AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1030710

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1030710 MtrunA17_Chr7g0251841 89.326 178 13 2 1 178 1 172 6.87e-71 212
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1030710 AT1G12830.1 67.500 80 23 1 91 170 116 192 1.76e-16 74.3

Find 59 sgRNAs with CRISPR-Local

Find 68 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTTCGTGGTTGTTGGTTT+CGG 0.192971 7_1:+64922630 None:intergenic
CGTCGATGAGGTTGGATTCT+TGG 0.206975 7_1:+64922515 None:intergenic
TCTTCGTGGTTGTTGGTTTC+GGG 0.218487 7_1:+64922631 None:intergenic
CAGACTGGAGTGCACATTTC+TGG 0.227098 7_1:-64922148 Msa1030710:CDS
GATTCTGACGGCAATGTTTC+GGG 0.258012 7_1:-64922256 Msa1030710:CDS
TCCACTTGCGGAGGTTGATT+TGG 0.320599 7_1:-64922209 Msa1030710:CDS
TGATTCTGACGGCAATGTTT+CGG 0.357245 7_1:-64922257 Msa1030710:CDS
TTCTTGATCGGGTTTGCGTT+TGG 0.373289 7_1:+64922594 None:intergenic
GGATTCTTGGTCTACGGTGG+TGG 0.378862 7_1:+64922528 None:intergenic
AGTAGAATCTAATCAGCATT+TGG 0.400189 7_1:+64922118 None:intergenic
GTGATGGGTTTCTTCTTGAT+CGG 0.423416 7_1:+64922582 None:intergenic
TTCGGGTTCGTTGTTGGGAA+CGG 0.430062 7_1:+64922456 None:intergenic
GTGGTGGGAGTAGTTATCTT+GGG 0.430123 7_1:+64922544 None:intergenic
TGTGGGTTCTTCGTGGTTGT+TGG 0.430236 7_1:+64922624 None:intergenic
TGATGGGTTTCTTCTTGATC+GGG 0.431013 7_1:+64922583 None:intergenic
TTTCCCTTCCTGTCCACCAC+AGG 0.432598 7_1:+64922373 None:intergenic
TTGCGTTTGGTGGGGAATGT+GGG 0.446781 7_1:+64922607 None:intergenic
TGATCGGGTTTGCGTTTGGT+GGG 0.446814 7_1:+64922598 None:intergenic
GTGGTGGACAGGAAGGGAAA+AGG 0.452668 7_1:-64922370 Msa1030710:CDS
TTTGCGTTTGGTGGGGAATG+TGG 0.460274 7_1:+64922606 None:intergenic
ATTGACGGTGGTGGGAAGTT+CGG 0.464983 7_1:+64922492 None:intergenic
ACATTCTTCCGTCTAGGACT+CGG 0.465560 7_1:-64922183 Msa1030710:CDS
TTCGTTGTTGGGAACGGCGT+CGG 0.465767 7_1:+64922462 None:intergenic
GGTGGTGGGAGTAGTTATCT+TGG 0.470330 7_1:+64922543 None:intergenic
TTGATCGGGTTTGCGTTTGG+TGG 0.477903 7_1:+64922597 None:intergenic
ATGCGCGATGACAAGGGAAA+AGG 0.483216 7_1:-64922343 Msa1030710:CDS
TGCGCGATGACAAGGGAAAA+GGG 0.486464 7_1:-64922342 Msa1030710:CDS
ATGAAGAGCCTGTGGTGGAC+AGG 0.489672 7_1:-64922381 Msa1030710:CDS
TGGGGAATGTGGGTTCTTCG+TGG 0.491435 7_1:+64922617 None:intergenic
TGGTGGACAGGAAGGGAAAA+GGG 0.491635 7_1:-64922369 Msa1030710:CDS
GAGGTTGGATTCTTGGTCTA+CGG 0.496324 7_1:+64922522 None:intergenic
GATTCTTGGTCTACGGTGGT+GGG 0.496695 7_1:+64922529 None:intergenic
CGGCGGCGAACTGCTCAGAC+TGG 0.498986 7_1:-64922163 Msa1030710:CDS
GGAAGAAGAATTGACGGTGG+TGG 0.527818 7_1:+64922483 None:intergenic
AAGTTCGGCGTCGATGAGGT+TGG 0.528090 7_1:+64922507 None:intergenic
TGGATAACATTCTTCCGTCT+AGG 0.534730 7_1:-64922189 Msa1030710:CDS
GATCGGGTTTGCGTTTGGTG+GGG 0.540763 7_1:+64922599 None:intergenic
TGGTGGGAGTAGTTATCTTG+GGG 0.541044 7_1:+64922545 None:intergenic
GAAGAAGATGAGGATGATGA+TGG 0.543991 7_1:-64922307 Msa1030710:CDS
GAAGAAGAATTGACGGTGGT+GGG 0.545012 7_1:+64922484 None:intergenic
AGAGCCTGTGGTGGACAGGA+AGG 0.545443 7_1:-64922377 Msa1030710:CDS
TCCAAATCAACCTCCGCAAG+TGG 0.550043 7_1:+64922208 None:intergenic
GGCGTCGGAAGAAGAATTGA+CGG 0.559067 7_1:+64922477 None:intergenic
GTCCACCACAGGCTCTTCAT+CGG 0.559628 7_1:+64922384 None:intergenic
AGGGATTATGCGCGATGACA+AGG 0.562364 7_1:-64922350 Msa1030710:CDS
AATGATTGAAGAAGAAGATG+AGG 0.573565 7_1:-64922317 Msa1030710:CDS
GGGATTATGCGCGATGACAA+GGG 0.589841 7_1:-64922349 Msa1030710:CDS
GAGCCTGTGGTGGACAGGAA+GGG 0.598333 7_1:-64922376 Msa1030710:CDS
TTCTGATGATCCACTTGCGG+AGG 0.598405 7_1:-64922218 Msa1030710:CDS
TTCCGATGAAGAGCCTGTGG+TGG 0.608098 7_1:-64922386 Msa1030710:CDS
TGGGAAGTTCGGCGTCGATG+AGG 0.608955 7_1:+64922503 None:intergenic
GGTGGGAGTAGTTATCTTGG+GGG 0.650526 7_1:+64922546 None:intergenic
CGATGATGAAGACGACGACG+AGG 0.653015 7_1:-64922416 Msa1030710:CDS
GTTGGATTCTTGGTCTACGG+TGG 0.656018 7_1:+64922525 None:intergenic
ACTGGAGTGCACATTTCTGG+TGG 0.678942 7_1:-64922145 Msa1030710:CDS
GATAGCGATGATGATTCTGA+CGG 0.698753 7_1:-64922268 Msa1030710:CDS
GAATTCCGATGAAGAGCCTG+TGG 0.723860 7_1:-64922389 Msa1030710:CDS
TTCTTCCGTCTAGGACTCGG+CGG 0.732545 7_1:-64922180 Msa1030710:CDS
GTCGGAAGAAGAATTGACGG+TGG 0.750092 7_1:+64922480 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AATGATTGAAGAAGAAGATG+AGG - chr7_1:64922449-64922468 Msa1030710:CDS 30.0%
! TTTTTCTGATGATCCACTTG+CGG - chr7_1:64922545-64922564 Msa1030710:CDS 35.0%
!! TTCTTCGTGGTTGTTGGTTT+CGG + chr7_1:64922139-64922158 None:intergenic 40.0%
!! TGATGGGTTTCTTCTTGATC+GGG + chr7_1:64922186-64922205 None:intergenic 40.0%
!! GTGATGGGTTTCTTCTTGAT+CGG + chr7_1:64922187-64922206 None:intergenic 40.0%
!!! GGTTTTGTTAGGAAGGTGAT+GGG + chr7_1:64922202-64922221 None:intergenic 40.0%
!!! GTTATCTTGGGGGTTTTGTT+AGG + chr7_1:64922213-64922232 None:intergenic 40.0%
!!! TTGTTTTCGGGTTCGTTGTT+GGG + chr7_1:64922318-64922337 None:intergenic 40.0%
!!! TCATCGTCAGTGTTGTTTTC+GGG + chr7_1:64922330-64922349 None:intergenic 40.0%
!!! GTCATCGTCAGTGTTGTTTT+CGG + chr7_1:64922331-64922350 None:intergenic 40.0%
GAAGAAGATGAGGATGATGA+TGG - chr7_1:64922459-64922478 Msa1030710:CDS 40.0%
GATAGCGATGATGATTCTGA+CGG - chr7_1:64922498-64922517 Msa1030710:CDS 40.0%
TGATTCTGACGGCAATGTTT+CGG - chr7_1:64922509-64922528 Msa1030710:CDS 40.0%
TGGATAACATTCTTCCGTCT+AGG - chr7_1:64922577-64922596 Msa1030710:CDS 40.0%
!! TCTTCGTGGTTGTTGGTTTC+GGG + chr7_1:64922138-64922157 None:intergenic 45.0%
TTCTTGATCGGGTTTGCGTT+TGG + chr7_1:64922175-64922194 None:intergenic 45.0%
!!! GGGTTTTGTTAGGAAGGTGA+TGG + chr7_1:64922203-64922222 None:intergenic 45.0%
!!! TCTTGGGGGTTTTGTTAGGA+AGG + chr7_1:64922209-64922228 None:intergenic 45.0%
TGGTGGGAGTAGTTATCTTG+GGG + chr7_1:64922224-64922243 None:intergenic 45.0%
! GTGGTGGGAGTAGTTATCTT+GGG + chr7_1:64922225-64922244 None:intergenic 45.0%
GAGGTTGGATTCTTGGTCTA+CGG + chr7_1:64922247-64922266 None:intergenic 45.0%
GAAGAAGAATTGACGGTGGT+GGG + chr7_1:64922285-64922304 None:intergenic 45.0%
!!! GTTGTTTTCGGGTTCGTTGT+TGG + chr7_1:64922319-64922338 None:intergenic 45.0%
GATTCTGACGGCAATGTTTC+GGG - chr7_1:64922510-64922529 Msa1030710:CDS 45.0%
! ACATTCTTCCGTCTAGGACT+CGG - chr7_1:64922583-64922602 Msa1030710:CDS 45.0%
TGTGGGTTCTTCGTGGTTGT+TGG + chr7_1:64922145-64922164 None:intergenic 50.0%
! TTGCGTTTGGTGGGGAATGT+GGG + chr7_1:64922162-64922181 None:intergenic 50.0%
! TTTGCGTTTGGTGGGGAATG+TGG + chr7_1:64922163-64922182 None:intergenic 50.0%
TGATCGGGTTTGCGTTTGGT+GGG + chr7_1:64922171-64922190 None:intergenic 50.0%
TTGATCGGGTTTGCGTTTGG+TGG + chr7_1:64922172-64922191 None:intergenic 50.0%
GGTGGGAGTAGTTATCTTGG+GGG + chr7_1:64922223-64922242 None:intergenic 50.0%
!! GGTGGTGGGAGTAGTTATCT+TGG + chr7_1:64922226-64922245 None:intergenic 50.0%
GATTCTTGGTCTACGGTGGT+GGG + chr7_1:64922240-64922259 None:intergenic 50.0%
GTTGGATTCTTGGTCTACGG+TGG + chr7_1:64922244-64922263 None:intergenic 50.0%
CGTCGATGAGGTTGGATTCT+TGG + chr7_1:64922254-64922273 None:intergenic 50.0%
!! ATTGACGGTGGTGGGAAGTT+CGG + chr7_1:64922277-64922296 None:intergenic 50.0%
GGAAGAAGAATTGACGGTGG+TGG + chr7_1:64922286-64922305 None:intergenic 50.0%
GTCGGAAGAAGAATTGACGG+TGG + chr7_1:64922289-64922308 None:intergenic 50.0%
! GGCGTCGGAAGAAGAATTGA+CGG + chr7_1:64922292-64922311 None:intergenic 50.0%
! TTCGGGTTCGTTGTTGGGAA+CGG + chr7_1:64922313-64922332 None:intergenic 50.0%
GAATTCCGATGAAGAGCCTG+TGG - chr7_1:64922377-64922396 Msa1030710:CDS 50.0%
! TGGTGGACAGGAAGGGAAAA+GGG - chr7_1:64922397-64922416 Msa1030710:CDS 50.0%
AGGGATTATGCGCGATGACA+AGG - chr7_1:64922416-64922435 Msa1030710:CDS 50.0%
GGGATTATGCGCGATGACAA+GGG - chr7_1:64922417-64922436 Msa1030710:CDS 50.0%
ATGCGCGATGACAAGGGAAA+AGG - chr7_1:64922423-64922442 Msa1030710:CDS 50.0%
TGCGCGATGACAAGGGAAAA+GGG - chr7_1:64922424-64922443 Msa1030710:CDS 50.0%
TTCTGATGATCCACTTGCGG+AGG - chr7_1:64922548-64922567 Msa1030710:CDS 50.0%
! TCCACTTGCGGAGGTTGATT+TGG - chr7_1:64922557-64922576 Msa1030710:CDS 50.0%
TCCAAATCAACCTCCGCAAG+TGG + chr7_1:64922561-64922580 None:intergenic 50.0%
CAGACTGGAGTGCACATTTC+TGG - chr7_1:64922618-64922637 Msa1030710:CDS 50.0%
! ACTGGAGTGCACATTTCTGG+TGG - chr7_1:64922621-64922640 Msa1030710:CDS 50.0%
TGGGGAATGTGGGTTCTTCG+TGG + chr7_1:64922152-64922171 None:intergenic 55.0%
! GATCGGGTTTGCGTTTGGTG+GGG + chr7_1:64922170-64922189 None:intergenic 55.0%
GGATTCTTGGTCTACGGTGG+TGG + chr7_1:64922241-64922260 None:intergenic 55.0%
!! AAGTTCGGCGTCGATGAGGT+TGG + chr7_1:64922262-64922281 None:intergenic 55.0%
TTCGTTGTTGGGAACGGCGT+CGG + chr7_1:64922307-64922326 None:intergenic 55.0%
CGATGATGAAGACGACGACG+AGG - chr7_1:64922350-64922369 Msa1030710:CDS 55.0%
TTCCGATGAAGAGCCTGTGG+TGG - chr7_1:64922380-64922399 Msa1030710:CDS 55.0%
GTCCACCACAGGCTCTTCAT+CGG + chr7_1:64922385-64922404 None:intergenic 55.0%
!! ATGAAGAGCCTGTGGTGGAC+AGG - chr7_1:64922385-64922404 Msa1030710:CDS 55.0%
TTTCCCTTCCTGTCCACCAC+AGG + chr7_1:64922396-64922415 None:intergenic 55.0%
!! GTGGTGGACAGGAAGGGAAA+AGG - chr7_1:64922396-64922415 Msa1030710:CDS 55.0%
! TTCTTCCGTCTAGGACTCGG+CGG - chr7_1:64922586-64922605 Msa1030710:CDS 55.0%
!! TGGGAAGTTCGGCGTCGATG+AGG + chr7_1:64922266-64922285 None:intergenic 60.0%
!! AGAGCCTGTGGTGGACAGGA+AGG - chr7_1:64922389-64922408 Msa1030710:CDS 60.0%
!! GAGCCTGTGGTGGACAGGAA+GGG - chr7_1:64922390-64922409 Msa1030710:CDS 60.0%
GTTCGCCGCCGAGTCCTAGA+CGG + chr7_1:64922594-64922613 None:intergenic 65.0%
CGGCGGCGAACTGCTCAGAC+TGG - chr7_1:64922603-64922622 Msa1030710:CDS 70.0%
Chromosome Type Strat End Strand Name
chr7_1 gene 64922126 64922662 64922126 ID=Msa1030710;Name=Msa1030710
chr7_1 mRNA 64922126 64922662 64922126 ID=Msa1030710-mRNA-1;Parent=Msa1030710;Name=Msa1030710-mRNA-1;_AED=0.22;_eAED=0.22;_QI=0|-1|0|1|-1|1|1|0|178
chr7_1 exon 64922126 64922662 64922126 ID=Msa1030710-mRNA-1:exon:14339;Parent=Msa1030710-mRNA-1
chr7_1 CDS 64922126 64922662 64922126 ID=Msa1030710-mRNA-1:cds;Parent=Msa1030710-mRNA-1
Gene Sequence

>Msa1030710

ATGGCTGAACCCGAAACCAACAACCACGAAGAACCCACATTCCCCACCAAACGCAAACCCGATCAAGAAGAAACCCATCACCTTCCTAACAAAACCCCCAAGATAACTACTCCCACCACCGTAGACCAAGAATCCAACCTCATCGACGCCGAACTTCCCACCACCGTCAATTCTTCTTCCGACGCCGTTCCCAACAACGAACCCGAAAACAACACTGACGATGACGATGATGAAGACGACGACGAGGATGAGAATTCCGATGAAGAGCCTGTGGTGGACAGGAAGGGAAAAGGGATTATGCGCGATGACAAGGGAAAAGGGAAAATGATTGAAGAAGAAGATGAGGATGATGATGGCAGTGACGATAGTGATGATAGCGATGATGATTCTGACGGCAATGTTTCGGGTAGTGACAGTGATTTTTCTGATGATCCACTTGCGGAGGTTGATTTGGATAACATTCTTCCGTCTAGGACTCGGCGGCGAACTGCTCAGACTGGAGTGCACATTTCTGGTGGCACGCCAAATGCTGATTAG
Protein sequence

>Msa1030710

MAEPETNNHEEPTFPTKRKPDQEETHHLPNKTPKITTPTTVDQESNLIDAELPTTVNSSSDAVPNNEPENNTDDDDDEDDDEDENSDEEPVVDRKGKGIMRDDKGKGKMIEEEDEDDDGSDDSDDSDDDSDGNVSGSDSDFSDDPLAEVDLDNILPSRTRRRTAQTGVHISGGTPNAD*