Contig-U12856-1
Contig ID Contig-U12856-1
Contig update 2002.12.18
Contig sequence
>Contig-U12856-1 (Contig-U12856-1Q) /CSM_Contig/Contig-U12856-1Q.Seq.d
ATAATCCCATCAAACTTTTATACATATACACACGCACACACTTTGTGTAT
TTGTTTCTCATTGTTATTTGTTTTTTTTTTTTTAAAAAATTTTTTTTTTT
TTNAAAAAAAAATTTTNNNNNNNNN

Gap no gap
Contig length 125
Chromosome number (1..6, M) 2
Chromosome length 8467578
Start point 6863988
End point 6863873
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 1
Link to clone list U12856
List of clone(s)

est1=AHR481F,1,116
Translated Amino Acid sequence
IIPSNFYTYTHAHTLCICFSLLFVFFFLKNFFFFXKKIXXX


Translated Amino Acid sequence (All Frames)
Frame A:
IIPSNFYTYTHAHTLCICFSLLFVFFFLKNFFFFXKKIXXX


Frame B:
*shqtfihihthtlcvfvshcylffff*kifffxkkkfxxx


Frame C:
npikllyiytrthfvylflivicffffkkffffxkknfxxx


own update 2004. 6.10
Homology vs CSM-cDNA
Query= Contig-U12856-1 (Contig-U12856-1Q)
/CSM_Contig/Contig-U12856-1Q.Seq.d
(125 letters)

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


Score E
Sequences producing significant alignments: (bits) Value

Contig-U12856-1 (Contig-U12856-1Q) /CSM_Contig/Conti... 139 7e-34
Contig-U13039-1 (Contig-U13039-1Q) /CSM_Contig/Conti... 38 0.002
Contig-U10840-1 (Contig-U10840-1Q) /CSM_Contig/Conti... 32 0.12
Contig-U09379-1 (Contig-U09379-1Q) /CSM_Contig/Conti... 30 0.49
Contig-U14026-1 (Contig-U14026-1Q) /CSM_Contig/Conti... 28 1.9
Contig-U13822-1 (Contig-U13822-1Q) /CSM_Contig/Conti... 28 1.9
Contig-U12745-1 (Contig-U12745-1Q) /CSM_Contig/Conti... 28 1.9
Contig-U11073-1 (Contig-U11073-1Q) /CSM_Contig/Conti... 28 1.9
Contig-U06379-1 (Contig-U06379-1Q) /CSM_Contig/Conti... 28 1.9
Contig-U04840-1 (Contig-U04840-1Q) /CSM_Contig/Conti... 28 1.9

>Contig-U12856-1 (Contig-U12856-1Q) /CSM_Contig/Contig-U12856-1Q.Seq.d
Length = 125

Score = 139 bits (70), Expect = 7e-34
Identities = 70/70 (100%)
Strand = Plus / Plus


Query: 1 ataatcccatcaaacttttatacatatacacacgcacacactttgtgtatttgtttctca 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1 ataatcccatcaaacttttatacatatacacacgcacacactttgtgtatttgtttctca 60


Query: 61 ttgttatttg 70
||||||||||
Sbjct: 61 ttgttatttg 70


>Contig-U13039-1 (Contig-U13039-1Q) /CSM_Contig/Contig-U13039-1Q.Seq.d
Length = 142

Score = 38.2 bits (19), Expect = 0.002
Identities = 22/23 (95%)
Strand = Plus / Plus


Query: 19 tatacatatacacacgcacacac 41
||||||||||||||| |||||||
Sbjct: 69 tatacatatacacacacacacac 91


>Contig-U10840-1 (Contig-U10840-1Q) /CSM_Contig/Contig-U10840-1Q.Seq.d
Length = 1997

Score = 32.2 bits (16), Expect = 0.12
Identities = 16/16 (100%)
Strand = Plus / Minus


Query: 18 ttatacatatacacac 33
||||||||||||||||
Sbjct: 70 ttatacatatacacac 55


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: 540
Number of Sequences: 6905
Number of extensions: 540
Number of successful extensions: 164
Number of sequences better than 10.0: 70
length of query: 125
length of database: 5,674,871
effective HSP length: 14
effective length of query: 111
effective length of database: 5,578,201
effective search space: 619180311
effective search space used: 619180311
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. 4
Homology vs DNA
Query= Contig-U12856-1 (Contig-U12856-1Q) /CSM_Contig/Contig-U12856-1Q.Seq.d
(125 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

(BJ339548) Dictyostelium discoideum cDNA clone:dda65b22, 5' ... 139 2e-29 1
(AC114263) Dictyostelium discoideum chromosome 2 map 215673-... 131 6e-27 1
(BX957362) Zebrafish DNA sequence from clone CH211-122F10 in... 50 0.016 1
(BX957235) Zebrafish DNA sequence from clone DKEY-84K17 in l... 50 0.016 1
(BX936404) Zebrafish DNA sequence from clone CH211-237F6 in ... 50 0.016 1
(CU856397) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 48 0.065 2
(AC135938) Rattus norvegicus clone CH230-345C4, WORKING DRAF... 48 0.065 1
(AC118493) Rattus norvegicus clone CH230-354I10, WORKING DRA... 48 0.065 1
(AC107542) Rattus norvegicus clone CH230-221J16, WORKING DRA... 48 0.065 1
(AC098048) Rattus norvegicus clone CH230-115I10, WORKING DRA... 48 0.065 1
(AQ714021) HS_5397_B2_C10_SP6E RPCI-11 Human Male BAC Librar... 42 0.23 2
(CR381646) Zebrafish DNA sequence from clone DKEY-241L7 in l... 46 0.26 1
(CR339044) Zebrafish DNA sequence from clone CH211-122G23 in... 46 0.26 1
(AC111733) Rattus norvegicus 13 BAC CH230-170L19 (Children's... 46 0.26 1
(CU019620) S.lycopersicum DNA sequence from clone LE_HBa-50I... 46 0.26 1
(AC107049) Homo sapiens BAC clone RP11-163G23 from 4, comple... 46 0.26 1
(AC022274) Homo sapiens BAC clone RP11-697M17 from 8, comple... 46 0.26 1
(AC147858) Macropus eugenii clone ME_KBa-270F7, WORKING DRAF... 46 0.26 1
(AC147734) Macropus eugenii clone ME_KBa-560K2, WORKING DRAF... 46 0.26 1
(AC112612) Rattus norvegicus clone CH230-31F19, WORKING DRAF... 46 0.26 1
(AC106389) Rattus norvegicus clone CH230-140G24, WORKING DRA... 46 0.26 1
(CU682341) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 46 0.26 1
(AC087607) Homo sapiens chromosome 4 clone RP11-163G23 map 4... 46 0.26 1
(AC044874) Homo sapiens clone RP11-614N10, WORKING DRAFT SEQ... 46 0.26 1
(CU469427) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 46 0.26 1
(CU468853) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 46 0.26 1
(CU019553) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS... 46 0.26 1
(CT005269) Leishmania major chromosome 32 strain Friedlin, c... 46 0.26 1
(AL499622) Leishmania major Friedlin assembled shotgun reads... 46 0.26 1
(AC023290) Homo sapiens clone RP11-13P8, WORKING DRAFT SEQUE... 46 0.26 1
(AL285305) Tetraodon nigroviridis genome survey sequence T7 ... 46 0.26 1
(EG327087) EST_903 Caste=Male, Stage=Adult Vespula squamosa ... 46 0.26 1
(AC105753) Homo sapiens chromosome 3 clone RP11-189A1, compl... 38 0.42 3
(AC103170) Rattus norvegicus clone CH230-89F11, WORKING DRAF... 36 0.54 2
(CR790387) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS... 34 0.55 2
(AL627236) Mouse DNA sequence from clone RP23-384G12 on chro... 34 0.55 2
(AC216148) Cavia porcellus clone CH234-57K11, WORKING DRAFT ... 34 0.56 2
(CU302432) Mouse DNA sequence *** SEQUENCING CANCELLED *** f... 34 0.56 2
(CU210874) Mouse DNA sequence from clone DN-375D1 on chromos... 34 0.59 2
(AC099775) Homo sapiens chromosome 3 clone RP11-169G24, comp... 38 0.61 3
(CR925704) Zebrafish DNA sequence from clone CH211-156P21 in... 44 1.0 1
(CR854822) Zebrafish DNA sequence from clone DKEY-34K3 in li... 44 1.0 1
(BX927212) Zebrafish DNA sequence from clone CH211-262A5 in ... 44 1.0 1
(BX005109) Zebrafish DNA sequence from clone CH211-284K5 in ... 44 1.0 1
(AM084745) Grus americana microsatellite locus WC-AC-B. 44 1.0 1
(AC163452) Mus musculus chromosome 19, clone RP23-405C7, com... 44 1.0 1
(AC163089) Mus musculus chromosome 5, clone RP23-346P15, com... 44 1.0 1
(AC140320) Mus musculus BAC clone RP23-401C13 from chromosom... 44 1.0 1
(AC140282) Mus musculus BAC clone RP24-501L1 from 1, complet... 44 1.0 1
(AC136710) Mus musculus chromosome 19, clone RP23-35B13, com... 44 1.0 1
(AC132100) Mus musculus BAC clone RP24-294D10 from chromosom... 44 1.0 1
(AC122801) Mus musculus BAC clone RP23-471L3 from chromosome... 44 1.0 1
(AC114342) Mus musculus chromosome 5, clone RP24-143H14, com... 44 1.0 1
(AC217025) Pan troglodytes BAC clone CH251-730F11 from chrom... 44 1.0 1
(AC142323) Pan troglodytes BAC clone RP43-72N8 from chromoso... 44 1.0 1
(AY020848) Oryza sativa microsatellite MRG3173 containing (T... 44 1.0 1
(AP008212) Oryza sativa (japonica cultivar-group) genomic DN... 44 1.0 1
(AP004741) Oryza sativa Japonica Group genomic DNA, chromoso... 44 1.0 1
(AP003525) Oryza sativa Japonica Group genomic DNA, chromoso... 44 1.0 1
(EA707627) Sequence 86506 from patent US 7365185. 44 1.0 1
(DD315064) Primary Rat Hepatocyte Toxicity Modeling. 44 1.0 1
(DQ095178) Otocolobus manul sex-determining region Y protein... 44 1.0 1
(AE014298) Drosophila melanogaster chromosome X, complete se... 44 1.0 1
(AC108481) Drosophila melanogaster 3L BAC RP98-1O19 (Roswell... 44 1.0 1
(AP006287) Homo sapiens genomic DNA, chromosome 11 clone:RP1... 44 1.0 1
(AL158218) Human DNA sequence from clone RP5-831K15 on chrom... 44 1.0 1
(AC138972) Homo sapiens 3 BAC RP11-1005I1 (Roswell Park Canc... 44 1.0 1
(AC112643) Homo sapiens 3 BAC RP11-328G15 (Roswell Park Canc... 44 1.0 1
(AC080164) Homo sapiens BAC clone RP11-550H11 from 2, comple... 44 1.0 1
(AC027004) Homo sapiens chromosome 15, clone RP11-143C19, co... 44 1.0 1
(AC010387) Homo sapiens chromosome 5 clone CTD-2074D8, compl... 44 1.0 1
(AC006212) Homo sapiens, clone hRPK.14_A_1, complete sequence. 44 1.0 1
(AC162048) Bos taurus clone CH240-111C13, WORKING DRAFT SEQU... 44 1.0 1
(AC156220) Bos taurus clone CH240-49E14, WORKING DRAFT SEQUE... 44 1.0 1
(AC152773) Bos taurus clone CH240-15N19, WORKING DRAFT SEQUE... 44 1.0 1
(AC128528) Rattus norvegicus clone CH230-149A1, *** SEQUENCI... 44 1.0 1
(AC117160) Rattus norvegicus clone CH230-227G23, *** SEQUENC... 44 1.0 1
(AC113912) Rattus norvegicus clone CH230-393M16, WORKING DRA... 44 1.0 1
(AC106488) Rattus norvegicus clone CH230-174D18, WORKING DRA... 44 1.0 1
(AC105800) Rattus norvegicus clone CH230-258G9, *** SEQUENCI... 44 1.0 1
(AC099471) Rattus norvegicus clone CH230-221M23, *** SEQUENC... 44 1.0 1
(AC095756) Rattus norvegicus clone CH230-8D16, WORKING DRAFT... 44 1.0 1
(CU464018) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 44 1.0 1
(CU311198) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 44 1.0 1
(AP004322) Oryza sativa Japonica Group genomic DNA, chromoso... 44 1.0 1
(AP001201) Homo sapiens genomic DNA, chromosome 11, clone:RP... 44 1.0 1
(AP001191) Homo sapiens genomic DNA, chromosome 11q13 clone:... 44 1.0 1
(AP000592) Homo sapiens genomic DNA, chromosome 11q13 clone:... 44 1.0 1
(AP000586) Homo sapiens genomic DNA, chromosome 11q13 clone:... 44 1.0 1
(AL121812) Drosophila melanogaster clone BACR33H2 WORKING DR... 44 1.0 1
(AC223185) Bos taurus clone CH240-426J15, WORKING DRAFT SEQU... 44 1.0 1
(AC221206) Bos taurus clone CH240-399I22, WORKING DRAFT SEQU... 44 1.0 1
(AC217480) Atelerix albiventris clone LB4-379M5, WORKING DRA... 44 1.0 1
(AC186265) Felis catus clone RP86-2D24, WORKING DRAFT SEQUEN... 44 1.0 1
(AC020052) Drosophila melanogaster, *** SEQUENCING IN PROGRE... 44 1.0 1
(AC012059) Homo sapiens clone RP11-19A2, WORKING DRAFT SEQUE... 44 1.0 1
(AQ549572) RPCI-11-429A9.TV RPCI-11 Homo sapiens genomic clo... 44 1.0 1
(AQ027933) CIT-HSP-2313J3.TR CIT-HSP Homo sapiens genomic cl... 44 1.0 1
(DH830352) Rattus norvegicus DNA, BAC clone: RNB1-437J05, 3'... 44 1.0 1
(DH668822) Rattus norvegicus DNA, BAC clone: RNB1-217O12, 3'... 44 1.0 1

>(BJ339548) Dictyostelium discoideum cDNA clone:dda65b22, 5' end,
single read.
Length = 116

Score = 139 bits (70), Expect = 2e-29
Identities = 70/70 (100%)
Strand = Plus / Plus


Query: 1 ataatcccatcaaacttttatacatatacacacgcacacactttgtgtatttgtttctca 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1 ataatcccatcaaacttttatacatatacacacgcacacactttgtgtatttgtttctca 60


Query: 61 ttgttatttg 70
||||||||||
Sbjct: 61 ttgttatttg 70

Lambda K H
1.37 0.711 1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 89,575,236
Number of extensions: 7078343
Number of successful extensions: 2501501
Number of sequences better than 10.0: 342
Length of query: 125
Length of database: 95,242,211,685
Length adjustment: 22
Effective length of query: 103
Effective length of database: 93,199,600,587
Effective search space: 9599558860461
Effective search space used: 9599558860461
X1: 11 (21.8 bits)
S2: 20 (40.1 bits)

protein update 2009. 7. 5
Homology vs Protein
Query= Contig-U12856-1 (Contig-U12856-1Q) /CSM_Contig/Contig-U12856-1Q.Seq.d
(125 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: 128,713,905
Number of extensions: 1155161
Number of successful extensions: 2437
Number of sequences better than 10.0: 0
Number of HSP's gapped: 2380
Number of HSP's successfully gapped: 0
Length of query: 41
Length of database: 1,051,180,864
Length adjustment: 15
Effective length of query: 26
Effective length of database: 1,002,632,479
Effective search space: 26068444454
Effective search space used: 26068444454
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: 1.02 gvh: 0.40 alm: 0.24 top: 0.60 tms: 0.07 mit: 0.40 mip: 0.00
nuc: 0.00 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: 1.00 tyr: 0.00 leu: 0.17 gpi: 0.00 myr: 0.00
dna: 0.00 rib: 0.00 bac: 0.00 m1a: 0.00 m1b: 1.00 m2 : 0.00 mNt: 0.00
m3a: 0.00 m3b: 0.00 m_ : 0.00

28.0 %: cytoplasmic
24.0 %: mitochondrial
24.0 %: nuclear
8.0 %: plasma membrane
8.0 %: endoplasmic reticulum
4.0 %: vesicles of secretory system
4.0 %: peroxisomal

>> prediction for Contig-U12856-1 is cyt

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