AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0312750


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0312750 MtrunA17_Chr2g0282171 94.937 237 11 1 1 237 1 236 8.56e-160 442
Msa0312750 MtrunA17_Chr4g0047381 55.172 232 80 8 1 223 1 217 1.98e-73 223
Msa0312750 MtrunA17_Chr4g0047371 43.443 244 86 8 1 237 1 199 1.18e-53 171
Msa0312750 MtrunA17_Chr4g0021321 40.851 235 113 7 12 237 27 244 7.16e-47 155
Msa0312750 MtrunA17_Chr8g0360011 41.048 229 123 6 4 223 11 236 2.90e-45 151
Msa0312750 MtrunA17_Chr2g0324261 40.367 218 106 5 19 225 31 235 3.14e-44 149
Msa0312750 MtrunA17_Chr2g0324291 51.923 104 44 3 28 130 30 128 9.24e-29 106
Msa0312750 MtrunA17_Chr2g0324281 56.322 87 25 2 28 114 18 91 2.37e-27 103
Msa0312750 MtrunA17_Chr7g0258821 40.000 120 58 3 10 125 148 257 3.98e-24 99.8
Msa0312750 MtrunA17_Chr1g0175871 44.330 97 52 2 23 117 50 146 4.03e-23 92.8
Msa0312750 MtrunA17_Chr1g0154561 47.253 91 40 2 26 116 30 112 1.06e-22 92.4
Msa0312750 MtrunA17_Chr1g0175571 45.055 91 43 2 26 116 120 203 5.51e-22 90.5
Msa0312750 MtrunA17_Chr5g0403521 54.412 68 24 1 26 93 33 93 9.34e-22 90.1
Msa0312750 MtrunA17_Chr1g0175641 53.125 64 24 1 28 91 76 133 4.03e-21 87.0
Msa0312750 MtrunA17_Chr2g0308681 39.080 87 39 2 14 93 86 165 1.29e-15 73.6
Msa0312750 MtrunA17_Chr1g0150921 36.000 75 38 1 16 90 352 416 3.58e-11 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0312750 AT4G03510.3 40.000 240 106 9 13 237 33 249 1.21e-44 150
Msa0312750 AT4G03510.1 40.000 240 106 9 13 237 33 249 1.21e-44 150
Msa0312750 AT4G03510.2 40.000 240 106 9 13 237 33 249 1.21e-44 150
Msa0312750 AT4G03510.4 40.000 240 106 9 13 237 33 249 1.21e-44 150
Msa0312750 AT4G27470.1 41.150 226 99 11 10 223 26 229 1.93e-39 137
Msa0312750 AT4G28270.1 34.375 224 94 5 23 237 14 193 9.93e-37 128
Msa0312750 AT1G74990.1 43.443 122 56 4 11 131 3 112 7.23e-26 98.6
Msa0312750 AT3G58030.4 39.695 131 58 4 16 142 121 234 1.21e-24 101
Msa0312750 AT3G58030.2 39.695 131 58 4 16 142 121 234 1.21e-24 101
Msa0312750 AT3G58030.1 39.695 131 58 4 16 142 121 234 1.21e-24 101
Msa0312750 AT3G58030.3 39.695 131 58 4 16 142 121 234 1.21e-24 101
Msa0312750 AT2G42030.1 44.231 104 47 2 28 131 139 231 1.02e-23 98.6
Msa0312750 AT1G19310.1 59.091 66 20 1 28 93 21 79 5.54e-23 93.6
Msa0312750 AT2G23780.3 49.333 75 31 1 19 93 17 84 1.01e-21 90.1
Msa0312750 AT2G23780.2 49.333 75 31 1 19 93 17 84 1.01e-21 90.1
Msa0312750 AT2G23780.1 49.333 75 31 1 19 93 17 84 1.01e-21 90.1
Msa0312750 AT2G44410.1 33.981 103 49 4 26 122 121 210 3.64e-14 71.6

Find 58 sgRNAs with CRISPR-Local

Find 66 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTGCTTCTGACATGGAATT+TGG 0.134595 2_4:+7906321 None:intergenic
TTCAGGTGCTCAAGCTCTTT+TGG 0.228650 2_4:-7906016 Msa0312750:CDS
TCCGTATCGAAATCCTTATC+AGG 0.353516 2_4:-7905959 Msa0312750:CDS
TTTAAATATTGTCCCTGATA+AGG 0.360067 2_4:+7905946 None:intergenic
CCACCAAGACCAACTGCTTC+AGG 0.366329 2_4:-7906033 Msa0312750:CDS
CCCACCATCTGATAAGAATT+CGG 0.384732 2_4:+7905781 None:intergenic
ACCCTCTTGTTGTTGGTATG+AGG 0.406828 2_4:+7905918 None:intergenic
TTTGTGGCCACCTTTACTGC+TGG 0.418114 2_4:-7906233 Msa0312750:CDS
TAGCATCACCCTCTTGTTGT+TGG 0.423010 2_4:+7905911 None:intergenic
GCACCTGAAGCAGTTGGTCT+TGG 0.423857 2_4:+7906030 None:intergenic
GTTCAAAGTGATGATTCTCT+TGG 0.429642 2_4:-7906186 Msa0312750:CDS
CTTAGACTTCGCCAACGAAC+CGG 0.433237 2_4:-7906265 Msa0312750:CDS
ACCACAATGGTCCCATTGTA+TGG 0.455188 2_4:-7906114 Msa0312750:CDS
CCTGAAGCAGTTGGTCTTGG+TGG 0.457076 2_4:+7906033 None:intergenic
GGCCACCGCGGCCATACAAT+GGG 0.462138 2_4:+7906103 None:intergenic
TCCTCGAACATTCCAACCAC+TGG 0.475584 2_4:+7905835 None:intergenic
CGGCGGGTGGCCGACTACTC+CGG 0.478519 2_4:+7905801 None:intergenic
TGGCCACCGCGGCCATACAA+TGG 0.491039 2_4:+7906102 None:intergenic
TTCTGACATGGAATTTGGAA+TGG 0.496636 2_4:+7906326 None:intergenic
GAACCGGTAGTCACCCTTTG+TGG 0.499048 2_4:-7906249 Msa0312750:CDS
AGATGCAAGGCCAGCAGTAA+AGG 0.499222 2_4:+7906223 None:intergenic
GTTGCAATCAAAACAACCAT+TGG 0.524152 2_4:+7906293 None:intergenic
ACTTCACAAATGCTTAGTCT+TGG 0.524773 2_4:-7905889 Msa0312750:CDS
CCCTGATAAGGATTTCGATA+CGG 0.531451 2_4:+7905958 None:intergenic
GCAGTAAAGGTGGCCACAAA+GGG 0.540437 2_4:+7906236 None:intergenic
ACATTCCAACCACTGGATGC+TGG 0.540579 2_4:+7905842 None:intergenic
TGGATGCTGGCGAGATCTTG+AGG 0.540737 2_4:+7905855 None:intergenic
GGAATCTTCTGCTTCTGACA+TGG 0.544972 2_4:+7906314 None:intergenic
TCTCGCCAGCATCCAGTGGT+TGG 0.552848 2_4:-7905847 Msa0312750:CDS
AGCAGTAAAGGTGGCCACAA+AGG 0.557862 2_4:+7906235 None:intergenic
TCCAGTGGTTGGAATGTTCG+AGG 0.560000 2_4:-7905836 Msa0312750:CDS
CCATCTGATAAGAATTCGGC+GGG 0.562245 2_4:+7905785 None:intergenic
ATGGTCCCATTGTATGGCCG+CGG 0.566563 2_4:-7906108 Msa0312750:CDS
GCCGAATTCTTATCAGATGG+TGG 0.576950 2_4:-7905782 Msa0312750:CDS
AAGGGTGACTACCGGTTCGT+TGG 0.577209 2_4:+7906254 None:intergenic
GCTGGCCTTGCATCTACAAG+TGG 0.589809 2_4:-7906215 Msa0312750:CDS
GTCCCATTGTATGGCCGCGG+TGG 0.589992 2_4:-7906105 Msa0312750:CDS
GCTTGAGCACCTGAAGCAGT+TGG 0.591446 2_4:+7906024 None:intergenic
ATAATAGCTCTAGATTGAGA+AGG 0.602529 2_4:-7905756 Msa0312750:CDS
TGGCCACAAAGGGTGACTAC+CGG 0.604390 2_4:+7906246 None:intergenic
TGGAGCCACTTGTAGATGCA+AGG 0.606645 2_4:+7906210 None:intergenic
CCCGCCGAATTCTTATCAGA+TGG 0.609487 2_4:-7905785 Msa0312750:CDS
TGCAAGGCCAGCAGTAAAGG+TGG 0.611126 2_4:+7906226 None:intergenic
CCGAATTCTTATCAGATGGT+GGG 0.611382 2_4:-7905781 Msa0312750:CDS
TCTTTGCATACAGGACATTG+TGG 0.614114 2_4:+7906150 None:intergenic
TTCCTCATACCAACAACAAG+AGG 0.616354 2_4:-7905920 Msa0312750:CDS
GAGAATCATCACTTTGAACA+TGG 0.619892 2_4:+7906190 None:intergenic
CCGTATCGAAATCCTTATCA+GGG 0.628835 2_4:-7905958 Msa0312750:CDS
TCGGTGGAGCGTGGCCACCG+CGG 0.635955 2_4:+7906091 None:intergenic
AAGATCTCGCCAGCATCCAG+TGG 0.636201 2_4:-7905851 Msa0312750:CDS
TCTGATAAGAATTCGGCGGG+TGG 0.643245 2_4:+7905788 None:intergenic
ACCATCTGATAAGAATTCGG+CGG 0.653831 2_4:+7905784 None:intergenic
GCGAGATCTTGAGGTCGTTG+AGG 0.655268 2_4:+7905864 None:intergenic
GCCATACAATGGGACCATTG+TGG 0.655448 2_4:+7906113 None:intergenic
TCAGAAGCAGAAGATTCCAA+TGG 0.671202 2_4:-7906309 Msa0312750:CDS
TCCTCATACCAACAACAAGA+GGG 0.675909 2_4:-7905919 Msa0312750:CDS
AAATATATCACATACCACAA+TGG 0.681589 2_4:-7906127 Msa0312750:CDS
GGTGGCCACGCTCCACCGAG+TGG 0.693866 2_4:-7906087 Msa0312750:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GATATATTTTCTTTGCATAC+AGG + chr2_4:7905897-7905916 None:intergenic 25.0%
! AAATATATCACATACCACAA+TGG - chr2_4:7905908-7905927 Msa0312750:CDS 25.0%
! TTTAAATATTGTCCCTGATA+AGG + chr2_4:7906092-7906111 None:intergenic 25.0%
! TGGAATGGTTTTCAATTCAT+GGG + chr2_4:7905697-7905716 None:intergenic 30.0%
! TTGGAATGGTTTTCAATTCA+TGG + chr2_4:7905698-7905717 None:intergenic 30.0%
!! ATAATAGCTCTAGATTGAGA+AGG - chr2_4:7906279-7906298 Msa0312750:CDS 30.0%
TTCTGACATGGAATTTGGAA+TGG + chr2_4:7905712-7905731 None:intergenic 35.0%
GTTGCAATCAAAACAACCAT+TGG + chr2_4:7905745-7905764 None:intergenic 35.0%
GAGAATCATCACTTTGAACA+TGG + chr2_4:7905848-7905867 None:intergenic 35.0%
GTTCAAAGTGATGATTCTCT+TGG - chr2_4:7905849-7905868 Msa0312750:CDS 35.0%
! CAACAAGAAGATTTTCCACT+CGG + chr2_4:7905966-7905985 None:intergenic 35.0%
ACTTCACAAATGCTTAGTCT+TGG - chr2_4:7906146-7906165 Msa0312750:CDS 35.0%
TCTGCTTCTGACATGGAATT+TGG + chr2_4:7905717-7905736 None:intergenic 40.0%
TCAGAAGCAGAAGATTCCAA+TGG - chr2_4:7905726-7905745 Msa0312750:CDS 40.0%
TCTTTGCATACAGGACATTG+TGG + chr2_4:7905888-7905907 None:intergenic 40.0%
TCCGTATCGAAATCCTTATC+AGG - chr2_4:7906076-7906095 Msa0312750:CDS 40.0%
CCCTGATAAGGATTTCGATA+CGG + chr2_4:7906080-7906099 None:intergenic 40.0%
CCGTATCGAAATCCTTATCA+GGG - chr2_4:7906077-7906096 Msa0312750:CDS 40.0%
TTCCTCATACCAACAACAAG+AGG - chr2_4:7906115-7906134 Msa0312750:CDS 40.0%
TCCTCATACCAACAACAAGA+GGG - chr2_4:7906116-7906135 Msa0312750:CDS 40.0%
! TTCGAGGAGATGATTTTTGC+CGG - chr2_4:7906215-7906234 Msa0312750:CDS 40.0%
! ATGATTTTTGCCGGAGTAGT+CGG - chr2_4:7906224-7906243 Msa0312750:CDS 40.0%
ACCATCTGATAAGAATTCGG+CGG + chr2_4:7906254-7906273 None:intergenic 40.0%
CCCACCATCTGATAAGAATT+CGG + chr2_4:7906257-7906276 None:intergenic 40.0%
CCGAATTCTTATCAGATGGT+GGG - chr2_4:7906254-7906273 Msa0312750:CDS 40.0%
GGAATCTTCTGCTTCTGACA+TGG + chr2_4:7905724-7905743 None:intergenic 45.0%
ACCACAATGGTCCCATTGTA+TGG - chr2_4:7905921-7905940 Msa0312750:CDS 45.0%
! CAAGAAGATTTTCCACTCGG+TGG + chr2_4:7905963-7905982 None:intergenic 45.0%
! TTCAGGTGCTCAAGCTCTTT+TGG - chr2_4:7906019-7906038 Msa0312750:CDS 45.0%
!! ACCCTCTTGTTGTTGGTATG+AGG + chr2_4:7906120-7906139 None:intergenic 45.0%
! TAGCATCACCCTCTTGTTGT+TGG + chr2_4:7906127-7906146 None:intergenic 45.0%
CCATCTGATAAGAATTCGGC+GGG + chr2_4:7906253-7906272 None:intergenic 45.0%
GCCGAATTCTTATCAGATGG+TGG - chr2_4:7906253-7906272 Msa0312750:CDS 45.0%
CTTAGACTTCGCCAACGAAC+CGG - chr2_4:7905770-7905789 Msa0312750:CDS 50.0%
GCAGTAAAGGTGGCCACAAA+GGG + chr2_4:7905802-7905821 None:intergenic 50.0%
AGCAGTAAAGGTGGCCACAA+AGG + chr2_4:7905803-7905822 None:intergenic 50.0%
TTTGTGGCCACCTTTACTGC+TGG - chr2_4:7905802-7905821 Msa0312750:CDS 50.0%
AGATGCAAGGCCAGCAGTAA+AGG + chr2_4:7905815-7905834 None:intergenic 50.0%
TGGAGCCACTTGTAGATGCA+AGG + chr2_4:7905828-7905847 None:intergenic 50.0%
GCCATACAATGGGACCATTG+TGG + chr2_4:7905925-7905944 None:intergenic 50.0%
ACATTCCAACCACTGGATGC+TGG + chr2_4:7906196-7906215 None:intergenic 50.0%
TCCAGTGGTTGGAATGTTCG+AGG - chr2_4:7906199-7906218 Msa0312750:CDS 50.0%
TCCTCGAACATTCCAACCAC+TGG + chr2_4:7906203-7906222 None:intergenic 50.0%
TCTGATAAGAATTCGGCGGG+TGG + chr2_4:7906250-7906269 None:intergenic 50.0%
CCCGCCGAATTCTTATCAGA+TGG - chr2_4:7906250-7906269 Msa0312750:CDS 50.0%
!! AAGGGTGACTACCGGTTCGT+TGG + chr2_4:7905784-7905803 None:intergenic 55.0%
GAACCGGTAGTCACCCTTTG+TGG - chr2_4:7905786-7905805 Msa0312750:CDS 55.0%
TGGCCACAAAGGGTGACTAC+CGG + chr2_4:7905792-7905811 None:intergenic 55.0%
TGCAAGGCCAGCAGTAAAGG+TGG + chr2_4:7905812-7905831 None:intergenic 55.0%
!! GCTGGCCTTGCATCTACAAG+TGG - chr2_4:7905820-7905839 Msa0312750:CDS 55.0%
ATGGTCCCATTGTATGGCCG+CGG - chr2_4:7905927-7905946 Msa0312750:CDS 55.0%
!! ATTTTCCACTCGGTGGAGCG+TGG + chr2_4:7905956-7905975 None:intergenic 55.0%
!! CCTGAAGCAGTTGGTCTTGG+TGG + chr2_4:7906005-7906024 None:intergenic 55.0%
CCACCAAGACCAACTGCTTC+AGG - chr2_4:7906002-7906021 Msa0312750:CDS 55.0%
! GCACCTGAAGCAGTTGGTCT+TGG + chr2_4:7906008-7906027 None:intergenic 55.0%
GCTTGAGCACCTGAAGCAGT+TGG + chr2_4:7906014-7906033 None:intergenic 55.0%
GCGAGATCTTGAGGTCGTTG+AGG + chr2_4:7906174-7906193 None:intergenic 55.0%
TGGATGCTGGCGAGATCTTG+AGG + chr2_4:7906183-7906202 None:intergenic 55.0%
AAGATCTCGCCAGCATCCAG+TGG - chr2_4:7906184-7906203 Msa0312750:CDS 55.0%
TCTCGCCAGCATCCAGTGGT+TGG - chr2_4:7906188-7906207 Msa0312750:CDS 60.0%
GTCCCATTGTATGGCCGCGG+TGG - chr2_4:7905930-7905949 Msa0312750:CDS 65.0%
GGCCACCGCGGCCATACAAT+GGG + chr2_4:7905935-7905954 None:intergenic 65.0%
TGGCCACCGCGGCCATACAA+TGG + chr2_4:7905936-7905955 None:intergenic 65.0%
TCGGTGGAGCGTGGCCACCG+CGG + chr2_4:7905947-7905966 None:intergenic 75.0%
GGTGGCCACGCTCCACCGAG+TGG - chr2_4:7905948-7905967 Msa0312750:CDS 75.0%
CGGCGGGTGGCCGACTACTC+CGG + chr2_4:7906237-7906256 None:intergenic 75.0%
Chromosome Type Strat End Strand Name
chr2_4 gene 7905672 7906385 7905672 ID=Msa0312750;Name=Msa0312750
chr2_4 mRNA 7905672 7906385 7905672 ID=Msa0312750-mRNA-1;Parent=Msa0312750;Name=Msa0312750-mRNA-1;_AED=0.20;_eAED=0.21;_QI=0|-1|0|1|-1|1|1|0|237
chr2_4 exon 7905672 7906385 7905672 ID=Msa0312750-mRNA-1:exon:3115;Parent=Msa0312750-mRNA-1
chr2_4 CDS 7905672 7906385 7905672 ID=Msa0312750-mRNA-1:cds;Parent=Msa0312750-mRNA-1
Gene Sequence

>Msa0312750

ATGGCATTTGAGCACTGTTTTTCCCATGAATTGAAAACCATTCCAAATTCCATGTCAGAAGCAGAAGATTCCAATGGTTGTTTTGATTGCAACATCTGCTTAGACTTCGCCAACGAACCGGTAGTCACCCTTTGTGGCCACCTTTACTGCTGGCCTTGCATCTACAAGTGGCTCCATGTTCAAAGTGATGATTCTCTTGGATCTGATGAACATCCACAATGTCCTGTATGCAAAGAAAATATATCACATACCACAATGGTCCCATTGTATGGCCGCGGTGGCCACGCTCCACCGAGTGGAAAATCTTCTTGTTGTGATGATAATTTTGTACCACCAAGACCAACTGCTTCAGGTGCTCAAGCTCTTTTGGCAACAGCTTCTCAAAGTGATCATCATCAGCGACTTCCGTATCGAAATCCTTATCAGGGACAATATTTAAACTCTTCCTCATACCAACAACAAGAGGGTGATGCTACTTCACAAATGCTTAGTCTTGGTGCCTCAACGACCTCAAGATCTCGCCAGCATCCAGTGGTTGGAATGTTCGAGGAGATGATTTTTGCCGGAGTAGTCGGCCACCCGCCGAATTCTTATCAGATGGTGGGAAATAATAGCTCTAGATTGAGAAGGCAAGAGTTGCAGACTGATAAATTTTTGAACAGAATTTCAAATTTTCTATTTTGCTGTTTTCTTTTGTGTCTTATTGTCTTTTGA

Protein sequence

>Msa0312750

MAFEHCFSHELKTIPNSMSEAEDSNGCFDCNICLDFANEPVVTLCGHLYCWPCIYKWLHVQSDDSLGSDEHPQCPVCKENISHTTMVPLYGRGGHAPPSGKSSCCDDNFVPPRPTASGAQALLATASQSDHHQRLPYRNPYQGQYLNSSSYQQQEGDATSQMLSLGASTTSRSRQHPVVGMFEEMIFAGVVGHPPNSYQMVGNNSSRLRRQELQTDKFLNRISNFLFCCFLLCLIVF*