AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0528990


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0528990 MtrunA17_Chr1g0187161 90.000 70 7 0 1 70 1 70 4.19e-42 131
Msa0528990 MtrunA17_Chr1g0187221 83.824 68 11 0 3 70 5 72 1.46e-36 117
Msa0528990 MtrunA17_Chr5g0442291 84.286 70 11 0 1 70 1 70 2.17e-36 116
Msa0528990 MtrunA17_Chr1g0187201 79.412 68 14 0 3 70 4 71 6.68e-32 105
Msa0528990 MtrunA17_Chr1g0184401 57.576 66 28 0 5 70 8 73 9.20e-23 82.4
Msa0528990 MtrunA17_Chr1g0184411 54.286 70 32 0 1 70 1 70 7.06e-22 80.1
Msa0528990 MtrunA17_Chr5g0419531 53.731 67 31 0 4 70 3 69 5.34e-19 72.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0528990 AT2G38870.1 52.857 70 33 0 1 70 1 70 1.51e-21 79.7
Msa0528990 AT5G43580.1 55.556 72 30 1 1 70 28 99 5.06e-21 79.0
Msa0528990 AT3G46860.1 46.032 63 34 0 8 70 23 85 4.13e-13 58.5
Msa0528990 AT5G43570.1 46.575 73 33 1 1 67 1 73 6.27e-12 56.2
Msa0528990 AT2G38900.1 42.188 64 37 0 7 70 10 73 2.12e-11 53.9
Msa0528990 AT2G38900.2 42.188 64 37 0 7 70 25 88 3.22e-11 53.9
Msa0528990 AT5G43570.2 50.000 60 30 0 8 67 24 83 6.66e-11 53.9

Find 32 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTTCCACTCCAACCAATTC+TGG 0.174728 4_1:+1991215 None:intergenic
CTGTGACAGGGTTTGGGTTT+GGG 0.259063 4_1:-1991102 Msa0528990:CDS
ACTTCCGCTGTGACAGGGTT+TGG 0.267379 4_1:-1991109 Msa0528990:CDS
CTTCCGCTGTGACAGGGTTT+GGG 0.309008 4_1:-1991108 Msa0528990:CDS
TATATACCACAAACACAAAT+AGG 0.312173 4_1:-1991421 Msa0528990:five_prime_UTR
GCTGTGACAGGGTTTGGGTT+TGG 0.326505 4_1:-1991103 Msa0528990:CDS
TAAAGATGGAATTGTCTATC+AGG 0.326953 4_1:-1991075 Msa0528990:CDS
CCTTTGACTTCCGCTGTGAC+AGG 0.333094 4_1:-1991115 Msa0528990:CDS
ATAAATTTAATGTTACAATA+AGG 0.340780 4_1:-1990995 Msa0528990:three_prime_UTR
TAAGAGTTCATGGCCAGAAT+TGG 0.414180 4_1:-1991228 Msa0528990:CDS
ATAGTAGTATAGTATAGAAT+TGG 0.416384 4_1:+1990957 None:intergenic
TGGGTTTGGGTTAATAAAGA+TGG 0.418377 4_1:-1991089 Msa0528990:CDS
TGTGGTCAGGTAAGAGTTCA+TGG 0.426967 4_1:-1991238 Msa0528990:intron
GTAACATTAAATTTATAACT+TGG 0.441318 4_1:+1991002 None:intergenic
AAATTGGATAGAAAGTTTCA+TGG 0.443912 4_1:-1991046 Msa0528990:exon
CTTTGACTTCCGCTGTGACA+GGG 0.463269 4_1:-1991114 Msa0528990:CDS
CTGTCACAGCGGAAGTCAAA+GGG 0.467050 4_1:+1991116 None:intergenic
GATGCCATCATTGTGCTAGA+AGG 0.504821 4_1:-1991149 Msa0528990:CDS
CCAGAATTGGTTGGAGTGGA+AGG 0.515293 4_1:-1991215 Msa0528990:CDS
AGTTCCTTCTAGCACAATGA+TGG 0.538007 4_1:+1991145 None:intergenic
AATTCAGAGGGAGAATCCAT+TGG 0.542280 4_1:-1991174 Msa0528990:CDS
ATATAATGCATTGCAATGTA+TGG 0.542822 4_1:+1991439 None:intergenic
CCTGTCACAGCGGAAGTCAA+AGG 0.545493 4_1:+1991115 None:intergenic
ATGGCCAGAATTGGTTGGAG+TGG 0.561764 4_1:-1991219 Msa0528990:CDS
AGTTCATGGCCAGAATTGGT+TGG 0.565712 4_1:-1991224 Msa0528990:CDS
ATTGGTTGGAGTGGAAGGAA+AGG 0.570071 4_1:-1991210 Msa0528990:CDS
AGCAGAAGCTACAATTCAGA+GGG 0.593359 4_1:-1991186 Msa0528990:CDS
TAGCAGAAGCTACAATTCAG+AGG 0.596029 4_1:-1991187 Msa0528990:CDS
ACAATGATGGCATCAACCAA+TGG 0.650325 4_1:+1991158 None:intergenic
AAAATGTCTGATGAATGCAA+AGG 0.675933 4_1:-1991392 Msa0528990:intron
TGTCACAGCGGAAGTCAAAG+GGG 0.698463 4_1:+1991117 None:intergenic
AAACCCAAACCCTGTCACAG+CGG 0.730650 4_1:+1991105 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATATGAATAATAAATTGAA+TGG - chr4_1:1991037-1991056 Msa0528990:three_prime_UTR 10.0%
!! ATAAATTTAATGTTACAATA+AGG - chr4_1:1991350-1991369 Msa0528990:intron 10.0%
!!! TTACATGCATATATATTTTT+TGG - chr4_1:1991000-1991019 Msa0528990:three_prime_UTR 15.0%
!! GTAACATTAAATTTATAACT+TGG + chr4_1:1991346-1991365 None:intergenic 15.0%
!! TTGTAATAAAAAAACCCATA+AGG - chr4_1:1990856-1990875 Msa0528990:three_prime_UTR 20.0%
!! ATAGTAGTATAGTATAGAAT+TGG + chr4_1:1991391-1991410 None:intergenic 20.0%
!!! GTATTTATAGTAGTTTTTGG+TGG + chr4_1:1990885-1990904 None:intergenic 25.0%
!! GGTGTATTTATAGTAGTTTT+TGG + chr4_1:1990888-1990907 None:intergenic 25.0%
! ATATAATGCATTGCAATGTA+TGG + chr4_1:1990909-1990928 None:intergenic 25.0%
! TATATACCACAAACACAAAT+AGG - chr4_1:1990924-1990943 Msa0528990:three_prime_UTR 25.0%
! TTGAATGAATCAATATTGTG+TGG - chr4_1:1991089-1991108 Msa0528990:CDS 25.0%
!! GAAACTTTCTATCCAATTTT+TGG + chr4_1:1991298-1991317 None:intergenic 25.0%
! AAATTGGATAGAAAGTTTCA+TGG - chr4_1:1991299-1991318 Msa0528990:intron 25.0%
!! AACTTGTAATTCGTTTTCTT+TGG - chr4_1:1991458-1991477 Msa0528990:five_prime_UTR 25.0%
! TTTTTGCCTATTTGTGTTTG+TGG + chr4_1:1990933-1990952 None:intergenic 30.0%
AAAATGTCTGATGAATGCAA+AGG - chr4_1:1990953-1990972 Msa0528990:three_prime_UTR 30.0%
TAAAGATGGAATTGTCTATC+AGG - chr4_1:1991270-1991289 Msa0528990:intron 30.0%
!!! GTTTTTGGTGGAAACCTTAT+GGG + chr4_1:1990873-1990892 None:intergenic 35.0%
!!! AGTTTTTGGTGGAAACCTTA+TGG + chr4_1:1990874-1990893 None:intergenic 35.0%
TGAATCAATATTGTGTGGTC+AGG - chr4_1:1991094-1991113 Msa0528990:CDS 35.0%
! TGGGTTTGGGTTAATAAAGA+TGG - chr4_1:1991256-1991275 Msa0528990:intron 35.0%
GTCTATCAGGTTCCAAAAAT+TGG - chr4_1:1991283-1991302 Msa0528990:intron 35.0%
GTCTGATGAATGCAAAGGTA+AGG - chr4_1:1990958-1990977 Msa0528990:three_prime_UTR 40.0%
TAAGAGTTCATGGCCAGAAT+TGG - chr4_1:1991117-1991136 Msa0528990:CDS 40.0%
TAGCAGAAGCTACAATTCAG+AGG - chr4_1:1991158-1991177 Msa0528990:CDS 40.0%
AGCAGAAGCTACAATTCAGA+GGG - chr4_1:1991159-1991178 Msa0528990:CDS 40.0%
AATTCAGAGGGAGAATCCAT+TGG - chr4_1:1991171-1991190 Msa0528990:CDS 40.0%
ACAATGATGGCATCAACCAA+TGG + chr4_1:1991190-1991209 None:intergenic 40.0%
AGTTCCTTCTAGCACAATGA+TGG + chr4_1:1991203-1991222 None:intergenic 40.0%
TGTGGTCAGGTAAGAGTTCA+TGG - chr4_1:1991107-1991126 Msa0528990:CDS 45.0%
AGTTCATGGCCAGAATTGGT+TGG - chr4_1:1991121-1991140 Msa0528990:CDS 45.0%
ATTGGTTGGAGTGGAAGGAA+AGG - chr4_1:1991135-1991154 Msa0528990:CDS 45.0%
GATGCCATCATTGTGCTAGA+AGG - chr4_1:1991196-1991215 Msa0528990:CDS 45.0%
ATGGCCAGAATTGGTTGGAG+TGG - chr4_1:1991126-1991145 Msa0528990:CDS 50.0%
CCTTCCACTCCAACCAATTC+TGG + chr4_1:1991133-1991152 None:intergenic 50.0%
CCAGAATTGGTTGGAGTGGA+AGG - chr4_1:1991130-1991149 Msa0528990:CDS 50.0%
TGTCACAGCGGAAGTCAAAG+GGG + chr4_1:1991231-1991250 None:intergenic 50.0%
CTGTCACAGCGGAAGTCAAA+GGG + chr4_1:1991232-1991251 None:intergenic 50.0%
! CTTTGACTTCCGCTGTGACA+GGG - chr4_1:1991231-1991250 Msa0528990:CDS 50.0%
AAACCCAAACCCTGTCACAG+CGG + chr4_1:1991243-1991262 None:intergenic 50.0%
! CTGTGACAGGGTTTGGGTTT+GGG - chr4_1:1991243-1991262 Msa0528990:intron 50.0%
CCTGTCACAGCGGAAGTCAA+AGG + chr4_1:1991233-1991252 None:intergenic 55.0%
! CCTTTGACTTCCGCTGTGAC+AGG - chr4_1:1991230-1991249 Msa0528990:CDS 55.0%
ACTTCCGCTGTGACAGGGTT+TGG - chr4_1:1991236-1991255 Msa0528990:intron 55.0%
CTTCCGCTGTGACAGGGTTT+GGG - chr4_1:1991237-1991256 Msa0528990:intron 55.0%
! GCTGTGACAGGGTTTGGGTT+TGG - chr4_1:1991242-1991261 Msa0528990:intron 55.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 1990856 1991511 1990856 ID=Msa0528990;Name=Msa0528990
chr4_1 mRNA 1990856 1991511 1990856 ID=Msa0528990-mRNA-1;Parent=Msa0528990;Name=Msa0528990-mRNA-1;_AED=0.00;_eAED=0.00;_QI=100|1|1|1|1|1|2|202|70
chr4_1 exon 1990856 1991251 1990856 ID=Msa0528990-mRNA-1:exon:642;Parent=Msa0528990-mRNA-1
chr4_1 exon 1991393 1991511 1991393 ID=Msa0528990-mRNA-1:exon:641;Parent=Msa0528990-mRNA-1
chr4_1 five_prime_UTR 1991412 1991511 1991412 ID=Msa0528990-mRNA-1:five_prime_utr;Parent=Msa0528990-mRNA-1
chr4_1 CDS 1991393 1991411 1991393 ID=Msa0528990-mRNA-1:cds;Parent=Msa0528990-mRNA-1
chr4_1 CDS 1991058 1991251 1991058 ID=Msa0528990-mRNA-1:cds;Parent=Msa0528990-mRNA-1
chr4_1 three_prime_UTR 1990856 1991057 1990856 ID=Msa0528990-mRNA-1:three_prime_utr;Parent=Msa0528990-mRNA-1
Gene Sequence

>Msa0528990

ATGTCTGATGAATGCAAAGGTAAGAGTTCATGGCCAGAATTGGTTGGAGTGGAAGGAAAGGTAGCAGAAGCTACAATTCAGAGGGAGAATCCATTGGTTGATGCCATCATTGTGCTAGAAGGAACTGATGTCCCCTTTGACTTCCGCTGTGACAGGGTTTGGGTTTGGGTTAATAAAGATGGAATTGTCTATCAGGTTCCAAAAATTGGATAG

Protein sequence

>Msa0528990

MSDECKGKSSWPELVGVEGKVAEATIQRENPLVDAIIVLEGTDVPFDFRCDRVWVWVNKDGIVYQVPKIG*