AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene76520


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene76520.t1 MTR_2g101430 90.110 273 19 1 1 265 1 273 3.09e-179 494
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene76520.t1 AT1G51080 48.416 221 103 4 47 259 63 280 1.31e-55 180

Find 75 sgRNAs with CRISPR-Local

Find 74 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGACCTTCTCGGCACTTCTA+AGG 0.214375 2.3:-2645574 MS.gene76520:CDS
TTTGCTCTTAATGTGTTAAA+TGG 0.235237 2.3:-2645717 MS.gene76520:CDS
TCATGTTTACTTTATGTTTC+GGG 0.243260 2.3:-2646006 MS.gene76520:CDS
GTTAGGTTGGGTGTTGGTAT+TGG 0.289295 2.3:+2645509 None:intergenic
ATCATGTTTACTTTATGTTT+CGG 0.295381 2.3:-2646007 MS.gene76520:CDS
TAGCAGGTGGGTGGTTAGGT+TGG 0.367914 2.3:+2645496 None:intergenic
AAAGTTGATTTCGACCTTCT+CGG 0.376013 2.3:-2645585 MS.gene76520:CDS
TAGGATGCTGCCATGGTTGA+TGG 0.394720 2.3:+2645263 None:intergenic
AGAGACAGAATAATAGATTT+CGG 0.398637 2.3:-2645891 MS.gene76520:CDS
TCAATGCGGTCTTTGTAGAT+TGG 0.399152 2.3:+2645747 None:intergenic
GAAATCTATTATTCTGTCTC+TGG 0.401072 2.3:+2645893 None:intergenic
CTTAAGAGCACGCGAGTTTG+AGG 0.411946 2.3:-2645805 MS.gene76520:CDS
CTAGTAGCAGGTGGGTGGTT+AGG 0.415512 2.3:+2645492 None:intergenic
CAATCCATTCCCCGGACGTC+AGG 0.418797 2.3:-2645301 MS.gene76520:CDS
TCTGCTGCTGCTAGATCCAT+TGG 0.419249 2.3:-2645681 MS.gene76520:CDS
CTTTGTAGATTGGGTCTAGA+AGG 0.419945 2.3:+2645757 None:intergenic
CAATGCGGTCTTTGTAGATT+GGG 0.420162 2.3:+2645748 None:intergenic
TTTAAAGTTGAGTTTAGCTT+AGG 0.423436 2.3:+2645244 None:intergenic
AGCAGGTGGGTGGTTAGGTT+GGG 0.433268 2.3:+2645497 None:intergenic
CAGGAGATAAGCAAGAGATT+TGG 0.434593 2.3:-2645639 MS.gene76520:CDS
TTCAGAAAGAGAAATTAAAC+TGG 0.440028 2.3:-2645916 MS.gene76520:CDS
TGGGTGGTTAGGTTGGGTGT+TGG 0.441793 2.3:+2645503 None:intergenic
CTCAGAATCTGCCGCTCCAA+TGG 0.465779 2.3:+2645665 None:intergenic
ACGGAGAAGAGCCTGACGTC+CGG 0.467710 2.3:+2645290 None:intergenic
AAATCAAAAGCAGCGTTATG+TGG 0.472830 2.3:-2645967 MS.gene76520:CDS
GATAAGCAAGAGATTTGGTT+GGG 0.481364 2.3:-2645634 MS.gene76520:CDS
AGAGCCTGACGTCCGGGGAA+TGG 0.482518 2.3:+2645297 None:intergenic
AAATACAAGGGGAAGATGTT+GGG 0.485271 2.3:-2645867 MS.gene76520:CDS
CGGAGAAGAGCCTGACGTCC+GGG 0.490784 2.3:+2645291 None:intergenic
GACCTTCTCGGCACTTCTAA+GGG 0.491235 2.3:-2645573 MS.gene76520:CDS
AAAATACAAGGGGAAGATGT+TGG 0.491381 2.3:-2645868 MS.gene76520:CDS
CTGACGTCCGGGGAATGGAT+TGG 0.498352 2.3:+2645302 None:intergenic
AGCGGCAGATTCTGAGCTGC+AGG 0.508668 2.3:-2645658 MS.gene76520:CDS
CCACATTGTTGTCCTTCTGT+TGG 0.509399 2.3:+2645370 None:intergenic
TGCCATGGTTGATGGCCTTA+CGG 0.514572 2.3:+2645271 None:intergenic
TCGCTGAAATTGACAAGTCT+CGG 0.520757 2.3:+2645540 None:intergenic
TTCCGTCGAGCTACCTCAAG+TGG 0.521226 2.3:-2645839 MS.gene76520:CDS
AGCACGCGAGTTTGAGGAGT+GGG 0.522721 2.3:-2645799 MS.gene76520:CDS
ACAGTAGTAGTAGGACTAAG+AGG 0.528829 2.3:-2645446 MS.gene76520:CDS
AATAGATTTCGGAAAATACA+AGG 0.531136 2.3:-2645880 MS.gene76520:CDS
GCCATTGCCAATCCATTCCC+CGG 0.538546 2.3:-2645309 MS.gene76520:CDS
ACGGTAGTAACAGTAGTAGT+AGG 0.539912 2.3:-2645455 MS.gene76520:CDS
CTCCCTTAGAAGTGCCGAGA+AGG 0.555291 2.3:+2645571 None:intergenic
AATCAAAAGCAGCGTTATGT+GGG 0.565427 2.3:-2645966 MS.gene76520:CDS
TGCTCCAACCAACTTTGTCA+AGG 0.565623 2.3:+2645607 None:intergenic
ACGTCAGGCTCTTCTCCGTA+AGG 0.566162 2.3:-2645286 MS.gene76520:CDS
AAATGAAGCGCACCAACAGA+AGG 0.567882 2.3:-2645382 MS.gene76520:CDS
AGATAAGCAAGAGATTTGGT+TGG 0.569741 2.3:-2645635 MS.gene76520:CDS
TAGTAGTAGGACTAAGAGGA+TGG 0.572795 2.3:-2645442 MS.gene76520:CDS
TCCGGGGAATGGATTGGCAA+TGG 0.584712 2.3:+2645308 None:intergenic
ACTAGTATCGTTGGTAGCAA+CGG 0.585566 2.3:-2645474 MS.gene76520:CDS
TGGGATAACCTTGACAAAGT+TGG 0.586673 2.3:-2645615 MS.gene76520:CDS
ATAACCTTGACAAAGTTGGT+TGG 0.591237 2.3:-2645611 MS.gene76520:CDS
TTCTCGGCACTTCTAAGGGA+GGG 0.601983 2.3:-2645569 MS.gene76520:CDS
TTTAGCTTAGGATGCTGCCA+TGG 0.602732 2.3:+2645256 None:intergenic
CTACCAACGATACTAGTAGC+AGG 0.604969 2.3:+2645480 None:intergenic
CTCCGTAAGGCCATCAACCA+TGG 0.607049 2.3:-2645273 MS.gene76520:CDS
TCTACAAAGACCGCATTGAG+TGG 0.608441 2.3:-2645743 MS.gene76520:CDS
TCCGTCGAGCTACCTCAAGT+GGG 0.610493 2.3:-2645838 MS.gene76520:CDS
ATAGATTTCGGAAAATACAA+GGG 0.628131 2.3:-2645879 MS.gene76520:CDS
CCACCTGCTACTAGTATCGT+TGG 0.631045 2.3:-2645483 MS.gene76520:CDS
CGAGACAGAAAATGAGATCG+AGG 0.635307 2.3:-2645410 MS.gene76520:CDS
CTACAAAGACCGCATTGAGT+GGG 0.639133 2.3:-2645742 MS.gene76520:CDS
GGAGAAGAGCCTGACGTCCG+GGG 0.642345 2.3:+2645292 None:intergenic
CGATACTAGTAGCAGGTGGG+TGG 0.643375 2.3:+2645487 None:intergenic
CTTCTCGGCACTTCTAAGGG+AGG 0.649267 2.3:-2645570 MS.gene76520:CDS
TAGATTTCGGAAAATACAAG+GGG 0.656423 2.3:-2645878 MS.gene76520:CDS
CCAACGATACTAGTAGCAGG+TGG 0.663999 2.3:+2645483 None:intergenic
ACTTGAGGTAGCTCGACGGA+AGG 0.664751 2.3:+2645841 None:intergenic
TGCTGCTAGATCCATTGGAG+CGG 0.676565 2.3:-2645676 MS.gene76520:CDS
ACCCACTTGAGGTAGCTCGA+CGG 0.680643 2.3:+2645837 None:intergenic
CAACGATACTAGTAGCAGGT+GGG 0.693048 2.3:+2645484 None:intergenic
CCAACAGAAGGACAACAATG+TGG 0.706083 2.3:-2645370 MS.gene76520:CDS
GAGCAAACTCCCACTCAATG+CGG 0.708509 2.3:+2645733 None:intergenic
GAGCACGCGAGTTTGAGGAG+TGG 0.717265 2.3:-2645800 MS.gene76520:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATCATGTTTACTTTATGTTT+CGG - chr2.3:2645282-2645301 MS.gene76520:CDS 20.0%
! AATAGATTTCGGAAAATACA+AGG - chr2.3:2645409-2645428 MS.gene76520:CDS 25.0%
! AGAGACAGAATAATAGATTT+CGG - chr2.3:2645398-2645417 MS.gene76520:CDS 25.0%
! ATAGATTTCGGAAAATACAA+GGG - chr2.3:2645410-2645429 MS.gene76520:CDS 25.0%
! TCATGTTTACTTTATGTTTC+GGG - chr2.3:2645283-2645302 MS.gene76520:CDS 25.0%
! TTCAGAAAGAGAAATTAAAC+TGG - chr2.3:2645373-2645392 MS.gene76520:CDS 25.0%
! TTTGCTCTTAATGTGTTAAA+TGG - chr2.3:2645572-2645591 MS.gene76520:CDS 25.0%
GAAATCTATTATTCTGTCTC+TGG + chr2.3:2645399-2645418 None:intergenic 30.0%
TAGATTTCGGAAAATACAAG+GGG - chr2.3:2645411-2645430 MS.gene76520:CDS 30.0%
AAAATACAAGGGGAAGATGT+TGG - chr2.3:2645421-2645440 MS.gene76520:CDS 35.0%
AAATACAAGGGGAAGATGTT+GGG - chr2.3:2645422-2645441 MS.gene76520:CDS 35.0%
AAATCAAAAGCAGCGTTATG+TGG - chr2.3:2645322-2645341 MS.gene76520:CDS 35.0%
AATCAAAAGCAGCGTTATGT+GGG - chr2.3:2645323-2645342 MS.gene76520:CDS 35.0%
! AAAGTTGATTTCGACCTTCT+CGG - chr2.3:2645704-2645723 MS.gene76520:CDS 35.0%
! AGATAAGCAAGAGATTTGGT+TGG - chr2.3:2645654-2645673 MS.gene76520:CDS 35.0%
! ATAACCTTGACAAAGTTGGT+TGG - chr2.3:2645678-2645697 MS.gene76520:CDS 35.0%
! GATAAGCAAGAGATTTGGTT+GGG - chr2.3:2645655-2645674 MS.gene76520:CDS 35.0%
!!! AGTTTTTTGAAACCCACTTG+AGG + chr2.3:2645466-2645485 None:intergenic 35.0%
ACAGTAGTAGTAGGACTAAG+AGG - chr2.3:2645843-2645862 MS.gene76520:CDS 40.0%
ACGGTAGTAACAGTAGTAGT+AGG - chr2.3:2645834-2645853 MS.gene76520:CDS 40.0%
CAATGCGGTCTTTGTAGATT+GGG + chr2.3:2645544-2645563 None:intergenic 40.0%
CAGGAGATAAGCAAGAGATT+TGG - chr2.3:2645650-2645669 MS.gene76520:CDS 40.0%
CTTTGTAGATTGGGTCTAGA+AGG + chr2.3:2645535-2645554 None:intergenic 40.0%
TAGTAGTAGGACTAAGAGGA+TGG - chr2.3:2645847-2645866 MS.gene76520:CDS 40.0%
TCAATGCGGTCTTTGTAGAT+TGG + chr2.3:2645545-2645564 None:intergenic 40.0%
TCGCTGAAATTGACAAGTCT+CGG + chr2.3:2645752-2645771 None:intergenic 40.0%
TGGGATAACCTTGACAAAGT+TGG - chr2.3:2645674-2645693 MS.gene76520:CDS 40.0%
!! ACTAGTATCGTTGGTAGCAA+CGG - chr2.3:2645815-2645834 MS.gene76520:CDS 40.0%
AAATGAAGCGCACCAACAGA+AGG - chr2.3:2645907-2645926 MS.gene76520:CDS 45.0%
CAACGATACTAGTAGCAGGT+GGG + chr2.3:2645808-2645827 None:intergenic 45.0%
CCAACAGAAGGACAACAATG+TGG - chr2.3:2645919-2645938 MS.gene76520:CDS 45.0%
CCACATTGTTGTCCTTCTGT+TGG + chr2.3:2645922-2645941 None:intergenic 45.0%
CGAGACAGAAAATGAGATCG+AGG - chr2.3:2645879-2645898 MS.gene76520:CDS 45.0%
CTACAAAGACCGCATTGAGT+GGG - chr2.3:2645547-2645566 MS.gene76520:CDS 45.0%
CTACCAACGATACTAGTAGC+AGG + chr2.3:2645812-2645831 None:intergenic 45.0%
TCTACAAAGACCGCATTGAG+TGG - chr2.3:2645546-2645565 MS.gene76520:CDS 45.0%
TGCTCCAACCAACTTTGTCA+AGG + chr2.3:2645685-2645704 None:intergenic 45.0%
!! GTTAGGTTGGGTGTTGGTAT+TGG + chr2.3:2645783-2645802 None:intergenic 45.0%
CCAACGATACTAGTAGCAGG+TGG + chr2.3:2645809-2645828 None:intergenic 50.0%
CCACCTGCTACTAGTATCGT+TGG - chr2.3:2645806-2645825 MS.gene76520:CDS 50.0%
GACCTTCTCGGCACTTCTAA+GGG - chr2.3:2645716-2645735 MS.gene76520:CDS 50.0%
GAGCAAACTCCCACTCAATG+CGG + chr2.3:2645559-2645578 None:intergenic 50.0%
TAGGATGCTGCCATGGTTGA+TGG + chr2.3:2646029-2646048 None:intergenic 50.0%
TCTGCTGCTGCTAGATCCAT+TGG - chr2.3:2645608-2645627 MS.gene76520:CDS 50.0%
TGCTGCTAGATCCATTGGAG+CGG - chr2.3:2645613-2645632 MS.gene76520:CDS 50.0%
! CTTAAGAGCACGCGAGTTTG+AGG - chr2.3:2645484-2645503 MS.gene76520:CDS 50.0%
! TTCTCGGCACTTCTAAGGGA+GGG - chr2.3:2645720-2645739 MS.gene76520:CDS 50.0%
!! TGCCATGGTTGATGGCCTTA+CGG + chr2.3:2646021-2646040 None:intergenic 50.0%
ACCCACTTGAGGTAGCTCGA+CGG + chr2.3:2645455-2645474 None:intergenic 55.0%
ACGTCAGGCTCTTCTCCGTA+AGG - chr2.3:2646003-2646022 MS.gene76520:CDS 55.0%
ACTTGAGGTAGCTCGACGGA+AGG + chr2.3:2645451-2645470 None:intergenic 55.0%
AGCACGCGAGTTTGAGGAGT+GGG - chr2.3:2645490-2645509 MS.gene76520:CDS 55.0%
AGCAGGTGGGTGGTTAGGTT+GGG + chr2.3:2645795-2645814 None:intergenic 55.0%
CGACCTTCTCGGCACTTCTA+AGG - chr2.3:2645715-2645734 MS.gene76520:CDS 55.0%
CGATACTAGTAGCAGGTGGG+TGG + chr2.3:2645805-2645824 None:intergenic 55.0%
CTAGTAGCAGGTGGGTGGTT+AGG + chr2.3:2645800-2645819 None:intergenic 55.0%
CTCAGAATCTGCCGCTCCAA+TGG + chr2.3:2645627-2645646 None:intergenic 55.0%
CTCCGTAAGGCCATCAACCA+TGG - chr2.3:2646016-2646035 MS.gene76520:CDS 55.0%
GCCATTGCCAATCCATTCCC+CGG - chr2.3:2645980-2645999 MS.gene76520:CDS 55.0%
TAGCAGGTGGGTGGTTAGGT+TGG + chr2.3:2645796-2645815 None:intergenic 55.0%
TCCGTCGAGCTACCTCAAGT+GGG - chr2.3:2645451-2645470 MS.gene76520:CDS 55.0%
TTCCGTCGAGCTACCTCAAG+TGG - chr2.3:2645450-2645469 MS.gene76520:CDS 55.0%
! CTTCTCGGCACTTCTAAGGG+AGG - chr2.3:2645719-2645738 MS.gene76520:CDS 55.0%
!! CTCCCTTAGAAGTGCCGAGA+AGG + chr2.3:2645721-2645740 None:intergenic 55.0%
!! TCCGGGGAATGGATTGGCAA+TGG + chr2.3:2645984-2646003 None:intergenic 55.0%
!! TGGGTGGTTAGGTTGGGTGT+TGG + chr2.3:2645789-2645808 None:intergenic 55.0%
ACGGAGAAGAGCCTGACGTC+CGG + chr2.3:2646002-2646021 None:intergenic 60.0%
AGCGGCAGATTCTGAGCTGC+AGG - chr2.3:2645631-2645650 MS.gene76520:CDS 60.0%
CAATCCATTCCCCGGACGTC+AGG - chr2.3:2645988-2646007 MS.gene76520:CDS 60.0%
CTGACGTCCGGGGAATGGAT+TGG + chr2.3:2645990-2646009 None:intergenic 60.0%
GAGCACGCGAGTTTGAGGAG+TGG - chr2.3:2645489-2645508 MS.gene76520:CDS 60.0%
AGAGCCTGACGTCCGGGGAA+TGG + chr2.3:2645995-2646014 None:intergenic 65.0%
CGGAGAAGAGCCTGACGTCC+GGG + chr2.3:2646001-2646020 None:intergenic 65.0%
GGAGAAGAGCCTGACGTCCG+GGG + chr2.3:2646000-2646019 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 2645257 2646054 2645257 ID=MS.gene76520
chr2.3 mRNA 2645257 2646054 2645257 ID=MS.gene76520.t1;Parent=MS.gene76520
chr2.3 exon 2645257 2646054 2645257 ID=MS.gene76520.t1.exon1;Parent=MS.gene76520.t1
chr2.3 CDS 2645257 2646054 2645257 ID=cds.MS.gene76520.t1;Parent=MS.gene76520.t1
Gene Sequence

>MS.gene76520

ATGCATCTGTTATTGCAGCAGCAGCATCATGTTTACTTTATGTTTCGGGACACTTGTTGTATAACAAATCAAAAGCAGCGTTATGTGGGAGTGACAGTAACATCGTTGAGACGCAATTCAGAAAGAGAAATTAAACTGGCCAGAGACAGAATAATAGATTTCGGAAAATACAAGGGGAAGATGTTGGGAAGCCTTCCGTCGAGCTACCTCAAGTGGGTTTCAAAAAACTTAAGAGCACGCGAGTTTGAGGAGTGGGCAATTCTTGCAGATCAAGTCCTTCTAGACCCAATCTACAAAGACCGCATTGAGTGGGAGTTTGCTCTTAATGTGTTAAATGGCAACAACATTTCTTCTGCTGCTGCTAGATCCATTGGAGCGGCAGATTCTGAGCTGCAGGAGATAAGCAAGAGATTTGGTTGGGATAACCTTGACAAAGTTGGTTGGAGCAAAGTTGATTTCGACCTTCTCGGCACTTCTAAGGGAGGGAGAATTCCGAGACTTGTCAATTTCAGCGACAGTGACGCCAATACCAACACCCAACCTAACCACCCACCTGCTACTAGTATCGTTGGTAGCAACGGTAGTAACAGTAGTAGTAGGACTAAGAGGATGGAGAGAAGAGCGAGACAGAAAATGAGATCGAGGACGACAAATGAAGCGCACCAACAGAAGGACAACAATGTGGTTGATATTGAAGAAGTTGAAGATGATAACATTAATATAGCCATTGCCAATCCATTCCCCGGACGTCAGGCTCTTCTCCGTAAGGCCATCAACCATGGCAGCATCCTAAGCTAA

Protein sequence

>MS.gene76520.t1

MHLLLQQQHHVYFMFRDTCCITNQKQRYVGVTVTSLRRNSEREIKLARDRIIDFGKYKGKMLGSLPSSYLKWVSKNLRAREFEEWAILADQVLLDPIYKDRIEWEFALNVLNGNNISSAAARSIGAADSELQEISKRFGWDNLDKVGWSKVDFDLLGTSKGGRIPRLVNFSDSDANTNTQPNHPPATSIVGSNGSNSSSRTKRMERRARQKMRSRTTNEAHQQKDNNVVDIEEVEDDNINIAIANPFPGRQALLRKAINHGSILS