AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene91276


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene91276.t1 MTR_2g084535 90.000 140 8 1 1 134 363 502 4.56e-87 262
MS.gene91276.t1 MTR_2g075300 64.567 127 45 0 1 127 348 474 2.41e-59 190
MS.gene91276.t1 MTR_7g105400 50.382 131 64 1 1 130 368 498 1.13e-41 144
MS.gene91276.t1 MTR_4g097590 50.781 128 62 1 1 127 391 518 1.82e-38 136
MS.gene91276.t1 MTR_7g105390 45.113 133 72 1 1 132 334 466 1.97e-34 124
MS.gene91276.t1 MTR_7g105390 45.113 133 72 1 1 132 368 500 3.05e-34 124
MS.gene91276.t1 MTR_2g078180 63.415 41 15 0 91 131 119 159 1.41e-11 58.9
MS.gene91276.t1 MTR_2g075270 46.154 52 27 1 76 127 32 82 2.65e-11 56.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene91276.t1 AT5G22860 53.333 135 62 1 1 134 365 499 2.40e-47 159
MS.gene91276.t1 AT2G24280 52.308 130 62 0 1 130 361 490 6.58e-44 150
MS.gene91276.t1 AT5G65760 46.154 130 69 1 1 129 374 503 9.49e-36 128
MS.gene91276.t1 AT5G22860 54.839 93 41 1 1 92 365 457 1.52e-30 114
MS.gene91276.t1 AT5G22860 57.333 75 31 1 1 74 365 439 6.47e-25 98.6
MS.gene91276.t1 AT5G22860 57.333 75 31 1 1 74 365 439 6.47e-25 98.6
MS.gene91276.t1 AT2G24280 55.405 74 33 0 1 74 361 434 5.21e-23 93.2

Find 30 sgRNAs with CRISPR-Local

Find 76 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATTGGATTACTACTTATTA+TGG 0.189882 2.3:-13469395 MS.gene91276:CDS
AAACGAGTTCTTCAAAAGTT+TGG 0.309801 2.3:-13468915 MS.gene91276:CDS
TATTGCAGGATCCCATTGTT+TGG 0.351682 2.3:-13468034 MS.gene91276:intron
GGCCAGTATTATATTGATCT+TGG 0.358230 2.3:-13467928 MS.gene91276:CDS
CGTTGTTCAATCAACCATCT+TGG 0.362655 2.3:+13467985 None:intergenic
GCTTACCCGGCACTACTATA+AGG 0.362908 2.3:+13468858 None:intergenic
CCGCAACAAGACTCTTTGAT+AGG 0.388564 2.3:+13468733 None:intergenic
GAAAGATGCAAGAAAGAATA+TGG 0.398219 2.3:-13469434 MS.gene91276:CDS
GTGTCTCACCTCGCCCTCAT+TGG 0.398503 2.3:-13469412 MS.gene91276:CDS
ACAAATCTCTTTAAGTCAAA+AGG 0.401588 2.3:+13469458 None:intergenic
CACCAAGATCAATATAATAC+TGG 0.419795 2.3:+13467926 None:intergenic
AAAGATCCTTATAGTAGTGC+CGG 0.462281 2.3:-13468864 MS.gene91276:CDS
ATGGTGATGCCTTTCGCTAT+AGG 0.480405 2.3:-13469506 MS.gene91276:CDS
ATTGATCTTGGTGCACTCCA+TGG 0.511982 2.3:-13467916 None:intergenic
AGATAGAATATCCAAACAAT+GGG 0.517359 2.3:+13468023 None:intergenic
GTTGCGGTCCATGCGATCAA+TGG 0.519229 2.3:-13468717 MS.gene91276:intron
AAGATAGAATATCCAAACAA+TGG 0.524080 2.3:+13468022 None:intergenic
GAGATTATTCAAGAGTGGAT+TGG 0.526156 2.3:-13467949 MS.gene91276:CDS
CTCTTTAAGTCAAAAGGAGA+AGG 0.546964 2.3:+13469464 None:intergenic
CAAAAGAAAGTGATCCAAGA+TGG 0.547883 2.3:-13467999 MS.gene91276:CDS
AAGATCCTTATAGTAGTGCC+GGG 0.557200 2.3:-13468863 MS.gene91276:intron
TGGATTACTACTTATTATGG+AGG 0.567337 2.3:-13469392 MS.gene91276:CDS
GATTGAACAACGAAATAAAG+AGG 0.581874 2.3:-13467974 MS.gene91276:CDS
AAGACATACCATTGATCGCA+TGG 0.584348 2.3:+13468709 None:intergenic
AGGTCGAGATTATTCAAGAG+TGG 0.591638 2.3:-13467954 MS.gene91276:CDS
AATAAGTAGTAATCCAATGA+GGG 0.598968 2.3:+13469399 None:intergenic
GTAGTAATCCAATGAGGGCG+AGG 0.600782 2.3:+13469404 None:intergenic
GTATCATTTCCTATAGCGAA+AGG 0.619045 2.3:+13469497 None:intergenic
TAATAAGTAGTAATCCAATG+AGG 0.619229 2.3:+13469398 None:intergenic
CCTATCAAAGAGTCTTGTTG+CGG 0.666760 2.3:-13468733 MS.gene91276:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTATATTTATAATAATTTTA+AGG + chr2.3:13469158-13469177 None:intergenic 0.0%
!! TTATGTATGTAAATTTATAA+TGG - chr2.3:13468946-13468965 MS.gene91276:intron 10.0%
!! AAAAAAAGACATTTAAATCA+AGG + chr2.3:13468380-13468399 None:intergenic 15.0%
!! AAATAATTTAGTGACTAAAT+TGG - chr2.3:13469289-13469308 MS.gene91276:intron 15.0%
!! ATCAGTTAAGTTAAAATTTA+TGG + chr2.3:13468865-13468884 None:intergenic 15.0%
!! TTTATACTACTAAAATATTG+TGG - chr2.3:13469219-13469238 MS.gene91276:intron 15.0%
!!! CAATTCAATTTTGAATTTTA+TGG + chr2.3:13468592-13468611 None:intergenic 15.0%
!!! GATTTAAATGTCTTTTTTTA+AGG - chr2.3:13468381-13468400 MS.gene91276:intron 15.0%
!!! GTCTTGTTATATATATATAA+GGG - chr2.3:13468765-13468784 MS.gene91276:intron 15.0%
!!! TCTTGTTATATATATATAAG+GGG - chr2.3:13468766-13468785 MS.gene91276:intron 15.0%
!!! TGTCTTGTTATATATATATA+AGG - chr2.3:13468764-13468783 MS.gene91276:intron 15.0%
!! AATTATTACATCAAAGAAAG+AGG - chr2.3:13468136-13468155 MS.gene91276:intron 20.0%
!! CAATGTTATAAAATATTGCA+GGG - chr2.3:13468657-13468676 MS.gene91276:intron 20.0%
!! TAGACAATCTAAATTAATGT+AGG + chr2.3:13468169-13468188 None:intergenic 20.0%
!!! ACAAGAAATTAATTTTGTTG+TGG - chr2.3:13468463-13468482 MS.gene91276:intron 20.0%
!!! TGTTTTTTCTTGATAAAGAA+AGG + chr2.3:13469064-13469083 None:intergenic 20.0%
! AAGATAGAATATCCAAACAA+TGG + chr2.3:13469404-13469423 None:intergenic 25.0%
! AATAAGTAGTAATCCAATGA+GGG + chr2.3:13468027-13468046 None:intergenic 25.0%
! AATTTAGTGACTAAATTGGA+GGG - chr2.3:13469293-13469312 MS.gene91276:intron 25.0%
! ACAAATCTCTTTAAGTCAAA+AGG + chr2.3:13467968-13467987 None:intergenic 25.0%
! AGATAGAATATCCAAACAAT+GGG + chr2.3:13469403-13469422 None:intergenic 25.0%
! ATACATAAATGAAGTTGTCA+GGG + chr2.3:13468934-13468953 None:intergenic 25.0%
! ATAGACATTAATTCTATTGC+AGG - chr2.3:13469375-13469394 MS.gene91276:intron 25.0%
! CATTGGATTACTACTTATTA+TGG - chr2.3:13468028-13468047 MS.gene91276:CDS 25.0%
! GCAATGTTATAAAATATTGC+AGG - chr2.3:13468656-13468675 MS.gene91276:intron 25.0%
! TAATAAGTAGTAATCCAATG+AGG + chr2.3:13468028-13468047 None:intergenic 25.0%
! TAATTTAGTGACTAAATTGG+AGG - chr2.3:13469292-13469311 MS.gene91276:intron 25.0%
! TATCTGTCATGTTCTATAAT+TGG + chr2.3:13469094-13469113 None:intergenic 25.0%
!! AATATTGTGGACTAAATTGA+TGG - chr2.3:13469232-13469251 MS.gene91276:intron 25.0%
!! AGAAAAAAGAAGTACAAACA+TGG + chr2.3:13468057-13468076 None:intergenic 25.0%
!! AGCAACATTATATTTTCGAA+TGG - chr2.3:13468532-13468551 MS.gene91276:intron 25.0%
!! GATGGATCACATATATTTTA+AGG - chr2.3:13469250-13469269 MS.gene91276:intron 25.0%
!!! AACACTTTTTACACTTTTGA+AGG + chr2.3:13468284-13468303 None:intergenic 25.0%
!!! ACACCTTAATGTTTTTATGT+GGG + chr2.3:13468805-13468824 None:intergenic 25.0%
!!! TACACCTTAATGTTTTTATG+TGG + chr2.3:13468806-13468825 None:intergenic 25.0%
!!! TTTTGACTTAAAGAGATTTG+TGG - chr2.3:13467967-13467986 MS.gene91276:CDS 25.0%
AAACGAGTTCTTCAAAAGTT+TGG - chr2.3:13468508-13468527 MS.gene91276:intron 30.0%
ACACCCACATAAAAACATTA+AGG - chr2.3:13468799-13468818 MS.gene91276:intron 30.0%
CACCAAGATCAATATAATAC+TGG + chr2.3:13469500-13469519 None:intergenic 30.0%
CATACATAAATGAAGTTGTC+AGG + chr2.3:13468935-13468954 None:intergenic 30.0%
GAAAGATGCAAGAAAGAATA+TGG - chr2.3:13467989-13468008 MS.gene91276:CDS 30.0%
GATTGAACAACGAAATAAAG+AGG - chr2.3:13469449-13469468 MS.gene91276:CDS 30.0%
TCTCAATAAAAAGAAGAGCT+AGG + chr2.3:13469034-13469053 None:intergenic 30.0%
TGGATTACTACTTATTATGG+AGG - chr2.3:13468031-13468050 MS.gene91276:intron 30.0%
!!! TTTGTTGTGGTTTTGACTAA+TGG - chr2.3:13468476-13468495 MS.gene91276:intron 30.0%
AAAGATCCTTATAGTAGTGC+CGG - chr2.3:13468559-13468578 MS.gene91276:intron 35.0%
AGCTAGGAAAAATAGAACGA+GGG + chr2.3:13469018-13469037 None:intergenic 35.0%
CAAAAGAAAGTGATCCAAGA+TGG - chr2.3:13469424-13469443 MS.gene91276:CDS 35.0%
CTCTTTAAGTCAAAAGGAGA+AGG + chr2.3:13467962-13467981 None:intergenic 35.0%
GAGATTATTCAAGAGTGGAT+TGG - chr2.3:13469474-13469493 MS.gene91276:CDS 35.0%
GGCCAGTATTATATTGATCT+TGG - chr2.3:13469495-13469514 MS.gene91276:CDS 35.0%
GTATCATTTCCTATAGCGAA+AGG + chr2.3:13467929-13467948 None:intergenic 35.0%
TGGACAAAGAAATACACTAG+TGG + chr2.3:13468845-13468864 None:intergenic 35.0%
! TGAATTTTATGGTGCTTACC+CGG + chr2.3:13468581-13468600 None:intergenic 35.0%
AAGACATACCATTGATCGCA+TGG + chr2.3:13468717-13468736 None:intergenic 40.0%
AAGATCCTTATAGTAGTGCC+GGG - chr2.3:13468560-13468579 MS.gene91276:intron 40.0%
AGGTCGAGATTATTCAAGAG+TGG - chr2.3:13469469-13469488 MS.gene91276:CDS 40.0%
CGTTGTTCAATCAACCATCT+TGG + chr2.3:13469441-13469460 None:intergenic 40.0%
GAGCTAGGAAAAATAGAACG+AGG + chr2.3:13469019-13469038 None:intergenic 40.0%
TATTGCAGGATCCCATTGTT+TGG - chr2.3:13469389-13469408 MS.gene91276:CDS 40.0%
!! CCTATCAAAGAGTCTTGTTG+CGG - chr2.3:13468690-13468709 MS.gene91276:intron 40.0%
!! TGTTCTGAGGACAATGGTTA+AGG + chr2.3:13468338-13468357 None:intergenic 40.0%
!!! TTGTGGTTTTGACTAATGGC+AGG - chr2.3:13468480-13468499 MS.gene91276:intron 40.0%
CCGCAACAAGACTCTTTGAT+AGG + chr2.3:13468693-13468712 None:intergenic 45.0%
TGCTCTCACAGTAGTGGTTA+AGG - chr2.3:13468216-13468235 MS.gene91276:intron 45.0%
TTAACCAGTGTCGTGTTCTG+AGG + chr2.3:13468351-13468370 None:intergenic 45.0%
! ATGGTGATGCCTTTCGCTAT+AGG - chr2.3:13467917-13467936 MS.gene91276:CDS 45.0%
!!! TTTTTTTTTTTTTTAAAGAA+TGG - chr2.3:13468739-13468758 MS.gene91276:CDS 5.0%
AACCAGTGCTCTCACAGTAG+TGG - chr2.3:13468210-13468229 MS.gene91276:intron 50.0%
GCTTACCCGGCACTACTATA+AGG + chr2.3:13468568-13468587 None:intergenic 50.0%
GTAGTAATCCAATGAGGGCG+AGG + chr2.3:13468022-13468041 None:intergenic 50.0%
TTGTCCTCAGAACACGACAC+TGG - chr2.3:13468344-13468363 MS.gene91276:intron 50.0%
! AACCACTACTGTGAGAGCAC+TGG + chr2.3:13468215-13468234 None:intergenic 50.0%
!! GTGTCGTGTTCTGAGGACAA+TGG + chr2.3:13468344-13468363 None:intergenic 50.0%
GTTGCGGTCCATGCGATCAA+TGG - chr2.3:13468706-13468725 MS.gene91276:intron 55.0%
GTGTCTCACCTCGCCCTCAT+TGG - chr2.3:13468011-13468030 MS.gene91276:CDS 60.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 13467917 13469528 13467917 ID=MS.gene91276
chr2.3 mRNA 13467917 13469528 13467917 ID=MS.gene91276.t1;Parent=MS.gene91276
chr2.3 exon 13469388 13469528 13469388 ID=MS.gene91276.t1.exon1;Parent=MS.gene91276.t1
chr2.3 CDS 13469388 13469528 13469388 ID=cds.MS.gene91276.t1;Parent=MS.gene91276.t1
chr2.3 exon 13468864 13468943 13468864 ID=MS.gene91276.t1.exon2;Parent=MS.gene91276.t1
chr2.3 CDS 13468864 13468943 13468864 ID=cds.MS.gene91276.t1;Parent=MS.gene91276.t1
chr2.3 exon 13468718 13468767 13468718 ID=MS.gene91276.t1.exon3;Parent=MS.gene91276.t1
chr2.3 CDS 13468718 13468767 13468718 ID=cds.MS.gene91276.t1;Parent=MS.gene91276.t1
chr2.3 exon 13467917 13468048 13467917 ID=MS.gene91276.t1.exon4;Parent=MS.gene91276.t1
chr2.3 CDS 13467917 13468048 13467917 ID=cds.MS.gene91276.t1;Parent=MS.gene91276.t1
Gene Sequence

>MS.gene91276

ATGGTGATGCCTTTCGCTATAGGAAATGATACTATGTTTCAACCTTCTCCTTTTGACTTAAAGAGATTTGTGGAAAGATGCAAGAAAGAATATGGTGTCTCACCTCGCCCTCATTGGATTACTACTTATTATGGAGGCCATGTTTGTACTTCTTTTTTCTCATCTATATAACATTATTTACTTCACATAGTTTTCTTCAAATGATTTTCTATATTTATTAATTATTACATCAAAGAAAGAGGATATCAACCTACATTAATTTAGATTGTCTACATTAATTTAAAAGAAATGTTAACCAGTGCTCTCACAGTAGTGGTTAAGGAAACAAATATAATAGTATTGCATTGAAACTTGTATAATCAATCCTTCAAAAGTGTAAAAAGTGTTGTTTTCTATTTAAATTTTTTTTTTTTTACTTCCTTAACCATTGTCCTCAGAACACGACACTGGTTAACATGATCCTTGATTTAAATGTCTTTTTTTAAGGTTTAAATCTCATTTTGATTGTAATATAACTAAAGTAACAATAAGAAAAATGTAACAGTAACAAGAAATTAATTTTGTTGTGGTTTTGACTAATGGCAGGATATAAAACGAGTTCTTCAAAAGTTTGGTAGCAACATTATATTTTCGAATGGACTAAAAGATCCTTATAGTAGTGCCGGGTAAGCACCATAAAATTCAAAATTGAATTGATCTCTTTGATTATTTTTGAACAAAATGTATGAAATTAAATATTGCAATGTTATAAAATATTGCAGGGTTTTGCACAACCTATCAAAGAGTCTTGTTGCGGTCCATGCGATCAATGGTATGTCTTGTTTTTTTTTTTTTTTAAAGAATGGTATGTCTTGTTATATATATATAAGGGGCTGTTAATTTACACCCACATAAAAACATTAAGGTGTAAATTAACAAACTACATCCACTAGTGTATTTCTTTGTCCATAAATTTTAACTTAACTGATGAAAATGTTGAAATCTTTAAGTCAGACGTTATCATCAAAATTTGAACCCTGACAACTTCATTTATGTATGTAAATTTATAATGGTTTTACAATTTTATCTGTATAAAAAAAAAAAAAAAAAACATTTTGTCCCTCGTTCTATTTTTCCTAGCTCTTCTTTTTATTGAGAATTGATGCCTTTCTTTATCAAGAAAAAACACTAAGAACCAATTATAGAACATGACAGATACATACACATAGAACATTGTATCACTTTATCTTCAATTTTGTCCTTAAAATTATTATAAATATAATAAATAATTTCTAGAATATATATATAATTCGTCGATTTATATTTATACTACTAAAATATTGTGGACTAAATTGATGGATCACATATATTTTAAGGATTTCATATTACATTTAAATAATTTAGTGACTAAATTGGAGGGAAAATTTTATTTTAAAGATTAAATTATAGTGCTTTATTCTATACATGTGTGTGTATTTGATAGACATTAATTCTATTGCAGGATCCCATTGTTTGGATATTCTATCTTCAAAAGAAAGTGATCCAAGATGGTTGATTGAACAACGAAATAAAGAGGTCGAGATTATTCAAGAGTGGATTGGCCAGTATTATATTGATCTTGGTGCACTCCATG

Protein sequence

>MS.gene91276.t1

MVMPFAIGNDTMFQPSPFDLKRFVERCKKEYGVSPRPHWITTYYGGHDIKRVLQKFGSNIIFSNGLKDPYSSAGVLHNLSKSLVAVHAINGSHCLDILSSKESDPRWLIEQRNKEVEIIQEWIGQYYIDLGALH