AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene067503

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene067503.t1 MTR_2g105850 94.309 246 11 2 1 243 1 246 1.21e-165 457
MS.gene067503.t1 MTR_2g105850 74.797 246 10 3 1 243 1 197 1.13e-124 352
MS.gene067503.t1 MTR_4g113520 29.900 301 136 8 13 242 15 311 1.87e-38 136
MS.gene067503.t1 MTR_3g087920 47.222 144 73 1 51 191 31 174 1.93e-36 131
MS.gene067503.t1 MTR_3g087920 42.500 80 38 2 171 242 245 324 5.20e-11 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene067503.t1 AT1G50440 69.444 252 66 3 1 243 1 250 1.57e-128 363
MS.gene067503.t1 AT1G50440 69.444 252 66 3 1 243 1 250 1.57e-128 363
MS.gene067503.t1 AT1G50440 69.444 252 66 3 1 243 1 250 1.57e-128 363
MS.gene067503.t1 AT1G50440 68.919 222 59 2 1 213 1 221 1.07e-112 322
MS.gene067503.t1 AT1G50440 58.294 211 76 3 1 202 1 208 1.85e-84 251
MS.gene067503.t1 AT1G11020 37.319 276 95 7 38 242 52 320 2.74e-46 157
MS.gene067503.t1 AT2G22120 43.421 152 79 2 24 172 7 154 1.00e-36 132
MS.gene067503.t1 AT2G22120 46.269 67 31 1 181 242 257 323 9.39e-11 61.2
MS.gene067503.t1 AT2G22120 43.421 152 79 2 24 172 7 154 1.20e-36 132
MS.gene067503.t1 AT2G22120 42.683 82 40 2 168 242 242 323 9.66e-11 61.2

Find 57 sgRNAs with CRISPR-Local

Find 91 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCAGTTCTCGCCATTATTT+TGG 0.183622 2.2:+131358 MS.gene067503:intron
TGCACAGGTTGTTGCTTTCT+TGG 0.234683 2.2:+131105 MS.gene067503:intron
TTCACAGAGGTGATTCAATA+TGG 0.242810 2.2:-130658 None:intergenic
ATGATCTGTGGACATACTTT+TGG 0.267771 2.2:-130830 None:intergenic
CTCAACCACCATCGATCTTT+AGG 0.272819 2.2:-130942 None:intergenic
GTGCTTATTTATAAATTCTA+TGG 0.292569 2.2:+131130 MS.gene067503:CDS
TTGTCAGACGTGGCAGAAAT+AGG 0.331431 2.2:-130687 None:intergenic
TTGGGTACCTTTGCAATGGC+AGG 0.331526 2.2:-130811 None:intergenic
GACCTTTGTCAATTCTTGTT+TGG 0.347635 2.2:-131456 None:intergenic
ACAGATCATGTCTCGATAAC+TGG 0.347729 2.2:+130844 MS.gene067503:CDS
GCACAGGTTGTTGCTTTCTT+GGG 0.351526 2.2:+131106 MS.gene067503:intron
CATCGATCTTTAGGGACATT+TGG 0.365167 2.2:-130933 None:intergenic
CCTTAGTTCTGTCACATGGC+TGG 0.365929 2.2:-131848 None:intergenic
TCAACCACCATCGATCTTTA+GGG 0.389036 2.2:-130941 None:intergenic
CTTAGTTCTGTCACATGGCT+GGG 0.400790 2.2:-131847 None:intergenic
TTTCTGAAGAAGAAGAATCT+TGG 0.402422 2.2:-130629 None:intergenic
GAGCAAACCCACCAAAATAA+TGG 0.405865 2.2:-131369 None:intergenic
TTCTTTATAGCAATAATATG+TGG 0.428860 2.2:+131398 MS.gene067503:CDS
TGCCGGATATGCCTTGATCT+TGG 0.432553 2.2:+130768 MS.gene067503:CDS
GATGAACTTAGAGAAATGTT+TGG 0.432617 2.2:+131154 MS.gene067503:CDS
ACATGGCTGGGGTCGAGTTC+AGG 0.434273 2.2:-131835 None:intergenic
GAGGTGATTCAATATGGGTT+GGG 0.457987 2.2:-130652 None:intergenic
CTCCAAGATCAAGGCATATC+CGG 0.463345 2.2:-130770 None:intergenic
GGGTACCTTTGCAATGGCAG+GGG 0.470794 2.2:-130809 None:intergenic
TCACAGAGGTGATTCAATAT+GGG 0.474068 2.2:-130657 None:intergenic
GTGACAGAACTAAGGATGTT+GGG 0.491109 2.2:+131856 MS.gene067503:CDS
TGGGTACCTTTGCAATGGCA+GGG 0.492265 2.2:-130810 None:intergenic
GAAAATGAATGCATGATCTC+TGG 0.494455 2.2:-130988 None:intergenic
CGGATATGCCTTGATCTTGG+AGG 0.499840 2.2:+130771 MS.gene067503:CDS
AGAGGTGATTCAATATGGGT+TGG 0.514100 2.2:-130653 None:intergenic
CAAGGCATATCCGGCATTGT+GGG 0.523063 2.2:-130761 None:intergenic
TGTGACAGAACTAAGGATGT+TGG 0.527888 2.2:+131855 MS.gene067503:CDS
AGTCTTCTCCTCCAAGATCA+AGG 0.530295 2.2:-130779 None:intergenic
TCTTTATAGCAATAATATGT+GGG 0.533500 2.2:+131399 MS.gene067503:CDS
AGAAGAAGAATCTTGGTTGT+CGG 0.545346 2.2:-130622 None:intergenic
TTAGTTCTGTCACATGGCTG+GGG 0.552531 2.2:-131846 None:intergenic
ATGCTGATCACCCACAATGC+CGG 0.553024 2.2:+130751 MS.gene067503:CDS
GTTTGGCAAGAACATGGTAG+TGG 0.554746 2.2:-131439 None:intergenic
CCAGCCATGTGACAGAACTA+AGG 0.558116 2.2:+131848 MS.gene067503:CDS
TCAAGGCATATCCGGCATTG+TGG 0.559551 2.2:-130762 None:intergenic
GCCATTGTGTAAAATCCGTA+TGG 0.559880 2.2:-131190 None:intergenic
ATACATATACCAGCTAGTAA+AGG 0.563392 2.2:-131879 None:intergenic
GGTACCTTTGCAATGGCAGG+GGG 0.567201 2.2:-130808 None:intergenic
AACTGGAGGTCTACCAAGGA+GGG 0.573090 2.2:+130861 MS.gene067503:CDS
AGAAGATCGAGAACATGTAA+AGG 0.577463 2.2:+131807 MS.gene067503:CDS
GGTTATGAAGAACATCCATA+CGG 0.581353 2.2:+131175 MS.gene067503:CDS
ATTCTTGTTTGGCAAGAACA+TGG 0.604029 2.2:-131445 None:intergenic
CAAATGTCCCTAAAGATCGA+TGG 0.630129 2.2:+130934 MS.gene067503:CDS
ACATCCTTAGTTCTGTCACA+TGG 0.650556 2.2:-131852 None:intergenic
CGATAACTGGAGGTCTACCA+AGG 0.652909 2.2:+130857 MS.gene067503:CDS
TGCCAAACAAGAATTGACAA+AGG 0.654420 2.2:+131454 MS.gene067503:CDS
AGTTATCGAGACATGATCTG+TGG 0.663655 2.2:-130842 None:intergenic
TAACTGGAGGTCTACCAAGG+AGG 0.663726 2.2:+130860 MS.gene067503:CDS
ATGTCCCTAAAGATCGATGG+TGG 0.685209 2.2:+130937 MS.gene067503:CDS
GATCATGTCTCGATAACTGG+AGG 0.685887 2.2:+130847 MS.gene067503:CDS
TATATCATGATTGTCAGACG+TGG 0.692189 2.2:-130697 None:intergenic
AAATAGGAATAATTTCACAG+AGG 0.778628 2.2:-130671 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ACCTTAAATTTTTATAAAAA+AGG - chr2.2:131736-131755 None:intergenic 10.0%
!!! TCCTTTTTTATAAAAATTTA+AGG + chr2.2:131732-131751 MS.gene067503:intron 10.0%
!! GTGCTTATTTATAAATTCTA+TGG + chr2.2:131130-131149 MS.gene067503:CDS 20.0%
!! TAAACAATACAATACAAGAA+CGG - chr2.2:131674-131693 None:intergenic 20.0%
!! TCTTTATAGCAATAATATGT+GGG + chr2.2:131399-131418 MS.gene067503:CDS 20.0%
!! TTCTTGTATTGTATTGTTTA+AGG + chr2.2:131674-131693 MS.gene067503:intron 20.0%
!! TTCTTTATAGCAATAATATG+TGG + chr2.2:131398-131417 MS.gene067503:CDS 20.0%
! AAACAATACAATACAAGAAC+GGG - chr2.2:131673-131692 None:intergenic 25.0%
! AAATAGGAATAATTTCACAG+AGG - chr2.2:130674-130693 None:intergenic 25.0%
!! AATTGATTCTGAGTCATATA+AGG + chr2.2:131702-131721 MS.gene067503:intron 25.0%
AAAAGCTGCAAACAAACATT+GGG - chr2.2:131252-131271 None:intergenic 30.0%
AACCAACTTATTACATGCAA+TGG + chr2.2:131311-131330 MS.gene067503:intron 30.0%
ATTTGAGAGTGGTGAATAAA+TGG - chr2.2:131224-131243 None:intergenic 30.0%
GATGAACTTAGAGAAATGTT+TGG + chr2.2:131154-131173 MS.gene067503:CDS 30.0%
GGTCATAAGATATGCAATTT+CGG + chr2.2:131628-131647 MS.gene067503:intron 30.0%
GTCATAAGATATGCAATTTC+GGG + chr2.2:131629-131648 MS.gene067503:intron 30.0%
TCTCTGAATGAAATACATAG+AGG - chr2.2:131047-131066 None:intergenic 30.0%
TGTGCAATTAGAAAAGGAAA+AGG - chr2.2:131091-131110 None:intergenic 30.0%
TTCCATTGCATGTAATAAGT+TGG - chr2.2:131316-131335 None:intergenic 30.0%
TTTGAGAGTGGTGAATAAAT+GGG - chr2.2:131223-131242 None:intergenic 30.0%
! TTTCTGAAGAAGAAGAATCT+TGG - chr2.2:130632-130651 None:intergenic 30.0%
! TTTTCCTTTTCTAATTGCAC+AGG + chr2.2:131090-131109 MS.gene067503:intron 30.0%
!! TAACATGCTTCACTTTTATG+TGG - chr2.2:131534-131553 None:intergenic 30.0%
ACAACCTGTGCAATTAGAAA+AGG - chr2.2:131097-131116 None:intergenic 35.0%
ACGAAAAAGTCAGAAATGAG+TGG - chr2.2:131275-131294 None:intergenic 35.0%
AGAAGAAGAATCTTGGTTGT+CGG - chr2.2:130625-130644 None:intergenic 35.0%
AGAAGATCGAGAACATGTAA+AGG + chr2.2:131807-131826 MS.gene067503:CDS 35.0%
GAAAAGCTGCAAACAAACAT+TGG - chr2.2:131253-131272 None:intergenic 35.0%
GAAAATGAATGCATGATCTC+TGG - chr2.2:130991-131010 None:intergenic 35.0%
GACCTTTGTCAATTCTTGTT+TGG - chr2.2:131459-131478 None:intergenic 35.0%
GGTTATGAAGAACATCCATA+CGG + chr2.2:131175-131194 MS.gene067503:CDS 35.0%
TATATCATGATTGTCAGACG+TGG - chr2.2:130700-130719 None:intergenic 35.0%
TCACAGAGGTGATTCAATAT+GGG - chr2.2:130660-130679 None:intergenic 35.0%
TGCCAAACAAGAATTGACAA+AGG + chr2.2:131454-131473 MS.gene067503:CDS 35.0%
TTCACAGAGGTGATTCAATA+TGG - chr2.2:130661-130680 None:intergenic 35.0%
! ATGATCTGTGGACATACTTT+TGG - chr2.2:130833-130852 None:intergenic 35.0%
! ATTCTTGTTTGGCAAGAACA+TGG - chr2.2:131448-131467 None:intergenic 35.0%
! TCCATACGGATTTTACACAA+TGG + chr2.2:131189-131208 MS.gene067503:CDS 35.0%
! TGATCTGTGGACATACTTTT+GGG - chr2.2:130832-130851 None:intergenic 35.0%
!! TGCTTCACTTTTATGTGGAT+TGG - chr2.2:131529-131548 None:intergenic 35.0%
!!! CTGTTTACTTTTTTGACGTC+AGG + chr2.2:131774-131793 MS.gene067503:intron 35.0%
ACAGATCATGTCTCGATAAC+TGG + chr2.2:130844-130863 MS.gene067503:CDS 40.0%
AGAGGTGATTCAATATGGGT+TGG - chr2.2:130656-130675 None:intergenic 40.0%
AGTTATCGAGACATGATCTG+TGG - chr2.2:130845-130864 None:intergenic 40.0%
ATTGGGCATGAATTTGAGAG+TGG - chr2.2:131235-131254 None:intergenic 40.0%
CAAATGTCCCTAAAGATCGA+TGG + chr2.2:130934-130953 MS.gene067503:CDS 40.0%
CTTGCTGCAAAACACATCTT+TGG + chr2.2:131607-131626 MS.gene067503:intron 40.0%
GAGCAAACCCACCAAAATAA+TGG - chr2.2:131372-131391 None:intergenic 40.0%
GAGGTGATTCAATATGGGTT+GGG - chr2.2:130655-130674 None:intergenic 40.0%
GCCATTGTGTAAAATCCGTA+TGG - chr2.2:131193-131212 None:intergenic 40.0%
GTGACAGAACTAAGGATGTT+GGG + chr2.2:131856-131875 MS.gene067503:CDS 40.0%
TCAACCACCATCGATCTTTA+GGG - chr2.2:130944-130963 None:intergenic 40.0%
TGTGACAGAACTAAGGATGT+TGG + chr2.2:131855-131874 MS.gene067503:CDS 40.0%
! CATCGATCTTTAGGGACATT+TGG - chr2.2:130936-130955 None:intergenic 40.0%
! TACGGATTTTACACAATGGC+TGG + chr2.2:131193-131212 MS.gene067503:CDS 40.0%
! TGCAGTTCTCGCCATTATTT+TGG + chr2.2:131358-131377 MS.gene067503:intron 40.0%
!! ACATCCTTAGTTCTGTCACA+TGG - chr2.2:131855-131874 None:intergenic 40.0%
!! ACTTTTGGGTACCTTTGCAA+TGG - chr2.2:130818-130837 None:intergenic 40.0%
!! TTTTTGACGTCAGGAGTATG+TGG + chr2.2:131783-131802 MS.gene067503:intron 40.0%
!!! AGTTCTCGCCATTATTTTGG+TGG + chr2.2:131361-131380 MS.gene067503:intron 40.0%
!!! ATTTTGGTGGGTTTGCTCTA+TGG + chr2.2:131374-131393 MS.gene067503:CDS 40.0%
!!! GTTCTCGCCATTATTTTGGT+GGG + chr2.2:131362-131381 MS.gene067503:intron 40.0%
AGAAAAAGCAAAGCCCTCCT+TGG - chr2.2:130877-130896 None:intergenic 45.0%
AGTCTTCTCCTCCAAGATCA+AGG - chr2.2:130782-130801 None:intergenic 45.0%
ATGTCCCTAAAGATCGATGG+TGG + chr2.2:130937-130956 MS.gene067503:CDS 45.0%
CTCAACCACCATCGATCTTT+AGG - chr2.2:130945-130964 None:intergenic 45.0%
CTCCAAGATCAAGGCATATC+CGG - chr2.2:130773-130792 None:intergenic 45.0%
CTTGCTGCAAAACACGTCTT+TGG + chr2.2:131572-131591 MS.gene067503:intron 45.0%
GATCATGTCTCGATAACTGG+AGG + chr2.2:130847-130866 MS.gene067503:CDS 45.0%
GTTTGGCAAGAACATGGTAG+TGG - chr2.2:131442-131461 None:intergenic 45.0%
TTGTCAGACGTGGCAGAAAT+AGG - chr2.2:130690-130709 None:intergenic 45.0%
!! CTTAGTTCTGTCACATGGCT+GGG - chr2.2:131850-131869 None:intergenic 45.0%
!! GCACAGGTTGTTGCTTTCTT+GGG + chr2.2:131106-131125 MS.gene067503:intron 45.0%
!! TGCACAGGTTGTTGCTTTCT+TGG + chr2.2:131105-131124 MS.gene067503:intron 45.0%
!! TTAGTTCTGTCACATGGCTG+GGG - chr2.2:131849-131868 None:intergenic 45.0%
AACTGGAGGTCTACCAAGGA+GGG + chr2.2:130861-130880 MS.gene067503:CDS 50.0%
ATGCTGATCACCCACAATGC+CGG + chr2.2:130751-130770 MS.gene067503:CDS 50.0%
CAAGGCATATCCGGCATTGT+GGG - chr2.2:130764-130783 None:intergenic 50.0%
CCAGCCATGTGACAGAACTA+AGG + chr2.2:131848-131867 MS.gene067503:CDS 50.0%
CGATAACTGGAGGTCTACCA+AGG + chr2.2:130857-130876 MS.gene067503:CDS 50.0%
CGGATATGCCTTGATCTTGG+AGG + chr2.2:130771-130790 MS.gene067503:CDS 50.0%
TAACTGGAGGTCTACCAAGG+AGG + chr2.2:130860-130879 MS.gene067503:CDS 50.0%
TCAAGGCATATCCGGCATTG+TGG - chr2.2:130765-130784 None:intergenic 50.0%
TGCCGGATATGCCTTGATCT+TGG + chr2.2:130768-130787 MS.gene067503:CDS 50.0%
TGGGTACCTTTGCAATGGCA+GGG - chr2.2:130813-130832 None:intergenic 50.0%
TTGGGTACCTTTGCAATGGC+AGG - chr2.2:130814-130833 None:intergenic 50.0%
!! CCTTAGTTCTGTCACATGGC+TGG - chr2.2:131851-131870 None:intergenic 50.0%
ATTGCCCCCTGCCATTGCAA+AGG + chr2.2:130804-130823 MS.gene067503:CDS 55.0%
GGGTACCTTTGCAATGGCAG+GGG - chr2.2:130812-130831 None:intergenic 55.0%
GGTACCTTTGCAATGGCAGG+GGG - chr2.2:130811-130830 None:intergenic 55.0%
ACATGGCTGGGGTCGAGTTC+AGG - chr2.2:131838-131857 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 130603 131888 130603 ID=MS.gene067503
chr2.2 mRNA 130603 131888 130603 ID=MS.gene067503.t1;Parent=MS.gene067503
chr2.2 exon 130603 131025 130603 ID=MS.gene067503.t1.exon1;Parent=MS.gene067503.t1
chr2.2 CDS 130603 131025 130603 ID=cds.MS.gene067503.t1;Parent=MS.gene067503.t1
chr2.2 exon 131112 131214 131112 ID=MS.gene067503.t1.exon2;Parent=MS.gene067503.t1
chr2.2 CDS 131112 131214 131112 ID=cds.MS.gene067503.t1;Parent=MS.gene067503.t1
chr2.2 exon 131363 131475 131363 ID=MS.gene067503.t1.exon3;Parent=MS.gene067503.t1
chr2.2 CDS 131363 131475 131363 ID=cds.MS.gene067503.t1;Parent=MS.gene067503.t1
chr2.2 exon 131796 131888 131796 ID=MS.gene067503.t1.exon4;Parent=MS.gene067503.t1
chr2.2 CDS 131796 131888 131796 ID=cds.MS.gene067503.t1;Parent=MS.gene067503.t1
Gene Sequence

>MS.gene067503

ATGCAATTAGCTTCAAACACCGACAACCAAGATTCTTCTTCTTCAGAAACCCAACCCATATTGAATCACCTCTGTGAAATTATTCCTATTTCTGCCACGTCTGACAATCATGATATAGAGAATGAGTCTTCTCGTCTTGTTGTTGTAAATGCTGATCACCCACAATGCCGGATATGCCTTGATCTTGGAGGAGAAGACTTAATTGCCCCCTGCCATTGCAAAGGTACCCAAAAGTATGTCCACAGATCATGTCTCGATAACTGGAGGTCTACCAAGGAGGGCTTTGCTTTTTCTCACTGTACAGAATGCAGAGCTGTCTTCATAATTCGACCAAATGTCCCTAAAGATCGATGGTGGTTGAGATTGAAATTTCAGTTTCTTGTTGCCAGAGATCATGCATTCATTTTCATCATTGTTCAACTCGTATGTATATGTATCTATCCTCTATGTATTTCATTCAGAGAATATGTCTGTTAATTTCTTTTCCTTTTCCTTTTCTAATTGCACAGGTTGTTGCTTTCTTGGGAGTGCTTATTTATAAATTCTATGGAGATGAACTTAGAGAAATGTTTGGTTATGAAGAACATCCATACGGATTTTACACAATGGCTGGTATTCCCATTTATTCACCACTCTCAAATTCATGCCCAATGTTTGTTTGCAGCTTTTCCACTCATTTCTGACTTTTTCGTAAATTCAATGTGTAACAACCAACTTATTACATGCAATGGAAACTTGATAATTTTGCTTTGTTTTGCAGTTCTCGCCATTATTTTGGTGGGTTTGCTCTATGGCTTCTTTATAGCAATAATATGTGGGCAAAGAATCAATGAACGCCACTACCATGTTCTTGCCAAACAAGAATTGACAAAGGTCTGCTATGTAATAGTAATAAATGCTTTCAAATTACTTTGACTTACAATCCAATCCACATAAAAGTGAAGCATGTTACTCAAAACTAGTAATATGCTTGCTGCAAAACACGTCTTTGGTCATAAGATATACTTGCTGCAAAACACATCTTTGGTCATAAGATATGCAATTTCGGGAAAACAATCATTTAACTACCCGTTCTTGTATTGTATTGTTTAAGGATTATAATTGATTCTGAGTCATATAAGGACTATATTCCTTTTTTATAAAAATTTAAGGTATTCAACTCTTCACTCTGCTGTTTACTTTTTTGACGTCAGGAGTATGTGGTAGAAGATCGAGAACATGTAAAGGATGTGCCTGAACTCGACCCCAGCCATGTGACAGAACTAAGGATGTTGGGCCTTTACTAG
Protein sequence

>MS.gene067503.t1

MQLASNTDNQDSSSSETQPILNHLCEIIPISATSDNHDIENESSRLVVVNADHPQCRICLDLGGEDLIAPCHCKGTQKYVHRSCLDNWRSTKEGFAFSHCTECRAVFIIRPNVPKDRWWLRLKFQFLVARDHAFIFIIVQLVVAFLGVLIYKFYGDELREMFGYEEHPYGFYTMAVLAIILVGLLYGFFIAIICGQRINERHYHVLAKQELTKEYVVEDREHVKDVPELDPSHVTELRMLGLY