AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene040272

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene040272.t1 MTR_7g063520 62.992 254 61 5 1 221 1 254 2.81e-92 271
MS.gene040272.t1 MTR_5g080880 34.884 258 126 8 1 220 1 254 3.57e-36 130
MS.gene040272.t1 MTR_5g080870 32.039 206 122 6 31 220 16 219 4.56e-22 92.4
MS.gene040272.t1 MTR_4g006560 32.075 159 77 4 89 221 83 236 2.33e-15 72.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene040272.t1 AT5G02050 35.484 279 110 10 1 221 1 267 1.65e-38 134
MS.gene040272.t1 AT2G39795 32.411 253 136 10 1 221 1 250 2.06e-29 110
MS.gene040272.t1 AT3G55605 36.585 164 75 3 87 221 95 258 1.50e-24 97.8
MS.gene040272.t1 AT5G05990 33.714 175 80 3 82 220 84 258 7.57e-24 95.9
MS.gene040272.t1 AT2G39790 31.020 245 138 10 1 220 1 239 6.60e-23 93.2
MS.gene040272.t1 AT1G15870 29.381 194 116 5 49 221 48 241 1.62e-17 79.0
MS.gene040272.t1 AT1G80720 28.351 194 118 6 49 221 48 241 2.08e-13 67.4
MS.gene040272.t1 AT1G80720 28.571 189 114 6 54 221 1 189 4.22e-13 65.9

Find 38 sgRNAs with CRISPR-Local

Find 76 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGATTCATCCGGCTTCTTT+AGG 0.139781 7.1:+65813750 None:intergenic
ATGGAGTGTGTCTGGAGTTT+GGG 0.192697 7.1:-65813814 MS.gene040272:CDS
AATGGAGTGTGTCTGGAGTT+TGG 0.285363 7.1:-65813815 MS.gene040272:CDS
TGATTCATCCGGCTTCTTTA+GGG 0.306067 7.1:+65813751 None:intergenic
ATTTCTCAATGAAGCTCTTC+AGG 0.341876 7.1:+65813478 None:intergenic
GATAGCGCTGTGGAAGGTTC+TGG 0.396323 7.1:+65814457 None:intergenic
TTCTTTGTGGCAAAGGTTAA+CGG 0.402077 7.1:+65814433 None:intergenic
CAAAGGAAATGGAGTGTGTC+TGG 0.417993 7.1:-65813822 MS.gene040272:CDS
TTGCTGATGCACGGCGAGAA+AGG 0.418141 7.1:+65814486 None:intergenic
CAAAAGGAGTGGTTTCTTTG+TGG 0.429970 7.1:+65814420 None:intergenic
AGCTGTTCTTCTGATTCATC+CGG 0.443725 7.1:+65813740 None:intergenic
CATGTTCAACAAAGACAAAA+AGG 0.444344 7.1:-65813523 MS.gene040272:CDS
GAGAGGGACTGCAGCGGCGG+TGG 0.453065 7.1:+65814508 None:intergenic
AAGTAGTGAGAGGGCACAAA+AGG 0.468209 7.1:+65814404 None:intergenic
CTGCAGCGGCGGTGGCGCGA+CGG 0.501759 7.1:+65814516 None:intergenic
TTTGAGATTGTGGACAACCC+TGG 0.521588 7.1:-65813983 MS.gene040272:CDS
GGGTTGTCCACAATCTCAAA+AGG 0.524335 7.1:+65813986 None:intergenic
GAGTGGTTTCTTTGTGGCAA+AGG 0.529220 7.1:+65814426 None:intergenic
TGAAATCAACTGTGCTCTTG+AGG 0.545087 7.1:-65814342 MS.gene040272:CDS
TAGATTGTCCCTAAAGAAGC+CGG 0.552974 7.1:-65813759 MS.gene040272:CDS
CGCTAAAGCTAAGTAGTGAG+AGG 0.553225 7.1:+65814394 None:intergenic
GGATGAATCAGAAGAACAGC+TGG 0.573263 7.1:-65813738 MS.gene040272:intron
TGGAGGAAGTTGCTGATGCA+CGG 0.580939 7.1:+65814477 None:intergenic
CTCAAGTATCTCAAGATCCG+AGG 0.590793 7.1:-65813582 MS.gene040272:CDS
TAGTAATCGTAACATAATCA+CGG 0.602610 7.1:+65813780 None:intergenic
AAGGAGAGGGACTGCAGCGG+CGG 0.602717 7.1:+65814505 None:intergenic
AACGGCGATAGCGCTGTGGA+AGG 0.604965 7.1:+65814451 None:intergenic
AGAAAGGAGAGGGACTGCAG+CGG 0.618940 7.1:+65814502 None:intergenic
ATGCACGGCGAGAAAGGAGA+GGG 0.621384 7.1:+65814492 None:intergenic
ATCTCAAAAGGAAAATAACC+AGG 0.622881 7.1:+65813998 None:intergenic
GTGAGAGGGCACAAAAGGAG+TGG 0.624862 7.1:+65814409 None:intergenic
TCAAGTATCTCAAGATCCGA+GGG 0.626132 7.1:-65813581 MS.gene040272:CDS
TGGAGTGTGTCTGGAGTTTG+GGG 0.633955 7.1:-65813813 MS.gene040272:CDS
GGTTAACGGCGATAGCGCTG+TGG 0.644254 7.1:+65814447 None:intergenic
GCTAAAGCTAAGTAGTGAGA+GGG 0.647721 7.1:+65814395 None:intergenic
GATGCACGGCGAGAAAGGAG+AGG 0.652935 7.1:+65814491 None:intergenic
AGCGCTGTGGAAGGTTCTGG+AGG 0.653512 7.1:+65814460 None:intergenic
GAGCACAGTTGATTTCACGA+AGG 0.726616 7.1:+65814348 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAAAAACTTAAACTTAAAA+CGG + chr7.1:65813878-65813897 None:intergenic 10.0%
!! AATATTCATATGATTGAAAA+AGG + chr7.1:65813914-65813933 None:intergenic 15.0%
!!! GTTTTAAGTTTAAGTTTTTA+AGG - chr7.1:65813877-65813896 MS.gene040272:CDS 15.0%
!!! TTTATTTTGTTTTTTCTGTT+TGG - chr7.1:65813727-65813746 MS.gene040272:intron 15.0%
! TAGTAATCGTAACATAATCA+CGG + chr7.1:65814235-65814254 None:intergenic 25.0%
! TGCAAAAATTTGGTTATCTT+GGG + chr7.1:65814463-65814482 None:intergenic 25.0%
! TTGCAAAGTTAAATAACCAT+CGG + chr7.1:65813847-65813866 None:intergenic 25.0%
! TTTCCAATTATTTACTCGTA+GGG - chr7.1:65813765-65813784 MS.gene040272:CDS 25.0%
!! AGTTGAAAAATATTTTCTCC+AGG + chr7.1:65814050-65814069 None:intergenic 25.0%
!! CGTAGGGTTTAATAAATTTT+AGG - chr7.1:65813781-65813800 MS.gene040272:CDS 25.0%
!! GTTGAAAAATATTTTCTCCA+GGG + chr7.1:65814049-65814068 None:intergenic 25.0%
!! TACATTGTGTCTATTTTCAA+AGG - chr7.1:65814136-65814155 MS.gene040272:intron 25.0%
!! TGTTATCTTTTGCAGTATAT+TGG - chr7.1:65814384-65814403 MS.gene040272:CDS 25.0%
!! TTAGTTGTGTCTATTTTCAA+AGG - chr7.1:65814173-65814192 MS.gene040272:intron 25.0%
!! TTTTCCAATTATTTACTCGT+AGG - chr7.1:65813764-65813783 MS.gene040272:CDS 25.0%
!!! TTATTTTCCTTTTGAGATTG+TGG - chr7.1:65814019-65814038 MS.gene040272:intron 25.0%
AAACCCTACGAGTAAATAAT+TGG + chr7.1:65813771-65813790 None:intergenic 30.0%
ATCTCAAAAGGAAAATAACC+AGG + chr7.1:65814017-65814036 None:intergenic 30.0%
CAAAGACAAAAAGGAATACT+TGG - chr7.1:65814498-65814517 MS.gene040272:CDS 30.0%
CATGTATTGCTGCAAAAATT+TGG + chr7.1:65814473-65814492 None:intergenic 30.0%
CATGTTCAACAAAGACAAAA+AGG - chr7.1:65814489-65814508 MS.gene040272:CDS 30.0%
CTGCAAAAATTTGGTTATCT+TGG + chr7.1:65814464-65814483 None:intergenic 30.0%
TACAAAACTATCGTACAAGA+AGG + chr7.1:65813824-65813843 None:intergenic 30.0%
! GATGGTTATTTAACTTTGCA+AGG - chr7.1:65813846-65813865 MS.gene040272:CDS 30.0%
! GTGTCTATTTTCAAAGGAAA+AGG - chr7.1:65814142-65814161 MS.gene040272:intron 30.0%
! GTGTCTATTTTCAAAGGAAA+TGG - chr7.1:65814142-65814161 MS.gene040272:intron 30.0%
! TGGTATATAACGGAAAAATC+AGG - chr7.1:65814294-65814313 MS.gene040272:intron 30.0%
! TTTTAGGCCAAATATCTCTT+TGG - chr7.1:65813797-65813816 MS.gene040272:CDS 30.0%
AATAACCAGGAAATTCAAGC+TGG + chr7.1:65814004-65814023 None:intergenic 35.0%
AGAAGGACCAAAGAGATATT+TGG + chr7.1:65813807-65813826 None:intergenic 35.0%
AGTGACAGAGAACTTAATGA+AGG + chr7.1:65813967-65813986 None:intergenic 35.0%
ATTTCTCAATGAAGCTCTTC+AGG + chr7.1:65814537-65814556 None:intergenic 35.0%
CAGTATATTGGATGAAAACC+TGG - chr7.1:65814396-65814415 MS.gene040272:CDS 35.0%
GAAGAACAGCTGGTATATAA+CGG - chr7.1:65814284-65814303 MS.gene040272:intron 35.0%
TTCTTTGTGGCAAAGGTTAA+CGG + chr7.1:65813582-65813601 None:intergenic 35.0%
! ACAAAAAGGAATACTTGGTG+TGG - chr7.1:65814503-65814522 MS.gene040272:CDS 35.0%
! TTTTTCCAGCTTGAATTTCC+TGG - chr7.1:65813996-65814015 MS.gene040272:CDS 35.0%
!! TTATCTTGGGTTTTATCCCT+CGG + chr7.1:65814450-65814469 None:intergenic 35.0%
AGCTGTTCTTCTGATTCATC+CGG + chr7.1:65814275-65814294 None:intergenic 40.0%
ATTGGATGAAAACCTGGAGA+AGG - chr7.1:65814402-65814421 MS.gene040272:CDS 40.0%
CAAAAGGAGTGGTTTCTTTG+TGG + chr7.1:65813595-65813614 None:intergenic 40.0%
GCTAAAGCTAAGTAGTGAGA+GGG + chr7.1:65813620-65813639 None:intergenic 40.0%
TAGATTGTCCCTAAAGAAGC+CGG - chr7.1:65814253-65814272 MS.gene040272:intron 40.0%
TCAAGTATCTCAAGATCCGA+GGG - chr7.1:65814431-65814450 MS.gene040272:CDS 40.0%
TGAAATCAACTGTGCTCTTG+AGG - chr7.1:65813670-65813689 MS.gene040272:intron 40.0%
TGATTCATCCGGCTTCTTTA+GGG + chr7.1:65814264-65814283 None:intergenic 40.0%
!!! GTACGATAGTTTTGTACCGA+TGG - chr7.1:65813828-65813847 MS.gene040272:CDS 40.0%
ACTTGAGAATAGCCTTCTCC+AGG + chr7.1:65814417-65814436 None:intergenic 45.0%
CAAAACGTTGCAGCAAACGT+AGG - chr7.1:65813698-65813717 MS.gene040272:intron 45.0%
CAAAGGAAATGGAGTGTGTC+TGG - chr7.1:65814190-65814209 MS.gene040272:intron 45.0%
CGCTAAAGCTAAGTAGTGAG+AGG + chr7.1:65813621-65813640 None:intergenic 45.0%
CTCAAGTATCTCAAGATCCG+AGG - chr7.1:65814430-65814449 MS.gene040272:CDS 45.0%
CTGATTCATCCGGCTTCTTT+AGG + chr7.1:65814265-65814284 None:intergenic 45.0%
GAGTGGTTTCTTTGTGGCAA+AGG + chr7.1:65813589-65813608 None:intergenic 45.0%
GGATGAATCAGAAGAACAGC+TGG - chr7.1:65814274-65814293 MS.gene040272:intron 45.0%
GGGTTGTCCACAATCTCAAA+AGG + chr7.1:65814029-65814048 None:intergenic 45.0%
! AAGTAGTGAGAGGGCACAAA+AGG + chr7.1:65813611-65813630 None:intergenic 45.0%
! AATGGAGTGTGTCTGGAGTT+TGG - chr7.1:65814197-65814216 MS.gene040272:intron 45.0%
! ATGGAGTGTGTCTGGAGTTT+GGG - chr7.1:65814198-65814217 MS.gene040272:intron 45.0%
! GAGCACAGTTGATTTCACGA+AGG + chr7.1:65813667-65813686 None:intergenic 45.0%
! TTTGAGATTGTGGACAACCC+TGG - chr7.1:65814029-65814048 MS.gene040272:intron 45.0%
TGGAGGAAGTTGCTGATGCA+CGG + chr7.1:65813538-65813557 None:intergenic 50.0%
! TGGAGTGTGTCTGGAGTTTG+GGG - chr7.1:65814199-65814218 MS.gene040272:intron 50.0%
AGAAAGGAGAGGGACTGCAG+CGG + chr7.1:65813513-65813532 None:intergenic 55.0%
ATGCACGGCGAGAAAGGAGA+GGG + chr7.1:65813523-65813542 None:intergenic 55.0%
CGTTGCAGCAAACGTAGGTC+TGG - chr7.1:65813703-65813722 MS.gene040272:intron 55.0%
GATAGCGCTGTGGAAGGTTC+TGG + chr7.1:65813558-65813577 None:intergenic 55.0%
TTGCTGATGCACGGCGAGAA+AGG + chr7.1:65813529-65813548 None:intergenic 55.0%
! GTGAGAGGGCACAAAAGGAG+TGG + chr7.1:65813606-65813625 None:intergenic 55.0%
AACGGCGATAGCGCTGTGGA+AGG + chr7.1:65813564-65813583 None:intergenic 60.0%
GATGCACGGCGAGAAAGGAG+AGG + chr7.1:65813524-65813543 None:intergenic 60.0%
GGTTAACGGCGATAGCGCTG+TGG + chr7.1:65813568-65813587 None:intergenic 60.0%
! AGCGCTGTGGAAGGTTCTGG+AGG + chr7.1:65813555-65813574 None:intergenic 60.0%
AAGGAGAGGGACTGCAGCGG+CGG + chr7.1:65813510-65813529 None:intergenic 65.0%
GAGAGGGACTGCAGCGGCGG+TGG + chr7.1:65813507-65813526 None:intergenic 75.0%
! CTGCAGCGGCGGTGGCGCGA+CGG + chr7.1:65813499-65813518 None:intergenic 80.0%


Chromosome Type Strat End Strand Name
chr7.1 gene 65813476 65814558 65813476 ID=MS.gene040272
chr7.1 mRNA 65813476 65814558 65813476 ID=MS.gene040272.t1;Parent=MS.gene040272
chr7.1 exon 65814319 65814558 65814319 ID=MS.gene040272.t1.exon1;Parent=MS.gene040272.t1
chr7.1 CDS 65814319 65814558 65814319 ID=cds.MS.gene040272.t1;Parent=MS.gene040272.t1
chr7.1 exon 65813739 65814029 65813739 ID=MS.gene040272.t1.exon2;Parent=MS.gene040272.t1
chr7.1 CDS 65813739 65814029 65813739 ID=cds.MS.gene040272.t1;Parent=MS.gene040272.t1
chr7.1 exon 65813476 65813610 65813476 ID=MS.gene040272.t1.exon3;Parent=MS.gene040272.t1
chr7.1 CDS 65813476 65813610 65813476 ID=cds.MS.gene040272.t1;Parent=MS.gene040272.t1
Gene Sequence

>MS.gene040272

ATGGCTATGTACACTGCTCTCCGTCGCGCCACCGCCGCTGCAGTCCCTCTCCTTTCTCGCCGTGCATCAGCAACTTCCTCCAGAACCTTCCACAGCGCTATCGCCGTTAACCTTTGCCACAAAGAAACCACTCCTTTTGTGCCCTCTCACTACTTAGCTTTAGCGAAAACTTTCGCAGATGATAGCATCCTTCGTGAAATCAACTGTGCTCTTGAGGATAATCAAAACGTTGCAGCAAACGTAGGTCTGGATTTATTTTGTTTTTTCTGTTTGGATTCTTCGTTTGTATTTTCCAATTATTTACTCGTAGGGTTTAATAAATTTTAGGCCAAATATCTCTTTGGTCCTTCTTGTACGATAGTTTTGTACCGATGGTTATTTAACTTTGCAAGGTTTATACCGTTTTAAGTTTAAGTTTTTAAGGTTTACACGTTACCTTTTTCAATCATATGAATATTTTATGTCAACACATTTGCTTTTGATATTAACCTTCATTAAGTTCTCTGTCACTTTTGTGTAATTTTTCCAGCTTGAATTTCCTGGTTATTTTCCTTTTGAGATTGTGGACAACCCTGGAGAAAATATTTTTCAACTAAAAAGACAATTTGAAGATGAAACTATCACAGTTCAAGTTGACATCACTCACGTGAGTGACGATGATACATTGTGTCTATTTTCAAAGGAAAAGGAGTGTCTATTAGTTGTGTCTATTTTCAAAGGAAATGGAGTGTGTCTGGAGTTTGGGGTGATTGCTTTCCGTGATTATGTTACGATTACTAGATTGTCCCTAAAGAAGCCGGATGAATCAGAAGAACAGCTGGTATATAACGGAAAAATCAGGTAAGCATTTATCAATTGTCATTTAACATTATCAAATGATAATGTCTCTATTACAGATTCTGAATGTTTGTTATCTTTTGCAGTATATTGGATGAAAACCTGGAGAAGGCTATTCTCAAGTATCTCAAGATCCGAGGGATAAAACCCAAGATAACCAAATTTTTGCAGCAATACATGTTCAACAAAGACAAAAAGGAATACTTGGTGTGGCTGAAGAACCTGAAGAGCTTCATTGAGAAATGA
Protein sequence

>MS.gene040272.t1

MAMYTALRRATAAAVPLLSRRASATSSRTFHSAIAVNLCHKETTPFVPSHYLALAKTFADDSILREINCALEDNQNVAANLEFPGYFPFEIVDNPGENIFQLKRQFEDETITVQVDITHVSDDDTLCLFSKEKECLLVVSIFKGNGVCLEFGVIAFRDYVTITRLSLKKPDESEEQLAILKYLKIRGIKPKITKFLQQYMFNKDKKEYLVWLKNLKSFIEK