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Dicty_cDB
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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-U10279-1
Contig ID Contig-U10279-1
Contig update 2002. 9.13
Contig sequence 
>Contig-U10279-1 (Contig-U10279-1Q) /CSM_Contig/Contig-U10279-1Q.Seq.d
CAAAACAATAGAAATGTCAGTTTACCAAAAAACCGTTACTCATGCACCAG
CAACTTTAAACAAAGCAAATCAAGTCGATGACGATGATGATTTCGAAACT
GATCCAGATTACGTTAATGATATTAGCGAAAAAGATACTCGTTGGGGTTC
TAAAATCATTGGTACTGATAAAGGTAACGGAAAAGATATGGAAGAAATTA
GATCAAATGCATTCAATAAACATCAAACTATAACCCAAGAAGAATATGAA
AATAAGAAAATGCTTTATGGTGGTGATCGTGCTGCACAAAATAAAAAAGA
TTAATTTAATACATAAAACAAAAAAAAGCAATAGTAGCAAAGTATTAAAA
AGAATAAGAAAACAATTTTTAATTAAATAATAATAAAAAATAAATAAAAT
ATAAAAATATAATAAAAATTGTTCATTGTAACATTATAAAAAAAAAATAA
AAAAAAAAAATAATAAAAAAAAAAAAAAATTTATATATTATAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAA
Gap no gap
Contig length 563
Chromosome number (1..6, M) 5
Chromosome length 5062330
Start point 1439610
End point 1439042
Strand (PLUS/MINUS) MINUS
Number of clones 5
Number of EST 7
Link to clone list U10279
List of clone(s) 

est1=SSC267F,1,414
est2=VFI568F,7,324
est3=VSH610F,16,324
est4=VSH838F,16,324
est5=VSC216Z,142,564
est6=VSH610Z,247,420
est7=VFI568Z,287,416
Translated Amino Acid sequence 
KTIEMSVYQKTVTHAPATLNKANQVDDDDDFETDPDYVNDISEKDTRWGSKIIGTDKGNG
KDMEEIRSNAFNKHQTITQEEYENKKMLYGGDRAAQNKKD*fnt*nkkkq**qsikknkk
tifn*iiiknk*niki**klfivtl*kknkkkk**kkkkiyil*kkkkkkkkkkkkkkkk
kkkkkkk
Translated Amino Acid sequence (All Frames) 
Frame A:
qnnrnvslpknrysctsnfkqskssr*r**frn*srlr**y*rkryslgf*nhwy**r*r
krygrn*ikciq*tsnynprri*k*enalww*scctk*krli*yikqkkaivaky*ke*e
nnf*lnnnkk*ikykniikivhcniikkk*kkkiikkkknlyiikkkkkkkkkkkkkkkk
kkkkkkk


Frame B:
KTIEMSVYQKTVTHAPATLNKANQVDDDDDFETDPDYVNDISEKDTRWGSKIIGTDKGNG
KDMEEIRSNAFNKHQTITQEEYENKKMLYGGDRAAQNKKD*fnt*nkkkq**qsikknkk
tifn*iiiknk*niki**klfivtl*kknkkkk**kkkkiyil*kkkkkkkkkkkkkkkk
kkkkkkk


Frame C:
kq*kcqftkkpllmhqql*tkqiksmtmmiskliqitlmilakkilvgvlkslvlikvte
kiwkkldqmhsinikl*pkknmkirkcfmvvivlhkikkinlihktkksnsskvlkrirk
qflik***kinki*kynkncsl*hykkkikkknnkkkkkfiyykkkkkkkkkkkkkkkkk
kkkkkkk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U10279-1 (Contig-U10279-1Q)
/CSM_Contig/Contig-U10279-1Q.Seq.d
         (563 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U10279-1 (Contig-U10279-1Q) /CSM_Contig/Conti...   632  0.0
Contig-U06513-1 (Contig-U06513-1Q) /CSM_Contig/Conti...    38  0.010
Contig-U05702-1 (Contig-U05702-1Q) /CSM_Contig/Conti...    36  0.039
Contig-U10257-1 (Contig-U10257-1Q) /CSM_Contig/Conti...    34  0.15
Contig-U09745-1 (Contig-U09745-1Q) /CSM_Contig/Conti...    34  0.15
Contig-U09227-1 (Contig-U09227-1Q) /CSM_Contig/Conti...    34  0.15
Contig-U14684-1 (Contig-U14684-1Q) /CSM_Contig/Conti...    32  0.61
Contig-U14077-1 (Contig-U14077-1Q) /CSM_Contig/Conti...    32  0.61
Contig-U13201-1 (Contig-U13201-1Q) /CSM_Contig/Conti...    32  0.61
Contig-U12406-1 (Contig-U12406-1Q) /CSM_Contig/Conti...    32  0.61

>Contig-U10279-1 (Contig-U10279-1Q) /CSM_Contig/Contig-U10279-1Q.Seq.d
          Length = 563

 Score =  632 bits (319), Expect = 0.0
 Identities = 319/319 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   caaaacaatagaaatgtcagtttaccaaaaaaccgttactcatgcaccagcaactttaaa 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   caaaacaatagaaatgtcagtttaccaaaaaaccgttactcatgcaccagcaactttaaa 60

                                                                       
Query: 61  caaagcaaatcaagtcgatgacgatgatgatttcgaaactgatccagattacgttaatga 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  caaagcaaatcaagtcgatgacgatgatgatttcgaaactgatccagattacgttaatga 120

                                                                       
Query: 121 tattagcgaaaaagatactcgttggggttctaaaatcattggtactgataaaggtaacgg 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 tattagcgaaaaagatactcgttggggttctaaaatcattggtactgataaaggtaacgg 180

                                                                       
Query: 181 aaaagatatggaagaaattagatcaaatgcattcaataaacatcaaactataacccaaga 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 aaaagatatggaagaaattagatcaaatgcattcaataaacatcaaactataacccaaga 240

                                                                       
Query: 241 agaatatgaaaataagaaaatgctttatggtggtgatcgtgctgcacaaaataaaaaaga 300
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 agaatatgaaaataagaaaatgctttatggtggtgatcgtgctgcacaaaataaaaaaga 300

                              
Query: 301 ttaatttaatacataaaac 319
           |||||||||||||||||||
Sbjct: 301 ttaatttaatacataaaac 319


>Contig-U06513-1 (Contig-U06513-1Q) /CSM_Contig/Contig-U06513-1Q.Seq.d
          Length = 284

 Score = 38.2 bits (19), Expect = 0.010
 Identities = 19/19 (100%)
 Strand = Plus / Plus

                              
Query: 288 aaaataaaaaagattaatt 306
           |||||||||||||||||||
Sbjct: 248 aaaataaaaaagattaatt 266


>Contig-U05702-1 (Contig-U05702-1Q) /CSM_Contig/Contig-U05702-1Q.Seq.d
          Length = 956

 Score = 36.2 bits (18), Expect = 0.039
 Identities = 21/22 (95%)
 Strand = Plus / Minus

                                 
Query: 288 aaaataaaaaagattaatttaa 309
           |||| |||||||||||||||||
Sbjct: 23  aaaaaaaaaaagattaatttaa 2


  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: 7272
Number of Sequences: 6905
Number of extensions: 7272
Number of successful extensions: 609
Number of sequences better than 10.0: 244
length of query: 563
length of database: 5,674,871
effective HSP length: 16
effective length of query: 547
effective length of database: 5,564,391
effective search space: 3043721877
effective search space used: 3043721877
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 2008.11.18
Homology vs DNA 
Query= Contig-U10279-1 (Contig-U10279-1Q) /CSM_Contig/Contig-U10279-1Q.Seq.d
         (563 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

(BJ414266) Dictyostelium discoideum cDNA clone:ddv18g17, 5' ...   557   e-154  1
(AU268048) Dictyostelium discoideum vegetative cDNA clone:VS...   539   e-149  1
(AU267703) Dictyostelium discoideum vegetative cDNA clone:VS...   539   e-149  1
(AU071686) Dictyostelium discoideum slug cDNA, clone SSC267.      476   e-130  1
(AU262401) Dictyostelium discoideum vegetative cDNA clone:VS...   268   2e-67  1
(EX007668) HTAB-aad62h12.b1 Heterorhabditis_bacteriophora_HT...    50   0.086  1
(EB030953) lk_hhin_0004e15.pDNRF2 lk_hhin Hippoglossus hippo...    48   0.34   1
(AG305167) Mus musculus molossinus DNA, clone:MSMg01-085K09....    46   1.3    1
(CP000153) Sulfurimonas denitrificans DSM 1251, complete gen...    46   1.3    1
(BX005299) Zebrafish DNA sequence from clone CH211-107C24.         44   5.3    1
(CR382133) Debaryomyces hansenii chromosome A of strain CBS7...    44   5.3    1
(AE014845) Plasmodium falciparum 3D7 chromosome 12, section ...    44   5.3    1
(AC123016) Rattus norvegicus clone CH230-45K8, WORKING DRAFT...    44   5.3    1
(AC103188) Rattus norvegicus clone CH230-108J24, *** SEQUENC...    44   5.3    1
(AC195693) Myotis lucifugus clone CH235-394J5, WORKING DRAFT...    44   5.3    1
(AC006281) Plasmodium falciparum chromosome 12 clone 3D7, **...    44   5.3    1
(BH342372) CH230-195E20.TJ CHORI-230 Segment 1 Rattus norveg...    44   5.3    1
(BH284757) CH230-49O4.TJ CHORI-230 Segment 1 Rattus norvegic...    44   5.3    1
(EJ115750) 1092343318782 Global-Ocean-Sampling_GS-27-01-01-1...    44   5.3    1
(DU879898) 295530 Tomato HindIII BAC Library Solanum lycoper...    44   5.3    1
(CF694112) CCAHW62TF C.neoformans strain JEC21 Cryptococcus ...    44   5.3    1
(BJ069851) Xenopus laevis cDNA clone:XL054m10, 5' end, singl...    44   5.3    1
(BF298793) 021PbD11 Pb cDNA #20, Charles Yowell and Jane Car...    44   5.3    1
(FD548783) RR3EN59TF RR3(NY) Raphanus raphanistrum subsp. ra...    44   5.3    1
(FD544926) RR3EN59JQ RR3(NY) Raphanus raphanistrum subsp. ra...    44   5.3    1
(BX908798) Parachlamydia-related symbiont UWE25, complete ge...    44   5.3    1
(AC168107) Bos taurus clone CH240-204A1, WORKING DRAFT SEQUE...    40   5.9    2
(FH623447) CHO_OF4948xh05r1.ab1 CHO_OF4 Nicotiana tabacum ge...    34   9.7    2

>(BJ414266) Dictyostelium discoideum cDNA clone:ddv18g17, 5' end,
           single read.
          Length = 318

 Score =  557 bits (281), Expect = e-154
 Identities = 281/281 (100%)
 Strand = Plus / Plus


Query: 7   aatagaaatgtcagtttaccaaaaaaccgttactcatgcaccagcaactttaaacaaagc 66
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   aatagaaatgtcagtttaccaaaaaaccgttactcatgcaccagcaactttaaacaaagc 60


Query: 67  aaatcaagtcgatgacgatgatgatttcgaaactgatccagattacgttaatgatattag 126
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  aaatcaagtcgatgacgatgatgatttcgaaactgatccagattacgttaatgatattag 120


Query: 127 cgaaaaagatactcgttggggttctaaaatcattggtactgataaaggtaacggaaaaga 186
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 cgaaaaagatactcgttggggttctaaaatcattggtactgataaaggtaacggaaaaga 180


Query: 187 tatggaagaaattagatcaaatgcattcaataaacatcaaactataacccaagaagaata 246
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 tatggaagaaattagatcaaatgcattcaataaacatcaaactataacccaagaagaata 240


Query: 247 tgaaaataagaaaatgctttatggtggtgatcgtgctgcac 287
           |||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 tgaaaataagaaaatgctttatggtggtgatcgtgctgcac 281

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 333,718,754
Number of extensions: 19298363
Number of successful extensions: 1730099
Number of sequences better than 10.0: 29
Length of query: 563
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 540
Effective length of database: 93,106,754,628
Effective search space: 50277647499120
Effective search space used: 50277647499120
X1: 11 (21.8 bits)
S2: 22 (44.1 bits)
protein update 2009. 6.27
Homology vs Protein 
Query= Contig-U10279-1 (Contig-U10279-1Q) /CSM_Contig/Contig-U10279-1Q.Seq.d
         (563 letters)

Database: nrp_A
           3,204,285 sequences; 1,040,966,779 total letters

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

(Q01406) RecName: Full=Src substrate protein p85; AltName: Full=...    48   2e-04
BC033889_1(BC033889|pid:none) Homo sapiens cortactin, mRNA (cDNA...    46   8e-04
AB036705_1(AB036705|pid:none) Homo sapiens EMS1 gene for cortact...    46   8e-04
AY892324_1(AY892324|pid:none) Synthetic construct Homo sapiens c...    46   8e-04
AK165555_1(AK165555|pid:none) Mus musculus bladder RCB-0544 MBT-...    46   8e-04
(Q14247) RecName: Full=Src substrate cortactin; AltName: Full=Am...    46   8e-04
A48063(A48063) mammary tumor/squamous cell carcinoma-associated ...    46   8e-04
AK084249_1(AK084249|pid:none) Mus musculus 12 days embryo eyebal...    44   0.004
CR861394_1(CR861394|pid:none) Pongo abelii mRNA; cDNA DKFZp459H1...    43   0.007
BC060434_1(BC060434|pid:none) Xenopus laevis hypothetical protei...    42   0.014
BC073454_1(BC073454|pid:none) Xenopus laevis MGC80961 protein, m...    41   0.019
AB027611_1(AB027611|pid:none) Xenopus laevis mRNA for cortactin,...    39   0.072
AK298696_1(AK298696|pid:none) Homo sapiens cDNA FLJ59379 complet...    39   0.072
(P14317) RecName: Full=Hematopoietic lineage cell-specific prote...    39   0.072
BC169873_1(BC169873|pid:none) Xenopus laevis cortactin, mRNA (cD...    39   0.072
BC103355_1(BC103355|pid:none) Bos taurus hematopoietic cell-spec...    39   0.094
(P49710) RecName: Full=Hematopoietic lineage cell-specific prote...    39   0.094
BC167645_1(BC167645|pid:none) Xenopus tropicalis cortactin, mRNA...    39   0.12
BC079081_1(BC079081|pid:none) Rattus norvegicus hematopoietic ce...    39   0.12
BC125934_1(BC125934|pid:none) Danio rerio si:dkey-9a20.6, mRNA (...    37   0.47
AF064260_1(AF064260|pid:none) Strongylocentrotus purpuratus SRC8...    33   3.9
BC162578_1(BC162578|pid:none) Danio rerio cortactin, mRNA (cDNA ...    33   3.9
AF527956_1(AF527956|pid:none) Danio rerio cortactin mRNA, comple...    33   3.9

>(Q01406) RecName: Full=Src substrate protein p85; AltName:
           Full=p80; AltName: Full=Cortactin;  &A41530(A41530)
           &M73705_1(M73705|pid:none)
          Length = 563

 Score = 47.8 bits (112), Expect = 2e-04
 Identities = 23/51 (45%), Positives = 35/51 (68%), Gaps = 4/51 (7%)
 Frame = +2

Query: 110 YVNDISEKDTRWGSKIIGTDKGNGK----DMEEIRSNAFNKHQTITQEEYE 250
           +VND+SEK+ RWG+K   T KG+G     ++ ++R N F +HQTI ++E E
Sbjct: 37  FVNDVSEKEQRWGAK---TVKGSGHQEHINIHQLRENVFQEHQTIKEKELE 84

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: 452,959,862
Number of extensions: 6113052
Number of successful extensions: 19298
Number of sequences better than 10.0: 23
Number of HSP's gapped: 19284
Number of HSP's successfully gapped: 23
Length of query: 187
Length of database: 1,040,966,779
Length adjustment: 121
Effective length of query: 66
Effective length of database: 653,248,294
Effective search space: 43114387404
Effective search space used: 43114387404
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: 30 (16.2 bits)
PSORT 

 psg: 0.84  gvh: 0.36  alm: 0.58  top: 0.53  tms: 0.00  mit: 0.26  mip: 0.00
 nuc: 0.00  erl: 0.00  erm: 0.40  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
	  8.0 %: vacuolar
	  4.0 %: cytoskeletal
	  4.0 %: mitochondrial

>> prediction for Contig-U10279-1 is nuc
VS (DIR, S) 3
VH (FL, L) 0
VF (FL, S) 1
AH (FL, L) 0
AF (FL, S) 0
SL (DIR, L) 0
SS (DIR, S) 1
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