AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1172040

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1172040 MtrunA17_Chr4g0059251 95.395 152 4 1 1 152 1 149 6.87e-106 298
Msa1172040 MtrunA17_Chr3g0117901 50.407 123 32 5 22 135 20 122 3.59e-31 109
Msa1172040 MtrunA17_Chr6g0451141 42.857 126 57 6 17 137 25 140 6.72e-24 90.9
Msa1172040 MtrunA17_Chr2g0305131 46.835 79 35 4 58 134 57 130 3.28e-13 62.8
Msa1172040 MtrunA17_Chr4g0065221 28.889 135 88 4 1 133 9 137 3.84e-12 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1172040 AT5G62865.1 41.447 152 66 7 3 139 1 144 9.02e-19 78.6
Msa1172040 AT3G01430.1 34.194 155 59 6 14 137 21 163 1.08e-17 75.9
Msa1172040 AT3G48020.1 37.705 122 55 4 26 139 14 122 1.99e-16 71.6
Msa1172040 AT5G14895.1 35.252 139 60 7 17 137 24 150 3.40e-16 71.6

Find 56 sgRNAs with CRISPR-Local

Find 61 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCAGGCTCGGAGTTTCTTTA+AGG 0.198226 8_1:+1930541 None:intergenic
CCGGAACCGGAGGGTGAAAT+TGG 0.303837 8_1:-1930317 Msa1172040:CDS
CGAATGAAATTCTTCCATCT+TGG 0.312826 8_1:+1930500 None:intergenic
CCAATTTCACCCTCCGGTTC+CGG 0.326252 8_1:+1930317 None:intergenic
TGGTTGTGGTGGTGGTGGGA+TGG 0.347361 8_1:+1930597 None:intergenic
GGCGGTGGTTGTGGTGGTGG+TGG 0.369594 8_1:+1930592 None:intergenic
GGTTGTGGTGGTGGTGGGAT+GGG 0.371805 8_1:+1930598 None:intergenic
CCATCTATCGGCGGTGGTTG+TGG 0.375414 8_1:+1930583 None:intergenic
TAAGTCTGTTGCGCCGGAAC+CGG 0.391391 8_1:-1930330 Msa1172040:CDS
CACGCCGCCGTTCCGTTTGG+TGG 0.400297 8_1:-1930652 Msa1172040:CDS
CCACAACCACCGCCGATAGA+TGG 0.401522 8_1:-1930583 Msa1172040:CDS
GTCTGTTGCGCCGGAACCGG+AGG 0.417562 8_1:-1930327 Msa1172040:CDS
ATCGGCGGTGGTTGTGGTGG+TGG 0.420574 8_1:+1930589 None:intergenic
CCTCACGCCGCCGTTCCGTT+TGG 0.424502 8_1:-1930655 Msa1172040:CDS
GCCTGGTCGGAGATCGTCGC+TGG 0.451987 8_1:-1930524 Msa1172040:CDS
CGCAACAGACTTAATATTAA+CGG 0.461558 8_1:+1930340 None:intergenic
CCTTAAAGAAACTCCGAGCC+TGG 0.463778 8_1:-1930541 Msa1172040:CDS
TTGTCATACGCTTCGATCGA+TGG 0.470318 8_1:+1930465 None:intergenic
ACGGCGGCGTGAGGCGAAGC+AGG 0.472114 8_1:+1930664 None:intergenic
ATGAAGATAGCCACGACGAC+GGG 0.475007 8_1:-1930391 Msa1172040:CDS
CAAGATGGAAGAATTTCATT+CGG 0.477769 8_1:-1930499 Msa1172040:CDS
GCGGTGGTTGTGGTGGTGGT+GGG 0.485464 8_1:+1930593 None:intergenic
GAAGCAGGTGGGGAAACATA+AGG 0.500761 8_1:+1930679 None:intergenic
AACCCGCCAATTTCACCCTC+CGG 0.509850 8_1:+1930311 None:intergenic
GGTGGGATGGGATTGAGAAA+AGG 0.511993 8_1:+1930610 None:intergenic
AACCGGAGGGTGAAATTGGC+GGG 0.518811 8_1:-1930313 Msa1172040:CDS
GAACCGGAGGGTGAAATTGG+CGG 0.518878 8_1:-1930314 Msa1172040:CDS
GGCGTGAGGCGAAGCAGGTG+GGG 0.526513 8_1:+1930669 None:intergenic
GCGGCGTGAGGCGAAGCAGG+TGG 0.527709 8_1:+1930667 None:intergenic
CGACGATCTCCGACCAGGCT+CGG 0.535045 8_1:+1930528 None:intergenic
ACGCCGCCGTTCCGTTTGGT+GGG 0.538378 8_1:-1930651 Msa1172040:CDS
TAATATTAAGTCTGTTGCGC+CGG 0.541424 8_1:-1930336 Msa1172040:CDS
ACCAGCGACGATCTCCGACC+AGG 0.547492 8_1:+1930523 None:intergenic
GCGAACACGTTCCCACCAAA+CGG 0.551665 8_1:+1930640 None:intergenic
AGATCGTCGCTGGTCCAAGA+TGG 0.560579 8_1:-1930514 Msa1172040:CDS
GCCGCGAGACCACCATCTAT+CGG 0.563498 8_1:+1930571 None:intergenic
CACGTTCCCACCAAACGGAA+CGG 0.587139 8_1:+1930645 None:intergenic
AGACCACCATCTATCGGCGG+TGG 0.590655 8_1:+1930577 None:intergenic
CCAAACGGAACGGCGGCGTG+AGG 0.591562 8_1:+1930655 None:intergenic
TCTATCGGCGGTGGTTGTGG+TGG 0.591878 8_1:+1930586 None:intergenic
TATGCGTTAAACTTTGATGA+GGG 0.593416 8_1:-1930419 Msa1172040:CDS
GGGATGGGATTGAGAAAAGG+AGG 0.601763 8_1:+1930613 None:intergenic
TTATGCGTTAAACTTTGATG+AGG 0.610573 8_1:-1930420 Msa1172040:CDS
GCCGATAGATGGTGGTCTCG+CGG 0.626739 8_1:-1930572 Msa1172040:CDS
TCTGTTGCGCCGGAACCGGA+GGG 0.629319 8_1:-1930326 Msa1172040:CDS
AATGAAGATAGCCACGACGA+CGG 0.629695 8_1:-1930392 Msa1172040:CDS
AATTCCGAAACCCGTCGTCG+TGG 0.629946 8_1:+1930381 None:intergenic
ATGGGATTGAGAAAAGGAGG+CGG 0.635403 8_1:+1930616 None:intergenic
AAAGAAACTCCGAGCCTGGT+CGG 0.644913 8_1:-1930537 Msa1172040:CDS
TGATTCAAGCTCTAGCTCAA+CGG 0.647004 8_1:+1930736 None:intergenic
AAGTTTAACGCATAACTCAA+CGG 0.651799 8_1:+1930428 None:intergenic
GGAGTTTCTTTAAGGCGTTG+AGG 0.656051 8_1:+1930549 None:intergenic
CAACCACCGCCGATAGATGG+TGG 0.659317 8_1:-1930580 Msa1172040:CDS
GTTCCCACCAAACGGAACGG+CGG 0.663196 8_1:+1930648 None:intergenic
AACAGACTTAATATTAACGG+CGG 0.721385 8_1:+1930343 None:intergenic
GCGAGACCACCATCTATCGG+CGG 0.723063 8_1:+1930574 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
CAAGATGGAAGAATTTCATT+CGG - chr8_1:1930545-1930564 Msa1172040:CDS 30.0%
AAGTTTAACGCATAACTCAA+CGG + chr8_1:1930619-1930638 None:intergenic 30.0%
TTATGCGTTAAACTTTGATG+AGG - chr8_1:1930624-1930643 Msa1172040:CDS 30.0%
TATGCGTTAAACTTTGATGA+GGG - chr8_1:1930625-1930644 Msa1172040:CDS 30.0%
AACAGACTTAATATTAACGG+CGG + chr8_1:1930704-1930723 None:intergenic 30.0%
CGCAACAGACTTAATATTAA+CGG + chr8_1:1930707-1930726 None:intergenic 30.0%
CGAATGAAATTCTTCCATCT+TGG + chr8_1:1930547-1930566 None:intergenic 35.0%
TAATATTAAGTCTGTTGCGC+CGG - chr8_1:1930708-1930727 Msa1172040:CDS 35.0%
! TGATTCAAGCTCTAGCTCAA+CGG + chr8_1:1930311-1930330 None:intergenic 40.0%
! TCTCTTTTGTTGGAGATGAG+CGG + chr8_1:1930338-1930357 None:intergenic 40.0%
! TTTTGTTGGAGATGAGCGGT+TGG + chr8_1:1930334-1930353 None:intergenic 45.0%
! AGGCGCTTGATCTCTTTTGT+TGG + chr8_1:1930348-1930367 None:intergenic 45.0%
ATGGGATTGAGAAAAGGAGG+CGG + chr8_1:1930431-1930450 None:intergenic 45.0%
!! GGAGTTTCTTTAAGGCGTTG+AGG + chr8_1:1930498-1930517 None:intergenic 45.0%
TTGTCATACGCTTCGATCGA+TGG + chr8_1:1930582-1930601 None:intergenic 45.0%
AATGAAGATAGCCACGACGA+CGG - chr8_1:1930652-1930671 Msa1172040:CDS 45.0%
GAAGCAGGTGGGGAAACATA+AGG + chr8_1:1930368-1930387 None:intergenic 50.0%
GGGATGGGATTGAGAAAAGG+AGG + chr8_1:1930434-1930453 None:intergenic 50.0%
GGTGGGATGGGATTGAGAAA+AGG + chr8_1:1930437-1930456 None:intergenic 50.0%
CCAGGCTCGGAGTTTCTTTA+AGG + chr8_1:1930506-1930525 None:intergenic 50.0%
CCTTAAAGAAACTCCGAGCC+TGG - chr8_1:1930503-1930522 Msa1172040:CDS 50.0%
AAAGAAACTCCGAGCCTGGT+CGG - chr8_1:1930507-1930526 Msa1172040:CDS 50.0%
ATGAAGATAGCCACGACGAC+GGG - chr8_1:1930653-1930672 Msa1172040:CDS 50.0%
CACGTTCCCACCAAACGGAA+CGG + chr8_1:1930402-1930421 None:intergenic 55.0%
GCGAACACGTTCCCACCAAA+CGG + chr8_1:1930407-1930426 None:intergenic 55.0%
AGATCGTCGCTGGTCCAAGA+TGG - chr8_1:1930530-1930549 Msa1172040:CDS 55.0%
! ATAGCCACGACGACGGGTTT+CGG - chr8_1:1930659-1930678 Msa1172040:CDS 55.0%
AATTCCGAAACCCGTCGTCG+TGG + chr8_1:1930666-1930685 None:intergenic 55.0%
TAAGTCTGTTGCGCCGGAAC+CGG - chr8_1:1930714-1930733 Msa1172040:CDS 55.0%
CCAATTTCACCCTCCGGTTC+CGG + chr8_1:1930730-1930749 None:intergenic 55.0%
GAACCGGAGGGTGAAATTGG+CGG - chr8_1:1930730-1930749 Msa1172040:CDS 55.0%
AACCGGAGGGTGAAATTGGC+GGG - chr8_1:1930731-1930750 Msa1172040:CDS 55.0%
AACCCGCCAATTTCACCCTC+CGG + chr8_1:1930736-1930755 None:intergenic 55.0%
GTTCCCACCAAACGGAACGG+CGG + chr8_1:1930399-1930418 None:intergenic 60.0%
!! GGTTGTGGTGGTGGTGGGAT+GGG + chr8_1:1930449-1930468 None:intergenic 60.0%
!! TGGTTGTGGTGGTGGTGGGA+TGG + chr8_1:1930450-1930469 None:intergenic 60.0%
TCTATCGGCGGTGGTTGTGG+TGG + chr8_1:1930461-1930480 None:intergenic 60.0%
CCATCTATCGGCGGTGGTTG+TGG + chr8_1:1930464-1930483 None:intergenic 60.0%
CCACAACCACCGCCGATAGA+TGG - chr8_1:1930461-1930480 Msa1172040:CDS 60.0%
CAACCACCGCCGATAGATGG+TGG - chr8_1:1930464-1930483 Msa1172040:CDS 60.0%
AGACCACCATCTATCGGCGG+TGG + chr8_1:1930470-1930489 None:intergenic 60.0%
GCGAGACCACCATCTATCGG+CGG + chr8_1:1930473-1930492 None:intergenic 60.0%
! GCCGATAGATGGTGGTCTCG+CGG - chr8_1:1930472-1930491 Msa1172040:CDS 60.0%
GCCGCGAGACCACCATCTAT+CGG + chr8_1:1930476-1930495 None:intergenic 60.0%
CCGGAACCGGAGGGTGAAAT+TGG - chr8_1:1930727-1930746 Msa1172040:CDS 60.0%
ACGCCGCCGTTCCGTTTGGT+GGG - chr8_1:1930393-1930412 Msa1172040:CDS 65.0%
!! GCGGTGGTTGTGGTGGTGGT+GGG + chr8_1:1930454-1930473 None:intergenic 65.0%
ATCGGCGGTGGTTGTGGTGG+TGG + chr8_1:1930458-1930477 None:intergenic 65.0%
CGACGATCTCCGACCAGGCT+CGG + chr8_1:1930519-1930538 None:intergenic 65.0%
ACCAGCGACGATCTCCGACC+AGG + chr8_1:1930524-1930543 None:intergenic 65.0%
TCTGTTGCGCCGGAACCGGA+GGG - chr8_1:1930718-1930737 Msa1172040:CDS 65.0%
GGCGTGAGGCGAAGCAGGTG+GGG + chr8_1:1930378-1930397 None:intergenic 70.0%
CGGCGTGAGGCGAAGCAGGT+GGG + chr8_1:1930379-1930398 None:intergenic 70.0%
CCAAACGGAACGGCGGCGTG+AGG + chr8_1:1930392-1930411 None:intergenic 70.0%
CCTCACGCCGCCGTTCCGTT+TGG - chr8_1:1930389-1930408 Msa1172040:CDS 70.0%
CACGCCGCCGTTCCGTTTGG+TGG - chr8_1:1930392-1930411 Msa1172040:CDS 70.0%
!! GGCGGTGGTTGTGGTGGTGG+TGG + chr8_1:1930455-1930474 None:intergenic 70.0%
GCCTGGTCGGAGATCGTCGC+TGG - chr8_1:1930520-1930539 Msa1172040:CDS 70.0%
GTCTGTTGCGCCGGAACCGG+AGG - chr8_1:1930717-1930736 Msa1172040:CDS 70.0%
GCGGCGTGAGGCGAAGCAGG+TGG + chr8_1:1930380-1930399 None:intergenic 75.0%
ACGGCGGCGTGAGGCGAAGC+AGG + chr8_1:1930383-1930402 None:intergenic 75.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 1930304 1930762 1930304 ID=Msa1172040;Name=Msa1172040
chr8_1 mRNA 1930304 1930762 1930304 ID=Msa1172040-mRNA-1;Parent=Msa1172040;Name=Msa1172040-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|152
chr8_1 exon 1930304 1930762 1930304 ID=Msa1172040-mRNA-1:exon:731;Parent=Msa1172040-mRNA-1
chr8_1 CDS 1930304 1930762 1930304 ID=Msa1172040-mRNA-1:cds;Parent=Msa1172040-mRNA-1
Gene Sequence

>Msa1172040

ATGTCCGTTGAGCTAGAGCTTGAATCACCAACCGCTCATCTCCAACAAAAGAGATCAAGCGCCTTATGTTTCCCCACCTGCTTCGCCTCACGCCGCCGTTCCGTTTGGTGGGAACGTGTTCGCTCCGCCTCCTTTTCTCAATCCCATCCCACCACCACCACAACCACCGCCGATAGATGGTGGTCTCGCGGCCTCAACGCCTTAAAGAAACTCCGAGCCTGGTCGGAGATCGTCGCTGGTCCAAGATGGAAGAATTTCATTCGGAAATTCAACAACCATCGATCGAAGCGTATGACAAAGTGTCAATACGATCCGTTGAGTTATGCGTTAAACTTTGATGAGGGACAGAATGAAGATAGCCACGACGACGGGTTTCGGAATTTCTCTACGCGTTACGCCGCCGTTAATATTAAGTCTGTTGCGCCGGAACCGGAGGGTGAAATTGGCGGGTTAGTTTGA
Protein sequence

>Msa1172040

MSVELELESPTAHLQQKRSSALCFPTCFASRRRSVWWERVRSASFSQSHPTTTTTTADRWWSRGLNALKKLRAWSEIVAGPRWKNFIRKFNNHRSKRMTKCQYDPLSYALNFDEGQNEDSHDDGFRNFSTRYAAVNIKSVAPEPEGEIGGLV*