AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1157580

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1157580 MtrunA17_Chr7g0251841 89.326 178 13 2 1 178 1 172 4.89e-71 212
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1157580 AT1G12830.1 68.750 80 22 1 91 170 116 192 8.86e-17 75.1

Find 58 sgRNAs with CRISPR-Local

Find 67 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTTCGTGGTTGTTGGTTT+CGG 0.192971 7_4:+46608652 None:intergenic
CGTCGATGAGGTTGGATTCT+TGG 0.206975 7_4:+46608537 None:intergenic
TCTTCGTGGTTGTTGGTTTC+GGG 0.218487 7_4:+46608653 None:intergenic
CAGACTGGAGTGCACATTTC+TGG 0.227098 7_4:-46608170 Msa1157580:CDS
GATTCTGACGGCAATGTTTC+GGG 0.258012 7_4:-46608278 Msa1157580:CDS
TCCACTTGCGGAGGTTGATT+TGG 0.320599 7_4:-46608231 Msa1157580:CDS
TGATTCTGACGGCAATGTTT+CGG 0.357245 7_4:-46608279 Msa1157580:CDS
TTCTTGATCGGGTTTGCGTT+TGG 0.373289 7_4:+46608616 None:intergenic
GGATTCTTGGTCTACGGTGG+TGG 0.378862 7_4:+46608550 None:intergenic
AGGGATTATGCGCGATGATA+AGG 0.420684 7_4:-46608372 Msa1157580:CDS
GTGATGGGTTTCTTCTTGAT+CGG 0.423416 7_4:+46608604 None:intergenic
TTCGGGTTCGTTGTTGGGAA+CGG 0.430062 7_4:+46608478 None:intergenic
GTGGTGGGAGTAGTTATCTT+GGG 0.430123 7_4:+46608566 None:intergenic
TGTGGGTTCTTCGTGGTTGT+TGG 0.430236 7_4:+46608646 None:intergenic
TGATGGGTTTCTTCTTGATC+GGG 0.431013 7_4:+46608605 None:intergenic
TTTCCCTTCCTGTCCACCAC+AGG 0.432598 7_4:+46608395 None:intergenic
TTGCGTTTGGTGGGGAATGT+GGG 0.446781 7_4:+46608629 None:intergenic
TGATCGGGTTTGCGTTTGGT+GGG 0.446814 7_4:+46608620 None:intergenic
GTGGTGGACAGGAAGGGAAA+AGG 0.452668 7_4:-46608392 Msa1157580:CDS
TTTGCGTTTGGTGGGGAATG+TGG 0.460274 7_4:+46608628 None:intergenic
GGGATTATGCGCGATGATAA+GGG 0.461736 7_4:-46608371 Msa1157580:CDS
ATTGACGGTGGTGGGAAGTT+CGG 0.464983 7_4:+46608514 None:intergenic
ACATTCTTCCGTCTAGGACT+CGG 0.465560 7_4:-46608205 Msa1157580:CDS
TTCGTTGTTGGGAACGGCGT+CGG 0.465767 7_4:+46608484 None:intergenic
GGTGGTGGGAGTAGTTATCT+TGG 0.470330 7_4:+46608565 None:intergenic
TTGATCGGGTTTGCGTTTGG+TGG 0.477903 7_4:+46608619 None:intergenic
ATGAAGAGCCTGTGGTGGAC+AGG 0.489672 7_4:-46608403 Msa1157580:CDS
TGCGCGATGATAAGGGAAAA+GGG 0.491143 7_4:-46608364 Msa1157580:CDS
TGGGGAATGTGGGTTCTTCG+TGG 0.491435 7_4:+46608639 None:intergenic
TGGTGGACAGGAAGGGAAAA+GGG 0.491635 7_4:-46608391 Msa1157580:CDS
ATGCGCGATGATAAGGGAAA+AGG 0.491640 7_4:-46608365 Msa1157580:CDS
GAGGTTGGATTCTTGGTCTA+CGG 0.496324 7_4:+46608544 None:intergenic
GATTCTTGGTCTACGGTGGT+GGG 0.496695 7_4:+46608551 None:intergenic
CGGCGGCGAACTGCTCAGAC+TGG 0.498986 7_4:-46608185 Msa1157580:CDS
AGTAGAATCTAATCAGCATT+CGG 0.511857 7_4:+46608140 None:intergenic
GGAAGAAGAATTGACGGTGG+TGG 0.527818 7_4:+46608505 None:intergenic
AAGTTCGGCGTCGATGAGGT+TGG 0.528090 7_4:+46608529 None:intergenic
TGGATAACATTCTTCCGTCT+AGG 0.534730 7_4:-46608211 Msa1157580:CDS
GATCGGGTTTGCGTTTGGTG+GGG 0.540763 7_4:+46608621 None:intergenic
TGGTGGGAGTAGTTATCTTG+GGG 0.541044 7_4:+46608567 None:intergenic
GAAGAAGAATTGACGGTGGT+GGG 0.545012 7_4:+46608506 None:intergenic
AGAGCCTGTGGTGGACAGGA+AGG 0.545443 7_4:-46608399 Msa1157580:CDS
TCCAAATCAACCTCCGCAAG+TGG 0.550043 7_4:+46608230 None:intergenic
GGCGTCGGAAGAAGAATTGA+CGG 0.559067 7_4:+46608499 None:intergenic
GTCCACCACAGGCTCTTCAT+CGG 0.559628 7_4:+46608406 None:intergenic
AATGATTGAAGAAGAAGATG+AGG 0.573565 7_4:-46608339 Msa1157580:CDS
GAGCCTGTGGTGGACAGGAA+GGG 0.598333 7_4:-46608398 Msa1157580:CDS
TTCTGATGATCCACTTGCGG+AGG 0.598405 7_4:-46608240 Msa1157580:CDS
TTCCGATGAAGAGCCTGTGG+TGG 0.608098 7_4:-46608408 Msa1157580:CDS
TGGGAAGTTCGGCGTCGATG+AGG 0.608955 7_4:+46608525 None:intergenic
GGTGGGAGTAGTTATCTTGG+GGG 0.650526 7_4:+46608568 None:intergenic
CGATGATGAAGACGACGACG+AGG 0.653015 7_4:-46608438 Msa1157580:CDS
GTTGGATTCTTGGTCTACGG+TGG 0.656018 7_4:+46608547 None:intergenic
ACTGGAGTGCACATTTCTGG+TGG 0.678942 7_4:-46608167 Msa1157580:CDS
GATAGCGATGATGATTCTGA+CGG 0.698753 7_4:-46608290 Msa1157580:CDS
GAATTCCGATGAAGAGCCTG+TGG 0.723860 7_4:-46608411 Msa1157580:CDS
TTCTTCCGTCTAGGACTCGG+CGG 0.732545 7_4:-46608202 Msa1157580:CDS
GTCGGAAGAAGAATTGACGG+TGG 0.750092 7_4:+46608502 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AATGATTGAAGAAGAAGATG+AGG - chr7_4:46608471-46608490 Msa1157580:CDS 30.0%
! TTTTTCTGATGATCCACTTG+CGG - chr7_4:46608567-46608586 Msa1157580:CDS 35.0%
!! TTCTTCGTGGTTGTTGGTTT+CGG + chr7_4:46608161-46608180 None:intergenic 40.0%
!! TGATGGGTTTCTTCTTGATC+GGG + chr7_4:46608208-46608227 None:intergenic 40.0%
!! GTGATGGGTTTCTTCTTGAT+CGG + chr7_4:46608209-46608228 None:intergenic 40.0%
!!! GGTTTTGTTAGGAAGGTGAT+GGG + chr7_4:46608224-46608243 None:intergenic 40.0%
!!! GTTATCTTGGGGGTTTTGTT+AGG + chr7_4:46608235-46608254 None:intergenic 40.0%
!!! TTGTTTTCGGGTTCGTTGTT+GGG + chr7_4:46608340-46608359 None:intergenic 40.0%
!!! TCATCGTCAGTGTTGTTTTC+GGG + chr7_4:46608352-46608371 None:intergenic 40.0%
!!! GTCATCGTCAGTGTTGTTTT+CGG + chr7_4:46608353-46608372 None:intergenic 40.0%
GATAGCGATGATGATTCTGA+CGG - chr7_4:46608520-46608539 Msa1157580:CDS 40.0%
TGATTCTGACGGCAATGTTT+CGG - chr7_4:46608531-46608550 Msa1157580:CDS 40.0%
TGGATAACATTCTTCCGTCT+AGG - chr7_4:46608599-46608618 Msa1157580:CDS 40.0%
!! TCTTCGTGGTTGTTGGTTTC+GGG + chr7_4:46608160-46608179 None:intergenic 45.0%
TTCTTGATCGGGTTTGCGTT+TGG + chr7_4:46608197-46608216 None:intergenic 45.0%
!!! GGGTTTTGTTAGGAAGGTGA+TGG + chr7_4:46608225-46608244 None:intergenic 45.0%
!!! TCTTGGGGGTTTTGTTAGGA+AGG + chr7_4:46608231-46608250 None:intergenic 45.0%
TGGTGGGAGTAGTTATCTTG+GGG + chr7_4:46608246-46608265 None:intergenic 45.0%
! GTGGTGGGAGTAGTTATCTT+GGG + chr7_4:46608247-46608266 None:intergenic 45.0%
GAGGTTGGATTCTTGGTCTA+CGG + chr7_4:46608269-46608288 None:intergenic 45.0%
GAAGAAGAATTGACGGTGGT+GGG + chr7_4:46608307-46608326 None:intergenic 45.0%
!!! GTTGTTTTCGGGTTCGTTGT+TGG + chr7_4:46608341-46608360 None:intergenic 45.0%
AGGGATTATGCGCGATGATA+AGG - chr7_4:46608438-46608457 Msa1157580:CDS 45.0%
GGGATTATGCGCGATGATAA+GGG - chr7_4:46608439-46608458 Msa1157580:CDS 45.0%
ATGCGCGATGATAAGGGAAA+AGG - chr7_4:46608445-46608464 Msa1157580:CDS 45.0%
TGCGCGATGATAAGGGAAAA+GGG - chr7_4:46608446-46608465 Msa1157580:CDS 45.0%
GATTCTGACGGCAATGTTTC+GGG - chr7_4:46608532-46608551 Msa1157580:CDS 45.0%
! ACATTCTTCCGTCTAGGACT+CGG - chr7_4:46608605-46608624 Msa1157580:CDS 45.0%
TGTGGGTTCTTCGTGGTTGT+TGG + chr7_4:46608167-46608186 None:intergenic 50.0%
! TTGCGTTTGGTGGGGAATGT+GGG + chr7_4:46608184-46608203 None:intergenic 50.0%
! TTTGCGTTTGGTGGGGAATG+TGG + chr7_4:46608185-46608204 None:intergenic 50.0%
TGATCGGGTTTGCGTTTGGT+GGG + chr7_4:46608193-46608212 None:intergenic 50.0%
TTGATCGGGTTTGCGTTTGG+TGG + chr7_4:46608194-46608213 None:intergenic 50.0%
GGTGGGAGTAGTTATCTTGG+GGG + chr7_4:46608245-46608264 None:intergenic 50.0%
!! GGTGGTGGGAGTAGTTATCT+TGG + chr7_4:46608248-46608267 None:intergenic 50.0%
GATTCTTGGTCTACGGTGGT+GGG + chr7_4:46608262-46608281 None:intergenic 50.0%
GTTGGATTCTTGGTCTACGG+TGG + chr7_4:46608266-46608285 None:intergenic 50.0%
CGTCGATGAGGTTGGATTCT+TGG + chr7_4:46608276-46608295 None:intergenic 50.0%
!! ATTGACGGTGGTGGGAAGTT+CGG + chr7_4:46608299-46608318 None:intergenic 50.0%
GGAAGAAGAATTGACGGTGG+TGG + chr7_4:46608308-46608327 None:intergenic 50.0%
GTCGGAAGAAGAATTGACGG+TGG + chr7_4:46608311-46608330 None:intergenic 50.0%
! GGCGTCGGAAGAAGAATTGA+CGG + chr7_4:46608314-46608333 None:intergenic 50.0%
! TTCGGGTTCGTTGTTGGGAA+CGG + chr7_4:46608335-46608354 None:intergenic 50.0%
GAATTCCGATGAAGAGCCTG+TGG - chr7_4:46608399-46608418 Msa1157580:CDS 50.0%
! TGGTGGACAGGAAGGGAAAA+GGG - chr7_4:46608419-46608438 Msa1157580:CDS 50.0%
TTCTGATGATCCACTTGCGG+AGG - chr7_4:46608570-46608589 Msa1157580:CDS 50.0%
! TCCACTTGCGGAGGTTGATT+TGG - chr7_4:46608579-46608598 Msa1157580:CDS 50.0%
TCCAAATCAACCTCCGCAAG+TGG + chr7_4:46608583-46608602 None:intergenic 50.0%
CAGACTGGAGTGCACATTTC+TGG - chr7_4:46608640-46608659 Msa1157580:CDS 50.0%
! ACTGGAGTGCACATTTCTGG+TGG - chr7_4:46608643-46608662 Msa1157580:CDS 50.0%
TGGGGAATGTGGGTTCTTCG+TGG + chr7_4:46608174-46608193 None:intergenic 55.0%
! GATCGGGTTTGCGTTTGGTG+GGG + chr7_4:46608192-46608211 None:intergenic 55.0%
GGATTCTTGGTCTACGGTGG+TGG + chr7_4:46608263-46608282 None:intergenic 55.0%
!! AAGTTCGGCGTCGATGAGGT+TGG + chr7_4:46608284-46608303 None:intergenic 55.0%
TTCGTTGTTGGGAACGGCGT+CGG + chr7_4:46608329-46608348 None:intergenic 55.0%
CGATGATGAAGACGACGACG+AGG - chr7_4:46608372-46608391 Msa1157580:CDS 55.0%
TTCCGATGAAGAGCCTGTGG+TGG - chr7_4:46608402-46608421 Msa1157580:CDS 55.0%
GTCCACCACAGGCTCTTCAT+CGG + chr7_4:46608407-46608426 None:intergenic 55.0%
!! ATGAAGAGCCTGTGGTGGAC+AGG - chr7_4:46608407-46608426 Msa1157580:CDS 55.0%
TTTCCCTTCCTGTCCACCAC+AGG + chr7_4:46608418-46608437 None:intergenic 55.0%
!! GTGGTGGACAGGAAGGGAAA+AGG - chr7_4:46608418-46608437 Msa1157580:CDS 55.0%
! TTCTTCCGTCTAGGACTCGG+CGG - chr7_4:46608608-46608627 Msa1157580:CDS 55.0%
!! TGGGAAGTTCGGCGTCGATG+AGG + chr7_4:46608288-46608307 None:intergenic 60.0%
!! AGAGCCTGTGGTGGACAGGA+AGG - chr7_4:46608411-46608430 Msa1157580:CDS 60.0%
!! GAGCCTGTGGTGGACAGGAA+GGG - chr7_4:46608412-46608431 Msa1157580:CDS 60.0%
GTTCGCCGCCGAGTCCTAGA+CGG + chr7_4:46608616-46608635 None:intergenic 65.0%
CGGCGGCGAACTGCTCAGAC+TGG - chr7_4:46608625-46608644 Msa1157580:CDS 70.0%
Chromosome Type Strat End Strand Name
chr7_4 gene 46608148 46608684 46608148 ID=Msa1157580;Name=Msa1157580
chr7_4 mRNA 46608148 46608684 46608148 ID=Msa1157580-mRNA-1;Parent=Msa1157580;Name=Msa1157580-mRNA-1;_AED=0.24;_eAED=0.24;_QI=0|-1|0|1|-1|1|1|0|178
chr7_4 exon 46608148 46608684 46608148 ID=Msa1157580-mRNA-1:exon:12255;Parent=Msa1157580-mRNA-1
chr7_4 CDS 46608148 46608684 46608148 ID=Msa1157580-mRNA-1:cds;Parent=Msa1157580-mRNA-1
Gene Sequence

>Msa1157580

ATGGCTGAACCCGAAACCAACAACCACGAAGAACCCACATTCCCCACCAAACGCAAACCCGATCAAGAAGAAACCCATCACCTTCCTAACAAAACCCCCAAGATAACTACTCCCACCACCGTAGACCAAGAATCCAACCTCATCGACGCCGAACTTCCCACCACCGTCAATTCTTCTTCCGACGCCGTTCCCAACAACGAACCCGAAAACAACACTGACGATGACGATGATGAAGACGACGACGAGGATGAGAATTCCGATGAAGAGCCTGTGGTGGACAGGAAGGGAAAAGGGATTATGCGCGATGATAAGGGAAAAGGGAAAATGATTGAAGAAGAAGATGAGGATGATGATGACAGTCACGATAGTGATGATAGCGATGATGATTCTGACGGCAATGTTTCGGGTAGTGACAGTGATTTTTCTGATGATCCACTTGCGGAGGTTGATTTGGATAACATTCTTCCGTCTAGGACTCGGCGGCGAACTGCTCAGACTGGAGTGCACATTTCTGGTGGCACGCCGAATGCTGATTAG
Protein sequence

>Msa1157580

MAEPETNNHEEPTFPTKRKPDQEETHHLPNKTPKITTPTTVDQESNLIDAELPTTVNSSSDAVPNNEPENNTDDDDDEDDDEDENSDEEPVVDRKGKGIMRDDKGKGKMIEEEDEDDDDSHDSDDSDDDSDGNVSGSDSDFSDDPLAEVDLDNILPSRTRRRTAQTGVHISGGTPNAD*