AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0540510

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0540510 MtrunA17_Chr5g0393501 29.146 199 114 4 2 173 43 241 4.70e-22 89.4
Msa0540510 MtrunA17_Chr4g0044671 26.630 184 111 2 1 160 25 208 1.44e-11 60.8
Msa0540510 MtrunA17_Chr4g0034781 26.087 184 112 2 1 160 19 202 8.62e-11 58.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 39 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGAAGTTCCTATCTGGATA+TGG 0.289906 4_1:+22846579 Msa0540510:CDS
GTACCTTTGAAGTTCCTATC+TGG 0.333773 4_1:+22846573 Msa0540510:CDS
AGGAATTTGCCGAAAGTATC+AGG 0.335653 4_1:-22846726 None:intergenic
AATCGTGATGTTTCACTCTA+AGG 0.341127 4_1:-22846746 None:intergenic
TAGGAACTACCTGATACTTT+CGG 0.400617 4_1:+22846717 Msa0540510:intron
TCCGAACATCACATTTGGTA+TGG 0.417548 4_1:-22846832 None:intergenic
ATCTACTTCCACCAAGGTAC+TGG 0.428620 4_1:-22846467 None:intergenic
CCGAACATCACATTTGGTAT+GGG 0.451435 4_1:-22846831 None:intergenic
GAGCAATGGCACTTGCTAGA+TGG 0.455163 4_1:+22846327 Msa0540510:CDS
AAATATTTAGCAACAAAGAA+TGG 0.465634 4_1:-22846291 None:intergenic
CCAAATGTGATGTTCGGAAA+AGG 0.475440 4_1:+22846837 Msa0540510:CDS
CCCATACCAAATGTGATGTT+CGG 0.477035 4_1:+22846831 Msa0540510:CDS
TCGTCGATCCATATCCAGAT+AGG 0.486078 4_1:-22846587 None:intergenic
GGCCGTTGTTGACAGATGGT+TGG 0.487397 4_1:+22846394 Msa0540510:CDS
TGTGATGCCAATGGTATTGA+GGG 0.488792 4_1:+22846873 Msa0540510:CDS
GTCATGCGTTTATCAACGCT+TGG 0.500774 4_1:-22846955 None:intergenic
CACGATTACGTCATGTTGTA+CGG 0.501494 4_1:+22846762 Msa0540510:CDS
TTGTGATGCCAATGGTATTG+AGG 0.502693 4_1:+22846872 Msa0540510:CDS
TAAATATTTCTACGAGCTAC+CGG 0.507354 4_1:+22846305 Msa0540510:CDS
ATTATTGCTTTCCAGTACCT+TGG 0.508515 4_1:+22846456 Msa0540510:CDS
ACAGGAATGATATTGTCATA+AGG 0.528831 4_1:-22846786 None:intergenic
AGTCGGCCGTTGTTGACAGA+TGG 0.531450 4_1:+22846390 Msa0540510:CDS
TCTAGCAAGTGCCATTGCTC+CGG 0.534587 4_1:-22846324 None:intergenic
ATTGCTTTCCAGTACCTTGG+TGG 0.549152 4_1:+22846459 Msa0540510:CDS
CGAACATCACATTTGGTATG+GGG 0.552019 4_1:-22846830 None:intergenic
GTCTCCGCCCTCAATACCAT+TGG 0.575295 4_1:-22846880 None:intergenic
CTGACTAACTTCTAGGATGT+CGG 0.584798 4_1:+22846258 None:intergenic
TGGCACTTGCTAGATGGTGA+TGG 0.587936 4_1:+22846333 Msa0540510:CDS
ACTAACTGATTTGTTGAACA+TGG 0.595544 4_1:-22846370 None:intergenic
TATCCAGATAGGAACTTCAA+AGG 0.596572 4_1:-22846576 None:intergenic
ATGTGATGTTCGGAAAAGGT+TGG 0.606400 4_1:+22846841 Msa0540510:CDS
GGCACTTGCTAGATGGTGAT+GGG 0.608333 4_1:+22846334 Msa0540510:CDS
TGTTCAACAAATCAGTTAGT+CGG 0.609582 4_1:+22846373 Msa0540510:CDS
TCTACGAGCTACCGGAGCAA+TGG 0.612965 4_1:+22846313 Msa0540510:CDS
TTTCAAGTACAAGTGTGTCG+TGG 0.648578 4_1:+22846911 Msa0540510:CDS
TTTGAAATCTACTTCCACCA+AGG 0.670569 4_1:-22846473 None:intergenic
CTCCAACCATCTGTCAACAA+CGG 0.679074 4_1:-22846396 None:intergenic
TGGATCGACGAAATCACCGA+AGG 0.700849 4_1:+22846599 Msa0540510:CDS
GATGCCAATGGTATTGAGGG+CGG 0.755038 4_1:+22846876 Msa0540510:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTTTATATATGCTATAATAA+AGG + chr4_1:22846657-22846676 Msa0540510:intron 15.0%
!!! CAGTTTTTTTTCTTTTTTTT+AGG + chr4_1:22846698-22846717 Msa0540510:intron 15.0%
!! AAATATTTAGCAACAAAGAA+TGG - chr4_1:22846294-22846313 None:intergenic 20.0%
!! AAAAAACAATAAACAACCTT+CGG - chr4_1:22846618-22846637 None:intergenic 20.0%
!! TTTTGATGCTATTCATTTAG+AGG + chr4_1:22846635-22846654 Msa0540510:intron 25.0%
!!! TCTGTATATTTTAATCTCAC+AGG - chr4_1:22846807-22846826 None:intergenic 25.0%
! TAAATATTTCTACGAGCTAC+CGG + chr4_1:22846305-22846324 Msa0540510:CDS 30.0%
!! ACTAACTGATTTGTTGAACA+TGG - chr4_1:22846373-22846392 None:intergenic 30.0%
TGTTCAACAAATCAGTTAGT+CGG + chr4_1:22846373-22846392 Msa0540510:CDS 30.0%
ACAGGAATGATATTGTCATA+AGG - chr4_1:22846789-22846808 None:intergenic 30.0%
ATTATTGCTTTCCAGTACCT+TGG + chr4_1:22846456-22846475 Msa0540510:CDS 35.0%
! TTTGAAATCTACTTCCACCA+AGG - chr4_1:22846476-22846495 None:intergenic 35.0%
TATCCAGATAGGAACTTCAA+AGG - chr4_1:22846579-22846598 None:intergenic 35.0%
TTGAAGTTCCTATCTGGATA+TGG + chr4_1:22846579-22846598 Msa0540510:CDS 35.0%
TAGGAACTACCTGATACTTT+CGG + chr4_1:22846717-22846736 Msa0540510:intron 35.0%
AATCGTGATGTTTCACTCTA+AGG - chr4_1:22846749-22846768 None:intergenic 35.0%
TGATAGGGTGGATAATCAGT+TGG - chr4_1:22846524-22846543 None:intergenic 40.0%
!! GTACCTTTGAAGTTCCTATC+TGG + chr4_1:22846573-22846592 Msa0540510:CDS 40.0%
!! AGGAATTTGCCGAAAGTATC+AGG - chr4_1:22846729-22846748 None:intergenic 40.0%
CACGATTACGTCATGTTGTA+CGG + chr4_1:22846762-22846781 Msa0540510:CDS 40.0%
CGAACATCACATTTGGTATG+GGG - chr4_1:22846833-22846852 None:intergenic 40.0%
CCGAACATCACATTTGGTAT+GGG - chr4_1:22846834-22846853 None:intergenic 40.0%
CCCATACCAAATGTGATGTT+CGG + chr4_1:22846831-22846850 Msa0540510:CDS 40.0%
TCCGAACATCACATTTGGTA+TGG - chr4_1:22846835-22846854 None:intergenic 40.0%
! CCTTTTCCGAACATCACATT+TGG - chr4_1:22846840-22846859 None:intergenic 40.0%
CCAAATGTGATGTTCGGAAA+AGG + chr4_1:22846837-22846856 Msa0540510:CDS 40.0%
ATGTGATGTTCGGAAAAGGT+TGG + chr4_1:22846841-22846860 Msa0540510:CDS 40.0%
! ACGAGTTTTTGTGATGCCAA+TGG + chr4_1:22846864-22846883 Msa0540510:CDS 40.0%
TTGTGATGCCAATGGTATTG+AGG + chr4_1:22846872-22846891 Msa0540510:CDS 40.0%
! TGTGATGCCAATGGTATTGA+GGG + chr4_1:22846873-22846892 Msa0540510:CDS 40.0%
! TTTCAAGTACAAGTGTGTCG+TGG + chr4_1:22846911-22846930 Msa0540510:CDS 40.0%
CTCCAACCATCTGTCAACAA+CGG - chr4_1:22846399-22846418 None:intergenic 45.0%
ATTGCTTTCCAGTACCTTGG+TGG + chr4_1:22846459-22846478 Msa0540510:CDS 45.0%
ATCTACTTCCACCAAGGTAC+TGG - chr4_1:22846470-22846489 None:intergenic 45.0%
ACCCTATCATTCCATGAGTG+CGG + chr4_1:22846535-22846554 Msa0540510:intron 45.0%
TCGTCGATCCATATCCAGAT+AGG - chr4_1:22846590-22846609 None:intergenic 45.0%
! TCTAGCAAGTGCCATTGCTC+CGG - chr4_1:22846327-22846346 None:intergenic 50.0%
! GAGCAATGGCACTTGCTAGA+TGG + chr4_1:22846327-22846346 Msa0540510:CDS 50.0%
! TGGCACTTGCTAGATGGTGA+TGG + chr4_1:22846333-22846352 Msa0540510:CDS 50.0%
! GGCACTTGCTAGATGGTGAT+GGG + chr4_1:22846334-22846353 Msa0540510:CDS 50.0%
GCACTCATGGAATGATAGGG+TGG - chr4_1:22846536-22846555 None:intergenic 50.0%
GCCGCACTCATGGAATGATA+GGG - chr4_1:22846539-22846558 None:intergenic 50.0%
TGCCGCACTCATGGAATGAT+AGG - chr4_1:22846540-22846559 None:intergenic 50.0%
TGGATCGACGAAATCACCGA+AGG + chr4_1:22846599-22846618 Msa0540510:CDS 50.0%
! GATGCCAATGGTATTGAGGG+CGG + chr4_1:22846876-22846895 Msa0540510:CDS 50.0%
TCTACGAGCTACCGGAGCAA+TGG + chr4_1:22846313-22846332 Msa0540510:CDS 55.0%
AGTCGGCCGTTGTTGACAGA+TGG + chr4_1:22846390-22846409 Msa0540510:CDS 55.0%
GGCCGTTGTTGACAGATGGT+TGG + chr4_1:22846394-22846413 Msa0540510:CDS 55.0%
ACACGATGTTGCCGCACTCA+TGG - chr4_1:22846549-22846568 None:intergenic 55.0%
GTCTCCGCCCTCAATACCAT+TGG - chr4_1:22846883-22846902 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 22846273 22846965 22846273 ID=Msa0540510;Name=Msa0540510
chr4_1 mRNA 22846273 22846965 22846273 ID=Msa0540510-mRNA-1;Parent=Msa0540510;Name=Msa0540510-mRNA-1;_AED=0.21;_eAED=0.21;_QI=0|0.5|0|1|0.5|0.33|3|0|174
chr4_1 exon 22846273 22846483 22846273 ID=Msa0540510-mRNA-1:exon:6346;Parent=Msa0540510-mRNA-1
chr4_1 exon 22846553 22846620 22846553 ID=Msa0540510-mRNA-1:exon:6347;Parent=Msa0540510-mRNA-1
chr4_1 exon 22846720 22846965 22846720 ID=Msa0540510-mRNA-1:exon:6348;Parent=Msa0540510-mRNA-1
chr4_1 CDS 22846273 22846483 22846273 ID=Msa0540510-mRNA-1:cds;Parent=Msa0540510-mRNA-1
chr4_1 CDS 22846553 22846620 22846553 ID=Msa0540510-mRNA-1:cds;Parent=Msa0540510-mRNA-1
chr4_1 CDS 22846720 22846965 22846720 ID=Msa0540510-mRNA-1:cds;Parent=Msa0540510-mRNA-1
Gene Sequence

>Msa0540510

GATGTCGGAGAACTACAACCATTCTTTGTTGCTAAATATTTCTACGAGCTACCGGAGCAATGGCACTTGCTAGATGGTGATGGGAATACTCATAACGCCATGTTCAACAAATCAGTTAGTCGGCCGTTGTTGACAGATGGTTGGAGTGCATTGCGATTATTCTACGAGTTTAGTAGAAGTACGATTATTGCTTTCCAGTACCTTGGTGGAATGCGGCAACATCGTGTTATTGTACCTTTGAAGTTCCTATCTGGATATGGATCGACGAAATCACCGAAGGAACTACCTGATACTTTCGGCAAATTCCTTAGAGTGAAACATCACGATTACGTCATGTTGTACGGACCTTATGACAATATCATTCCTGTGAGATTAAAATATACAGACGACCCCATACCAAATGTGATGTTCGGAAAAGGTTGGACGAGTTTTTGTGATGCCAATGGTATTGAGGGCGGAGACGTGTTGATTTTCAAGTACAAGTGTGTCGTGGACAAAAAATATGTTATCGTATCCAAGCGTTGA
Protein sequence

>Msa0540510

DVGELQPFFVAKYFYELPEQWHLLDGDGNTHNAMFNKSVSRPLLTDGWSALRLFYEFSRSTIIAFQYLGGMRQHRVIVPLKFLSGYGSTKSPKELPDTFGKFLRVKHHDYVMLYGPYDNIIPVRLKYTDDPIPNVMFGKGWTSFCDANGIEGGDVLIFKYKCVVDKKYVIVSKR*