AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene052941

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene052941.t1 MTR_0206s0010 83.740 123 15 2 1 121 1 120 3.76e-60 181
MS.gene052941.t1 MTR_4g012950 83.740 123 15 2 1 121 1 120 7.17e-59 177
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene052941.t1 AT1G15230 42.405 158 52 4 1 122 1 155 5.65e-23 87.8

Find 37 sgRNAs with CRISPR-Local

Find 42 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCATCCTCGCCGGCCGGCTT+TGG 0.289427 4.1:+83464601 None:intergenic
GAGCCGGGAGCTTGTGTTGA+TGG 0.317537 4.1:-83464541 MS.gene052941:CDS
CAGCAAACCTGGTTGTTTCT+CGG 0.368726 4.1:+83464774 None:intergenic
TGTTGATGGGTTGCAAGGTT+TGG 0.372075 4.1:-83464527 MS.gene052941:CDS
TCGAAAATATTCACATCTTC+CGG 0.378538 4.1:-83464646 MS.gene052941:CDS
AATGCTTCGTGGATTGATTC+CGG 0.400340 4.1:+83464694 None:intergenic
ACATAGCCACCAACCAAGAT+AGG 0.434082 4.1:+83464442 None:intergenic
CGGCTTTGAGAAATGCTTCG+TGG 0.446691 4.1:+83464683 None:intergenic
GAAAGAGAAGAAACCTATCT+TGG 0.464765 4.1:-83464455 MS.gene052941:CDS
TTTCGATTTCACGGCGGCGG+CGG 0.471497 4.1:+83464663 None:intergenic
GAAAGATGATGTGAAGGAAA+AGG 0.485530 4.1:-83464503 MS.gene052941:CDS
CGAAGATCCTGCACTTCCAC+CGG 0.490722 4.1:-83464713 MS.gene052941:CDS
ATAATCTGCTGCAGCAAACC+TGG 0.498161 4.1:+83464763 None:intergenic
AGCCGGGAGCTTGTGTTGAT+GGG 0.502950 4.1:-83464540 MS.gene052941:CDS
TGAGCCGGAAAACGAGGAGC+CGG 0.504878 4.1:-83464557 MS.gene052941:CDS
ATTGATTCCGGTGGAAGTGC+AGG 0.512710 4.1:+83464706 None:intergenic
GAGCCGGAAAACGAGGAGCC+GGG 0.513089 4.1:-83464556 MS.gene052941:CDS
GCTTGTGTTGATGGGTTGCA+AGG 0.538167 4.1:-83464532 MS.gene052941:CDS
GAGAAGAAACCTATCTTGGT+TGG 0.545774 4.1:-83464451 MS.gene052941:CDS
CGATCCAAAGCCGGCCGGCG+AGG 0.558176 4.1:-83464605 MS.gene052941:CDS
GACATCTGAAGCATCCTCGC+CGG 0.571070 4.1:+83464591 None:intergenic
GTCGATGCAATCATCTTCGC+CGG 0.573460 4.1:+83464627 None:intergenic
TTTGGAGAAAGATGATGTGA+AGG 0.575030 4.1:-83464509 MS.gene052941:CDS
GAGTCCACCGAGAAACAACC+AGG 0.578103 4.1:-83464781 MS.gene052941:CDS
TTGCATCGACGATCCAAAGC+CGG 0.583740 4.1:-83464614 MS.gene052941:CDS
AACCCATCAACACAAGCTCC+CGG 0.588157 4.1:+83464538 None:intergenic
ATCGACGATCCAAAGCCGGC+CGG 0.592029 4.1:-83464610 MS.gene052941:CDS
TCTGAAGCATCCTCGCCGGC+CGG 0.595069 4.1:+83464595 None:intergenic
AAGAAACCTATCTTGGTTGG+TGG 0.604979 4.1:-83464448 MS.gene052941:CDS
GAGGATGCTTCAGATGTCGT+TGG 0.615781 4.1:-83464586 MS.gene052941:CDS
CAAACCTGGTTGTTTCTCGG+TGG 0.627408 4.1:+83464777 None:intergenic
TGTCGTTGGTGTGATTGAGC+CGG 0.633135 4.1:-83464572 MS.gene052941:CDS
GCTTCGTGGATTGATTCCGG+TGG 0.637305 4.1:+83464697 None:intergenic
TGTGATTGAGCCGGAAAACG+AGG 0.638081 4.1:-83464563 MS.gene052941:CDS
AGACCAGCGTCTTCTAGACG+CGG 0.719055 4.1:+83464736 None:intergenic
CCACCGCGTCTAGAAGACGC+TGG 0.721185 4.1:-83464739 MS.gene052941:CDS
CCAGCGTCTTCTAGACGCGG+TGG 0.725582 4.1:+83464739 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAGGAAAAAAGTGAAGAAA+AGG - chr4.1:83464737-83464756 MS.gene052941:CDS 25.0%
!! TGTGAATATTTTCGATTTCA+CGG + chr4.1:83464571-83464590 None:intergenic 25.0%
TCGAAAATATTCACATCTTC+CGG - chr4.1:83464576-83464595 MS.gene052941:CDS 30.0%
GAAAGAGAAGAAACCTATCT+TGG - chr4.1:83464767-83464786 MS.gene052941:CDS 35.0%
GAAAGATGATGTGAAGGAAA+AGG - chr4.1:83464719-83464738 MS.gene052941:CDS 35.0%
TTTGGAGAAAGATGATGTGA+AGG - chr4.1:83464713-83464732 MS.gene052941:CDS 35.0%
! GAATATTTTCGATTTCACGG+CGG + chr4.1:83464568-83464587 None:intergenic 35.0%
AAGAAACCTATCTTGGTTGG+TGG - chr4.1:83464774-83464793 MS.gene052941:CDS 40.0%
GAGAAGAAACCTATCTTGGT+TGG - chr4.1:83464771-83464790 MS.gene052941:CDS 40.0%
! AATGCTTCGTGGATTGATTC+CGG + chr4.1:83464531-83464550 None:intergenic 40.0%
ACATAGCCACCAACCAAGAT+AGG + chr4.1:83464783-83464802 None:intergenic 45.0%
ATAATCTGCTGCAGCAAACC+TGG + chr4.1:83464462-83464481 None:intergenic 45.0%
! TATTTTCGATTTCACGGCGG+CGG + chr4.1:83464565-83464584 None:intergenic 45.0%
!! CAGCAAACCTGGTTGTTTCT+CGG + chr4.1:83464451-83464470 None:intergenic 45.0%
!! TGTTGATGGGTTGCAAGGTT+TGG - chr4.1:83464695-83464714 MS.gene052941:CDS 45.0%
AACCCATCAACACAAGCTCC+CGG + chr4.1:83464687-83464706 None:intergenic 50.0%
GAGGATGCTTCAGATGTCGT+TGG - chr4.1:83464636-83464655 MS.gene052941:CDS 50.0%
GTCGATGCAATCATCTTCGC+CGG + chr4.1:83464598-83464617 None:intergenic 50.0%
TGTCGTTGGTGTGATTGAGC+CGG - chr4.1:83464650-83464669 MS.gene052941:CDS 50.0%
TGTGATTGAGCCGGAAAACG+AGG - chr4.1:83464659-83464678 MS.gene052941:CDS 50.0%
! ATTGATTCCGGTGGAAGTGC+AGG + chr4.1:83464519-83464538 None:intergenic 50.0%
! TTGCATCGACGATCCAAAGC+CGG - chr4.1:83464608-83464627 MS.gene052941:CDS 50.0%
!! CAAACCTGGTTGTTTCTCGG+TGG + chr4.1:83464448-83464467 None:intergenic 50.0%
!! CGGCTTTGAGAAATGCTTCG+TGG + chr4.1:83464542-83464561 None:intergenic 50.0%
!! GCTTGTGTTGATGGGTTGCA+AGG - chr4.1:83464690-83464709 MS.gene052941:CDS 50.0%
AGACCAGCGTCTTCTAGACG+CGG + chr4.1:83464489-83464508 None:intergenic 55.0%
CGAAGATCCTGCACTTCCAC+CGG - chr4.1:83464509-83464528 MS.gene052941:CDS 55.0%
GAGTCCACCGAGAAACAACC+AGG - chr4.1:83464441-83464460 MS.gene052941:CDS 55.0%
! AGCCGGGAGCTTGTGTTGAT+GGG - chr4.1:83464682-83464701 MS.gene052941:CDS 55.0%
! GACATCTGAAGCATCCTCGC+CGG + chr4.1:83464634-83464653 None:intergenic 55.0%
! GCTTCGTGGATTGATTCCGG+TGG + chr4.1:83464528-83464547 None:intergenic 55.0%
ATCGACGATCCAAAGCCGGC+CGG - chr4.1:83464612-83464631 MS.gene052941:CDS 60.0%
GAGCCGGGAGCTTGTGTTGA+TGG - chr4.1:83464681-83464700 MS.gene052941:CDS 60.0%
TGAGCCGGAAAACGAGGAGC+CGG - chr4.1:83464665-83464684 MS.gene052941:CDS 60.0%
TTTCGATTTCACGGCGGCGG+CGG + chr4.1:83464562-83464581 None:intergenic 60.0%
CCACCGCGTCTAGAAGACGC+TGG - chr4.1:83464483-83464502 MS.gene052941:CDS 65.0%
CCAGCGTCTTCTAGACGCGG+TGG + chr4.1:83464486-83464505 None:intergenic 65.0%
GAGCCGGAAAACGAGGAGCC+GGG - chr4.1:83464666-83464685 MS.gene052941:CDS 65.0%
! GCTCCCGGCTCCTCGTTTTC+CGG + chr4.1:83464672-83464691 None:intergenic 65.0%
! TCTGAAGCATCCTCGCCGGC+CGG + chr4.1:83464630-83464649 None:intergenic 65.0%
CGATCCAAAGCCGGCCGGCG+AGG - chr4.1:83464617-83464636 MS.gene052941:CDS 75.0%
! GCATCCTCGCCGGCCGGCTT+TGG + chr4.1:83464624-83464643 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 83464438 83464806 83464438 ID=MS.gene052941
chr4.1 mRNA 83464438 83464806 83464438 ID=MS.gene052941.t1;Parent=MS.gene052941
chr4.1 exon 83464438 83464806 83464438 ID=MS.gene052941.t1.exon1;Parent=MS.gene052941.t1
chr4.1 CDS 83464438 83464806 83464438 ID=cds.MS.gene052941.t1;Parent=MS.gene052941.t1
Gene Sequence

>MS.gene052941

ATGGAGTCCACCGAGAAACAACCAGGTTTGCTGCAGCAGATTATACCACCGCGTCTAGAAGACGCTGGTCTCGAAGATCCTGCACTTCCACCGGAATCAATCCACGAAGCATTTCTCAAAGCCGCCGCCGCCGTGAAATCGAAAATATTCACATCTTCCGGCGAAGATGATTGCATCGACGATCCAAAGCCGGCCGGCGAGGATGCTTCAGATGTCGTTGGTGTGATTGAGCCGGAAAACGAGGAGCCGGGAGCTTGTGTTGATGGGTTGCAAGGTTTGGAGAAAGATGATGTGAAGGAAAAGGAAAAAAGTGAAGAAAAGGAGAAGAAGAAAGAGAAGAAACCTATCTTGGTTGGTGGCTATGTTTGA
Protein sequence

>MS.gene052941.t1

MESTEKQPGLLQQIIPPRLEDAGLEDPALPPESIHEAFLKAAAAVKSKIFTSSGEDDCIDDPKPAGEDASDVVGVIEPENEEPGACVDGLQGLEKDDVKEKEKSEEKEKKKEKKPILVGGYV