AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0515130


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0515130 MtrunA17_Chr3g0124061 93.970 199 12 0 1 199 1 199 7.28e-141 390
Msa0515130 MtrunA17_Chr3g0124111 88.945 199 22 0 1 199 1 199 7.68e-133 370
Msa0515130 MtrunA17_Chr3g0124141 86.935 199 26 0 1 199 1 199 4.41e-127 356
Msa0515130 MtrunA17_Chr3g0124091 85.075 201 27 2 1 199 1 200 9.55e-122 342
Msa0515130 MtrunA17_Chr3g0124151 84.906 106 16 0 94 199 1 106 1.18e-62 189
Msa0515130 MtrunA17_Chr3g0124131 80.000 50 10 0 1 50 1 50 4.66e-24 89.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0515130 AT5G65030.1 30.964 197 124 3 11 199 10 202 2.00e-26 100
Msa0515130 AT5G10210.1 32.124 193 109 7 15 196 13 194 2.03e-24 95.5

Find 36 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTTGCCCCAAAGAATTCT+TGG 0.233772 3_4:-66165170 Msa0515130:CDS
CTACCAAATCAGTACCCTTT+TGG 0.251571 3_4:-66165216 Msa0515130:CDS
ATAAGAGTAGGTTGAATAAT+TGG 0.258714 3_4:-66164901 Msa0515130:CDS
TTAATCTCCACTTCTACTTC+TGG 0.271949 3_4:+66164962 None:intergenic
TGCGCTTGGCGCAGCTTTGG+AGG 0.349292 3_4:-66164810 Msa0515130:CDS
AGCTAAGGCAAAGGAAGATA+TGG 0.356544 3_4:-66165117 Msa0515130:CDS
ATTTGCGCTTGGCGCAGCTT+TGG 0.402289 3_4:-66164813 Msa0515130:CDS
GCTCCAACACTAGGCTTTGT+TGG 0.406615 3_4:+66165137 None:intergenic
AGTGGCTTCGGTTCATGAAA+TGG 0.417821 3_4:-66164933 Msa0515130:CDS
GTCCCAAAAGGGTACTGATT+TGG 0.428896 3_4:+66165213 None:intergenic
GATTCAAGAATCACTTTCCA+TGG 0.437928 3_4:+66165064 None:intergenic
GCAAGGCTGTATCTTCCAAC+AGG 0.447411 3_4:-66165277 Msa0515130:CDS
GATTAAAATAAGAGTGGCTT+CGG 0.448073 3_4:-66164945 Msa0515130:CDS
TGCACCAAGCGCGATGATCA+TGG 0.461361 3_4:+66164855 None:intergenic
GCTAAGGCAAAGGAAGATAT+GGG 0.463318 3_4:-66165116 Msa0515130:CDS
ATTAAATGACTCGTCCCAAA+AGG 0.469911 3_4:+66165201 None:intergenic
TTGGAAAAGGTGAGATTCCA+TGG 0.470388 3_4:-66165081 Msa0515130:CDS
AAAGCCTAGTGTTGGAGCTA+AGG 0.499139 3_4:-66165132 Msa0515130:CDS
TTTGCCTTAGCTCCAACACT+AGG 0.507447 3_4:+66165128 None:intergenic
CAACTGAAGTTTGCATATGC+AGG 0.509989 3_4:+66165361 None:intergenic
GGGTCACAACTTATTGGAAA+AGG 0.523568 3_4:-66165094 Msa0515130:CDS
TTAAATGACTCGTCCCAAAA+GGG 0.547621 3_4:+66165202 None:intergenic
AGTGGAGATTAAAATAAGAG+TGG 0.548596 3_4:-66164951 Msa0515130:CDS
AATGAGTGTGGATGCAAGAA+TGG 0.549203 3_4:-66164878 Msa0515130:CDS
ATGGCCATGATCATCGCGCT+TGG 0.550412 3_4:-66164859 Msa0515130:CDS
GATTGTGATATATTTGCGCT+TGG 0.560902 3_4:-66164824 Msa0515130:CDS
TAACCAACAAAGCCTAGTGT+TGG 0.564525 3_4:-66165140 Msa0515130:CDS
CTCAACACCAGAAGTAGAAG+TGG 0.577557 3_4:-66164969 Msa0515130:CDS
TTGAATAATTGGAATGAGTG+TGG 0.579695 3_4:-66164890 Msa0515130:CDS
GATTCTTGAATCACAAAACA+TGG 0.583125 3_4:-66165053 Msa0515130:CDS
TAGTGTTGGAGCTAAGGCAA+AGG 0.590191 3_4:-66165126 Msa0515130:CDS
TTGAAGATGTATTTAGTGAG+TGG 0.629374 3_4:-66165016 Msa0515130:CDS
GAGTGGAAGTGATTGCAAAG+AGG 0.644927 3_4:-66164999 Msa0515130:CDS
AAACGTTGAATTCATCAAGT+CGG 0.660973 3_4:-66165314 Msa0515130:CDS
CTAAGGCAAAGGAAGATATG+GGG 0.679009 3_4:-66165115 Msa0515130:CDS
TAAGGCAAAGGAAGATATGG+GGG 0.682962 3_4:-66165114 Msa0515130:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGATTTTCCAAGAATTCTTT+GGG + chr3_4:66165021-66165040 None:intergenic 25.0%
!! AAGATTTTCCAAGAATTCTT+TGG + chr3_4:66165022-66165041 None:intergenic 25.0%
! AAAACATGGAGTTGAAAAAA+TGG - chr3_4:66165142-66165161 Msa0515130:CDS 25.0%
! TGGAAAAGAAAAATAAGAGT+AGG - chr3_4:66165268-66165287 Msa0515130:CDS 25.0%
!! ATAAGAGTAGGTTGAATAAT+TGG - chr3_4:66165280-66165299 Msa0515130:CDS 25.0%
AAACGTTGAATTCATCAAGT+CGG - chr3_4:66164867-66164886 Msa0515130:CDS 30.0%
!!! ATACTTTTGTTGTTTCCTGT+TGG + chr3_4:66164922-66164941 None:intergenic 30.0%
! GATTTTCCAAGAATTCTTTG+GGG + chr3_4:66165020-66165039 None:intergenic 30.0%
GATTCTTGAATCACAAAACA+TGG - chr3_4:66165128-66165147 Msa0515130:CDS 30.0%
TTGAAGATGTATTTAGTGAG+TGG - chr3_4:66165165-66165184 Msa0515130:CDS 30.0%
AGTGGAGATTAAAATAAGAG+TGG - chr3_4:66165230-66165249 Msa0515130:CDS 30.0%
GATTAAAATAAGAGTGGCTT+CGG - chr3_4:66165236-66165255 Msa0515130:CDS 30.0%
TTGAATAATTGGAATGAGTG+TGG - chr3_4:66165291-66165310 Msa0515130:CDS 30.0%
! TACCAAATCAGTACCCTTTT+GGG - chr3_4:66164966-66164985 Msa0515130:CDS 35.0%
TTAAATGACTCGTCCCAAAA+GGG + chr3_4:66164982-66165001 None:intergenic 35.0%
ATTAAATGACTCGTCCCAAA+AGG + chr3_4:66164983-66165002 None:intergenic 35.0%
GATTCAAGAATCACTTTCCA+TGG + chr3_4:66165120-66165139 None:intergenic 35.0%
TTAATCTCCACTTCTACTTC+TGG + chr3_4:66165222-66165241 None:intergenic 35.0%
GATTGTGATATATTTGCGCT+TGG - chr3_4:66165357-66165376 Msa0515130:CDS 35.0%
CAACTGAAGTTTGCATATGC+AGG + chr3_4:66164823-66164842 None:intergenic 40.0%
CGGCAAAAAACATGTTTGCA+AGG - chr3_4:66164887-66164906 Msa0515130:CDS 40.0%
! CTACCAAATCAGTACCCTTT+TGG - chr3_4:66164965-66164984 Msa0515130:CDS 40.0%
TTCTTGCCCCAAAGAATTCT+TGG - chr3_4:66165011-66165030 Msa0515130:CDS 40.0%
TAACCAACAAAGCCTAGTGT+TGG - chr3_4:66165041-66165060 Msa0515130:CDS 40.0%
AGCTAAGGCAAAGGAAGATA+TGG - chr3_4:66165064-66165083 Msa0515130:CDS 40.0%
GCTAAGGCAAAGGAAGATAT+GGG - chr3_4:66165065-66165084 Msa0515130:CDS 40.0%
CTAAGGCAAAGGAAGATATG+GGG - chr3_4:66165066-66165085 Msa0515130:CDS 40.0%
TAAGGCAAAGGAAGATATGG+GGG - chr3_4:66165067-66165086 Msa0515130:CDS 40.0%
ATATGGGGGTCACAACTTAT+TGG - chr3_4:66165081-66165100 Msa0515130:CDS 40.0%
GGGTCACAACTTATTGGAAA+AGG - chr3_4:66165087-66165106 Msa0515130:CDS 40.0%
TTGGAAAAGGTGAGATTCCA+TGG - chr3_4:66165100-66165119 Msa0515130:CDS 40.0%
AATGAGTGTGGATGCAAGAA+TGG - chr3_4:66165303-66165322 Msa0515130:CDS 40.0%
! GCATATGCAGGTGTTTTCGA+TGG + chr3_4:66164811-66164830 None:intergenic 45.0%
!! GTCCCAAAAGGGTACTGATT+TGG + chr3_4:66164971-66164990 None:intergenic 45.0%
! AAAGCCTAGTGTTGGAGCTA+AGG - chr3_4:66165049-66165068 Msa0515130:CDS 45.0%
TTTGCCTTAGCTCCAACACT+AGG + chr3_4:66165056-66165075 None:intergenic 45.0%
! TAGTGTTGGAGCTAAGGCAA+AGG - chr3_4:66165055-66165074 Msa0515130:CDS 45.0%
GAGTGGAAGTGATTGCAAAG+AGG - chr3_4:66165182-66165201 Msa0515130:CDS 45.0%
CTCAACACCAGAAGTAGAAG+TGG - chr3_4:66165212-66165231 Msa0515130:CDS 45.0%
AGTGGCTTCGGTTCATGAAA+TGG - chr3_4:66165248-66165267 Msa0515130:CDS 45.0%
GCAAGGCTGTATCTTCCAAC+AGG - chr3_4:66164904-66164923 Msa0515130:CDS 50.0%
! GCTCCAACACTAGGCTTTGT+TGG + chr3_4:66165047-66165066 None:intergenic 50.0%
ATGGCCATGATCATCGCGCT+TGG - chr3_4:66165322-66165341 Msa0515130:CDS 55.0%
TGCACCAAGCGCGATGATCA+TGG + chr3_4:66165329-66165348 None:intergenic 55.0%
ATTTGCGCTTGGCGCAGCTT+TGG - chr3_4:66165368-66165387 Msa0515130:CDS 55.0%
! TGCGCTTGGCGCAGCTTTGG+AGG - chr3_4:66165371-66165390 Msa0515130:CDS 65.0%
Chromosome Type Strat End Strand Name
chr3_4 gene 66164802 66165401 66164802 ID=Msa0515130;Name=Msa0515130
chr3_4 mRNA 66164802 66165401 66164802 ID=Msa0515130-mRNA-1;Parent=Msa0515130;Name=Msa0515130-mRNA-1;_AED=0.40;_eAED=0.40;_QI=0|-1|0|1|-1|1|1|0|199
chr3_4 exon 66164802 66165401 66164802 ID=Msa0515130-mRNA-1:exon:17025;Parent=Msa0515130-mRNA-1
chr3_4 CDS 66164802 66165401 66164802 ID=Msa0515130-mRNA-1:cds;Parent=Msa0515130-mRNA-1
Gene Sequence

>Msa0515130

ATGGATCCATCGAAAACACCTGCATATGCAAACTTCAGTTGTGAACTGAGAATAATACAAGCACGAAACGTTGAATTCATCAAGTCGGCAAAAAACATGTTTGCAAGGCTGTATCTTCCAACAGGAAACAACAAAAGTATTCAACTCAACAGCAAAAAAGTTTCTACCAAATCAGTACCCTTTTGGGACGAGTCATTTAATCTAGATTGTTCTTGCCCCAAAGAATTCTTGGAAAATCTTAACCAACAAAGCCTAGTGTTGGAGCTAAGGCAAAGGAAGATATGGGGGTCACAACTTATTGGAAAAGGTGAGATTCCATGGAAAGTGATTCTTGAATCACAAAACATGGAGTTGAAAAAATGGTTGAAGATGTATTTAGTGAGTGGAAGTGATTGCAAAGAGGAAATGTTCTCAACACCAGAAGTAGAAGTGGAGATTAAAATAAGAGTGGCTTCGGTTCATGAAATGGAAAAGAAAAATAAGAGTAGGTTGAATAATTGGAATGAGTGTGGATGCAAGAATGGCCATGATCATCGCGCTTGGTGCAGCGCTGAAGATTGTGATATATTTGCGCTTGGCGCAGCTTTGGAGGCTTTTTGA

Protein sequence

>Msa0515130

MDPSKTPAYANFSCELRIIQARNVEFIKSAKNMFARLYLPTGNNKSIQLNSKKVSTKSVPFWDESFNLDCSCPKEFLENLNQQSLVLELRQRKIWGSQLIGKGEIPWKVILESQNMELKKWLKMYLVSGSDCKEEMFSTPEVEVEIKIRVASVHEMEKKNKSRLNNWNECGCKNGHDHRAWCSAEDCDIFALGAALEAF*