AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene053288


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene053288.t1 MTR_1g103420 95.122 205 3 1 1 205 20 217 4.24e-130 365
MS.gene053288.t1 MTR_5g006940 59.512 205 71 5 1 205 20 212 5.20e-63 194
MS.gene053288.t1 MTR_1g071720 56.190 105 42 4 8 109 27 130 1.53e-31 113
MS.gene053288.t1 MTR_1g071720 56.190 105 42 4 8 109 27 130 1.68e-31 113
MS.gene053288.t1 MTR_7g095250 48.544 103 46 3 18 113 2 104 7.93e-23 90.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene053288.t1 AT1G05450 60.993 141 48 3 7 147 27 160 2.39e-46 152
MS.gene053288.t1 AT3G22620 47.692 195 80 6 13 205 29 203 2.62e-41 139
MS.gene053288.t1 AT2G48140 50.331 151 63 6 1 140 15 164 5.44e-35 122
MS.gene053288.t1 AT2G48140 57.009 107 44 2 1 106 15 120 2.56e-34 119

Find 66 sgRNAs with CRISPR-Local

Find 81 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACTCTCTTCACACCTTGTA+TGG 0.248146 1.4:-2322659 MS.gene053288:CDS
AATCCATGCCACTACTTGTT+AGG 0.277189 1.4:+2322569 None:intergenic
AAGAGAGTGCTTATTGTAGA+AGG 0.288971 1.4:+2322673 None:intergenic
GGAGATGAAGTTGGTGAAGC+TGG 0.347569 1.4:+2321819 None:intergenic
ATAGCTAAGGTTCTATTGAT+TGG 0.350447 1.4:+2322505 None:intergenic
CTTACAGGTAGTAGTGCTAA+TGG 0.358055 1.4:-2322631 MS.gene053288:CDS
CCATCGCCGTCGGTGAATTC+CGG 0.375246 1.4:-2321753 MS.gene053288:CDS
GTCATTAATATTGTCATGGC+TGG 0.381229 1.4:-2322730 None:intergenic
CTTCCAGTTGTCGATGTAGA+TGG 0.386358 1.4:+2321726 None:intergenic
TACTGTTCTATTGATTGCAC+TGG 0.398561 1.4:-2321649 MS.gene053288:CDS
GAGATGAAGTTGGTGAAGCT+GGG 0.416122 1.4:+2321820 None:intergenic
GGCGATGGCGGAGTCAAAAT+AGG 0.422484 1.4:+2321768 None:intergenic
TGCTAATAACCTTGAGGACT+AGG 0.423773 1.4:+2321965 None:intergenic
CTTATTGTAGAAGGGTTACA+TGG 0.446986 1.4:+2322682 None:intergenic
TCACCTGCATCTTCTCCCTC+AGG 0.449806 1.4:-2322001 MS.gene053288:CDS
ATCCATGCCACTACTTGTTA+GGG 0.450316 1.4:+2322570 None:intergenic
TGGGGTGTTGATTTGTGCAT+TGG 0.461296 1.4:+2322702 None:intergenic
TGAGACATTGTAAGATGTAA+TGG 0.469321 1.4:+2321674 None:intergenic
GCTAATAACCTTGAGGACTA+GGG 0.472496 1.4:+2321966 None:intergenic
TTCACCAACTTCATCTCCTC+TGG 0.485231 1.4:-2321814 MS.gene053288:CDS
CCTCGTGCTTGTAACATGCC+TGG 0.487865 1.4:-2322475 MS.gene053288:CDS
ATTCCATCTACATCGACAAC+TGG 0.490256 1.4:-2321729 MS.gene053288:CDS
GCTTCACCACTTCCTGCTCC+TGG 0.495227 1.4:-2322304 MS.gene053288:intron
GCATTACCAGGAGCAGGAAG+TGG 0.522233 1.4:+2322298 None:intergenic
AGAGAGTGCTTATTGTAGAA+GGG 0.525567 1.4:+2322674 None:intergenic
AATCCTGAGGGAGAAGATGC+AGG 0.533311 1.4:+2321998 None:intergenic
AGCAGGAAGTGGTGAAGCTG+AGG 0.535400 1.4:+2322309 None:intergenic
CCGGAATTCACCGACGGCGA+TGG 0.538150 1.4:+2321753 None:intergenic
ATTCCAACCCCTAGTCCTCA+AGG 0.540237 1.4:-2321974 MS.gene053288:intron
ACTCTCTTCACACCTTGTAT+GGG 0.540459 1.4:-2322658 MS.gene053288:CDS
AATTTGGCATTACCAGGAGC+AGG 0.546347 1.4:+2322292 None:intergenic
TTCACAGGTCCTGTGGCTCT+AGG 0.546401 1.4:-2322034 MS.gene053288:intron
TAACCTTGAGGACTAGGGGT+TGG 0.546635 1.4:+2321971 None:intergenic
ATGTATATTCACAGGTCCTG+TGG 0.548141 1.4:-2322041 MS.gene053288:intron
ATCCCTAACAAGTAGTGGCA+TGG 0.551127 1.4:-2322572 MS.gene053288:CDS
CTTAAATCCCTAACAAGTAG+TGG 0.551269 1.4:-2322577 MS.gene053288:CDS
TGTCGATGTAGATGGAATAC+CGG 0.553646 1.4:+2321734 None:intergenic
TGAGATGGTCCTAGAGCCAC+AGG 0.556902 1.4:+2322025 None:intergenic
ACTGTTCTATTGATTGCACT+GGG 0.566423 1.4:-2321648 MS.gene053288:CDS
CCTGTAAGAAAACCCATACA+AGG 0.567820 1.4:+2322646 None:intergenic
TAAGATGTAATGGCAGATGA+TGG 0.568483 1.4:+2321684 None:intergenic
TTGCATTGAACTGGAACACC+AGG 0.568933 1.4:+2322457 None:intergenic
GGAACATTTGTGTCTTGTTG+TGG 0.569274 1.4:+2321789 None:intergenic
AAGAGCACCGCAACATTCAG+TGG 0.581316 1.4:+2322597 None:intergenic
TTTGACTCCGCCATCGCCGT+CGG 0.585425 1.4:-2321763 MS.gene053288:CDS
AGGGAACACTAGCAGTTACA+AGG 0.586483 1.4:+2322536 None:intergenic
AGTGCAATCAATAGAACAGT+AGG 0.586789 1.4:+2321651 None:intergenic
GTGTCTTGTTGTGGTGCCAG+AGG 0.590812 1.4:+2321798 None:intergenic
GCACCGCAACATTCAGTGGT+TGG 0.593515 1.4:+2322601 None:intergenic
TCTACATCGACAACTGGAAG+CGG 0.603015 1.4:-2321723 MS.gene053288:CDS
GAAGATGCAGGTGAATGAGA+TGG 0.607870 1.4:+2322010 None:intergenic
GAATTCACCGACGGCGATGG+CGG 0.628016 1.4:+2321756 None:intergenic
GGTGTTCCAGTTCAATGCAA+AGG 0.630148 1.4:-2322454 MS.gene053288:intron
CCAGGCATGTTACAAGCACG+AGG 0.631598 1.4:+2322475 None:intergenic
ACGAGGGAGAGAGATAGCTA+AGG 0.635982 1.4:+2322492 None:intergenic
TGGTGAAGCTGGGAGATCAG+AGG 0.637738 1.4:+2321830 None:intergenic
CTAATAACCTTGAGGACTAG+GGG 0.642081 1.4:+2321967 None:intergenic
TCACCAACCACTGAATGTTG+CGG 0.642405 1.4:-2322604 MS.gene053288:CDS
TTATTGTAGAAGGGTTACAT+GGG 0.644859 1.4:+2322683 None:intergenic
GCAACATTCAGTGGTTGGTG+AGG 0.651267 1.4:+2322606 None:intergenic
GGGGTTGGAATAAATCCTGA+GGG 0.662198 1.4:+2321986 None:intergenic
AGGGGTTGGAATAAATCCTG+AGG 0.672890 1.4:+2321985 None:intergenic
GGTGCCAGAGGAGATGAAGT+TGG 0.674504 1.4:+2321810 None:intergenic
TATTGTAGAAGGGTTACATG+GGG 0.692481 1.4:+2322684 None:intergenic
GGAATACCGGAATTCACCGA+CGG 0.713881 1.4:+2321747 None:intergenic
CAGGCATGTTACAAGCACGA+GGG 0.748196 1.4:+2322476 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATTATTGAAATTGAAATT+TGG + chr1.4:2322065-2322084 None:intergenic 10.0%
!! CATTATTAAGATTAATTCAA+AGG + chr1.4:2322271-2322290 None:intergenic 15.0%
!!! GTTAGAAAATATTTTTGTTA+GGG + chr1.4:2322123-2322142 None:intergenic 15.0%
!!! TGTTAGAAAATATTTTTGTT+AGG + chr1.4:2322124-2322143 None:intergenic 15.0%
! TCAAAGAAAAATGTAAGAGT+TGG + chr1.4:2322481-2322500 None:intergenic 25.0%
! TCAAAGGAAAAATAGTTTAG+AGG + chr1.4:2322255-2322274 None:intergenic 25.0%
!! TTTTGTTAGGGATTATAGAA+GGG + chr1.4:2322111-2322130 None:intergenic 25.0%
!! TTTTTGTTAGGGATTATAGA+AGG + chr1.4:2322112-2322131 None:intergenic 25.0%
!!! CTATTGATTGGAATTTTGAA+GGG + chr1.4:2321824-2321843 None:intergenic 25.0%
!!! TCTATTGATTGGAATTTTGA+AGG + chr1.4:2321825-2321844 None:intergenic 25.0%
!!! TGATTTTGATGTATATTCAC+AGG - chr1.4:2322289-2322308 MS.gene053288:intron 25.0%
AATTGAAATTTGGCATTACC+AGG + chr1.4:2322055-2322074 None:intergenic 30.0%
ATAGCTAAGGTTCTATTGAT+TGG + chr1.4:2321836-2321855 None:intergenic 30.0%
CTATCATCTAGTAACATTGT+AGG - chr1.4:2322222-2322241 MS.gene053288:intron 30.0%
TGAGACATTGTAAGATGTAA+TGG + chr1.4:2322667-2322686 None:intergenic 30.0%
TTATTGTAGAAGGGTTACAT+GGG + chr1.4:2321658-2321677 None:intergenic 30.0%
! TTTTTACCTTTGCATTGAAC+TGG + chr1.4:2321893-2321912 None:intergenic 30.0%
AGTGCAATCAATAGAACAGT+AGG + chr1.4:2322690-2322709 None:intergenic 35.0%
CTTAAATCCCTAACAAGTAG+TGG - chr1.4:2321761-2321780 MS.gene053288:CDS 35.0%
CTTATTGTAGAAGGGTTACA+TGG + chr1.4:2321659-2321678 None:intergenic 35.0%
GTGTAATGCTAATAACCTTG+AGG + chr1.4:2322382-2322401 None:intergenic 35.0%
TAAGATGTAATGGCAGATGA+TGG + chr1.4:2322657-2322676 None:intergenic 35.0%
TATTGTAGAAGGGTTACATG+GGG + chr1.4:2321657-2321676 None:intergenic 35.0%
! ACTGTTCTATTGATTGCACT+GGG - chr1.4:2322690-2322709 MS.gene053288:CDS 35.0%
! TACTGTTCTATTGATTGCAC+TGG - chr1.4:2322689-2322708 MS.gene053288:CDS 35.0%
!! AAGAGAGTGCTTATTGTAGA+AGG + chr1.4:2321668-2321687 None:intergenic 35.0%
!! AGAGAGTGCTTATTGTAGAA+GGG + chr1.4:2321667-2321686 None:intergenic 35.0%
AATCCATGCCACTACTTGTT+AGG + chr1.4:2321772-2321791 None:intergenic 40.0%
ACTCTCTTCACACCTTGTAT+GGG - chr1.4:2321680-2321699 MS.gene053288:CDS 40.0%
ATGTATATTCACAGGTCCTG+TGG - chr1.4:2322297-2322316 MS.gene053288:intron 40.0%
ATTCCATCTACATCGACAAC+TGG - chr1.4:2322609-2322628 MS.gene053288:CDS 40.0%
CCTGTAAGAAAACCCATACA+AGG + chr1.4:2321695-2321714 None:intergenic 40.0%
CTAATAACCTTGAGGACTAG+GGG + chr1.4:2322374-2322393 None:intergenic 40.0%
CTTACAGGTAGTAGTGCTAA+TGG - chr1.4:2321707-2321726 MS.gene053288:CDS 40.0%
GCTAATAACCTTGAGGACTA+GGG + chr1.4:2322375-2322394 None:intergenic 40.0%
TGCTAATAACCTTGAGGACT+AGG + chr1.4:2322376-2322395 None:intergenic 40.0%
TGTCGATGTAGATGGAATAC+CGG + chr1.4:2322607-2322626 None:intergenic 40.0%
! ATCCATGCCACTACTTGTTA+GGG + chr1.4:2321771-2321790 None:intergenic 40.0%
! CCTTGTATGGGTTTTCTTAC+AGG - chr1.4:2321692-2321711 MS.gene053288:CDS 40.0%
! GGAACATTTGTGTCTTGTTG+TGG + chr1.4:2322552-2322571 None:intergenic 40.0%
AATTTGGCATTACCAGGAGC+AGG + chr1.4:2322049-2322068 None:intergenic 45.0%
AGGGAACACTAGCAGTTACA+AGG + chr1.4:2321805-2321824 None:intergenic 45.0%
AGGGGTTGGAATAAATCCTG+AGG + chr1.4:2322356-2322375 None:intergenic 45.0%
ATCCCTAACAAGTAGTGGCA+TGG - chr1.4:2321766-2321785 MS.gene053288:CDS 45.0%
CACTCTCTTCACACCTTGTA+TGG - chr1.4:2321679-2321698 MS.gene053288:CDS 45.0%
CTTCCAGTTGTCGATGTAGA+TGG + chr1.4:2322615-2322634 None:intergenic 45.0%
GAAGATGCAGGTGAATGAGA+TGG + chr1.4:2322331-2322350 None:intergenic 45.0%
GGGGTTGGAATAAATCCTGA+GGG + chr1.4:2322355-2322374 None:intergenic 45.0%
GGTGTTCCAGTTCAATGCAA+AGG - chr1.4:2321884-2321903 MS.gene053288:intron 45.0%
TCACCAACCACTGAATGTTG+CGG - chr1.4:2321734-2321753 MS.gene053288:CDS 45.0%
TCTACATCGACAACTGGAAG+CGG - chr1.4:2322615-2322634 MS.gene053288:CDS 45.0%
TTCACCAACTTCATCTCCTC+TGG - chr1.4:2322524-2322543 MS.gene053288:CDS 45.0%
TTGCATTGAACTGGAACACC+AGG + chr1.4:2321884-2321903 None:intergenic 45.0%
!! GAGATGAAGTTGGTGAAGCT+GGG + chr1.4:2322521-2322540 None:intergenic 45.0%
!! TGGGGTGTTGATTTGTGCAT+TGG + chr1.4:2321639-2321658 None:intergenic 45.0%
AATCCTGAGGGAGAAGATGC+AGG + chr1.4:2322343-2322362 None:intergenic 50.0%
ACGAGGGAGAGAGATAGCTA+AGG + chr1.4:2321849-2321868 None:intergenic 50.0%
ATTCCAACCCCTAGTCCTCA+AGG - chr1.4:2322364-2322383 MS.gene053288:intron 50.0%
CAGGCATGTTACAAGCACGA+GGG + chr1.4:2321865-2321884 None:intergenic 50.0%
GGAATACCGGAATTCACCGA+CGG + chr1.4:2322594-2322613 None:intergenic 50.0%
TAACCTTGAGGACTAGGGGT+TGG + chr1.4:2322370-2322389 None:intergenic 50.0%
! GCAACATTCAGTGGTTGGTG+AGG + chr1.4:2321735-2321754 None:intergenic 50.0%
!! AAGAGCACCGCAACATTCAG+TGG + chr1.4:2321744-2321763 None:intergenic 50.0%
!! GGAGATGAAGTTGGTGAAGC+TGG + chr1.4:2322522-2322541 None:intergenic 50.0%
AGCAGGAAGTGGTGAAGCTG+AGG + chr1.4:2322032-2322051 None:intergenic 55.0%
CCAGGCATGTTACAAGCACG+AGG + chr1.4:2321866-2321885 None:intergenic 55.0%
CCTCGTGCTTGTAACATGCC+TGG - chr1.4:2321863-2321882 MS.gene053288:intron 55.0%
GCACCGCAACATTCAGTGGT+TGG + chr1.4:2321740-2321759 None:intergenic 55.0%
GCATTACCAGGAGCAGGAAG+TGG + chr1.4:2322043-2322062 None:intergenic 55.0%
GGTGCCAGAGGAGATGAAGT+TGG + chr1.4:2322531-2322550 None:intergenic 55.0%
TCACCTGCATCTTCTCCCTC+AGG - chr1.4:2322337-2322356 MS.gene053288:intron 55.0%
TGAGATGGTCCTAGAGCCAC+AGG + chr1.4:2322316-2322335 None:intergenic 55.0%
TGGTGAAGCTGGGAGATCAG+AGG + chr1.4:2322511-2322530 None:intergenic 55.0%
TTCACAGGTCCTGTGGCTCT+AGG - chr1.4:2322304-2322323 MS.gene053288:intron 55.0%
! GTGTCTTGTTGTGGTGCCAG+AGG + chr1.4:2322543-2322562 None:intergenic 55.0%
!! GGCGATGGCGGAGTCAAAAT+AGG + chr1.4:2322573-2322592 None:intergenic 55.0%
CCATCGCCGTCGGTGAATTC+CGG - chr1.4:2322585-2322604 MS.gene053288:CDS 60.0%
GAATTCACCGACGGCGATGG+CGG + chr1.4:2322585-2322604 None:intergenic 60.0%
GCTTCACCACTTCCTGCTCC+TGG - chr1.4:2322034-2322053 MS.gene053288:intron 60.0%
TTTGACTCCGCCATCGCCGT+CGG - chr1.4:2322575-2322594 MS.gene053288:CDS 60.0%
CCGGAATTCACCGACGGCGA+TGG + chr1.4:2322588-2322607 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 2321623 2322737 2321623 ID=MS.gene053288
chr1.4 mRNA 2321623 2322737 2321623 ID=MS.gene053288.t1;Parent=MS.gene053288
chr1.4 exon 2322455 2322737 2322455 ID=MS.gene053288.t1.exon1;Parent=MS.gene053288.t1
chr1.4 CDS 2322455 2322737 2322455 ID=cds.MS.gene053288.t1;Parent=MS.gene053288.t1
chr1.4 exon 2322305 2322331 2322305 ID=MS.gene053288.t1.exon2;Parent=MS.gene053288.t1
chr1.4 CDS 2322305 2322331 2322305 ID=cds.MS.gene053288.t1;Parent=MS.gene053288.t1
chr1.4 exon 2321975 2322049 2321975 ID=MS.gene053288.t1.exon3;Parent=MS.gene053288.t1
chr1.4 CDS 2321975 2322049 2321975 ID=cds.MS.gene053288.t1;Parent=MS.gene053288.t1
chr1.4 exon 2321623 2321855 2321623 ID=MS.gene053288.t1.exon4;Parent=MS.gene053288.t1
chr1.4 CDS 2321623 2321855 2321623 ID=cds.MS.gene053288.t1;Parent=MS.gene053288.t1
Gene Sequence

>MS.gene053288

ATGGCTGGACAAGCCAATGCACAAATCAACACCCCATGTAACCCTTCTACAATAAGCACTCTCTTCACACCTTGTATGGGTTTTCTTACAGGTAGTAGTGCTAATGGCACCTCACCAACCACTGAATGTTGCGGTGCTCTTAAATCCCTAACAAGTAGTGGCATGGATTGTTTGTGTCTCCTTGTAACTGCTAGTGTTCCCTTCAAAATTCCAATCAATAGAACCTTAGCTATCTCTCTCCCTCGTGCTTGTAACATGCCTGGTGTTCCAGTTCAATGCAAAGGTAAAAAAAAAAAAAAAACTACAATATTTTTCTCGTGTTTGTAACTTTGTAGAGTAAAATTTGTTATTCTCACTACAATAATAAAGCTAAGATGTTACTTTTTTTTTTTTTTTTACTTTGCAGCCTCAGCTTCACCACTTCCTGCTCCTGGTAATGCCAAATTTCAATTTCAATAATTTTTGTACACAAATTCTTACATAAACCCTTCTATAATCCCTAACAAAAATATTTTCTAACAAACTCTTCGCGACATGTGAATTTCATTTCTTTACTTAGAAATTGAGTCATGCTAAATAAGAAATGAAACTAGCATGATCTATCATCTAGTAACATTGTAGGTTTAATTCCTCTAAACTATTTTTCCTTTGAATTAATCTTAATAATGATTTTGATGTATATTCACAGGTCCTGTGGCTCTAGGACCATCTCATTCACCTGCATCTTCTCCCTCAGGATTTATTCCAACCCCTAGTCCTCAAGGTTATTAGCATTACACTATTCTATTACAATACAAGCTTATACAAGTTTAAACTTTTCATAGTGCTAAGAGCTTCTTAATGTGTTACTAACATCCAACTCTTACATTTTTCTTTGAGCAGCATCCTCTGATCTCCCAGCTTCACCAACTTCATCTCCTCTGGCACCACAACAAGACACAAATGTTCCTATTTTGACTCCGCCATCGCCGTCGGTGAATTCCGGTATTCCATCTACATCGACAACTGGAAGCGGTCGCTCTTCTCTGACTCCATCATCTGCCATTACATCTTACAATGTCTCACCTACTGTTCTATTGATTGCACTGGGATTTGTTGCTCTCAAATACTACTAG

Protein sequence

>MS.gene053288.t1

MAGQANAQINTPCNPSTISTLFTPCMGFLTGSSANGTSPTTECCGALKSLTSSGMDCLCLLVTASVPFKIPINRTLAISLPRACNMPGVPVQCKASASPLPAPGPVALGPSHSPASSPSGFIPTPSPQASSDLPASPTSSPLAPQQDTNVPILTPPSPSVNSGIPSTSTTGSGRSSLTPSSAITSYNVSPTVLLIALGFVALKYY