Contig-U13193-1
Contig ID Contig-U13193-1
Contig update 2002.12.18
Contig sequence
>Contig-U13193-1 (Contig-U13193-1Q) /CSM_Contig/Contig-U13193-1Q.Seq.d
NNNNNNNNNNTNAATAGAGGNACCCNACATGGTGAACTTGGNCAAAGAAA
TCATAGATTTNAATTGAAAATCGATTCATTNCCAGGGGCAATTATGCATC
ATGATTTGGTNTCAAGATTAAGTGCTTTAAAGNTATTGAAGTTTCATGAT
AGNTTTAGACCNTCCTACTATGGGACNTTTTNTAAAACTAGNNAACNAAT
CCCCGCTAAGAACCCNTTCAAAAAAGATTTAACNATCGATTATGATTATG
ATAGNTCTGATGAATGGGAGGAANAGAAAGATGATGATCNAGCTGAGAAA
ATTACNTCTGCTGATGAAAAANAAGAAGATCNAGATGCTGATGAAGAAGA
AAATGAAGAAGATAGAGCNTGGATTGATGATATTGGNTTGAATGATGATG
ATGANACCCNAGTTGATAATTCCACCNANATCNCNG

Gap no gap
Contig length 436
Chromosome number (1..6, M) 5
Chromosome length 5062330
Start point 756668
End point 757094
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 1
Link to clone list U13193
List of clone(s)

est1=SFI557Z,1,427
Translated Amino Acid sequence
XXXXNRGTXHGELGQRNHRFXLKIDSXPGAIMHHDLVSRLSALKXLKFHDXFRPSYYGTF
XKTXXXIPAKNPFKKDLTIDYDYDXSDEWEEXKDDDXAEKITSADEKXEDXDADEEENEE
DRAWIDDIGLNDDDXTXVDNSTXIX


Translated Amino Acid sequence (All Frames)
Frame A:
XXXXNRGTXHGELGQRNHRFXLKIDSXPGAIMHHDLVSRLSALKXLKFHDXFRPSYYGTF
XKTXXXIPAKNPFKKDLTIDYDYDXSDEWEEXKDDDXAEKITSADEKXEDXDADEEENEE
DRAWIDDIGLNDDDXTXVDNSTXIX


Frame B:
xxxxiexpxmvnlxkeiidxn*ksihxqgqlcimiwxqd*vl*xy*sfmixldxptmgxf
xklxnxsplrtxskki*xsimimixlmngrxrkmmixlrklxllmkxkkixmlmkkkmkk
iexglmilx*mmmmxpxliippxsx


Frame C:
xxxx*rxptw*twxkks*ixienrfixrgnyas*fgxkikcfkxievs**x*txllwdxx
*n*xtnpr*epxqkrfnxrl*l**x**mggxer**ss*enyxc**kxrrsrc**rrk*rr
*sxd**ywxe****xps**fhxxx


own update 2004. 6.10
Homology vs CSM-cDNA
Query= Contig-U13193-1 (Contig-U13193-1Q)
/CSM_Contig/Contig-U13193-1Q.Seq.d
(436 letters)

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


Score E
Sequences producing significant alignments: (bits) Value

Contig-U13193-1 (Contig-U13193-1Q) /CSM_Contig/Conti... 595 e-170
Contig-U08437-1 (Contig-U08437-1Q) /CSM_Contig/Conti... 54 1e-07
Contig-U11573-1 (Contig-U11573-1Q) /CSM_Contig/Conti... 44 1e-04
Contig-U14238-1 (Contig-U14238-1Q) /CSM_Contig/Conti... 42 5e-04
Contig-U12528-1 (Contig-U12528-1Q) /CSM_Contig/Conti... 38 0.008
Contig-U12206-1 (Contig-U12206-1Q) /CSM_Contig/Conti... 38 0.008
Contig-U10351-1 (Contig-U10351-1Q) /CSM_Contig/Conti... 38 0.008
Contig-U02486-1 (Contig-U02486-1Q) /CSM_Contig/Conti... 38 0.008
Contig-U14570-1 (Contig-U14570-1Q) /CSM_Contig/Conti... 36 0.030
Contig-U14177-1 (Contig-U14177-1Q) /CSM_Contig/Conti... 36 0.030

>Contig-U13193-1 (Contig-U13193-1Q) /CSM_Contig/Contig-U13193-1Q.Seq.d
Length = 436

Score = 595 bits (300), Expect = e-170
Identities = 402/414 (97%)
Strand = Plus / Plus


Query: 13 aatagaggnacccnacatggtgaacttggncaaagaaatcatagatttnaattgaaaatc 72
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 13 aatagaggnacccnacatggtgaacttggncaaagaaatcatagatttnaattgaaaatc 72


Query: 73 gattcattnccaggggcaattatgcatcatgatttggtntcaagattaagtgctttaaag 132
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 73 gattcattnccaggggcaattatgcatcatgatttggtntcaagattaagtgctttaaag 132


Query: 133 ntattgaagtttcatgatagntttagaccntcctactatgggacnnnnnnnaaaactagn 192
||||||||||||||||||||||||||||||||||||||||||||| | |||||||||
Sbjct: 133 ntattgaagtttcatgatagntttagaccntcctactatgggacnttttntaaaactagn 192


Query: 193 naacnaatccccgctaagaacccnttcaaaaaagatttaacnatcgattatgattatgat 252
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 193 naacnaatccccgctaagaacccnttcaaaaaagatttaacnatcgattatgattatgat 252


Query: 253 agntctgatgaatgggaggaanagaaagatgatgatcnagctgagaaaattacntctgct 312
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 253 agntctgatgaatgggaggaanagaaagatgatgatcnagctgagaaaattacntctgct 312


Query: 313 gatgnnnnnnnngaagatcnagatgctgatgaagaagaaaatgaagaagatagagcntgg 372
|||| | ||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 313 gatgaaaaanaagaagatcnagatgctgatgaagaagaaaatgaagaagatagagcntgg 372


Query: 373 attgatgatattggnttgaatgatgatgatganacccnagttgataattccacc 426
||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 373 attgatgatattggnttgaatgatgatgatganacccnagttgataattccacc 426


>Contig-U08437-1 (Contig-U08437-1Q) /CSM_Contig/Contig-U08437-1Q.Seq.d
Length = 1122

Score = 54.0 bits (27), Expect = 1e-07
Identities = 30/31 (96%)
Strand = Plus / Minus


Query: 333 agatgctgatgaagaagaaaatgaagaagat 363
||||| |||||||||||||||||||||||||
Sbjct: 748 agatgatgatgaagaagaaaatgaagaagat 718


Score = 38.2 bits (19), Expect = 0.008
Identities = 22/23 (95%)
Strand = Plus / Minus


Query: 340 gatgaagaagaaaatgaagaaga 362
||||||||||||||||| |||||
Sbjct: 825 gatgaagaagaaaatgatgaaga 803


Score = 38.2 bits (19), Expect = 0.008
Identities = 22/23 (95%)
Strand = Plus / Minus


Query: 341 atgaagaagaaaatgaagaagat 363
|||| ||||||||||||||||||
Sbjct: 812 atgatgaagaaaatgaagaagat 790


Score = 36.2 bits (18), Expect = 0.030
Identities = 18/18 (100%)
Strand = Plus / Minus


Query: 346 gaagaaaatgaagaagat 363
||||||||||||||||||
Sbjct: 789 gaagaaaatgaagaagat 772


Score = 36.2 bits (18), Expect = 0.030
Identities = 18/18 (100%)
Strand = Plus / Minus


Query: 346 gaagaaaatgaagaagat 363
||||||||||||||||||
Sbjct: 762 gaagaaaatgaagaagat 745


Score = 32.2 bits (16), Expect = 0.47
Identities = 19/20 (95%)
Strand = Plus / Minus


Query: 340 gatgaagaagaaaatgaaga 359
||||| ||||||||||||||
Sbjct: 843 gatgatgaagaaaatgaaga 824


Score = 28.2 bits (14), Expect = 7.3
Identities = 17/18 (94%)
Strand = Plus / Minus


Query: 346 gaagaaaatgaagaagat 363
|||||| |||||||||||
Sbjct: 780 gaagaagatgaagaagat 763


>Contig-U11573-1 (Contig-U11573-1Q) /CSM_Contig/Contig-U11573-1Q.Seq.d
Length = 1479

Score = 44.1 bits (22), Expect = 1e-04
Identities = 25/26 (96%)
Strand = Plus / Plus


Query: 333 agatgctgatgaagaagaaaatgaag 358
||||| ||||||||||||||||||||
Sbjct: 516 agatgatgatgaagaagaaaatgaag 541


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: 5376
Number of Sequences: 6905
Number of extensions: 5376
Number of successful extensions: 1388
Number of sequences better than 10.0: 220
length of query: 436
length of database: 5,674,871
effective HSP length: 16
effective length of query: 420
effective length of database: 5,564,391
effective search space: 2337044220
effective search space used: 2337044220
T: 0
A: 40
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 14 (28.2 bits)
dna update 2008.12. 7
Homology vs DNA
Query= Contig-U13193-1 (Contig-U13193-1Q) /CSM_Contig/Contig-U13193-1Q.Seq.d
(436 letters)

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

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

Score E
Sequences producing significant alignments: (bits) Value N

(BJ402855) Dictyostelium discoideum cDNA clone:dds18a15, 3' ... 474 e-150 2
(AC213809) Oryza glaberrima clone OG_BBa0026F03, *** SEQUENC... 32 7.6 2

>(BJ402855) Dictyostelium discoideum cDNA clone:dds18a15, 3' end,
single read.
Length = 427

Score = 474 bits (239), Expect(2) = e-150
Identities = 299/299 (100%)
Strand = Plus / Minus


Query: 13 aatagaggnacccnacatggtgaacttggncaaagaaatcatagatttnaattgaaaatc 72
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 425 aatagaggnacccnacatggtgaacttggncaaagaaatcatagatttnaattgaaaatc 366


Query: 73 gattcattnccaggggcaattatgcatcatgatttggtntcaagattaagtgctttaaag 132
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 365 gattcattnccaggggcaattatgcatcatgatttggtntcaagattaagtgctttaaag 306


Query: 133 ntattgaagtttcatgatagntttagaccntcctactatgggacnttttntaaaactagn 192
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 305 ntattgaagtttcatgatagntttagaccntcctactatgggacnttttntaaaactagn 246


Query: 193 naacnaatccccgctaagaacccnttcaaaaaagatttaacnatcgattatgattatgat 252
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 245 naacnaatccccgctaagaacccnttcaaaaaagatttaacnatcgattatgattatgat 186


Query: 253 agntctgatgaatgggaggaanagaaagatgatgatcnagctgagaaaattacntctgc 311
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 185 agntctgatgaatgggaggaanagaaagatgatgatcnagctgagaaaattacntctgc 127

Score = 95.6 bits (48), Expect(2) = e-150
Identities = 63/63 (100%)
Strand = Plus / Minus


Query: 370 tggattgatgatattggnttgaatgatgatgatganacccnagttgataattccaccnan 429
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 68 tggattgatgatattggnttgaatgatgatgatganacccnagttgataattccaccnan 9


Query: 430 atc 432
|||
Sbjct: 8 atc 6

Lambda K H
1.37 0.711 1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 226,121,317
Number of extensions: 14413777
Number of successful extensions: 1532783
Number of sequences better than 10.0: 2
Length of query: 436
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 413
Effective length of database: 93,106,754,628
Effective search space: 38453089661364
Effective search space used: 38453089661364
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)

protein update 2009. 7. 6
Homology vs Protein
Query= Contig-U13193-1 (Contig-U13193-1Q) /CSM_Contig/Contig-U13193-1Q.Seq.d
(436 letters)

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

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

Score E
Sequences producing significant alignments: (bits) Value

BX005201_4(BX005201|pid:none) Zebrafish DNA sequence from clone ... 38 0.13
(Q5R1T0) RecName: Full=Chromatin assembly factor 1 subunit A; ... 34 1.4
AP008213_684(AP008213|pid:none) Oryza sativa (japonica cultivar-... 33 2.4
AP005880_6(AP005880|pid:none) Oryza sativa Japonica Group genomi... 33 2.4
CP000884_3759(CP000884|pid:none) Delftia acidovorans SPH-1, comp... 33 3.1
AK161016_1(AK161016|pid:none) Mus musculus 16 days embryo head c... 33 3.1
(Q9QWF0) RecName: Full=Chromatin assembly factor 1 subunit A; ... 33 3.1
AE014298_1265(AE014298|pid:none) Drosophila melanogaster chromos... 33 4.1
AY069784_1(AY069784|pid:none) Drosophila melanogaster SD02526 fu... 33 4.1
BC067093_1(BC067093|pid:none) Homo sapiens chromatin assembly fa... 32 5.3
FN357680_5(FN357680|pid:none) Schistosoma mansoni genome sequenc... 32 5.3
A56731(A56731) chromatin assembly factor I p150 chain - human &... 32 5.3
CR382137_680(CR382137|pid:none) Debaryomyces hansenii strain CBS... 32 6.9

>BX005201_4(BX005201|pid:none) Zebrafish DNA sequence from clone
CH211-129C21 in linkage group 22 Contains the gene for a
novel protein similar to vertebrate chromatin assembly
factor 1 subunit A, p150 (CHAF1A), the gene for a novel
protein similar to vertebrate secretory carrier membrane
protein 4 (SCAMP4), the 5' end of the hdgfrp2 gene for
hepatoma-derived growth factor, related protein 2, the
gene for a novel protein similar to vertebrate sema,
immunoglobulin (Ig), transmembrane (TM) and short
cytoplasmic domain, semaphorin 4D (SEMA4D), a novel gene
and a CpG island, complete sequence.
Length = 798

Score = 37.7 bits (86), Expect = 0.13
Identities = 16/39 (41%), Positives = 23/39 (58%)
Frame = +1

Query: 112 SRLSALKXLKFHDXFRPSYYGTFXKTXXXIPAKNPFKKD 228
SR +K L FHD +RP+Y+GT+ K I + P + D
Sbjct: 401 SRYGRMKLLHFHDNYRPAYWGTWSKKSTHISPRCPLRLD 439

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: 303,986,356
Number of extensions: 3401259
Number of successful extensions: 2780
Number of sequences better than 10.0: 13
Number of HSP's gapped: 2780
Number of HSP's successfully gapped: 13
Length of query: 145
Length of database: 1,051,180,864
Length adjustment: 108
Effective length of query: 37
Effective length of database: 701,632,492
Effective search space: 25960402204
Effective search space used: 25960402204
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: 29 (15.8 bits)

PSORT

psg: 0.45 gvh: 0.48 alm: 0.52 top: 0.53 tms: 0.00 mit: 0.27 mip: 0.04
nuc: 0.00 erl: 0.00 erm: 0.20 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

48.0 %: cytoplasmic
24.0 %: mitochondrial
20.0 %: nuclear
4.0 %: extracellular, including cell wall
4.0 %: peroxisomal

>> prediction for Contig-U13193-1 is cyt

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) 1
CH (FL, L) 0
CF (FL, S) 0
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0