Contig-U13161-1
Contig ID Contig-U13161-1
Contig update 2002.12.18
Contig sequence
>Contig-U13161-1 (Contig-U13161-1Q) /CSM_Contig/Contig-U13161-1Q.Seq.d
NNNNNNNNNNTTTAANNGGAANTGAAACCCCNCNAATANATCGNCNTTGN
AAAAATAAAAAAAAAANNTATTCCCNNNANGTANNGATAAAAAAAAAAAA
GTAAAAAAAAAAAAA

Gap no gap
Contig length 115
Chromosome number (1..6, M) -
Chromosome length -
Start point -
End point -
Strand (PLUS/MINUS) -
Number of clones 1
Number of EST 1
Link to clone list U13161
List of clone(s)

est1=CHR746Z,1,106
Translated Amino Acid sequence
XXXLXGXETPXIXRXXKNKKKXYSXXVXIKKKK*kkk


Translated Amino Acid sequence (All Frames)
Frame A:
xxxx*xexkpxxxixxxkikkkxipxxxx*kkkskkkk


Frame B:
xxxfxxx*npxnxsxlxk*kkxxfpxxxdkkkkvkkkk


Frame C:
XXXLXGXETPXIXRXXKNKKKXYSXXVXIKKKK*kkk


own update 2004. 6.10
Homology vs CSM-cDNA
Query= Contig-U13161-1 (Contig-U13161-1Q)
/CSM_Contig/Contig-U13161-1Q.Seq.d
(115 letters)

Database: CSM
6905 sequences; 5,674,871 total letters


***** No hits found ******

Database: CSM
Posted date: Jun 9, 2004 7:35 PM
Number of letters in database: 5,674,871
Number of sequences in database: 6905

Lambda K H
1.37 0.711 1.31

Gapped
Lambda K H
1.37 0.711 1.31


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Hits to DB: 0
Number of Sequences: 6905
Number of extensions: 0
Number of successful extensions: 0
Number of sequences better than 10.0: 0
length of query: 115
length of database: 5,674,871
effective HSP length: 14
effective length of query: 101
effective length of database: 5,578,201
effective search space: 563398301
effective search space used: 563398301
T: 0
A: 40
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 13 (26.3 bits)
dna update 2008.12. 6
Homology vs DNA
Query= Contig-U13161-1 (Contig-U13161-1Q) /CSM_Contig/Contig-U13161-1Q.Seq.d
(115 letters)

Database: ddbj_A
92,845,959 sequences; 95,242,211,685 total letters

Searching..................................................done

***** No hits found ******

Lambda K H
1.37 0.711 1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 2,241,238
Number of extensions: 220576
Number of successful extensions: 2
Number of sequences better than 10.0: 0
Length of query: 115
Length of database: 95,242,211,685
Length adjustment: 22
Effective length of query: 93
Effective length of database: 93,199,600,587
Effective search space: 8667562854591
Effective search space used: 8667562854591
X1: 11 (21.8 bits)
S2: 20 (40.1 bits)

protein update 2009. 7. 6
Homology vs Protein
Query= Contig-U13161-1 (Contig-U13161-1Q) /CSM_Contig/Contig-U13161-1Q.Seq.d
(115 letters)

Database: nrp_B
3,236,559 sequences; 1,051,180,864 total letters

Searching..................................................done

***** No hits found ******

Lambda K H
0.318 0.134 0.401

Gapped
Lambda K H
0.267 0.0410 0.140

Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 3236559
Number of Hits to DB: 42,819,463
Number of extensions: 3658277
Number of successful extensions: 242
Number of sequences better than 10.0: 0
Number of HSP's gapped: 236
Number of HSP's successfully gapped: 0
Length of query: 38
Length of database: 1,051,180,864
Length adjustment: 12
Effective length of query: 26
Effective length of database: 1,012,342,156
Effective search space: 26320896056
Effective search space used: 26320896056
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 24 (13.9 bits)

PSORT

psg: 0.34 gvh: 0.12 alm: 0.79 top: 0.53 tms: 0.00 mit: 0.30 mip: 0.00
nuc: 0.28 erl: 0.00 erm: 0.60 pox: 0.00 px2: 0.00 vac: 0.00 rnp: 0.00
act: 0.00 caa: 0.00 yqr: 0.00 tyr: 0.00 leu: 0.00 gpi: 0.00 myr: 0.00
dna: 0.00 rib: 0.00 bac: 0.00 m1a: 0.00 m1b: 0.00 m2 : 0.00 mNt: 0.00
m3a: 0.00 m3b: 0.00 m_ : 1.00

68.0 %: nuclear
20.0 %: cytoplasmic
8.0 %: mitochondrial
4.0 %: cytoskeletal

>> prediction for Contig-U13161-1 is nuc

VS (DIR, S) 0
VH (FL, L) 0
VF (FL, S) 0
AH (FL, L) 0
AF (FL, S) 0
SL (DIR, L) 0
SS (DIR, S) 0
SH (FL, L) 0
SF (FL, S) 0
CH (FL, L) 1
CF (FL, S) 0
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0