AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene77419


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene77419.t1 MTR_5g040340 92.144 471 24 2 1 464 1 465 0.0 874
MS.gene77419.t1 MTR_8g055860 46.245 506 171 25 17 464 29 491 1.22e-98 305
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene77419.t1 AT2G02950 36.341 410 171 20 55 439 76 420 3.26e-47 169
MS.gene77419.t1 AT1G14280 33.570 423 173 23 52 435 63 416 6.46e-42 154

Find 69 sgRNAs with CRISPR-Local

Find 77 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAGAAGAAGATGGAGAAAT+TGG 0.158218 5.1:-30455659 MS.gene77419:CDS
GAATTAAACGATGTTCTTAT+TGG 0.158853 5.1:+30454720 None:intergenic
TCACTTGGTGCATAGAAATT+TGG 0.171246 5.1:+30454840 None:intergenic
GCCTCAGATGACAAGGTTTA+AGG 0.196735 5.1:-30454550 MS.gene77419:CDS
TTTCAAGTACTTGAGTTTAT+TGG 0.250362 5.1:+30455568 None:intergenic
TGCACTTTCTATTCTCTTGT+TGG 0.253513 5.1:+30455543 None:intergenic
TTGCATCTTTCATCTAATAT+TGG 0.263596 5.1:+30455104 None:intergenic
CTTGAGTTTATTGGCATCTA+AGG 0.270047 5.1:+30455577 None:intergenic
TTCCTTTCTGTTGCTGATAA+AGG 0.278838 5.1:+30455703 None:intergenic
TCCTTTCTGTTGCTGATAAA+GGG 0.296457 5.1:+30455704 None:intergenic
AAGAGTCTTCTTGCTACTAT+TGG 0.302021 5.1:-30455398 MS.gene77419:CDS
CAGAAAGCTGTTGGTGTTGC+TGG 0.351018 5.1:-30454624 MS.gene77419:CDS
AGGTTTAAGGTGGAAAGTTT+TGG 0.354957 5.1:-30454537 MS.gene77419:CDS
AGGAAAACATTGGAAGTGTT+TGG 0.359214 5.1:-30455131 MS.gene77419:CDS
AGAAAGTGCAAAGTTCAATA+TGG 0.368278 5.1:-30455530 MS.gene77419:CDS
ACAACATCACATGTTGCTTC+TGG 0.368292 5.1:-30454873 MS.gene77419:CDS
CATTCAATGCTTGCTTCACT+TGG 0.371898 5.1:+30454825 None:intergenic
AGAAATGAACAACATGGTTA+TGG 0.378020 5.1:-30454510 MS.gene77419:CDS
CTTGATTCTGAGCCAACACT+TGG 0.447581 5.1:+30455503 None:intergenic
CGGCGTCATGGAAAATTGTT+GGG 0.449202 5.1:-30454657 MS.gene77419:CDS
CTTCTTCTTTCTTTACTCCA+AGG 0.457657 5.1:+30455672 None:intergenic
GCGGCGTCATGGAAAATTGT+TGG 0.460904 5.1:-30454658 MS.gene77419:CDS
AGTCAATAAGCTTTGATATG+AGG 0.461128 5.1:-30455082 MS.gene77419:CDS
TTCAACAAAAGTGCAGTTCA+AGG 0.462298 5.1:-30455311 MS.gene77419:CDS
AAGGTTCAGTAGTAACTATA+AGG 0.462753 5.1:-30454746 MS.gene77419:CDS
TTTGAGATTGAAAGCTTCAC+TGG 0.464240 5.1:-30454927 MS.gene77419:CDS
GAAGACTCTTTCTATGAACT+TGG 0.474532 5.1:+30455411 None:intergenic
TTTGTAGCAGCTTCCCAAGA+TGG 0.486138 5.1:+30455050 None:intergenic
GCATCTAAGGTAGCAAGTCT+TGG 0.492321 5.1:+30455590 None:intergenic
CTTGAACAACAAGGAAGTAA+AGG 0.492569 5.1:-30455750 MS.gene77419:CDS
TTCTGTTGCTGATAAAGGGG+TGG 0.493694 5.1:+30455708 None:intergenic
TTCCGCTGCAGCACGAGTCT+CGG 0.494266 5.1:+30455217 None:intergenic
GTTTCAGATCATGAAGATCA+AGG 0.495758 5.1:-30454765 MS.gene77419:CDS
GGTGAATTTGATCTCTTAAG+AGG 0.500716 5.1:+30454480 None:intergenic
CAAGTGAAGCAAGCATTGAA+TGG 0.508457 5.1:-30454824 MS.gene77419:CDS
GGGTGGATTGAATCAGCAAA+AGG 0.523505 5.1:+30455725 None:intergenic
ACATCGTTTAATTCATCGAA+TGG 0.528036 5.1:-30454711 MS.gene77419:CDS
TTCTTTACTCCAAGGTGAAG+AGG 0.529025 5.1:+30455680 None:intergenic
CCTTTCTGTTGCTGATAAAG+GGG 0.530407 5.1:+30455705 None:intergenic
GAGATGCCGAGGCGGCGTCA+TGG 0.530887 5.1:-30454669 MS.gene77419:CDS
GGAGTAAAGAAAGAAGAAGA+TGG 0.538350 5.1:-30455668 MS.gene77419:CDS
ACCTTAAACCTTGTCATCTG+AGG 0.538940 5.1:+30454549 None:intergenic
AACCGAGACTCGTGCTGCAG+CGG 0.552008 5.1:-30455219 MS.gene77419:CDS
TTCAACAAGTAGAGAATCCA+AGG 0.552480 5.1:-30455151 MS.gene77419:CDS
CCCCTTTATCAGCAACAGAA+AGG 0.557673 5.1:-30455705 MS.gene77419:CDS
AGAGAATCCAAGGAAAACAT+TGG 0.562983 5.1:-30455141 MS.gene77419:CDS
GTTATTCTGAGAGGTGAAAG+TGG 0.569101 5.1:+30455808 None:intergenic
TGTAATAGTCAGAAAGCTGT+TGG 0.572244 5.1:-30454633 MS.gene77419:CDS
GTTATTGTTGTTATTCTGAG+AGG 0.577463 5.1:+30455799 None:intergenic
CAGGTTGTAAAAGTGCACTT+TGG 0.581251 5.1:+30455471 None:intergenic
CAATATGGAACTCCAAGTGT+TGG 0.581850 5.1:-30455515 MS.gene77419:CDS
GAATTTGATCTCTTAAGAGG+TGG 0.585210 5.1:+30454483 None:intergenic
CTCTTCATACTTGAACAACA+AGG 0.600465 5.1:-30455759 MS.gene77419:CDS
AGAAAGGAACCTCTTCACCT+TGG 0.604048 5.1:-30455689 MS.gene77419:CDS
AAATGTTGCCTCAGATGACA+AGG 0.605171 5.1:-30454557 MS.gene77419:CDS
TCAGATGACAAGGTTTAAGG+TGG 0.630245 5.1:-30454547 MS.gene77419:CDS
AAATCAACAAAGAGATGCCG+AGG 0.636605 5.1:-30454680 MS.gene77419:CDS
GGTGCAAGAAATGAACAACA+TGG 0.655080 5.1:-30454516 MS.gene77419:CDS
TCAACAAAGAGATGCCGAGG+CGG 0.670252 5.1:-30454677 MS.gene77419:CDS
AAGAGATCAAATTCACCACA+TGG 0.683671 5.1:-30454474 MS.gene77419:CDS
AACAACAATAACCTCCGTGG+TGG 0.687252 5.1:-30455788 MS.gene77419:CDS
GTTGATGTAAGTGATCATGC+AGG 0.688347 5.1:-30455344 MS.gene77419:CDS
ACAACAACAAATGAGAAACA+TGG 0.697642 5.1:-30454591 MS.gene77419:CDS
AGCAAGCATTGAATGGAGTG+TGG 0.726329 5.1:-30454817 MS.gene77419:CDS
ATGAAGAGAAAGAACCACCA+CGG 0.734637 5.1:+30455774 None:intergenic
TACAAAAGTTGTGCACCATG+TGG 0.736641 5.1:+30454459 None:intergenic
AATAACAACAATAACCTCCG+TGG 0.749739 5.1:-30455791 MS.gene77419:CDS
AGTGGTTGCTGAGATAACCA+TGG 0.758373 5.1:+30455826 None:intergenic
AAGAGAAAGAACCACCACGG+AGG 0.793634 5.1:+30455777 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! GAATTAAACGATGTTCTTAT+TGG + chr5.1:30455559-30455578 None:intergenic 25.0%
! TTGCATCTTTCATCTAATAT+TGG + chr5.1:30455175-30455194 None:intergenic 25.0%
!! TTTCAAGTACTTGAGTTTAT+TGG + chr5.1:30454711-30454730 None:intergenic 25.0%
AAAGAAGAAGATGGAGAAAT+TGG - chr5.1:30454617-30454636 MS.gene77419:CDS 30.0%
AAGGTTCAGTAGTAACTATA+AGG - chr5.1:30455530-30455549 MS.gene77419:CDS 30.0%
ACAACAACAAATGAGAAACA+TGG - chr5.1:30455685-30455704 MS.gene77419:CDS 30.0%
ACATCGTTTAATTCATCGAA+TGG - chr5.1:30455565-30455584 MS.gene77419:CDS 30.0%
AGAAATGAACAACATGGTTA+TGG - chr5.1:30455766-30455785 MS.gene77419:CDS 30.0%
GATGCTGAAAAATACTTCAA+TGG - chr5.1:30454647-30454666 MS.gene77419:CDS 30.0%
! AATGATGATGATGATGATGT+TGG - chr5.1:30455304-30455323 MS.gene77419:CDS 30.0%
! AGAAAGTGCAAAGTTCAATA+TGG - chr5.1:30454746-30454765 MS.gene77419:CDS 30.0%
! AGTCAATAAGCTTTGATATG+AGG - chr5.1:30455194-30455213 MS.gene77419:CDS 30.0%
! ATGTTTGAAGAGTTTTTCTG+AGG + chr5.1:30454999-30455018 None:intergenic 30.0%
! GTTATTGTTGTTATTCTGAG+AGG + chr5.1:30454480-30454499 None:intergenic 30.0%
!! GAAGTAGAATTTTTCAAAGC+AGG + chr5.1:30454827-30454846 None:intergenic 30.0%
AAGAGATCAAATTCACCACA+TGG - chr5.1:30455802-30455821 MS.gene77419:CDS 35.0%
AAGAGTCTTCTTGCTACTAT+TGG - chr5.1:30454878-30454897 MS.gene77419:CDS 35.0%
AATAACAACAATAACCTCCG+TGG - chr5.1:30454485-30454504 MS.gene77419:CDS 35.0%
AGAGAATCCAAGGAAAACAT+TGG - chr5.1:30455135-30455154 MS.gene77419:CDS 35.0%
CTCTTCATACTTGAACAACA+AGG - chr5.1:30454517-30454536 MS.gene77419:CDS 35.0%
CTTCTTCTTTCTTTACTCCA+AGG + chr5.1:30454607-30454626 None:intergenic 35.0%
CTTGAACAACAAGGAAGTAA+AGG - chr5.1:30454526-30454545 MS.gene77419:CDS 35.0%
CTTGAGTTTATTGGCATCTA+AGG + chr5.1:30454702-30454721 None:intergenic 35.0%
GAAGACTCTTTCTATGAACT+TGG + chr5.1:30454868-30454887 None:intergenic 35.0%
GAATTTGATCTCTTAAGAGG+TGG + chr5.1:30455796-30455815 None:intergenic 35.0%
GAGGCTAAAAATACCATCTT+GGG - chr5.1:30455213-30455232 MS.gene77419:CDS 35.0%
GGAGTAAAGAAAGAAGAAGA+TGG - chr5.1:30454608-30454627 MS.gene77419:CDS 35.0%
GGTGAATTTGATCTCTTAAG+AGG + chr5.1:30455799-30455818 None:intergenic 35.0%
GTTTCAGATCATGAAGATCA+AGG - chr5.1:30455511-30455530 MS.gene77419:CDS 35.0%
TCCTTTCTGTTGCTGATAAA+GGG + chr5.1:30454575-30454594 None:intergenic 35.0%
TGAGGCTAAAAATACCATCT+TGG - chr5.1:30455212-30455231 MS.gene77419:CDS 35.0%
TGCACTTTCTATTCTCTTGT+TGG + chr5.1:30454736-30454755 None:intergenic 35.0%
TGTAATAGTCAGAAAGCTGT+TGG - chr5.1:30455643-30455662 MS.gene77419:CDS 35.0%
TTCAACAAGTAGAGAATCCA+AGG - chr5.1:30455125-30455144 MS.gene77419:CDS 35.0%
TTCCTTTCTGTTGCTGATAA+AGG + chr5.1:30454576-30454595 None:intergenic 35.0%
! AACACTTCCAATGTTTTCCT+TGG + chr5.1:30455145-30455164 None:intergenic 35.0%
! TTCAACAAAAGTGCAGTTCA+AGG - chr5.1:30454965-30454984 MS.gene77419:CDS 35.0%
! TTTGAGATTGAAAGCTTCAC+TGG - chr5.1:30455349-30455368 MS.gene77419:CDS 35.0%
!! AGGAAAACATTGGAAGTGTT+TGG - chr5.1:30455145-30455164 MS.gene77419:CDS 35.0%
!! AGGTTTAAGGTGGAAAGTTT+TGG - chr5.1:30455739-30455758 MS.gene77419:CDS 35.0%
!! TCACTTGGTGCATAGAAATT+TGG + chr5.1:30455439-30455458 None:intergenic 35.0%
AAATCAACAAAGAGATGCCG+AGG - chr5.1:30455596-30455615 MS.gene77419:CDS 40.0%
AAATGTTGCCTCAGATGACA+AGG - chr5.1:30455719-30455738 MS.gene77419:CDS 40.0%
ACCTTAAACCTTGTCATCTG+AGG + chr5.1:30455730-30455749 None:intergenic 40.0%
ATGAAGAGAAAGAACCACCA+CGG + chr5.1:30454505-30454524 None:intergenic 40.0%
CAATATGGAACTCCAAGTGT+TGG - chr5.1:30454761-30454780 MS.gene77419:CDS 40.0%
CATTCAATGCTTGCTTCACT+TGG + chr5.1:30455454-30455473 None:intergenic 40.0%
CCTTTCTGTTGCTGATAAAG+GGG + chr5.1:30454574-30454593 None:intergenic 40.0%
GGTGCAAGAAATGAACAACA+TGG - chr5.1:30455760-30455779 MS.gene77419:CDS 40.0%
GTTGATGTAAGTGATCATGC+AGG - chr5.1:30454932-30454951 MS.gene77419:CDS 40.0%
TACAAAAGTTGTGCACCATG+TGG + chr5.1:30455820-30455839 None:intergenic 40.0%
TCAGATGACAAGGTTTAAGG+TGG - chr5.1:30455729-30455748 MS.gene77419:CDS 40.0%
TTCTTTACTCCAAGGTGAAG+AGG + chr5.1:30454599-30454618 None:intergenic 40.0%
! ACAACATCACATGTTGCTTC+TGG - chr5.1:30455403-30455422 MS.gene77419:CDS 40.0%
! CAGGTTGTAAAAGTGCACTT+TGG + chr5.1:30454808-30454827 None:intergenic 40.0%
! GTTATTCTGAGAGGTGAAAG+TGG + chr5.1:30454471-30454490 None:intergenic 40.0%
!! CAAGTGAAGCAAGCATTGAA+TGG - chr5.1:30455452-30455471 MS.gene77419:CDS 40.0%
!! GTCATCTGAGGCAACATTTT+TGG + chr5.1:30455718-30455737 None:intergenic 40.0%
AACAACAATAACCTCCGTGG+TGG - chr5.1:30454488-30454507 MS.gene77419:CDS 45.0%
AGAAAGGAACCTCTTCACCT+TGG - chr5.1:30454587-30454606 MS.gene77419:CDS 45.0%
CCCCTTTATCAGCAACAGAA+AGG - chr5.1:30454571-30454590 MS.gene77419:CDS 45.0%
CGGCGTCATGGAAAATTGTT+GGG - chr5.1:30455619-30455638 MS.gene77419:CDS 45.0%
CTTGATTCTGAGCCAACACT+TGG + chr5.1:30454776-30454795 None:intergenic 45.0%
GCCTCAGATGACAAGGTTTA+AGG - chr5.1:30455726-30455745 MS.gene77419:CDS 45.0%
TTCTGTTGCTGATAAAGGGG+TGG + chr5.1:30454571-30454590 None:intergenic 45.0%
TTTGTAGCAGCTTCCCAAGA+TGG + chr5.1:30455229-30455248 None:intergenic 45.0%
! GCATCTAAGGTAGCAAGTCT+TGG + chr5.1:30454689-30454708 None:intergenic 45.0%
!! AGCAAGCATTGAATGGAGTG+TGG - chr5.1:30455459-30455478 MS.gene77419:CDS 45.0%
!! GGGTGGATTGAATCAGCAAA+AGG + chr5.1:30454554-30454573 None:intergenic 45.0%
AAGAGAAAGAACCACCACGG+AGG + chr5.1:30454502-30454521 None:intergenic 50.0%
GCGGCGTCATGGAAAATTGT+TGG - chr5.1:30455618-30455637 MS.gene77419:CDS 50.0%
TCAACAAAGAGATGCCGAGG+CGG - chr5.1:30455599-30455618 MS.gene77419:CDS 50.0%
! AATTTTCCATGACGCCGCCT+CGG + chr5.1:30455616-30455635 None:intergenic 50.0%
!! CAGAAAGCTGTTGGTGTTGC+TGG - chr5.1:30455652-30455671 MS.gene77419:CDS 50.0%
AACCGAGACTCGTGCTGCAG+CGG - chr5.1:30455057-30455076 MS.gene77419:CDS 60.0%
TTCCGCTGCAGCACGAGTCT+CGG + chr5.1:30455062-30455081 None:intergenic 60.0%
GAGATGCCGAGGCGGCGTCA+TGG - chr5.1:30455607-30455626 MS.gene77419:CDS 70.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 30454452 30455846 30454452 ID=MS.gene77419
chr5.1 mRNA 30454452 30455846 30454452 ID=MS.gene77419.t1;Parent=MS.gene77419
chr5.1 exon 30454452 30455846 30454452 ID=MS.gene77419.t1.exon1;Parent=MS.gene77419.t1
chr5.1 CDS 30454452 30455846 30454452 ID=cds.MS.gene77419.t1;Parent=MS.gene77419.t1
Gene Sequence

>MS.gene77419

ATGGTTATCTCAGCAACCACTTTCACCTCTCAGAATAACAACAATAACCTCCGTGGTGGTTCTTTCTCTTCATACTTGAACAACAAGGAAGTAAAGGATCCTTTTGCTGATTCAATCCACCCCTTTATCAGCAACAGAAAGGAACCTCTTCACCTTGGAGTAAAGAAAGAAGAAGATGGAGAAATTGGAGTATTTGATGCTGAAAAATACTTCAATGGAGTTGAAATAGAAACTCCAAGACTTGCTACCTTAGATGCCAATAAACTCAAGTACTTGAAAGACCAACAAGAGAATAGAAAGTGCAAAGTTCAATATGGAACTCCAAGTGTTGGCTCAGAATCAAGCTTGAATAGCCAAAGTGCACTTTTACAACCTGCTTTGAAAAATTCTACTTCAAGTAACAGTAGAAAAAACCAAGTTCATAGAAAGAGTCTTCTTGCTACTATTGGTTGCAAATGCTCTTGTTATGATAAGAATTCTGTTGATGTAAGTGATCATGCAGGTGAAATCAGCTTCAACAAAAGTGCAGTTCAAGGAAAAACAACCTCAGAAAAACTCTTCAAACATGATCAAGATGCTTCTGATCATTCAATTAAGAATAAGAAAACCGAGACTCGTGCTGCAGCGGAACTCTTGATGAACAAAGAAAAGATTTCTACTTACAAAATGCAACTTCAACAAGTAGAGAATCCAAGGAAAACATTGGAAGTGTTTGGTTCACCAATATTAGATGAAAGATGCAAGTCAATAAGCTTTGATATGAGGCTAAAAATACCATCTTGGGAAGCTGCTACAAAACTTGAAGAAGAAGAAATTGATTTTTCTACAAATTGTGATGAAAACAACTATGATAATGATGATGATGATGATGTTGGAAGTGATGCAAGTTCAGATTTATTTGAGATTGAAAGCTTCACTGGTAATAAAACAAGCTCATTTTTATCAAGAACAACAACATCACATGTTGCTTCTGGTTGCACTAGTCCAAATTTCTATGCACCAAGTGAAGCAAGCATTGAATGGAGTGTGGTAACTGCAAGTGCAATTGATTATTCAGCTGTTTCAGATCATGAAGATCAAGGTTCAGTAGTAACTATAAGGAGTCCAATAAGAACATCGTTTAATTCATCGAATGGTAAACACAAAATCAACAAAGAGATGCCGAGGCGGCGTCATGGAAAATTGTTGGGTTGTAATAGTCAGAAAGCTGTTGGTGTTGCTGGTGATGCTTTCACAACAACAAATGAGAAACATGGTACAAATCCAAAAATGTTGCCTCAGATGACAAGGTTTAAGGTGGAAAGTTTTGGTGCAAGAAATGAACAACATGGTTATGGAAAACCACCTCTTAAGAGATCAAATTCACCACATGGTGCACAACTTTTGTATATTTAG

Protein sequence

>MS.gene77419.t1

MVISATTFTSQNNNNNLRGGSFSSYLNNKEVKDPFADSIHPFISNRKEPLHLGVKKEEDGEIGVFDAEKYFNGVEIETPRLATLDANKLKYLKDQQENRKCKVQYGTPSVGSESSLNSQSALLQPALKNSTSSNSRKNQVHRKSLLATIGCKCSCYDKNSVDVSDHAGEISFNKSAVQGKTTSEKLFKHDQDASDHSIKNKKTETRAAAELLMNKEKISTYKMQLQQVENPRKTLEVFGSPILDERCKSISFDMRLKIPSWEAATKLEEEEIDFSTNCDENNYDNDDDDDVGSDASSDLFEIESFTGNKTSSFLSRTTTSHVASGCTSPNFYAPSEASIEWSVVTASAIDYSAVSDHEDQGSVVTIRSPIRTSFNSSNGKHKINKEMPRRRHGKLLGCNSQKAVGVAGDAFTTTNEKHGTNPKMLPQMTRFKVESFGARNEQHGYGKPPLKRSNSPHGAQLLYI