NBDC - アーカイブトップ - ヘルプ
データベースの説明 | データ項目の説明 | 利用許諾 | ヘルプ
Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
NBDC - LSDB Archive
Description of this DB | Description of data items | Download | License
Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
SSJ446
Library SS
(Link to library)
Clone ID SSJ446
Atlas ID -
NBRP ID
dictyBase ID
Link to Contig Contig-U02608-1
Original site URL
Representative seq. ID SSJ446P
(Link to Original site)
Representative DNA sequence 
>SSJ446 (SSJ446Q) /CSM/SS/SSJ4-B/SSJ446Q.Seq.d/
TTTTTTTACATTGTTCTAAAATTTTAAAAGATACAAAAAAAAAAAAAAAGTTTCTTCTTT
TTTTTTTTTTTTTTAATTTTATTATACACCATCTTGCCCAAAATCATTAGTGAATTCAAC
ATATCTATCTAAATCAGCTTTATTAACAGATGGTTTAATAACTCTTAAACTCTTTAAACA
ATCGGCGATTGTAATTTCAGGTTCNTTTAATTTAGTTGGGTCAATATCCATCCAAGTCAT
CTCTTGAGCCAATGGATCACCAGGTGAACAAGGTGTGACATAATCGGTCATAACTGAAGG
ATCCTCTCTAGAGGGTGCTCTAATTTGTTTGAAATGAGTTGCACATTGAACTGCACGAAC
TGGTTGCATAATTGCATCCTTTACCAATGAACCAATATCTGAACCCGAGTAACCCTCGGT
TAAATCTGCCAACTTTTTATAATCTGCTTGAACTAATGTATTTGGAGTTGAACCAATATG
AATTTGAAACATTTTGGCTCTTGCTTGTGGTTCTGGTAAACCGATATATATTCTCTTTTC
AAAACGTCTACGAATTGCTAAATCCAAACCCCATGGAATATTTGTTGCTGCCAATACCAA
TATACCATCGGAATCATTACCAACACCATTCATTTGAATGAGAAACTCTGTCTTTATACG
TCTTGCTGATTCAGATTCTTGATCATTACGTGATGAACATAAAGAATCAACTTCATCAAT
AAXXXXXXXXXXGCACCATTTGCACTACCAGCACTATTACTTTTATTACCACCAACTGCT
ACTGGTTTCTTATTCTTTGATTTATCTAAATATTCTNTTAATTGTTCTGCTCTTTGAAGA
TATTCTAATGTTTTTGCTTTAATTGTTGCTTTTGATCTTTCGCTTTTTTCATATTTTAAA
GCTGTTGTAAACCATTCTAAACTTTGGATATATAATCTATGTGCTTCTGCATAATTTTTT
GCATTATCTTGTTCTGTTGCTTGTTGAACAATTTGAATTGCTTTTTGTAAGAAATTAACA
TCACCCATTATTAGTTGTATTGGATTTTTTTTTGGTTTTCTTTTTTTTTTTTTTTGGTTT
TTATGAATCGTCCATAGTATTTGTTTTAATTTCTAAAAAAAAAAAAAT
sequence update 1998.11.17
Translated Amino Acid sequence 
fftlf*nfkrykkkkkvssfffff*fyytpscpkslvnstylsksalltdglitlklfkq
saivisgsfnlvgsisiqvis*angspgeqgvt*svitegsslegaliclk*vah*tart
gciiasftnepisepe*psvksanfl*sa*tnvfgvepi*i*nilalacgsgkpiyilfs
krlriakskphgifvaantnipseslptpfi*mrnsvfirladsds*SLRDEHKESTSSI
---

---HHLHYQHYYFYYHQLLLVSYSLIYLNILLIVLLFEDILMFLL*llllifrffhilkl
l*tilnfgyiiyvllhnflhylvlllveqfellfvrn*hhpllvvldfflvffffffgfy
essivfvliskkkk
Translated Amino Acid sequence (All Frames) 
Frame A:
ffyivlkf*kiqkkkksffffffflillytilpkiisefnisi*isfinrwfnns*tl*t
igdcnfrfx*fswvnihpshllsqwitr*trcdiighn*rilsrgcsnlfemsctlnctn
wlhncilyq*tni*trvtlg*icqlfiicln*ciws*tnmnlkhfgsclwfw*tdiyslf
ktstnc*iqtpwnicccqyqytigiitntihlneklclytsc*frfliit**t*rinfin
---

---apfalpalllllpptatgflffdlskysxncsal*rysnvfalivafdlslfsyfka
vvnhsklwiynlcasa*ffalscsvac*ti*iafckkltspiiscigfffgflffffwfl
*ivhsicfnf*kkkn

Frame B:
fftlf*nfkrykkkkkvssfffff*fyytpscpkslvnstylsksalltdglitlklfkq
saivisgsfnlvgsisiqvis*angspgeqgvt*svitegsslegaliclk*vah*tart
gciiasftnepisepe*psvksanfl*sa*tnvfgvepi*i*nilalacgsgkpiyilfs
krlriakskphgifvaantnipseslptpfi*mrnsvfirladsds*SLRDEHKESTSSI
---

---HHLHYQHYYFYYHQLLLVSYSLIYLNILLIVLLFEDILMFLL*llllifrffhilkl
l*tilnfgyiiyvllhnflhylvlllveqfellfvrn*hhpllvvldfflvffffffgfy
essivfvliskkkk

Frame C:
flhcskilkdtkkkkkfllfffffnfiihhlaqnh**iqhiylnqly*qmv**llnslnn
rrl*fqvxli*lgqypsksslepmdhqvnkv*hnrs*lkdpl*rvl*fv*nelhielhel
va*lhplpmnqylnpsnprlnlptfynllelmylelnqyefetfwlllvvlvnryifsfq
nvyellnpnpmeylllpipiyhrnhyqhhsfe*etlslyvlliqildhyvmniknqlhq*
---

---ticttstitfittncywflil*fi*ifx*lfcslkif*cfcfnccf*sfaffif*sc
ckpf*tldi*smcfciifciilfccllnnlncfl*einithy*lywiffwfsfffflvfm
nrp*ylf*flkkkk
Homology vs CSM-cDNA 

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

SSJ446 (SSJ446Q) /CSM/SS/SSJ4-B/SSJ446Q.Seq.d/                       1463   0.0
AFF478 (AFF478Q) /CSM/AF/AFF4-D/AFF478Q.Seq.d/                       1178   0.0
SSA176 (SSA176Q) /CSM/SS/SSA1-D/SSA176Q.Seq.d/                       1132   0.0
SSB762 (SSB762Q) /CSM/SS/SSB7-C/SSB762Q.Seq.d/                        589   e-167
SLJ282 (SLJ282Q) /CSM/SL/SLJ2-D/SLJ282Q.Seq.d/                        492   e-138
SSI783 (SSI783Q) /CSM/SS/SSI7-D/SSI783Q.Seq.d/                        343   4e-93
AFE779 (AFE779Q) /CSM/AF/AFE7-D/AFE779Q.Seq.d/                        220   4e-56
VFG111 (VFG111Q) /CSM/VF/VFG1-A/VFG111Q.Seq.d/                         40   0.072
CHL686 (CHL686Q) /CSM/CH/CHL6-D/CHL686Q.Seq.d/                         40   0.072
VSF163 (VSF163Q) /CSM/VS/VSF1-C/VSF163Q.Seq.d/                         38   0.28
own update 2004.12.25
Homology vs DNA 

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

BI745667|BI745667.1 rk83g09.y4 Meloidogyne javanica egg pAMP1 v6 Chiapelli McCarter Meloidogyne javanica cDNA 5' similar to SW:SKD1_MOUSE P46467 SKD1 PROTEIN. [1] ;, mRNA sequence.    56   2e-08  2
CD080841|CD080841.1 MA3-9999U-M315-E10-U.B MA3-0001 Schistosoma mansoni cDNA clone MA3-9999U-M315-E10.B, mRNA sequence.    32   3e-08  4
CD190528|CD190528.1 MS1-0064U-A263-A04-U.B MS1-0064 Schistosoma mansoni cDNA clone MS1-0064U-A263-A04.B, mRNA sequence.    32   3e-08  4
CD184281|CD184281.1 MS1-0044T-R200-A01-U.G MS1-0044 Schistosoma mansoni cDNA clone MS1-0044T-R200-A01.G, mRNA sequence.    32   3e-08  4
CD178977|CD178977.1 MS1-0014P-A285-G05-U.G MS1-0014 Schistosoma mansoni cDNA clone MS1-0014P-A285-G05.G, mRNA sequence.    32   3e-08  4
CF400358|CF400358.1 RTWW1_4_D05.g1_A015 Well-watered loblolly pine roots WW1 Pinus taeda cDNA clone RTWW1_4_D05_A015 5', mRNA sequence.    54   1e-06  2
CF400261|CF400261.1 RTWW1_4_D05.b1_A015 Well-watered loblolly pine roots WW1 Pinus taeda cDNA clone RTWW1_4_D05_A015 3', mRNA sequence.    54   1e-06  2
CD492322|CD492322.1 RGMP 63 Touchdown PCR for candidate resistance genes pg FG 11-32 Haematobia irritans irritans cDNA similar to Vacuolar sorting protein SKD1, mRNA sequence.    58   3e-04  1
AC020874|AC020874.2 Mus musculus clone RP23-333M14, *** SEQUENCING IN PROGRESS ***, 64 unordered pieces.    42   0.004  6
AY077834|AY077834.1 Sheeppox virus strain NISKHI, complete genome.    32   0.020  11
dna update 2004. 2.16
Homology vs Protein 

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

(Q54PT2) RecName: Full=Vacuolar protein sorting-associating prot...   425   e-117
AJ719395_1(AJ719395|pid:none) Gallus gallus mRNA for hypothetica...   288   2e-76
AJ720732_1(AJ720732|pid:none) Gallus gallus mRNA for hypothetica...   288   2e-76
AF038960_1(AF038960|pid:none) Homo sapiens SKD1 homolog mRNA, co...   282   2e-74
BC055202_1(BC055202|pid:none) Danio rerio vacuolar protein sorti...   281   3e-74
CU207344_1(CU207344|pid:none) Zebrafish DNA sequence from clone ...   281   3e-74
BC152663_1(BC152663|pid:none) Danio rerio vacuolar protein sorti...   281   3e-74
(Q5R658) RecName: Full=Vacuolar protein sorting-associating prot...   280   8e-74
(O75351) RecName: Full=Vacuolar protein sorting-associating prot...   280   8e-74
AK291253_1(AK291253|pid:none) Homo sapiens cDNA FLJ75934 complet...   279   1e-73
protein update 2009. 6.14
PSORT 

 psg: 0.75  gvh: 0.46  alm: 0.22  top: 0.23  tms: 0.07  mit: 0.26  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: 0.92  leu: 0.13  gpi: 0.00  myr: 0.00
 dna: 0.00  rib: 0.00  bac: 0.00  m1a: 0.00  m1b: 0.00  m2 : 1.00  mNt: 0.00
 m3a: 0.00  m3b: 0.00  m_ : 0.00 

	 40.0 %: mitochondrial
	 20.0 %: Golgi
	 16.0 %: nuclear
	 12.0 %: endoplasmic reticulum
	  8.0 %: cytoplasmic
	  4.0 %: vacuolar

>> prediction for SSJ446 is mit
5' end seq. ID SSJ446F
5' end seq. 
>SSJ446F.Seq
TTTTTTTACATTGTTCTAAAATTTTAAAAGATACAAAAAAAAAAAAAAAGTTTCTTCTTT
TTTTTTTTTTTTTTAATTTTATTATACACCATCTTGCCCAAAATCATTAGTGAATTCAAC
ATATCTATCTAAATCAGCTTTATTAACAGATGGTTTAATAACTCTTAAACTCTTTAAACA
ATCGGCGATTGTAATTTCAGGTTCNTTTAATTTAGTTGGGTCAATATCCATCCAAGTCAT
CTCTTGAGCCAATGGATCACCAGGTGAACAAGGTGTGACATAATCGGTCATAACTGAAGG
ATCCTCTCTAGAGGGTGCTCTAATTTGTTTGAAATGAGTTGCACATTGAACTGCACGAAC
TGGTTGCATAATTGCATCCTTTACCAATGAACCAATATCTGAACCCGAGTAACCCTCGGT
TAAATCTGCCAACTTTTTATAATCTGCTTGAACTAATGTATTTGGAGTTGAACCAATATG
AATTTGAAACATTTTGGCTCTTGCTTGTGGTTCTGGTAAACCGATATATATTCTCTTTTC
AAAACGTCTACGAATTGCTAAATCCAAACCCCATGGAATATTTGTTGCTGCCAATACCAA
TATACCATCGGAATCATTACCAACACCATTCATTTGAATGAGAAACTCTGTCTTTATACG
TCTTGCTGATTCAGATTCTTGATCATTACGTGATGAACATAAAGAATCAACTTCATCAAT
AA----------
Length of 5' end seq. 722
3' end seq. ID SSJ446Z
3' end seq. 
>SSJ446Z.Seq
----------GCACCATTTGCACTACCAGCACTATTACTTTTATTACCACCAACTGCTAC
TGGTTTCTTATTCTTTGATTTATCTAAATATTCTNTTAATTGTTCTGCTCTTTGAAGATA
TTCTAATGTTTTTGCTTTAATTGTTGCTTTTGATCTTTCGCTTTTTTCATATTTTAAAGC
TGTTGTAAACCATTCTAAACTTTGGATATATAATCTATGTGCTTCTGCATAATTTTTTGC
ATTATCTTGTTCTGTTGCTTGTTGAACAATTTGAATTGCTTTTTGTAAGAAATTAACATC
ACCCATTATTAGTTGTATTGGATTTTTTTTTGGTTTTCTTTTTTTTTTTTTTTGGTTTTT
ATGAATCGTCCATAGTATTTGTTTTAATTTCTAAAAAAAAAAAAAT
Length of 3' end seq. 396
Connected seq. ID SSJ446P
Connected seq. 
>SSJ446P.Seq
TTTTTTTACATTGTTCTAAAATTTTAAAAGATACAAAAAAAAAAAAAAAGTTTCTTCTTT
TTTTTTTTTTTTTTAATTTTATTATACACCATCTTGCCCAAAATCATTAGTGAATTCAAC
ATATCTATCTAAATCAGCTTTATTAACAGATGGTTTAATAACTCTTAAACTCTTTAAACA
ATCGGCGATTGTAATTTCAGGTTCNTTTAATTTAGTTGGGTCAATATCCATCCAAGTCAT
CTCTTGAGCCAATGGATCACCAGGTGAACAAGGTGTGACATAATCGGTCATAACTGAAGG
ATCCTCTCTAGAGGGTGCTCTAATTTGTTTGAAATGAGTTGCACATTGAACTGCACGAAC
TGGTTGCATAATTGCATCCTTTACCAATGAACCAATATCTGAACCCGAGTAACCCTCGGT
TAAATCTGCCAACTTTTTATAATCTGCTTGAACTAATGTATTTGGAGTTGAACCAATATG
AATTTGAAACATTTTGGCTCTTGCTTGTGGTTCTGGTAAACCGATATATATTCTCTTTTC
AAAACGTCTACGAATTGCTAAATCCAAACCCCATGGAATATTTGTTGCTGCCAATACCAA
TATACCATCGGAATCATTACCAACACCATTCATTTGAATGAGAAACTCTGTCTTTATACG
TCTTGCTGATTCAGATTCTTGATCATTACGTGATGAACATAAAGAATCAACTTCATCAAT
AA----------GCACCATTTGCACTACCAGCACTATTACTTTTATTACCACCAACTGCT
ACTGGTTTCTTATTCTTTGATTTATCTAAATATTCTNTTAATTGTTCTGCTCTTTGAAGA
TATTCTAATGTTTTTGCTTTAATTGTTGCTTTTGATCTTTCGCTTTTTTCATATTTTAAA
GCTGTTGTAAACCATTCTAAACTTTGGATATATAATCTATGTGCTTCTGCATAATTTTTT
GCATTATCTTGTTCTGTTGCTTGTTGAACAATTTGAATTGCTTTTTGTAAGAAATTAACA
TCACCCATTATTAGTTGTATTGGATTTTTTTTTGGTTTTCTTTTTTTTTTTTTTTGGTTT
TTATGAATCGTCCATAGTATTTGTTTTAATTTCTAAAAAAAAAAAAAT
Length of connected seq. 1118
Full length Seq ID -
Full length Seq. -
Length of full length seq. -