AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0272550


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0272550 MtrunA17_Chr2g0282171 94.937 237 11 1 1 237 1 236 8.56e-160 442
Msa0272550 MtrunA17_Chr4g0047381 55.172 232 80 8 1 223 1 217 1.98e-73 223
Msa0272550 MtrunA17_Chr4g0047371 43.443 244 86 8 1 237 1 199 1.18e-53 171
Msa0272550 MtrunA17_Chr4g0021321 40.851 235 113 7 12 237 27 244 7.16e-47 155
Msa0272550 MtrunA17_Chr8g0360011 41.048 229 123 6 4 223 11 236 2.90e-45 151
Msa0272550 MtrunA17_Chr2g0324261 40.367 218 106 5 19 225 31 235 3.14e-44 149
Msa0272550 MtrunA17_Chr2g0324291 51.923 104 44 3 28 130 30 128 9.24e-29 106
Msa0272550 MtrunA17_Chr2g0324281 56.322 87 25 2 28 114 18 91 2.37e-27 103
Msa0272550 MtrunA17_Chr7g0258821 40.000 120 58 3 10 125 148 257 3.98e-24 99.8
Msa0272550 MtrunA17_Chr1g0175871 44.330 97 52 2 23 117 50 146 4.03e-23 92.8
Msa0272550 MtrunA17_Chr1g0154561 47.253 91 40 2 26 116 30 112 1.06e-22 92.4
Msa0272550 MtrunA17_Chr1g0175571 45.055 91 43 2 26 116 120 203 5.51e-22 90.5
Msa0272550 MtrunA17_Chr5g0403521 54.412 68 24 1 26 93 33 93 9.34e-22 90.1
Msa0272550 MtrunA17_Chr1g0175641 53.125 64 24 1 28 91 76 133 4.03e-21 87.0
Msa0272550 MtrunA17_Chr2g0308681 39.080 87 39 2 14 93 86 165 1.29e-15 73.6
Msa0272550 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
Msa0272550 AT4G03510.3 40.000 240 106 9 13 237 33 249 1.21e-44 150
Msa0272550 AT4G03510.1 40.000 240 106 9 13 237 33 249 1.21e-44 150
Msa0272550 AT4G03510.2 40.000 240 106 9 13 237 33 249 1.21e-44 150
Msa0272550 AT4G03510.4 40.000 240 106 9 13 237 33 249 1.21e-44 150
Msa0272550 AT4G27470.1 41.150 226 99 11 10 223 26 229 1.93e-39 137
Msa0272550 AT4G28270.1 34.375 224 94 5 23 237 14 193 9.93e-37 128
Msa0272550 AT1G74990.1 43.443 122 56 4 11 131 3 112 7.23e-26 98.6
Msa0272550 AT3G58030.4 39.695 131 58 4 16 142 121 234 1.21e-24 101
Msa0272550 AT3G58030.2 39.695 131 58 4 16 142 121 234 1.21e-24 101
Msa0272550 AT3G58030.1 39.695 131 58 4 16 142 121 234 1.21e-24 101
Msa0272550 AT3G58030.3 39.695 131 58 4 16 142 121 234 1.21e-24 101
Msa0272550 AT2G42030.1 44.231 104 47 2 28 131 139 231 1.02e-23 98.6
Msa0272550 AT1G19310.1 59.091 66 20 1 28 93 21 79 5.54e-23 93.6
Msa0272550 AT2G23780.3 49.333 75 31 1 19 93 17 84 1.01e-21 90.1
Msa0272550 AT2G23780.2 49.333 75 31 1 19 93 17 84 1.01e-21 90.1
Msa0272550 AT2G23780.1 49.333 75 31 1 19 93 17 84 1.01e-21 90.1
Msa0272550 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_3:+4082208 None:intergenic
TTCAGGTGCTCAAGCTCTTT+TGG 0.228650 2_3:-4081903 Msa0272550:CDS
TCCGTATCGAAATCCTTATC+AGG 0.353516 2_3:-4081846 Msa0272550:CDS
TTTAAATATTGTCCCTGATA+AGG 0.360067 2_3:+4081833 None:intergenic
CCACCAAGACCAACTGCTTC+AGG 0.366329 2_3:-4081920 Msa0272550:CDS
CCCACCATCTGATAAGAATT+CGG 0.384732 2_3:+4081668 None:intergenic
ACCCTCTTGTTGTTGGTATG+AGG 0.406828 2_3:+4081805 None:intergenic
TTTGTGGCCACCTTTACTGC+TGG 0.418114 2_3:-4082120 Msa0272550:CDS
TAGCATCACCCTCTTGTTGT+TGG 0.423010 2_3:+4081798 None:intergenic
GCACCTGAAGCAGTTGGTCT+TGG 0.423857 2_3:+4081917 None:intergenic
GTTCAAAGTGATGATTCTCT+TGG 0.429642 2_3:-4082073 Msa0272550:CDS
CTTAGACTTCGCCAACGAAC+CGG 0.433237 2_3:-4082152 Msa0272550:CDS
ACCACAATGGTCCCATTGTA+TGG 0.455188 2_3:-4082001 Msa0272550:CDS
CCTGAAGCAGTTGGTCTTGG+TGG 0.457076 2_3:+4081920 None:intergenic
GGCCACCGCGGCCATACAAT+GGG 0.462138 2_3:+4081990 None:intergenic
CGGCGGGTGGCCGACTACTC+CGG 0.478519 2_3:+4081688 None:intergenic
TGGCCACCGCGGCCATACAA+TGG 0.491039 2_3:+4081989 None:intergenic
TTCTGACATGGAATTTGGAA+TGG 0.496636 2_3:+4082213 None:intergenic
GAACCGGTAGTCACCCTTTG+TGG 0.499048 2_3:-4082136 Msa0272550:CDS
AGATGCAAGGCCAGCAGTAA+AGG 0.499222 2_3:+4082110 None:intergenic
GTTGCAATCAAAACAACCAT+TGG 0.524152 2_3:+4082180 None:intergenic
ACTTCACAAATGCTTAGTCT+TGG 0.524773 2_3:-4081776 Msa0272550:CDS
CCCTGATAAGGATTTCGATA+CGG 0.531451 2_3:+4081845 None:intergenic
GCAGTAAAGGTGGCCACAAA+GGG 0.540437 2_3:+4082123 None:intergenic
GGAATCTTCTGCTTCTGACA+TGG 0.544972 2_3:+4082201 None:intergenic
ACATTCCAACCACAGGATGC+TGG 0.545754 2_3:+4081729 None:intergenic
TCCTGTGGTTGGAATGTTCG+AGG 0.548858 2_3:-4081723 Msa0272550:CDS
TCTCGCCAGCATCCTGTGGT+TGG 0.550366 2_3:-4081734 Msa0272550:CDS
AGCAGTAAAGGTGGCCACAA+AGG 0.557862 2_3:+4082122 None:intergenic
CCATCTGATAAGAATTCGGC+GGG 0.562245 2_3:+4081672 None:intergenic
AGGATGCTGGCGAGATCTTG+AGG 0.565005 2_3:+4081742 None:intergenic
ATGGTCCCATTGTATGGCCG+CGG 0.566563 2_3:-4081995 Msa0272550:CDS
TCCTCGAACATTCCAACCAC+AGG 0.567924 2_3:+4081722 None:intergenic
GCCGAATTCTTATCAGATGG+TGG 0.576950 2_3:-4081669 Msa0272550:CDS
AAGGGTGACTACCGGTTCGT+TGG 0.577209 2_3:+4082141 None:intergenic
GCTGGCCTTGCATCTACAAG+TGG 0.589809 2_3:-4082102 Msa0272550:CDS
GTCCCATTGTATGGCCGCGG+TGG 0.589992 2_3:-4081992 Msa0272550:CDS
AAGATCTCGCCAGCATCCTG+TGG 0.590620 2_3:-4081738 Msa0272550:CDS
GCTTGAGCACCTGAAGCAGT+TGG 0.591446 2_3:+4081911 None:intergenic
ATAATAGCTCTAGATTGAGA+AGG 0.602529 2_3:-4081643 Msa0272550:CDS
TGGCCACAAAGGGTGACTAC+CGG 0.604390 2_3:+4082133 None:intergenic
TGGAGCCACTTGTAGATGCA+AGG 0.606645 2_3:+4082097 None:intergenic
CCCGCCGAATTCTTATCAGA+TGG 0.609487 2_3:-4081672 Msa0272550:CDS
TGCAAGGCCAGCAGTAAAGG+TGG 0.611126 2_3:+4082113 None:intergenic
CCGAATTCTTATCAGATGGT+GGG 0.611382 2_3:-4081668 Msa0272550:CDS
TCTTTGCATACAGGACATTG+TGG 0.614114 2_3:+4082037 None:intergenic
TTCCTCATACCAACAACAAG+AGG 0.616354 2_3:-4081807 Msa0272550:CDS
GAGAATCATCACTTTGAACA+TGG 0.619892 2_3:+4082077 None:intergenic
CCGTATCGAAATCCTTATCA+GGG 0.628835 2_3:-4081845 Msa0272550:CDS
TCGGTGGAGCGTGGCCACCG+CGG 0.635955 2_3:+4081978 None:intergenic
TCTGATAAGAATTCGGCGGG+TGG 0.643245 2_3:+4081675 None:intergenic
ACCATCTGATAAGAATTCGG+CGG 0.653831 2_3:+4081671 None:intergenic
GCGAGATCTTGAGGTCGTTG+AGG 0.655268 2_3:+4081751 None:intergenic
GCCATACAATGGGACCATTG+TGG 0.655448 2_3:+4082000 None:intergenic
TCAGAAGCAGAAGATTCCAA+TGG 0.671202 2_3:-4082196 Msa0272550:CDS
TCCTCATACCAACAACAAGA+GGG 0.675909 2_3:-4081806 Msa0272550:CDS
AAATATATCACATACCACAA+TGG 0.681589 2_3:-4082014 Msa0272550:CDS
GGTGGCCACGCTCCACCGAG+TGG 0.693866 2_3:-4081974 Msa0272550:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GATATATTTTCTTTGCATAC+AGG + chr2_3:4081784-4081803 None:intergenic 25.0%
! AAATATATCACATACCACAA+TGG - chr2_3:4081795-4081814 Msa0272550:CDS 25.0%
! TTTAAATATTGTCCCTGATA+AGG + chr2_3:4081979-4081998 None:intergenic 25.0%
! TGGAATGGTTTTCAATTCAT+GGG + chr2_3:4081584-4081603 None:intergenic 30.0%
! TTGGAATGGTTTTCAATTCA+TGG + chr2_3:4081585-4081604 None:intergenic 30.0%
!! ATAATAGCTCTAGATTGAGA+AGG - chr2_3:4082166-4082185 Msa0272550:CDS 30.0%
TTCTGACATGGAATTTGGAA+TGG + chr2_3:4081599-4081618 None:intergenic 35.0%
GTTGCAATCAAAACAACCAT+TGG + chr2_3:4081632-4081651 None:intergenic 35.0%
GAGAATCATCACTTTGAACA+TGG + chr2_3:4081735-4081754 None:intergenic 35.0%
GTTCAAAGTGATGATTCTCT+TGG - chr2_3:4081736-4081755 Msa0272550:CDS 35.0%
! CAACAAGAAGATTTTCCACT+CGG + chr2_3:4081853-4081872 None:intergenic 35.0%
ACTTCACAAATGCTTAGTCT+TGG - chr2_3:4082033-4082052 Msa0272550:CDS 35.0%
TCTGCTTCTGACATGGAATT+TGG + chr2_3:4081604-4081623 None:intergenic 40.0%
TCAGAAGCAGAAGATTCCAA+TGG - chr2_3:4081613-4081632 Msa0272550:CDS 40.0%
TCTTTGCATACAGGACATTG+TGG + chr2_3:4081775-4081794 None:intergenic 40.0%
TCCGTATCGAAATCCTTATC+AGG - chr2_3:4081963-4081982 Msa0272550:CDS 40.0%
CCCTGATAAGGATTTCGATA+CGG + chr2_3:4081967-4081986 None:intergenic 40.0%
CCGTATCGAAATCCTTATCA+GGG - chr2_3:4081964-4081983 Msa0272550:CDS 40.0%
TTCCTCATACCAACAACAAG+AGG - chr2_3:4082002-4082021 Msa0272550:CDS 40.0%
TCCTCATACCAACAACAAGA+GGG - chr2_3:4082003-4082022 Msa0272550:CDS 40.0%
! TTCGAGGAGATGATTTTTGC+CGG - chr2_3:4082102-4082121 Msa0272550:CDS 40.0%
! ATGATTTTTGCCGGAGTAGT+CGG - chr2_3:4082111-4082130 Msa0272550:CDS 40.0%
ACCATCTGATAAGAATTCGG+CGG + chr2_3:4082141-4082160 None:intergenic 40.0%
CCCACCATCTGATAAGAATT+CGG + chr2_3:4082144-4082163 None:intergenic 40.0%
CCGAATTCTTATCAGATGGT+GGG - chr2_3:4082141-4082160 Msa0272550:CDS 40.0%
GGAATCTTCTGCTTCTGACA+TGG + chr2_3:4081611-4081630 None:intergenic 45.0%
ACCACAATGGTCCCATTGTA+TGG - chr2_3:4081808-4081827 Msa0272550:CDS 45.0%
! CAAGAAGATTTTCCACTCGG+TGG + chr2_3:4081850-4081869 None:intergenic 45.0%
! TTCAGGTGCTCAAGCTCTTT+TGG - chr2_3:4081906-4081925 Msa0272550:CDS 45.0%
!! ACCCTCTTGTTGTTGGTATG+AGG + chr2_3:4082007-4082026 None:intergenic 45.0%
! TAGCATCACCCTCTTGTTGT+TGG + chr2_3:4082014-4082033 None:intergenic 45.0%
CCATCTGATAAGAATTCGGC+GGG + chr2_3:4082140-4082159 None:intergenic 45.0%
GCCGAATTCTTATCAGATGG+TGG - chr2_3:4082140-4082159 Msa0272550:CDS 45.0%
CTTAGACTTCGCCAACGAAC+CGG - chr2_3:4081657-4081676 Msa0272550:CDS 50.0%
GCAGTAAAGGTGGCCACAAA+GGG + chr2_3:4081689-4081708 None:intergenic 50.0%
AGCAGTAAAGGTGGCCACAA+AGG + chr2_3:4081690-4081709 None:intergenic 50.0%
TTTGTGGCCACCTTTACTGC+TGG - chr2_3:4081689-4081708 Msa0272550:CDS 50.0%
AGATGCAAGGCCAGCAGTAA+AGG + chr2_3:4081702-4081721 None:intergenic 50.0%
TGGAGCCACTTGTAGATGCA+AGG + chr2_3:4081715-4081734 None:intergenic 50.0%
GCCATACAATGGGACCATTG+TGG + chr2_3:4081812-4081831 None:intergenic 50.0%
ACATTCCAACCACAGGATGC+TGG + chr2_3:4082083-4082102 None:intergenic 50.0%
TCCTGTGGTTGGAATGTTCG+AGG - chr2_3:4082086-4082105 Msa0272550:CDS 50.0%
TCCTCGAACATTCCAACCAC+AGG + chr2_3:4082090-4082109 None:intergenic 50.0%
TCTGATAAGAATTCGGCGGG+TGG + chr2_3:4082137-4082156 None:intergenic 50.0%
CCCGCCGAATTCTTATCAGA+TGG - chr2_3:4082137-4082156 Msa0272550:CDS 50.0%
!! AAGGGTGACTACCGGTTCGT+TGG + chr2_3:4081671-4081690 None:intergenic 55.0%
GAACCGGTAGTCACCCTTTG+TGG - chr2_3:4081673-4081692 Msa0272550:CDS 55.0%
TGGCCACAAAGGGTGACTAC+CGG + chr2_3:4081679-4081698 None:intergenic 55.0%
TGCAAGGCCAGCAGTAAAGG+TGG + chr2_3:4081699-4081718 None:intergenic 55.0%
!! GCTGGCCTTGCATCTACAAG+TGG - chr2_3:4081707-4081726 Msa0272550:CDS 55.0%
ATGGTCCCATTGTATGGCCG+CGG - chr2_3:4081814-4081833 Msa0272550:CDS 55.0%
!! ATTTTCCACTCGGTGGAGCG+TGG + chr2_3:4081843-4081862 None:intergenic 55.0%
!! CCTGAAGCAGTTGGTCTTGG+TGG + chr2_3:4081892-4081911 None:intergenic 55.0%
CCACCAAGACCAACTGCTTC+AGG - chr2_3:4081889-4081908 Msa0272550:CDS 55.0%
! GCACCTGAAGCAGTTGGTCT+TGG + chr2_3:4081895-4081914 None:intergenic 55.0%
GCTTGAGCACCTGAAGCAGT+TGG + chr2_3:4081901-4081920 None:intergenic 55.0%
GCGAGATCTTGAGGTCGTTG+AGG + chr2_3:4082061-4082080 None:intergenic 55.0%
AGGATGCTGGCGAGATCTTG+AGG + chr2_3:4082070-4082089 None:intergenic 55.0%
AAGATCTCGCCAGCATCCTG+TGG - chr2_3:4082071-4082090 Msa0272550:CDS 55.0%
TCTCGCCAGCATCCTGTGGT+TGG - chr2_3:4082075-4082094 Msa0272550:CDS 60.0%
GTCCCATTGTATGGCCGCGG+TGG - chr2_3:4081817-4081836 Msa0272550:CDS 65.0%
GGCCACCGCGGCCATACAAT+GGG + chr2_3:4081822-4081841 None:intergenic 65.0%
TGGCCACCGCGGCCATACAA+TGG + chr2_3:4081823-4081842 None:intergenic 65.0%
TCGGTGGAGCGTGGCCACCG+CGG + chr2_3:4081834-4081853 None:intergenic 75.0%
GGTGGCCACGCTCCACCGAG+TGG - chr2_3:4081835-4081854 Msa0272550:CDS 75.0%
CGGCGGGTGGCCGACTACTC+CGG + chr2_3:4082124-4082143 None:intergenic 75.0%
Chromosome Type Strat End Strand Name
chr2_3 gene 4081559 4082272 4081559 ID=Msa0272550;Name=Msa0272550
chr2_3 mRNA 4081559 4082272 4081559 ID=Msa0272550-mRNA-1;Parent=Msa0272550;Name=Msa0272550-mRNA-1;_AED=0.20;_eAED=0.21;_QI=0|-1|0|1|-1|1|1|0|237
chr2_3 exon 4081559 4082272 4081559 ID=Msa0272550-mRNA-1:exon:2061;Parent=Msa0272550-mRNA-1
chr2_3 CDS 4081559 4082272 4081559 ID=Msa0272550-mRNA-1:cds;Parent=Msa0272550-mRNA-1
Gene Sequence

>Msa0272550

ATGGCATTTGAGCACTGTTTTTCCCATGAATTGAAAACCATTCCAAATTCCATGTCAGAAGCAGAAGATTCCAATGGTTGTTTTGATTGCAACATCTGCTTAGACTTCGCCAACGAACCGGTAGTCACCCTTTGTGGCCACCTTTACTGCTGGCCTTGCATCTACAAGTGGCTCCATGTTCAAAGTGATGATTCTCTTGGATCTGATGAACATCCACAATGTCCTGTATGCAAAGAAAATATATCACATACCACAATGGTCCCATTGTATGGCCGCGGTGGCCACGCTCCACCGAGTGGAAAATCTTCTTGTTGTGATGATAATTTTGTACCACCAAGACCAACTGCTTCAGGTGCTCAAGCTCTTTTGGCAACAGCTTCTCAAAGTGATCATCATCAGCGACTTCCGTATCGAAATCCTTATCAGGGACAATATTTAAACTCTTCCTCATACCAACAACAAGAGGGTGATGCTACTTCACAAATGCTTAGTCTTGGTGCCTCAACGACCTCAAGATCTCGCCAGCATCCTGTGGTTGGAATGTTCGAGGAGATGATTTTTGCCGGAGTAGTCGGCCACCCGCCGAATTCTTATCAGATGGTGGGAAATAATAGCTCTAGATTGAGAAGGCAAGAGTTGCAGACTGATAAATTTTTGAACAGAATTTCAAATTTTCTATTTTGCTGTTTTCTTTTGTGTCTTATTGTCTTTTGA

Protein sequence

>Msa0272550

MAFEHCFSHELKTIPNSMSEAEDSNGCFDCNICLDFANEPVVTLCGHLYCWPCIYKWLHVQSDDSLGSDEHPQCPVCKENISHTTMVPLYGRGGHAPPSGKSSCCDDNFVPPRPTASGAQALLATASQSDHHQRLPYRNPYQGQYLNSSSYQQQEGDATSQMLSLGASTTSRSRQHPVVGMFEEMIFAGVVGHPPNSYQMVGNNSSRLRRQELQTDKFLNRISNFLFCCFLLCLIVF*