AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0212100

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0212100 MtrunA17_Chr7g0253751 51.250 80 35 1 11 90 24 99 1.14e-22 85.9
Msa0212100 MtrunA17_Chr3g0142071 55.556 63 28 0 27 89 45 107 5.21e-18 78.2
Msa0212100 MtrunA17_Chr2g0311391 54.688 64 29 0 33 96 37 100 1.04e-16 74.3
Msa0212100 MtrunA17_Chr2g0311471 49.206 63 32 0 33 95 37 99 6.06e-14 66.2
Msa0212100 MtrunA17_Chr2g0311091 48.438 64 33 0 33 96 35 98 8.09e-14 64.3
Msa0212100 MtrunA17_Chr2g0311381 48.438 64 33 0 32 95 36 99 9.86e-14 65.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0212100 AT1G09850.1 45.833 72 38 1 27 97 27 98 1.21e-15 72.0
Msa0212100 AT3G43960.1 41.791 67 39 0 27 93 36 102 6.72e-13 63.9
Msa0212100 AT4G35350.1 51.515 66 31 1 28 93 47 111 7.04e-13 63.9
Msa0212100 AT4G35350.2 51.515 66 31 1 28 93 47 111 7.22e-13 63.5

Find 42 sgRNAs with CRISPR-Local

Find 112 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCAATGGAACAACCATAAT+TGG 0.195557 2_1:-53870949 None:intergenic
TGATCAGTTTATGAAATAAA+AGG 0.223384 2_1:-53870465 None:intergenic
GTGGTTGTGTTGAGTGATTC+TGG 0.223931 2_1:-53870859 None:intergenic
TTTGATTATATTAAAACTAT+TGG 0.232195 2_1:+53871124 Msa0212100:three_prime_UTR
TCCATCTTAATATCAATAAA+TGG 0.249277 2_1:+53871210 Msa0212100:three_prime_UTR
GAGGAATTTACGTCCAATTA+TGG 0.252320 2_1:+53870936 Msa0212100:CDS
TAAGATGGAAGTTCAAGATT+TGG 0.319820 2_1:-53871196 None:intergenic
TTGATTATATTAAAACTATT+GGG 0.332489 2_1:+53871125 Msa0212100:three_prime_UTR
TTCTTGAAGCTTGGAGTTGG+AGG 0.392872 2_1:-53870601 None:intergenic
TGAGTAATTCAACTCGTAGA+TGG 0.395615 2_1:-53870517 None:intergenic
AGAATAACAAACCGATGGTT+GGG 0.404177 2_1:-53870634 None:intergenic
CTGTTCTTGAAGCTTGGAGT+TGG 0.411197 2_1:-53870604 None:intergenic
CCGGATGATCTTGAAAAGTT+AGG 0.423858 2_1:+53870987 Msa0212100:CDS
AAAACTTCATTGATGTTTGA+CGG 0.433536 2_1:-53871018 None:intergenic
TCCATGAAATATTTGAAAAG+TGG 0.434083 2_1:+53870760 Msa0212100:CDS
AGGAATCTGTTCTTGAAGCT+TGG 0.443942 2_1:-53870610 None:intergenic
GTAGCTTCAAAATATGTCAT+AGG 0.453381 2_1:+53870489 Msa0212100:five_prime_UTR
ACCATTTATTGATATTAAGA+TGG 0.454456 2_1:-53871211 None:intergenic
ATTAAAACTATTGGGCTAAG+AGG 0.456850 2_1:+53871133 Msa0212100:three_prime_UTR
AAACTTCATTGATGTTTGAC+GGG 0.458766 2_1:-53871017 None:intergenic
AACGTTGTGTCTCTATTCAA+TGG 0.461032 2_1:+53870560 Msa0212100:exon
CAACTATTAACACTTCATCT+TGG 0.461354 2_1:-53871171 None:intergenic
GATCAGTTTATGAAATAAAA+GGG 0.463851 2_1:-53870464 None:intergenic
TGAATATAAGGCTCCTGGTT+CGG 0.465353 2_1:+53870734 Msa0212100:intron
AATTGTGAATATAAGGCTCC+TGG 0.479700 2_1:+53870729 Msa0212100:intron
CGAAGGTGAGATCAGAGAAC+TGG 0.488939 2_1:-53870914 None:intergenic
TGATTTCAACGATGTCCATC+CGG 0.494998 2_1:+53870968 Msa0212100:CDS
TAGAATAACAAACCGATGGT+TGG 0.501861 2_1:-53870635 None:intergenic
GTTCTCTGATCTCACCTTCG+AGG 0.507841 2_1:+53870917 Msa0212100:CDS
ATGGACATCGTTGAAATCAA+TGG 0.510440 2_1:-53870964 None:intergenic
CGACAAAACATATTCTTCAA+AGG 0.513620 2_1:+53870794 Msa0212100:CDS
ATATAATCAAAGGTGGTGAC+AGG 0.523055 2_1:-53871112 None:intergenic
GAATAACAAACCGATGGTTG+GGG 0.564507 2_1:-53870633 None:intergenic
AAAACTATTGGGCTAAGAGG+AGG 0.564725 2_1:+53871136 Msa0212100:three_prime_UTR
ACAGATTCCTCCCCAACCAT+CGG 0.584110 2_1:+53870623 Msa0212100:CDS
ATTTCATGGATGTCCGAACC+AGG 0.584248 2_1:-53870747 None:intergenic
AAACTATTGGGCTAAGAGGA+GGG 0.592370 2_1:+53871137 Msa0212100:three_prime_UTR
TGAGATCAGAGAACTGGTTG+AGG 0.597092 2_1:-53870908 None:intergenic
AATATTTGAAAAGTGGTGCA+AGG 0.602264 2_1:+53870767 Msa0212100:CDS
TAACAAACCGATGGTTGGGG+AGG 0.622332 2_1:-53870630 None:intergenic
ATTGGACGTAAATTCCTCGA+AGG 0.638330 2_1:-53870931 None:intergenic
ATTGAATAGAGACACAACGT+TGG 0.699795 2_1:-53870558 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAATTTTAATTGTGAATATA+AGG + chr2_1:53870722-53870741 Msa0212100:intron 10.0%
!!! AATAGTTTTAATATAATCAA+AGG - chr2_1:53871125-53871144 None:intergenic 10.0%
!! TTTGATTATATTAAAACTAT+TGG + chr2_1:53871124-53871143 Msa0212100:three_prime_UTR 10.0%
!! TTGATTATATTAAAACTATT+GGG + chr2_1:53871125-53871144 Msa0212100:three_prime_UTR 10.0%
!!! TAATTTTAATTGTGAATATA+AGG + chr2_1:53870722-53870741 Msa0212100:intron 10.0%
!!! AATAGTTTTAATATAATCAA+AGG - chr2_1:53871125-53871144 None:intergenic 10.0%
!! TTTGATTATATTAAAACTAT+TGG + chr2_1:53871124-53871143 Msa0212100:three_prime_UTR 10.0%
!! TTGATTATATTAAAACTATT+GGG + chr2_1:53871125-53871144 Msa0212100:three_prime_UTR 10.0%
!!! AGTTTTAATATAATCAAAGG+TGG - chr2_1:53871122-53871141 None:intergenic 20.0%
!! TCCATCTTAATATCAATAAA+TGG + chr2_1:53871210-53871229 Msa0212100:three_prime_UTR 20.0%
!! ACCATTTATTGATATTAAGA+TGG - chr2_1:53871214-53871233 None:intergenic 20.0%
!!! AGTTTTAATATAATCAAAGG+TGG - chr2_1:53871122-53871141 None:intergenic 20.0%
!! TCCATCTTAATATCAATAAA+TGG + chr2_1:53871210-53871229 Msa0212100:three_prime_UTR 20.0%
!! ACCATTTATTGATATTAAGA+TGG - chr2_1:53871214-53871233 None:intergenic 20.0%
! AAATCATGAGAGAAATTGAA+GGG - chr2_1:53870662-53870681 None:intergenic 25.0%
! AAAATCATGAGAGAAATTGA+AGG - chr2_1:53870663-53870682 None:intergenic 25.0%
! TCCATGAAATATTTGAAAAG+TGG + chr2_1:53870760-53870779 Msa0212100:CDS 25.0%
!!! ACCACTTTTCAAATATTTCA+TGG - chr2_1:53870764-53870783 None:intergenic 25.0%
! AAAACTTCATTGATGTTTGA+CGG - chr2_1:53871021-53871040 None:intergenic 25.0%
! ACAAAAAACACCACAATTAT+TGG - chr2_1:53871046-53871065 None:intergenic 25.0%
! AAATCATGAGAGAAATTGAA+GGG - chr2_1:53870662-53870681 None:intergenic 25.0%
! AAAATCATGAGAGAAATTGA+AGG - chr2_1:53870663-53870682 None:intergenic 25.0%
! TCCATGAAATATTTGAAAAG+TGG + chr2_1:53870760-53870779 Msa0212100:CDS 25.0%
!!! ACCACTTTTCAAATATTTCA+TGG - chr2_1:53870764-53870783 None:intergenic 25.0%
! AAAACTTCATTGATGTTTGA+CGG - chr2_1:53871021-53871040 None:intergenic 25.0%
! ACAAAAAACACCACAATTAT+TGG - chr2_1:53871046-53871065 None:intergenic 25.0%
GTAGCTTCAAAATATGTCAT+AGG + chr2_1:53870489-53870508 Msa0212100:five_prime_UTR 30.0%
AATATTTGAAAAGTGGTGCA+AGG + chr2_1:53870767-53870786 Msa0212100:CDS 30.0%
CGACAAAACATATTCTTCAA+AGG + chr2_1:53870794-53870813 Msa0212100:CDS 30.0%
! AAAAATTCTGGTTACACTCT+AGG + chr2_1:53870885-53870904 Msa0212100:CDS 30.0%
ATCAATGGAACAACCATAAT+TGG - chr2_1:53870952-53870971 None:intergenic 30.0%
AAACTTCATTGATGTTTGAC+GGG - chr2_1:53871020-53871039 None:intergenic 30.0%
!! GAAGTTTTGTCCAATAATTG+TGG + chr2_1:53871033-53871052 Msa0212100:exon 30.0%
ATTAAAACTATTGGGCTAAG+AGG + chr2_1:53871133-53871152 Msa0212100:three_prime_UTR 30.0%
CAACTATTAACACTTCATCT+TGG - chr2_1:53871174-53871193 None:intergenic 30.0%
TAAGATGGAAGTTCAAGATT+TGG - chr2_1:53871199-53871218 None:intergenic 30.0%
GTAGCTTCAAAATATGTCAT+AGG + chr2_1:53870489-53870508 Msa0212100:five_prime_UTR 30.0%
AATATTTGAAAAGTGGTGCA+AGG + chr2_1:53870767-53870786 Msa0212100:CDS 30.0%
CGACAAAACATATTCTTCAA+AGG + chr2_1:53870794-53870813 Msa0212100:CDS 30.0%
! AAAAATTCTGGTTACACTCT+AGG + chr2_1:53870885-53870904 Msa0212100:CDS 30.0%
ATCAATGGAACAACCATAAT+TGG - chr2_1:53870952-53870971 None:intergenic 30.0%
AAACTTCATTGATGTTTGAC+GGG - chr2_1:53871020-53871039 None:intergenic 30.0%
!! GAAGTTTTGTCCAATAATTG+TGG + chr2_1:53871033-53871052 Msa0212100:exon 30.0%
ATTAAAACTATTGGGCTAAG+AGG + chr2_1:53871133-53871152 Msa0212100:three_prime_UTR 30.0%
CAACTATTAACACTTCATCT+TGG - chr2_1:53871174-53871193 None:intergenic 30.0%
TAAGATGGAAGTTCAAGATT+TGG - chr2_1:53871199-53871218 None:intergenic 30.0%
TGAGTAATTCAACTCGTAGA+TGG - chr2_1:53870520-53870539 None:intergenic 35.0%
ATTGAATAGAGACACAACGT+TGG - chr2_1:53870561-53870580 None:intergenic 35.0%
AACGTTGTGTCTCTATTCAA+TGG + chr2_1:53870560-53870579 Msa0212100:exon 35.0%
AGAATAACAAACCGATGGTT+GGG - chr2_1:53870637-53870656 None:intergenic 35.0%
TAGAATAACAAACCGATGGT+TGG - chr2_1:53870638-53870657 None:intergenic 35.0%
AATTGTGAATATAAGGCTCC+TGG + chr2_1:53870729-53870748 Msa0212100:intron 35.0%
CAAAGGAAGAAAAACAGTAC+AGG + chr2_1:53870811-53870830 Msa0212100:CDS 35.0%
!!! TGTAACCAGAATTTTTCAGG+TGG - chr2_1:53870881-53870900 None:intergenic 35.0%
! GAGTGTAACCAGAATTTTTC+AGG - chr2_1:53870884-53870903 None:intergenic 35.0%
GAGGAATTTACGTCCAATTA+TGG + chr2_1:53870936-53870955 Msa0212100:CDS 35.0%
ATGGACATCGTTGAAATCAA+TGG - chr2_1:53870967-53870986 None:intergenic 35.0%
!! CCTAACTTTTCAAGATCATC+CGG - chr2_1:53870990-53871009 None:intergenic 35.0%
ATATAATCAAAGGTGGTGAC+AGG - chr2_1:53871115-53871134 None:intergenic 35.0%
TGAGTAATTCAACTCGTAGA+TGG - chr2_1:53870520-53870539 None:intergenic 35.0%
ATTGAATAGAGACACAACGT+TGG - chr2_1:53870561-53870580 None:intergenic 35.0%
AACGTTGTGTCTCTATTCAA+TGG + chr2_1:53870560-53870579 Msa0212100:exon 35.0%
AGAATAACAAACCGATGGTT+GGG - chr2_1:53870637-53870656 None:intergenic 35.0%
TAGAATAACAAACCGATGGT+TGG - chr2_1:53870638-53870657 None:intergenic 35.0%
AATTGTGAATATAAGGCTCC+TGG + chr2_1:53870729-53870748 Msa0212100:intron 35.0%
CAAAGGAAGAAAAACAGTAC+AGG + chr2_1:53870811-53870830 Msa0212100:CDS 35.0%
!!! TGTAACCAGAATTTTTCAGG+TGG - chr2_1:53870881-53870900 None:intergenic 35.0%
! GAGTGTAACCAGAATTTTTC+AGG - chr2_1:53870884-53870903 None:intergenic 35.0%
GAGGAATTTACGTCCAATTA+TGG + chr2_1:53870936-53870955 Msa0212100:CDS 35.0%
ATGGACATCGTTGAAATCAA+TGG - chr2_1:53870967-53870986 None:intergenic 35.0%
!! CCTAACTTTTCAAGATCATC+CGG - chr2_1:53870990-53871009 None:intergenic 35.0%
ATATAATCAAAGGTGGTGAC+AGG - chr2_1:53871115-53871134 None:intergenic 35.0%
AGGAATCTGTTCTTGAAGCT+TGG - chr2_1:53870613-53870632 None:intergenic 40.0%
GAATAACAAACCGATGGTTG+GGG - chr2_1:53870636-53870655 None:intergenic 40.0%
GGGATAGAATAACAAACCGA+TGG - chr2_1:53870642-53870661 None:intergenic 40.0%
TGAATATAAGGCTCCTGGTT+CGG + chr2_1:53870734-53870753 Msa0212100:intron 40.0%
CACAACCACCTGAAAAATTC+TGG + chr2_1:53870873-53870892 Msa0212100:CDS 40.0%
ATTGGACGTAAATTCCTCGA+AGG - chr2_1:53870934-53870953 None:intergenic 40.0%
TGATTTCAACGATGTCCATC+CGG + chr2_1:53870968-53870987 Msa0212100:CDS 40.0%
!! ACTTTTCAAGATCATCCGGA+TGG - chr2_1:53870986-53871005 None:intergenic 40.0%
CCGGATGATCTTGAAAAGTT+AGG + chr2_1:53870987-53871006 Msa0212100:CDS 40.0%
AAAACTATTGGGCTAAGAGG+AGG + chr2_1:53871136-53871155 Msa0212100:three_prime_UTR 40.0%
AAACTATTGGGCTAAGAGGA+GGG + chr2_1:53871137-53871156 Msa0212100:three_prime_UTR 40.0%
AGGAATCTGTTCTTGAAGCT+TGG - chr2_1:53870613-53870632 None:intergenic 40.0%
GAATAACAAACCGATGGTTG+GGG - chr2_1:53870636-53870655 None:intergenic 40.0%
GGGATAGAATAACAAACCGA+TGG - chr2_1:53870642-53870661 None:intergenic 40.0%
TGAATATAAGGCTCCTGGTT+CGG + chr2_1:53870734-53870753 Msa0212100:intron 40.0%
CACAACCACCTGAAAAATTC+TGG + chr2_1:53870873-53870892 Msa0212100:CDS 40.0%
ATTGGACGTAAATTCCTCGA+AGG - chr2_1:53870934-53870953 None:intergenic 40.0%
TGATTTCAACGATGTCCATC+CGG + chr2_1:53870968-53870987 Msa0212100:CDS 40.0%
!! ACTTTTCAAGATCATCCGGA+TGG - chr2_1:53870986-53871005 None:intergenic 40.0%
CCGGATGATCTTGAAAAGTT+AGG + chr2_1:53870987-53871006 Msa0212100:CDS 40.0%
AAAACTATTGGGCTAAGAGG+AGG + chr2_1:53871136-53871155 Msa0212100:three_prime_UTR 40.0%
AAACTATTGGGCTAAGAGGA+GGG + chr2_1:53871137-53871156 Msa0212100:three_prime_UTR 40.0%
TTCTTGAAGCTTGGAGTTGG+AGG - chr2_1:53870604-53870623 None:intergenic 45.0%
CTGTTCTTGAAGCTTGGAGT+TGG - chr2_1:53870607-53870626 None:intergenic 45.0%
ATTTCATGGATGTCCGAACC+AGG - chr2_1:53870750-53870769 None:intergenic 45.0%
GTGGTTGTGTTGAGTGATTC+TGG - chr2_1:53870862-53870881 None:intergenic 45.0%
TGAGATCAGAGAACTGGTTG+AGG - chr2_1:53870911-53870930 None:intergenic 45.0%
TTCTTGAAGCTTGGAGTTGG+AGG - chr2_1:53870604-53870623 None:intergenic 45.0%
CTGTTCTTGAAGCTTGGAGT+TGG - chr2_1:53870607-53870626 None:intergenic 45.0%
ATTTCATGGATGTCCGAACC+AGG - chr2_1:53870750-53870769 None:intergenic 45.0%
GTGGTTGTGTTGAGTGATTC+TGG - chr2_1:53870862-53870881 None:intergenic 45.0%
TGAGATCAGAGAACTGGTTG+AGG - chr2_1:53870911-53870930 None:intergenic 45.0%
ACAGATTCCTCCCCAACCAT+CGG + chr2_1:53870623-53870642 Msa0212100:CDS 50.0%
TAACAAACCGATGGTTGGGG+AGG - chr2_1:53870633-53870652 None:intergenic 50.0%
CGAAGGTGAGATCAGAGAAC+TGG - chr2_1:53870917-53870936 None:intergenic 50.0%
GTTCTCTGATCTCACCTTCG+AGG + chr2_1:53870917-53870936 Msa0212100:CDS 50.0%
ACAGATTCCTCCCCAACCAT+CGG + chr2_1:53870623-53870642 Msa0212100:CDS 50.0%
TAACAAACCGATGGTTGGGG+AGG - chr2_1:53870633-53870652 None:intergenic 50.0%
CGAAGGTGAGATCAGAGAAC+TGG - chr2_1:53870917-53870936 None:intergenic 50.0%
GTTCTCTGATCTCACCTTCG+AGG + chr2_1:53870917-53870936 Msa0212100:CDS 50.0%
Chromosome Type Strat End Strand Name
chr2_1 gene 53870466 53871257 53870466 ID=Msa0212100;Name=Msa0212100
chr2_1 mRNA 53870466 53871257 53870466 ID=Msa0212100-mRNA-1;Parent=Msa0212100;Name=Msa0212100-mRNA-1;_AED=0.22;_eAED=0.22;_QI=113|1|1|1|1|1|2|223|118
chr2_1 exon 53870466 53870644 53870466 ID=Msa0212100-mRNA-1:exon:14973;Parent=Msa0212100-mRNA-1
chr2_1 exon 53870744 53871257 53870744 ID=Msa0212100-mRNA-1:exon:14974;Parent=Msa0212100-mRNA-1
chr2_1 five_prime_UTR 53870466 53870578 53870466 ID=Msa0212100-mRNA-1:five_prime_utr;Parent=Msa0212100-mRNA-1
chr2_1 CDS 53870579 53870644 53870579 ID=Msa0212100-mRNA-1:cds;Parent=Msa0212100-mRNA-1
chr2_1 CDS 53870744 53871034 53870744 ID=Msa0212100-mRNA-1:cds;Parent=Msa0212100-mRNA-1
chr2_1 three_prime_UTR 53871035 53871257 53871035 ID=Msa0212100-mRNA-1:three_prime_utr;Parent=Msa0212100-mRNA-1
Gene Sequence

>Msa0212100

ATGGATGTAAACAGTGAGCTAACCTCCAACTCCAAGCTTCAAGAACAGATTCCTCCCCAACCATCGGCTCCTGGTTCGGACATCCATGAAATATTTGAAAAGTGGTGCAAGGAATTCGACAAAACATATTCTTCAAAGGAAGAAAAACAGTACAGGTTCAAAGTGTTTGAAGAAAGATATGCCAGAATCACTCAACACAACCACCTGAAAAATTCTGGTTACACTCTAGGCCTCAACCAGTTCTCTGATCTCACCTTCGAGGAATTTACGTCCAATTATGGTTGTTCCATTGATTTCAACGATGTCCATCCGGATGATCTTGAAAAGTTAGGCATTAAACCCGTCAAACATCAATGA
Protein sequence

>Msa0212100

MDVNSELTSNSKLQEQIPPQPSAPGSDIHEIFEKWCKEFDKTYSSKEEKQYRFKVFEERYARITQHNHLKNSGYTLGLNQFSDLTFEEFTSNYGCSIDFNDVHPDDLEKLGIKPVKHQ*