AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0185790

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0185790 MtrunA17_Chr5g0400901 93.631 157 10 0 1 157 1 157 3.07e-107 302
Msa0185790 MtrunA17_Chr4g0054291 55.172 174 61 6 1 157 1 174 3.28e-53 166
Msa0185790 MtrunA17_Chr3g0135061 41.085 129 60 3 11 136 16 131 1.17e-16 72.0
Msa0185790 MtrunA17_Chr1g0152241 53.086 81 38 0 60 140 59 139 2.60e-15 68.6
Msa0185790 MtrunA17_Chr7g0225661 40.625 96 50 1 58 153 81 169 1.16e-14 68.2
Msa0185790 MtrunA17_Chr4g0035414 43.210 81 46 0 58 138 27 107 3.91e-14 65.9
Msa0185790 MtrunA17_Chr8g0341311 39.583 96 51 1 58 153 71 159 1.14e-13 65.1
Msa0185790 MtrunA17_Chr3g0144941 37.500 96 52 1 58 145 27 122 3.64e-12 60.5
Msa0185790 MtrunA17_Chr1g0194681 36.667 90 42 2 36 125 8 82 6.97e-12 59.7
Msa0185790 MtrunA17_Chr1g0155551 36.792 106 63 1 36 137 1 106 1.13e-11 59.3
Msa0185790 MtrunA17_Chr8g0378901 42.683 82 39 3 59 136 33 110 1.16e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0185790 AT3G49760.1 38.129 139 85 1 5 142 15 153 2.03e-27 100
Msa0185790 AT4G37730.1 43.609 133 60 3 7 124 135 267 3.23e-19 82.4
Msa0185790 AT2G22850.1 47.059 85 45 0 59 143 127 211 3.13e-18 78.6
Msa0185790 AT2G22850.2 47.059 85 45 0 59 143 127 211 3.13e-18 78.6
Msa0185790 AT3G30530.1 40.000 120 67 2 27 146 49 163 4.82e-15 68.9
Msa0185790 AT1G75390.1 35.833 120 76 1 31 149 10 129 2.87e-13 64.3
Msa0185790 AT2G18160.1 50.820 61 23 1 52 105 15 75 9.12e-13 62.8
Msa0185790 AT1G75390.2 38.384 99 60 1 31 128 10 108 2.27e-12 60.8
Msa0185790 AT1G13600.1 45.679 81 37 1 58 138 83 156 4.56e-12 61.6
Msa0185790 AT4G34590.1 40.000 85 51 0 58 142 24 108 4.82e-12 60.8
Msa0185790 AT2G04038.1 38.835 103 51 2 36 138 54 144 1.79e-11 59.3
Msa0185790 AT4G36730.1 33.628 113 56 2 48 141 194 306 1.85e-11 61.2
Msa0185790 AT4G36730.2 33.628 113 56 2 48 141 192 304 2.05e-11 60.8
Msa0185790 AT5G15830.1 47.945 73 32 1 33 105 52 118 5.36e-11 58.5

Find 52 sgRNAs with CRISPR-Local

Find 59 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAGACATCTAGAGAATTTA+CGG 0.286559 2_1:+4550 Msa0185790:CDS
GGATGGCTCGAACCGGAATA+TGG 0.309967 2_1:+4461 Msa0185790:CDS
GGGCTGGTGGGTTGGAAGGG+TGG 0.313437 2_1:-4387 None:intergenic
ATATCATTCTCCTCCGCTTT+CGG 0.329484 2_1:-4488 None:intergenic
GCAACCCGTTGTTCAATTCC+CGG 0.358900 2_1:-4602 None:intergenic
CAACCGGAGCCACTCACTTT+CGG 0.360505 2_1:-4658 None:intergenic
GTGACCTCCGTGCCGATTCC+CGG 0.363167 2_1:-4515 None:intergenic
TTCTTCTAACTCCGTGAAAT+CGG 0.384933 2_1:-4331 None:intergenic
GCTTTCGGTCCTCCATATTC+CGG 0.399400 2_1:-4473 None:intergenic
CTTAGGGCTGGTGGGTTGGA+AGG 0.408872 2_1:-4391 None:intergenic
ACCGGTTTAGAGTTGAAAAC+CGG 0.409929 2_1:+4583 Msa0185790:CDS
CCGGTTGGAACGAACCATGC+TGG 0.411515 2_1:+4674 Msa0185790:CDS
TCTCTATGCCTCCGATTTCA+CGG 0.417032 2_1:+4320 Msa0185790:CDS
CTCACTTCAAGCTCCGGTTC+AGG 0.426863 2_1:+4414 Msa0185790:CDS
CCGGAGCTTGAAGTGAGCTT+AGG 0.429061 2_1:-4408 None:intergenic
AAAACCGGGAATTGAACAAC+GGG 0.452979 2_1:+4598 Msa0185790:CDS
ATTTACGGAACCAGGTGAAC+CGG 0.455271 2_1:+4565 Msa0185790:CDS
CCAGCATGGTTCGTTCCAAC+CGG 0.461195 2_1:-4674 None:intergenic
TGAAGTGAGCTTAGGGCTGG+TGG 0.471435 2_1:-4400 None:intergenic
CAACTCTAAACCGGTTCACC+TGG 0.478647 2_1:-4575 None:intergenic
CGGAGCTTGAAGTGAGCTTA+GGG 0.479442 2_1:-4407 None:intergenic
TTAGGGCTGGTGGGTTGGAA+GGG 0.484445 2_1:-4390 None:intergenic
CGGTCATGGATGGCTCGAAC+CGG 0.489104 2_1:+4454 Msa0185790:CDS
CGGTTCGAGCCATCCATGAC+CGG 0.490515 2_1:-4453 None:intergenic
TTCAACCTTTCTCATCTGCA+TGG 0.491200 2_1:+4733 Msa0185790:CDS
GGAGGAGAATGATATCAAAC+CGG 0.491685 2_1:+4496 Msa0185790:CDS
AATGATATCAAACCGGGAAT+CGG 0.493933 2_1:+4503 Msa0185790:CDS
GAACCGAAAGTGAGTGGCTC+CGG 0.506432 2_1:+4655 Msa0185790:CDS
TGAGCTTAGGGCTGGTGGGT+TGG 0.515513 2_1:-4395 None:intergenic
CCTAAGCTCACTTCAAGCTC+CGG 0.518730 2_1:+4408 Msa0185790:CDS
CGGTTGGAACGAACCATGCT+GGG 0.526524 2_1:+4675 Msa0185790:CDS
GAAGTGAGCTTAGGGCTGGT+GGG 0.547493 2_1:-4399 None:intergenic
GGCATAGAGAGAAGAGAGCA+TGG 0.571054 2_1:-4307 None:intergenic
CATGGCCATGCAGATGAGAA+AGG 0.571565 2_1:-4738 None:intergenic
GCTTGAAGTGAGCTTAGGGC+TGG 0.571567 2_1:-4403 None:intergenic
AGAAGAAAGTTTAACGCCGT+GGG 0.579656 2_1:+4347 Msa0185790:CDS
CCGGTTTAGAGTTGAAAACC+GGG 0.582456 2_1:+4584 Msa0185790:CDS
TCTAGAGAATTTACGGAACC+AGG 0.588686 2_1:+4557 Msa0185790:CDS
TAGAAGAAAGTTTAACGCCG+TGG 0.593173 2_1:+4346 Msa0185790:CDS
CGAAAGTGAGTGGCTCCGGT+TGG 0.593366 2_1:+4659 Msa0185790:CDS
TATCAAACCGGGAATCGGCA+CGG 0.599707 2_1:+4508 Msa0185790:CDS
GTCTACGAACCGAAAGTGAG+TGG 0.602935 2_1:+4649 Msa0185790:CDS
TTCTAACTCCGTGAAATCGG+AGG 0.604958 2_1:-4328 None:intergenic
GGTCAAAAGTTGTCAAACAT+AGG 0.610074 2_1:+4696 Msa0185790:CDS
GGAATATGGAGGACCGAAAG+CGG 0.611264 2_1:+4475 Msa0185790:CDS
GAGGAGAATGATATCAAACC+GGG 0.616694 2_1:+4497 Msa0185790:CDS
TCAGCTGTGACAATATTGCA+TGG 0.636378 2_1:-4756 None:intergenic
GTCAAACATAGGTCAAAACA+TGG 0.654401 2_1:+4707 Msa0185790:CDS
GAAAACCGGGAATTGAACAA+CGG 0.656607 2_1:+4597 Msa0185790:CDS
ATATGGAGGACCGAAAGCGG+AGG 0.670255 2_1:+4478 Msa0185790:CDS
TGGCTCGAACCGGAATATGG+AGG 0.676236 2_1:+4464 Msa0185790:CDS
CAAACCGGGAATCGGCACGG+AGG 0.765542 2_1:+4511 Msa0185790:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAGACATCTAGAGAATTTA+CGG + chr2_1:4550-4569 Msa0185790:CDS 25.0%
AGAATGTTAGAAAAATCCCA+CGG - chr2_1:4366-4385 None:intergenic 30.0%
TTCTTCTAACTCCGTGAAAT+CGG - chr2_1:4334-4353 None:intergenic 35.0%
AATGATATCAAACCGGGAAT+CGG + chr2_1:4503-4522 Msa0185790:CDS 35.0%
GGTCAAAAGTTGTCAAACAT+AGG + chr2_1:4696-4715 Msa0185790:CDS 35.0%
GTCAAACATAGGTCAAAACA+TGG + chr2_1:4707-4726 Msa0185790:CDS 35.0%
TAGAAGAAAGTTTAACGCCG+TGG + chr2_1:4346-4365 Msa0185790:CDS 40.0%
AGAAGAAAGTTTAACGCCGT+GGG + chr2_1:4347-4366 Msa0185790:CDS 40.0%
AGGCGAACCAAAAGAAAAAC+CGG + chr2_1:4434-4453 Msa0185790:CDS 40.0%
ACCAAAAGAAAAACCGGTCA+TGG + chr2_1:4440-4459 Msa0185790:CDS 40.0%
!! TCCATGACCGGTTTTTCTTT+TGG - chr2_1:4444-4463 None:intergenic 40.0%
AAAGAAAAACCGGTCATGGA+TGG + chr2_1:4444-4463 Msa0185790:CDS 40.0%
ATATCATTCTCCTCCGCTTT+CGG - chr2_1:4491-4510 None:intergenic 40.0%
GGAGGAGAATGATATCAAAC+CGG + chr2_1:4496-4515 Msa0185790:CDS 40.0%
GAGGAGAATGATATCAAACC+GGG + chr2_1:4497-4516 Msa0185790:CDS 40.0%
TCTAGAGAATTTACGGAACC+AGG + chr2_1:4557-4576 Msa0185790:CDS 40.0%
! ACCGGTTTAGAGTTGAAAAC+CGG + chr2_1:4583-4602 Msa0185790:CDS 40.0%
GAAAACCGGGAATTGAACAA+CGG + chr2_1:4597-4616 Msa0185790:CDS 40.0%
AAAACCGGGAATTGAACAAC+GGG + chr2_1:4598-4617 Msa0185790:CDS 40.0%
TTCAACCTTTCTCATCTGCA+TGG + chr2_1:4733-4752 Msa0185790:CDS 40.0%
TCAGCTGTGACAATATTGCA+TGG - chr2_1:4759-4778 None:intergenic 40.0%
TCTCTATGCCTCCGATTTCA+CGG + chr2_1:4320-4339 Msa0185790:CDS 45.0%
TTCTAACTCCGTGAAATCGG+AGG - chr2_1:4331-4350 None:intergenic 45.0%
!!! TTCTTTTGGTTCGCCTGAAC+CGG - chr2_1:4430-4449 None:intergenic 45.0%
ATTTACGGAACCAGGTGAAC+CGG + chr2_1:4565-4584 Msa0185790:CDS 45.0%
! CCCGGTTTTCAACTCTAAAC+CGG - chr2_1:4587-4606 None:intergenic 45.0%
! CCGGTTTAGAGTTGAAAACC+GGG + chr2_1:4584-4603 Msa0185790:CDS 45.0%
! TGACAACTTTTGACCCAGCA+TGG - chr2_1:4691-4710 None:intergenic 45.0%
CGGAGCTTGAAGTGAGCTTA+GGG - chr2_1:4410-4429 None:intergenic 50.0%
CCTAAGCTCACTTCAAGCTC+CGG + chr2_1:4408-4427 Msa0185790:CDS 50.0%
GCTTTCGGTCCTCCATATTC+CGG - chr2_1:4476-4495 None:intergenic 50.0%
GGAATATGGAGGACCGAAAG+CGG + chr2_1:4475-4494 Msa0185790:CDS 50.0%
TATCAAACCGGGAATCGGCA+CGG + chr2_1:4508-4527 Msa0185790:CDS 50.0%
! CAACTCTAAACCGGTTCACC+TGG - chr2_1:4578-4597 None:intergenic 50.0%
GCAACCCGTTGTTCAATTCC+CGG - chr2_1:4605-4624 None:intergenic 50.0%
GTCTACGAACCGAAAGTGAG+TGG + chr2_1:4649-4668 Msa0185790:CDS 50.0%
CATGGCCATGCAGATGAGAA+AGG - chr2_1:4741-4760 None:intergenic 50.0%
!! TTAGGGCTGGTGGGTTGGAA+GGG - chr2_1:4393-4412 None:intergenic 55.0%
! GAAGTGAGCTTAGGGCTGGT+GGG - chr2_1:4402-4421 None:intergenic 55.0%
TGAAGTGAGCTTAGGGCTGG+TGG - chr2_1:4403-4422 None:intergenic 55.0%
GCTTGAAGTGAGCTTAGGGC+TGG - chr2_1:4406-4425 None:intergenic 55.0%
CCGGAGCTTGAAGTGAGCTT+AGG - chr2_1:4411-4430 None:intergenic 55.0%
CTCACTTCAAGCTCCGGTTC+AGG + chr2_1:4414-4433 Msa0185790:CDS 55.0%
GGATGGCTCGAACCGGAATA+TGG + chr2_1:4461-4480 Msa0185790:CDS 55.0%
TGGCTCGAACCGGAATATGG+AGG + chr2_1:4464-4483 Msa0185790:CDS 55.0%
ATATGGAGGACCGAAAGCGG+AGG + chr2_1:4478-4497 Msa0185790:CDS 55.0%
GAACCGAAAGTGAGTGGCTC+CGG + chr2_1:4655-4674 Msa0185790:CDS 55.0%
CAACCGGAGCCACTCACTTT+CGG - chr2_1:4661-4680 None:intergenic 55.0%
CCAGCATGGTTCGTTCCAAC+CGG - chr2_1:4677-4696 None:intergenic 55.0%
CGGTTGGAACGAACCATGCT+GGG + chr2_1:4675-4694 Msa0185790:CDS 55.0%
!! CTTAGGGCTGGTGGGTTGGA+AGG - chr2_1:4394-4413 None:intergenic 60.0%
! TGAGCTTAGGGCTGGTGGGT+TGG - chr2_1:4398-4417 None:intergenic 60.0%
CGGTTCGAGCCATCCATGAC+CGG - chr2_1:4456-4475 None:intergenic 60.0%
CGGTCATGGATGGCTCGAAC+CGG + chr2_1:4454-4473 Msa0185790:CDS 60.0%
CGAAAGTGAGTGGCTCCGGT+TGG + chr2_1:4659-4678 Msa0185790:CDS 60.0%
CCGGTTGGAACGAACCATGC+TGG + chr2_1:4674-4693 Msa0185790:CDS 60.0%
CAAACCGGGAATCGGCACGG+AGG + chr2_1:4511-4530 Msa0185790:CDS 65.0%
!! GTGACCTCCGTGCCGATTCC+CGG - chr2_1:4518-4537 None:intergenic 65.0%
!! GGGCTGGTGGGTTGGAAGGG+TGG - chr2_1:4390-4409 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr2_1 gene 4309 4782 4309 ID=Msa0185790;Name=Msa0185790
chr2_1 mRNA 4309 4782 4309 ID=Msa0185790-mRNA-1;Parent=Msa0185790;Name=Msa0185790-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|157
chr2_1 exon 4309 4782 4309 ID=Msa0185790-mRNA-1:exon:1;Parent=Msa0185790-mRNA-1
chr2_1 CDS 4309 4782 4309 ID=Msa0185790-mRNA-1:cds;Parent=Msa0185790-mRNA-1
Gene Sequence

>Msa0185790

ATGCTCTCTTCTCTCTATGCCTCCGATTTCACGGAGTTAGAAGAAAGTTTAACGCCGTGGGATTTTTCTAACATTCTGCCACCCTTCCAACCCACCAGCCCTAAGCTCACTTCAAGCTCCGGTTCAGGCGAACCAAAAGAAAAACCGGTCATGGATGGCTCGAACCGGAATATGGAGGACCGAAAGCGGAGGAGAATGATATCAAACCGGGAATCGGCACGGAGGTCACGTATGAGAAAACAAAGACATCTAGAGAATTTACGGAACCAGGTGAACCGGTTTAGAGTTGAAAACCGGGAATTGAACAACGGGTTGCAGTTTTTGCTGTATCAATGCAATCGTCTACGAACCGAAAGTGAGTGGCTCCGGTTGGAACGAACCATGCTGGGTCAAAAGTTGTCAAACATAGGTCAAAACATGGTTTTTCAACCTTTCTCATCTGCATGGCCATGCAATATTGTCACAGCTGAATAA
Protein sequence

>Msa0185790

MLSSLYASDFTELEESLTPWDFSNILPPFQPTSPKLTSSSGSGEPKEKPVMDGSNRNMEDRKRRRMISNRESARRSRMRKQRHLENLRNQVNRFRVENRELNNGLQFLLYQCNRLRTESEWLRLERTMLGQKLSNIGQNMVFQPFSSAWPCNIVTAE*