Search for expression mechanisms, i.e. Carotenoid Synthesis @
http://www.ncbi.nlm.nih.gov/protein
example gene to search for (and variants):
carotenoid synthesis gene clusters in DC416 & DC260: "crtEXYIBZ" is the classical organization
The carotenoid synthesis gene cluster isolated from Algo- riphagus sp. KK10202C has been deposited in GenBank under accession number DQ286432 (via http://getentry.ddbj.nig.ac.jp/)
- Searched http://getentry.ddbj.nig.ac.jp/ for accession number DQ286432 to get "gene name" = crtI (and others)
- Searched crtI under "gene name" and got many results, including the DC416 and DC260 above:
DQ090835 Enterobacteriaceae bacterium DC416 carotenoid synthesis gene
DQ090833 Enterobacteriaceae bacterium DC260 carotenoid synthesis gene
LOCUS DQ090833 6999 bp DNA linear BCT 06-DEC-2005
DEFINITION Enterobacteriaceae bacterium DC260 carotenoid synthesis gene
cluster, complete sequence.
gene 3685..5166
/gene="crtI"
CDS 3685..5166
/gene="crtI"
/function="desaturates phytoene to lycopene"
/codon_start=1
/transl_table=11
/product="phytoene desaturase"
/protein_id="AAZ73130.1"
/db_xref="GI:72536062"
/translation="MKRTYVIGAGFGGLALAIRLQAAGIPTTLLEQRDKPGGRAYVFE
DSGFTFDAGPTVITDPSAIEELFTLAGKSLSDYVELMPVTPFYRLCWEDGKQLDYDNN
QPLLEQQIATFNPQDVEGYRQFLAYSREVFREGYLKLGTVPFLQVRDMLRVAPQLGRL
QAWRSVYSMVAKFIQDDHLRQAFSFHSLLVGGNPFATSSIYTLIHALEREWGVWFPRG
GTGALVQGMARLFEDLGGELLLNAEVSQLETSGNRISGVQLEGGRRFDAAAVASNADV
VHTYDKLLRHHPLAMKRATSLKRKRMSNSLFVLYFGLNQPHEQLAHHTVCFGPRYREL
IDEIFNSSQLADDFSLYLHAPCSSDPSLAPPGCGSFYVLAPVPHLGTADIDWQQEGPR
LRDRIFAYLEQHYMPGLRQQLVTHRMFTPFDFRDTLHAHHGSAFSLEPILTQSAWFRP
HNRDADISNLYLVGAGTHPGAGVPGVIGSAKATARLMLEDRAE"
BASE COUNT 1457 a 2008 c 2015 g 1519 t
ORIGIN
1 gcgatggcaa tggaaaatgt tgcgtgagct tttcgtctaa ctgcggcatc agcggctgaa
61 taatcagcac ggcaggtttg gtattcgtca ttttattgtc cattagcggt atttatttac
121 caccagccta acggagttat ttatgttacg gcgttgctgt tacttatttc gctaataaga
181 tcacgcatag cattattaac aatatttacc tggtgcgcat gaatacgcac cctacaaagt
241 caagtccctc gctggcgaac tcaccttacg cagtctacgg ttaatcaaaa agcataaaaa
301 tttcaccaac catggatagc cattatgacc acccatgtcg acaccacagc acatcagaca
361 agcgaactcc ttcagctgca gcaaatttta caggcgcatc ttgaacattt actgcctgcc
421 ggacagcaaa gcgatcgcgt gcgtgccgcg atgcgtgccg gaacgctggc gcagggcaaa
481 cgtattcgtc ctttattact gctgctggca gcgcgcgata tgggttgcga gctgacgcaa
541 aatggcgttc tcgatctcgc ctgtgcagtg gaaatggtgc acgcggcatc gctgattctg
601 gatgacattc cctcgatgga taacgcgcag atgcgtcgtg gtcgccctac cgtgcatcgc
661 gaatttggtg aaaacgtggc gattctcgcc gccatcgcgc tgcttagccg cgcatttgaa
721 gtgattgcca ttgcacccgg tttgcctgcc atacataaat ctgaagcgat tgctgaactc
781 tccgctgccg tcggcctgca gggcttagtg caagggcaat tccaggatct gcacgacggc
841 acgcagagcc gcagcccgga agcgatcgcc atgaccaacg aactgaaaac cagcgtgctg
901 tttcgcgcca cgctgcaaat ggcggcgatt gccgctgacg cttcaccgca ggtgcggcaa
961 agacttagct tcttcgccca ggatttgggc caggcgtttc aactgctcga cgacctcgcc
1021 gacggttgca aacacaccgg taaagatgtg caccaggatc agggcaaatc cacgctggta
1081 cagatgctcg gtgctgacgg cgcggaacgt cgcctgcgcg atcacctgcg cagcgcagat
1141 gcacaccttg cctgcgcctg ccatcgcggc atcgccactc gccaatatat gcacgcgctg
1201 tttaatcaac agctagcgat attcaactga gcgcggctca gccggtgggc cactttgcgg
1261 tgatcgcgcc gccgctctac agccactttc acgcgttgca ggcgttagca caaacgctgc
1321 tggcgcgcgg ccatcgcatc acattcatcc agcaagccga tgcccgcact ttgcttagcg
1381 acgaacgcat cgattttgtt gccgtcggcc aacagacgca tcctgccggt tcgctggcgc
1441 ccgtgttgca tcggctggcc tcgccgggcg gcctgtcgct gtttcgcgtg atcgacgatc
1501 tcgcgtcctg caccgatatg ctgtgccgcg aactgcctgc ggtactgaaa gcattgaaca
1561 tcgatggcgt gatcgccgac gaaatggaag cggcgggcgg attggtcgct gaagcgctgc
1621 atctgccgtt tgtttcggtg gcctgcgcct tgccggtcaa tcgtgaagcc gggattccgc
1681 ttgcggtgat gcccttccgt tttgcacagg atgacaaagc gctgaaacgt tttcaggcca
1741 gcagcgatat ctatgatcgc atcatgcgtc gtcacggcga cgtgatcctc aaacacgcgc
1801 gggcgtttaa tttgacggag cggcgcggat tacatcagtg cctgtcgccg ctggcacaaa
1861 tcagccagat ggtgccggcc tttgattttc cacgtcagca actgcccgcc tgctatcacg
1921 ccgtggggcc actccgcgcc ccggtttctc ctgcgccgct ccatgcgccc tggccagcgc
1981 tgcgtcagcc ggtggtttat gcctcgctgg gtacgctgca aggccatcgc ttccggctgt
2041 ttctgcatct ggcgcaggcg tgccgccagc tgcggctatc gctggtgatc gcccattgtg
2101 ggggattaaa cgccgaacag acgcatcagc tggagctcgc tggcgcggcg tgggtgacgg
2161 atttcgtcga tcagcgcgca gccctacagc acgcgcagct gtttatcact catgccgggt
2221 taaacagcgc gctggaagca ctggaatgcg gtacgccgat gctggcgctg ccgattgctt
2281 ttgatcagcc cggcgtggcg gcgcgcattg agtggcatga cgttggtcgc cgcgcatcac
2341 gctttagccg tgttcatcaa ctggagcagc atctgcaaca gctgctgacc gacgatcgtt
2401 acgcgctacg gatgtcagcg attcaggcgc agctgcagcg cgcaggcggt tgccagcgtg
2461 ccgccgacat cgtcgagcag gcgctgtgcc agcagcaagt cgtgctggcg gaggcgacct
2521 gatgcgcacg caatacgatg tgattttggt cggtgctgga ctggcgaatg gcttgattgc
2581 gctgcgtctg cgtcaattgc agccacaact gaaatgcctg ttgctggaga gcgatgcgca
2641 tccggcaggc aatcatacct ggtcgtttca tcacagcgat ctcagcgccg aacaacttcg
2701 ctggctgcaa ccgctgatta ccgtgcgttg gtcaggttat caggtgcgtt ttcctgcgct
2761 gcgccgcaat ctggacgggg attattgttc catcgcatca ggcgattttg cccgccatct
2821 ttacgcggcg atgggtgacg atctgtggac aaacacagcc gtacaacagg taaaacccac
2881 gcaggtgacg ctggcggatg gccgtgaact tgctgcgcaa gtggtgattg atggtcgcgg
2941 cctgcagccg acgccacatc tgcagctggg ttatcaggtg tttcttggac aagagtggca
3001 gctggcgcag ccgcacggcc tgcagcagcc gatcctgatg gatgccaccg tcgatcagca
3061 agcgggttat cgttttgtct acacgctgcc gctcagcgcc gatcggctat tgattgaaga
3121 tacccattac gttaaccagc ccgcgctggc ggagaacacc gctcgtcagc acatcgccga
3181 ctatgccaat cagcaaggct ggacgctgag tacgctgctg cgtgaagagc acggcatatt
3241 accgattacc ctgagcggca acatcgatcg attctggcaa cagcagcgcg gccaagcgtg
3301 cagcggcctg cgcgccgggc tgtttcatgc caccaccggt tactccttgc cgtccgccgt
3361 ggcgctagcg gagttggtag cagcgctgtt gcccaccgat gccctcacgc tcagccaaca
3421 tatcgaacgc tttgcccgtc agcagtggcg cgaacagcga tttttccgtc tgctaaaccg
3481 catgctgttt ttggccggta agccgcagca gcgctggcgc gtgatgcaac gtttttaccg
3541 gctcgatgcc gggttaatta gccgctttta cgccgggcaa ctgcgcctgc gcgataaaac
3601 gcggattctg tgcggcaagc cgccggtgcc catcggtgaa gcgctgcgcg cgctgttgaa
3661 ttctgtcgaa ccagggaaga aaaaatgaaa cgcacttatg tgattggcgc aggctttggc
3721 ggcctggcgc tggcgattcg cctgcaagcg gcgggcatac caaccacctt actcgagcag
3781 cgcgacaaac cgggcggacg cgcctatgtg tttgaggaca gtggctttac cttcgatgcc
3841 ggacccacgg tgatcaccga tcccagcgcc atcgaagagt tgttcacgct ggcaggaaaa
3901 tcgctcagcg attacgtcga gctgatgccg gtaacgccct tctatcgcct gtgctgggaa
3961 gatggcaaac agcttgatta cgacaataat cagccgctgc tggagcagca gatcgccacg
4021 ttcaatccgc aagatgtaga aggctatcgt caatttcttg cctattcacg tgaagtattt
4081 agagagggtt atctgaaact cggcacggtg ccgtttctgc aggtgcgtga catgctgcgc
4141 gtcgcgccgc agttgggacg tctgcaagca tggcgcagcg tctacagcat ggtggcgaaa
4201 tttattcagg acgatcatct gcgtcaggcg ttttccttcc actcattgct ggtgggcggt
4261 aatccttttg caacgtcatc gatctatacc ttaattcatg cgctggagcg tgaatggggc
4321 gtgtggtttc cgcgcggcgg caccggcgcg ctggtgcagg gcatggcgcg actgttcgag
4381 gacttgggcg gcgagctgtt actgaatgcc gaagtgagcc agctggaaac cagcggcaat
4441 cgcattagcg gcgttcagtt agagggcgga cgacgcttcg atgccgccgc tgtggcctcc
4501 aatgccgacg tggtgcatac ctacgacaaa ctgcttcgcc accatccgct ggcaatgaaa
4561 cgtgcgacat cgctgaagcg taagcgcatg agcaactcgc tgtttgtact ctattttggc
4621 ctgaatcagc cgcatgaaca gctcgcgcac cacaccgtct gttttggccc gcgttatcgt
4681 gagttgatcg atgagatttt caacagcagc cagctggcag acgatttttc actttacctg
4741 cacgcgccct gcagcagcga tccgtcgctg gcaccgcccg gctgcggcag cttttatgtg
4801 ttagcgccgg tgccgcatct cggcaccgct gacatcgact ggcaacagga aggaccgcgc
4861 ttgcgcgatc gaatttttgc ttatctggag cagcactaca tgccgggatt acgtcagcaa
4921 ttagtgacac acagaatgtt tacgccgttt gattttcgcg acacgctgca tgcccatcac
4981 ggctcggcgt tttcgctgga gccgattttg acgcaaagcg cctggttccg cccgcataac
5041 cgcgatgccg atatcagcaa tctctatctg gtgggtgccg gtacgcatcc aggcgcgggc
5101 gtgcccggcg tgatcggttc ggccaaggcc accgccaggc tgatgctgga ggatcgcgcc
5161 gaatgaatcg acagccttta cttgagcaag taacgcaaac catggcggtg ggctcgaaga
5221 gtttcgccac cgccgccaag ctgtttgatg caccgacgcg ccgcagcacg ctgatgctgt
5281 atgcgtggtg tcgtcactgc gatgatgtga ttgatgggca aacgctgggc gaaggcggca
5341 cgcagcatgc cgtcgaagac gcgcaggcac gtatgcagca tctgcaaatt gaaacccgcc
5401 gcgcctacag cggcgcgcac atggatgaac cggcgtttag ggcgtttcag gaagtggcga
5461 tcattcacca gctgccgcaa caactggcgt ttgatcatct ggaaggcttc gctatggatg
5521 cacgcaacga acattacgcg agcttcgatg acacgctgcg ttactgctat cacgtcgcgg
5581 gcgtggtcgg tttgatgatg gcgcgcgtaa tgggcgtgcg cgacgaagcg gtgctcgatc
5641 acgcctgcga tttaggactg gcgttccagc tcactaacat tgcgcgcgac attgtagaag
5701 atgccgaaaa tggtcgctgc tatctgccgc aatcctggct cgatcaggcg ggattacgcg
5761 ccgatacgct gactgcaccg caacatcgtg cagcgctcgc ctcactggca gcgcgtttag
5821 tggcggaggc ggaaccctat tatcactcgg cgcgatccgg tttaccgggt ttaccgctgc
5881 gctcggcgtg ggccatcgct acggctcgcg gcgtttatcg cgaaattggc gtcaaagttc
5941 agcacgccgg tgtgcacgcc tgggattcac ggcagcgcac cagtaaaggt gaaaaactgg
6001 cgctgctggt gaaaggggca ggtttggcga tcacttcgcg tgtgtctcgt cctgaaccgc
6061 gtccggctgg tctgtggcag cgtcctcgtt gattttacgt ccgtgacgct ggcgcagcgt
6121 ggcttgcagc ttattcagcg gtggcgcgta gaggaaacca aacgacacgc agccttcacg
6181 cccgcgcacc gcatgatgca tgcggtgcgc catgtataag cgcttaagat agcctttgcg
6241 cgggatatag cggaacggcc agcgttgatg caccaggcca tcgtgcacca tgaagtagag
6301 cgcgccgtac gtcgtcattc cggcaccaat ccactgcagc ggccacatgc cttgcacacc
6361 gacataaatc agcacaatcg ccagtaccgc aaacaccacc gcataaagat cgttgagctc
6421 aaacttaccg ctgtgcggtt catggtgcga cagatgccag ccccatcccc aaccgtgcat
6481 gatgtattta tgcgacagcg ccgctacgat ttccatcacc accacggttg ccaacaagat
6541 aagcacgttc cataaccaga gcattgttcg tccatttgtg gaaaagggaa gtactaaagg
6601 tggacgcgga tgagtgatgg cgcaaggttt accatgttta gaaattttaa aagtccataa
6661 cacgttatga acgctgcatt gcagaaagcg cagatttcac acatactcac cacacttatc
6721 aatacacgtg ttaactacat gggggattta tgccttctac agccgtaaga caaaaaaaaa
6781 ctgtcagtgt gacacttgaa cctgctctac tcgagcaagc cagagaggca gggctcaatt
6841 tatccgccat cctatccaaa gctttgcaac atgaaattcg cacgactgca gcagaaagat
6901 ggaagcgtga aaacagtgaa ggtttgcagg aactcaatcg cataaccgaa gagcacggtt
6961 tattgtcgga tgaatacagg acgttttaga catgcaata
====
LOCUS DQ090835 8675 bp DNA linear BCT 06-DEC-2005
DEFINITION Enterobacteriaceae bacterium DC416 carotenoid synthesis gene
cluster, complete sequence.
gene 4572..6053
/gene="crtI"
CDS 4572..6053
/gene="crtI"
/function="desaturates phytoene to lycopene"
/codon_start=1
/transl_table=11
/product="phytoene desaturase"
/protein_id="AAZ73142.1"
/db_xref="GI:72536076"
/translation="MKRTYVIGAGFGGLALAIRLQAAGVPVTLLEQRDKPGGRAYVYQ
DQGFTFDAGPTVITDPSAIEALFTLAGKQLSDYVDLMPVTPFYRLCWEDGRQLDYDNN
QAQLEQQIATFNPQDVAGYRQFLAYSQDVFREGYLKLGTVPFLHFRDMLRAGPQLGRL
QAWRSVYSMVAKFIHDDHLRQAFSFHSLLVGGNPFATSSIYTLIHALEREWGVWFPRG
GTGALVDGMARLFRDLGGELLLNAEVSQLETEGNRISGVQLKDGRRFAAAAVASNADV
VHTYDRLLSQHPAARKRAATLKRKRMSNSLFVLYFGLNHAHPQLAHHTVCFGPRYREL
IDEIFNSSQLAEDFSLYLHAPCSSDPSLAPAGCGSFYVLAPVPHLGTAAIDWQQEGPR
LRDRIFAYLEEHYMPGLRQQLVTHRMFTPFDFRDTLHAHQGSAFSLEPILTQSAWFRP
HNRDADITNLYLVGAGTHPGAGVPGVIGSAKATAQLMVEDLTG"
BASE COUNT 1592 a 2652 c 2629 g 1802 t
ORIGIN
1 aacccgggct aatgggggtg acaagcccca ggccggccaa acaatcaggt ggaagggccc
61 ggtgccgagg caatttgctc gatttgcaac gcaccagccg tggcaaacag cgcacggtag
121 cgctcacgaa actgatcggc gatggcacta tgagtcgacg gcggagcgcc cggatcggcc
181 aggtgatcga gatccagcgc ctgtaacagt aaccgcccgc cgccgtccgg ccgcacgttc
241 agctgcggag aaatcaggtt ggtgccaagc gataacggct gtggtgcggt gcgcgccaga
301 aagctgcagg ccaccgcatc aggcttgctg gtgtcaatca gcgccagttc cagaccaagc
361 gtatgcagca gctgattggc ccagcgtccg gtcgccagca ccagacgatc accctgccac
421 cgctcaccct gctccagctg caccgtcacg ccttccgcat tttcactaat gtgctgaatc
481 gcctgatgct gatgcagtac cgcgccgtgc gcctgcgcct ctgaccacag ccgtgccaga
541 tacagcgctg gatagagcac cgattccgtt ggaaaatgcc agatgctgcc gtgtaccgca
601 gacgcgcgca gttcaggaat ttcctgctgc agctcggcca gcgtcctttg ccgtgccgca
661 tagccagcgg cctgcaaggc ggtggcacgc tgctgcagtt gctgttcggc ttcacccgtg
721 ccggcccact cccaggtgcc acaaggttcc agccagcgca cgccattggt ctgcgtcagc
781 tgcagccgga tatgctcctc catcgccagc gcattgaggc ggtgatagct ggcaggctgt
841 tttccgttgg agtttaccca ggcaaatgtg gtgctgctgg tgcccgcgcc catgtgttgc
901 cggtcaaaga gggtcacctg cgccccctgc cgcgccagcg cccacgccac ggcgaggccg
961 atcacacccg caccgattac cgccactttt tgcgtcgtca tagctgtctc ctctgctcgc
1021 ccaacatcat aacagtcacc gcagcgaaaa ctggcctgag ggtcatagga attacttctc
1081 agattattca ataaataaaa aaagcgtgac ggtgcgttaa agtcgcttcg ctcgctggcg
1141 cactcccctt accgggtcta cggttaattg aaaaagcaca agaatttaac taaccatgga
1201 aagccgctat gaccgcccat gtcgatacca cagcaagcca ggaaagcgat ctccttcagt
1261 tgcatcacgc attgcaggcc catcttgaac atttattgcc tgccgggcag caggccgatc
1321 gcgttcgggc cgccatgcgt gccggcacgc tggcaccggg caaacgtatt cgtccgctct
1381 tgctgctgct ggcagcacgc gatatgggct gtgacgtggc gcagcagggc atccttgatc
1441 ttgcctgtgc ggtcgaaatg gtgcacgctg cctcactgat cctcgacgac attccatcaa
1501 tggataacgc ccggatgcga cgtgggcgcc cggcaatcca ctgtgaatat ggggaaaacg
1561 tggcgatcct ggcagcggtc gcgctactca gccgcgcctt tgaggtgatt gccctcgcgc
1621 cgggtctgcc agcaacgcac aaagccgaag ccattgccga gctctcctct gccgtgggcc
1681 tgcagggact ggttcagggt cagttccagg atctgcatga cggcgcacac agccgcagtc
1741 cggaagccat caccctgacc aatgaactga aaaccagcgt cctgtttcgc gccacgctgc
1801 agatggcggc gattgcggcc gatgcgtcag tgcaggtacg tcagcgttta agctattttg
1861 cgcaggattt aggtcaggct ttccagttac tggacgacct ggcggatggc tctaagcaca
1921 ccggcaagga ctgtcatcag gatcagggca aatccacgct ggtgcagatg ctgggcccgg
1981 aaggggctga gcgtcgtctg cgcgaccatc taagcagcgc cgatgcacac cttgcctgcg
2041 cctgccatcg cggtgtcgcc acccgtcaat atatgcacgc cctgtttaat caacagctgg
2101 cgatgttcaa ctgaagccgg tcatacctat ggggcatttt gccgttattg cgccaccgct
2161 ctacagccac tttcacgcat tgcaggcgct ggcgcaaacg ctgctggcgc gcggacatcg
2221 catcaccttt atccagcaaa gtgatgcacg caccttgctg agcgacgagc gcattgcctt
2281 tgtggccgtc ggcgagcgca cgcatcctgc cggatcgctc tccagcgaac tcaggcggct
2341 ggccgcaccg ggcgggctgt cgctgtttcg cgtgattcac gatctggcca gcaccaccga
2401 tatgctatgc cgcgaactgc ccgcggtgct gcaacggctg caggtcgatg gcgtgattgc
2461 cgatcaaatg gaagcggctg gtggtctggt ggcagaggcg ttacagctgc cgttcgtgtc
2521 ggtggcctgc gcgctgccgg tcaatcgcga agcggccatt ccgctggtgg tgatgccctt
2581 tcgctttgct caggatgaga aagcgctgca gcgctatcag gccagcagtg acatctacga
2641 ccgcatcatg cgtcgtcatg gcgctgtcat cgctcgtcat gcgcgcgcct tcggcctgcc
2701 cgaacgccat ggcttacatc agtgtctgtc gccgctggcg caaatcagtc agctggtgcc
2761 cgcttttgat tttccacgcc agcaactgcc agcctgctat cacagcgtgg gtccgctgcg
2821 gactccagtt gctagcggcg cgctcgccgc accctggcca gcgctgcgcc agccggtggt
2881 gtatgcctcg ctgggcacgc tacaggggca tcgctttcgc ctgtttctgc atctggctca
2941 ggcctgccgc aatcagcagc tgtcgctggt ggtggcacac tgtggcgggt tgaccgccag
3001 ccaggcacat cagctcagac tggccggtgc tgcgtgggtg accgattttg tggatcagcg
3061 ggcggcgctg cagcatgcgc aactgtttat cactcacgcc ggtctgaaca gtgcgctgga
3121 agcactggag tgtggcacgc cgatgctggc gctgccgatc gccttcgatc agcccggcgt
3181 ggcggcacgt attgagtggc acggcgtcgg ccggcgcgcc tcacgtttca gccgggtcgc
3241 gcagctggag caccacctgc aacagttgct gagtgacgat cgctatcgtc tgcgcatgtc
3301 agccattcag gcgcagctgc agcgggccgg tggctgtacg cgcgcggctg atattgtcga
3361 gcaggcgctg tgtcagcagc aaatcgtgct ggcggaggcc acctgatgcg cgcaccttat
3421 gatgtcattc tggtcggtgc cggcctggct aacgggctga ttgcgctgcg tttacgccag
3481 ctgcagcccg cacttaaggt tttgctactg gagagtcagg cgcagccggc cggcaatcat
3541 acctggtcgt tccatcgcga agacgtcagc gaagcgcagt ttcgctggct cgagccgctg
3601 ctttcggcgc gctggcccgg ttatcaggta cgcttcccca ccctgcgtcg ccagctggat
3661 ggtgaatatt gctcgattgc ctcggaggat tttgcccggc acttacagca ggtgctcggt
3721 gccgcgctac gcaccgcagc gccggtcagc gaggtctcac ccaccggggt cagactggcg
3781 gatggcggga tgttacaggc gcaggcggtg attgacggac gcgggctgca gccgacaccg
3841 catctgcagc tcggctatca ggcatttgtc ggtcaggagt ggcaactggc cgcgccgcat
3901 ggcctgcagc agccaatatt gatggacgcc agcgtcgatc agcagcaggg ttatcgcttt
3961 gtttacaccc tgccgctcag tgccagccgt ttactgattg aagataccca ctacatcaac
4021 catgccacgc tggatgccgc acaggcgcgc cgtcacatta cggattatgc ccaccagcgc
4081 ggctggaatt tgcgccagct gctgcgcgag gagcacggct cgctgccgat cacgctcagc
4141 ggcgatatcg atcagttctg gcaacagcag cacgggcaac cgtgcagcgg gctgcgcgcc
4201 ggactgtttc acgccaccac cggttactcg ctgcccgccg cggtggcgct ggcggagaag
4261 attgccagca cgctgcccgc cgacgctcac acgctgagcc actgcatcga atcctttgcc
4321 cgtcagcact ggcgcgagca gcgctttttc cgtctgttaa atcgcatgct gtttcttgcc
4381 ggacggcctg aacagcgctg gcgcgtaatg cagcgttttt accggcttga cgccggattg
4441 attagccgct tttacgccgg gcaactgcgc ctcagcgata aagcacgcat tctgtgcggc
4501 aaaccgccgg tccctctcgg cgaagcgctg cgcgcattga tgatgacctc tccgttacca
4561 gggaagaaat aatgaaacgc acctatgtga ttggcgcagg cttcggtggc ctggcgctgg
4621 cgattcgtct gcaagcggcc ggcgtgccgg tcacgctgct ggaacagcgc gataagcctg
4681 gcgggcgcgc ctatgtgtat caggatcagg gttttacctt tgatgccggt ccgacggtga
4741 ttaccgatcc cagcgctatc gaggcgctgt ttacgctggc aggcaagcaa ctcagtgatt
4801 atgtcgacct gatgccggtg acgccatttt atcgcctgtg ctgggaagac ggcaggcagc
4861 tggactacga caacaatcag gcgcagctgg agcagcagat tgccactttt aatccccagg
4921 atgtcgccgg ttaccgccag tttctggcct attcacagga tgtgtttcgt gagggctatc
4981 tgaaactggg caccgtacct tttctgcatt tccgcgacat gctgcgtgcc gggccacagc
5041 tgggtcggct gcaggcctgg cgcagtgtct acagcatggt ggcgaaattt attcatgacg
5101 atcatctgcg ccaggctttt tcctttcact cgttgctggt cggcggtaat ccttttgcaa
5161 cgtcttcgat ctatacctta attcacgcac tggagcgcga atggggcgtg tggtttccgc
5221 gcggcggtac cggtgcgctg gttgatggca tggcgcggct gtttcgcgat ttgggcggtg
5281 aactgctgct caacgccgaa gtcagccagc tggagaccga gggtaaccgc atcagcggtg
5341 tccagctgaa ggatgggcgc cgttttgccg ccgccgccgt tgcgtcaaat gctgacgtgg
5401 tgcataccta cgatcgcctg ttaagccagc atcctgcggc gcgtaaacgc gcggcaacgc
5461 tgaagcgcaa gcggatgagc aactcgctgt ttgtactcta ttttggtctt aatcatgccc
5521 acccgcagct ggcgcaccac acggtgtgct ttggtccgcg ctatcgtgaa ttgatcgatg
5581 agatcttcaa tagcagccag ctggcggaag atttctcgct gtatctgcat gcgccctgct
5641 ccagcgatcc gtcgctggca ccggcgggct gcggcagttt ttacgtgctg gcgccggtgc
5701 cgcatctcgg taccgccgca attgactggc aacaggaagg gccgcgcttg cgcgatcgca
5761 tttttgctta tctggaggag cactatatgc cgggtctgcg acagcagtta gtgacacacc
5821 gtatgtttac gccgtttgat tttcgcgaca cgctgcacgc gcatcagggc tcagcgtttt
5881 cgctcgaacc cattttgacg caaagcgcct ggttccggcc gcataaccgc gatgccgaca
5941 ttactaacct ttatctggtg ggggctggca cgcatcccgg tgccggtgtg ccaggcgtga
6001 tcggctccgc gaaagcgacc gcccagctga tggtggagga tctgaccgga tgaaccaacc
6061 gccgctgatt gagcaggtca cgcaaaccat ggcgcagggc tccaaaagtt tcgccagcgc
6121 tacccggcta tttgatcctt caacgcgccg cagtacgctg atgctgtacg cctggtgtcg
6181 tcactgtgac gatgtgatag atggtcagac gctgggcgaa ggcggcacgc agcacgcggt
6241 ggcggatgca caggcgcgga tgcgccacct gcaaatcgaa acccgccgcg cctacagcgg
6301 tgcccacatg gatgaaccag cgtttcgtgc ctttcaggaa gtggcgctga cgcatcagct
6361 tccccagcag ctggcttttg atcatctgga agggtttgcg atggatgcgc gtgaagaacg
6421 ttatgcgtgt ttcggggaca cgctgcgtta ctgctatcac gtggccggcg tggtggggtt
6481 aatgatggcg cgcgtgatgg gcgtacgtga tgagcgcgta ctcgatcacg cctgtgattt
6541 gggtctggcg tttcagctta ccaatatcgc acgggatatc gttgaggacg cggagaatgg
6601 ccgttgctat ctgccacaaa gctggctgga tgaggccgga ctgagcgccg cccagcttgc
6661 cgatccgcaa catcgcgcag cgctggcccc gctggcagcg cgtctggtgc gcgaggccga
6721 gccgtactat cagtcagcgc gcagcgggct gccaggattg ccgctccgtt cggcgtgggc
6781 gatcgccacc gcgcgcggcg tttaccggga aattggcgta aaagtgcagc atgccggtgc
6841 ccgggcatgg gatacgcgcc agcgcaccag taaaggcgaa aagctggcgc tgctggtgaa
6901 aggtgccggc gtcgcgctta cttcgcgcct tgctcatccc gaggcgcgtc ctgccggtct
6961 gtggcagcgt ccgcgttgac acgacgccca tggcgctggc gcagcgtcgc ctgcagcttg
7021 tgcaacggtg gggcgtaaag aaagccaaag gaaacgcagc cttcccgtcc ccgcaccgca
7081 tgatgcatgc ggtgcgccat atacaaccgc ttcagatagc ctttgcgtgg aatatagcga
7141 aacggccagc gttgatggac caggccgtca tgcaccataa aatagagagc gccataggtc
7201 gtcatgccag cgccaatcca ctgcagcggc cagacgccgt tgacacccag ccaaatcagg
7261 ccaatcgaca acagcgcaaa caccacggca tacaggtcgt tgagctcaaa tttgctctca
7321 tgtggttcat gatgcgacaa atgccagccc catccccagc catgcataat gtatttatgc
7381 gacagcgccg cgacgatctc catcagtatc acggtagcca gcaggataag cgcattccat
7441 aaccagagca tcattggtcc atttgcgaag agtgagagta taaaggtgga cgtggatagc
7501 gaaaggcgca agtccccggc aaaaaaacgc accggcagcg taaataccag ccaggtcacg
7561 gacgcgtgct atcaccttca gacaagcaaa gcggcaagag ggttatcctg catggcggcc
7621 gggtgggtct gctttacatc gatttaacag ctggttagta tagccagcgg ttcagcggtc
7681 caggctgctg cgtacgcgtt aacgtcaatc aacgcaccat atgcagagac tttctgcctc
7741 atttctatgg tgcgcaacat gtcccatacc gctttatctg ctgattctgc cctgcgtcgt
7801 tccggctttt tcctgctgct actgttactc accgccgcca acttacgcac gcccatcacc
7861 gctaccgggc cggtactgga aaatattcgc ctgacatttg gcctgagcgc cagcgctgcc
7921 ggcgtgatta actttttacc gctgctgatg tttgccacgc tggctccgcc agccgcctgg
7981 tttggcaatc gctttggcct ggagcgcagt ctgtgggggg ctttactcct gatcgtcctg
8041 ggttcactgc tgcgaatcag cggcagcgaa acggcactgt ggctgggtac gctgattctc
8101 agcagcggga tcgcggcggc caacgtcctg ctgccgccgc tgattaagcg ggattacacc
8161 gcgcacaccg cgcgttatat cgggctgtat gccatgacca tgggcatcac cgccagcatc
8221 gcttccggcg tggccgtgcc gctggccgaa ctcagcagcg ccggctggcg tctgtcgctg
8281 gcggtctggc tgattccggc tctggtcgcg ctactggcgt ggctgccgca gctgaaaaat
8341 cccgcgacgc gtgagcagcg cgcgacagag gtcaccgtaa cgcgttcgcc gtgtcgttcc
8401 gcgatcggct ggcaggtgtc gctgttcatg gccagccagt cgctgctgtt ttataccctg
8461 attggctggt ttaccccgtt cgcacaggat aatggcatca gtcagcttca ggcaggcagc
8521 atgttgtttg tctatcaaat tgtggcgatc gcctccaatc tggcctgtat gcgggcgctg
8581 aagcagctgc gcgatcagcg tctgatcggg ctactggcct cgctgtcgat cttcatcgcg
8641 gtgaccggcc tgctgctggc acccgcatgg tctct
//
Theor Appl Genet. 2010 Apr 22. [Epub ahead of print]
Carotenoid biosynthesis genes provide evidence of geographical subdivision and extensive linkage disequilibrium in the carrot.
Clotault J, Geoffriau E, Lionneton E, Briard M, Peltier D.
Agrocampus Ouest, INHP, IFR 149 Quasav, UMR 1259 GenHort, 2 Rue Le Nτtre, 49045, Angers, France.
Abstract
According to the history of the cultivated carrot, root colour can be considered as a structural factor of carrot germplasm. Therefore, molecular variations of carotenoid biosynthesis genes, these being involved in colour traits, represent a good putative source of polymorphism related to diversity structure. Seven candidate genes involved in the carotenoid biosynthesis pathway have been analysed from a sample of 48 individual plants, each one from a different cultivar of
carrot (Daucus carota L. ssp. sativus).
The cultivars were chosen to represent a large diversity and a wide range of root colour. A high single nucleotide polymorphism (SNP) frequency of 1 SNP per 22 bp (mean pi (sil) = 0.020) was found on average within these genes. The analysis of genetic structure from carotenoid biosynthesis gene sequences and 17 putatively neutral microsatellites showed moderate genetic differentiation between cultivars originating from the West and the East (F (ST) = 0.072), this being consistent with breeding history, but not previously evidenced by molecular tools. Surprisingly, carotenoid biosynthesis genes did not exhibit decay of LD (mean r ( 2 ) = 0.635) within the 700-1,000 bp analysed, even though a fast decay level of LD is expected in outcrossing species. The high level of intralocus LD found for carotenoid biosynthesis genes implies that candidate-gene association mapping for carrot root colour should be useful to validate gene function, but may be unable to identify precisely the causative variations involved in trait determinism. Finally this study affords the first molecular evidence of a genetic structure in cultivated carrot germplasm related to phylogeography.
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Search results for Daucus carota
http://www.ncbi.nlm.nih.gov/sites/gquery?term=Daucus+carota
DEFINITION Daucus carota DcECP63 mRNA for ECP63 protein, complete cds.
ACCESSION AB495352