AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene73844

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene73844.t1 MTR_4g079580 91.034 145 12 1 1 145 1 144 1.10e-89 267
MS.gene73844.t1 MTR_4g079580 96.629 89 3 0 136 224 247 335 2.76e-45 154
MS.gene73844.t1 MTR_2g090960 68.504 127 37 2 1 125 3 128 1.26e-53 175
MS.gene73844.t1 MTR_2g090960 56.627 83 33 3 138 217 239 321 8.92e-21 89.0
MS.gene73844.t1 MTR_8g463380 83.908 87 14 0 3 89 34 120 9.72e-47 160
MS.gene73844.t1 MTR_2g078200 79.762 84 17 0 6 89 3 86 7.94e-45 151
MS.gene73844.t1 MTR_7g015010 59.740 77 31 0 17 93 51 127 2.85e-25 101
MS.gene73844.t1 MTR_6g015350 61.250 80 28 1 17 96 43 119 9.10e-23 94.7
MS.gene73844.t1 MTR_4g109660 58.824 68 28 0 17 84 50 117 1.51e-20 88.2
MS.gene73844.t1 MTR_3g026050 46.392 97 45 2 17 107 51 146 4.53e-20 87.8
MS.gene73844.t1 MTR_6g017055 48.148 81 41 1 3 83 107 186 2.51e-18 83.2
MS.gene73844.t1 MTR_1g103380 55.000 60 27 0 23 82 201 260 5.54e-17 79.3
MS.gene73844.t1 MTR_4g111935 46.250 80 42 1 3 82 113 191 1.24e-15 75.1
MS.gene73844.t1 MTR_7g018500 53.448 58 27 0 25 82 122 179 2.92e-15 73.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene73844.t1 AT3G15030 84.706 85 13 0 5 89 27 111 3.64e-47 160
MS.gene73844.t1 AT3G15030 84.706 85 13 0 5 89 27 111 3.64e-47 160
MS.gene73844.t1 AT3G15030 84.706 85 13 0 5 89 27 111 3.64e-47 160
MS.gene73844.t1 AT3G15030 84.706 85 13 0 5 89 27 111 3.64e-47 160
MS.gene73844.t1 AT1G53230 81.176 85 16 0 5 89 31 115 9.29e-45 154
MS.gene73844.t1 AT1G53230 81.176 85 16 0 5 89 31 115 9.29e-45 154
MS.gene73844.t1 AT2G31070 88.312 77 9 0 5 81 11 87 1.51e-44 152
MS.gene73844.t1 AT4G18390 59.184 98 29 3 17 109 36 127 3.35e-27 107
MS.gene73844.t1 AT4G18390 59.184 98 29 3 17 109 36 127 3.35e-27 107
MS.gene73844.t1 AT1G30210 66.176 68 23 0 17 84 44 111 2.24e-23 96.3
MS.gene73844.t1 AT1G30210 66.176 68 23 0 17 84 44 111 2.24e-23 96.3
MS.gene73844.t1 AT3G02150 63.768 69 25 0 17 85 68 136 1.28e-22 93.2
MS.gene73844.t1 AT3G02150 63.768 69 25 0 17 85 68 136 1.99e-22 94.0
MS.gene73844.t1 AT5G60970 53.012 83 37 1 17 99 57 137 1.10e-20 89.4
MS.gene73844.t1 AT5G08070 51.220 82 37 1 17 95 27 108 1.56e-20 87.0
MS.gene73844.t1 AT5G08070 51.220 82 37 1 17 95 27 108 1.56e-20 87.0
MS.gene73844.t1 AT1G68800 53.846 65 30 0 19 83 108 172 2.28e-19 85.5
MS.gene73844.t1 AT1G68800 53.846 65 30 0 19 83 108 172 2.39e-19 85.5
MS.gene73844.t1 AT1G67260 50.000 66 33 0 18 83 82 147 9.62e-18 80.9
MS.gene73844.t1 AT1G67260 50.000 66 33 0 18 83 82 147 9.62e-18 80.9
MS.gene73844.t1 AT1G67260 50.000 66 33 0 18 83 82 147 1.05e-17 80.9
MS.gene73844.t1 AT3G18550 50.769 65 32 0 18 82 143 207 3.28e-15 74.3
MS.gene73844.t1 AT3G18550 50.769 65 32 0 18 82 143 207 3.28e-15 74.3
MS.gene73844.t1 AT3G18550 54.098 61 28 0 22 82 147 207 3.35e-15 74.3
MS.gene73844.t1 AT3G18550 50.769 65 32 0 18 82 143 207 3.51e-15 73.9

Find 50 sgRNAs with CRISPR-Local

Find 82 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTCATCAAGCTTCAATCTT+TGG 0.193207 4.2:+30591345 MS.gene73844:CDS
TGTCCACCTTGAACTGTATC+AGG 0.337666 4.2:-30591408 None:intergenic
TTCGACTGAAGGGCCTCATT+TGG 0.352467 4.2:-30591243 None:intergenic
AGGAGAAGAAGAAGGTCTAT+TGG 0.357996 4.2:-30591451 None:intergenic
GAAGTAGGGATGAGGAGTAC+TGG 0.386702 4.2:+30590466 None:intergenic
TGCATTCCTGATACAGTTCA+AGG 0.398078 4.2:+30591402 MS.gene73844:CDS
AGCCAATCCACTGCTTTGCT+TGG 0.398100 4.2:-30590661 None:intergenic
GGAGAGATAGTTCAGGTAGA+AGG 0.398765 4.2:+30590493 MS.gene73844:CDS
TAGAAGGAGGACACATAGTT+CGG 0.402620 4.2:+30590509 MS.gene73844:CDS
GGAAGCAGGTTTGTTTCTGA+TGG 0.414475 4.2:+30591366 MS.gene73844:CDS
TTTGTTTCTGATGGATTAGC+AGG 0.421645 4.2:+30591375 MS.gene73844:CDS
AACTTTGCTCAGTTGTGGTT+AGG 0.425546 4.2:-30591471 None:intergenic
AAGCTTCAATCTTTGGAAGC+AGG 0.461093 4.2:+30591352 MS.gene73844:CDS
TGGAGGAGGAGAGATAGTTC+AGG 0.462988 4.2:+30590486 MS.gene73844:CDS
CAAAAGGTCCTCGTGATCGC+AGG 0.468784 4.2:+30590572 MS.gene73844:CDS
GGAGAAACATCAGAATCTAA+TGG 0.478617 4.2:+30590817 MS.gene73844:CDS
AGAAGGAGGACACATAGTTC+GGG 0.484476 4.2:+30590510 MS.gene73844:CDS
TTTCGCATTCTGTTAGTACA+TGG 0.488530 4.2:+30591268 MS.gene73844:CDS
AGCAAGGTTTACACATCAAA+AGG 0.489089 4.2:+30590556 MS.gene73844:CDS
AACTCAAGTGGAATGGTTGT+TGG 0.490485 4.2:+30590796 MS.gene73844:CDS
CTTCAGAGGTTCATCATCAC+AGG 0.503181 4.2:+30591313 MS.gene73844:CDS
AAGCTCCGCGAGCTTGTCAA+TGG 0.510986 4.2:-30590704 None:intergenic
GGGATGAGGAGTACTGGAGG+AGG 0.516880 4.2:+30590472 None:intergenic
TCCTATGGATTCTTCTTCAG+AGG 0.520790 4.2:+30591299 MS.gene73844:CDS
GACCAAGCAAAGCAGTGGAT+TGG 0.524360 4.2:+30590659 MS.gene73844:CDS
CTTCCTCCATGGCATCCAAT+CGG 0.535397 4.2:+30590724 MS.gene73844:CDS
TAGAAAACTTTGCTCAGTTG+TGG 0.537314 4.2:-30591476 None:intergenic
TACATGGAATGAGATTCCTA+TGG 0.537407 4.2:+30591284 MS.gene73844:CDS
AAAGTAGTTGCAAACTCAAG+TGG 0.543287 4.2:+30590784 MS.gene73844:CDS
AGACAATTGAGTGAGAATCA+AGG 0.556151 4.2:+30590859 MS.gene73844:CDS
GTAGGGATGAGGAGTACTGG+AGG 0.556752 4.2:+30590469 None:intergenic
AGCTCGCGGAGCTTCCTCCA+TGG 0.559593 4.2:+30590713 MS.gene73844:CDS
AGTTGCAAACTCAAGTGGAA+TGG 0.583308 4.2:+30590789 MS.gene73844:CDS
ACTTTCTGAACTTCTTCTAG+AGG 0.585901 4.2:-30590766 None:intergenic
TTCAGAATACTCTCCAAATG+AGG 0.589921 4.2:+30591230 MS.gene73844:CDS
ACAGTTCAAGGTGGACAAGA+GGG 0.596091 4.2:+30591414 MS.gene73844:CDS
AAAAGGTCCTCGTGATCGCA+GGG 0.597089 4.2:+30590573 MS.gene73844:CDS
TACAGTTCAAGGTGGACAAG+AGG 0.610010 4.2:+30591413 MS.gene73844:CDS
TGCTTGGTCTGTCATAGCCG+AGG 0.612632 4.2:-30590645 None:intergenic
TACGATGTTCAAGATCGCCT+CGG 0.620277 4.2:+30590628 MS.gene73844:CDS
AGTCGAACCCTGCGATCACG+AGG 0.621133 4.2:-30590580 None:intergenic
AGTATTCTGAACCTGAACCT+TGG 0.621967 4.2:-30591218 None:intergenic
GAGATAGTTCAGGTAGAAGG+AGG 0.622890 4.2:+30590496 MS.gene73844:CDS
TTGAACATCGTAGAATTCGA+TGG 0.627660 4.2:-30590617 None:intergenic
TGACAGACCAAGCAAAGCAG+TGG 0.629311 4.2:+30590654 MS.gene73844:CDS
TTGTGGTTAGGAGAAGAAGA+AGG 0.640804 4.2:-30591459 None:intergenic
TCGCCGATTGGATGCCATGG+AGG 0.652394 4.2:-30590727 None:intergenic
ACCTCTGAAGAAGAATCCAT+AGG 0.653923 4.2:-30591300 None:intergenic
GTCTTCCATTGACAAGCTCG+CGG 0.658985 4.2:+30590699 MS.gene73844:CDS
ATTCCTGATACAGTTCAAGG+TGG 0.774068 4.2:+30591405 MS.gene73844:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACTTTCTTTATATAATCAT+TGG - chr4.2:30591166-30591185 None:intergenic 15.0%
!! AATGATTATATAAAGAAAGT+TGG + chr4.2:30591165-30591184 MS.gene73844:intron 15.0%
!! AATATCATAGAATTGAGAAT+TGG + chr4.2:30591127-30591146 MS.gene73844:intron 20.0%
!! AATTCTCAATTCTATGATAT+TGG - chr4.2:30591128-30591147 None:intergenic 20.0%
! GTGAAATGAAAGTTGAATTA+TGG - chr4.2:30590888-30590907 None:intergenic 25.0%
! TATAAAGAAAGTTGGATTCA+TGG + chr4.2:30591173-30591192 MS.gene73844:intron 25.0%
!! ATTGGTTCTCAAAAAAAGTT+TGG - chr4.2:30591110-30591129 None:intergenic 25.0%
!!! AAAAAGTTTGGTTTTGGTTT+TGG - chr4.2:30591098-30591117 None:intergenic 25.0%
!!! TCTCAAAAAAAGTTTGGTTT+TGG - chr4.2:30591104-30591123 None:intergenic 25.0%
!! GGTTTTCATTTGAAGTTTCA+TGG - chr4.2:30591077-30591096 None:intergenic 30.0%
AAAGTAGTTGCAAACTCAAG+TGG + chr4.2:30590784-30590803 MS.gene73844:CDS 35.0%
AATGCGAAAAATTCGACTGA+AGG - chr4.2:30591257-30591276 None:intergenic 35.0%
ACTTTCTGAACTTCTTCTAG+AGG - chr4.2:30590769-30590788 None:intergenic 35.0%
AGACAATTGAGTGAGAATCA+AGG + chr4.2:30590859-30590878 MS.gene73844:CDS 35.0%
AGCAAGGTTTACACATCAAA+AGG + chr4.2:30590556-30590575 MS.gene73844:CDS 35.0%
ATCACAATGGTTTCATTCCA+TGG + chr4.2:30591028-30591047 MS.gene73844:intron 35.0%
ATGCGAAAAATTCGACTGAA+GGG - chr4.2:30591256-30591275 None:intergenic 35.0%
GAATGAAACCATTGTGATCT+TGG - chr4.2:30591026-30591045 None:intergenic 35.0%
GGAGAAACATCAGAATCTAA+TGG + chr4.2:30590817-30590836 MS.gene73844:CDS 35.0%
GGATCAGTTTCAACATTATG+TGG - chr4.2:30590910-30590929 None:intergenic 35.0%
GTTCATCAAGCTTCAATCTT+TGG + chr4.2:30591345-30591364 MS.gene73844:CDS 35.0%
TAAAAAAGATCGTCACAGCA+AGG + chr4.2:30590540-30590559 MS.gene73844:CDS 35.0%
TACATGGAATGAGATTCCTA+TGG + chr4.2:30591284-30591303 MS.gene73844:CDS 35.0%
TTCAGAATACTCTCCAAATG+AGG + chr4.2:30591230-30591249 MS.gene73844:CDS 35.0%
TTGAACATCGTAGAATTCGA+TGG - chr4.2:30590620-30590639 None:intergenic 35.0%
TTTCGCATTCTGTTAGTACA+TGG + chr4.2:30591268-30591287 MS.gene73844:CDS 35.0%
! GTAGTTGGAAAGAAAGGTAT+AGG - chr4.2:30590931-30590950 None:intergenic 35.0%
!! AGGGTAGTTCTGAAAATTGA+TGG - chr4.2:30590971-30590990 None:intergenic 35.0%
!! TTTGTTTCTGATGGATTAGC+AGG + chr4.2:30591375-30591394 MS.gene73844:CDS 35.0%
!!! GTAAACTCACAGCCATTTTT+AGG + chr4.2:30591195-30591214 MS.gene73844:intron 35.0%
AACTCAAGTGGAATGGTTGT+TGG + chr4.2:30590796-30590815 MS.gene73844:CDS 40.0%
AGGAGAAGAAGAAGGTCTAT+TGG - chr4.2:30591454-30591473 None:intergenic 40.0%
AGTATTCTGAACCTGAACCT+TGG - chr4.2:30591221-30591240 None:intergenic 40.0%
AGTTGCAAACTCAAGTGGAA+TGG + chr4.2:30590789-30590808 MS.gene73844:CDS 40.0%
ATTCCTGATACAGTTCAAGG+TGG + chr4.2:30591405-30591424 MS.gene73844:CDS 40.0%
CATTCCTTCCAAGATCACAA+TGG + chr4.2:30591015-30591034 MS.gene73844:intron 40.0%
GAAACCATTGTGATCTTGGA+AGG - chr4.2:30591022-30591041 None:intergenic 40.0%
GAAGAAGTAGAAGAGGTAGT+TGG - chr4.2:30590946-30590965 None:intergenic 40.0%
GAAGAGGTAGTTGGAAAGAA+AGG - chr4.2:30590937-30590956 None:intergenic 40.0%
GATGGATGAAGAAGTAGAAG+AGG - chr4.2:30590953-30590972 None:intergenic 40.0%
TAGAAGGAGGACACATAGTT+CGG + chr4.2:30590509-30590528 MS.gene73844:CDS 40.0%
TCCTATGGATTCTTCTTCAG+AGG + chr4.2:30591299-30591318 MS.gene73844:CDS 40.0%
TGCATTCCTGATACAGTTCA+AGG + chr4.2:30591402-30591421 MS.gene73844:CDS 40.0%
TTGTGGTTAGGAGAAGAAGA+AGG - chr4.2:30591462-30591481 None:intergenic 40.0%
! AACTACCCTTCTGAAAACCT+TGG + chr4.2:30590982-30591001 MS.gene73844:intron 40.0%
! AAGCTTCAATCTTTGGAAGC+AGG + chr4.2:30591352-30591371 MS.gene73844:CDS 40.0%
! ACCTCTGAAGAAGAATCCAT+AGG - chr4.2:30591303-30591322 None:intergenic 40.0%
!! AGAGTTTGATTTTCGCCGAT+TGG - chr4.2:30590742-30590761 None:intergenic 40.0%
!! CATACTTGTTGTGATTGCCA+TGG - chr4.2:30591048-30591067 None:intergenic 40.0%
!!! GCTGTGACGATCTTTTTTAC+TGG - chr4.2:30590539-30590558 None:intergenic 40.0%
!!! GTGACGATCTTTTTTACTGG+TGG - chr4.2:30590536-30590555 None:intergenic 40.0%
ACAGTTCAAGGTGGACAAGA+GGG + chr4.2:30591414-30591433 MS.gene73844:CDS 45.0%
AGAAGGAGGACACATAGTTC+GGG + chr4.2:30590510-30590529 MS.gene73844:CDS 45.0%
CCTGAACCTTGGCCTAAAAA+TGG - chr4.2:30591210-30591229 None:intergenic 45.0%
CTTCAGAGGTTCATCATCAC+AGG + chr4.2:30591313-30591332 MS.gene73844:CDS 45.0%
CTTGGAAGGAATGAAGAGAG+AGG - chr4.2:30591008-30591027 None:intergenic 45.0%
GAGATAGTTCAGGTAGAAGG+AGG + chr4.2:30590496-30590515 MS.gene73844:CDS 45.0%
GGAGAGATAGTTCAGGTAGA+AGG + chr4.2:30590493-30590512 MS.gene73844:CDS 45.0%
TACAGTTCAAGGTGGACAAG+AGG + chr4.2:30591413-30591432 MS.gene73844:CDS 45.0%
TACGATGTTCAAGATCGCCT+CGG + chr4.2:30590628-30590647 MS.gene73844:CDS 45.0%
TGTCCACCTTGAACTGTATC+AGG - chr4.2:30591411-30591430 None:intergenic 45.0%
! AGAGGCCAAGGTTTTCAGAA+GGG - chr4.2:30590990-30591009 None:intergenic 45.0%
!! CCATTTTTAGGCCAAGGTTC+AGG + chr4.2:30591207-30591226 MS.gene73844:intron 45.0%
!! GGAAGCAGGTTTGTTTCTGA+TGG + chr4.2:30591366-30591385 MS.gene73844:CDS 45.0%
!!! TCACAGCCATTTTTAGGCCA+AGG + chr4.2:30591201-30591220 MS.gene73844:intron 45.0%
AAAAGGTCCTCGTGATCGCA+GGG + chr4.2:30590573-30590592 MS.gene73844:CDS 50.0%
AGCCAATCCACTGCTTTGCT+TGG - chr4.2:30590664-30590683 None:intergenic 50.0%
AGGAATGAAGAGAGAGGCCA+AGG - chr4.2:30591002-30591021 None:intergenic 50.0%
CTTCCTCCATGGCATCCAAT+CGG + chr4.2:30590724-30590743 MS.gene73844:CDS 50.0%
GACCAAGCAAAGCAGTGGAT+TGG + chr4.2:30590659-30590678 MS.gene73844:CDS 50.0%
GTCTTCCATTGACAAGCTCG+CGG + chr4.2:30590699-30590718 MS.gene73844:CDS 50.0%
TGACAGACCAAGCAAAGCAG+TGG + chr4.2:30590654-30590673 MS.gene73844:CDS 50.0%
TGGAGGAGGAGAGATAGTTC+AGG + chr4.2:30590486-30590505 MS.gene73844:CDS 50.0%
TTCGACTGAAGGGCCTCATT+TGG - chr4.2:30591246-30591265 None:intergenic 50.0%
! GAGAGGCCAAGGTTTTCAGA+AGG - chr4.2:30590991-30591010 None:intergenic 50.0%
!! TTTTCGCCGATTGGATGCCA+TGG - chr4.2:30590733-30590752 None:intergenic 50.0%
AAGCTCCGCGAGCTTGTCAA+TGG - chr4.2:30590707-30590726 None:intergenic 55.0%
CAAAAGGTCCTCGTGATCGC+AGG + chr4.2:30590572-30590591 MS.gene73844:CDS 55.0%
TGCTTGGTCTGTCATAGCCG+AGG - chr4.2:30590648-30590667 None:intergenic 55.0%
AGTCGAACCCTGCGATCACG+AGG - chr4.2:30590583-30590602 None:intergenic 60.0%
! TCGCCGATTGGATGCCATGG+AGG - chr4.2:30590730-30590749 None:intergenic 60.0%
AGCTCGCGGAGCTTCCTCCA+TGG + chr4.2:30590713-30590732 MS.gene73844:CDS 65.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 30590475 30591485 30590475 ID=MS.gene73844
chr4.2 mRNA 30590475 30591485 30590475 ID=MS.gene73844.t1;Parent=MS.gene73844
chr4.2 exon 30590475 30590880 30590475 ID=MS.gene73844.t1.exon1;Parent=MS.gene73844.t1
chr4.2 CDS 30590475 30590880 30590475 ID=cds.MS.gene73844.t1;Parent=MS.gene73844.t1
chr4.2 exon 30591217 30591485 30591217 ID=MS.gene73844.t1.exon2;Parent=MS.gene73844.t1
chr4.2 CDS 30591217 30591485 30591217 ID=cds.MS.gene73844.t1;Parent=MS.gene73844.t1
Gene Sequence

>MS.gene73844

ATGAGGAGTACTGGAGGAGGAGAGATAGTTCAGGTAGAAGGAGGACACATAGTTCGGGCCACCAGTAAAAAAGATCGTCACAGCAAGGTTTACACATCAAAAGGTCCTCGTGATCGCAGGGTTCGACTCTCAGCACACACAGCCATCGAATTCTACGATGTTCAAGATCGCCTCGGCTATGACAGACCAAGCAAAGCAGTGGATTGGCTCATCAAGAAAGCAAAGTCTTCCATTGACAAGCTCGCGGAGCTTCCTCCATGGCATCCAATCGGCGAAAATCAAACTCTGAAACCTCTAGAAGAAGTTCAGAAAGTAGTTGCAAACTCAAGTGGAATGGTTGTTGGAGAAACATCAGAATCTAATGGTTACAATTTTCATTTTTTAAGACAATTGAGTGAGAATCAAGGTAACCATAATTCAACTTTCATTTCACCACATAATGTTGAAACTGATCCTATACCTTTCTTTCCAACTACCTCTTCTACTTCTTCATCCATCAATTTTCAGAACTACCCTTCTGAAAACCTTGGCCTCTCTCTTCATTCCTTCCAAGATCACAATGGTTTCATTCCATGGCAATCACAACAAGTATGTGAAAACCATGAAACTTCAAATGAAAACCAAAACCAAAACCAAACTTTTTTTGAGAACCAATATCATAGAATTGAGAATTGGAACAATGAAACAACCAATGATTATATAAAGAAAGTTGGATTCATGGTAAACTCACAGCCATTTTTAGGCCAAGGTTCAGGTTCAGAATACTCTCCAAATGAGGCCCTTCAGTCGAATTTTTCGCATTCTGTTAGTACATGGAATGAGATTCCTATGGATTCTTCTTCAGAGGTTCATCATCACAGGTCTCAACAAGTTCATCAAGCTTCAATCTTTGGAAGCAGGTTTGTTTCTGATGGATTAGCAGGTTTCTGCATTCCTGATACAGTTCAAGGTGGACAAGAGGGTCATAGAGTTTCTTCCAATAGACCTTCTTCTTCTCCTAACCACAACTGA
Protein sequence

>MS.gene73844.t1

MRSTGGGEIVQVEGGHIVRATSKKDRHSKVYTSKGPRDRRVRLSAHTAIEFYDVQDRLGYDRPSKAVDWLIKKAKSSIDKLAELPPWHPIGENQTLKPLEEVQKVVANSSGMVVGETSESNGYNFHFLRQLSENQGQGSGSEYSPNEALQSNFSHSVSTWNEIPMDSSSEVHHHRSQQVHQASIFGSRFVSDGLAGFCIPDTVQGGQEGHRVSSNRPSSSPNHN