AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene004572

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene004572.t1 MTR_8g040560 64.179 134 48 0 99 232 744 877 4.20e-52 181
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene004572.t1 AT3G12280 58.209 134 52 3 99 232 735 864 9.73e-42 151
MS.gene004572.t1 AT3G12280 58.209 134 52 3 99 232 735 864 9.74e-42 151

Find 46 sgRNAs with CRISPR-Local

Find 100 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCTGTAGAGCCACTGCTTT+TGG 0.167941 2.2:+52331838 MS.gene004572:CDS
TGTTGGGTGAAGTCAGAATT+AGG 0.300929 2.2:+52331399 MS.gene004572:CDS
TTGGGAGCAGTCAGAATAAA+TGG 0.315321 2.2:+52330610 MS.gene004572:CDS
GCTCGGAACATTGAGTTAAA+TGG 0.362997 2.2:-52331083 None:intergenic
GCATGCCAGGACTCAGTATC+TGG 0.374643 2.2:+52331755 MS.gene004572:CDS
TTTCTCCTAGATCATTATGT+TGG 0.375290 2.2:+52331382 MS.gene004572:intron
CGTATTTGTTGATTGGTCAT+TGG 0.390654 2.2:+52331733 MS.gene004572:CDS
TTGATAGCGTATTTGTTGAT+TGG 0.394006 2.2:+52331726 MS.gene004572:CDS
TTCATAGTGAATTTGTTGAT+TGG 0.400565 2.2:+52330930 MS.gene004572:CDS
TCAGTATCTGGTAAAACAAT+AGG 0.407377 2.2:+52331767 MS.gene004572:CDS
GGCCATTGGCACGCATGGAC+TGG 0.408428 2.2:+52330951 MS.gene004572:CDS
TTCTCCTAGATCATTATGTT+GGG 0.426785 2.2:+52331383 MS.gene004572:intron
GGAGCGTGGTTGAAATGCTT+GGG 0.443007 2.2:+52331420 MS.gene004572:CDS
CTGTGGTTGCATTCTATAGC+TGG 0.451262 2.2:-52330891 None:intergenic
AGGAGCGTGGTTGAAATGCT+TGG 0.453033 2.2:+52331419 MS.gene004572:CDS
TCTGTCGATGAAGAATTATC+TGG 0.461758 2.2:-52331481 None:intergenic
GCACGCATGGACTGGCCATA+TGG 0.467219 2.2:+52330959 MS.gene004572:CDS
GTTTCCTAGATCATTATGTT+GGG 0.473365 2.2:+52330592 None:intergenic
TGATTGGTCATTGGCATGCC+AGG 0.482497 2.2:+52331742 MS.gene004572:CDS
TTATAACCTCCTTAAAAGTC+AGG 0.483868 2.2:-52331664 None:intergenic
CTATAATCTCTCGATAAGTT+AGG 0.506862 2.2:-52330868 None:intergenic
GGCCAGTCCATGCGTGCCAA+TGG 0.508439 2.2:-52330953 None:intergenic
AGAATTATCTCACAAGATAG+AGG 0.512835 2.2:+52330648 MS.gene004572:CDS
TTGGGTTATCTCAGCAGATA+AGG 0.519446 2.2:+52331438 MS.gene004572:CDS
TGATTGGCCATTGGCACGCA+TGG 0.524304 2.2:+52330946 MS.gene004572:CDS
CTATGCATGTGTCTCTCCAA+TGG 0.533378 2.2:+52331170 MS.gene004572:CDS
TATGCATGTGTCTCTCCAAT+GGG 0.533482 2.2:+52331171 MS.gene004572:CDS
ACCTCCTTAAAAGTCAGGCT+CGG 0.541985 2.2:-52331659 None:intergenic
TGGGTTATCTCAGCAGATAA+GGG 0.545719 2.2:+52331439 MS.gene004572:CDS
CAAAAGCAGTGGCTCTACAG+AGG 0.551471 2.2:-52331837 None:intergenic
TGAATTTGTTGATTGGCCAT+TGG 0.561366 2.2:+52330937 MS.gene004572:CDS
AAGCCTTTCTGTTATGTCTG+TGG 0.562011 2.2:+52331128 MS.gene004572:CDS
CTTCCACAGACATAACAGAA+AGG 0.576860 2.2:-52331131 None:intergenic
TTTGGAACTTGGCGTTGAAG+TGG 0.581032 2.2:+52331856 MS.gene004572:CDS
AAAAGCAGTGGCTCTACAGA+GGG 0.599947 2.2:-52331836 None:intergenic
AGTACCTCGGATGATCCCAT+TGG 0.608676 2.2:-52331186 None:intergenic
TTGCTTCTGTGCAGTCACAA+AGG 0.625881 2.2:+52331547 MS.gene004572:CDS
CTCTCCAATGGGATCATCCG+AGG 0.629524 2.2:+52331182 MS.gene004572:CDS
AGCAGTCAGAATAAATGGCA+TGG 0.631825 2.2:+52330615 MS.gene004572:CDS
AAAACTCGTGGGTTGCATTG+CGG 0.634698 2.2:-52331704 None:intergenic
ACGCCAAGTTCCAAAAGCAG+TGG 0.646767 2.2:-52331848 None:intergenic
AGAAGCAACACACAATGATG+TGG 0.674691 2.2:-52331532 None:intergenic
CAATGATGTGGTCAATATGA+CGG 0.678181 2.2:-52331520 None:intergenic
TGAAGTCAGAATTAGGAGCG+TGG 0.693278 2.2:+52331406 MS.gene004572:CDS
AAAACTGATGGTGGGCACTG+TGG 0.743278 2.2:-52330908 None:intergenic
AGAGACACATGCATAGTGTG+TGG 0.766106 2.2:-52331163 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATAGATAATTTTATGTCAA+AGG + chr2.2:52331335-52331354 MS.gene004572:intron 15.0%
!! AATTAGGTCAATATGAAAAT+CGG - chr2.2:52330740-52330759 None:intergenic 20.0%
!! CTATAAAAAGAATGAGAAAA+CGG - chr2.2:52330841-52330860 None:intergenic 20.0%
!! TTGTTTAAATTGAGAAACTT+GGG + chr2.2:52331573-52331592 MS.gene004572:intron 20.0%
!! TTTGTTTAAATTGAGAAACT+TGG + chr2.2:52331572-52331591 MS.gene004572:intron 20.0%
!!! CTTGTGAAAGTTAATATTTT+AGG - chr2.2:52331111-52331130 None:intergenic 20.0%
! AATTCACTATGAAAAACTGA+TGG - chr2.2:52330923-52330942 None:intergenic 25.0%
! ACCAACTAGAAATAGTATAT+GGG - chr2.2:52331251-52331270 None:intergenic 25.0%
! ATACTAAAAACATAGTACCT+CGG - chr2.2:52331202-52331221 None:intergenic 25.0%
!! TATGTCAAAGGTTTACATTT+TGG + chr2.2:52331347-52331366 MS.gene004572:intron 25.0%
!!! GTGAAAGTTAATATTTTAGG+AGG - chr2.2:52331108-52331127 None:intergenic 25.0%
!!! TCAGTTTTAGTAATTTGAGA+GGG + chr2.2:52330799-52330818 MS.gene004572:intron 25.0%
!!! TTCAGTTTTAGTAATTTGAG+AGG + chr2.2:52330798-52330817 MS.gene004572:intron 25.0%
!!! TTCATAGTGAATTTGTTGAT+TGG + chr2.2:52330930-52330949 MS.gene004572:CDS 25.0%
AAAGAATAGGATGAGAAAAC+GGG - chr2.2:52331623-52331642 None:intergenic 30.0%
AGAATTATCTCACAAGATAG+AGG + chr2.2:52330648-52330667 MS.gene004572:CDS 30.0%
CAATTGAAAGTAACTTAGCT+AGG - chr2.2:52330999-52331018 None:intergenic 30.0%
CACCAACTAGAAATAGTATA+TGG - chr2.2:52331252-52331271 None:intergenic 30.0%
CTATAATCTCTCGATAAGTT+AGG - chr2.2:52330871-52330890 None:intergenic 30.0%
GAAAGAATAGGATGAGAAAA+CGG - chr2.2:52331624-52331643 None:intergenic 30.0%
GGAAGCAACACAAAATAATT+AGG - chr2.2:52330756-52330775 None:intergenic 30.0%
TCAGTATCTGGTAAAACAAT+AGG + chr2.2:52331767-52331786 MS.gene004572:CDS 30.0%
TGAAATCTGCAAGAAAGAAT+AGG - chr2.2:52331636-52331655 None:intergenic 30.0%
TGAGTTAAATGGTCTGTAAA+TGG - chr2.2:52331075-52331094 None:intergenic 30.0%
TTATAACCTCCTTAAAAGTC+AGG - chr2.2:52331667-52331686 None:intergenic 30.0%
TTCTCCTAGATCATTATGTT+GGG + chr2.2:52331383-52331402 MS.gene004572:intron 30.0%
TTTCTCCTAGATCATTATGT+TGG + chr2.2:52331382-52331401 MS.gene004572:intron 30.0%
! CTCATTCTTTTTATAGTGCA+GGG + chr2.2:52330845-52330864 MS.gene004572:intron 30.0%
! TCTCATTCTTTTTATAGTGC+AGG + chr2.2:52330844-52330863 MS.gene004572:intron 30.0%
!! AGTTAATATTTTAGGAGGCT+CGG - chr2.2:52331103-52331122 None:intergenic 30.0%
!! TTGATAGCGTATTTGTTGAT+TGG + chr2.2:52331726-52331745 MS.gene004572:CDS 30.0%
!!! ATTATTTTGTGTTGCTTCCA+TGG + chr2.2:52330757-52330776 MS.gene004572:intron 30.0%
!!! GTTTTTAGTATGTCTTTCCT+TGG + chr2.2:52331211-52331230 MS.gene004572:intron 30.0%
AATACGCTATCAAAAACTCG+TGG - chr2.2:52331719-52331738 None:intergenic 35.0%
ACAAGATAGAGGTGAATGTA+GGG + chr2.2:52330659-52330678 MS.gene004572:intron 35.0%
ATACGCTATCAAAAACTCGT+GGG - chr2.2:52331718-52331737 None:intergenic 35.0%
ATGAAAATCGGAGAAGAGAT+GGG - chr2.2:52330728-52330747 None:intergenic 35.0%
CAATGATGTGGTCAATATGA+CGG - chr2.2:52331523-52331542 None:intergenic 35.0%
CACTATGAAAAACTGATGGT+GGG - chr2.2:52330919-52330938 None:intergenic 35.0%
GCAAATGAACAAGTACCATA+TGG - chr2.2:52330977-52330996 None:intergenic 35.0%
TATGAAAATCGGAGAAGAGA+TGG - chr2.2:52330729-52330748 None:intergenic 35.0%
TCACTATGAAAAACTGATGG+TGG - chr2.2:52330920-52330939 None:intergenic 35.0%
TCTGTCGATGAAGAATTATC+TGG - chr2.2:52331484-52331503 None:intergenic 35.0%
TTCACCCAACATAATGATCT+AGG - chr2.2:52331390-52331409 None:intergenic 35.0%
! CGTATTTGTTGATTGGTCAT+TGG + chr2.2:52331733-52331752 MS.gene004572:CDS 35.0%
!! GCCCATATACTATTTCTAGT+TGG + chr2.2:52331247-52331266 MS.gene004572:intron 35.0%
!! TGAATTTGTTGATTGGCCAT+TGG + chr2.2:52330937-52330956 MS.gene004572:CDS 35.0%
AAATGGAGCACACAAGTCAA+TGG - chr2.2:52331058-52331077 None:intergenic 40.0%
AAGCCTTTCTGTTATGTCTG+TGG + chr2.2:52331128-52331147 MS.gene004572:CDS 40.0%
AGAAGCAACACACAATGATG+TGG - chr2.2:52331535-52331554 None:intergenic 40.0%
AGCAGTCAGAATAAATGGCA+TGG + chr2.2:52330615-52330634 MS.gene004572:CDS 40.0%
CAAGATAGAGGTGAATGTAG+GGG + chr2.2:52330660-52330679 MS.gene004572:intron 40.0%
CACAAGATAGAGGTGAATGT+AGG + chr2.2:52330658-52330677 MS.gene004572:intron 40.0%
CTTCCACAGACATAACAGAA+AGG - chr2.2:52331134-52331153 None:intergenic 40.0%
CTTGCATAGAAATGGAAGTC+AGG - chr2.2:52331026-52331045 None:intergenic 40.0%
GCTCGGAACATTGAGTTAAA+TGG - chr2.2:52331086-52331105 None:intergenic 40.0%
GGGCAAAATGAAAAAGTCCA+AGG - chr2.2:52331231-52331250 None:intergenic 40.0%
TATGCATGTGTCTCTCCAAT+GGG + chr2.2:52331171-52331190 MS.gene004572:CDS 40.0%
TGAAAATCGGAGAAGAGATG+GGG - chr2.2:52330727-52330746 None:intergenic 40.0%
TGGGTTATCTCAGCAGATAA+GGG + chr2.2:52331439-52331458 MS.gene004572:CDS 40.0%
TGTTGGGTGAAGTCAGAATT+AGG + chr2.2:52331399-52331418 MS.gene004572:CDS 40.0%
TTGCAGGACTTGCATAGAAA+TGG - chr2.2:52331034-52331053 None:intergenic 40.0%
TTGGGAGCAGTCAGAATAAA+TGG + chr2.2:52330610-52330629 MS.gene004572:CDS 40.0%
TTGGGTTATCTCAGCAGATA+AGG + chr2.2:52331438-52331457 MS.gene004572:CDS 40.0%
! AAAACCGAGCCTGACTTTTA+AGG + chr2.2:52331655-52331674 MS.gene004572:CDS 40.0%
! TTTTACCAGATACTGAGTCC+TGG - chr2.2:52331763-52331782 None:intergenic 40.0%
ACCTCCTTAAAAGTCAGGCT+CGG - chr2.2:52331662-52331681 None:intergenic 45.0%
AGAGACACATGCATAGTGTG+TGG - chr2.2:52331166-52331185 None:intergenic 45.0%
CTATGCATGTGTCTCTCCAA+TGG + chr2.2:52331170-52331189 MS.gene004572:CDS 45.0%
CTGTGGTTGCATTCTATAGC+TGG - chr2.2:52330894-52330913 None:intergenic 45.0%
GAGAAACCTTTGCAACTCCA+TGG - chr2.2:52330777-52330796 None:intergenic 45.0%
GTTGGTGCAAAACACTCAAC+TGG + chr2.2:52331265-52331284 MS.gene004572:intron 45.0%
TGAAGTCAGAATTAGGAGCG+TGG + chr2.2:52331406-52331425 MS.gene004572:CDS 45.0%
TTGCTTCCATGGAGTTGCAA+AGG + chr2.2:52330768-52330787 MS.gene004572:intron 45.0%
TTGCTTCTGTGCAGTCACAA+AGG + chr2.2:52331547-52331566 MS.gene004572:CDS 45.0%
! AAAACTCGTGGGTTGCATTG+CGG - chr2.2:52331707-52331726 None:intergenic 45.0%
! AAAAGCAGTGGCTCTACAGA+GGG - chr2.2:52331839-52331858 None:intergenic 45.0%
! ACACTCAACTGGCATTTTCC+TGG + chr2.2:52331276-52331295 MS.gene004572:intron 45.0%
! TTTGGAACTTGGCGTTGAAG+TGG + chr2.2:52331856-52331875 MS.gene004572:CDS 45.0%
!! CACACAAGTCAATGGATTGC+AGG - chr2.2:52331050-52331069 None:intergenic 45.0%
ACGCCAAGTTCCAAAAGCAG+TGG - chr2.2:52331851-52331870 None:intergenic 50.0%
AGAGATGGGGCTGTTGAGTT+AGG - chr2.2:52330714-52330733 None:intergenic 50.0%
AGTACCTCGGATGATCCCAT+TGG - chr2.2:52331189-52331208 None:intergenic 50.0%
GCTGTTGAGTTAGGATTCGC+TGG - chr2.2:52330705-52330724 None:intergenic 50.0%
GGAGCGTGGTTGAAATGCTT+GGG + chr2.2:52331420-52331439 MS.gene004572:CDS 50.0%
! AGGAGCGTGGTTGAAATGCT+TGG + chr2.2:52331419-52331438 MS.gene004572:CDS 50.0%
! CAAAAGCAGTGGCTCTACAG+AGG - chr2.2:52331840-52331859 None:intergenic 50.0%
! CCTCGTGTACTTCTTTTGCC+AGG - chr2.2:52331297-52331316 None:intergenic 50.0%
! CCTGGCAAAAGAAGTACACG+AGG + chr2.2:52331294-52331313 MS.gene004572:intron 50.0%
! CTCTGTAGAGCCACTGCTTT+TGG + chr2.2:52331838-52331857 MS.gene004572:CDS 50.0%
! TGATTGGTCATTGGCATGCC+AGG + chr2.2:52331742-52331761 MS.gene004572:CDS 50.0%
!! AAAACTGATGGTGGGCACTG+TGG - chr2.2:52330911-52330930 None:intergenic 50.0%
!! ACCGAGCCTGACTTTTAAGG+AGG + chr2.2:52331658-52331677 MS.gene004572:CDS 50.0%
!!! GAGCCACTGCTTTTGGAACT+TGG + chr2.2:52331845-52331864 MS.gene004572:CDS 50.0%
CTCTCCAATGGGATCATCCG+AGG + chr2.2:52331182-52331201 MS.gene004572:CDS 55.0%
GCATGCCAGGACTCAGTATC+TGG + chr2.2:52331755-52331774 MS.gene004572:CDS 55.0%
! TGATTGGCCATTGGCACGCA+TGG + chr2.2:52330946-52330965 MS.gene004572:CDS 55.0%
!! GCACGCATGGACTGGCCATA+TGG + chr2.2:52330959-52330978 MS.gene004572:CDS 60.0%
GGCCAGTCCATGCGTGCCAA+TGG - chr2.2:52330956-52330975 None:intergenic 65.0%
GGCCATTGGCACGCATGGAC+TGG + chr2.2:52330951-52330970 MS.gene004572:CDS 65.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 52330607 52331889 52330607 ID=MS.gene004572
chr2.2 mRNA 52330607 52331889 52330607 ID=MS.gene004572.t1;Parent=MS.gene004572
chr2.2 exon 52330607 52330669 52330607 ID=MS.gene004572.t1.exon1;Parent=MS.gene004572.t1
chr2.2 CDS 52330607 52330669 52330607 ID=cds.MS.gene004572.t1;Parent=MS.gene004572.t1
chr2.2 exon 52330866 52330980 52330866 ID=MS.gene004572.t1.exon2;Parent=MS.gene004572.t1
chr2.2 CDS 52330866 52330980 52330866 ID=cds.MS.gene004572.t1;Parent=MS.gene004572.t1
chr2.2 exon 52331082 52331203 52331082 ID=MS.gene004572.t1.exon3;Parent=MS.gene004572.t1
chr2.2 CDS 52331082 52331203 52331082 ID=cds.MS.gene004572.t1;Parent=MS.gene004572.t1
chr2.2 exon 52331392 52331568 52331392 ID=MS.gene004572.t1.exon4;Parent=MS.gene004572.t1
chr2.2 CDS 52331392 52331568 52331392 ID=cds.MS.gene004572.t1;Parent=MS.gene004572.t1
chr2.2 exon 52331650 52331889 52331650 ID=MS.gene004572.t1.exon5;Parent=MS.gene004572.t1
chr2.2 CDS 52331650 52331889 52331650 ID=cds.MS.gene004572.t1;Parent=MS.gene004572.t1
Gene Sequence

>MS.gene004572

ATGTTGGGAGCAGTCAGAATAAATGGCATGGCTGAAAAGCTAGAATTATCTCACAAGATAGAGGTGAATGTAGGGGAGAATGTATACTATATTTTCCAGCGAATCCTAACTCAACAGCCCCATCTCTTCTCCGATTTTCATATTGACCTAATTATTTTGTGTTGCTTCCATGGAGTTGCAAAGGTTTCTCTTTCAGTTTTAGTAATTTGAGAGGGTAATGTTCTACAGTTGCCGTTTTCTCATTCTTTTTATAGTGCAGGGCCTAACTTATCGAGAGATTATAGCCAGCTATAGAATGCAACCACAGTGCCCACCATCAGTTTTTCATAGTGAATTTGTTGATTGGCCATTGGCACGCATGGACTGGCCATATGGTACTTGTTCATTTGCCTAGCTAAGTTACTTTCAATTGTTTTCCTGACTTCCATTTCTATGCAAGTCCTGCAATCCATTGACTTGTGTGCTCCATTTACAGACCATTTAACTCAATGTTCCGAGCCTCCTAAAATATTAACTTTCACAAGCCTTTCTGTTATGTCTGTGGAAGAAGTGTCTGCCACACACTATGCATGTGTCTCTCCAATGGGATCATCCGAGGTACTATGTTTTTAGTATGTCTTTCCTTGGACTTTTTCATTTTGCCCATATACTATTTCTAGTTGGTGCAAAACACTCAACTGGCATTTTCCTGGCAAAAGAAGTACACGAGGCTGTGACTCTCGTGCGCTTATAGATAATTTTATGTCAAAGGTTTACATTTTGGTTGCATTTCTTATTTCTCCTAGATCATTATGTTGGGTGAAGTCAGAATTAGGAGCGTGGTTGAAATGCTTGGGTTATCTCAGCAGATAAGGGAGAATGTATACAGTCTGTTCCAGATAATTCTTCATCGACAGACATCTCTCTTCTTCAACCGTCATATTGACCACATCATTGTGTGTTGCTTCTGTGCAGTCACAAAGGTTTTTGTTTAAATTGAGAAACTTGGGAGTATAAGTTTATGTGCTTCAATTCCCGTTTTCTCATCCTATTCTTTCTTGCAGATTTCAAAACCGAGCCTGACTTTTAAGGAGGTTATAAGCATCTATAAGAAGCAACCGCAATGCAACCCACGAGTTTTTGATAGCGTATTTGTTGATTGGTCATTGGCATGCCAGGACTCAGTATCTGGTAAAACAATAGGAAATGAGCATCTCGACATTATTACATTCTGCAATGATATATTTGTTCCCTCTGTAGAGCCACTGCTTTTGGAACTTGGCGTTGAAGTGGAGAAGCTGTGA
Protein sequence

>MS.gene004572.t1

MLGAVRINGMAEKLELSHKIEGLTYREIIASYRMQPQCPPSVFHSEFVDWPLARMDWPYDHLTQCSEPPKILTFTSLSVMSVEEVSATHYACVSPMGSSEIIMLGEVRIRSVVEMLGLSQQIRENVYSLFQIILHRQTSLFFNRHIDHIIVCCFCAVTKISKPSLTFKEVISIYKKQPQCNPRVFDSVFVDWSLACQDSVSGKTIGNEHLDIITFCNDIFVPSVEPLLLELGVEVEKL