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[173129_s_at] seryl-tRNA synthetase

Description AV183073_rc /REP_DB=TREMBL Accession /FEA=EST Transcript /REVCOMP /GB=AV183073 /DEF=Caenorhabditis elegans cDNA clone:yk646b9 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 63      6grp_high1_10_10 > 36      4grp_highest_8_8 > 22      4grp_high_8_8 > 06      6grp_highest_nonorm > 36      6grp_total > 36      4grp_total > 01      6grp_highest_sub > Cu      6grp_cgc > 15      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 7932
1 2 3 4 range
A 5560.3
(-2.9)
P 		5473.4
(-3)
P 		6087.5
(-2.4)
P 		12018.7
(3)
P 		6545
B 5662.7
(-2.3)
P 		4738.2
(-3)
P 		5809.8
(-2.1)
P 		12191.8
(3)
P 		7454
C 4932.1
(-2.5)
P 		4260.2
(-3)
P 		5723.1
(-1.9)
P 		11995.8
(3)
P 		7736
avr 5385
(-2.5) 		4823.9
(-3) 		5873.5
(-2.1) 		12068.8
(3) 		7245

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1957
1 2 3 4 5 6 range
A 4207.8
(-0.7)
P 		4803.3
(3)
P 		3973.7
(-2.1)
P 		3981.6
(-2.1)
P 		3834.7
(-3)
P 		4738.3
(2.6)
P 		969
B 4907.8
(3)
P 		4586.7
(1.9)
P 		3075.7
(-3)
P 		3890
(-0.3)
P 		3665.6
(-1.1)
P 		4184.9
(0.6)
P 		1832
C 5032.9
(3)
P 		4404.2
(0.1)
P 		4787.9
(1.9)
P 		4434.7
(0.2)
P 		3747.8
(-3)
P 		4384
(-0)
P 		1285
avr 4716.2
(3) 		4598.1
(2.3) 		3945.8
(-1.8) 		4102.1
(-0.8) 		3749.4
(-3) 		4435.7
(1.3) 		967
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1428
1 2 3 4 range
A 2024.5
(3)
P 		1188.1
(-3)
P 		1591.4
(-0.1)
P 		1759.3
(1.1)
P 		836
B 1805.8
(-0.3)
P 		1170.2
(-3)
P 		1346.3
(-2.3)
P 		2598.1
(3)
P 		1428
C 1632.7
(0.1)
P 		1224.8
(-3)
P 		1994.7
(2.8)
P 		2022.7
(3)
P 		798
avr 1821
(1) 		1194.4
(-3) 		1644.1
(-0.1) 		2126.7
(3) 		932

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1119
1 2 3 4 5 6 range
A 775.7
(-3)
P 		1708.3
(3)
P 		865.4
(-2.4)
P 		1009.8
(-1.5)
P 		1157.1
(-0.5)
P 		1153.6
(-0.6)
P 		933
B 1707.7
(3)
P 		1526.7
(1.9)
P 		746.9
(-3)
P 		1030.3
(-1.2)
P 		1489.3
(1.6)
P 		1560.5
(2.1)
P 		961
C 1865.5
(3)
P 		1343.8
(-0.2)
P 		1218.6
(-1)
P 		891.8
(-3)
P 		1212.7
(-1)
P 		1467.6
(0.5)
P 		974
avr 1449.6
(2.2) 		1526.3
(3) 		943.6
(-3) 		977.3
(-2.7) 		1286.4
(0.5) 		1393.9
(1.6) 		583
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173129_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.26829
Sequence Type Exemplar sequence
Representative Public ID AV183073 NCBI
Target Description AV183073_rc /REP_DB=TREMBL Accession /FEA=EST Transcript /REVCOMP /GB=AV183073 /DEF=Caenorhabditis elegans cDNA clone:yk646b9 : 3prime end, single read.
Cluster Evidence This cluster is supported by a EST Transcript.
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_069403(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069403 NCBI Caenorhabditis elegans Seryl tRNA Synthetase family member (srs-2) (srs-2) mRNA, complete cds. 11/11 A 
SNAP00000021573 ENSEMBL cdna:SNAP chromosome:CEL140:IV:10003726:10005396:1 11/11 None
GENEFINDER00000021588 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:10003726:10005396:1 11/11 None
C47E12.1.2 ENSEMBL cdna:known chromosome:CEL140:IV:10003671:10005551:1 gene:C47E12.1 11/11 None
C47E12.1.4 ENSEMBL cdna:known chromosome:CEL140:IV:10003692:10005529:1 gene:C47E12.1 11/11 None
C47E12.1.3 ENSEMBL cdna:known chromosome:CEL140:IV:10003698:10005550:1 gene:C47E12.1 11/11 None
C47E12.1.1 ENSEMBL cdna:known chromosome:CEL140:IV:10003698:10005551:1 gene:C47E12.1 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:10005149-10005459(+) 84.67 84.67
Public Domain and Genome References
Gene Title seryl-tRNA synthetase
Gene Symbol srs-2
Ensembl C47E12.1
Entrez Gene 177859 Entrez gene
SwissProt Q18678 EMBL-EBI
WormBase CE05445 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:20545_AT seryl-tRNA synthetase / serine--tRNA ligase at
ATH1-121501:246780_AT seryl-tRNA synthetase / serine--tRNA ligase at
CANINE:1602740_S_AT similar to seryl-tRNA synthetase cfa
CANINE:1596298_AT similar to seryl-tRNA synthetase cfa
CANINE:1588781_AT similar to seryl-tRNA synthetase cfa
CANINE:1587051_AT similar to seryl-tRNA synthetase cfa
CANINE:1584564_S_AT similar to seryl-tRNA synthetase cfa
CANINE:1584563_AT similar to seryl-tRNA synthetase cfa
CANINE_2:CFA.18627.1.S1_S_AT similar to seryl-tRNA synthetase cfa
CANINE_2:CFA.19116.1.S1_S_AT similar to seryl-tRNA synthetase cfa
CANINE_2:CFA.6293.1.A1_AT similar to seryl-tRNA synthetase cfa
CANINE_2:CFA.7872.1.A1_A_AT similar to seryl-tRNA synthetase cfa
CANINE_2:CFA.7872.1.A1_S_AT similar to seryl-tRNA synthetase cfa
CANINE_2:CFAAFFX.30372.1.S1_AT similar to seryl-tRNA synthetase cfa
DROSOPHILA_2:1638642_AT dm
DROSGENOME1:142167_AT dm
CHICKEN:GGAAFFX.335.1.S1_S_AT seryl-tRNA synthetase gga
HG-U133_PLUS_2:200802_AT seryl-tRNA synthetase hs
HG-U133A:200802_AT seryl-tRNA synthetase hs
HG-FOCUS:200802_AT seryl-tRNA synthetase hs
HG-U133A_2:200802_AT seryl-tRNA synthetase hs
HUGENEFL:X91257_AT seryl-tRNA synthetase hs
U133_X3P:G5730028_3P_AT seryl-tRNA synthetase hs
HG-U95AV2:34849_AT seryl-tRNA synthetase hs
HG-U95E:75529_AT seryl-tRNA synthetase hs
HG-U133_PLUS_2:231894_AT Seryl-tRNA synthetase hs
HG-U133B:231894_AT Seryl-tRNA synthetase hs
HU35KSUBA:RC_AA406640_S_AT Seryl-tRNA synthetase hs
U133_X3P:HS.18498.0.S1_3P_AT Seryl-tRNA synthetase hs
HG-U95B:51666_I_AT Seryl-tRNA synthetase hs
HG-U95B:51667_F_AT Seryl-tRNA synthetase hs
HG-U133_PLUS_2:237689_AT Seryl-tRNA synthetase hs
HG-U133B:237689_AT Seryl-tRNA synthetase hs
U133_X3P:HS.144063.0.A1_3P_AT Seryl-tRNA synthetase hs
MU11KSUBA:AA497681_S_AT seryl-aminoacyl-tRNA synthetase 1 mm
MU11KSUBB:MSA.3900.0_S_AT seryl-aminoacyl-tRNA synthetase 1 mm
MU11KSUBB:MSA.34802.0_S_AT seryl-aminoacyl-tRNA synthetase 1 mm
MU11KSUBB:MSA.42131.0_F_AT seryl-aminoacyl-tRNA synthetase 1 mm
MG-U74AV2:98936_AT seryl-aminoacyl-tRNA synthetase 1 mm
MOE430A:1426257_A_AT seryl-aminoacyl-tRNA synthetase 1 mm
MOUSE430A_2:1426257_A_AT seryl-aminoacyl-tRNA synthetase 1 mm
MOUSE430_2:1426257_A_AT seryl-aminoacyl-tRNA synthetase 1 mm
MOE430A:1452000_S_AT seryl-aminoacyl-tRNA synthetase 1 mm
MOUSE430A_2:1452000_S_AT seryl-aminoacyl-tRNA synthetase 1 mm
MOUSE430_2:1452000_S_AT seryl-aminoacyl-tRNA synthetase 1 mm
MU19KSUBA:TC17090_AT Seryl-aminoacyl-tRNA synthetase 1, mRNA (cDNA clone MGC:7162 IMAGE:3257101) mm
MU19KSUBB:TC33952_AT Seryl-aminoacyl-tRNA synthetase 1, mRNA (cDNA clone MGC:7162 IMAGE:3257101) mm
RG-U34B:RC_AA957307_AT seryl-aminoacyl-tRNA synthetase 1 rn
RAE230A:1375441_AT seryl-aminoacyl-tRNA synthetase 1 rn
RAT230_2:1375441_AT seryl-aminoacyl-tRNA synthetase 1 rn
RAE230B:1392262_AT Seryl-aminoacyl-tRNA synthetase 1 rn
RAT230_2:1392262_AT Seryl-aminoacyl-tRNA synthetase 1 rn
YEAST_2:1776877_AT Cytosolic seryl-tRNA synthetase, class II aminoacyl-tRNA synthetase that aminoacylates tRNA(Ser), displays tRNA-dependent amino acid recognition which enhances discrimination of the serine substrate, interacts with peroxin Pex21p Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6418 tRNA aminoacylation for protein translation inferred from electronic annotation QuickGO AmiGO
6434 seryl-tRNA aminoacylation inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
4812 tRNA ligase activity inferred from electronic annotation QuickGO AmiGO
4828 serine-tRNA ligase activity inferred from electronic annotation QuickGO AmiGO
5524 ATP binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA93105 Hypothetical protein C47E12.1 [Caenorhabditis elegans] ref|NP_501804.1| Seryl tRNA Synthetase family member (srs-2) [Caenorhabditis elegans] sp|Q18678|SYS_CAEEL Probable seryl-tRNA synthetase (Serine--tRNA ligase) (SerRS) 0.0
blast CAE59948 Hypothetical protein CBG03435 [Caenorhabditis briggsae] 0.0
blast AAH67920 Seryl-aminoacyl-tRNA synthetase 1 [Xenopus tropicalis] ref|NP_998852.1| seryl-aminoacyl-tRNA synthetase 1 [Xenopus tropicalis] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR002314 EMBL-EBI tRNA synthetases, class-II (G, H, P and S) 3.7E-56
Pfam IPR002317 EMBL-EBI Seryl-tRNA synthetase, class IIa 4.8E-29
Sequence
Target Sequence 
>C. ELEGANS:173129_S_AT
atttgtacatatgctcaacgcaacaatgtgtgctacaactcgtgtcatttgcgccatcct
cgaaaataatcaaactgaagaaggaatcaatgtaccaaccgctattcaacaatggatgcc
agaaaactaccgtacattcattccattcgttaaaccagcgccgatcgacgaggatgccaa
aa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATTTGTACATATGCTCAACGCAACA 625 17 13 Antisense
GCTCAACGCAACAATGTGTGCTACA 557 301 25 Antisense
GTGCTACAACTCGTGTCATTTGCGC 313 479 42 Antisense
TCATTTGCGCCATCCTCGAAAATAA 615 619 57 Antisense
GCGCCATCCTCGAAAATAATCAAAC 584 287 63 Antisense
AAGGAATCAATGTACCAACCGCTAT 73 161 93 Antisense
GTACCAACCGCTATTCAACAATGGA 12 457 104 Antisense
ACTACCGTACATTCATTCCATTCGT 599 101 138 Antisense
CATTCCATTCGTTAAACCAGCGCCG 18 217 151 Antisense
TCGTTAAACCAGCGCCGATCGACGA 167 581 159 Antisense
GCGCCGATCGACGAGGATGCCAAAA 379 287 170 Antisense
Sequence Source Affymetrix Proprietary Database