AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene72733


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene72733.t1 MTR_2g049710 40.306 196 79 1 120 315 5 162 2.12e-43 151
MS.gene72733.t1 MTR_1g054530 44.809 183 87 2 148 316 70 252 2.36e-42 147
MS.gene72733.t1 MTR_8g032820 40.580 138 82 0 191 328 66 203 3.23e-28 112
MS.gene72733.t1 MTR_7g025210 39.316 117 71 0 212 328 86 202 9.61e-24 100
MS.gene72733.t1 MTR_4g109010 38.686 137 81 1 192 328 919 1052 8.89e-23 99.8
MS.gene72733.t1 MTR_0010s0390 73.214 56 15 0 262 317 57 112 7.03e-21 86.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene72733.t1 AT3G29763 46.646 328 175 0 1 328 93 420 1.59e-108 325
MS.gene72733.t1 AT1G19260 46.341 328 176 0 1 328 225 552 3.73e-106 327
MS.gene72733.t1 AT3G29765 46.708 319 170 0 10 328 1 319 5.63e-106 320
MS.gene72733.t1 AT4G09660 43.293 328 166 1 1 328 189 496 7.16e-92 287
MS.gene72733.t1 AT3G29450 43.902 328 162 1 1 328 131 436 1.51e-89 277
MS.gene72733.t1 AT1G41920 43.072 332 183 2 1 328 48 377 9.73e-89 275
MS.gene72733.t1 AT2G06541 37.963 324 139 4 1 324 158 419 1.91e-67 222
MS.gene72733.t1 AT2G06541 45.178 197 104 1 1 197 158 350 1.89e-56 192
MS.gene72733.t1 AT3G31402 43.373 83 47 0 30 112 89 171 4.86e-17 81.6
MS.gene72733.t1 AT3G31402 30.488 164 84 4 172 314 173 327 3.52e-13 70.1
MS.gene72733.t1 AT3G29794 20.690 319 225 5 15 325 30 328 4.13e-15 75.9
MS.gene72733.t1 AT1G42710 51.667 60 29 0 55 114 121 180 2.57e-14 71.2
MS.gene72733.t1 AT3G31402 30.488 164 84 4 172 314 91 245 2.42e-13 70.1

Find 43 sgRNAs with CRISPR-Local

Find 84 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATCATTAATGTTATGAATT+TGG 0.136942 5.4:+16584706 MS.gene72733:CDS
GATCTTGGAGATGAATTATT+TGG 0.205909 5.4:+16583921 MS.gene72733:CDS
TTTGCGTTATGTTAACAAAA+AGG 0.209858 5.4:+16583998 MS.gene72733:CDS
TCCACTTTATTAAATGTTGT+TGG 0.337683 5.4:+16584317 MS.gene72733:CDS
GGCTTAGTGTATCAAGAATT+CGG 0.337788 5.4:+16584117 MS.gene72733:CDS
CCACTTTATTAAATGTTGTT+GGG 0.343025 5.4:+16584318 MS.gene72733:CDS
TATTCTTAATGTAGTTGCTT+TGG 0.353716 5.4:+16583875 MS.gene72733:CDS
AGTTCCTAGTGGACAAGGTT+TGG 0.364335 5.4:+16584415 MS.gene72733:CDS
AGTGCTATTATAAGTGATCT+TGG 0.373494 5.4:+16583906 MS.gene72733:CDS
TGGTCTCAAAAGTTTGATCT+TGG 0.381765 5.4:+16584184 MS.gene72733:CDS
GCTTAGTGTATCAAGAATTC+GGG 0.382792 5.4:+16584118 MS.gene72733:CDS
AACATTGTTGAACGTTTACT+TGG 0.405740 5.4:+16584023 MS.gene72733:CDS
CAATGCACATAAAATGCATA+AGG 0.408341 5.4:-16584215 None:intergenic
TCATAACATTAATGATGTCT+TGG 0.453741 5.4:-16584700 None:intergenic
TCTCAAAAGTTTGATCTTGG+AGG 0.471671 5.4:+16584187 MS.gene72733:CDS
CCCAACAACATTTAATAAAG+TGG 0.475868 5.4:-16584318 None:intergenic
CACTTTATTAAATGTTGTTG+GGG 0.479138 5.4:+16584319 MS.gene72733:CDS
CATATCAAATAAGTGGCAAA+TGG 0.484382 5.4:+16583968 MS.gene72733:CDS
GATCACTCCAACAATTCAAA+AGG 0.486430 5.4:+16583851 MS.gene72733:CDS
CTCGTGACATATCAAATAAG+TGG 0.488071 5.4:+16583961 MS.gene72733:CDS
TTAGGCTGCTTGCTTCTACT+AGG 0.493369 5.4:+16585554 MS.gene72733:intron
TGATCCAAACCTTGTCCACT+AGG 0.498873 5.4:-16584419 None:intergenic
GTTAGAGAGGCATTGAGAAA+AGG 0.512328 5.4:+16584389 MS.gene72733:CDS
AATGCACATAAAATGCATAA+GGG 0.514943 5.4:-16584214 None:intergenic
AAGCTATGAGGGATGATGGA+TGG 0.535499 5.4:+16584753 MS.gene72733:CDS
AAACAAAAGTAGAAGACCAT+TGG 0.539281 5.4:-16584588 None:intergenic
TTACAAGCTATGAGGGATGA+TGG 0.541196 5.4:+16584749 MS.gene72733:CDS
ATCACTTATAATAGCACTAG+TGG 0.542048 5.4:-16583901 None:intergenic
AGCTATGAGGGATGATGGAT+GGG 0.543141 5.4:+16584754 MS.gene72733:CDS
AGCAATTGTTACAAGCTATG+AGG 0.551497 5.4:+16584741 MS.gene72733:CDS
TTGAGACCAGAAAATACCTC+TGG 0.554003 5.4:-16584170 None:intergenic
AAAGAGCTACGGATACTCGC+TGG 0.562733 5.4:+16584456 MS.gene72733:CDS
GCAATTGTTACAAGCTATGA+GGG 0.563032 5.4:+16584742 MS.gene72733:CDS
ATTCGGGGACAAGGTTATGA+TGG 0.567827 5.4:+16584134 MS.gene72733:CDS
AGCACGTCATGTTGCTTGCA+TGG 0.569802 5.4:-16584344 None:intergenic
GATCAAAGAGCTGAAGCCAA+TGG 0.579682 5.4:+16584572 MS.gene72733:CDS
AATTAGTCTCAAAAGAGCTA+CGG 0.582583 5.4:+16584445 MS.gene72733:CDS
ACAAATAGTCAATGTTAGAG+AGG 0.587628 5.4:+16584376 MS.gene72733:CDS
GGAAAAGTTCCTAGTGGACA+AGG 0.588211 5.4:+16584410 MS.gene72733:CDS
GTATCAAGAATTCGGGGACA+AGG 0.601912 5.4:+16584125 MS.gene72733:CDS
TGGTGCTAGCAACGTGCCAG+AGG 0.640295 5.4:+16584154 MS.gene72733:CDS
AGAAAAGGAAAAGTTCCTAG+TGG 0.671947 5.4:+16584404 MS.gene72733:CDS
CTTAGTGTATCAAGAATTCG+GGG 0.791104 5.4:+16584119 MS.gene72733:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CATCATTAATGTTATGAATT+TGG + chr5.4:16584706-16584725 MS.gene72733:CDS 20.0%
!! TTCAAAAGAAGATAAACTAA+CGG - chr5.4:16585235-16585254 None:intergenic 20.0%
!!! TGAATTATTTTATACTGTTG+TGG + chr5.4:16584919-16584938 MS.gene72733:intron 20.0%
! AAAGTAGAGAACTTATTAGT+TGG - chr5.4:16585022-16585041 None:intergenic 25.0%
! AATGCACATAAAATGCATAA+GGG - chr5.4:16584217-16584236 None:intergenic 25.0%
! CACTTTATTAAATGTTGTTG+GGG + chr5.4:16584319-16584338 MS.gene72733:CDS 25.0%
! CATTTGATGAAAAATGTCTT+GGG + chr5.4:16584638-16584657 MS.gene72733:CDS 25.0%
! CCACTTTATTAAATGTTGTT+GGG + chr5.4:16584318-16584337 MS.gene72733:CDS 25.0%
! GATGAATTTGCATCTTTAAA+AGG + chr5.4:16585157-16585176 MS.gene72733:intron 25.0%
! TATTCTTAATGTAGTTGCTT+TGG + chr5.4:16583875-16583894 MS.gene72733:CDS 25.0%
! TCATAACATTAATGATGTCT+TGG - chr5.4:16584703-16584722 None:intergenic 25.0%
! TCCACTTTATTAAATGTTGT+TGG + chr5.4:16584317-16584336 MS.gene72733:CDS 25.0%
! TTGCGTTATGTTAACAAAAA+GGG + chr5.4:16583999-16584018 MS.gene72733:CDS 25.0%
! TTTGCGTTATGTTAACAAAA+AGG + chr5.4:16583998-16584017 MS.gene72733:CDS 25.0%
!! AGAATATCCTTTTGAATTGT+TGG - chr5.4:16583861-16583880 None:intergenic 25.0%
!!! ATTTTTGGCAATAGCAATTA+AGG - chr5.4:16584264-16584283 None:intergenic 25.0%
AAAATATATTCTGTCCCAAG+GGG + chr5.4:16584840-16584859 MS.gene72733:intron 30.0%
AAACAAAAGTAGAAGACCAT+TGG - chr5.4:16584591-16584610 None:intergenic 30.0%
AACATTGTTGAACGTTTACT+TGG + chr5.4:16584023-16584042 MS.gene72733:CDS 30.0%
ACAAATAGTCAATGTTAGAG+AGG + chr5.4:16584376-16584395 MS.gene72733:CDS 30.0%
ATCACTTATAATAGCACTAG+TGG - chr5.4:16583904-16583923 None:intergenic 30.0%
CAATGCACATAAAATGCATA+AGG - chr5.4:16584218-16584237 None:intergenic 30.0%
CATATCAAATAAGTGGCAAA+TGG + chr5.4:16583968-16583987 MS.gene72733:CDS 30.0%
CCCAACAACATTTAATAAAG+TGG - chr5.4:16584321-16584340 None:intergenic 30.0%
GAAAATATATTCTGTCCCAA+GGG + chr5.4:16584839-16584858 MS.gene72733:intron 30.0%
GATCTTGGAGATGAATTATT+TGG + chr5.4:16583921-16583940 MS.gene72733:CDS 30.0%
GCATTTGATGAAAAATGTCT+TGG + chr5.4:16584637-16584656 MS.gene72733:CDS 30.0%
GGACAACAAATTAAAAAGAG+AGG - chr5.4:16584300-16584319 None:intergenic 30.0%
TCAAGCATTAGCAATTCAAT+AGG - chr5.4:16585097-16585116 None:intergenic 30.0%
TCGCGTAATGAACAATTATA+AGG + chr5.4:16585449-16585468 MS.gene72733:intron 30.0%
TTCCATGTGAGGAATATTAA+TGG - chr5.4:16584822-16584841 None:intergenic 30.0%
! AATTAGTCTCAAAAGAGCTA+CGG + chr5.4:16584445-16584464 MS.gene72733:CDS 30.0%
! AGTGCTATTATAAGTGATCT+TGG + chr5.4:16583906-16583925 MS.gene72733:CDS 30.0%
! CAATGATCTTTCTGAAAAGT+TGG + chr5.4:16585183-16585202 MS.gene72733:intron 30.0%
! CAGAATATATTTTCCATGTG+AGG - chr5.4:16584833-16584852 None:intergenic 30.0%
!! CTCTACTTTTGATAAGACAA+GGG + chr5.4:16585033-16585052 MS.gene72733:intron 30.0%
!! GTTCAACAACATTGATAATG+AGG + chr5.4:16585396-16585415 MS.gene72733:intron 30.0%
!! GTTGAATTGTTTTGCAAACA+CGG + chr5.4:16584095-16584114 MS.gene72733:CDS 30.0%
!! TCTCTACTTTTGATAAGACA+AGG + chr5.4:16585032-16585051 MS.gene72733:intron 30.0%
!! TTGAATTGTTTTGCAAACAC+GGG + chr5.4:16584096-16584115 MS.gene72733:CDS 30.0%
AGAAAAGGAAAAGTTCCTAG+TGG + chr5.4:16584404-16584423 MS.gene72733:CDS 35.0%
AGCAATTGTTACAAGCTATG+AGG + chr5.4:16584741-16584760 MS.gene72733:CDS 35.0%
ATGGATGAATGATTGTCTAG+TGG + chr5.4:16585354-16585373 MS.gene72733:intron 35.0%
CACAAACTTCATAGCAGAAA+AGG - chr5.4:16585302-16585321 None:intergenic 35.0%
CTCGTGACATATCAAATAAG+TGG + chr5.4:16583961-16583980 MS.gene72733:CDS 35.0%
CTTAGTGTATCAAGAATTCG+GGG + chr5.4:16584119-16584138 MS.gene72733:CDS 35.0%
GATCACTCCAACAATTCAAA+AGG + chr5.4:16583851-16583870 MS.gene72733:CDS 35.0%
GCAATTGTTACAAGCTATGA+GGG + chr5.4:16584742-16584761 MS.gene72733:CDS 35.0%
GCTTAGTGTATCAAGAATTC+GGG + chr5.4:16584118-16584137 MS.gene72733:CDS 35.0%
GGAAAATATATTCTGTCCCA+AGG + chr5.4:16584838-16584857 MS.gene72733:intron 35.0%
GGCTTAGTGTATCAAGAATT+CGG + chr5.4:16584117-16584136 MS.gene72733:CDS 35.0%
GTAATCGAATAGCAGATGAA+TGG + chr5.4:16585335-16585354 MS.gene72733:intron 35.0%
GTTTCACTGTGACAAATACT+CGG + chr5.4:16584969-16584988 MS.gene72733:intron 35.0%
TCAATAGGAGAAAATTCACG+AGG - chr5.4:16585082-16585101 None:intergenic 35.0%
TCTCAAAAGTTTGATCTTGG+AGG + chr5.4:16584187-16584206 MS.gene72733:CDS 35.0%
TGCCATTAATATTCCTCACA+TGG + chr5.4:16584817-16584836 MS.gene72733:intron 35.0%
TGGTCTCAAAAGTTTGATCT+TGG + chr5.4:16584184-16584203 MS.gene72733:CDS 35.0%
! GGCAACTTGAATGTGATTTT+TGG - chr5.4:16584279-16584298 None:intergenic 35.0%
! TTTTGATAAGACAAGGGTGA+TGG + chr5.4:16585039-16585058 MS.gene72733:intron 35.0%
!! TGGTCTTCTACTTTTGTTTG+AGG + chr5.4:16584592-16584611 MS.gene72733:CDS 35.0%
TACTCGGTTGCTTCTTTGTA+TGG + chr5.4:16584985-16585004 MS.gene72733:intron 40.0%
TTACAAGCTATGAGGGATGA+TGG + chr5.4:16584749-16584768 MS.gene72733:CDS 40.0%
TTGAGACCAGAAAATACCTC+TGG - chr5.4:16584173-16584192 None:intergenic 40.0%
!! GTTAGAGAGGCATTGAGAAA+AGG + chr5.4:16584389-16584408 MS.gene72733:CDS 40.0%
AGCAGAAAAGGCTCTTTCAG+TGG - chr5.4:16585290-16585309 None:intergenic 45.0%
ATTCGGGGACAAGGTTATGA+TGG + chr5.4:16584134-16584153 MS.gene72733:CDS 45.0%
GATCAAAGAGCTGAAGCCAA+TGG + chr5.4:16584572-16584591 MS.gene72733:CDS 45.0%
GTATCAAGAATTCGGGGACA+AGG + chr5.4:16584125-16584144 MS.gene72733:CDS 45.0%
TGATCCAAACCTTGTCCACT+AGG - chr5.4:16584422-16584441 None:intergenic 45.0%
TGTTGTGGACATGCAACTTC+AGG + chr5.4:16584934-16584953 MS.gene72733:intron 45.0%
! AGTTCCTAGTGGACAAGGTT+TGG + chr5.4:16584415-16584434 MS.gene72733:CDS 45.0%
! GGAAAAGTTCCTAGTGGACA+AGG + chr5.4:16584410-16584429 MS.gene72733:CDS 45.0%
!! AAGCTATGAGGGATGATGGA+TGG + chr5.4:16584753-16584772 MS.gene72733:CDS 45.0%
!! AGCTATGAGGGATGATGGAT+GGG + chr5.4:16584754-16584773 MS.gene72733:CDS 45.0%
!!! AACGTGCCAGAGGTATTTTC+TGG + chr5.4:16584164-16584183 MS.gene72733:CDS 45.0%
!!! ATAACAATTAATATTATTTT+AGG + chr5.4:16585536-16585555 MS.gene72733:intron 5.0%
AAAGAGCTACGGATACTCGC+TGG + chr5.4:16584456-16584475 MS.gene72733:CDS 50.0%
! AGCACGTCATGTTGCTTGCA+TGG - chr5.4:16584347-16584366 None:intergenic 50.0%
! GGCTCTTTCAGTGGTTGATG+TGG - chr5.4:16585281-16585300 None:intergenic 50.0%
! TCAGTGGTTGATGTGGCGAC+AGG - chr5.4:16585274-16585293 None:intergenic 55.0%
CCCAAGGGGAAGTCACGACA+CGG + chr5.4:16584854-16584873 MS.gene72733:intron 60.0%
CCGTGTCGTGACTTCCCCTT+GGG - chr5.4:16584857-16584876 None:intergenic 60.0%
TCCGTGTCGTGACTTCCCCT+TGG - chr5.4:16584858-16584877 None:intergenic 60.0%
! TGGTGCTAGCAACGTGCCAG+AGG + chr5.4:16584154-16584173 MS.gene72733:CDS 60.0%


Chromosome Type Strat End Strand Name
chr5.4 gene 16583822 16585575 16583822 ID=MS.gene72733
chr5.4 mRNA 16583822 16585575 16583822 ID=MS.gene72733.t1;Parent=MS.gene72733
chr5.4 exon 16583822 16584793 16583822 ID=MS.gene72733.t1.exon1;Parent=MS.gene72733.t1
chr5.4 CDS 16583822 16584793 16583822 ID=cds.MS.gene72733.t1;Parent=MS.gene72733.t1
chr5.4 exon 16585558 16585575 16585558 ID=MS.gene72733.t1.exon2;Parent=MS.gene72733.t1
chr5.4 CDS 16585558 16585575 16585558 ID=cds.MS.gene72733.t1;Parent=MS.gene72733.t1
Gene Sequence

>MS.gene72733

ATGGAAAATGCTTCAGAAAATGATCAATTGATCACTCCAACAATTCAAAAGGATATTCTTAATGTAGTTGCTTTGGAAACCACTAGTGCTATTATAAGTGATCTTGGAGATGAATTATTTGGTATTCATGTCGATGAAGCTCGTGACATATCAAATAAGTGGCAAATGGTTGTTGCTTTGCGTTATGTTAACAAAAAGGGAAACATTGTTGAACGTTTACTTGGTATTGTTCACGTTAAAGATGTTACAGCTTTATCATTTAAAATGCAAATTGTTGAATTGTTTTGCAAACACGGGCTTAGTGTATCAAGAATTCGGGGACAAGGTTATGATGGTGCTAGCAACGTGCCAGAGGTATTTTCTGGTCTCAAAAGTTTGATCTTGGAGGAGAACCCTTATGCATTTTATGTGCATTGTTTTGCTCATCAATTACAACTTACCTTAATTGCTATTGCCAAAAATCACATTCAAGTTGCCTCTCTTTTTAATTTGTTGTCCACTTTATTAAATGTTGTTGGGGCACCATGCAAGCAACATGACGTGCTTCGTGAAAGACAAATAGTCAATGTTAGAGAGGCATTGAGAAAAGGAAAAGTTCCTAGTGGACAAGGTTTGGATCAAGAAATTAGTCTCAAAAGAGCTACGGATACTCGCTGGAGTTCACATTATGTAACTCTGATTAATTTGATATTAATGCATTCTGATATAACTGATGTTCTTGAAATTGTGAAAGAAGATGCATTAAATGCAGATCAAAGAGCTGAAGCCAATGGTCTTCTACTTTTGTTTGAGGAGTTTGATTTCGCATTCACATTGCATTTGATGAAAAATGTCTTGGGTATATCATATGAATTGTCGCAAACAATTGAAAGAAAAGACCAAGACATCATTAATGTTATGAATTTGGTTGATATAGTGAAGCAATTGTTACAAGCTATGAGGGATGATGGATGGGAGTCTTTATTGCAAGAAGTAATTTTATTTTGTAATACGCATGCCATTAATATTCCTCACATGGAAAATATATTCTGTCCCAAGGGGAAGTCACGACACGGAGACAAAGCTCAAGCTATTACAATAGAGCATCATTATCGTGTTGAATTATTTTATACTGTTGTGGACATGCAACTTCAGGAACTTAATGATCGTTTCACTGTGACAAATACTCGGTTGCTTCTTTGTATGGCGTGTTTGAGTCCAACTAATAAGTTCTCTACTTTTGATAAGACAAGGGTGATGGAATTTGCAAATTTTTATCCTCGTGAATTTTCTCCTATTGAATTGCTAATGCTTGATGATCAACTTGAGAATTACATCATTGACGTGCGTAGTGATGATGAATTTGCATCTTTAAAAGGAATCAATGATCTTTCTGAAAAGTTGGTCAAAACTAGAAAACATATTGTTTATCCGTTAGTTTATCTTCTTTTGAAGTTAGCTATGATTTTGCCTGTCGCCACATCAACCACTGAAAGAGCCTTTTCTGCTATGAAGTTTGTGAAGAGTACATTGTGTAATCGAATAGCAGATGAATGGATGAATGATTGTCTAGTGGCTTATATTGAGAAAGATGTGTTCAACAACATTGATAATGAGGTGATCATTCAAACAATTTCAAAACATGAAATCGCGTAATGAACAATTATAAGGTATCTATGTACTAGTAGATATATTACAATTTTTTGATTGAATTTGTTTTAACTTTTATTTCATGATAACAATTAATATTATTTTAGGCTGCTTGCTTCTACTAG

Protein sequence

>MS.gene72733.t1

MENASENDQLITPTIQKDILNVVALETTSAIISDLGDELFGIHVDEARDISNKWQMVVALRYVNKKGNIVERLLGIVHVKDVTALSFKMQIVELFCKHGLSVSRIRGQGYDGASNVPEVFSGLKSLILEENPYAFYVHCFAHQLQLTLIAIAKNHIQVASLFNLLSTLLNVVGAPCKQHDVLRERQIVNVREALRKGKVPSGQGLDQEISLKRATDTRWSSHYVTLINLILMHSDITDVLEIVKEDALNADQRAEANGLLLLFEEFDFAFTLHLMKNVLGISYELSQTIERKDQDIINVMNLVDIVKQLLQAMRDDGWESLLQEAACFY