AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1109880


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1109880 MtrunA17_Chr7g0244341 90.370 135 13 0 1 135 92 226 4.93e-92 265
Msa1109880 MtrunA17_Chr7g0244371 86.885 122 16 0 1 122 90 211 4.62e-79 232
Msa1109880 MtrunA17_Chr7g0244331 83.333 120 20 0 1 120 92 211 1.19e-74 221
Msa1109880 MtrunA17_Chr7g0244111 81.513 119 22 0 1 119 4 122 6.81e-74 216
Msa1109880 MtrunA17_Chr7g0244321 83.333 120 20 0 1 120 92 211 9.43e-74 219
Msa1109880 MtrunA17_Chr7g0244361 79.508 122 25 0 1 122 121 242 9.61e-70 209
Msa1109880 MtrunA17_Chr4g0013291 68.067 119 38 0 1 119 80 198 3.19e-58 179
Msa1109880 MtrunA17_Chr1g0150081 58.407 113 43 2 1 113 77 185 1.05e-38 129
Msa1109880 MtrunA17_Chr1g0150101 56.098 82 32 2 32 113 2 79 1.51e-21 82.0
Msa1109880 MtrunA17_Chr1g0150091 41.732 127 53 4 3 113 10 131 2.58e-20 80.5
Msa1109880 MtrunA17_Chr2g0333101 30.252 119 77 4 2 118 90 204 8.24e-17 73.6
Msa1109880 MtrunA17_Chr4g0003271 27.966 118 81 4 2 118 79 193 7.19e-16 70.9
Msa1109880 MtrunA17_Chr5g0432221 35.780 109 65 3 7 112 105 211 7.38e-16 70.9
Msa1109880 MtrunA17_Chr2g0333111 27.500 120 81 4 2 119 91 206 3.65e-12 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1109880 AT5G01750.2 64.754 122 43 0 1 122 96 217 1.28e-60 186
Msa1109880 AT3G11740.1 65.000 120 41 1 1 119 72 191 1.58e-55 172
Msa1109880 AT2G14560.1 54.135 133 59 1 1 133 76 206 4.55e-47 151
Msa1109880 AT2G14560.3 54.135 133 59 1 1 133 136 266 5.74e-46 150
Msa1109880 AT1G33840.1 58.621 116 48 0 1 116 96 211 1.04e-45 148
Msa1109880 AT5G01750.1 63.636 77 28 0 1 77 96 172 5.59e-34 117
Msa1109880 AT3G16900.1 46.491 114 49 3 4 116 78 180 1.21e-32 114
Msa1109880 AT2G14560.2 57.692 78 33 0 1 78 76 153 3.15e-30 107
Msa1109880 AT2G14560.4 57.692 78 33 0 1 78 136 213 4.72e-29 106
Msa1109880 AT1G33840.2 53.846 78 36 0 1 78 96 173 1.09e-26 98.6
Msa1109880 AT3G56180.2 37.607 117 68 2 1 114 87 201 2.89e-20 82.8
Msa1109880 AT3G56180.1 36.752 117 67 3 1 114 87 199 4.88e-18 76.6
Msa1109880 AT3G15810.1 27.731 119 82 2 2 120 92 206 2.27e-17 75.5
Msa1109880 AT2G30270.1 33.645 107 65 3 7 112 78 179 6.35e-16 70.9
Msa1109880 AT1G80120.1 29.565 115 75 3 7 119 84 194 2.11e-14 67.4
Msa1109880 AT3G10986.1 31.933 119 76 2 1 114 74 192 3.27e-14 66.6

Find 22 sgRNAs with CRISPR-Local

Find 74 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTGGTCTTCAATTGCATTA+TGG 0.249654 7_3:+54338635 None:intergenic
GAAGTCACAAACATCTTCTT+TGG 0.264338 7_3:+54338587 None:intergenic
AGCAAGAAACACGTCTAATT+TGG 0.276680 7_3:+54338617 None:intergenic
GAAGAAAAGGGAAGTGAATC+AGG 0.376536 7_3:-54338006 Msa1109880:CDS
GATTGGTAAAGACCATTTCA+TGG 0.376637 7_3:-54338100 Msa1109880:CDS
TGAGATTAACAGTGAAGAAA+AGG 0.382281 7_3:-54338019 Msa1109880:CDS
AACAATGTTGTTTGATTCAC+CGG 0.422881 7_3:+54338521 None:intergenic
GAGATTAACAGTGAAGAAAA+GGG 0.427156 7_3:-54338018 Msa1109880:CDS
GTTTGATTCACCGGCATAAA+CGG 0.431148 7_3:+54338530 None:intergenic
ACTTCAAAGTCAAAGGTAGT+TGG 0.472279 7_3:-54338569 Msa1109880:CDS
TGATCGGTGGGAAGCTTACA+TGG 0.483103 7_3:-54338706 Msa1109880:CDS
ATGAAAGCGTAATCAACATT+GGG 0.498374 7_3:+54338066 None:intergenic
TATGAAAGCGTAATCAACAT+TGG 0.519673 7_3:+54338065 None:intergenic
CGATCTTGCACCGTTTATGC+CGG 0.523467 7_3:-54338540 Msa1109880:CDS
ATCAAACAACATTGTTGCAC+AGG 0.532488 7_3:-54338514 Msa1109880:intron
TGTTGATTACGCTTTCATAG+TGG 0.534696 7_3:-54338061 Msa1109880:CDS
GATAAACTGTGACCATGAAA+TGG 0.538015 7_3:+54338088 None:intergenic
GTTTGTGACTTCAAAGTCAA+AGG 0.540662 7_3:-54338576 Msa1109880:CDS
AATGACTATGCATGATCGGT+GGG 0.582075 7_3:-54338718 Msa1109880:CDS
TAATGACTATGCATGATCGG+TGG 0.599736 7_3:-54338719 Msa1109880:CDS
AGATAATGACTATGCATGAT+CGG 0.641095 7_3:-54338722 None:intergenic
GATCGGTGGGAAGCTTACAT+GGG 0.678160 7_3:-54338705 Msa1109880:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GAAACTTTTTTTTTTTTTTG+AGG - chr7_3:54338354-54338373 Msa1109880:intron 15.0%
!!! AATTAACAAATCAACTTTTA+TGG - chr7_3:54338517-54338536 Msa1109880:CDS 15.0%
!!! GAAACTTTTTTTTTTTTTTG+AGG - chr7_3:54338354-54338373 Msa1109880:intron 15.0%
!!! AATTAACAAATCAACTTTTA+TGG - chr7_3:54338517-54338536 Msa1109880:CDS 15.0%
!!! ACAAAGAAGAAATTTTATCT+TGG - chr7_3:54338310-54338329 Msa1109880:intron 20.0%
!!! CAAAGAAGAAATTTTATCTT+GGG - chr7_3:54338311-54338330 Msa1109880:intron 20.0%
!!! ACTTGTTAATGATTCAAAAA+AGG + chr7_3:54338438-54338457 None:intergenic 20.0%
!! TCCAGTGATAATTAAATTAA+GGG + chr7_3:54338486-54338505 None:intergenic 20.0%
!!! ACAAAGAAGAAATTTTATCT+TGG - chr7_3:54338310-54338329 Msa1109880:intron 20.0%
!!! CAAAGAAGAAATTTTATCTT+GGG - chr7_3:54338311-54338330 Msa1109880:intron 20.0%
!!! ACTTGTTAATGATTCAAAAA+AGG + chr7_3:54338438-54338457 None:intergenic 20.0%
!! TCCAGTGATAATTAAATTAA+GGG + chr7_3:54338486-54338505 None:intergenic 20.0%
!!! CTTCTTAAAAAGTGTCTTAA+GGG + chr7_3:54338289-54338308 None:intergenic 25.0%
!!! ACTTCTTAAAAAGTGTCTTA+AGG + chr7_3:54338290-54338309 None:intergenic 25.0%
! ACCCTTAATTTAATTATCAC+TGG - chr7_3:54338482-54338501 Msa1109880:intron 25.0%
! GTCCAGTGATAATTAAATTA+AGG + chr7_3:54338487-54338506 None:intergenic 25.0%
!!! TTACTTGATGAAGTTTTGTT+CGG - chr7_3:54338707-54338726 Msa1109880:CDS 25.0%
!!! CTTCTTAAAAAGTGTCTTAA+GGG + chr7_3:54338289-54338308 None:intergenic 25.0%
!!! ACTTCTTAAAAAGTGTCTTA+AGG + chr7_3:54338290-54338309 None:intergenic 25.0%
! ACCCTTAATTTAATTATCAC+TGG - chr7_3:54338482-54338501 Msa1109880:intron 25.0%
! GTCCAGTGATAATTAAATTA+AGG + chr7_3:54338487-54338506 None:intergenic 25.0%
!!! TTACTTGATGAAGTTTTGTT+CGG - chr7_3:54338707-54338726 Msa1109880:CDS 25.0%
! TTTGGTCTTCAATTGCATTA+TGG + chr7_3:54338057-54338076 None:intergenic 30.0%
! AACAATGTTGTTTGATTCAC+CGG + chr7_3:54338171-54338190 None:intergenic 30.0%
AAAACTAAATATTCGCGTGT+TGG + chr7_3:54338228-54338247 None:intergenic 30.0%
! ATGAAAGCGTAATCAACATT+GGG + chr7_3:54338626-54338645 None:intergenic 30.0%
! TATGAAAGCGTAATCAACAT+TGG + chr7_3:54338627-54338646 None:intergenic 30.0%
TGAGATTAACAGTGAAGAAA+AGG - chr7_3:54338670-54338689 Msa1109880:CDS 30.0%
GAGATTAACAGTGAAGAAAA+GGG - chr7_3:54338671-54338690 Msa1109880:CDS 30.0%
!!! TACTTGATGAAGTTTTGTTC+GGG - chr7_3:54338708-54338727 Msa1109880:CDS 30.0%
! TTTGGTCTTCAATTGCATTA+TGG + chr7_3:54338057-54338076 None:intergenic 30.0%
! AACAATGTTGTTTGATTCAC+CGG + chr7_3:54338171-54338190 None:intergenic 30.0%
AAAACTAAATATTCGCGTGT+TGG + chr7_3:54338228-54338247 None:intergenic 30.0%
! ATGAAAGCGTAATCAACATT+GGG + chr7_3:54338626-54338645 None:intergenic 30.0%
! TATGAAAGCGTAATCAACAT+TGG + chr7_3:54338627-54338646 None:intergenic 30.0%
TGAGATTAACAGTGAAGAAA+AGG - chr7_3:54338670-54338689 Msa1109880:CDS 30.0%
GAGATTAACAGTGAAGAAAA+GGG - chr7_3:54338671-54338690 Msa1109880:CDS 30.0%
!!! TACTTGATGAAGTTTTGTTC+GGG - chr7_3:54338708-54338727 Msa1109880:CDS 30.0%
AGCAAGAAACACGTCTAATT+TGG + chr7_3:54338075-54338094 None:intergenic 35.0%
GAAGTCACAAACATCTTCTT+TGG + chr7_3:54338105-54338124 None:intergenic 35.0%
GTTTGTGACTTCAAAGTCAA+AGG - chr7_3:54338113-54338132 Msa1109880:CDS 35.0%
ACTTCAAAGTCAAAGGTAGT+TGG - chr7_3:54338120-54338139 Msa1109880:CDS 35.0%
ATCAAACAACATTGTTGCAC+AGG - chr7_3:54338175-54338194 Msa1109880:intron 35.0%
!! TATTCGCGTGTTGGTTATAT+AGG + chr7_3:54338219-54338238 None:intergenic 35.0%
! ACTGTTCAGAGTCTTTTGAT+TGG - chr7_3:54338572-54338591 Msa1109880:CDS 35.0%
GATTGGTAAAGACCATTTCA+TGG - chr7_3:54338589-54338608 Msa1109880:CDS 35.0%
GATAAACTGTGACCATGAAA+TGG + chr7_3:54338604-54338623 None:intergenic 35.0%
! TGTTGATTACGCTTTCATAG+TGG - chr7_3:54338628-54338647 Msa1109880:CDS 35.0%
!!! ACTTGATGAAGTTTTGTTCG+GGG - chr7_3:54338709-54338728 Msa1109880:CDS 35.0%
AGCAAGAAACACGTCTAATT+TGG + chr7_3:54338075-54338094 None:intergenic 35.0%
GAAGTCACAAACATCTTCTT+TGG + chr7_3:54338105-54338124 None:intergenic 35.0%
GTTTGTGACTTCAAAGTCAA+AGG - chr7_3:54338113-54338132 Msa1109880:CDS 35.0%
ACTTCAAAGTCAAAGGTAGT+TGG - chr7_3:54338120-54338139 Msa1109880:CDS 35.0%
ATCAAACAACATTGTTGCAC+AGG - chr7_3:54338175-54338194 Msa1109880:intron 35.0%
!! TATTCGCGTGTTGGTTATAT+AGG + chr7_3:54338219-54338238 None:intergenic 35.0%
! ACTGTTCAGAGTCTTTTGAT+TGG - chr7_3:54338572-54338591 Msa1109880:CDS 35.0%
GATTGGTAAAGACCATTTCA+TGG - chr7_3:54338589-54338608 Msa1109880:CDS 35.0%
GATAAACTGTGACCATGAAA+TGG + chr7_3:54338604-54338623 None:intergenic 35.0%
! TGTTGATTACGCTTTCATAG+TGG - chr7_3:54338628-54338647 Msa1109880:CDS 35.0%
!!! ACTTGATGAAGTTTTGTTCG+GGG - chr7_3:54338709-54338728 Msa1109880:CDS 35.0%
GTTTGATTCACCGGCATAAA+CGG + chr7_3:54338162-54338181 None:intergenic 40.0%
TCATGCTAACAAGTGCTCTT+AGG + chr7_3:54338463-54338482 None:intergenic 40.0%
GAAGAAAAGGGAAGTGAATC+AGG - chr7_3:54338683-54338702 Msa1109880:CDS 40.0%
!!! CTTGATGAAGTTTTGTTCGG+GGG - chr7_3:54338710-54338729 Msa1109880:CDS 40.0%
GTTTGATTCACCGGCATAAA+CGG + chr7_3:54338162-54338181 None:intergenic 40.0%
TCATGCTAACAAGTGCTCTT+AGG + chr7_3:54338463-54338482 None:intergenic 40.0%
GAAGAAAAGGGAAGTGAATC+AGG - chr7_3:54338683-54338702 Msa1109880:CDS 40.0%
!!! CTTGATGAAGTTTTGTTCGG+GGG - chr7_3:54338710-54338729 Msa1109880:CDS 40.0%
TGATCGGTGGGAAGCTTACA+TGG - chr7_3:54337983-54338002 Msa1109880:CDS 50.0%
GATCGGTGGGAAGCTTACAT+GGG - chr7_3:54337984-54338003 Msa1109880:CDS 50.0%
CGATCTTGCACCGTTTATGC+CGG - chr7_3:54338149-54338168 Msa1109880:intron 50.0%
TGATCGGTGGGAAGCTTACA+TGG - chr7_3:54337983-54338002 Msa1109880:CDS 50.0%
GATCGGTGGGAAGCTTACAT+GGG - chr7_3:54337984-54338003 Msa1109880:CDS 50.0%
CGATCTTGCACCGTTTATGC+CGG - chr7_3:54338149-54338168 Msa1109880:intron 50.0%
Chromosome Type Strat End Strand Name
chr7_3 gene 54337972 54338739 54337972 ID=Msa1109880;Name=Msa1109880
chr7_3 mRNA 54337972 54338739 54337972 ID=Msa1109880-mRNA-1;Parent=Msa1109880;Name=Msa1109880-mRNA-1;_AED=0.11;_eAED=0.11;_QI=0|0|0|1|1|1|2|0|135
chr7_3 exon 54338515 54338739 54338515 ID=Msa1109880-mRNA-1:exon:11425;Parent=Msa1109880-mRNA-1
chr7_3 exon 54337972 54338154 54337972 ID=Msa1109880-mRNA-1:exon:11424;Parent=Msa1109880-mRNA-1
chr7_3 CDS 54338515 54338739 54338515 ID=Msa1109880-mRNA-1:cds;Parent=Msa1109880-mRNA-1
chr7_3 CDS 54337972 54338154 54337972 ID=Msa1109880-mRNA-1:cds;Parent=Msa1109880-mRNA-1
Gene Sequence

>Msa1109880

ATGACTATGCATGATCGGTGGGAAGCTTACATGGGTGAAAGCACAAATGCTAAAGATCTAGTATTTACATTGAAACGATCGTCCATAATGCAATTGAAGACCAAATTAGACGTGTTTCTTGCTAATAACACCAAAGAAGATGTTTGTGACTTCAAAGTCAAAGGTAGTTGGTTCGAACGATCTTGCACCGTTTATGCCGGTGAATCAAACAACATTGTTGCACAGATGCACAAAAAGCACACTGTTCAGAGTCTTTTGATTGGTAAAGACCATTTCATGGTCACAGTTTATCCCAATGTTGATTACGCTTTCATAGTGGCATTAATCGTGATTCTTAATGAGATTAACAGTGAAGAAAAGGGAAGTGAATCAGGCTTACTTGATGAAGTTTTGTTCGGGGGTGTTTAA

Protein sequence

>Msa1109880

MTMHDRWEAYMGESTNAKDLVFTLKRSSIMQLKTKLDVFLANNTKEDVCDFKVKGSWFERSCTVYAGESNNIVAQMHKKHTVQSLLIGKDHFMVTVYPNVDYAFIVALIVILNEINSEEKGSESGLLDEVLFGGV*