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Dicty_cDB
Contig List | Clone List | cDNA Library List
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NBDC - LSDB Archive
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U07081-1
Contig ID Contig-U07081-1
Contig update 2002. 9.13
Contig sequence 
>Contig-U07081-1 (Contig-U07081-1Q) /CSM_Contig/Contig-U07081-1Q.Seq.d
AAGCAGCCTTCCTTCTATCAAAAGGTGTTGAACTCTATGGTATTAGGGAT
TTAATTATGGGTGATTCTGTTTTATCTTTATCAAGTAAATTAAAATCTTT
TGAATTACAAGAAAGATTGATAAAACAAAATCCTCAATAAATCTGTAAAT
TATAAAAGTTTTATCTTTTATAATTTACATTTTTTTTTTTTTTTTTNATT
TTCCCCCCAAAATN
Gap no gap
Contig length 214
Chromosome number (1..6, M) 3
Chromosome length 6358359
Start point 4469312
End point 4469526
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 1
Link to clone list U07081
List of clone(s) 

est1=VSK280F,1,215
Translated Amino Acid sequence 
AAFLLSKGVELYGIRDLIMGDSVLSLSSKLKSFELQERLIKQNPQ*ickl*kfyll*ftf
ffffxifppk
Translated Amino Acid sequence (All Frames) 
Frame A:
kqpsfyqkvlnsmvlgi*lwvilfylyqvn*nllnykkd**nkilnksvnyksfifynlh
fffffxfspqn


Frame B:
sslpsikrc*tlwy*gfnyg*fcfifik*ikif*itrkidktkssinl*iikvlsfiiyi
fffffxfppkx


Frame C:
AAFLLSKGVELYGIRDLIMGDSVLSLSSKLKSFELQERLIKQNPQ*ickl*kfyll*ftf
ffffxifppk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U07081-1 (Contig-U07081-1Q)
/CSM_Contig/Contig-U07081-1Q.Seq.d
         (214 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U07081-1 (Contig-U07081-1Q) /CSM_Contig/Conti...   355  1e-98
Contig-U14284-1 (Contig-U14284-1Q) /CSM_Contig/Conti...    42  2e-04
Contig-U01338-1 (Contig-U01338-1Q) /CSM_Contig/Conti...    40  0.001
Contig-U12179-1 (Contig-U12179-1Q) /CSM_Contig/Conti...    34  0.056
Contig-U04873-1 (Contig-U04873-1Q) /CSM_Contig/Conti...    34  0.056
Contig-U01043-1 (Contig-U01043-1Q) /CSM_Contig/Conti...    34  0.056
Contig-U14874-1 (Contig-U14874-1Q) /CSM_Contig/Conti...    32  0.22
Contig-U12703-1 (Contig-U12703-1Q) /CSM_Contig/Conti...    32  0.22
Contig-U07951-1 (Contig-U07951-1Q) /CSM_Contig/Conti...    32  0.22
Contig-U11586-1 (Contig-U11586-1Q) /CSM_Contig/Conti...    28  3.5

>Contig-U07081-1 (Contig-U07081-1Q) /CSM_Contig/Contig-U07081-1Q.Seq.d
          Length = 214

 Score =  355 bits (179), Expect = 1e-98
 Identities = 179/179 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   aagcagccttccttctatcaaaaggtgttgaactctatggtattagggatttaattatgg 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   aagcagccttccttctatcaaaaggtgttgaactctatggtattagggatttaattatgg 60

                                                                       
Query: 61  gtgattctgttttatctttatcaagtaaattaaaatcttttgaattacaagaaagattga 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  gtgattctgttttatctttatcaagtaaattaaaatcttttgaattacaagaaagattga 120

                                                                      
Query: 121 taaaacaaaatcctcaataaatctgtaaattataaaagttttatcttttataatttaca 179
           |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 taaaacaaaatcctcaataaatctgtaaattataaaagttttatcttttataatttaca 179


 Score = 40.1 bits (20), Expect = 0.001
 Identities = 32/36 (88%)
 Strand = Plus / Minus

                                               
Query: 144 tgtaaattataaaagttttatcttttataatttaca 179
           ||||||||||||||| |  | |||||||||||||||
Sbjct: 179 tgtaaattataaaagataaaacttttataatttaca 144


 Score = 32.2 bits (16), Expect = 0.22
 Identities = 16/16 (100%)
 Strand = Plus / Plus

                           
Query: 198 attttccccccaaaat 213
           ||||||||||||||||
Sbjct: 198 attttccccccaaaat 213


>Contig-U14284-1 (Contig-U14284-1Q) /CSM_Contig/Contig-U14284-1Q.Seq.d
          Length = 760

 Score = 42.1 bits (21), Expect = 2e-04
 Identities = 24/25 (96%)
 Strand = Plus / Minus

                                    
Query: 94  aatcttttgaattacaagaaagatt 118
           |||||||||||||| ||||||||||
Sbjct: 26  aatcttttgaattaaaagaaagatt 2


>Contig-U01338-1 (Contig-U01338-1Q) /CSM_Contig/Contig-U01338-1Q.Seq.d
          Length = 888

 Score = 40.1 bits (20), Expect = 0.001
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                               
Query: 69  gttttatctttatcaagtaa 88
           ||||||||||||||||||||
Sbjct: 227 gttttatctttatcaagtaa 246


  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: 3989
Number of Sequences: 6905
Number of extensions: 3989
Number of successful extensions: 1285
Number of sequences better than 10.0: 156
length of query: 214
length of database: 5,674,871
effective HSP length: 15
effective length of query: 199
effective length of database: 5,571,296
effective search space: 1108687904
effective search space used: 1108687904
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 2008.11.11
Homology vs DNA 
Query= Contig-U07081-1 (Contig-U07081-1Q) /CSM_Contig/Contig-U07081-1Q.Seq.d
         (214 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

(AU270930) Dictyostelium discoideum vegetative cDNA clone:VS...   355   2e-97  2
(AC104647) Homo sapiens BAC clone RP11-38D12 from 4, complet...    34   0.095  4
(EC095621) AAE00001943 Acetabularia acetabulum Non-normalize...    42   0.26   2
(EJ703907) 1092956046112 Global-Ocean-Sampling_GS-30-02-01-1...    38   0.33   2
(AL355379) Human DNA sequence from clone RP3-508D13 on chrom...    44   0.37   2
(AC111689) Rattus norvegicus clone CH230-66C23, *** SEQUENCI...    46   0.48   1
(DX338558) OR_ABa0264N07.r OR_ABa Oryza ridleyi genomic clon...    46   0.48   1
(DX225915) OR_ABa0104E02.f OR_ABa Oryza ridleyi genomic clon...    46   0.48   1
(AC189976) Glycine tomentella clone gtd1-48g18, WORKING DRAF...    30   0.49   6
(EJ220394) 1092351227794 Global-Ocean-Sampling_GS-27-01-01-1...    40   0.98   2
(CT820304) Paramecium tetraurelia 5-PRIME EST from clone LK0...    36   1.0    2
(DX529597) GH_MBb0035B08f GH_MBb Gossypium hirsutum genomic ...    30   1.0    3
(EK431693) 1095516156715 Global-Ocean-Sampling_GS-31-01-01-1...    38   1.4    2
(AL805979) Mouse DNA sequence from clone RP23-172B20 on chro...    34   1.7    4
(AB169468) Macaca fascicularis testis cDNA, clone: QtsA-2126...    44   1.9    1
(CT967317) M.truncatula DNA sequence from clone MTH2-34B8 on...    44   1.9    1
(AC145219) Medicago truncatula clone mth2-6m1, complete sequ...    44   1.9    1
(DD411476) PIBF.                                                   44   1.9    1
(DD411467) PIBF.                                                   44   1.9    1
(DD313104) METHOD FOR DETECTING REMOTE HOMOLOGUES AND NOVEL ...    44   1.9    1
(DD218782) STRUCTURAL AND CYTOSKELETON-ASSOCIATED PROTEINS.        44   1.9    1
(DD025940) Method for diagnosing a tumor in a patient determ...    44   1.9    1
(DD025931) Method for diagnosing a tumor in a patient determ...    44   1.9    1
(CS351075) Sequence 459 from Patent WO2006013561.                  44   1.9    1
(CQ725365) Sequence 11299 from Patent WO02068579.                  44   1.9    1
(CQ725125) Sequence 11059 from Patent WO02068579.                  44   1.9    1
(CQ700584) Sequence 45510 from Patent WO02070737.                  44   1.9    1
(AX958732) Sequence 3 from Patent WO03100428.                      44   1.9    1
(AX452726) Sequence 21 from Patent WO0244734.                      44   1.9    1
(AX452708) Sequence 3 from Patent WO0244734.                       44   1.9    1
(Y09631) H.sapiens mRNA for PIBF1 protein, complete.               44   1.9    1
(BC051911) Homo sapiens progesterone immunomodulatory bindin...    44   1.9    1
(BC041806) Homo sapiens progesterone immunomodulatory bindin...    44   1.9    1
(AL391384) Human DNA sequence from clone RP11-555G22 on chro...    44   1.9    1
(AF330046) Homo sapiens progesterone-induced blocking factor...    44   1.9    1
(AC025524) Homo sapiens chromosome 8, clone RP11-705O24, com...    44   1.9    1
(AC011239) Homo sapiens BAC clone RP11-414D15 from 2, comple...    44   1.9    1
(AC011179) Homo sapiens, clone RP11-11N24, complete sequence.      44   1.9    1
(AC007773) Homo sapiens chromosome 19, BAC 275282 (CIT-B-325...    44   1.9    1
(AC005953) Homo sapiens chromosome 19, cosmid R26349, comple...    44   1.9    1
(AC160791) Bos taurus clone CH240-85E17, WORKING DRAFT SEQUE...    44   1.9    1
(AC142196) Homo sapiens chromosome 16 clone RP11-104K9, WORK...    44   1.9    1
(CU638845) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   1.9    1
(AL139181) Human DNA sequence *** SEQUENCING CANCELLED *** f...    44   1.9    1
(AK309828) Homo sapiens cDNA, FLJ99869.                            44   1.9    1
(ER450565) 1092963848186 Global-Ocean-Sampling_GS-35-01-01-1...    44   1.9    1
(EK300145) 1095462362413 Global-Ocean-Sampling_GS-31-01-01-1...    44   1.9    1
(AQ153343) HS_2233_A1_G02_MR CIT Approved Human Genomic Sper...    44   1.9    1
(EJ095568) 1095462006420 Global-Ocean-Sampling_GS-26-01-01-1...    44   1.9    1
(DQ048476) Pan troglodytes PIBF1 gene, VIRTUAL TRANSCRIPT, p...    44   1.9    1
(DQ048475) Homo sapiens PIBF1 gene, VIRTUAL TRANSCRIPT, part...    44   1.9    1
(AG252950) Lotus japonicus DNA, clone:LjT33c13_sfi.                44   1.9    1
(AV703156) Homo sapiens cDNA clone:ADBCFG01, 5'end, expresse...    44   1.9    1
(DA075156) Homo sapiens cDNA clone BRACE2026893, 5' end, mRN...    44   1.9    1
(D31319) Homo sapiens fetal-lung cDNA 5'-end sequence, HUML1...    44   1.9    1
(CK902732) in53b10.x5 HR85 islet Homo sapiens cDNA clone IMA...    44   1.9    1
(AJ680361) Sus scrofa EST, clone C0001787_N17.                     44   1.9    1
(AJ651836) Sus scrofa EST, clone C0005179_P10.                     44   1.9    1
(CD088590) MC1-0051T-L118-H06-U.B MC1-0051 Schistosoma manso...    44   1.9    1
(CD088559) MC1-0051T-L118-E04-U.B MC1-0051 Schistosoma manso...    44   1.9    1
(CD088496) MC1-0051T-L116-A10-U.B MC1-0051 Schistosoma manso...    44   1.9    1
(AI915158) tx04b01.x1 NCI_CGAP_Ut4 Homo sapiens cDNA clone I...    44   1.9    1
(AI809069) wf68a08.x1 Soares_NFL_T_GBC_S1 Homo sapiens cDNA ...    44   1.9    1
(BX835130) Arabidopsis thaliana Full-length cDNA 3PRIM end o...    44   1.9    1
(BW956317) Sus scrofa mRNA, clone:AMP010018C03, 5' end, expr...    44   1.9    1
(BU786299) in53b10.y1 HR85 islet Homo sapiens cDNA clone IMA...    44   1.9    1
(BU561566) AGENCOURT_10275734 NIH_MGC_82 Homo sapiens cDNA c...    44   1.9    1
(AI014561) ou40g05.x1 Soares_NFL_T_GBC_S1 Homo sapiens cDNA ...    44   1.9    1
(BP382990) Homo sapiens cDNA clone: kaia1277, Sugano cDNA li...    44   1.9    1
(BM763165) K-EST0044442 S13KMS5 Homo sapiens cDNA clone S13K...    44   1.9    1
(BM714785) UI-E-EJ0-ahs-d-11-0-UI.r1 UI-E-EJ0 Homo sapiens c...    44   1.9    1
(BG943946) ax44b06.x1 Hembase; Erythroid Progenitor Cells (L...    44   1.9    1
(BG187438) RST6429 Athersys RAGE Library Homo sapiens cDNA, ...    44   1.9    1
(AA806027) oc19h06.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone ...    44   1.9    1
(BF669414) 602120114F1 NIH_MGC_56 Homo sapiens cDNA clone IM...    44   1.9    1
(BF666676) 602121364F1 NIH_MGC_56 Homo sapiens cDNA clone IM...    44   1.9    1
(BF240060) 601906085F1 NIH_MGC_54 Homo sapiens cDNA clone IM...    44   1.9    1
(AW978222) EST390331 MAGE resequences, MAGP Homo sapiens cDN...    44   1.9    1
(N40036) yw71f10.r1 Soares_placenta_8to9weeks_2NbHP8to9W Hom...    44   1.9    1
(H64996) yu66c12.s1 Weizmann Olfactory Epithelium Homo sapie...    44   1.9    1
(EX297408) 1611569_5_D23_094 PY06 Carica papaya cDNA, mRNA s...    44   1.9    1
(EW480349) rova008_o18.y1 ova Sus scrofa cDNA 5', mRNA seque...    44   1.9    1
(AM436224) Vitis vinifera contig VV78X013770.3, whole genome...    34   2.0    2
(AM440419) Vitis vinifera contig VV78X211814.5, whole genome...    36   2.5    2
(AC183213) Bos taurus clone CH240-98N11, WORKING DRAFT SEQUE...    40   2.5    4
(EJ106503) 1092343138819 Global-Ocean-Sampling_GS-27-01-01-1...    30   2.6    3
(AC104947) Homo sapiens chromosome 11, clone RP11-1029L14, c...    34   3.6    2
(AC024244) Homo sapiens chromosome 11 clone RP11-541L6, WORK...    34   3.6    2
(AC021723) Homo sapiens chromosome 11, clone RP11-313M3, com...    34   3.6    2
(AF542646) Campylobacter jejuni strain RM1479 RloE (rloE) an...    36   3.7    2
(AF542643) Campylobacter jejuni strain RM1158 RloE (rloE) an...    36   3.7    2
(AF542642) Campylobacter jejuni strain RM1052 RloE (rloE) an...    36   3.7    2
(AG044959) Pan troglodytes DNA, clone: PTB-023L18.F.               34   3.9    2
(BX908752) Zebrafish DNA sequence from clone DKEYP-12C7 in l...    34   4.2    3
(EA719552) Sequence 98431 from patent US 7365185.                  40   4.3    2
(AQ547535) RPCI-11-409G1.TV RPCI-11 Homo sapiens genomic clo...    34   4.9    2
(AQ791608) HS_5266_B2_G08_T7A RPCI-11 Human Male BAC Library...    34   4.9    2
(CO132861) GR__Eb45P04.f GR__Eb Gossypium raimondii cDNA clo...    32   5.0    2
(EJ440748) 1093015303932 Global-Ocean-Sampling_GS-28-01-01-1...    34   5.0    2
(AC011050) Homo sapiens clone RP11-9P22, WORKING DRAFT SEQUE...    36   5.3    5

>(AU270930) Dictyostelium discoideum vegetative cDNA clone:VSK280,
           5' end single read.
          Length = 215

 Score =  355 bits (179), Expect(2) = 2e-97
 Identities = 179/179 (100%)
 Strand = Plus / Plus


Query: 1   aagcagccttccttctatcaaaaggtgttgaactctatggtattagggatttaattatgg 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   aagcagccttccttctatcaaaaggtgttgaactctatggtattagggatttaattatgg 60


Query: 61  gtgattctgttttatctttatcaagtaaattaaaatcttttgaattacaagaaagattga 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  gtgattctgttttatctttatcaagtaaattaaaatcttttgaattacaagaaagattga 120


Query: 121 taaaacaaaatcctcaataaatctgtaaattataaaagttttatcttttataatttaca 179
           |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 taaaacaaaatcctcaataaatctgtaaattataaaagttttatcttttataatttaca 179

 Score = 32.2 bits (16), Expect(2) = 2e-97
 Identities = 16/16 (100%)
 Strand = Plus / Plus


Query: 198 attttccccccaaaat 213
           ||||||||||||||||
Sbjct: 198 attttccccccaaaat 213

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 290,565,689
Number of extensions: 19645424
Number of successful extensions: 5739360
Number of sequences better than 10.0: 167
Length of query: 214
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 191
Effective length of database: 93,106,754,628
Effective search space: 17783390133948
Effective search space used: 17783390133948
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 6.23
Homology vs Protein 
Query= Contig-U07081-1 (Contig-U07081-1Q) /CSM_Contig/Contig-U07081-1Q.Seq.d
         (214 letters)

Database: nrp_A
           3,204,285 sequences; 1,040,966,779 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: 3204285
Number of Hits to DB: 213,187,435
Number of extensions: 2578079
Number of successful extensions: 1589
Number of sequences better than 10.0: 0
Number of HSP's gapped: 1589
Number of HSP's successfully gapped: 0
Length of query: 71
Length of database: 1,040,966,779
Length adjustment: 42
Effective length of query: 29
Effective length of database: 906,386,809
Effective search space: 26285217461
Effective search space used: 26285217461
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: 27 (15.0 bits)
PSORT 

 psg: 0.66  gvh: 0.42  alm: 0.47  top: 0.53  tms: 0.00  mit: 0.19  mip: 0.00
 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 %: nuclear
	 36.0 %: cytoplasmic
	 12.0 %: mitochondrial
	  4.0 %: peroxisomal

>> prediction for Contig-U07081-1 is nuc
VS (DIR, S) 1
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) 0
CF (FL, S) 0
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0