AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0264130

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0264130 MtrunA17_Chr2g0327671 48.750 160 33 6 3 113 437 596 3.80e-32 118
Msa0264130 MtrunA17_Chr4g0030441 73.585 53 13 1 62 113 541 593 8.14e-19 80.5
Msa0264130 MtrunA17_Chr2g0318301 51.250 80 37 2 35 113 517 595 4.74e-16 72.8
Msa0264130 MtrunA17_Chr8g0352381 71.429 42 12 0 62 103 572 613 7.71e-15 69.3
Msa0264130 MtrunA17_Chr2g0292501 50.725 69 33 1 35 103 536 603 9.63e-15 68.9
Msa0264130 MtrunA17_Chr7g0245131 46.591 88 30 3 35 113 550 629 3.90e-14 67.4
Msa0264130 MtrunA17_Chr4g0061081 64.286 42 15 0 62 103 568 609 8.23e-14 66.2
Msa0264130 MtrunA17_Chr4g0053561 60.377 53 20 1 62 113 482 534 5.46e-13 63.9
Msa0264130 MtrunA17_Chr4g0053521 65.909 44 15 0 60 103 1098 1141 6.43e-13 63.9
Msa0264130 MtrunA17_Chr7g0274261 61.905 42 16 0 62 103 568 609 2.95e-12 62.0
Msa0264130 MtrunA17_Chr1g0190581 59.524 42 17 0 62 103 563 604 3.31e-12 61.6
Msa0264130 MtrunA17_Chr5g0432871 64.286 42 15 0 62 103 657 698 4.09e-12 61.6
Msa0264130 MtrunA17_Chr6g0455321 54.717 53 23 1 62 113 577 629 4.40e-12 61.6
Msa0264130 MtrunA17_Chr7g0219681 45.070 71 35 2 37 103 536 606 1.05e-11 60.5
Msa0264130 MtrunA17_Chr3g0108361 64.286 42 15 0 62 103 663 704 1.35e-11 60.1
Msa0264130 MtrunA17_Chr4g0053571 66.667 42 14 0 62 103 539 580 2.17e-11 59.3
Msa0264130 MtrunA17_Chr1g0202711 56.818 44 19 0 60 103 542 585 2.25e-11 59.3
Msa0264130 MtrunA17_Chr7g0245221 59.524 42 17 0 62 103 662 703 6.37e-11 58.2
Msa0264130 MtrunA17_Chr4g0053591 61.364 44 17 0 60 103 187 230 7.66e-11 57.8
Msa0264130 MtrunA17_Chr7g0219571 60.976 41 16 0 62 102 576 616 9.24e-11 57.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0264130 AT3G46290.1 40.506 158 46 7 3 113 422 578 2.60e-20 85.5
Msa0264130 AT5G59700.1 85.714 42 6 0 62 103 523 564 8.72e-19 80.9
Msa0264130 AT5G54380.1 66.038 53 17 1 62 113 551 603 8.19e-16 72.4
Msa0264130 AT2G39360.1 71.429 42 12 0 62 103 528 569 9.08e-16 72.4
Msa0264130 AT5G61350.1 53.623 69 31 1 35 103 540 607 1.52e-15 71.6
Msa0264130 AT1G30570.1 73.810 42 11 0 62 103 561 602 5.87e-15 70.1
Msa0264130 AT3G51550.1 46.591 88 30 3 35 113 551 630 1.19e-14 69.3
Msa0264130 AT2G21480.1 71.429 42 12 0 62 103 566 607 2.73e-14 68.2
Msa0264130 AT4G39110.1 69.048 42 13 0 62 103 567 608 3.01e-14 68.2
Msa0264130 AT5G39000.1 50.000 72 30 2 35 103 533 601 5.54e-14 67.4
Msa0264130 AT5G38990.1 50.000 68 30 2 40 103 541 608 1.33e-13 66.2
Msa0264130 AT3G04690.1 56.604 53 22 1 62 113 558 610 1.32e-12 63.2
Msa0264130 AT5G28680.1 58.491 53 21 1 62 113 562 614 1.73e-12 63.2
Msa0264130 AT5G28680.2 58.491 53 21 1 62 113 562 614 1.73e-12 63.2
Msa0264130 AT2G23200.1 54.717 53 23 1 62 113 529 581 5.38e-12 61.6
Msa0264130 AT5G01950.6 61.905 42 16 0 62 103 667 708 3.01e-11 59.3
Msa0264130 AT5G01950.2 61.905 42 16 0 62 103 582 623 3.03e-11 59.3
Msa0264130 AT5G01950.3 61.905 42 16 0 62 103 667 708 3.05e-11 59.3
Msa0264130 AT5G01950.1 61.905 42 16 0 62 103 667 708 3.05e-11 59.3
Msa0264130 AT5G01950.4 61.905 42 16 0 62 103 667 708 3.05e-11 59.3
Msa0264130 AT5G01950.8 61.905 42 16 0 62 103 667 708 3.05e-11 59.3
Msa0264130 AT1G06840.1 61.905 42 16 0 62 103 666 707 3.08e-11 59.3
Msa0264130 AT5G01950.5 61.905 42 16 0 62 103 667 708 3.42e-11 59.3
Msa0264130 AT1G51860.1 40.278 72 35 2 35 103 599 665 5.82e-11 58.5
Msa0264130 AT1G51860.2 40.278 72 35 2 35 103 455 521 5.85e-11 58.5
Msa0264130 AT1G07560.1 41.791 67 36 1 40 103 586 652 6.72e-11 58.5

Find 35 sgRNAs with CRISPR-Local

Find 48 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTAATGGATGGCAGGAAAT+TGG 0.308418 2_2:+63985151 Msa0264130:CDS
TCACCATGTATTCATGTATA+AGG 0.310947 2_2:-63985297 None:intergenic
AGTATACAAGGGAGAGTTAA+TGG 0.311117 2_2:+63985136 Msa0264130:intron
CGACATCTGGTGTCTTTGAT+TGG 0.343051 2_2:+63985247 Msa0264130:CDS
TCAGTTCTGCCTGCGACATC+TGG 0.379508 2_2:+63985234 Msa0264130:CDS
ATTGTATCATTGACGGATAA+TGG 0.409966 2_2:-63984968 None:intergenic
CTCTCCTTCCAACTTAAGCT+TGG 0.433329 2_2:-63985356 None:intergenic
AGGAAATTGGTAGTGAAGAG+AGG 0.440075 2_2:+63985164 Msa0264130:CDS
TCTCCTTCCAACTTAAGCTT+GGG 0.460314 2_2:-63985355 None:intergenic
ATGATACAATCACATACAAT+GGG 0.503298 2_2:+63984981 Msa0264130:CDS
CGGGACTCCCAAGCTTAAGT+TGG 0.506548 2_2:+63985348 Msa0264130:CDS
GAGTTTGTTGTGTACTGTGC+AGG 0.510421 2_2:+63984900 Msa0264130:CDS
GTATGTGATTGTATCATTGA+CGG 0.522247 2_2:-63984975 None:intergenic
GTTGTGTACTGTGCAGGAAA+AGG 0.534414 2_2:+63984906 Msa0264130:CDS
AATGATACAATCACATACAA+TGG 0.537213 2_2:+63984980 Msa0264130:CDS
AGGGAGAGTTAATGGATGGC+AGG 0.538987 2_2:+63985144 Msa0264130:CDS
AGGGAATACACAGTTGCACC+AGG 0.539966 2_2:+63985184 Msa0264130:CDS
TCGTAAAACATAACAATGCC+CGG 0.542847 2_2:+63984878 None:intergenic
CTCAGAGTCGTCTACACGGT+CGG 0.547721 2_2:+63985328 Msa0264130:CDS
TCAGAGTCGTCTACACGGTC+GGG 0.548191 2_2:+63985329 Msa0264130:CDS
TCAATTTCAGTTCGAAACCC+TGG 0.553797 2_2:-63985202 None:intergenic
GCACAGTACACAACAAACTC+CGG 0.556299 2_2:-63984897 None:intergenic
CACAGTACACAACAAACTCC+GGG 0.562899 2_2:-63984896 None:intergenic
GGAAATTGGTAGTGAAGAGA+GGG 0.566151 2_2:+63985165 Msa0264130:CDS
GTGCAGGAAAAGGAAGTGGC+TGG 0.577030 2_2:+63984916 Msa0264130:CDS
GATCCTTATACATGAATACA+TGG 0.583030 2_2:+63985294 Msa0264130:CDS
TACTGTGCAGGAAAAGGAAG+TGG 0.588839 2_2:+63984912 Msa0264130:CDS
AACTCTCAGAGTCGTCTACA+CGG 0.596763 2_2:+63985324 Msa0264130:CDS
ACTCCCAAGCTTAAGTTGGA+AGG 0.605304 2_2:+63985352 Msa0264130:CDS
TCAAAGACACCAGATGTCGC+AGG 0.606175 2_2:-63985243 None:intergenic
TACAAGGGAGAGTTAATGGA+TGG 0.608918 2_2:+63985140 Msa0264130:CDS
ATACATGAATACATGGTGAA+CGG 0.627490 2_2:+63985301 Msa0264130:CDS
GGAAGTGGCTGGCAAGACAA+AGG 0.636359 2_2:+63984927 Msa0264130:CDS
GACAAAGGCAGTCAAAGACA+CGG 0.682941 2_2:+63984942 Msa0264130:CDS
GGGAATACACAGTTGCACCA+GGG 0.703383 2_2:+63985185 Msa0264130:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AATGATACAATCACATACAA+TGG + chr2_2:63984980-63984999 Msa0264130:CDS 25.0%
! ATGATACAATCACATACAAT+GGG + chr2_2:63984981-63985000 Msa0264130:CDS 25.0%
! ATTGTATCATTGACGGATAA+TGG - chr2_2:63984971-63984990 None:intergenic 30.0%
GTATGTGATTGTATCATTGA+CGG - chr2_2:63984978-63984997 None:intergenic 30.0%
ATGGGAAGTAAATATTCCAA+TGG + chr2_2:63984999-63985018 Msa0264130:intron 30.0%
! CAAACAATTTTGTTGAGAGT+TGG + chr2_2:63985087-63985106 Msa0264130:intron 30.0%
TTTGTTGAGAGTTGGATTAT+TGG + chr2_2:63985095-63985114 Msa0264130:intron 30.0%
TTGTTGAGAGTTGGATTATT+GGG + chr2_2:63985096-63985115 Msa0264130:intron 30.0%
GATCCTTATACATGAATACA+TGG + chr2_2:63985294-63985313 Msa0264130:CDS 30.0%
TCACCATGTATTCATGTATA+AGG - chr2_2:63985300-63985319 None:intergenic 30.0%
ATACATGAATACATGGTGAA+CGG + chr2_2:63985301-63985320 Msa0264130:CDS 30.0%
CCATCTTGAACTTATGCAAA+AGG - chr2_2:63985065-63985084 None:intergenic 35.0%
! CCTTTTGCATAAGTTCAAGA+TGG + chr2_2:63985062-63985081 Msa0264130:intron 35.0%
TGTTGAGAGTTGGATTATTG+GGG + chr2_2:63985097-63985116 Msa0264130:intron 35.0%
!! GGTTTTGCGAAAGTATACAA+GGG + chr2_2:63985125-63985144 Msa0264130:intron 35.0%
AGTATACAAGGGAGAGTTAA+TGG + chr2_2:63985136-63985155 Msa0264130:intron 35.0%
AGCATTTATTGTCGTGCCAT+TGG - chr2_2:63985018-63985037 None:intergenic 40.0%
AGAGTTGGATTATTGGGGTT+GGG + chr2_2:63985102-63985121 Msa0264130:intron 40.0%
!! GGGTTTTGCGAAAGTATACA+AGG + chr2_2:63985124-63985143 Msa0264130:intron 40.0%
TACAAGGGAGAGTTAATGGA+TGG + chr2_2:63985140-63985159 Msa0264130:CDS 40.0%
! GTTAATGGATGGCAGGAAAT+TGG + chr2_2:63985151-63985170 Msa0264130:CDS 40.0%
!! AGGAAATTGGTAGTGAAGAG+AGG + chr2_2:63985164-63985183 Msa0264130:CDS 40.0%
!! GGAAATTGGTAGTGAAGAGA+GGG + chr2_2:63985165-63985184 Msa0264130:CDS 40.0%
TCAATTTCAGTTCGAAACCC+TGG - chr2_2:63985205-63985224 None:intergenic 40.0%
TCTCCTTCCAACTTAAGCTT+GGG - chr2_2:63985358-63985377 None:intergenic 40.0%
CACAGTACACAACAAACTCC+GGG - chr2_2:63984899-63984918 None:intergenic 45.0%
GCACAGTACACAACAAACTC+CGG - chr2_2:63984900-63984919 None:intergenic 45.0%
!! GAGTTTGTTGTGTACTGTGC+AGG + chr2_2:63984900-63984919 Msa0264130:CDS 45.0%
GTTGTGTACTGTGCAGGAAA+AGG + chr2_2:63984906-63984925 Msa0264130:CDS 45.0%
TACTGTGCAGGAAAAGGAAG+TGG + chr2_2:63984912-63984931 Msa0264130:CDS 45.0%
GACAAAGGCAGTCAAAGACA+CGG + chr2_2:63984942-63984961 Msa0264130:CDS 45.0%
GAGAGTTGGATTATTGGGGT+TGG + chr2_2:63985101-63985120 Msa0264130:intron 45.0%
GAGTTGGATTATTGGGGTTG+GGG + chr2_2:63985103-63985122 Msa0264130:intron 45.0%
AGTTGGATTATTGGGGTTGG+GGG + chr2_2:63985104-63985123 Msa0264130:intron 45.0%
CGACATCTGGTGTCTTTGAT+TGG + chr2_2:63985247-63985266 Msa0264130:CDS 45.0%
AACTCTCAGAGTCGTCTACA+CGG + chr2_2:63985324-63985343 Msa0264130:CDS 45.0%
!! ACTCCCAAGCTTAAGTTGGA+AGG + chr2_2:63985352-63985371 Msa0264130:CDS 45.0%
CTCTCCTTCCAACTTAAGCT+TGG - chr2_2:63985359-63985378 None:intergenic 45.0%
! AGGGAGAGTTAATGGATGGC+AGG + chr2_2:63985144-63985163 Msa0264130:CDS 50.0%
AGGGAATACACAGTTGCACC+AGG + chr2_2:63985184-63985203 Msa0264130:CDS 50.0%
GGGAATACACAGTTGCACCA+GGG + chr2_2:63985185-63985204 Msa0264130:CDS 50.0%
TCAAAGACACCAGATGTCGC+AGG - chr2_2:63985246-63985265 None:intergenic 50.0%
GTGCAGGAAAAGGAAGTGGC+TGG + chr2_2:63984916-63984935 Msa0264130:CDS 55.0%
GGAAGTGGCTGGCAAGACAA+AGG + chr2_2:63984927-63984946 Msa0264130:CDS 55.0%
TCAGTTCTGCCTGCGACATC+TGG + chr2_2:63985234-63985253 Msa0264130:CDS 55.0%
CTCAGAGTCGTCTACACGGT+CGG + chr2_2:63985328-63985347 Msa0264130:CDS 55.0%
TCAGAGTCGTCTACACGGTC+GGG + chr2_2:63985329-63985348 Msa0264130:CDS 55.0%
CGGGACTCCCAAGCTTAAGT+TGG + chr2_2:63985348-63985367 Msa0264130:CDS 55.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 63984893 63985384 63984893 ID=Msa0264130;Name=Msa0264130
chr2_2 mRNA 63984893 63985384 63984893 ID=Msa0264130-mRNA-1;Parent=Msa0264130;Name=Msa0264130-mRNA-1;_AED=0.44;_eAED=0.44;_QI=0|0|0|1|0|0.5|2|0|119
chr2_2 exon 63984893 63985005 63984893 ID=Msa0264130-mRNA-1:exon:19895;Parent=Msa0264130-mRNA-1
chr2_2 exon 63985138 63985384 63985138 ID=Msa0264130-mRNA-1:exon:19896;Parent=Msa0264130-mRNA-1
chr2_2 CDS 63984893 63985005 63984893 ID=Msa0264130-mRNA-1:cds;Parent=Msa0264130-mRNA-1
chr2_2 CDS 63985138 63985384 63985138 ID=Msa0264130-mRNA-1:cds;Parent=Msa0264130-mRNA-1
Gene Sequence

>Msa0264130

ATGCCCGGAGTTTGTTGTGTACTGTGCAGGAAAAGGAAGTGGCTGGCAAGACAAAGGCAGTCAAAGACACGGATTCCATTATCCGTCAATGATACAATCACATACAATGGGAATATACAAGGGAGAGTTAATGGATGGCAGGAAATTGGTAGTGAAGAGAGGGAATACACAGTTGCACCAGGGTTTCGAACTGAAATTGAAATGTTATCTCAGTTCTGCCTGCGACATCTGGTGTCTTTGATTGGTTATTGTGATGAAAATAATGAAATGATCCTTATACATGAATACATGGTGAACGGAACTCTCAGAGTCGTCTACACGGTCGGGACTCCCAAGCTTAAGTTGGAAGGAGAGACTTGA
Protein sequence

>Msa0264130

MPGVCCVLCRKRKWLARQRQSKTRIPLSVNDTITYNGNIQGRVNGWQEIGSEEREYTVAPGFRTEIEMLSQFCLRHLVSLIGYCDENNEMILIHEYMVNGTLRVVYTVGTPKLKLEGET*