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[193894_at] 5-methyltetrahydrofolate-homocysteine methyltransferase

Description R03D7.1 /REP_DB=WormBase Gene ID /WP=CE01609 /TR=SW:Q09582 /GB=CAA86855.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=5-methyltetrahydrofolate-homocysteine methyltransferase
Cluster 6grp_highest_10_10 > 84      6grp_high1_10_10 > 47      4grp_highest_8_8 > 12      4grp_high_8_8 > 39      6grp_highest_nonorm > 66      6grp_total > 47      4grp_total > 32      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 3018
1 2 3 4 range
A 1215.4
(-3)
P 		2999.1
(0.8)
P 		4040
(3)
P 		3472.2
(1.8)
P 		2825
B 1262.4
(-3)
P 		2854.2
(0.7)
P 		3844.5
(2.9)
P 		3876.4
(3)
P 		2614
C 1021.7
(-3)
P 		2734.7
(1.1)
P 		3498.8
(3)
P 		3387.4
(2.7)
P 		2477
avr 1166.5
(-3) 		2862.7
(0.9) 		3794.4
(3) 		3578.7
(2.5) 		2628

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 852
1 2 3 4 5 6 range
A 1556
(1)
P 		1556.1
(1)
P 		986.7
(-3)
P 		1450.4
(0.3)
P 		1263.6
(-1)
P 		1838.6
(3)
P 		852
B 1514.4
(3)
P 		1471.8
(2.1)
P 		1362.6
(-0.3)
P 		1286.2
(-1.9)
P 		1237.1
(-3)
P 		1486.6
(2.4)
P 		277
C 1702.7
(3)
P 		1418.3
(-1.9)
P 		1579.3
(0.9)
P 		1352.4
(-3)
P 		1518.4
(-0.2)
P 		1688.1
(2.7)
P 		350
avr 1591
(1.7) 		1482.1
(-0.1) 		1309.5
(-3) 		1363
(-2.1) 		1339.7
(-2.5) 		1671.1
(3) 		362
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 881
1 2 3 4 range
A 442.5
(-3)
P 		651
(-1)
P 		1056.1
(3)
P 		508.3
(-2.4)
P 		614
B 402.6
(-3)
P 		704.9
(0.7)
P 		890.9
(3)
P 		826.1
(2.2)
P 		488
C 338.2
(-3)
P 		786.3
(0.1)
P 		1219.4
(3)
P 		571.2
(-1.4)
P 		881
avr 394.4
(-3) 		714.1
(-0.1) 		1055.5
(3) 		635.2
(-0.8) 		661

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 416
1 2 3 4 5 6 range
A 286.8
(-1.7)
P 		553.4
(3)
P 		214.9
(-3)
P 		367.9
(-0.3)
P 		381.3
(-0.1)
P 		447.7
(1.1)
P 		339
B 526.9
(2.3)
P 		489.9
(1.3)
P 		330.9
(-3)
P 		340.7
(-2.7)
P 		502.6
(1.6)
P 		554.4
(3)
P 		224
C 631.1
(3)
P 		432.8
(-0.3)
P 		402
(-0.8)
P 		272
(-3)
P 		491.3
(0.7)
P 		565.1
(1.9)
P 		359
avr 481.6
(1.8) 		492
(2.1) 		315.9
(-3) 		326.9
(-2.7) 		458.4
(1.1) 		522.4
(3) 		207
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193894_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.2609
Sequence Type Exemplar sequence
Representative Public ID R03D7.1 NCBI
Target Description R03D7.1 /REP_DB=WormBase Gene ID /WP=CE01609 /TR=SW:Q09582 /GB=CAA86855.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=5-methyltetrahydrofolate-homocysteine methyltransferase
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_063952(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063952 NCBI Caenorhabditis elegans R03D7.1 (R03D7.1) mRNA, complete cds. 11/11 None
SNAP00000040565 ENSEMBL cdna:SNAP chromosome:CEL140:II:10926475:10930794:1 11/11 None
GENEFINDER00000040581 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:10926475:10930794:1 11/11 None
R03D7.1 ENSEMBL cdna:known chromosome:CEL140:II:10926472:10931229:1 gene:R03D7.1 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
chrII:10926471-10930791(+) 100.0 100.0
Public Domain and Genome References
Gene Title 5-methyltetrahydrofolate-homocysteine methyltransferase
Ensembl R03D7.1
Entrez Gene 174681 Entrez gene
SwissProt Q09582 EMBL-EBI
WormBase CE01609 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1602578_AT similar to Methionine synthase (5-methyltetrahydrofolate--homocysteine methyltransferase) (Methionine synthase, vitamin-B12 dependent) (MS) cfa
CANINE_2:CFAAFFX.16559.1.S1_S_AT similar to Methionine synthase (5-methyltetrahydrofolate--homocysteine methyltransferase) (Methionine synthase, vitamin-B12 dependent) (MS) cfa
CHICKEN:GGAAFFX.12960.1.S1_AT 5-methyltetrahydrofolate-homocysteine methyltransferase gga
CHICKEN:GGAAFFX.1815.1.S1_S_AT 5-methyltetrahydrofolate-homocysteine methyltransferase gga
CHICKEN:GGAAFFX.6847.2.S1_S_AT 5-methyltetrahydrofolate-homocysteine methyltransferase gga
CHICKEN:GGAAFFX.9187.1.S1_S_AT 5-methyltetrahydrofolate-homocysteine methyltransferase gga
HG-U133_PLUS_2:203774_AT 5-methyltetrahydrofolate-homocysteine methyltransferase hs
HG-U133A:203774_AT 5-methyltetrahydrofolate-homocysteine methyltransferase hs
HG-FOCUS:203774_AT 5-methyltetrahydrofolate-homocysteine methyltransferase hs
HG-U133A_2:203774_AT 5-methyltetrahydrofolate-homocysteine methyltransferase hs
HUGENEFL:U73338_AT 5-methyltetrahydrofolate-homocysteine methyltransferase hs
U133_X3P:G4557764_3P_AT 5-methyltetrahydrofolate-homocysteine methyltransferase hs
HG-U95AV2:38383_AT 5-methyltetrahydrofolate-homocysteine methyltransferase hs
HG-U133_PLUS_2:244093_AT 5-methyltetrahydrofolate-homocysteine methyltransferase hs
HG-U133B:244093_AT 5-methyltetrahydrofolate-homocysteine methyltransferase hs
HG-U95C:60125_AT 5-methyltetrahydrofolate-homocysteine methyltransferase hs
HU35KSUBB:RC_N74501_AT 5-methyltetrahydrofolate-homocysteine methyltransferase hs
U133_X3P:HS.34504.0.A1_3P_AT 5-methyltetrahydrofolate-homocysteine methyltransferase hs
MOUSE430_2:1439811_AT 5-methyltetrahydrofolate-homocysteine methyltransferase mm
MOE430B:1439811_AT 5-methyltetrahydrofolate-homocysteine methyltransferase mm
MG-U74BV2:116994_AT 5-methyltetrahydrofolate-homocysteine methyltransferase mm
MOE430B:1458532_AT 5-methyltetrahydrofolate-homocysteine methyltransferase mm
MOUSE430_2:1458532_AT 5-methyltetrahydrofolate-homocysteine methyltransferase mm
MG-U74AV2:101660_AT 5-methyltetrahydrofolate-homocysteine methyltransferase mm
MU11KSUBA:AA415486_RC_AT 5-methyltetrahydrofolate-homocysteine methyltransferase mm
MU19KSUBC:TC36110_AT PREDICTED: 5-methyltetrahydrofolate-homocysteine methyltransferase [Mus musculus], mRNA sequence mm
RG-U34A:AF034214_AT 5-methyltetrahydrofolate-homocysteine methyltransferase rn
RAE230A:1387545_AT 5-methyltetrahydrofolate-homocysteine methyltransferase rn
RAT230_2:1387545_AT 5-methyltetrahydrofolate-homocysteine methyltransferase rn
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
9086 methionine biosynthesis inferred from electronic annotation QuickGO AmiGO
9396 folic acid and derivative biosynthesis inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5622 intracellular inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
4156 dihydropteroate synthase activity inferred from electronic annotation QuickGO AmiGO
8705 methionine synthase activity inferred from electronic annotation QuickGO AmiGO
8898 homocysteine S-methyltransferase activity inferred from electronic annotation QuickGO AmiGO
50897 cobalt ion binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA86855 Hypothetical protein R03D7.1 [Caenorhabditis elegans] ref|NP_496353.1| R03D7.1 [Caenorhabditis elegans] sp|Q09582|METH_CAEEL Probable methionine synthase (5-methyltetrahydrofolate--homocysteine methyltransferase) (Methionine synthase, vitamin-B12 dependent) (MS) 0.0
blast CAE73229 Hypothetical protein CBG20636 [Caenorhabditis briggsae] 0.0
blast NP_001025469 5-methyltetrahydrofolate-homocysteine methyltransferase [Bos taurus] gb|AAY86762.1| 5-methyltetrahydrofolate-homocysteine methyltransferase [Bos taurus] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000489 EMBL-EBI Dihydropteroate synthase, DHPS 9.0E-75
Pfam IPR004223 EMBL-EBI Vitamin B12 dependent methionine synthase activation domain 1.0E-126
Pfam IPR003759 EMBL-EBI Cobalamin-dependent methionine synthase, B12-binding 1.1E-46
Pfam IPR003726 EMBL-EBI Homocysteine S-methyltransferase 1.0E-126
Pfam IPR006158 EMBL-EBI Coenzyme B12-binding 1.0E-29
Sequence
Target Sequence 
>C. ELEGANS:193894_AT
aagctcgacacattctacggtcttcgccaacaatctggacgtgaacacgatcaaccacat
ttctgtctctcggatttcatcaagccactcaaaaatggcgtccctgatgattaccttggt
ctattcgcttgtactgctggtctcggagccgaagaatactgtaaaactcttgaaaagaat
catgatgattatgcttcaattatggtgaaagctcttgccgatcgtcttgccgaagcatac
gctgaatacttgcacaaagaagtgagaacgactctttggggatattcaaccaacgaagat
ctcaccgaatctgatcttttgtcgatcaaatatcaaggtattcgcccggcgtgtggctat
ccatctcaaccggatcacactgaaaagcgaactctttggaagctgcttgaggcggaaaag
aatggaattgggctcacggagcatcttgctatgcttccagctgcatcagtgtctggactc
tatttcgcgaat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AAGCTCGACACATTCTACGGTCTTC 512 149 3139 Antisense
GTCTTCGCCAACAATCTGGACGTGA 471 467 3158 Antisense
CGATCAACCACATTTCTGTCTCTCG 291 249 3186 Antisense
TGTCTCTCGGATTTCATCAAGCCAC 218 559 3202 Antisense
AAAATGGCGTCCCTGATGATTACCT 439 131 3230 Antisense
ATTACCTTGGTCTATTCGCTTGTAC 510 13 3248 Antisense
TATGGTGAAAGCTCTTGCCGATCGT 679 653 3339 Antisense
CCGATCGTCTTGCCGAAGCATACGC 169 265 3356 Antisense
ATCTCACCGAATCTGATCTTTTGTC 146 33 3437 Antisense
TATGCTTCCAGCTGCATCAGTGTCT 551 657 3588 Antisense
AGTGTCTGGACTCTATTTCGCGAAT 413 57 3606 Antisense
Sequence Source Affymetrix Proprietary Database