(3) 		91.5
(-1.2) 		113.8
(-0.1) 		54.5
(-3) 		121

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 109
1 2 3 4 5 6 range
A 64.3
(-3)
P 		139.9
(3)
P 		90.3
(-0.9)
P 		93.6
(-0.7)
P 		114.9
(1)
P 		112.2
(0.8)
P 		76
B 139.8
(0.6)
P 		135.7
(0.3)
P 		108.1
(-1.6)
P 		88.9
(-3)
P 		173.6
(3)
P 		172.6
(2.9)
P 		85
C 134
(1.4)
P 		150.5
(3)
P 		103.5
(-1.5)
P 		88.4
(-3)
P 		93.9
(-2.5)
P 		147
(2.7)
P 		62
avr 112.7
(-0.5) 		142
(2.8) 		100.6
(-1.8) 		90.3
(-3) 		127.5
(1.2) 		143.9
(3) 		54
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193951_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.9694
Sequence Type Exemplar sequence
Representative Public ID T23F6.4 NCBI
Target Description T23F6.4 /REP_DB=WormBase Gene ID /WP=CE18963 /TR=Q9XU67 /GB=CAB05631.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=RNA recognition motif. (aka RRM, RBD, or RNP domain) (6 domains)
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_070031(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_070031 NCBI Caenorhabditis elegans RBD (RNA binding domain) protein family member (rbd-1) (rbd-1) mRNA, complete cds. 11/11 None
SNAP00000000563 ENSEMBL cdna:SNAP chromosome:CEL140:IV:12724961:12729944:1 11/11 None
GENEFINDER00000000566 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:12724961:12729944:1 11/11 None
T23F6.4.1 ENSEMBL cdna:known chromosome:CEL140:IV:12724919:12730066:1 gene:T23F6.4 11/11 None
T23F6.4.2 ENSEMBL cdna:known chromosome:CEL140:IV:12724957:12730025:1 gene:T23F6.4 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
chrIV:12724966-12729950(+) 97.02 100.0
Public Domain and Genome References
Gene Title RNA recognition motif. (aka RRM, RBD, or RNP domain) (6 domains)
Gene Symbol rbd-1
Ensembl T23F6.4
Entrez Gene 178229 Entrez gene
SwissProt Q9XU67 EMBL-EBI
WormBase CE18963 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:15312_AT RNA recognition motif (RRM)-containing protein at
ATH1-121501:254527_AT RNA recognition motif (RRM)-containing protein at
CANINE:1605802_AT similar to Probable RNA-binding protein 19 (RNA binding motif protein 19) cfa
CANINE_2:CFAAFFX.14463.1.S1_S_AT similar to Probable RNA-binding protein 19 (RNA binding motif protein 19) cfa
DROSOPHILA_2:1631433_AT dm
DROSGENOME1:148477_AT dm
CHICKEN:GGA.6364.3.S1_AT similar to RNA binding motif protein 19 gga
CHICKEN:GGA.6364.3.S1_S_AT similar to RNA binding motif protein 19 gga
HG-U133_PLUS_2:206019_AT RNA binding motif protein 19 hs
HG-U133A:206019_AT RNA binding motif protein 19 hs
HG-U133A_2:206019_AT RNA binding motif protein 19 hs
HG-U133_PLUS_2:205115_S_AT RNA binding motif protein 19 hs
HG-U133A:205115_S_AT RNA binding motif protein 19 hs
HG-U133A_2:205115_S_AT RNA binding motif protein 19 hs
HU35KSUBB:RC_T25505_AT RNA binding motif protein 19 hs
HU35KSUBC:RC_AA406133_AT RNA binding motif protein 19 hs
HU35KSUBC:RC_AA122337_AT RNA binding motif protein 19 hs
U133_X3P:G7705364_3P_S_AT RNA binding motif protein 19 hs
U133_X3P:G7662249_3P_AT RNA binding motif protein 19 hs
HG-U95AV2:40377_AT RNA binding motif protein 19 hs
HG-U95B:51883_AT RNA binding motif protein 19 hs
HG-U95C:58578_AT RNA binding motif protein 19 hs
MOE430A:1451365_AT RNA binding motif protein 19 mm
MOUSE430A_2:1451365_AT RNA binding motif protein 19 mm
MOUSE430_2:1451365_AT RNA binding motif protein 19 mm
MG-U74BV2:164140_AT RNA binding motif protein 19 mm
MG-U74CV2:134208_AT RNA binding motif protein 19, mRNA (cDNA clone MGC:18721 IMAGE:4225239) mm
YEAST_2:1777153_AT Essential conserved protein that associates with 35S precursor rRNA and is required for its initial processing at the A(0)-A(2) cleavage sites, shows partial nucleolar localization, contains five consensus RNA-binding domains Sc
Protein Similarities
Method ID Description E-Value
blast CAB05631 Hypothetical protein T23F6.4 [Caenorhabditis elegans] ref|NP_502432.1| RBD (RNA binding domain) protein family member (rbd-1) [Caenorhabditis elegans] 0.0
blast CAE59999 Hypothetical protein CBG03493 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 3.1E-20
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 1.8E-4
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 1.4E-21
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 8.9E-7
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 1.8E-11
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 1.1E-15
Sequence
Target Sequence 
>C. ELEGANS:193951_AT
tggagacctcgttaaatctgcgcaaatctccaagaagctcaatccagcggagccaacgaa
gccactttccatgggattcggattcgttcagttctacactgcattcgacgcgaaaactgc
actgaaagatatgcaaggagagcttcttgatggtcattctctagaattgaagatttcgca
tagagagaacgccgacaagggagctctaaaacgaaaggaagtgaagcaaaaagagcaggg
agaatgtacgaagcttttggtcagaaatctaccatttgaagcatcagttaaagaagttga
aactctttttgaaacttttggagctgtaaaaaccattcgtattcctaaaaagccaggaca
aaagcaacaacatcgtggattcggattcgtcgattttatttcggcagatgaggctcatcg
agcatttgattctcttgttcactctactcatctgtacggaagacgtttagttttggaatg
ggctaaagacgatgaaactgtggaagaacttcgtgaaaagacggccgagaagtttgctgg
a

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGGAGACCTCGTTAAATCTGCGCAA 165 549 2007 Antisense
ATCTGCGCAAATCTCCAAGAAGCTC 283 33 2022 Antisense
GAAGCTCAATCCAGCGGAGCCAACG 592 341 2040 Antisense
GAAGCCACTTTCCATGGGATTCGGA 496 345 2064 Antisense
GATTCGGATTCGTTCAGTTCTACAC 411 431 2081 Antisense
TTCTACACTGCATTCGACGCGAAAA 540 691 2098 Antisense
GAGCTTCTTGATGGTCATTCTCTAG 625 387 2146 Antisense
GAGAACGCCGACAAGGGAGCTCTAA 34 393 2191 Antisense
ATTTGATTCTCTTGTTCACTCTACT 620 17 2430 Antisense
TCACTCTACTCATCTGTACGGAAGA 196 627 2445 Antisense
AAAGACGGCCGAGAAGTTTGCTGGA 564 113 2523 Antisense
Sequence Source Affymetrix Proprietary Database