Contig-U06991-1
Contig ID Contig-U06991-1
Contig update 2001. 8.30
Contig sequence
>Contig-U06991-1 (Contig-U06991-1Q) /CSM_Contig/Contig-U06991-1Q.Seq.d
AATTAATTAAAAAAGATAAAAAAGAAAAAAAAGAATTTGAAAATCAATTA
AAGATTGAATTTAATAAACAAGATGTATTTAGTATAAAAAGAAAAGAGGA
ATTAGGATATAAAGCAAAGAGATTAATTGATTATGGTAGATATTTATTTA
TTAAAGAAAAATTAAATTTACCAAATACAAAATTTTGGATTTATACAAAT
CAATCAAAAGAAAATTTATTTTTAGTTTCAAATAAATAAATTAAAAAATT
AATTTAAAATTAATTTANANAAAAA

Gap no gap
Contig length 275
Chromosome number (1..6, M) 6
Chromosome length 3595308
Start point 3240869
End point 3241135
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 2
Link to clone list U06991
List of clone(s)

est1=VSJ249F,1,276
est2=VSJ249Z,1,260
Translated Amino Acid sequence
LIKKDKKEKKEFENQLKIEFNKQDVFSIKRKEELGYKAKRLIDYGRYLFIKEKLNLPNTK
FWIYTNQSKENLFLVSNK*ikkli*n*fxxk


Translated Amino Acid sequence (All Frames)
Frame A:
n*lkkikkkkknlkin*rlnlinkmylv*kekrn*dikqrd*limvdiyllkkn*iyqiq
nfgfiqinqkkiyf*fqinklkn*fkinlxk


Frame B:
in*kr*krkkri*ksikd*i**trci*ykkkrgiri*skein*lw*ifiy*rkikftkyk
ildlyksikrkfifsfk*in*kinlklixxk


Frame C:
LIKKDKKEKKEFENQLKIEFNKQDVFSIKRKEELGYKAKRLIDYGRYLFIKEKLNLPNTK
FWIYTNQSKENLFLVSNK*ikkli*n*fxxk


own update 2004. 6.10
Homology vs CSM-cDNA
Query= Contig-U06991-1 (Contig-U06991-1Q)
/CSM_Contig/Contig-U06991-1Q.Seq.d
(275 letters)

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


Score E
Sequences producing significant alignments: (bits) Value

Contig-U06991-1 (Contig-U06991-1Q) /CSM_Contig/Conti... 317 3e-87
Contig-U13044-1 (Contig-U13044-1Q) /CSM_Contig/Conti... 38 0.005
Contig-U11429-1 (Contig-U11429-1Q) /CSM_Contig/Conti... 38 0.005
Contig-U09515-1 (Contig-U09515-1Q) /CSM_Contig/Conti... 36 0.019
Contig-U07866-1 (Contig-U07866-1Q) /CSM_Contig/Conti... 36 0.019
Contig-U04955-1 (Contig-U04955-1Q) /CSM_Contig/Conti... 36 0.019
Contig-U14147-1 (Contig-U14147-1Q) /CSM_Contig/Conti... 34 0.074
Contig-U12921-1 (Contig-U12921-1Q) /CSM_Contig/Conti... 34 0.074
Contig-U11828-1 (Contig-U11828-1Q) /CSM_Contig/Conti... 34 0.074
Contig-U10616-1 (Contig-U10616-1Q) /CSM_Contig/Conti... 34 0.074

>Contig-U06991-1 (Contig-U06991-1Q) /CSM_Contig/Contig-U06991-1Q.Seq.d
Length = 275

Score = 317 bits (160), Expect = 3e-87
Identities = 160/160 (100%)
Strand = Plus / Plus


Query: 33 gaatttgaaaatcaattaaagattgaatttaataaacaagatgtatttagtataaaaaga 92
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 33 gaatttgaaaatcaattaaagattgaatttaataaacaagatgtatttagtataaaaaga 92


Query: 93 aaagaggaattaggatataaagcaaagagattaattgattatggtagatatttatttatt 152
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 93 aaagaggaattaggatataaagcaaagagattaattgattatggtagatatttatttatt 152


Query: 153 aaagaaaaattaaatttaccaaatacaaaattttggattt 192
||||||||||||||||||||||||||||||||||||||||
Sbjct: 153 aaagaaaaattaaatttaccaaatacaaaattttggattt 192


>Contig-U13044-1 (Contig-U13044-1Q) /CSM_Contig/Contig-U13044-1Q.Seq.d
Length = 570

Score = 38.2 bits (19), Expect = 0.005
Identities = 19/19 (100%)
Strand = Plus / Plus


Query: 34 aatttgaaaatcaattaaa 52
|||||||||||||||||||
Sbjct: 500 aatttgaaaatcaattaaa 518


>Contig-U11429-1 (Contig-U11429-1Q) /CSM_Contig/Contig-U11429-1Q.Seq.d
Length = 3542

Score = 38.2 bits (19), Expect = 0.005
Identities = 19/19 (100%)
Strand = Plus / Plus


Query: 34 aatttgaaaatcaattaaa 52
|||||||||||||||||||
Sbjct: 3492 aatttgaaaatcaattaaa 3510


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: 8935
Number of Sequences: 6905
Number of extensions: 8935
Number of successful extensions: 4403
Number of sequences better than 10.0: 374
length of query: 275
length of database: 5,674,871
effective HSP length: 15
effective length of query: 260
effective length of database: 5,571,296
effective search space: 1448536960
effective search space used: 1448536960
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-U06991-1 (Contig-U06991-1Q) /CSM_Contig/Contig-U06991-1Q.Seq.d
(275 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

(AU269643) Dictyostelium discoideum vegetative cDNA clone:VS... 224 1e-54 1
(AU269642) Dictyostelium discoideum vegetative cDNA clone:VS... 224 1e-54 1
(ER531081) 1093015751296 Global-Ocean-Sampling_GS-35-01-01-1... 52 0.010 1
(AC151069) Bos taurus clone CH240-478N6, WORKING DRAFT SEQUE... 48 0.16 1
(AC165548) Bos taurus clone CH240-174E8, WORKING DRAFT SEQUE... 48 0.16 1
(AC122140) Mus musculus BAC clone RP24-270F2 from 17, comple... 34 0.35 2
(EF647600) Solanum lycopersicum chromosome 9 clone C09HBa007... 46 0.63 1
(AP007961) Lotus japonicus genomic DNA, chromosome 5, clone:... 46 0.63 1
(CP000109) Thiomicrospira crunogena XCL-2, complete genome. 46 0.63 1
(AC217519) Homo sapiens chromosome UNK clone ABC13-48642600E... 42 1.4 2
(CU302421) Mouse DNA sequence from clone CH29-115K17 on chro... 44 2.5 1
(AC160000) Mus musculus 6 BAC RP24-340J19 (Roswell Park Canc... 44 2.5 1
(AC138117) Mus musculus BAC clone RP24-146K16 from chromosom... 44 2.5 1
(AC116571) Mus musculus BAC clone RP23-97B18 from 6, complet... 44 2.5 1
(AP009017) Bombyx mori genomic DNA, chromosome 3, BAC clone:... 44 2.5 1
(AC152717) Bos taurus clone CH240-7B11, WORKING DRAFT SEQUEN... 44 2.5 1
(AC175187) Bos taurus clone CH240-27O18, WORKING DRAFT SEQUE... 44 2.5 1
(AC171857) Bos taurus clone CH240-308G23, WORKING DRAFT SEQU... 44 2.5 1
(DU957117) 227490 Tomato MboI BAC Library Solanum lycopersic... 44 2.5 1
(DE385848) Bombyx mori genomic DNA, BAC clone:7L4C. 44 2.5 1
(DE341020) Bombyx mori genomic DNA, BAC clone:BET_035_L02. 44 2.5 1
(FD933862) SmSal979 Orange wheat blossom midge salivary glan... 44 2.5 1
(CP000766) Rickettsia rickettsii str. Iowa, complete genome. 30 4.1 2
(CP000848) Rickettsia rickettsii str. 'Sheila Smith', comple... 30 4.1 2
(CU928685) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 42 4.6 2
(AL445563) Mycoplasma pulmonis (strain UAB CTIP) complete ge... 40 4.9 4
(AC079150) Homo sapiens BAC clone RP11-155F11 from 2, comple... 42 5.4 2
(AC169575) Bos taurus clone CH240-217F15, WORKING DRAFT SEQU... 36 5.5 2
(AE008662) Rickettsia conorii str. Malish 7, section 94 of 1... 30 5.5 2
(AZ524271) 230PbC11 Pb MBN #21 Plasmodium berghei genomic 3'... 30 6.4 2
(DB769383) Apis mellifera head cDNA, RIKEN full-length enric... 32 6.5 2
(EJ076244) 1095458124032 Global-Ocean-Sampling_GS-26-01-01-1... 34 8.7 2
(BX957256) Zebrafish DNA sequence from clone DKEY-23N7 in li... 42 9.8 1
(AY591713) Mus musculus clone IgKVk33-85 immunoglobulin kapp... 42 9.8 1
(AC153614) Mus musculus 6 BAC RP23-344N8 (Roswell Park Cance... 42 9.8 1
(AC127353) Mus musculus BAC clone RP23-81P21 from chromosome... 42 9.8 1
(AC124383) Mus musculus BAC clone RP24-411E14 from chromosom... 42 9.8 1
(AM457877) Vitis vinifera, whole genome shotgun sequence, co... 42 9.8 1
(AC102803) Homo sapiens chromosome 18, clone RP11-454J3, com... 42 9.8 1
(AC130008) Rattus norvegicus clone CH230-69H22, WORKING DRAF... 42 9.8 1
(AC127212) Rattus norvegicus clone CH230-32C10, *** SEQUENCI... 42 9.8 1
(CU468501) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 42 9.8 1
(AP001651) Homo sapiens genomic DNA, chromosome 18q22 clone:... 42 9.8 1
(AC216424) Solanum lycopersicum chromosome 7 clone C07HBa017... 42 9.8 1
(AC181244) Strongylocentrotus purpuratus clone R3-115K20, WO... 42 9.8 1
(AC178958) Strongylocentrotus purpuratus clone R3-3121K18, W... 42 9.8 1
(AC169471) Sorex araneus clone SA_Ba-215B23, WORKING DRAFT S... 42 9.8 1
(AC167109) Sorex araneus clone SA_Ba-538H24, WORKING DRAFT S... 42 9.8 1
(AC023972) Homo sapiens chromosome 18 clone RP11-778A8 map 1... 42 9.8 1
(FH590264) CHO_OF4908xm17r1.ab1 CHO_OF4 Nicotiana tabacum ge... 42 9.8 1
(FH129835) CHO_OF3500xc21r1.ab1 CHO_OF3 Nicotiana tabacum ge... 42 9.8 1
(FH097299) CHO_OF3025xc03f1.ab1 CHO_OF3 Nicotiana tabacum ge... 42 9.8 1
(ER614818) 1093016343078 Global-Ocean-Sampling_GS-36-01-01-2... 42 9.8 1
(EJ091370) 1095460186974 Global-Ocean-Sampling_GS-26-01-01-1... 42 9.8 1
(CU091912) Equus caballus GSS, BAC clone CH241-190M11, SP6 e... 42 9.8 1
(CL065686) CH216-105B20_Sp6.1 CH216 Xenopus (Silurana) tropi... 42 9.8 1
(CC223537) CH261-135O17_Sp6.1 CH261 Gallus gallus genomic cl... 42 9.8 1
(BX217297) Danio rerio genomic clone DKEY-258H6, genomic sur... 42 9.8 1
(ES512980) BIG_AF_20798 Brine Shrimp embryos, 10 hours after... 42 9.8 1
(ES508121) BIG_AF_15938 Brine Shrimp embryos, 10 hours after... 42 9.8 1
(DW204133) EST20397 Larval Stage 1 Aedes aegypti cDNA clone ... 42 9.8 1
(DT922103) BMSB13043 Hematopoietic stem cells Mus musculus c... 42 9.8 1
(AV112029) Mus musculus 10-day embryo cDNA, partial sequence... 42 9.8 1
(CJ103440) Mus musculus 14 days embryo whole body cDNA, RIKE... 42 9.8 1
(CJ098576) Mus musculus 14 days embryo whole body cDNA, RIKE... 42 9.8 1
(CB181153) AGENCOURT_11379769 NIH_MGC_164 Mus musculus cDNA ... 42 9.8 1
(BI988101) 3221-42 Mouse E14.5 retina lambda ZAP II Library ... 42 9.8 1
(EW349011) rplun0129_d14.y1 lun Sus scrofa cDNA 5', mRNA seq... 42 9.8 1
(CP001103) Alteromonas macleodii 'Deep ecotype', complete ge... 42 9.8 1

>(AU269643) Dictyostelium discoideum vegetative cDNA clone:VSJ249,
3' end single read.
Length = 260

Score = 224 bits (113), Expect = 1e-54
Identities = 113/113 (100%)
Strand = Plus / Plus


Query: 33 gaatttgaaaatcaattaaagattgaatttaataaacaagatgtatttagtataaaaaga 92
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 33 gaatttgaaaatcaattaaagattgaatttaataaacaagatgtatttagtataaaaaga 92


Query: 93 aaagaggaattaggatataaagcaaagagattaattgattatggtagatattt 145
|||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 93 aaagaggaattaggatataaagcaaagagattaattgattatggtagatattt 145

Lambda K H
1.37 0.711 1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 182,021,582
Number of extensions: 13926036
Number of successful extensions: 1134141
Number of sequences better than 10.0: 69
Length of query: 275
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 252
Effective length of database: 93,106,754,628
Effective search space: 23462902166256
Effective search space used: 23462902166256
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)

protein update 2009. 6.23
Homology vs Protein
Query= Contig-U06991-1 (Contig-U06991-1Q) /CSM_Contig/Contig-U06991-1Q.Seq.d
(275 letters)

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

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

Score E
Sequences producing significant alignments: (bits) Value

(Q54BD5) RecName: Full=tRNA guanosine-2'-O-methyltransferase TRM... 134 8e-31
EU637021_10(EU637021|pid:none) Philodina roseola hypothetical pr... 39 0.057
BC091859_1(BC091859|pid:none) Danio rerio coiled-coil domain con... 35 1.1
CP000361_1110(CP000361|pid:none) Arcobacter butzleri RM4018, com... 34 1.4
AJ890364_160(AJ890364|pid:none) Emiliania huxleyi virus 86 isola... 33 4.1
(Q9NUP7) RecName: Full=tRNA guanosine-2'-O-methyltransferase TRM... 32 7.0
AX405884_1(AX405884|pid:none) Sequence 299 from Patent WO0222660. 32 7.0
T15698(T15698) hypothetical protein C29F5.1 - Caenorhabditis ele... 32 9.2
(Q8BYH3) RecName: Full=tRNA guanosine-2'-O-methyltransferase TRM... 32 9.2

>(Q54BD5) RecName: Full=tRNA guanosine-2'-O-methyltransferase TRM13
homolog; EC=2.1.1.-; AltName: Full=tRNA [Gm4]
methyltransferase;
Length = 525

Score = 134 bits (338), Expect = 8e-31
Identities = 65/65 (100%), Positives = 65/65 (100%)
Frame = +3

Query: 42 NQLKIEFNKQDVFSIKRKEELGYKAKRLIDYGRYLFIKEKLNLPNTKFWIYTNQSKENLF 221
NQLKIEFNKQDVFSIKRKEELGYKAKRLIDYGRYLFIKEKLNLPNTKFWIYTNQSKENLF
Sbjct: 461 NQLKIEFNKQDVFSIKRKEELGYKAKRLIDYGRYLFIKEKLNLPNTKFWIYTNQSKENLF 520

Query: 222 LVSNK 236
LVSNK
Sbjct: 521 LVSNK 525

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: 199,076,338
Number of extensions: 2744614
Number of successful extensions: 8413
Number of sequences better than 10.0: 9
Number of HSP's gapped: 8407
Number of HSP's successfully gapped: 9
Length of query: 91
Length of database: 1,040,966,779
Length adjustment: 60
Effective length of query: 31
Effective length of database: 848,709,679
Effective search space: 26310000049
Effective search space used: 26310000049
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: 0.50 gvh: 0.18 alm: 0.60 top: 0.53 tms: 0.00 mit: 0.20 mip: 0.00
nuc: 0.12 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

64.0 %: nuclear
16.0 %: cytoplasmic
4.0 %: cytoskeletal
4.0 %: mitochondrial
4.0 %: vacuolar
4.0 %: plasma membrane
4.0 %: vesicles of secretory system

>> prediction for Contig-U06991-1 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