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[173262_s_at] aminomethytransferase

Description CEC3034_rc /REP_DB=TREMBL Accession /GB=C11303 /FEA=Transcript Cluster /DEF=C.elegans cDNA clone yk170c2 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 35      6grp_high1_10_10 > 53      4grp_highest_8_8 > 17      4grp_high_8_8 > 61      6grp_highest_nonorm > 24      6grp_total > 20      4grp_total > 59      6grp_highest_sub > 03      6grp_high1_sub > 03      6grp_total_sub > Hat      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 3476
1 2 3 4 range
A 4165.8
(0.2)
P 		4545.4
(1.1)
P 		5363
(3)
P 		2755.1
(-3)
P 		2608
B 4161.5
(0.9)
P 		5071.1
(3)
P 		4870
(2.5)
P 		2532.5
(-3)
P 		2539
C 4442.1
(0.6)
P 		4963.3
(1.5)
P 		5811
(3)
P 		2334.8
(-3)
P 		3476
avr 4256.5
(0.7) 		4859.9
(2) 		5348
(3) 		2540.8
(-3) 		2807

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2560
1 2 3 4 5 6 range
A 3016.9
(-1.4)
P 		4316.6
(2)
P 		4712.7
(3)
P 		3397.3
(-0.4)
P 		2385.6
(-3)
P 		2736.6
(-2.1)
P 		2327
B 2152.7
(-3)
P 		4032.7
(2.5)
P 		4206.1
(3)
P 		3213.8
(0.1)
P 		2501.2
(-2)
P 		2795.2
(-1.1)
P 		2053
C 2701.7
(-2.5)
P 		3253.5
(-1)
P 		4670.4
(3)
P 		2985.3
(-1.7)
P 		2536.2
(-3)
P 		3355.4
(-0.7)
P 		2134
avr 2623.8
(-2.6) 		3867.6
(1.1) 		4529.7
(3) 		3198.8
(-0.9) 		2474.3
(-3) 		2962.4
(-1.6) 		2055
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1632
1 2 3 4 range
A 1516.8
(3)
P 		986.7
(0.1)
P 		1402
(2.4)
P 		403.3
(-3)
P 		1114
B 1327.1
(3)
P 		1252.4
(2.4)
P 		1128.5
(1.5)
P 		539.7
(-3)
P 		787
C 1470.4
(1)
P 		1427
(0.8)
P 		2025.3
(3)
P 		393.7
(-3)
P 		1632
avr 1438.1
(2.5) 		1222
(1.3) 		1518.6
(3) 		445.6
(-3) 		1073

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 979
1 2 3 4 5 6 range
A 556.1
(-3)
P 		1535.2
(3)
P 		1026.3
(-0.1)
P 		861.6
(-1.1)
P 		719.9
(-2)
P 		666.3
(-2.3)
P 		979
B 749
(-3)
P 		1342.3
(3)
P 		1021.4
(-0.2)
P 		851.2
(-2)
P 		1016.2
(-0.3)
P 		1042.3
(-0)
P 		593
C 1001.4
(1.1)
P 		992.7
(1)
P 		1188.7
(3)
P 		600.3
(-3)
P 		820.7
(-0.8)
P 		1123.2
(2.3)
P 		588
avr 768.8
(-3) 		1290.1
(3) 		1078.8
(0.6) 		771
(-3) 		852.3
(-2) 		943.9
(-1) 		521
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173262_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.27815
Sequence Type Exemplar sequence
Representative Public ID CEC3034 NCBI
Target Description CEC3034_rc /REP_DB=TREMBL Accession /GB=C11303 /FEA=Transcript Cluster /DEF=C.elegans cDNA clone yk170c2 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Transcript 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_072101(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_072101 NCBI Caenorhabditis elegans F25B4.1 (aminomethytransferase) mRNA, complete cds. 11/11 A 
SNAP00000008368 ENSEMBL cdna:SNAP chromosome:CEL140:V:5716431:5717211:1 11/11 None
GENEFINDER00000008381 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:5716467:5717211:1 11/11 None
F25B4.1.1 ENSEMBL cdna:known chromosome:CEL140:V:5715498:5717351:1 gene:F25B4.1 11/11 None
F25B4.1.2 ENSEMBL cdna:known chromosome:CEL140:V:5715514:5717351:1 gene:F25B4.1 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
chrV:5716949-5717230(+) 75.27 75.27
Public Domain and Genome References
Gene Title aminomethytransferase
Ensembl F25B4.1
Entrez Gene 178960 Entrez gene
SwissProt Q22968 EMBL-EBI
WormBase CE09620 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:264394_AT aminomethyltransferase, putative at
ATGENOME1:17420_AT aminomethyltransferase, putative at
DROSOPHILA_2:1623839_AT dm
DROSGENOME1:151967_AT dm
HG-U133_PLUS_2:204294_AT aminomethyltransferase (glycine cleavage system protein T) hs
HG-U133A:204294_AT aminomethyltransferase (glycine cleavage system protein T) hs
HG-FOCUS:204294_AT aminomethyltransferase (glycine cleavage system protein T) hs
HG-U133A_2:204294_AT aminomethyltransferase (glycine cleavage system protein T) hs
HU35KSUBD:RC_N59532_S_AT aminomethyltransferase (glycine cleavage system protein T) hs
HUGENEFL:D14686_AT aminomethyltransferase (glycine cleavage system protein T) hs
U133_X3P:G4502082_3P_AT aminomethyltransferase (glycine cleavage system protein T) hs
HG-U95AV2:41120_AT aminomethyltransferase (glycine cleavage system protein T) hs
YEAST_2:1776596_AT T subunit of the mitochondrial glycine decarboxylase complex, required for the catabolism of glycine to 5,10-methylene-THF; expression is regulated by levels of levels of 5,10-methylene-THF in the cytoplasm Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6546 glycine catabolism inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
4047 aminomethyltransferase activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAB37080 Hypothetical protein F25B4.1 [Caenorhabditis elegans] ref|NP_504502.1| F25B4.1 [Caenorhabditis elegans] 0.0
blast CAE64583 Hypothetical protein CBG09336 [Caenorhabditis briggsae] 0.0
blast AAH83400 Zgc:103483 [Danio rerio] gb|AAZ08415.1| glycine cleavage system protein T [Danio rerio] ref|NP_001006021.1| hypothetical protein LOC450000 [Danio rerio] 1.0E-102
blast AAB37080 Hypothetical protein F25B4.1 [Caenorhabditis elegans] ref|NP_504502.1| F25B4.1 [Caenorhabditis elegans] 5.0E-76
Protein Domains
Database ID Description E-Value
Pfam IPR006222 EMBL-EBI Glycine cleavage T protein (aminomethyl transferase) 1.0E-126
Pfam IPR006222 EMBL-EBI Glycine cleavage T protein (aminomethyl transferase) 8.4E-65
Pfam IPR006222 EMBL-EBI Glycine cleavage T protein (aminomethyl transferase) 6.5E-38
Sequence
Target Sequence 
>C. ELEGANS:173262_S_AT
gtagatgccctcgatctcatctaccactcatcgatcctctcgataagtgttccatcggat
ttgtaacttctggatgcccatcgccaactctcggaaagaacattgcaatcgcctacgtcg
acaaatcgcattcaaagatcggaaccaagttcgtcgtggatttcggcgccaagcaggcgc
cagtagaagtcgtcaaaatgccatttgttccgacaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTAGATGCCCTCGATCTCATCTACC 355 457 77 Antisense
CCACTCATCGATCCTCTCGATAAGT 357 275 100 Antisense
GTGTTCCATCGGATTTGTAACTTCT 372 483 123 Antisense
TTTGTAACTTCTGGATGCCCATCGC 210 667 136 Antisense
CCATCGCCAACTCTCGGAAAGAACA 69 269 154 Antisense
AAAGAACATTGCAATCGCCTACGTC 596 123 171 Antisense
TCGCCTACGTCGACAAATCGCATTC 359 597 185 Antisense
AGATCGGAACCAAGTTCGTCGTGGA 346 67 212 Antisense
GTGGATTTCGGCGCCAAGCAGGCGC 71 491 232 Antisense
AGCAGGCGCCAGTAGAAGTCGTCAA 101 79 248 Antisense
GTCAAAATGCCATTTGTTCCGACAA 597 463 268 Antisense
Sequence Source Affymetrix Proprietary Database