SHD239
Library SH
(Link to library)
Clone ID SHD239
Atlas ID -
NBRP ID -
dictyBase ID -
Link to Contig Contig-U15709-1
Original site URL
Representative seq. ID
(Link to Original site)
Representative DNA sequence
>SHD239 (SHD239Q) /CSM/SH/SHD2-B/SHD239Q.Seq.d/
ATTTTTTATCAATATATATTTAAAATATATAAAAAAATAAAAAAATGCCTTTACGTTTAG
ATATTAAGAAAAAATTATCAACAAGATCAGATAGAGTTAAATCTGTTGATATTCACCCAA
CAGAACCATGGATTTTAGCAAGTTTATATGATGGTAATGTTTATATTTGGAATTATGAAA
CTCAAAATATGGTAAAATCATTTGAAGTTTCACCAAATAATCCAGTTAGAACAGCAAGAT
TCATTGCAAAGAAACAATGGATAGTTACAGGTAGTGATGATACATATATTAGAGTTTATA
ATTATAATACAATGGAAAAGATAAAATCATTTGAAGCACATGCCGATTATATTAGATGTA
TTATAGTTCATCCAACATTACCATATATATTATCATCATCGGATGATATGTTTATAAAGT
TATGGGATTATGAAAAGGGATGGAGTAACACTCAAGTCTTTGAAGGACATTCACATTACG
TCATGTCGATTGCATGGAATCCAAAGGATACCAATCAATTTGCAACCGCATCATTGGATA
AAACTGTGAAAGTGTGGAGTATAAACTCACCACATCCTCACTTTACATTGGAGGGACACG
AAAAGGGTATCAACAGTGTCGAGTATTTCTCTGGCXXXXXXXXXX
sequence update 2002.10.25
Translated Amino Acid sequence
flsiyi*ni*KNKKMPLRLDIKKKLSTRSDRVKSVDIHPTEPWILASLYDGNVYIWNYET
QNMVKSFEVSPNNPVRTARFIAKKQWIVTGSDDTYIRVYNYNTMEKIKSFEAHADYIRCI
IVHPTLPYILSSSDDMFIKLWDYEKGWSNTQVFEGHSHYVMSIAWNPKDTNQFATASLDK
TVKVWSINSPHPHFTLEGHEKGINSVEYFS---


Translated Amino Acid sequence (All Frames)
Frame A:
ifyqyifkiykkikkclyv*ilrknyqqdqielnlliftqqnhgf*qvymmvmfifgimk
lkiw*nhlkfhqiiqleqqdslqrnng*lqvvmihilefiiiiqwkr*nhlkhmpiildv
l*fiqhyhiyyhhrmicl*sygimkrdgvtlkslkdihitscrlhgiqripinlqphhwi
kl*kcgv*thhiltlhwrdtkrvstvssisl---


Frame B:
ffiniylkyikk*knaftfry*ekiinkir*s*ic*yspnrtmdfskfi*w*clylel*n
skygkii*sftk*ss*nskihcketmdsyr***yiy*sl*l*yngkdkii*stcrly*my
ysssnitiyiiiig*yvykvmgl*kgme*hssl*rtftlrhvdcmeskgyqsicnriig*
ncesveyklttsslyiggtrkgyqqcrvflw---


Frame C:
flsiyi*ni*KNKKMPLRLDIKKKLSTRSDRVKSVDIHPTEPWILASLYDGNVYIWNYET
QNMVKSFEVSPNNPVRTARFIAKKQWIVTGSDDTYIRVYNYNTMEKIKSFEAHADYIRCI
IVHPTLPYILSSSDDMFIKLWDYEKGWSNTQVFEGHSHYVMSIAWNPKDTNQFATASLDK
TVKVWSINSPHPHFTLEGHEKGINSVEYFS---


Homology vs CSM-cDNA

Score E
Sequences producing significant alignments: (bits) Value

SHL384 (SHL384Q) /CSM/SH/SHL3-D/SHL384Q.Seq.d/ 1170 0.0
SHD239 (SHD239Q) /CSM/SH/SHD2-B/SHD239Q.Seq.d/ 1170 0.0
AHQ130 (AHQ130Q) /CSM/AH/AHQ1-B/AHQ130Q.Seq.d/ 1170 0.0
AHE547 (AHE547Q) /CSM/AH/AHE5-B/AHE547Q.Seq.d/ 1170 0.0
AHD201 (AHD201Q) /CSM/AH/AHD2-A/AHD201Q.Seq.d/ 1170 0.0
AHA122 (AHA122Q) /CSM/AH/AHA1-A/AHA122Q.Seq.d/ 1170 0.0
SHL172 (SHL172Q) /CSM/SH/SHL1-C/SHL172Q.Seq.d/ 1162 0.0
SHK472 (SHK472Q) /CSM/SH/SHK4-C/SHK472Q.Seq.d/ 1162 0.0
SHG821 (SHG821Q) /CSM/SH/SHG8-A/SHG821Q.Seq.d/ 1162 0.0
AHN840 (AHN840Q) /CSM/AH/AHN8-B/AHN840Q.Seq.d/ 1158 0.0

own update 2002.10.17
Homology vs DNA

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

CN942611|CN942611.1 010921AVBC069045PG (AVBC) Royal Gala young shoot Malus x domesticacDNA clone AVBC069045, mRNA sequence. 78 8e-13 2
CN914665|CN914665.1 030110ABNB001773HT (ABNB) Braeburn cultured fruit cells, boron exposed, phytoremediation Malus x domestica cDNA clone ABNB001773, mRNA sequence. 78 9e-13 2
CN939139|CN939139.1 010616AVBC004822HT (AVBC) Royal Gala young shoot Malus x domestica cDNA clone AVBC004822, mRNA sequence. 78 1e-12 2
AZ684437|AZ684437.1 ENTLH77TR Entamoeba histolytica Sheared DNA Entamoeba histolytica genomic, DNA sequence. 66 2e-12 2
AY266451|AY266451.1 Plasmodium falciparum isolate 3D7 COPI protein (Sec27) mRNA, complete cds. 84 4e-12 1
AL929355|AL929355.1 Plasmodium falciparum strain 3D7, chromosome 9; segment 1/5. 84 4e-12 1
CL809452|CL809452.1 OR_CBa0024E02.f OR_CBa Oryza rufipogon genomic clone OR_CBa0024E02 5', genomic survey sequence. 46 9e-12 4
BP064336|BP064336.1 Lotus corniculatus var. japonicus cDNA, clone:GENLf038d07, 3' end. 68 2e-11 3
AP003487|AP003487.2 Oryza sativa (japonica cultivar-group) genomic DNA, chromosome 6, BAC clone:OSJNBa0007O20. 46 3e-11 3
AK111584|AK111584.1 Oryza sativa (japonica cultivar-group) cDNA clone:J013089O14, full insert sequence. 46 4e-11 3
dna update 2006. 1.29
Homology vs Protein

Score E
Sequences producing significant alignments: (bits) Value

(Q54YD8) RecName: Full=Coatomer subunit beta'; AltName: Full=Bet... 416 e-115
(Q6H8D5) RecName: Full=Coatomer subunit beta'-2; AltName: Full=B... 318 8e-86
(Q9C827) RecName: Full=Coatomer subunit beta'-2; AltName: Full=B... 318 8e-86
(Q9CAA0) RecName: Full=Coatomer subunit beta'-1; AltName: Full=B... 315 5e-85
BT036985_1(BT036985|pid:none) Zea mays full-length cDNA clone ZM... 311 7e-84
BC096500_1(BC096500|pid:none) Xenopus tropicalis hypothetical pr... 304 2e-81
AK304219_1(AK304219|pid:none) Homo sapiens cDNA FLJ61545 complet... 304 2e-81
(P35606) RecName: Full=Coatomer subunit beta'; AltName: Full=Bet... 304 2e-81
(P35605) RecName: Full=Coatomer subunit beta'; AltName: Full=Bet... 304 2e-81
S35312(S35312;S39811) coatomer complex beta' chain - bovine &X7... 304 2e-81
protein update 2009. 4.16
PSORT

psg: 0.43 gvh: 0.36 alm: 0.45 top: 0.53 tms: 0.00 mit: 0.34 mip: 0.03
nuc: 0.00 erl: 0.00 erm: 0.00 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

44.0 %: nuclear
28.0 %: cytoplasmic
16.0 %: mitochondrial
8.0 %: vesicles of secretory system
4.0 %: cytoskeletal

>> prediction for SHD239 is nuc

5' end seq. ID SHD239F
5' end seq.
>SHD239F.Seq
ATTTTTTATCAATATATATTTAAAATATATAAAAAAATAAAAAAATGCCTTTACGTTTAG
ATATTAAGAAAAAATTATCAACAAGATCAGATAGAGTTAAATCTGTTGATATTCACCCAA
CAGAACCATGGATTTTAGCAAGTTTATATGATGGTAATGTTTATATTTGGAATTATGAAA
CTCAAAATATGGTAAAATCATTTGAAGTTTCACCAAATAATCCAGTTAGAACAGCAAGAT
TCATTGCAAAGAAACAATGGATAGTTACAGGTAGTGATGATACATATATTAGAGTTTATA
ATTATAATACAATGGAAAAGATAAAATCATTTGAAGCACATGCCGATTATATTAGATGTA
TTATAGTTCATCCAACATTACCATATATATTATCATCATCGGATGATATGTTTATAAAGT
TATGGGATTATGAAAAGGGATGGAGTAACACTCAAGTCTTTGAAGGACATTCACATTACG
TCATGTCGATTGCATGGAATCCAAAGGATACCAATCAATTTGCAACCGCATCATTGGATA
AAACTGTGAAAGTGTGGAGTATAAACTCACCACATCCTCACTTTACATTGGAGGGACACG
AAAAGGGTATCAACAGTGTCGAGTATTTCTCTGGCNNNNNNNNNN
Length of 5' end seq. 645
3' end seq. ID -
3' end seq. -
Length of 3' end seq. -
Connected seq. ID -
Connected seq. -
Length of connected seq. -
Full length Seq ID -
Full length Seq. -
Length of full length seq. -