AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0463250

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0463250 MtrunA17_Chr3g0113431 99.167 120 1 0 1 120 11 130 1.17e-86 248
Msa0463250 MtrunA17_Chr2g0300391 46.250 80 43 0 26 105 6 85 3.78e-22 84.0
Msa0463250 MtrunA17_Chr4g0070681 52.857 70 33 0 36 105 17 86 4.43e-22 84.0
Msa0463250 MtrunA17_Chr8g0343731 42.500 80 46 0 26 105 6 85 3.07e-19 76.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0463250 AT2G40080.1 68.293 82 25 1 29 109 14 95 7.98e-35 116
Msa0463250 AT2G29950.1 50.549 91 44 1 24 113 21 111 1.46e-23 88.6
Msa0463250 AT2G06255.1 52.857 70 33 0 36 105 17 86 8.87e-22 83.6
Msa0463250 AT1G17455.2 47.500 80 42 0 26 105 6 85 1.22e-20 80.5
Msa0463250 AT1G17455.1 47.500 80 42 0 26 105 6 85 1.22e-20 80.5
Msa0463250 AT1G72630.1 46.250 80 43 0 26 105 10 89 4.61e-19 76.6

Find 38 sgRNAs with CRISPR-Local

Find 37 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCGGCGGCGTTGATTCTTCT+TGG 0.236721 3_3:-62596053 None:intergenic
ATCTAGAATGCCTGATAATA+TGG 0.270265 3_3:+62596237 Msa0463250:CDS
TTAAGGGTCTGCCATGCTTC+GGG 0.352696 3_3:-62596139 None:intergenic
GTTTGATTCAAGAGCTTAAT+GGG 0.355178 3_3:+62596272 Msa0463250:CDS
GTTAAGGGTCTGCCATGCTT+CGG 0.360927 3_3:-62596140 None:intergenic
ACGTTCTTCACCATATTATC+AGG 0.362205 3_3:-62596247 None:intergenic
AGTCGGTGCTTGACAGGAAC+AGG 0.378549 3_3:+62596182 Msa0463250:CDS
GGTTTGATTCAAGAGCTTAA+TGG 0.380169 3_3:+62596271 Msa0463250:CDS
TCGGAGTAGTCGTTGTTTGT+TGG 0.405287 3_3:-62596091 None:intergenic
TTGCCTGAAGCTCTTGTTAA+GGG 0.405821 3_3:-62596155 None:intergenic
GCTTAATGGGAATATCTCTA+AGG 0.425461 3_3:+62596285 Msa0463250:CDS
CTTGCCTGAAGCTCTTGTTA+AGG 0.452710 3_3:-62596156 None:intergenic
TATGAGAAGAACGCTGTTGC+TGG 0.458998 3_3:-62596357 None:intergenic
GTTGTTTGTTGGAGTGGCGG+AGG 0.471753 3_3:-62596080 None:intergenic
GGCGTTGATTCTTCTTGGAA+CGG 0.478309 3_3:-62596048 None:intergenic
TTGTTGGAGTGGCGGAGGGA+CGG 0.484279 3_3:-62596075 None:intergenic
ACGGTGGTTGGTGTCTTCCA+TGG 0.485355 3_3:-62596029 None:intergenic
GAACAGGGCAATAATTCAAC+AGG 0.485880 3_3:+62596198 Msa0463250:CDS
AAGTTCAGTCGGTGCTTGAC+AGG 0.488761 3_3:+62596176 Msa0463250:CDS
ATTCTTCTTGGAACGGTGGT+TGG 0.500480 3_3:-62596041 None:intergenic
GAGTGGCGGAGGGACGGCGG+CGG 0.507547 3_3:-62596069 None:intergenic
GTAGTCGTTGTTTGTTGGAG+TGG 0.524126 3_3:-62596086 None:intergenic
AGACCCTTAACAAGAGCTTC+AGG 0.525177 3_3:+62596152 Msa0463250:CDS
TTGTTTGTTGGAGTGGCGGA+GGG 0.536933 3_3:-62596079 None:intergenic
GTCGTTGTTTGTTGGAGTGG+CGG 0.547841 3_3:-62596083 None:intergenic
GCTAAAATCAGAATTAAGAT+CGG 0.560174 3_3:-62596323 None:intergenic
TTGGAGTGGCGGAGGGACGG+CGG 0.562226 3_3:-62596072 None:intergenic
GACGTGGAGGATGCTGAAGA+CGG 0.583878 3_3:+62596112 Msa0463250:CDS
AAGACGGCGATCCCGAAGCA+TGG 0.588795 3_3:+62596128 Msa0463250:CDS
GAGCTTCAGGCAAGTTCAGT+CGG 0.593643 3_3:+62596165 Msa0463250:CDS
GTTGATTCTTCTTGGAACGG+TGG 0.599566 3_3:-62596045 None:intergenic
TGATAATATGGTGAAGAACG+TGG 0.629062 3_3:+62596249 Msa0463250:CDS
GTCGGTGCTTGACAGGAACA+GGG 0.640394 3_3:+62596183 Msa0463250:CDS
GATAATATGGTGAAGAACGT+GGG 0.654854 3_3:+62596250 Msa0463250:CDS
CAACGACTACTCCGACGTGG+AGG 0.676846 3_3:+62596099 Msa0463250:CDS
GTCTTCAGCATCCTCCACGT+CGG 0.689723 3_3:-62596110 None:intergenic
CAGCGTTCTTCTCATAACCG+TGG 0.715942 3_3:+62596364 Msa0463250:CDS
AAACAACGACTACTCCGACG+TGG 0.738856 3_3:+62596096 Msa0463250:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! GCTAAAATCAGAATTAAGAT+CGG - chr3_3:62596326-62596345 None:intergenic 25.0%
! ATCTAGAATGCCTGATAATA+TGG + chr3_3:62596237-62596256 Msa0463250:CDS 30.0%
GTTTGATTCAAGAGCTTAAT+GGG + chr3_3:62596272-62596291 Msa0463250:CDS 30.0%
ACGTTCTTCACCATATTATC+AGG - chr3_3:62596250-62596269 None:intergenic 35.0%
TGATAATATGGTGAAGAACG+TGG + chr3_3:62596249-62596268 Msa0463250:CDS 35.0%
GATAATATGGTGAAGAACGT+GGG + chr3_3:62596250-62596269 Msa0463250:CDS 35.0%
GGTTTGATTCAAGAGCTTAA+TGG + chr3_3:62596271-62596290 Msa0463250:CDS 35.0%
GCTTAATGGGAATATCTCTA+AGG + chr3_3:62596285-62596304 Msa0463250:CDS 35.0%
TTGCCTGAAGCTCTTGTTAA+GGG - chr3_3:62596158-62596177 None:intergenic 40.0%
GAACAGGGCAATAATTCAAC+AGG + chr3_3:62596198-62596217 Msa0463250:CDS 40.0%
ATTCTTCTTGGAACGGTGGT+TGG - chr3_3:62596044-62596063 None:intergenic 45.0%
! GTTGATTCTTCTTGGAACGG+TGG - chr3_3:62596048-62596067 None:intergenic 45.0%
!! GGCGTTGATTCTTCTTGGAA+CGG - chr3_3:62596051-62596070 None:intergenic 45.0%
! GTAGTCGTTGTTTGTTGGAG+TGG - chr3_3:62596089-62596108 None:intergenic 45.0%
TCGGAGTAGTCGTTGTTTGT+TGG - chr3_3:62596094-62596113 None:intergenic 45.0%
AGACCCTTAACAAGAGCTTC+AGG + chr3_3:62596152-62596171 Msa0463250:CDS 45.0%
CTTGCCTGAAGCTCTTGTTA+AGG - chr3_3:62596159-62596178 None:intergenic 45.0%
TATGAGAAGAACGCTGTTGC+TGG - chr3_3:62596360-62596379 None:intergenic 45.0%
! TTGTTTGTTGGAGTGGCGGA+GGG - chr3_3:62596082-62596101 None:intergenic 50.0%
! GTCGTTGTTTGTTGGAGTGG+CGG - chr3_3:62596086-62596105 None:intergenic 50.0%
AAACAACGACTACTCCGACG+TGG + chr3_3:62596096-62596115 Msa0463250:CDS 50.0%
TTAAGGGTCTGCCATGCTTC+GGG - chr3_3:62596142-62596161 None:intergenic 50.0%
GTTAAGGGTCTGCCATGCTT+CGG - chr3_3:62596143-62596162 None:intergenic 50.0%
GAGCTTCAGGCAAGTTCAGT+CGG + chr3_3:62596165-62596184 Msa0463250:CDS 50.0%
! AAGTTCAGTCGGTGCTTGAC+AGG + chr3_3:62596176-62596195 Msa0463250:CDS 50.0%
CAGCGTTCTTCTCATAACCG+TGG + chr3_3:62596364-62596383 Msa0463250:CDS 50.0%
! GTTGTTTGTTGGAGTGGCGG+AGG - chr3_3:62596083-62596102 None:intergenic 55.0%
GTCTTCAGCATCCTCCACGT+CGG - chr3_3:62596113-62596132 None:intergenic 55.0%
GACGTGGAGGATGCTGAAGA+CGG + chr3_3:62596112-62596131 Msa0463250:CDS 55.0%
! AGTCGGTGCTTGACAGGAAC+AGG + chr3_3:62596182-62596201 Msa0463250:CDS 55.0%
! GTCGGTGCTTGACAGGAACA+GGG + chr3_3:62596183-62596202 Msa0463250:CDS 55.0%
!! GCGGCGGCGTTGATTCTTCT+TGG - chr3_3:62596056-62596075 None:intergenic 60.0%
! TTGTTGGAGTGGCGGAGGGA+CGG - chr3_3:62596078-62596097 None:intergenic 60.0%
CAACGACTACTCCGACGTGG+AGG + chr3_3:62596099-62596118 Msa0463250:CDS 60.0%
AAGACGGCGATCCCGAAGCA+TGG + chr3_3:62596128-62596147 Msa0463250:CDS 60.0%
! TTGGAGTGGCGGAGGGACGG+CGG - chr3_3:62596075-62596094 None:intergenic 70.0%
!! GAGTGGCGGAGGGACGGCGG+CGG - chr3_3:62596072-62596091 None:intergenic 80.0%
Chromosome Type Strat End Strand Name
chr3_3 gene 62596031 62596393 62596031 ID=Msa0463250;Name=Msa0463250
chr3_3 mRNA 62596031 62596393 62596031 ID=Msa0463250-mRNA-1;Parent=Msa0463250;Name=Msa0463250-mRNA-1;_AED=0.28;_eAED=0.28;_QI=0|-1|0|1|-1|1|1|0|120
chr3_3 exon 62596031 62596393 62596031 ID=Msa0463250-mRNA-1:exon:13444;Parent=Msa0463250-mRNA-1
chr3_3 CDS 62596031 62596393 62596031 ID=Msa0463250-mRNA-1:cds;Parent=Msa0463250-mRNA-1
Gene Sequence

>Msa0463250

ATGGAAGACACCAACCACCGTTCCAAGAAGAATCAACGCCGCCGCCGTCCCTCCGCCACTCCAACAAACAACGACTACTCCGACGTGGAGGATGCTGAAGACGGCGATCCCGAAGCATGGCAGACCCTTAACAAGAGCTTCAGGCAAGTTCAGTCGGTGCTTGACAGGAACAGGGCAATAATTCAACAGGTGAATGAGAATCAACAATCTAGAATGCCTGATAATATGGTGAAGAACGTGGGTTTGATTCAAGAGCTTAATGGGAATATCTCTAAGGTTGCTTCTCTTTATTCCGATCTTAATTCTGATTTTAGCAATATTTGTCACCAGCAACAGCGTTCTTCTCATAACCGTGGCAAGTGA
Protein sequence

>Msa0463250

MEDTNHRSKKNQRRRRPSATPTNNDYSDVEDAEDGDPEAWQTLNKSFRQVQSVLDRNRAIIQQVNENQQSRMPDNMVKNVGLIQELNGNISKVASLYSDLNSDFSNICHQQQRSSHNRGK*