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[173984_at] signal recognition particle protein (SRP54)

Description CE12D11 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F21D5.7 /5_PRIME_EXT_DB=WormBase Gene ID /GB=M88956 /WB_GENE_ID=F21D5.7 /WP=CE09524 /CHR=4 /FEA=Genomic Cluster /DEF=signal recognition particle protein (SRP54); CEL12D11 Chris Martin sorted cDNA library Caenorhabditis elegans cDNA clone cm12d11 5prime similar to signal recognition particle 54K protein homologous peptide, mRNA sequence.
Cluster 6grp_highest_10_10 > 01      6grp_high1_10_10 > 0      4grp_highest_8_8 > 34      4grp_high_8_8 > 57      6grp_highest_nonorm > 57      6grp_total > 09      4grp_total > 63      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1508
1 2 3 4 range
A 2767.5
(3)
P 		1435.7
(-2.3)
P 		2160.5
(0.6)
P 		1260
(-3)
P 		1508
B 1880.6
(3)
P 		1606.7
(-3)
P 		1760.5
(0.4)
P 		1629.6
(-2.5)
P 		274
C 1840.7
(-0.8)
P 		1673.7
(-1.6)
P 		2671.2
(3)
P 		1357.4
(-3)
P 		1314
avr 2162.9
(2.7) 		1572
(-1.8) 		2197.4
(3) 		1415.7
(-3) 		782

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1768
1 2 3 4 5 6 range
A 2413.9
(0.6)
P 		2460.2
(0.8)
P 		1750.4
(-3)
P 		2868.2
(3)
P 		2180
(-0.7)
P 		2140.7
(-0.9)
P 		1118
B 2573.8
(3)
P 		2230.7
(1.3)
P 		1387.6
(-3)
P 		2504.3
(2.6)
P 		1853
(-0.6)
P 		2062.3
(0.4)
P 		1186
C 2768.9
(1.5)
P 		2199.9
(-0.7)
P 		3155.3
(3)
P 		2505.9
(0.5)
P 		1923.9
(-1.8)
P 		1621.6
(-3)
P 		1534
avr 2585.5
(2.6) 		2296.9
(0.1) 		2097.8
(-1.6) 		2626.1
(3) 		1985.6
(-2.6) 		1941.5
(-3) 		685
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 823
1 2 3 4 range
A 1007.6
(3)
P 		311.6
(-2.1)
P 		564.8
(-0.2)
P 		184.4
(-3)
P 		823
B 599.7
(3)
P 		396.8
(-1.8)
P 		408
(-1.6)
P 		347.3
(-3)
P 		252
C 609.3
(0.3)
P 		481.2
(-0.8)
P 		931
(3)
P 		228.9
(-3)
P 		702
avr 738.9
(3) 		396.5
(-1.2) 		634.6
(1.7) 		253.5
(-3) 		485

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 689
1 2 3 4 5 6 range
A 445
(-2.2)
P 		875
(3)
P 		381.2
(-3)
P 		727.5
(1.2)
P 		657.8
(0.4)
P 		521.2
(-1.3)
P 		494
B 895.6
(3)
P 		742.5
(1.4)
P 		337
(-3)
P 		663.3
(0.5)
P 		752.9
(1.5)
P 		769
(1.6)
P 		559
C 1026.3
(3)
P 		671.2
(-1.1)
P 		803.1
(0.4)
P 		503.9
(-3)
P 		622.5
(-1.6)
P 		542.8
(-2.6)
P 		522
avr 789
(3) 		762.9
(2.4) 		507.1
(-3) 		631.6
(-0.4) 		677.7
(0.6) 		611
(-0.8) 		282
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173984_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.24802
Sequence Type Exemplar sequence
Representative Public ID CE12D11 NCBI
Target Description CE12D11 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F21D5.7 /5_PRIME_EXT_DB=WormBase Gene ID /GB=M88956 /WB_GENE_ID=F21D5.7 /WP=CE09524 /CHR=4 /FEA=Genomic Cluster /DEF=signal recognition particle protein (SRP54); CEL12D11 Chris Martin sorted cDNA library Caenorhabditis elegans cDNA clone cm12d11 5prime similar to signal recognition particle 54K protein homologous peptide, mRNA sequence.
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_069106(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069106 NCBI Caenorhabditis elegans F21D5.7 (F21D5.7) mRNA, complete cds. 11/11 None
F21D5.7.1 ENSEMBL cdna:known chromosome:CEL140:IV:8741378:8743688:-1 gene:F21D5.7 11/11 A 
F21D5.7.2 ENSEMBL cdna:known chromosome:CEL140:IV:8741494:8743686:-1 gene:F21D5.7 11/11 A 
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:8741524-8743687(-) 100.0 100.0
Public Domain and Genome References
Gene Title signal recognition particle protein (SRP54)
Ensembl F21D5.7
Entrez Gene 259584 Entrez gene
SwissProt Q19639 EMBL-EBI
WormBase CE09524 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:246628_AT signal recognition particle 54 kDa protein 3 / SRP54 (SRP-54C) at
ATGENOME1:17474_AT signal recognition particle 54 kDa protein 3 / SRP54 (SRP-54C) at
CANINE:1587448_AT signal recognition particle 54kDa cfa
CANINE_2:CFA.3810.1.S1_AT signal recognition particle 54kDa cfa
CANINE_2:CFAAFFX.20628.1.S1_S_AT signal recognition particle 54kDa cfa
DROSOPHILA_2:1633320_AT Signal recognition particle protein 54k dm
DROSGENOME1:143632_AT Signal recognition particle protein 54k dm
CHICKEN:GGA.1375.1.S1_AT similar to signal recognition particle 54kDa; signal recognition particle 54kD gga
CHICKEN:GGA.1375.2.S1_S_AT similar to signal recognition particle 54kDa; signal recognition particle 54kD gga
CHICKEN:GGA.1375.3.S1_S_AT similar to signal recognition particle 54kDa; signal recognition particle 54kD gga
HG-U133A:203605_AT signal recognition particle 54kDa hs
HG-U133A_2:203605_AT signal recognition particle 54kDa hs
HG-U133_PLUS_2:203605_AT signal recognition particle 54kDa hs
HG-FOCUS:203605_AT signal recognition particle 54kDa hs
HUGENEFL:U51920_AT signal recognition particle 54kDa hs
U133_X3P:G4507214_3P_AT signal recognition particle 54kDa hs
HG-U95AV2:36060_AT signal recognition particle 54kDa hs
HG-U95E:84475_AT signal recognition particle 54kDa hs
U133_X3P:HS2.167535.1.A1_3P_S_AT Signal recognition particle 54kDa hs
U133_X3P:HS2.167535.1.A1_3P_AT Signal recognition particle 54kDa hs
U133_X3P:1557505_3P_A_AT Signal recognition particle 54kDa hs
HG-U133_PLUS_2:1557504_AT Signal recognition particle 54kDa hs
HG-U133_PLUS_2:1557505_A_AT Signal recognition particle 54kDa hs
HG-U95D:91830_I_AT Signal recognition particle 54kDa hs
HG-U95D:91832_R_AT Signal recognition particle 54kDa hs
MOUSE430_2:1430476_AT signal recognition particle 54 mm
MOE430B:1430476_AT signal recognition particle 54 mm
MOUSE430_2:1425665_A_AT signal recognition particle 54 mm
MOE430A:1425665_A_AT signal recognition particle 54 mm
MOUSE430A_2:1425665_A_AT signal recognition particle 54 mm
MU11KSUBB:X16319_S_AT signal recognition particle 54 mm
MG-U74CV2:169765_AT signal recognition particle 54 mm
MOE430A:1416153_AT signal recognition particle 54 mm
MOUSE430A_2:1416153_AT signal recognition particle 54 mm
MOUSE430_2:1416153_AT signal recognition particle 54 mm
MOE430A:1416154_AT signal recognition particle 54 mm
MOUSE430A_2:1416154_AT signal recognition particle 54 mm
MOUSE430_2:1416154_AT signal recognition particle 54 mm
MG-U74AV2:160073_I_AT signal recognition particle 54 mm
MU19KSUBA:TC20784_S_AT Signal recognition particle 54, mRNA (cDNA clone MGC:30254 IMAGE:3708250) mm
MU19KSUBB:TC25941_AT Signal recognition particle 54, mRNA (cDNA clone MGC:30254 IMAGE:3708250) mm
MU19KSUBC:TC40902_AT Signal recognition particle 54, mRNA (cDNA clone MGC:30254 IMAGE:3708250) mm
RG-U34B:RC_AA924196_AT signal recognition particle 54 rn
RAE230B:1383410_AT signal recognition particle 54 rn
RAT230_2:1383410_AT signal recognition particle 54 rn
RAE230B:1385680_AT signal recognition particle 54 rn
RAT230_2:1385680_AT signal recognition particle 54 rn
RG-U34C:H32369_AT Signal recognition particle 54 rn
YEAST_2:1775642_AT Signal recognition particle (SRP) subunit (homolog of mammalian SRP54); contains the signal sequence-binding activity of SRP, interacts with the SRP RNA, and mediates binding of SRP to signal receptor; contains GTPase domain Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6605 protein targeting inferred from electronic annotation QuickGO AmiGO
6614 SRP-dependent cotranslational protein targeting to membrane inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5786 signal recognition particle (sensu Eukaryota) inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
166 nucleotide binding inferred from electronic annotation QuickGO AmiGO
3723 RNA binding inferred from electronic annotation QuickGO AmiGO
5525 GTP binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA92301 Hypothetical protein F21D5.7 [Caenorhabditis elegans] emb|CAA91040.1| Hypothetical protein F21D5.7 [Caenorhabditis elegans] ref|NP_501507.1| F21D5.7 [Caenorhabditis elegans] 0.0
blast CAE70021 Hypothetical protein CBG16436 [Caenorhabditis briggsae] 0.0
blast AAH44991 Srp54-prov protein [Xenopus laevis] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR004125 EMBL-EBI Signal peptide binding (SRP54) M-domain 8.6E-57
Pfam IPR000897 EMBL-EBI GTP-binding signal recognition particle (SRP54) G-domain 1.3E-19
Pfam IPR000897 EMBL-EBI GTP-binding signal recognition particle (SRP54) G-domain 4.4E-111
Sequence
Target Sequence 
>C. ELEGANS:173984_AT
aaatggatgcaattattttctgtagtttttgaaatgcctgttcccagttcccacaattca
ttctgactaaaacgttttttaataatatcaatatgatttctcgatttccctttcatcaga
atgtttcccaagttcattttttgtctagcagattctgtgattctaattag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AAATGGATGCAATTATTTTCTGTAG 89 121 1507 Antisense
GTAGTTTTTGAAATGCCTGTTCCCA 152 457 1528 Antisense
TTTTGAAATGCCTGTTCCCAGTTCC 422 675 1533 Antisense
TCCCAGTTCCCACAATTCATTCTGA 623 597 1548 Antisense
GTTCCCACAATTCATTCTGACTAAA 705 441 1553 Antisense
AATATGATTTCTCGATTTCCCTTTC 517 173 1596 Antisense
TCTCGATTTCCCTTTCATCAGAATG 507 611 1605 Antisense
TCCCTTTCATCAGAATGTTTCCCAA 275 597 1613 Antisense
TGTTTCCCAAGTTCATTTTTTGTCT 483 561 1628 Antisense
TCATTTTTTGTCTAGCAGATTCTGT 72 621 1640 Antisense
TAGCAGATTCTGTGATTCTAATTAG 395 649 1652 Antisense
Sequence Source Affymetrix Proprietary Database