AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0680070


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0680070 MtrunA17_Chr2g0325811 59.375 128 27 3 48 157 665 785 9.50e-41 145
Msa0680070 MtrunA17_Chr2g0280141 59.375 128 34 2 48 157 644 771 4.24e-38 137
Msa0680070 MtrunA17_Chr2g0325711 54.198 131 42 2 45 157 660 790 7.55e-37 134
Msa0680070 MtrunA17_Chr2g0325291 58.594 128 35 2 48 157 77 204 1.96e-35 122
Msa0680070 MtrunA17_Chr5g0434761 50.000 128 46 2 48 157 91 218 1.02e-32 116
Msa0680070 MtrunA17_Chr6g0471251 50.000 128 46 2 48 157 593 720 4.98e-31 117
Msa0680070 MtrunA17_Chr2g0325861 57.143 105 37 1 37 133 737 841 1.38e-29 113
Msa0680070 MtrunA17_Chr2g0325611 53.906 128 41 2 48 157 416 543 3.62e-29 111
Msa0680070 MtrunA17_Chr2g0325351 53.125 128 42 2 48 157 514 641 1.06e-27 107
Msa0680070 MtrunA17_Chr2g0325621 54.688 128 40 2 48 157 487 614 2.96e-27 106
Msa0680070 MtrunA17_Chr2g0325661 54.688 128 40 2 48 157 702 829 2.64e-25 100
Msa0680070 MtrunA17_Chr2g0325631 52.344 128 43 2 48 157 91 218 9.37e-25 96.3
Msa0680070 MtrunA17_Chr2g0325231 52.326 86 34 1 45 123 796 881 3.73e-22 92.0
Msa0680070 MtrunA17_Chr2g0325361 51.562 128 44 2 48 157 903 1030 1.31e-21 90.5
Msa0680070 MtrunA17_Chr2g0325221 69.643 56 7 1 112 157 599 654 1.27e-16 75.9
Msa0680070 MtrunA17_Chr5g0416271 50.000 72 28 1 48 111 411 482 2.09e-14 69.3
Msa0680070 MtrunA17_Chr3g0140591 53.333 75 27 1 48 114 98 172 2.66e-14 66.6
Msa0680070 MtrunA17_Chr8g0361651 43.363 113 50 3 45 145 226 336 2.03e-13 66.6
Msa0680070 MtrunA17_Chr2g0325701 60.563 71 21 1 48 111 519 589 2.80e-13 66.2
Msa0680070 MtrunA17_Chr2g0325761 64.815 54 9 1 114 157 594 647 1.09e-12 64.7
Msa0680070 MtrunA17_Chr7g0235921 51.807 83 33 1 48 123 13 95 2.58e-12 60.1
Msa0680070 MtrunA17_Chr2g0332951 48.000 75 28 2 48 111 133 207 3.24e-12 61.6
Msa0680070 MtrunA17_Chr2g0333341 57.143 70 22 1 48 109 537 606 3.84e-11 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 15 sgRNAs with CRISPR-Local

Find 75 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTACTCTTTCTGTCTATTTA+TGG 0.079226 4_4:-38866787 Msa0680070:CDS
TCTCTTCTCCATTTGAATAA+TGG 0.185917 4_4:+38866973 None:intergenic
CTCTTCTCCATTTGAATAAT+GGG 0.193830 4_4:+38866974 None:intergenic
AAGATAACTGTAGAGTTGTT+TGG 0.358335 4_4:-38866703 Msa0680070:CDS
CTTACACTAGGTCTATTATC+TGG 0.372712 4_4:+38866892 None:intergenic
TGGGGTTCTATATGATTTCC+AGG 0.376151 4_4:+38866993 None:intergenic
GTAGAGTTGTTTGGAACTCT+TGG 0.419084 4_4:-38866694 Msa0680070:CDS
ATAGAACCCCATTATTCAAA+TGG 0.454726 4_4:-38866981 Msa0680070:CDS
GGAAACTAACTGCATTGAAC+CGG 0.489489 4_4:-38866271 None:intergenic
AGATCTAGCAAAAGTTGTCC+TGG 0.490853 4_4:-38867011 Msa0680070:CDS
ATGTCATCTTCATTGAAAGA+AGG 0.546335 4_4:+38866757 None:intergenic
GAATGCTGAATTATTGATGA+TGG 0.552603 4_4:-38866952 Msa0680070:CDS
TCTTCTCCATTTGAATAATG+GGG 0.581882 4_4:+38866975 None:intergenic
AATTTCTGAGAGCAATTGCA+AGG 0.582735 4_4:-38866292 Msa0680070:CDS
TTCTTCTGCTCAAAGAACCG+AGG 0.657146 4_4:-38866924 Msa0680070:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTCATATAAAATAATATGTG+AGG + chr4_4:38866842-38866861 None:intergenic 15.0%
!!! TATATCTTCTATTTTCTAAA+CGG - chr4_4:38866897-38866916 Msa0680070:CDS 15.0%
!!! AACTTATTATATAGTTGTTT+TGG - chr4_4:38866978-38866997 Msa0680070:CDS 15.0%
!! TTCATATAAAATAATATGTG+AGG + chr4_4:38866842-38866861 None:intergenic 15.0%
!!! TATATCTTCTATTTTCTAAA+CGG - chr4_4:38866897-38866916 Msa0680070:CDS 15.0%
!!! AACTTATTATATAGTTGTTT+TGG - chr4_4:38866978-38866997 Msa0680070:CDS 15.0%
!! AAAAAAAAGATGAAGTAGAT+TGG + chr4_4:38866949-38866968 None:intergenic 20.0%
!! AAAAAAAAGATGAAGTAGAT+TGG + chr4_4:38866949-38866968 None:intergenic 20.0%
! AATGACAATAATCAAGTAGT+TGG - chr4_4:38867108-38867127 Msa0680070:intron 25.0%
! AATGACAATAATCAAGTAGT+TGG - chr4_4:38867108-38867127 Msa0680070:intron 25.0%
GAAAAATGTTGAACTTGAGT+CGG + chr4_4:38866354-38866373 None:intergenic 30.0%
! TTCAACATTTTTCTCACTTG+AGG - chr4_4:38866361-38866380 Msa0680070:CDS 30.0%
! TCAACATTTTTCTCACTTGA+GGG - chr4_4:38866362-38866381 Msa0680070:CDS 30.0%
ACTTGATTGATTACATGAGT+CGG - chr4_4:38866385-38866404 Msa0680070:CDS 30.0%
ATAGAACCCCATTATTCAAA+TGG - chr4_4:38866475-38866494 Msa0680070:intron 30.0%
TCTTCTCCATTTGAATAATG+GGG + chr4_4:38866484-38866503 None:intergenic 30.0%
CTCTTCTCCATTTGAATAAT+GGG + chr4_4:38866485-38866504 None:intergenic 30.0%
TCTCTTCTCCATTTGAATAA+TGG + chr4_4:38866486-38866505 None:intergenic 30.0%
GAATGCTGAATTATTGATGA+TGG - chr4_4:38866504-38866523 Msa0680070:intron 30.0%
AAAAATTATGCAGCGATTCT+AGG - chr4_4:38866642-38866661 Msa0680070:intron 30.0%
CTACTCTTTCTGTCTATTTA+TGG - chr4_4:38866669-38866688 Msa0680070:intron 30.0%
ATGTCATCTTCATTGAAAGA+AGG + chr4_4:38866702-38866721 None:intergenic 30.0%
!! GATGACATTTTTCAGCTTTT+TGG - chr4_4:38866714-38866733 Msa0680070:CDS 30.0%
AAGATAACTGTAGAGTTGTT+TGG - chr4_4:38866753-38866772 Msa0680070:CDS 30.0%
! TTTGAGAAATGTTTTGCTTC+AGG - chr4_4:38866814-38866833 Msa0680070:intron 30.0%
GAAAAATGTTGAACTTGAGT+CGG + chr4_4:38866354-38866373 None:intergenic 30.0%
! TTCAACATTTTTCTCACTTG+AGG - chr4_4:38866361-38866380 Msa0680070:CDS 30.0%
! TCAACATTTTTCTCACTTGA+GGG - chr4_4:38866362-38866381 Msa0680070:CDS 30.0%
ACTTGATTGATTACATGAGT+CGG - chr4_4:38866385-38866404 Msa0680070:CDS 30.0%
ATAGAACCCCATTATTCAAA+TGG - chr4_4:38866475-38866494 Msa0680070:intron 30.0%
TCTTCTCCATTTGAATAATG+GGG + chr4_4:38866484-38866503 None:intergenic 30.0%
CTCTTCTCCATTTGAATAAT+GGG + chr4_4:38866485-38866504 None:intergenic 30.0%
TCTCTTCTCCATTTGAATAA+TGG + chr4_4:38866486-38866505 None:intergenic 30.0%
GAATGCTGAATTATTGATGA+TGG - chr4_4:38866504-38866523 Msa0680070:intron 30.0%
AAAAATTATGCAGCGATTCT+AGG - chr4_4:38866642-38866661 Msa0680070:intron 30.0%
CTACTCTTTCTGTCTATTTA+TGG - chr4_4:38866669-38866688 Msa0680070:intron 30.0%
ATGTCATCTTCATTGAAAGA+AGG + chr4_4:38866702-38866721 None:intergenic 30.0%
!! GATGACATTTTTCAGCTTTT+TGG - chr4_4:38866714-38866733 Msa0680070:CDS 30.0%
AAGATAACTGTAGAGTTGTT+TGG - chr4_4:38866753-38866772 Msa0680070:CDS 30.0%
! TTTGAGAAATGTTTTGCTTC+AGG - chr4_4:38866814-38866833 Msa0680070:intron 30.0%
! ATTTCCAGGACAAATTTTGC+TGG - chr4_4:38866287-38866306 Msa0680070:CDS 35.0%
GACATTCTTGTTCGTCTTAA+AGG + chr4_4:38866323-38866342 None:intergenic 35.0%
! TTATCTGGTGAGATTTTCCT+CGG + chr4_4:38866552-38866571 None:intergenic 35.0%
CTTACACTAGGTCTATTATC+TGG + chr4_4:38866567-38866586 None:intergenic 35.0%
ATTGCTTCTTCTCTTACACT+AGG + chr4_4:38866579-38866598 None:intergenic 35.0%
! AATTTCTGAGAGCAATTGCA+AGG - chr4_4:38867164-38867183 Msa0680070:intron 35.0%
! GAAATTATCTAGAACCCCAT+CGG + chr4_4:38866272-38866291 None:intergenic 35.0%
! ATTTCCAGGACAAATTTTGC+TGG - chr4_4:38866287-38866306 Msa0680070:CDS 35.0%
GACATTCTTGTTCGTCTTAA+AGG + chr4_4:38866323-38866342 None:intergenic 35.0%
! TTATCTGGTGAGATTTTCCT+CGG + chr4_4:38866552-38866571 None:intergenic 35.0%
CTTACACTAGGTCTATTATC+TGG + chr4_4:38866567-38866586 None:intergenic 35.0%
ATTGCTTCTTCTCTTACACT+AGG + chr4_4:38866579-38866598 None:intergenic 35.0%
! AATTTCTGAGAGCAATTGCA+AGG - chr4_4:38867164-38867183 Msa0680070:intron 35.0%
!! TGGGGTTCTAGATAATTTCC+AGG - chr4_4:38866273-38866292 Msa0680070:CDS 40.0%
AGATCCAGCAAAATTTGTCC+TGG + chr4_4:38866294-38866313 None:intergenic 40.0%
! AGGACAAATTTTGCTGGATC+TGG - chr4_4:38866293-38866312 Msa0680070:CDS 40.0%
! AGGACAACTTTTGCTAGATC+TGG + chr4_4:38866446-38866465 None:intergenic 40.0%
AGATCTAGCAAAAGTTGTCC+TGG - chr4_4:38866445-38866464 Msa0680070:intron 40.0%
TGGGGTTCTATATGATTTCC+AGG + chr4_4:38866466-38866485 None:intergenic 40.0%
! GTAGAGTTGTTTGGAACTCT+TGG - chr4_4:38866762-38866781 Msa0680070:CDS 40.0%
! GGTTTTGCAGTTAAAGCTTC+TGG - chr4_4:38866783-38866802 Msa0680070:CDS 40.0%
!! TGGGGTTCTAGATAATTTCC+AGG - chr4_4:38866273-38866292 Msa0680070:CDS 40.0%
AGATCCAGCAAAATTTGTCC+TGG + chr4_4:38866294-38866313 None:intergenic 40.0%
! AGGACAAATTTTGCTGGATC+TGG - chr4_4:38866293-38866312 Msa0680070:CDS 40.0%
! AGGACAACTTTTGCTAGATC+TGG + chr4_4:38866446-38866465 None:intergenic 40.0%
AGATCTAGCAAAAGTTGTCC+TGG - chr4_4:38866445-38866464 Msa0680070:intron 40.0%
TGGGGTTCTATATGATTTCC+AGG + chr4_4:38866466-38866485 None:intergenic 40.0%
! GTAGAGTTGTTTGGAACTCT+TGG - chr4_4:38866762-38866781 Msa0680070:CDS 40.0%
! GGTTTTGCAGTTAAAGCTTC+TGG - chr4_4:38866783-38866802 Msa0680070:CDS 40.0%
ATTACATGAGTCGGTTGCCA+AGG - chr4_4:38866394-38866413 Msa0680070:CDS 45.0%
!! AAGACGAACAAGAGTGTCCT+TGG + chr4_4:38866414-38866433 None:intergenic 45.0%
TTCTTCTGCTCAAAGAACCG+AGG - chr4_4:38866532-38866551 Msa0680070:intron 45.0%
ATTACATGAGTCGGTTGCCA+AGG - chr4_4:38866394-38866413 Msa0680070:CDS 45.0%
!! AAGACGAACAAGAGTGTCCT+TGG + chr4_4:38866414-38866433 None:intergenic 45.0%
TTCTTCTGCTCAAAGAACCG+AGG - chr4_4:38866532-38866551 Msa0680070:intron 45.0%
Chromosome Type Strat End Strand Name
chr4_4 gene 38866272 38867206 38866272 ID=Msa0680070;Name=Msa0680070
chr4_4 mRNA 38866272 38867206 38866272 ID=Msa0680070-mRNA-1;Parent=Msa0680070;Name=Msa0680070-mRNA-1;_AED=0.13;_eAED=0.36;_QI=0|0|0|0.83|0.2|0.16|6|0|158
chr4_4 exon 38867202 38867206 38867202 ID=Msa0680070-mRNA-1:exon:9161;Parent=Msa0680070-mRNA-1
chr4_4 exon 38866897 38867031 38866897 ID=Msa0680070-mRNA-1:exon:9160;Parent=Msa0680070-mRNA-1
chr4_4 exon 38866848 38866891 38866848 ID=Msa0680070-mRNA-1:exon:9159;Parent=Msa0680070-mRNA-1
chr4_4 exon 38866674 38866823 38866674 ID=Msa0680070-mRNA-1:exon:9158;Parent=Msa0680070-mRNA-1
chr4_4 exon 38866356 38866441 38866356 ID=Msa0680070-mRNA-1:exon:9157;Parent=Msa0680070-mRNA-1
chr4_4 exon 38866272 38866325 38866272 ID=Msa0680070-mRNA-1:exon:9156;Parent=Msa0680070-mRNA-1
chr4_4 CDS 38867202 38867206 38867202 ID=Msa0680070-mRNA-1:cds;Parent=Msa0680070-mRNA-1
chr4_4 CDS 38866897 38867031 38866897 ID=Msa0680070-mRNA-1:cds;Parent=Msa0680070-mRNA-1
chr4_4 CDS 38866848 38866891 38866848 ID=Msa0680070-mRNA-1:cds;Parent=Msa0680070-mRNA-1
chr4_4 CDS 38866674 38866823 38866674 ID=Msa0680070-mRNA-1:cds;Parent=Msa0680070-mRNA-1
chr4_4 CDS 38866356 38866441 38866356 ID=Msa0680070-mRNA-1:cds;Parent=Msa0680070-mRNA-1
chr4_4 CDS 38866272 38866325 38866272 ID=Msa0680070-mRNA-1:cds;Parent=Msa0680070-mRNA-1
Gene Sequence

>Msa0680070

ATGGGATCTAGCAAAAGTTGTCCTGGAAATCATATAGAACCCCATTATTCAAATGGAGAAGAGAATGCTGAATTATTGATGATGGCGACATTCTTCTGCTCAAAGAACCGAGGAAAATCTCACCAGATAATAGACCTAGTAGAAGAAGCAATTAAGCTAGCTCTCGATGTGAAAGCGTACATAACGATTCTAGGTTTTCTACTCTTTCTGTCTATTTATGGACTGACTCCTTCTTTCAATGAAGATGACATTTTTCAGCTTTTTGGTTTTGCTGCTCAGCACAAGATAACTGTAGAGTTGTTTGGAACTCTTGGTTTTGCAGTTAAAGCTTCTGATGTTGTTGAGAATCTTATCAAGAGACAACAATACGATGAAGCTGTTAGATTCAGTCGTGCATATAACTTCAATGACAATAATCAAAACGTAAAACTAATTTCTGAGAGCAATTGCAAGGAAACTAACTGCATTGAACCG

Protein sequence

>Msa0680070

MGSSKSCPGNHIEPHYSNGEENAELLMMATFFCSKNRGKSHQIIDLVEEAIKLALDVKAYITILGFLLFLSIYGLTPSFNEDDIFQLFGFAAQHKITVELFGTLGFAVKASDVVENLIKRQQYDEAVRFSRAYNFNDNNQNVKLISESNCKETNCIEP