[Home] | [Total List]

[173779_at] RNA binding protein

Description CEC3753_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=C25A1.4 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C10375 /WB_GENE_ID=C25A1.4 /WP=CE08369 /CHR=1 /FEA=Genomic Cluster /DEF=RNA binding protein; C.elegans cDNA clone yk145b5 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 93      6grp_high1_10_10 > 48      4grp_highest_8_8 > 10      4grp_high_8_8 > 54      6grp_highest_nonorm > 81      6grp_total > 49      4grp_total > 57      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.
4 279
1 2 3 4 range
A 288.6
(2.4)
P 		254.8
(1.1)
P 		304.8
(3)
P 		143.9
(-3)
P 		161
B 204.2
(-3)
P 		328
(2.6)
P 		336.5
(3)
P 		248.9
(-1)
P 		132
C 168.7
(-2.3)
P 		415.1
(3)
P 		404.9
(2.8)
P 		135.9
(-3)
P 		279
avr 220.5
(-1.5) 		332.6
(2.4) 		348.7
(3) 		176.2
(-3) 		173

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 317
1 2 3 4 5 6 range
A 312.3
(3)
P 		193.7
(-0.9)
P 		233.3
(0.4)
P 		128.5
(-3)
P 		240.3
(0.6)
P 		306.7
(2.8)
P 		184
B 337.4
(2.3)
P 		284.8
(0.4)
P 		230.2
(-1.6)
P 		191.8
(-3)
P 		322.2
(1.8)
P 		355.2
(3)
P 		163
C 445.9
(3)
P 		231.4
(-2.6)
P 		216.3
(-3)
P 		266.7
(-1.7)
P 		283.2
(-1.3)
P 		328.3
(-0.1)
P 		230
avr 365.2
(3) 		236.6
(-1.6) 		226.6
(-1.9) 		195.7
(-3) 		281.9
(0.1) 		330.1
(1.8) 		170
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 120
1 2 3 4 range
A 105.1
(3)
P 		55.3
(-0.6)
P 		79.7
(1.2)
P 		21.1
(-3)
P 		84
B 65.1
(-0.4)
P 		81
(3)
P 		78
(2.4)
P 		53
(-3)
P 		28
C 55.8
(-1.3)
P 		119.3
(1.9)
P 		141.1
(3)
P 		22.9
(-3)
P 		118
avr 75.3
(0.8) 		85.2
(1.7) 		99.6
(3) 		32.3
(-3) 		67

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 133
1 2 3 4 5 6 range
A 57.6
(0.6)
P 		68.9
(2.2)
P 		50.8
(-0.4)
P 		32.6
(-3)
P 		72.5
(2.7)
P 		74.7
(3)
P 		42
B 117.4
(1.9)
P 		94.8
(0.2)
P 		55.9
(-2.6)
P 		50.8
(-3)
P 		130.9
(2.9)
P 		132.5
(3)
P 		82
C 165.3
(3)
P 		70.6
(-2.1)
P 		55.1
(-2.9)
P 		53.6
(-3)
P 		91.6
(-1)
P 		109.9
(0)
P 		112
avr 113.4
(3) 		78.1
(-0.1) 		53.9
(-2.3) 		45.7
(-3) 		98.3
(1.7) 		105.7
(2.3) 		68
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173779_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.22593
Sequence Type Exemplar sequence
Representative Public ID CEC3753 NCBI
Target Description CEC3753_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=C25A1.4 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C10375 /WB_GENE_ID=C25A1.4 /WP=CE08369 /CHR=1 /FEA=Genomic Cluster /DEF=RNA binding protein; C.elegans cDNA clone yk145b5 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_060276(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_060276 NCBI Caenorhabditis elegans C25A1.4 (C25A1.4) mRNA, complete cds. 11/11 None
C25A1.4.1 ENSEMBL cdna:known chromosome:CEL140:I:10177760:10180724:-1 gene:C25A1.4 11/11 None
C25A1.4.3 ENSEMBL cdna:known chromosome:CEL140:I:10177771:10180726:-1 gene:C25A1.4 11/11 None
C25A1.4.2 ENSEMBL cdna:known chromosome:CEL140:I:10177771:10181336:-1 gene:C25A1.4 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:10177703-10180620(-) 100.0 100.0
Public Domain and Genome References
Gene Title RNA binding protein
Ensembl C25A1.4
Entrez Gene 172881 Entrez gene
SwissProt Q9XVS2 EMBL-EBI
WormBase CE08369 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1604834_AT similar to heterogeneous nuclear ribonucleoprotein M isoform a cfa
CANINE:1599820_S_AT similar to heterogeneous nuclear ribonucleoprotein M isoform a cfa
CANINE_2:CFA.17567.1.S1_S_AT similar to heterogeneous nuclear ribonucleoprotein M isoform a cfa
CANINE_2:CFA.20749.1.S1_S_AT similar to heterogeneous nuclear ribonucleoprotein M isoform a cfa
CANINE_2:CFAAFFX.28323.1.S1_S_AT similar to heterogeneous nuclear ribonucleoprotein M isoform a cfa
DROSOPHILA_2:1633767_AT dm
DROSGENOME1:152373_AT dm
CHICKEN:GGAAFFX.11957.1.S1_AT heterogeneous nuclear ribonucleoprotein M gga
CHICKEN:GGAAFFX.11957.1.S1_S_AT heterogeneous nuclear ribonucleoprotein M gga
CHICKEN:GGAAFFX.240.5.S1_S_AT heterogeneous nuclear ribonucleoprotein M gga
PLASMODIUM_ANOPHELES:200072_S_AT heterogeneous nuclear ribonucleoprotein M hs
HG-U133B:200072_S_AT heterogeneous nuclear ribonucleoprotein M hs
HG-FOCUS:200072_S_AT heterogeneous nuclear ribonucleoprotein M hs
HG-U133A:200072_S_AT heterogeneous nuclear ribonucleoprotein M hs
HG-U133_PLUS_2:200072_S_AT heterogeneous nuclear ribonucleoprotein M hs
HG-U133A_2:200072_S_AT heterogeneous nuclear ribonucleoprotein M hs
U133_X3P:200072_S_AT heterogeneous nuclear ribonucleoprotein M hs
HG-U133_PLUS_2:233605_X_AT heterogeneous nuclear ribonucleoprotein M hs
HG-U133B:233605_X_AT heterogeneous nuclear ribonucleoprotein M hs
HG-U133_PLUS_2:214918_AT heterogeneous nuclear ribonucleoprotein M hs
HG-U133A_2:214918_AT heterogeneous nuclear ribonucleoprotein M hs
HG-U133A:214918_AT heterogeneous nuclear ribonucleoprotein M hs
HU35KSUBA:HUM_ALU_AT heterogeneous nuclear ribonucleoprotein M hs
HU35KSUBB:HUM_ALU_AT heterogeneous nuclear ribonucleoprotein M hs
HU35KSUBC:HUM_ALU_AT heterogeneous nuclear ribonucleoprotein M hs
HU35KSUBD:HUM_ALU_AT heterogeneous nuclear ribonucleoprotein M hs
HUGENEFL:HUM_ALU_AT heterogeneous nuclear ribonucleoprotein M hs
HC-G110:HUM_ALU_AT heterogeneous nuclear ribonucleoprotein M hs
HUGENEFL:L03532_AT heterogeneous nuclear ribonucleoprotein M hs
U133_X3P:G3126877_3P_S_AT heterogeneous nuclear ribonucleoprotein M hs
U133_X3P:HS2.385766.1.A1_3P_X_AT heterogeneous nuclear ribonucleoprotein M hs
U133_X3P:HS2.385766.1.A1_3P_AT heterogeneous nuclear ribonucleoprotein M hs
U133_X3P:HS.288823.0.A1_3P_AT heterogeneous nuclear ribonucleoprotein M hs
U133_X3P:HS.287652.0.S1_3P_X_AT heterogeneous nuclear ribonucleoprotein M hs
U133_X3P:214918_3P_AT heterogeneous nuclear ribonucleoprotein M hs
HG-U133_PLUS_2:1555844_S_AT heterogeneous nuclear ribonucleoprotein M hs
HG-U133_PLUS_2:1556084_AT heterogeneous nuclear ribonucleoprotein M hs
HG-U95AV2:37717_AT heterogeneous nuclear ribonucleoprotein M hs
HG-U133_PLUS_2:234035_AT Heterogeneous nuclear ribonucleoprotein M hs
HG-U133B:234035_AT Heterogeneous nuclear ribonucleoprotein M hs
U133_X3P:HS2.356878.1.A1_3P_AT Heterogeneous nuclear ribonucleoprotein M hs
U133_X3P:HS.288823.0.S1_3P_AT Heterogeneous nuclear ribonucleoprotein M hs
U133_X3P:HS.157975.0.A1_3P_AT Heterogeneous nuclear ribonucleoprotein M hs
HG-U133_PLUS_2:1555843_AT Heterogeneous nuclear ribonucleoprotein M hs
HG-U133_PLUS_2:230392_AT Heterogeneous nuclear ribonucleoprotein M hs
HG-U133B:230392_AT Heterogeneous nuclear ribonucleoprotein M hs
HG-U95E:67177_AT Heterogeneous nuclear ribonucleoprotein M hs
HG-U95E:83809_AT Heterogeneous nuclear ribonucleoprotein M hs
HG-U133_PLUS_2:238610_S_AT Heterogeneous nuclear ribonucleoprotein M hs
HG-U133B:238610_S_AT Heterogeneous nuclear ribonucleoprotein M hs
HG-U133_PLUS_2:238611_AT Heterogeneous nuclear ribonucleoprotein M hs
HG-U133B:238611_AT Heterogeneous nuclear ribonucleoprotein M hs
HG-U133_PLUS_2:243593_S_AT Heterogeneous nuclear ribonucleoprotein M hs
HG-U133B:243593_S_AT Heterogeneous nuclear ribonucleoprotein M hs
HG-U95B:51443_AT Heterogeneous nuclear ribonucleoprotein M hs
HG-U95D:73206_AT Heterogeneous nuclear ribonucleoprotein M hs
HU35KSUBD:RC_R01415_AT Heterogeneous nuclear ribonucleoprotein M hs
U133_X3P:HS.225026.0.A1_3P_AT Heterogeneous nuclear ribonucleoprotein M hs
U133_X3P:HS.225026.1.A1_3P_AT Heterogeneous nuclear ribonucleoprotein M hs
MU11KSUBA:AA117835_S_AT heterogeneous nuclear ribonucleoprotein M mm
MG-U74AV2:96266_AT heterogeneous nuclear ribonucleoprotein M mm
MG-U74CV2:136707_F_AT heterogeneous nuclear ribonucleoprotein M mm
MOE430A:1426698_A_AT heterogeneous nuclear ribonucleoprotein M mm
MOUSE430A_2:1426698_A_AT heterogeneous nuclear ribonucleoprotein M mm
MOUSE430_2:1426698_A_AT heterogeneous nuclear ribonucleoprotein M mm
MG-U74BV2:106484_AT Heterogeneous nuclear ribonucleoprotein M (Hnrpm), mRNA mm
MOE430B:1443872_AT Heterogeneous nuclear ribonucleoprotein M (Hnrpm), mRNA mm
MOUSE430_2:1443872_AT Heterogeneous nuclear ribonucleoprotein M (Hnrpm), mRNA mm
MU19KSUBB:TC27941_AT Heterogeneous nuclear ribonucleoprotein M (Hnrpm), mRNA mm
MU19KSUBB:TC27941_G_AT Heterogeneous nuclear ribonucleoprotein M (Hnrpm), mRNA mm
MU19KSUBC:TC39644_AT Heterogeneous nuclear ribonucleoprotein M (Hnrpm), mRNA mm
MU19KSUBC:TC40317_AT Heterogeneous nuclear ribonucleoprotein M (Hnrpm), mRNA mm
Protein Similarities
Method ID Description E-Value
blast CAB02757 Hypothetical protein C25A1.4 [Caenorhabditis elegans] ref|NP_492677.1| C25A1.4 [Caenorhabditis elegans] 0.0
blast CAE66858 Hypothetical protein CBG12231 [Caenorhabditis briggsae] 0.0
blast EAL38591 ENSANGP00000026392 [Anopheles gambiae str. PEST] ref|XP_551368.1| ENSANGP00000026392 [Anopheles gambiae str. PEST] 2.0E-43
Protein Domains
Database ID Description E-Value
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 8.6E-13
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 2.8E-14
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 2.6E-11
Sequence
Target Sequence 
>C. ELEGANS:173779_AT
ttcattccccctgttatatttgtatttgaaacttctcacgtttctcttgaatcatcatct
attatctttattttatccgttttttctccatctctatccttccttatccctttaaaaagg
cttccttgtcaacggaatctcaataatttaaaacatcttcctcattttcatcactctaaa
actatttctcat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTCATTCCCCCTGTTATATTTGTAT 464 689 1379 Antisense
ATTTGTATTTGAAACTTCTCACGTT 138 19 1396 Antisense
AACTTCTCACGTTTCTCTTGAATCA 636 137 1408 Antisense
CACGTTTCTCTTGAATCATCATCTA 701 199 1415 Antisense
GAATCATCATCTATTATCTTTATTT 12 329 1427 Antisense
ATCTATTATCTTTATTTTATCCGTT 641 31 1435 Antisense
AAGGCTTCCTTGTCAACGGAATCTC 670 159 1495 Antisense
TGTCAACGGAATCTCAATAATTTAA 512 559 1505 Antisense
AATAATTTAAAACATCTTCCTCATT 554 169 1520 Antisense
CTTCCTCATTTTCATCACTCTAAAA 295 219 1535 Antisense
TCATCACTCTAAAACTATTTCTCAT 326 621 1546 Antisense
Sequence Source Affymetrix Proprietary Database