AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene73093


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene73093.t1 MTR_3g053540 100.000 101 0 0 1 101 1 101 1.20e-72 211
MS.gene73093.t1 MTR_3g053520 98.020 101 2 0 1 101 1 101 2.23e-71 207
MS.gene73093.t1 MTR_8g010480 59.459 74 30 0 21 94 165 238 2.35e-27 102
MS.gene73093.t1 MTR_8g010480 61.972 71 27 0 23 93 244 314 1.33e-22 89.4
MS.gene73093.t1 MTR_8g010480 55.128 78 31 1 20 93 83 160 9.56e-22 87.0
MS.gene73093.t1 MTR_8g010480 43.678 87 46 2 15 100 2 86 5.60e-16 71.6
MS.gene73093.t1 MTR_8g010490 46.237 93 49 1 3 95 10 101 1.60e-26 97.1
MS.gene73093.t1 MTR_8g010490 52.632 76 36 0 23 98 108 183 7.15e-22 85.1
MS.gene73093.t1 MTR_8g085340 38.710 93 56 1 10 101 14 106 2.91e-18 74.3
MS.gene73093.t1 MTR_8g085320 33.333 99 65 1 1 98 1 99 8.80e-18 72.4
MS.gene73093.t1 MTR_3g053640 50.000 70 35 0 20 89 82 151 1.19e-15 70.9
MS.gene73093.t1 MTR_3g053640 51.562 64 31 0 29 92 15 78 1.71e-15 70.5
MS.gene73093.t1 MTR_0007s0030 64.103 39 14 0 48 86 1 39 1.53e-14 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene73093.t1 AT4G26840 90.000 90 9 0 7 96 2 91 3.86e-57 171
MS.gene73093.t1 AT5G55160 90.426 94 6 2 5 98 2 92 4.53e-57 171
MS.gene73093.t1 AT5G55160 79.439 107 6 3 5 98 2 105 1.64e-53 163
MS.gene73093.t1 AT5G55856 49.438 89 45 0 10 98 2 90 1.38e-26 94.4
MS.gene73093.t1 AT5G55170 51.685 89 41 1 12 98 5 93 1.03e-25 92.8
MS.gene73093.t1 AT5G55855 47.674 86 45 0 13 98 5 90 2.13e-24 89.0
MS.gene73093.t1 AT5G48710 46.591 88 46 1 12 98 17 104 9.67e-23 85.1
MS.gene73093.t1 AT5G48710 46.591 88 46 1 12 98 17 104 9.67e-23 85.1
MS.gene73093.t1 AT5G48710 46.591 88 46 1 12 98 17 104 9.67e-23 85.1
MS.gene73093.t1 AT5G55170 48.315 89 40 2 12 98 5 89 2.83e-21 81.3
MS.gene73093.t1 AT2G32765 37.778 90 55 1 10 98 14 103 1.98e-20 79.0
MS.gene73093.t1 AT5G55170 49.296 71 34 1 12 80 5 75 7.39e-18 72.4
MS.gene73093.t1 AT5G48700 42.222 90 50 2 11 98 19 108 9.23e-18 72.4
MS.gene73093.t1 AT5G48710 39.437 71 42 1 12 81 17 87 5.73e-14 62.4

Find 28 sgRNAs with CRISPR-Local

Find 99 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATGTGAGCACCACCTGCTT+CGG 0.338312 3.4:+50464258 None:intergenic
TTCTTGTCTTCCTCGGTGTT+GGG 0.340524 3.4:+50464283 None:intergenic
ATGTGAGCACCACCTGCTTC+GGG 0.344186 3.4:+50464259 None:intergenic
CTTCTTGTCTTCCTCGGTGT+TGG 0.351501 3.4:+50464282 None:intergenic
TCGTAAACACAAACCTCATC+TGG 0.362733 3.4:+50462783 None:intergenic
ATGGGAATGAAGTGTTCTTC+AGG 0.382849 3.4:-50462923 MS.gene73093:CDS
GAACCTGGCCTTTGACTTTG+AGG 0.404598 3.4:+50464233 None:intergenic
TTCGGGCTTCTTGTCTTCCT+CGG 0.415650 3.4:+50464276 None:intergenic
GAAGACAAGAAGCCCGAAGC+AGG 0.445397 3.4:-50464271 MS.gene73093:CDS
CGGAAACTGAAGATGTCGTC+AGG 0.500483 3.4:-50464316 None:intergenic
TTGCAGCTGGAAATGGAAGA+TGG 0.502872 3.4:-50462679 MS.gene73093:intron
CGTAAACACAAACCTCATCT+GGG 0.526755 3.4:+50462784 None:intergenic
CATCTGGGGTCTGCTCTGCA+CGG 0.560850 3.4:+50462799 None:intergenic
TGCAGCTGGAAATGGAAGAT+GGG 0.572615 3.4:-50462678 MS.gene73093:intron
GATGCCATGCTTCATCAGAC+AGG 0.575586 3.4:-50462646 MS.gene73093:CDS
CACATCAACCTCAAAGTCAA+AGG 0.580464 3.4:-50464241 MS.gene73093:CDS
ACCTCCTGTCTGATGAAGCA+TGG 0.580486 3.4:+50462642 None:intergenic
CCCATCAAATAGAAAAGCAA+TGG 0.583133 3.4:+50462830 None:intergenic
CAACCTCAAAGTCAAAGGCC+AGG 0.584554 3.4:-50464236 MS.gene73093:intron
AAGTGTTCTTCAGGATCAAG+AGG 0.592447 3.4:-50462914 MS.gene73093:CDS
GCCATGCTTCATCAGACAGG+AGG 0.614785 3.4:-50462643 MS.gene73093:CDS
GACAAGAAGCCCGAAGCAGG+TGG 0.627526 3.4:-50464268 MS.gene73093:CDS
TGCAGAGCAGACCCCAGATG+AGG 0.644394 3.4:-50462796 MS.gene73093:intron
TTACTGTGATCGTCAGTCTG+TGG 0.670146 3.4:-50462862 MS.gene73093:CDS
CTGGGGTCTGCTCTGCACGG+AGG 0.678982 3.4:+50462802 None:intergenic
GCAGCTGGAAATGGAAGATG+GGG 0.689173 3.4:-50462677 MS.gene73093:intron
GTAAACACAAACCTCATCTG+GGG 0.707969 3.4:+50462785 None:intergenic
TGCAGCTGCTCCCAACACCG+AGG 0.715016 3.4:-50464293 MS.gene73093:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAATACAATAAAAATGTT+TGG + chr3.4:50463586-50463605 None:intergenic 10.0%
!!! ATTTTATATGTTTAGATTAA+CGG - chr3.4:50462931-50462950 MS.gene73093:intron 10.0%
!! ATTTGATAAAAAATACACTT+TGG + chr3.4:50463525-50463544 None:intergenic 15.0%
!! TGAATTATATACAATTTGTA+AGG - chr3.4:50463097-50463116 MS.gene73093:intron 15.0%
!!! TTTTATATGTTTAGATTAAC+GGG - chr3.4:50462932-50462951 MS.gene73093:intron 15.0%
!! AATAAAAATGTTTGGATTGA+CGG + chr3.4:50463578-50463597 None:intergenic 20.0%
!! ACAAGATAACAATATCATAT+AGG + chr3.4:50463777-50463796 None:intergenic 20.0%
!! TTTATATGTTTAGATTAACG+GGG - chr3.4:50462933-50462952 MS.gene73093:intron 20.0%
!!! ATTCGATCGTTAATTTTTTA+GGG - chr3.4:50462785-50462804 MS.gene73093:intron 20.0%
!!! ATTTCTGTTATTAGTTTCAT+TGG - chr3.4:50463658-50463677 MS.gene73093:intron 20.0%
!!! ATTTTAATATGTTCTAGGAT+GGG - chr3.4:50463993-50464012 MS.gene73093:intron 20.0%
!!! GTATTTTTTATCAAATCACT+TGG - chr3.4:50463529-50463548 MS.gene73093:intron 20.0%
!!! TATTCGATCGTTAATTTTTT+AGG - chr3.4:50462784-50462803 MS.gene73093:intron 20.0%
!!! TTTGTAAGGAATTTTTGTTT+TGG - chr3.4:50463111-50463130 MS.gene73093:intron 20.0%
!!! TTTTTATTGAATTTGTGTGT+TGG - chr3.4:50463602-50463621 MS.gene73093:intron 20.0%
! TGCATTCATGTAAAACATAT+TGG - chr3.4:50463818-50463837 MS.gene73093:intron 25.0%
! TTTCTGTTATCAGTTTCATT+AGG - chr3.4:50463285-50463304 MS.gene73093:intron 25.0%
!! GAGTTATGTATGCTAATTTT+TGG - chr3.4:50463969-50463988 MS.gene73093:intron 25.0%
!! TATATTTGAAACTCTTGACA+TGG - chr3.4:50463877-50463896 MS.gene73093:intron 25.0%
!! TTTGTTTAAAACGTTGGTTA+GGG - chr3.4:50463249-50463268 MS.gene73093:intron 25.0%
!!! CATTTTAATATGTTCTAGGA+TGG - chr3.4:50463992-50464011 MS.gene73093:intron 25.0%
!!! GTATATGATTTGGTGAAAAT+AGG - chr3.4:50463414-50463433 MS.gene73093:intron 25.0%
!!! TTGGCATTTTAATATGTTCT+AGG - chr3.4:50463988-50464007 MS.gene73093:intron 25.0%
!!! TTTTTTTGAACAAGCCATAT+AGG + chr3.4:50463746-50463765 None:intergenic 25.0%
AACAATCACAAACACAACAA+AGG + chr3.4:50462821-50462840 None:intergenic 30.0%
AATCCAAACATAATTGAGAC+TGG - chr3.4:50463053-50463072 MS.gene73093:intron 30.0%
AATTATGTTTGGATTGACGA+TGG + chr3.4:50463048-50463067 None:intergenic 30.0%
ATCCAAAAAGTCCTAACATA+TGG + chr3.4:50463640-50463659 None:intergenic 30.0%
ATTCCAGTCTCAATTATGTT+TGG + chr3.4:50463059-50463078 None:intergenic 30.0%
CAAATATTGATGTTGCGTTA+TGG + chr3.4:50463205-50463224 None:intergenic 30.0%
GATAACAGAAACCCAAAAAA+AGG + chr3.4:50463276-50463295 None:intergenic 30.0%
TACGATATTGTTGAAGAACT+GGG - chr3.4:50463373-50463392 MS.gene73093:intron 30.0%
TAGTTCTTATCAGAATCACT+TGG - chr3.4:50463002-50463021 MS.gene73093:intron 30.0%
TGATTCTGATAAGAACTACA+CGG + chr3.4:50463000-50463019 None:intergenic 30.0%
! CTTTGTTTAAAACGTTGGTT+AGG - chr3.4:50463248-50463267 MS.gene73093:intron 30.0%
! GATTGTTTGTTGAAGAACTA+GGG - chr3.4:50462834-50462853 MS.gene73093:CDS 30.0%
! TACCATATGTTAGGACTTTT+TGG - chr3.4:50463635-50463654 MS.gene73093:intron 30.0%
! TGATTGTTTGTTGAAGAACT+AGG - chr3.4:50462833-50462852 MS.gene73093:CDS 30.0%
!! AAAATATGTTTTGTTGCAGC+TGG - chr3.4:50464242-50464261 MS.gene73093:CDS 30.0%
!! ACCAACGTTTTAAACAAAGT+TGG + chr3.4:50463247-50463266 None:intergenic 30.0%
!! CAACGTTTTAAACAAAGTTG+GGG + chr3.4:50463245-50463264 None:intergenic 30.0%
!! CCAACGTTTTAAACAAAGTT+GGG + chr3.4:50463246-50463265 None:intergenic 30.0%
!! CCATTGCTTTTCTATTTGAT+GGG - chr3.4:50464104-50464123 MS.gene73093:intron 30.0%
!! TGGAAATGATGCATTGATTT+CGG - chr3.4:50463131-50463150 MS.gene73093:intron 30.0%
AAAAATGTTTGGATTGACGG+TGG + chr3.4:50463575-50463594 None:intergenic 35.0%
AACAAAAACCCTAGAATCGA+AGG + chr3.4:50462738-50462757 None:intergenic 35.0%
ACGATATTGTTGAAGAACTG+GGG - chr3.4:50463374-50463393 MS.gene73093:intron 35.0%
ATATAGGAGACAAGTTAGAG+TGG + chr3.4:50463730-50463749 None:intergenic 35.0%
CCCATCAAATAGAAAAGCAA+TGG + chr3.4:50464107-50464126 None:intergenic 35.0%
CTGTTTGCATACCATATGTT+AGG - chr3.4:50463626-50463645 MS.gene73093:intron 35.0%
GTACGATATTGTTGAAGAAC+TGG - chr3.4:50463372-50463391 MS.gene73093:intron 35.0%
GTTCTTCAACAATATCGTAC+AGG + chr3.4:50463372-50463391 None:intergenic 35.0%
! ACTCTAACTTGTCTCCTATA+TGG - chr3.4:50463729-50463748 MS.gene73093:intron 35.0%
! CACACTAGGAGTATATGATT+TGG - chr3.4:50463404-50463423 MS.gene73093:intron 35.0%
! CCCAACTTTGTTTAAAACGT+TGG - chr3.4:50463243-50463262 MS.gene73093:intron 35.0%
!! GCCATTGCTTTTCTATTTGA+TGG - chr3.4:50464103-50464122 MS.gene73093:intron 35.0%
!!! TTGGTTAGGGTCCTTTTTTT+GGG - chr3.4:50463262-50463281 MS.gene73093:intron 35.0%
AAGTGTTCTTCAGGATCAAG+AGG - chr3.4:50464020-50464039 MS.gene73093:intron 40.0%
CACATCAACCTCAAAGTCAA+AGG - chr3.4:50462693-50462712 MS.gene73093:intron 40.0%
CGTAAACACAAACCTCATCT+GGG + chr3.4:50464153-50464172 None:intergenic 40.0%
GTAAACACAAACCTCATCTG+GGG + chr3.4:50464152-50464171 None:intergenic 40.0%
GTTTGGATTGACGATGGAAT+TGG + chr3.4:50463042-50463061 None:intergenic 40.0%
TCGTAAACACAAACCTCATC+TGG + chr3.4:50464154-50464173 None:intergenic 40.0%
TGTCTCTTCCTTCGATTCTA+GGG - chr3.4:50462727-50462746 MS.gene73093:intron 40.0%
TTGAAGAACTAGGGTTTCTC+TGG - chr3.4:50462843-50462862 MS.gene73093:CDS 40.0%
TTGTCTCTTCCTTCGATTCT+AGG - chr3.4:50462726-50462745 MS.gene73093:intron 40.0%
! AAAGTTCCGCAGTGATTTTG+TGG + chr3.4:50462963-50462982 None:intergenic 40.0%
! ATGGGAATGAAGTGTTCTTC+AGG - chr3.4:50464011-50464030 MS.gene73093:intron 40.0%
! TGATGTTGCGTTATGGATTG+CGG + chr3.4:50463198-50463217 None:intergenic 40.0%
!! TGTTTTGTTGCAGCTGGAAA+TGG - chr3.4:50464248-50464267 MS.gene73093:CDS 40.0%
!!! GTTGGTTAGGGTCCTTTTTT+TGG - chr3.4:50463261-50463280 MS.gene73093:intron 40.0%
AAGGAAGAGACAAACGAACC+TGG + chr3.4:50462719-50462738 None:intergenic 45.0%
ACTGGGGTTAATCTCACACT+AGG - chr3.4:50463390-50463409 MS.gene73093:intron 45.0%
CTGTGAGTTCGACAAACTCA+CGG - chr3.4:50463476-50463495 MS.gene73093:intron 45.0%
GGAGTTCCACAAAATCACTG+CGG - chr3.4:50462954-50462973 MS.gene73093:intron 45.0%
GTTTGGATTGACGGTGGAAT+TGG + chr3.4:50463569-50463588 None:intergenic 45.0%
TGCAGCTGGAAATGGAAGAT+GGG - chr3.4:50464256-50464275 MS.gene73093:CDS 45.0%
TTACTGTGATCGTCAGTCTG+TGG - chr3.4:50464072-50464091 MS.gene73093:intron 45.0%
TTGCAGCTGGAAATGGAAGA+TGG - chr3.4:50464255-50464274 MS.gene73093:CDS 45.0%
!! TTCTTGTCTTCCTCGGTGTT+GGG + chr3.4:50462654-50462673 None:intergenic 45.0%
ACAAAGTTGGGGCTGCGTTA+AGG + chr3.4:50463234-50463253 None:intergenic 50.0%
ACCTCCTGTCTGATGAAGCA+TGG + chr3.4:50464295-50464314 None:intergenic 50.0%
CAACCTCAAAGTCAAAGGCC+AGG - chr3.4:50462698-50462717 MS.gene73093:intron 50.0%
GATGCCATGCTTCATCAGAC+AGG - chr3.4:50464288-50464307 MS.gene73093:CDS 50.0%
GCAGCTGGAAATGGAAGATG+GGG - chr3.4:50464257-50464276 MS.gene73093:CDS 50.0%
TGAGTTCGACAAACTCACGG+TGG - chr3.4:50463479-50463498 MS.gene73093:intron 50.0%
TTCGGGCTTCTTGTCTTCCT+CGG + chr3.4:50462661-50462680 None:intergenic 50.0%
! CTTCTTGTCTTCCTCGGTGT+TGG + chr3.4:50462655-50462674 None:intergenic 50.0%
! GAACCTGGCCTTTGACTTTG+AGG + chr3.4:50462704-50462723 None:intergenic 50.0%
! GTTGCGTTATGGATTGCGGT+CGG + chr3.4:50463194-50463213 None:intergenic 50.0%
ATGTGAGCACCACCTGCTTC+GGG + chr3.4:50462678-50462697 None:intergenic 55.0%
GAAGACAAGAAGCCCGAAGC+AGG - chr3.4:50462663-50462682 MS.gene73093:CDS 55.0%
GATGTGAGCACCACCTGCTT+CGG + chr3.4:50462679-50462698 None:intergenic 55.0%
GCCATGCTTCATCAGACAGG+AGG - chr3.4:50464291-50464310 MS.gene73093:CDS 55.0%
GACAAGAAGCCCGAAGCAGG+TGG - chr3.4:50462666-50462685 MS.gene73093:CDS 60.0%
TGCAGAGCAGACCCCAGATG+AGG - chr3.4:50464138-50464157 MS.gene73093:intron 60.0%
! CATCTGGGGTCTGCTCTGCA+CGG + chr3.4:50464138-50464157 None:intergenic 60.0%
TGCAGCTGCTCCCAACACCG+AGG - chr3.4:50462641-50462660 MS.gene73093:CDS 65.0%
CTGGGGTCTGCTCTGCACGG+AGG + chr3.4:50464135-50464154 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 50462630 50464326 50462630 ID=MS.gene73093
chr3.4 mRNA 50462630 50464326 50462630 ID=MS.gene73093.t1;Parent=MS.gene73093
chr3.4 exon 50464237 50464326 50464237 ID=MS.gene73093.t1.exon1;Parent=MS.gene73093.t1
chr3.4 CDS 50464237 50464326 50464237 ID=cds.MS.gene73093.t1;Parent=MS.gene73093.t1
chr3.4 exon 50462797 50462946 50462797 ID=MS.gene73093.t1.exon2;Parent=MS.gene73093.t1
chr3.4 CDS 50462797 50462946 50462797 ID=cds.MS.gene73093.t1;Parent=MS.gene73093.t1
chr3.4 exon 50462630 50462695 50462630 ID=MS.gene73093.t1.exon3;Parent=MS.gene73093.t1
chr3.4 CDS 50462630 50462695 50462630 ID=cds.MS.gene73093.t1;Parent=MS.gene73093.t1
Gene Sequence

>MS.gene73093

ATGTCGTCAGGTGCAGCTGCTCCCAACACCGAGGAAGACAAGAAGCCCGAAGCAGGTGGTGCTCACATCAACCTCAAAGTCAAAGGCCAGGTTCGTTTGTCTCTTCCTTCGATTCTAGGGTTTTTGTTTTTTTATGAATCGTCTTATTCAAACGTATTCGATCGTTAATTTTTTAGGGTTTTTTTTTGCCTTTGTTGTGTTTGTGATTGTTTGTTGAAGAACTAGGGTTTCTCTGGTTTAATTTGATTGCTATTTGTGTTATATAGCATAAGTATGAAAAATTTTAAAAATAAAAAGAGAAATTTTATATGTTTAGATTAACGGGGAGTTCCACAAAATCACTGCGGAACTTTGATTTTGTGTAATTCCGTGTAGTTCTTATCAGAATCACTTGGTCACTGTGATTTTGCCAATTCCATCGTCAATCCAAACATAATTGAGACTGGAATTTATAGTGTTAATTTTATTGAATTATATACAATTTGTAAGGAATTTTTGTTTTGGAAATGATGCATTGATTTCGGTAAGATTTGTGCAATGTTATAATTAAATCACATCGCGCCGACCGCAATCCATAACGCAACATCAATATTTGCGAAATCCTTAACGCAGCCCCAACTTTGTTTAAAACGTTGGTTAGGGTCCTTTTTTTGGGTTTCTGTTATCAGTTTCATTAGGAAACTTTAGATGCTATGTATTAGTGTTCATTCTTCAGTTTATCGATCACTCTAACTTGTTTCCTGTACGATATTGTTGAAGAACTGGGGTTAATCTCACACTAGGAGTATATGATTTGGTGAAAATAGGATAATCACTAATGCTATTTTTTAAACATGTTTAAATTAACTGTGAGTTCGACAAACTCACGGTGGCACTTTGATTTAATGAAGTTCCAAAGTGTATTTTTTATCAAATCACTTGGTCACTGTGATTTTGCCAATTCCACCGTCAATCCAAACATTTTTATTGTATTTTTTATTGAATTTGTGTGTTGGACTGTTTGCATACCATATGTTAGGACTTTTTGGATTTCTGTTATTAGTTTCATTGGTAAACTTTAGATGCTATGTATTAGTGTTCATTCTTCAGTTTATCTACCACTCTAACTTGTCTCCTATATGGCTTGTTCAAAAAAAACATGTCTCCTATATGATATTGTTATCTTGTTCTTCGTTCGTTTCTTTATGTTGCATTCATGTAAAACATATTGGTCTAATCTTAAGTTATAACTTTTCAGAAATCGAAGTTATATTTGAAACTCTTGACATGGTTATAGTTTTCTATATTATTAGTCTTAGTTACTGTCAAAAGTTTTTAGTCATCATTGAAATTAGCATCAGAGTTATGTATGCTAATTTTTGGCATTTTAATATGTTCTAGGATGGGAATGAAGTGTTCTTCAGGATCAAGAGGAACACTCAACTGAAAAAGCTTATGAATGCTTACTGTGATCGTCAGTCTGTGGATTTCAATGCCATTGCTTTTCTATTTGATGGGCGTCGCCTCCGTGCAGAGCAGACCCCAGATGAGGTTTGTGTTTACGACATTTTTTCATCACTTTTTCTCTATCATAATGTTCAAATAAGTCTAACATTTGTGTTTTTATGACTTGAAAATATGTTTTGTTGCAGCTGGAAATGGAAGATGGGGACGAAATCGATGCCATGCTTCATCAGACAGGAGGTTCTGTTGTCTGA

Protein sequence

>MS.gene73093.t1

MSSGAAAPNTEEDKKPEAGGAHINLKVKGQDGNEVFFRIKRNTQLKKLMNAYCDRQSVDFNAIAFLFDGRRLRAEQTPDELEMEDGDEIDAMLHQTGGSVV