AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0301260

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0301260 MtrunA17_Chr2g0282561 97.260 73 2 0 1 73 40 112 5.67e-47 144
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0301260 AT5G44300.1 68.657 67 19 2 8 73 49 114 1.43e-25 91.3
Msa0301260 AT2G33830.2 71.429 63 16 2 12 73 47 108 5.02e-25 89.7
Msa0301260 AT2G33830.1 71.429 63 16 2 12 73 45 106 5.36e-25 89.4
Msa0301260 AT1G28330.1 73.469 49 12 1 26 73 74 122 3.74e-22 82.8
Msa0301260 AT1G28330.4 71.429 49 13 1 26 73 74 122 2.07e-21 80.9
Msa0301260 AT1G28330.5 73.684 38 9 1 26 62 74 111 1.60e-14 63.2
Msa0301260 AT1G28330.6 73.684 38 9 1 26 62 74 111 1.60e-14 63.2
Msa0301260 AT1G28330.3 60.417 48 18 1 26 72 74 121 2.75e-14 63.2
Msa0301260 AT1G28330.2 60.417 48 18 1 26 72 74 121 2.75e-14 63.2

Find 40 sgRNAs with CRISPR-Local

Find 118 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATGTGCCACCAAAACTTTC+TGG 0.166653 2_3:-57115990 Msa0301260:three_prime_UTR
TTAGCTAGATAAACCTATTA+AGG 0.299960 2_3:+57115795 None:intergenic
TGGAGGAGCGTGTTCAATCC+TGG 0.327841 2_3:-57116460 Msa0301260:CDS
TTATCTAGCTTTGCCTTAAT+AGG 0.332499 2_3:-57115808 Msa0301260:three_prime_UTR
CACGTAAAGTTGACAACGTT+TGG 0.347744 2_3:-57116480 Msa0301260:CDS
GCAATCAACCCAGAAAGTTT+TGG 0.362794 2_3:+57115981 None:intergenic
AACTCTGCTACTAAGACAAT+TGG 0.426460 2_3:-57116433 Msa0301260:CDS
CTTCTGAATATTGTAACAAA+TGG 0.444532 2_3:-57115699 Msa0301260:three_prime_UTR
ATTCCATCTTGGTAATAGCT+TGG 0.452319 2_3:-57115636 Msa0301260:three_prime_UTR
ATGTGCCACCAAAACTTTCT+GGG 0.468880 2_3:-57115989 Msa0301260:three_prime_UTR
GATGGAATTGCACAGTTACA+TGG 0.475449 2_3:+57115651 None:intergenic
GGAGGAGCGTGTTCAATCCT+GGG 0.490368 2_3:-57116459 Msa0301260:CDS
TGGCAGACGATCAACAAAAC+AGG 0.493537 2_3:+57115943 None:intergenic
GATCAGATCACGACACGTAA+TGG 0.493690 2_3:+57115907 None:intergenic
TCAACTTTACGTGCCGATTG+AGG 0.495412 2_3:+57116490 None:intergenic
GACTCCAACGACACCTCAAT+CGG 0.504134 2_3:-57116503 Msa0301260:CDS
ACCGGTGTTGTCGGTGTCGA+AGG 0.505007 2_3:+57116526 None:intergenic
TGAGGTGTCGTTGGAGTCAC+CGG 0.510899 2_3:+57116508 None:intergenic
TTGTATTTAGGTGTAGATGA+AGG 0.513685 2_3:-57116583 Msa0301260:five_prime_UTR
GTGATCGCAGGATGTACAGC+GGG 0.519197 2_3:-57116035 Msa0301260:intron
TTACGTGTCGTGATCTGATC+GGG 0.520466 2_3:-57115904 Msa0301260:three_prime_UTR
GTAACTGTGCAATTCCATCT+TGG 0.524557 2_3:-57115647 Msa0301260:three_prime_UTR
GTTGGAGTCACCGGTGTTGT+CGG 0.528758 2_3:+57116517 None:intergenic
TTAGTAGCAGAGTTACTCCC+AGG 0.531237 2_3:+57116442 None:intergenic
GGATGTACAGCGGGGACACA+AGG 0.536816 2_3:-57116026 Msa0301260:CDS
CGTGCCGATTGAGGTGTCGT+TGG 0.538925 2_3:+57116499 None:intergenic
AATCCAAGCTATTACCAAGA+TGG 0.547872 2_3:+57115633 None:intergenic
ATTACGTGTCGTGATCTGAT+CGG 0.563489 2_3:-57115905 Msa0301260:three_prime_UTR
TATTTAGGTGTAGATGAAGG+AGG 0.572856 2_3:-57116580 Msa0301260:five_prime_UTR
GTAAAGTTGACAACGTTTGG+AGG 0.589302 2_3:-57116477 Msa0301260:CDS
ACATACCAATCATAGACAGT+GGG 0.591016 2_3:+57116376 None:intergenic
GCCTTCGACACCGACAACAC+CGG 0.604941 2_3:-57116527 Msa0301260:CDS
ACAAAACTCAAATTAATACA+AGG 0.623205 2_3:+57115830 None:intergenic
GATTAATTAACACTTACAGA+AGG 0.629797 2_3:+57115759 None:intergenic
AACATACCAATCATAGACAG+TGG 0.664521 2_3:+57116375 None:intergenic
CATACCAATCATAGACAGTG+GGG 0.727901 2_3:+57116377 None:intergenic
TGTGATCGCAGGATGTACAG+CGG 0.734662 2_3:-57116036 Msa0301260:intron
ATACCAATCATAGACAGTGG+GGG 0.749000 2_3:+57116378 None:intergenic
TGATCGCAGGATGTACAGCG+GGG 0.761714 2_3:-57116034 Msa0301260:intron
GTAATGGTGATACAGACACG+TGG 0.778111 2_3:+57115923 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTGATTCTATATTTTATTTT+TGG - chr2_3:57115954-57115973 Msa0301260:three_prime_UTR 10.0%
!!! TTAAGAATTTTATATTACAA+AGG - chr2_3:57116587-57116606 Msa0301260:five_prime_UTR 10.0%
!!! TAAGAATTTTATATTACAAA+GGG - chr2_3:57116588-57116607 Msa0301260:five_prime_UTR 10.0%
!!! TTGATTCTATATTTTATTTT+TGG - chr2_3:57115954-57115973 Msa0301260:three_prime_UTR 10.0%
!!! TTAAGAATTTTATATTACAA+AGG - chr2_3:57116587-57116606 Msa0301260:five_prime_UTR 10.0%
!!! TAAGAATTTTATATTACAAA+GGG - chr2_3:57116588-57116607 Msa0301260:five_prime_UTR 10.0%
!! ACAAACATATAAAAATGAAT+TGG - chr2_3:57116131-57116150 Msa0301260:intron 15.0%
!! CAAACATATAAAAATGAATT+GGG - chr2_3:57116132-57116151 Msa0301260:intron 15.0%
!!! AAGAATTTTATATTACAAAG+GGG - chr2_3:57116589-57116608 Msa0301260:five_prime_UTR 15.0%
!! ACAAACATATAAAAATGAAT+TGG - chr2_3:57116131-57116150 Msa0301260:intron 15.0%
!! CAAACATATAAAAATGAATT+GGG - chr2_3:57116132-57116151 Msa0301260:intron 15.0%
!!! AAGAATTTTATATTACAAAG+GGG - chr2_3:57116589-57116608 Msa0301260:five_prime_UTR 15.0%
!! ACAAAACTCAAATTAATACA+AGG + chr2_3:57116369-57116388 None:intergenic 20.0%
!! AATATTCAGAAGAAGAAAAA+AGG + chr2_3:57116489-57116508 None:intergenic 20.0%
!! ACAAAACTCAAATTAATACA+AGG + chr2_3:57116369-57116388 None:intergenic 20.0%
!! AATATTCAGAAGAAGAAAAA+AGG + chr2_3:57116489-57116508 None:intergenic 20.0%
! TGTATAGTTCTTCTAACAAA+AGG + chr2_3:57116022-57116041 None:intergenic 25.0%
! TTAGCTAGATAAACCTATTA+AGG + chr2_3:57116404-57116423 None:intergenic 25.0%
! GATTAATTAACACTTACAGA+AGG + chr2_3:57116440-57116459 None:intergenic 25.0%
! CTTCTGAATATTGTAACAAA+TGG - chr2_3:57116497-57116516 Msa0301260:CDS 25.0%
! TGTATAGTTCTTCTAACAAA+AGG + chr2_3:57116022-57116041 None:intergenic 25.0%
! TTAGCTAGATAAACCTATTA+AGG + chr2_3:57116404-57116423 None:intergenic 25.0%
! GATTAATTAACACTTACAGA+AGG + chr2_3:57116440-57116459 None:intergenic 25.0%
! CTTCTGAATATTGTAACAAA+TGG - chr2_3:57116497-57116516 Msa0301260:CDS 25.0%
TTGTATTTAGGTGTAGATGA+AGG - chr2_3:57115613-57115632 Msa0301260:three_prime_UTR 30.0%
TGTTAGAAGAACTATACATG+TGG - chr2_3:57116024-57116043 Msa0301260:CDS 30.0%
!! TTATCTAGCTTTGCCTTAAT+AGG - chr2_3:57116388-57116407 Msa0301260:CDS 30.0%
TTGTATTTAGGTGTAGATGA+AGG - chr2_3:57115613-57115632 Msa0301260:three_prime_UTR 30.0%
TGTTAGAAGAACTATACATG+TGG - chr2_3:57116024-57116043 Msa0301260:CDS 30.0%
!! TTATCTAGCTTTGCCTTAAT+AGG - chr2_3:57116388-57116407 Msa0301260:CDS 30.0%
TATTTAGGTGTAGATGAAGG+AGG - chr2_3:57115616-57115635 Msa0301260:three_prime_UTR 35.0%
AACTCTGCTACTAAGACAAT+TGG - chr2_3:57115763-57115782 Msa0301260:three_prime_UTR 35.0%
ACATACCAATCATAGACAGT+GGG + chr2_3:57115823-57115842 None:intergenic 35.0%
AACATACCAATCATAGACAG+TGG + chr2_3:57115824-57115843 None:intergenic 35.0%
ACGCAAATTATAAGAGTGGT+TGG + chr2_3:57115864-57115883 None:intergenic 35.0%
ATGCACGCAAATTATAAGAG+TGG + chr2_3:57115868-57115887 None:intergenic 35.0%
! ATTCCATCTTGGTAATAGCT+TGG - chr2_3:57116560-57116579 Msa0301260:exon 35.0%
AATCCAAGCTATTACCAAGA+TGG + chr2_3:57116566-57116585 None:intergenic 35.0%
TATTTAGGTGTAGATGAAGG+AGG - chr2_3:57115616-57115635 Msa0301260:three_prime_UTR 35.0%
AACTCTGCTACTAAGACAAT+TGG - chr2_3:57115763-57115782 Msa0301260:three_prime_UTR 35.0%
ACATACCAATCATAGACAGT+GGG + chr2_3:57115823-57115842 None:intergenic 35.0%
AACATACCAATCATAGACAG+TGG + chr2_3:57115824-57115843 None:intergenic 35.0%
ACGCAAATTATAAGAGTGGT+TGG + chr2_3:57115864-57115883 None:intergenic 35.0%
ATGCACGCAAATTATAAGAG+TGG + chr2_3:57115868-57115887 None:intergenic 35.0%
! ATTCCATCTTGGTAATAGCT+TGG - chr2_3:57116560-57116579 Msa0301260:exon 35.0%
AATCCAAGCTATTACCAAGA+TGG + chr2_3:57116566-57116585 None:intergenic 35.0%
CACGTAAAGTTGACAACGTT+TGG - chr2_3:57115716-57115735 Msa0301260:three_prime_UTR 40.0%
GTAAAGTTGACAACGTTTGG+AGG - chr2_3:57115719-57115738 Msa0301260:three_prime_UTR 40.0%
ATACCAATCATAGACAGTGG+GGG + chr2_3:57115821-57115840 None:intergenic 40.0%
CATACCAATCATAGACAGTG+GGG + chr2_3:57115822-57115841 None:intergenic 40.0%
ATGTGCCACCAAAACTTTCT+GGG - chr2_3:57116207-57116226 Msa0301260:intron 40.0%
!! ATCAACCCAGAAAGTTTTGG+TGG + chr2_3:57116215-57116234 None:intergenic 40.0%
! GCAATCAACCCAGAAAGTTT+TGG + chr2_3:57116218-57116237 None:intergenic 40.0%
ATTACGTGTCGTGATCTGAT+CGG - chr2_3:57116291-57116310 Msa0301260:intron 40.0%
GATGGAATTGCACAGTTACA+TGG + chr2_3:57116548-57116567 None:intergenic 40.0%
GTAACTGTGCAATTCCATCT+TGG - chr2_3:57116549-57116568 Msa0301260:exon 40.0%
CACGTAAAGTTGACAACGTT+TGG - chr2_3:57115716-57115735 Msa0301260:three_prime_UTR 40.0%
GTAAAGTTGACAACGTTTGG+AGG - chr2_3:57115719-57115738 Msa0301260:three_prime_UTR 40.0%
ATACCAATCATAGACAGTGG+GGG + chr2_3:57115821-57115840 None:intergenic 40.0%
CATACCAATCATAGACAGTG+GGG + chr2_3:57115822-57115841 None:intergenic 40.0%
ATGTGCCACCAAAACTTTCT+GGG - chr2_3:57116207-57116226 Msa0301260:intron 40.0%
!! ATCAACCCAGAAAGTTTTGG+TGG + chr2_3:57116215-57116234 None:intergenic 40.0%
! GCAATCAACCCAGAAAGTTT+TGG + chr2_3:57116218-57116237 None:intergenic 40.0%
ATTACGTGTCGTGATCTGAT+CGG - chr2_3:57116291-57116310 Msa0301260:intron 40.0%
GATGGAATTGCACAGTTACA+TGG + chr2_3:57116548-57116567 None:intergenic 40.0%
GTAACTGTGCAATTCCATCT+TGG - chr2_3:57116549-57116568 Msa0301260:exon 40.0%
!! TCAACTTTACGTGCCGATTG+AGG + chr2_3:57115709-57115728 None:intergenic 45.0%
TTAGTAGCAGAGTTACTCCC+AGG + chr2_3:57115757-57115776 None:intergenic 45.0%
! ATTGGGTTGTATGTGATCGC+AGG - chr2_3:57116149-57116168 Msa0301260:intron 45.0%
!! AAGTTTTGGTGGCACATCAG+CGG + chr2_3:57116204-57116223 None:intergenic 45.0%
GATGTGCCACCAAAACTTTC+TGG - chr2_3:57116206-57116225 Msa0301260:intron 45.0%
TGGCAGACGATCAACAAAAC+AGG + chr2_3:57116256-57116275 None:intergenic 45.0%
GTAATGGTGATACAGACACG+TGG + chr2_3:57116276-57116295 None:intergenic 45.0%
GATCAGATCACGACACGTAA+TGG + chr2_3:57116292-57116311 None:intergenic 45.0%
TTACGTGTCGTGATCTGATC+GGG - chr2_3:57116292-57116311 Msa0301260:intron 45.0%
!! TCAACTTTACGTGCCGATTG+AGG + chr2_3:57115709-57115728 None:intergenic 45.0%
TTAGTAGCAGAGTTACTCCC+AGG + chr2_3:57115757-57115776 None:intergenic 45.0%
! ATTGGGTTGTATGTGATCGC+AGG - chr2_3:57116149-57116168 Msa0301260:intron 45.0%
!! AAGTTTTGGTGGCACATCAG+CGG + chr2_3:57116204-57116223 None:intergenic 45.0%
GATGTGCCACCAAAACTTTC+TGG - chr2_3:57116206-57116225 Msa0301260:intron 45.0%
TGGCAGACGATCAACAAAAC+AGG + chr2_3:57116256-57116275 None:intergenic 45.0%
GTAATGGTGATACAGACACG+TGG + chr2_3:57116276-57116295 None:intergenic 45.0%
GATCAGATCACGACACGTAA+TGG + chr2_3:57116292-57116311 None:intergenic 45.0%
TTACGTGTCGTGATCTGATC+GGG - chr2_3:57116292-57116311 Msa0301260:intron 45.0%
GACTCCAACGACACCTCAAT+CGG - chr2_3:57115693-57115712 Msa0301260:three_prime_UTR 50.0%
!! TCATAGACAGTGGGGGTGTT+GGG + chr2_3:57115814-57115833 None:intergenic 50.0%
! ATCATAGACAGTGGGGGTGT+TGG + chr2_3:57115815-57115834 None:intergenic 50.0%
ACACCCCCACTGTCTATGAT+TGG - chr2_3:57115815-57115834 Msa0301260:three_prime_UTR 50.0%
TGTGATCGCAGGATGTACAG+CGG - chr2_3:57116160-57116179 Msa0301260:intron 50.0%
GACTCCAACGACACCTCAAT+CGG - chr2_3:57115693-57115712 Msa0301260:three_prime_UTR 50.0%
!! TCATAGACAGTGGGGGTGTT+GGG + chr2_3:57115814-57115833 None:intergenic 50.0%
! ATCATAGACAGTGGGGGTGT+TGG + chr2_3:57115815-57115834 None:intergenic 50.0%
ACACCCCCACTGTCTATGAT+TGG - chr2_3:57115815-57115834 Msa0301260:three_prime_UTR 50.0%
TGTGATCGCAGGATGTACAG+CGG - chr2_3:57116160-57116179 Msa0301260:intron 50.0%
!! GTTGGAGTCACCGGTGTTGT+CGG + chr2_3:57115682-57115701 None:intergenic 55.0%
!! TGAGGTGTCGTTGGAGTCAC+CGG + chr2_3:57115691-57115710 None:intergenic 55.0%
! TGGAGGAGCGTGTTCAATCC+TGG - chr2_3:57115736-57115755 Msa0301260:three_prime_UTR 55.0%
! GGAGGAGCGTGTTCAATCCT+GGG - chr2_3:57115737-57115756 Msa0301260:three_prime_UTR 55.0%
!! CATAGACAGTGGGGGTGTTG+GGG + chr2_3:57115813-57115832 None:intergenic 55.0%
GTGATCGCAGGATGTACAGC+GGG - chr2_3:57116161-57116180 Msa0301260:intron 55.0%
TGATCGCAGGATGTACAGCG+GGG - chr2_3:57116162-57116181 Msa0301260:intron 55.0%
!! GTTGGAGTCACCGGTGTTGT+CGG + chr2_3:57115682-57115701 None:intergenic 55.0%
!! TGAGGTGTCGTTGGAGTCAC+CGG + chr2_3:57115691-57115710 None:intergenic 55.0%
! TGGAGGAGCGTGTTCAATCC+TGG - chr2_3:57115736-57115755 Msa0301260:three_prime_UTR 55.0%
! GGAGGAGCGTGTTCAATCCT+GGG - chr2_3:57115737-57115756 Msa0301260:three_prime_UTR 55.0%
!! CATAGACAGTGGGGGTGTTG+GGG + chr2_3:57115813-57115832 None:intergenic 55.0%
GTGATCGCAGGATGTACAGC+GGG - chr2_3:57116161-57116180 Msa0301260:intron 55.0%
TGATCGCAGGATGTACAGCG+GGG - chr2_3:57116162-57116181 Msa0301260:intron 55.0%
GCCTTCGACACCGACAACAC+CGG - chr2_3:57115669-57115688 Msa0301260:three_prime_UTR 60.0%
!! ACCGGTGTTGTCGGTGTCGA+AGG + chr2_3:57115673-57115692 None:intergenic 60.0%
!! CGTGCCGATTGAGGTGTCGT+TGG + chr2_3:57115700-57115719 None:intergenic 60.0%
GGATGTACAGCGGGGACACA+AGG - chr2_3:57116170-57116189 Msa0301260:intron 60.0%
GCCTTCGACACCGACAACAC+CGG - chr2_3:57115669-57115688 Msa0301260:three_prime_UTR 60.0%
!! ACCGGTGTTGTCGGTGTCGA+AGG + chr2_3:57115673-57115692 None:intergenic 60.0%
!! CGTGCCGATTGAGGTGTCGT+TGG + chr2_3:57115700-57115719 None:intergenic 60.0%
GGATGTACAGCGGGGACACA+AGG - chr2_3:57116170-57116189 Msa0301260:intron 60.0%
!! ACAGTGGGGGTGTTGGGGAG+TGG + chr2_3:57115808-57115827 None:intergenic 65.0%
!! ACAGTGGGGGTGTTGGGGAG+TGG + chr2_3:57115808-57115827 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr2_3 gene 57115606 57116612 57115606 ID=Msa0301260;Name=Msa0301260
chr2_3 mRNA 57115606 57116612 57115606 ID=Msa0301260-mRNA-1;Parent=Msa0301260;Name=Msa0301260-mRNA-1;_AED=0.01;_eAED=0.01;_QI=46|1|1|1|1|1|2|405|73
chr2_3 exon 57115606 57116047 57115606 ID=Msa0301260-mRNA-1:exon:18395;Parent=Msa0301260-mRNA-1
chr2_3 exon 57116382 57116612 57116382 ID=Msa0301260-mRNA-1:exon:18394;Parent=Msa0301260-mRNA-1
chr2_3 five_prime_UTR 57116567 57116612 57116567 ID=Msa0301260-mRNA-1:five_prime_utr;Parent=Msa0301260-mRNA-1
chr2_3 CDS 57116382 57116566 57116382 ID=Msa0301260-mRNA-1:cds;Parent=Msa0301260-mRNA-1
chr2_3 CDS 57116011 57116047 57116011 ID=Msa0301260-mRNA-1:cds;Parent=Msa0301260-mRNA-1
chr2_3 three_prime_UTR 57115606 57116010 57115606 ID=Msa0301260-mRNA-1:three_prime_utr;Parent=Msa0301260-mRNA-1
Gene Sequence

>Msa0301260

ATGAGAAACACGTCGTTGCCTTCGACACCGACAACACCGGTGACTCCAACGACACCTCAATCGGCACGTAAAGTTGACAACGTTTGGAGGAGCGTGTTCAATCCTGGGAGTAACTCTGCTACTAAGACAATTGGTGCTCATATGTTTGACAAACCACTCCCCAACACCCCCACTGTCTATGATTGGATGTACAGCGGGGACACAAGGAGCAAGCACCGCTGA
Protein sequence

>Msa0301260

MRNTSLPSTPTTPVTPTTPQSARKVDNVWRSVFNPGSNSATKTIGAHMFDKPLPNTPTVYDWMYSGDTRSKHR*