AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0192040


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0192040 MtrunA17_Chr2g0282171 94.515 237 12 1 1 237 1 236 4.29e-159 440
Msa0192040 MtrunA17_Chr4g0047381 55.172 232 80 8 1 223 1 217 2.33e-73 223
Msa0192040 MtrunA17_Chr4g0047371 43.443 244 86 8 1 237 1 199 1.03e-53 171
Msa0192040 MtrunA17_Chr4g0021321 40.851 235 113 7 12 237 27 244 8.69e-47 155
Msa0192040 MtrunA17_Chr8g0360011 41.048 229 123 6 4 223 11 236 4.22e-45 151
Msa0192040 MtrunA17_Chr2g0324261 40.367 218 106 5 19 225 31 235 3.32e-44 149
Msa0192040 MtrunA17_Chr2g0324291 51.923 104 44 3 28 130 30 128 9.95e-29 106
Msa0192040 MtrunA17_Chr2g0324281 56.322 87 25 2 28 114 18 91 2.37e-27 103
Msa0192040 MtrunA17_Chr7g0258821 40.000 120 58 3 10 125 148 257 4.23e-24 99.8
Msa0192040 MtrunA17_Chr1g0175871 44.330 97 52 2 23 117 50 146 4.03e-23 92.8
Msa0192040 MtrunA17_Chr1g0154561 47.253 91 40 2 26 116 30 112 1.11e-22 92.4
Msa0192040 MtrunA17_Chr1g0175571 45.055 91 43 2 26 116 120 203 5.39e-22 90.5
Msa0192040 MtrunA17_Chr5g0403521 54.412 68 24 1 26 93 33 93 9.53e-22 90.1
Msa0192040 MtrunA17_Chr1g0175641 53.125 64 24 1 28 91 76 133 4.11e-21 87.0
Msa0192040 MtrunA17_Chr2g0308681 39.080 87 39 2 14 93 86 165 1.28e-15 73.6
Msa0192040 MtrunA17_Chr1g0150921 36.000 75 38 1 16 90 352 416 3.49e-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
Msa0192040 AT4G03510.3 40.000 240 106 9 13 237 33 249 1.61e-44 150
Msa0192040 AT4G03510.1 40.000 240 106 9 13 237 33 249 1.61e-44 150
Msa0192040 AT4G03510.2 40.000 240 106 9 13 237 33 249 1.61e-44 150
Msa0192040 AT4G03510.4 40.000 240 106 9 13 237 33 249 1.61e-44 150
Msa0192040 AT4G27470.1 40.175 229 97 10 10 223 26 229 2.58e-39 136
Msa0192040 AT4G28270.1 34.375 224 94 5 23 237 14 193 1.51e-36 127
Msa0192040 AT1G74990.1 43.443 122 56 4 11 131 3 112 7.47e-26 98.6
Msa0192040 AT3G58030.4 39.695 131 58 4 16 142 121 234 1.31e-24 101
Msa0192040 AT3G58030.2 39.695 131 58 4 16 142 121 234 1.31e-24 101
Msa0192040 AT3G58030.1 39.695 131 58 4 16 142 121 234 1.31e-24 101
Msa0192040 AT3G58030.3 39.695 131 58 4 16 142 121 234 1.31e-24 101
Msa0192040 AT2G42030.1 44.231 104 47 2 28 131 139 231 1.08e-23 98.6
Msa0192040 AT1G19310.1 59.091 66 20 1 28 93 21 79 5.72e-23 93.6
Msa0192040 AT2G23780.3 49.333 75 31 1 19 93 17 84 9.68e-22 90.1
Msa0192040 AT2G23780.2 49.333 75 31 1 19 93 17 84 9.68e-22 90.1
Msa0192040 AT2G23780.1 49.333 75 31 1 19 93 17 84 9.68e-22 90.1
Msa0192040 AT2G44410.1 33.981 103 49 4 26 122 121 210 3.34e-14 71.6

Find 59 sgRNAs with CRISPR-Local

Find 67 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTGCTTCTGACATGGAATT+TGG 0.134595 2_1:-7783835 None:intergenic
TTCAGGTGCTCAAGCTCTTT+TGG 0.228650 2_1:+7784140 Msa0192040:CDS
TCCGTATCGAAATCCTTATC+AGG 0.353516 2_1:+7784197 Msa0192040:CDS
TTTAAATATTGTCCCTGATA+AGG 0.360067 2_1:-7784210 None:intergenic
CCACCAAGACCAACTGCTTC+AGG 0.366329 2_1:+7784123 Msa0192040:CDS
CCCACCATCCGATAAGAATT+CGG 0.404009 2_1:-7784375 None:intergenic
ACCCTCTTGTTGTTGGTATG+AGG 0.406828 2_1:-7784238 None:intergenic
TTTGTGGCCACCTTTACTGC+TGG 0.418114 2_1:+7783923 Msa0192040:CDS
TAGCATCACCCTCTTGTTGT+TGG 0.423010 2_1:-7784245 None:intergenic
GCACCTGAAGCAGTTGGTCT+TGG 0.423857 2_1:-7784126 None:intergenic
GTTCAAAGTGATGATTCTCT+TGG 0.429642 2_1:+7783970 Msa0192040:CDS
CTTAGACTTCGCCAACGAAC+CGG 0.433237 2_1:+7783891 Msa0192040:CDS
ACCACAATGGTCCCATTGTA+TGG 0.455188 2_1:+7784042 Msa0192040:CDS
CCTGAAGCAGTTGGTCTTGG+TGG 0.457076 2_1:-7784123 None:intergenic
GCCACCCGCCGAATTCTTAT+CGG 0.458532 2_1:+7784367 Msa0192040:CDS
GGCCACCGCGGCCATACAAT+GGG 0.462138 2_1:-7784053 None:intergenic
CGGCGGGTGGCCGACTACTC+CGG 0.478519 2_1:-7784355 None:intergenic
TGGCCACCGCGGCCATACAA+TGG 0.491039 2_1:-7784054 None:intergenic
TTCTGACATGGAATTTGGAA+TGG 0.496636 2_1:-7783830 None:intergenic
GAACCGGTAGTCACCCTTTG+TGG 0.499048 2_1:+7783907 Msa0192040:CDS
AGATGCAAGGCCAGCAGTAA+AGG 0.499222 2_1:-7783933 None:intergenic
GTTGCAATCAAAACAACCAT+TGG 0.524152 2_1:-7783863 None:intergenic
ACTTCACAAATGCTTAGTCT+TGG 0.524773 2_1:+7784267 Msa0192040:CDS
CCCTGATAAGGATTTCGATA+CGG 0.531451 2_1:-7784198 None:intergenic
GCAGTAAAGGTGGCCACAAA+GGG 0.540437 2_1:-7783920 None:intergenic
GGAATCTTCTGCTTCTGACA+TGG 0.544972 2_1:-7783842 None:intergenic
ACATTCCAACCACAGGATGC+TGG 0.545754 2_1:-7784314 None:intergenic
TCCTGTGGTTGGAATGTTCG+AGG 0.548858 2_1:+7784320 Msa0192040:CDS
TCTCGCCAGCATCCTGTGGT+TGG 0.550366 2_1:+7784309 Msa0192040:CDS
AGCAGTAAAGGTGGCCACAA+AGG 0.557862 2_1:-7783921 None:intergenic
AGGATGCTGGCGAGATCTTG+AGG 0.565005 2_1:-7784301 None:intergenic
ATGGTCCCATTGTATGGCCG+CGG 0.566563 2_1:+7784048 Msa0192040:CDS
TCCTCGAACATTCCAACCAC+AGG 0.567924 2_1:-7784321 None:intergenic
GCCGAATTCTTATCGGATGG+TGG 0.570212 2_1:+7784374 Msa0192040:CDS
AAGGGTGACTACCGGTTCGT+TGG 0.577209 2_1:-7783902 None:intergenic
CCATCCGATAAGAATTCGGC+GGG 0.577298 2_1:-7784371 None:intergenic
GCTGGCCTTGCATCTACAAG+TGG 0.589809 2_1:+7783941 Msa0192040:CDS
GTCCCATTGTATGGCCGCGG+TGG 0.589992 2_1:+7784051 Msa0192040:CDS
AAGATCTCGCCAGCATCCTG+TGG 0.590620 2_1:+7784305 Msa0192040:CDS
GCTTGAGCACCTGAAGCAGT+TGG 0.591446 2_1:-7784132 None:intergenic
CCGAATTCTTATCGGATGGT+GGG 0.591726 2_1:+7784375 Msa0192040:CDS
ATAATAGCTCTAGATTGAGA+AGG 0.602529 2_1:+7784400 Msa0192040:CDS
TCCGATAAGAATTCGGCGGG+TGG 0.603859 2_1:-7784368 None:intergenic
TGGCCACAAAGGGTGACTAC+CGG 0.604390 2_1:-7783910 None:intergenic
TGGAGCCACTTGTAGATGCA+AGG 0.606645 2_1:-7783946 None:intergenic
CCCGCCGAATTCTTATCGGA+TGG 0.607422 2_1:+7784371 Msa0192040:CDS
TGCAAGGCCAGCAGTAAAGG+TGG 0.611126 2_1:-7783930 None:intergenic
TCTTTGCATACAGGACATTG+TGG 0.614114 2_1:-7784006 None:intergenic
TTCCTCATACCAACAACAAG+AGG 0.616354 2_1:+7784236 Msa0192040:CDS
GAGAATCATCACTTTGAACA+TGG 0.619892 2_1:-7783966 None:intergenic
CCGTATCGAAATCCTTATCA+GGG 0.628835 2_1:+7784198 Msa0192040:CDS
TCGGTGGAGCGTGGCCACCG+CGG 0.635955 2_1:-7784065 None:intergenic
GCGAGATCTTGAGGTCGTTG+AGG 0.655268 2_1:-7784292 None:intergenic
GCCATACAATGGGACCATTG+TGG 0.655448 2_1:-7784043 None:intergenic
ACCATCCGATAAGAATTCGG+CGG 0.670812 2_1:-7784372 None:intergenic
TCAGAAGCAGAAGATTCCAA+TGG 0.671202 2_1:+7783847 Msa0192040:CDS
TCCTCATACCAACAACAAGA+GGG 0.675909 2_1:+7784237 Msa0192040:CDS
AAATATATCACATACCACAA+TGG 0.681589 2_1:+7784029 Msa0192040:CDS
GGTGGCCACGCTCCACCGAG+TGG 0.693866 2_1:+7784069 Msa0192040:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GATATATTTTCTTTGCATAC+AGG - chr2_1:7784018-7784037 None:intergenic 25.0%
! AAATATATCACATACCACAA+TGG + chr2_1:7784029-7784048 Msa0192040:CDS 25.0%
! TTTAAATATTGTCCCTGATA+AGG - chr2_1:7784213-7784232 None:intergenic 25.0%
! TGGAATGGTTTTCAATTCAT+GGG - chr2_1:7783818-7783837 None:intergenic 30.0%
! TTGGAATGGTTTTCAATTCA+TGG - chr2_1:7783819-7783838 None:intergenic 30.0%
!! ATAATAGCTCTAGATTGAGA+AGG + chr2_1:7784400-7784419 Msa0192040:CDS 30.0%
TTCTGACATGGAATTTGGAA+TGG - chr2_1:7783833-7783852 None:intergenic 35.0%
GTTGCAATCAAAACAACCAT+TGG - chr2_1:7783866-7783885 None:intergenic 35.0%
GAGAATCATCACTTTGAACA+TGG - chr2_1:7783969-7783988 None:intergenic 35.0%
GTTCAAAGTGATGATTCTCT+TGG + chr2_1:7783970-7783989 Msa0192040:CDS 35.0%
! CAACAAGAAGATTTTCCACT+CGG - chr2_1:7784087-7784106 None:intergenic 35.0%
ACTTCACAAATGCTTAGTCT+TGG + chr2_1:7784267-7784286 Msa0192040:CDS 35.0%
TCTGCTTCTGACATGGAATT+TGG - chr2_1:7783838-7783857 None:intergenic 40.0%
TCAGAAGCAGAAGATTCCAA+TGG + chr2_1:7783847-7783866 Msa0192040:CDS 40.0%
TCTTTGCATACAGGACATTG+TGG - chr2_1:7784009-7784028 None:intergenic 40.0%
TCCGTATCGAAATCCTTATC+AGG + chr2_1:7784197-7784216 Msa0192040:CDS 40.0%
CCCTGATAAGGATTTCGATA+CGG - chr2_1:7784201-7784220 None:intergenic 40.0%
CCGTATCGAAATCCTTATCA+GGG + chr2_1:7784198-7784217 Msa0192040:CDS 40.0%
TTCCTCATACCAACAACAAG+AGG + chr2_1:7784236-7784255 Msa0192040:CDS 40.0%
TCCTCATACCAACAACAAGA+GGG + chr2_1:7784237-7784256 Msa0192040:CDS 40.0%
! TTCGAGGAGATGATTTTTGC+CGG + chr2_1:7784336-7784355 Msa0192040:CDS 40.0%
! ATGATTTTTGCCGGAGTAGT+CGG + chr2_1:7784345-7784364 Msa0192040:CDS 40.0%
GGAATCTTCTGCTTCTGACA+TGG - chr2_1:7783845-7783864 None:intergenic 45.0%
ACCACAATGGTCCCATTGTA+TGG + chr2_1:7784042-7784061 Msa0192040:CDS 45.0%
! CAAGAAGATTTTCCACTCGG+TGG - chr2_1:7784084-7784103 None:intergenic 45.0%
! TTCAGGTGCTCAAGCTCTTT+TGG + chr2_1:7784140-7784159 Msa0192040:CDS 45.0%
!! ACCCTCTTGTTGTTGGTATG+AGG - chr2_1:7784241-7784260 None:intergenic 45.0%
! TAGCATCACCCTCTTGTTGT+TGG - chr2_1:7784248-7784267 None:intergenic 45.0%
ACCATCCGATAAGAATTCGG+CGG - chr2_1:7784375-7784394 None:intergenic 45.0%
CCCACCATCCGATAAGAATT+CGG - chr2_1:7784378-7784397 None:intergenic 45.0%
CCGAATTCTTATCGGATGGT+GGG + chr2_1:7784375-7784394 Msa0192040:CDS 45.0%
CTTAGACTTCGCCAACGAAC+CGG + chr2_1:7783891-7783910 Msa0192040:CDS 50.0%
GCAGTAAAGGTGGCCACAAA+GGG - chr2_1:7783923-7783942 None:intergenic 50.0%
AGCAGTAAAGGTGGCCACAA+AGG - chr2_1:7783924-7783943 None:intergenic 50.0%
TTTGTGGCCACCTTTACTGC+TGG + chr2_1:7783923-7783942 Msa0192040:CDS 50.0%
AGATGCAAGGCCAGCAGTAA+AGG - chr2_1:7783936-7783955 None:intergenic 50.0%
TGGAGCCACTTGTAGATGCA+AGG - chr2_1:7783949-7783968 None:intergenic 50.0%
GCCATACAATGGGACCATTG+TGG - chr2_1:7784046-7784065 None:intergenic 50.0%
ACATTCCAACCACAGGATGC+TGG - chr2_1:7784317-7784336 None:intergenic 50.0%
TCCTGTGGTTGGAATGTTCG+AGG + chr2_1:7784320-7784339 Msa0192040:CDS 50.0%
TCCTCGAACATTCCAACCAC+AGG - chr2_1:7784324-7784343 None:intergenic 50.0%
CCATCCGATAAGAATTCGGC+GGG - chr2_1:7784374-7784393 None:intergenic 50.0%
GCCGAATTCTTATCGGATGG+TGG + chr2_1:7784374-7784393 Msa0192040:CDS 50.0%
!! AAGGGTGACTACCGGTTCGT+TGG - chr2_1:7783905-7783924 None:intergenic 55.0%
GAACCGGTAGTCACCCTTTG+TGG + chr2_1:7783907-7783926 Msa0192040:CDS 55.0%
TGGCCACAAAGGGTGACTAC+CGG - chr2_1:7783913-7783932 None:intergenic 55.0%
TGCAAGGCCAGCAGTAAAGG+TGG - chr2_1:7783933-7783952 None:intergenic 55.0%
!! GCTGGCCTTGCATCTACAAG+TGG + chr2_1:7783941-7783960 Msa0192040:CDS 55.0%
ATGGTCCCATTGTATGGCCG+CGG + chr2_1:7784048-7784067 Msa0192040:CDS 55.0%
!! ATTTTCCACTCGGTGGAGCG+TGG - chr2_1:7784077-7784096 None:intergenic 55.0%
!! CCTGAAGCAGTTGGTCTTGG+TGG - chr2_1:7784126-7784145 None:intergenic 55.0%
CCACCAAGACCAACTGCTTC+AGG + chr2_1:7784123-7784142 Msa0192040:CDS 55.0%
! GCACCTGAAGCAGTTGGTCT+TGG - chr2_1:7784129-7784148 None:intergenic 55.0%
GCTTGAGCACCTGAAGCAGT+TGG - chr2_1:7784135-7784154 None:intergenic 55.0%
GCGAGATCTTGAGGTCGTTG+AGG - chr2_1:7784295-7784314 None:intergenic 55.0%
AGGATGCTGGCGAGATCTTG+AGG - chr2_1:7784304-7784323 None:intergenic 55.0%
AAGATCTCGCCAGCATCCTG+TGG + chr2_1:7784305-7784324 Msa0192040:CDS 55.0%
GCCACCCGCCGAATTCTTAT+CGG + chr2_1:7784367-7784386 Msa0192040:CDS 55.0%
TCCGATAAGAATTCGGCGGG+TGG - chr2_1:7784371-7784390 None:intergenic 55.0%
CCCGCCGAATTCTTATCGGA+TGG + chr2_1:7784371-7784390 Msa0192040:CDS 55.0%
TCTCGCCAGCATCCTGTGGT+TGG + chr2_1:7784309-7784328 Msa0192040:CDS 60.0%
GTCCCATTGTATGGCCGCGG+TGG + chr2_1:7784051-7784070 Msa0192040:CDS 65.0%
GGCCACCGCGGCCATACAAT+GGG - chr2_1:7784056-7784075 None:intergenic 65.0%
TGGCCACCGCGGCCATACAA+TGG - chr2_1:7784057-7784076 None:intergenic 65.0%
TCGGTGGAGCGTGGCCACCG+CGG - chr2_1:7784068-7784087 None:intergenic 75.0%
GGTGGCCACGCTCCACCGAG+TGG + chr2_1:7784069-7784088 Msa0192040:CDS 75.0%
CGGCGGGTGGCCGACTACTC+CGG - chr2_1:7784358-7784377 None:intergenic 75.0%
Chromosome Type Strat End Strand Name
chr2_1 gene 7783793 7784506 7783793 ID=Msa0192040;Name=Msa0192040
chr2_1 mRNA 7783793 7784506 7783793 ID=Msa0192040-mRNA-1;Parent=Msa0192040;Name=Msa0192040-mRNA-1;_AED=0.20;_eAED=0.21;_QI=0|-1|0|1|-1|1|1|0|237
chr2_1 exon 7783793 7784506 7783793 ID=Msa0192040-mRNA-1:exon:3576;Parent=Msa0192040-mRNA-1
chr2_1 CDS 7783793 7784506 7783793 ID=Msa0192040-mRNA-1:cds;Parent=Msa0192040-mRNA-1
Gene Sequence

>Msa0192040

ATGGCATTTGAGCACTGTTTTTCCCATGAATTGAAAACCATTCCAAATTCCATGTCAGAAGCAGAAGATTCCAATGGTTGTTTTGATTGCAACATCTGCTTAGACTTCGCCAACGAACCGGTAGTCACCCTTTGTGGCCACCTTTACTGCTGGCCTTGCATCTACAAGTGGCTCCATGTTCAAAGTGATGATTCTCTTGGATCTGATGAACATCCACAATGTCCTGTATGCAAAGAAAATATATCACATACCACAATGGTCCCATTGTATGGCCGCGGTGGCCACGCTCCACCGAGTGGAAAATCTTCTTGTTGTGATGATAATTTTGTACCACCAAGACCAACTGCTTCAGGTGCTCAAGCTCTTTTGGCAACAGCTTCTCAAAGTGATCATCATCAGCGACTTCCGTATCGAAATCCTTATCAGGGACAATATTTAAACTCTTCCTCATACCAACAACAAGAGGGTGATGCTACTTCACAAATGCTTAGTCTTGGTGCCTCAACGACCTCAAGATCTCGCCAGCATCCTGTGGTTGGAATGTTCGAGGAGATGATTTTTGCCGGAGTAGTCGGCCACCCGCCGAATTCTTATCGGATGGTGGGAAATAATAGCTCTAGATTGAGAAGGCAAGAGTTGCAGACTGATAAATTTTTGAACAGAATTTCAAATTTTCTATTTTGCTGTTTTCTTTTGTGTCTTATTGTCTTTTGA

Protein sequence

>Msa0192040

MAFEHCFSHELKTIPNSMSEAEDSNGCFDCNICLDFANEPVVTLCGHLYCWPCIYKWLHVQSDDSLGSDEHPQCPVCKENISHTTMVPLYGRGGHAPPSGKSSCCDDNFVPPRPTASGAQALLATASQSDHHQRLPYRNPYQGQYLNSSSYQQQEGDATSQMLSLGASTTSRSRQHPVVGMFEEMIFAGVVGHPPNSYRMVGNNSSRLRRQELQTDKFLNRISNFLFCCFLLCLIVF*