AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1126950

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1126950 MtrunA17_Chr7g0270601 61.272 173 21 4 1 127 282 454 1.88e-50 166
Msa1126950 MtrunA17_Chr7g0269191 69.697 99 19 3 40 127 1 99 7.92e-29 101
Msa1126950 MtrunA17_Chr7g0271391 39.167 120 63 3 18 127 504 623 3.99e-22 90.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1126950 AT3G62200.1 36.054 147 74 4 1 127 505 651 3.90e-21 88.2

Find 39 sgRNAs with CRISPR-Local

Find 114 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTTCATTTATCGGCAATTT+TGG 0.159196 7_3:+78483055 Msa1126950:CDS
GTACATTCCCATCTGCTTAC+TGG 0.214575 7_3:+78483513 Msa1126950:three_prime_UTR
GTACATTTCAATCTGCTTAC+TGG 0.250536 7_3:+78483573 Msa1126950:three_prime_UTR
CAATTCCTTGCTTCATTTAT+CGG 0.255799 7_3:+78483046 Msa1126950:CDS
CGTGGTTCCCAGACGCAATC+TGG 0.270910 7_3:+78483011 Msa1126950:CDS
TTAGCCTCTGTAAGTGAAAA+TGG 0.275804 7_3:-78483322 None:intergenic
GGGTGATGTACTTAAGATTT+TGG 0.277803 7_3:+78483239 Msa1126950:CDS
GATGACACAGATAGTGATTC+TGG 0.347850 7_3:+78483356 Msa1126950:three_prime_UTR
AAGGTGGTTAAACGAGTCTT+TGG 0.382873 7_3:+78482932 Msa1126950:intron
ATCCTAACCCAGATTGCGTC+TGG 0.396295 7_3:-78483019 None:intergenic
TTATACCTTGTCATTCTAGA+TGG 0.412658 7_3:+78483289 Msa1126950:CDS
GAATACACTGATGAATGAAA+TGG 0.416796 7_3:+78482805 Msa1126950:CDS
CTGTAAGTGAAAATGGTAAT+CGG 0.431067 7_3:-78483315 None:intergenic
TTGTTGCAAATGAGAATCTA+TGG 0.442211 7_3:+78482972 Msa1126950:CDS
TTATAATCACAATCAAGAAA+TGG 0.466378 7_3:+78483265 Msa1126950:CDS
CCTCTACATATCTCTAACTA+CGG 0.467900 7_3:-78483439 None:intergenic
TTGCGTCTGGGAACCACGTA+AGG 0.473407 7_3:-78483006 None:intergenic
TCCCAGACGCAATCTGGGTT+AGG 0.483088 7_3:+78483017 Msa1126950:CDS
AGCAGATGGGAATGTACAAA+AGG 0.496986 7_3:-78483507 None:intergenic
TGTCTTGAAGAGCTTGTGTT+GGG 0.501883 7_3:+78483219 Msa1126950:CDS
CATTTCAATCTGCTTACTGG+TGG 0.505776 7_3:+78483576 Msa1126950:three_prime_UTR
ATTCCCATCTGCTTACTGGT+GGG 0.506945 7_3:+78483517 Msa1126950:three_prime_UTR
TGAGAATTTGCAAGGACTTG+TGG 0.513544 7_3:+78482763 Msa1126950:CDS
CATTCCCATCTGCTTACTGG+TGG 0.519665 7_3:+78483516 Msa1126950:three_prime_UTR
TTCCCATCTGCTTACTGGTG+GGG 0.524628 7_3:+78483518 Msa1126950:three_prime_UTR
GTGTCTTGAAGAGCTTGTGT+TGG 0.527052 7_3:+78483218 Msa1126950:CDS
GTGGTTCCCAGACGCAATCT+GGG 0.539558 7_3:+78483012 Msa1126950:CDS
AGTCCCCACCAGTAAGCAGA+TGG 0.550048 7_3:-78483521 None:intergenic
TCCTAACCCAGATTGCGTCT+GGG 0.566146 7_3:-78483018 None:intergenic
GAGATATGTAGAGGAATTCG+TGG 0.572067 7_3:+78483448 Msa1126950:three_prime_UTR
CCGTAGTTAGAGATATGTAG+AGG 0.580945 7_3:+78483439 Msa1126950:three_prime_UTR
TGCGTCTGGGAACCACGTAA+GGG 0.598064 7_3:-78483005 None:intergenic
GTCCCCACCAGTAAGCAGAT+GGG 0.623279 7_3:-78483520 None:intergenic
AATTGCCGATAAATGAAGCA+AGG 0.623661 7_3:-78483051 None:intergenic
AAACTACGTGAGCTTTGACA+TGG 0.629175 7_3:+78483404 Msa1126950:three_prime_UTR
TCAACACATGAGAATTTGCA+AGG 0.634115 7_3:+78482755 Msa1126950:CDS
GCGTCTGGGAACCACGTAAG+GGG 0.647796 7_3:-78483004 None:intergenic
GGAAGTGTGAACCCCTTACG+TGG 0.663822 7_3:+78482993 Msa1126950:CDS
GGCTGCCATCTAGAATGACA+AGG 0.705174 7_3:-78483294 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACATATAATAAAAGACAAA+AGG - chr7_3:78483160-78483179 None:intergenic 15.0%
!! AACATATAATAAAAGACAAA+AGG - chr7_3:78483160-78483179 None:intergenic 15.0%
!! ATATCAAATGTCTCATATTT+GGG - chr7_3:78482878-78482897 None:intergenic 20.0%
!! AATATCAAATGTCTCATATT+TGG - chr7_3:78482879-78482898 None:intergenic 20.0%
!! AATATGAGACATTTGATATT+AGG + chr7_3:78482879-78482898 Msa1126950:intron 20.0%
!! TTATAATCACAATCAAGAAA+TGG + chr7_3:78483265-78483284 Msa1126950:CDS 20.0%
!! ATATCAAATGTCTCATATTT+GGG - chr7_3:78482878-78482897 None:intergenic 20.0%
!! AATATCAAATGTCTCATATT+TGG - chr7_3:78482879-78482898 None:intergenic 20.0%
!! AATATGAGACATTTGATATT+AGG + chr7_3:78482879-78482898 Msa1126950:intron 20.0%
!! TTATAATCACAATCAAGAAA+TGG + chr7_3:78483265-78483284 Msa1126950:CDS 20.0%
! GCAATCAATTATATTTCCTT+CGG - chr7_3:78482840-78482859 None:intergenic 25.0%
! ATAATTGATTGCATTCGTTA+TGG + chr7_3:78482848-78482867 Msa1126950:intron 25.0%
!!! TATTGTTTTTCTTAGTTCCT+TGG + chr7_3:78483100-78483119 Msa1126950:intron 25.0%
! GCAATCAATTATATTTCCTT+CGG - chr7_3:78482840-78482859 None:intergenic 25.0%
! ATAATTGATTGCATTCGTTA+TGG + chr7_3:78482848-78482867 Msa1126950:intron 25.0%
!!! TATTGTTTTTCTTAGTTCCT+TGG + chr7_3:78483100-78483119 Msa1126950:intron 25.0%
GAATACACTGATGAATGAAA+TGG + chr7_3:78482805-78482824 Msa1126950:CDS 30.0%
TCAATTATATTTCCTTCGGT+AGG - chr7_3:78482836-78482855 None:intergenic 30.0%
TGAGACATTTGATATTAGGA+AGG + chr7_3:78482883-78482902 Msa1126950:intron 30.0%
GAGACATTTGATATTAGGAA+GGG + chr7_3:78482884-78482903 Msa1126950:intron 30.0%
TTGTTGCAAATGAGAATCTA+TGG + chr7_3:78482972-78482991 Msa1126950:CDS 30.0%
CAATTCCTTGCTTCATTTAT+CGG + chr7_3:78483046-78483065 Msa1126950:CDS 30.0%
TAACAAGTAATAAAGCTCCA+AGG - chr7_3:78483120-78483139 None:intergenic 30.0%
TTATACCTTGTCATTCTAGA+TGG + chr7_3:78483289-78483308 Msa1126950:CDS 30.0%
CTGTAAGTGAAAATGGTAAT+CGG - chr7_3:78483318-78483337 None:intergenic 30.0%
! ATTACCATTTTCACTTACAG+AGG + chr7_3:78483318-78483337 Msa1126950:CDS 30.0%
GAATACACTGATGAATGAAA+TGG + chr7_3:78482805-78482824 Msa1126950:CDS 30.0%
TCAATTATATTTCCTTCGGT+AGG - chr7_3:78482836-78482855 None:intergenic 30.0%
TGAGACATTTGATATTAGGA+AGG + chr7_3:78482883-78482902 Msa1126950:intron 30.0%
GAGACATTTGATATTAGGAA+GGG + chr7_3:78482884-78482903 Msa1126950:intron 30.0%
TTGTTGCAAATGAGAATCTA+TGG + chr7_3:78482972-78482991 Msa1126950:CDS 30.0%
CAATTCCTTGCTTCATTTAT+CGG + chr7_3:78483046-78483065 Msa1126950:CDS 30.0%
TAACAAGTAATAAAGCTCCA+AGG - chr7_3:78483120-78483139 None:intergenic 30.0%
TTATACCTTGTCATTCTAGA+TGG + chr7_3:78483289-78483308 Msa1126950:CDS 30.0%
CTGTAAGTGAAAATGGTAAT+CGG - chr7_3:78483318-78483337 None:intergenic 30.0%
! ATTACCATTTTCACTTACAG+AGG + chr7_3:78483318-78483337 Msa1126950:CDS 30.0%
TCAACACATGAGAATTTGCA+AGG + chr7_3:78482755-78482774 Msa1126950:CDS 35.0%
AATTGCCGATAAATGAAGCA+AGG - chr7_3:78483054-78483073 None:intergenic 35.0%
! GCTTCATTTATCGGCAATTT+TGG + chr7_3:78483055-78483074 Msa1126950:CDS 35.0%
! GGGTGATGTACTTAAGATTT+TGG + chr7_3:78483239-78483258 Msa1126950:CDS 35.0%
TTAGCCTCTGTAAGTGAAAA+TGG - chr7_3:78483325-78483344 None:intergenic 35.0%
CCTCTACATATCTCTAACTA+CGG - chr7_3:78483442-78483461 None:intergenic 35.0%
GTACATTTCAATCTGCTTAC+TGG + chr7_3:78483573-78483592 Msa1126950:three_prime_UTR 35.0%
!!! CTTACTGGTGGATTTTTTGA+TGG + chr7_3:78483588-78483607 Msa1126950:three_prime_UTR 35.0%
TCAACACATGAGAATTTGCA+AGG + chr7_3:78482755-78482774 Msa1126950:CDS 35.0%
AATTGCCGATAAATGAAGCA+AGG - chr7_3:78483054-78483073 None:intergenic 35.0%
! GCTTCATTTATCGGCAATTT+TGG + chr7_3:78483055-78483074 Msa1126950:CDS 35.0%
! GGGTGATGTACTTAAGATTT+TGG + chr7_3:78483239-78483258 Msa1126950:CDS 35.0%
TTAGCCTCTGTAAGTGAAAA+TGG - chr7_3:78483325-78483344 None:intergenic 35.0%
CCTCTACATATCTCTAACTA+CGG - chr7_3:78483442-78483461 None:intergenic 35.0%
GTACATTTCAATCTGCTTAC+TGG + chr7_3:78483573-78483592 Msa1126950:three_prime_UTR 35.0%
!!! CTTACTGGTGGATTTTTTGA+TGG + chr7_3:78483588-78483607 Msa1126950:three_prime_UTR 35.0%
TGAGAATTTGCAAGGACTTG+TGG + chr7_3:78482763-78482782 Msa1126950:CDS 40.0%
! GAAATGGTTTTTCCTACCGA+AGG + chr7_3:78482821-78482840 Msa1126950:intron 40.0%
TTGTGCAATTGAGCAACAGA+AGG + chr7_3:78482913-78482932 Msa1126950:intron 40.0%
AAGGTGGTTAAACGAGTCTT+TGG + chr7_3:78482932-78482951 Msa1126950:intron 40.0%
!! CAATTTTGGCGTCTTGTAAC+AGG + chr7_3:78483069-78483088 Msa1126950:intron 40.0%
TGTCTTGAAGAGCTTGTGTT+GGG + chr7_3:78483219-78483238 Msa1126950:CDS 40.0%
GATGACACAGATAGTGATTC+TGG + chr7_3:78483356-78483375 Msa1126950:three_prime_UTR 40.0%
! AAACTACGTGAGCTTTGACA+TGG + chr7_3:78483404-78483423 Msa1126950:three_prime_UTR 40.0%
CCGTAGTTAGAGATATGTAG+AGG + chr7_3:78483439-78483458 Msa1126950:three_prime_UTR 40.0%
GAGATATGTAGAGGAATTCG+TGG + chr7_3:78483448-78483467 Msa1126950:three_prime_UTR 40.0%
AGCAGATGGGAATGTACAAA+AGG - chr7_3:78483510-78483529 None:intergenic 40.0%
CATTTCAATCTGCTTACTGG+TGG + chr7_3:78483576-78483595 Msa1126950:three_prime_UTR 40.0%
TGAGAATTTGCAAGGACTTG+TGG + chr7_3:78482763-78482782 Msa1126950:CDS 40.0%
! GAAATGGTTTTTCCTACCGA+AGG + chr7_3:78482821-78482840 Msa1126950:intron 40.0%
TTGTGCAATTGAGCAACAGA+AGG + chr7_3:78482913-78482932 Msa1126950:intron 40.0%
AAGGTGGTTAAACGAGTCTT+TGG + chr7_3:78482932-78482951 Msa1126950:intron 40.0%
!! CAATTTTGGCGTCTTGTAAC+AGG + chr7_3:78483069-78483088 Msa1126950:intron 40.0%
TGTCTTGAAGAGCTTGTGTT+GGG + chr7_3:78483219-78483238 Msa1126950:CDS 40.0%
GATGACACAGATAGTGATTC+TGG + chr7_3:78483356-78483375 Msa1126950:three_prime_UTR 40.0%
! AAACTACGTGAGCTTTGACA+TGG + chr7_3:78483404-78483423 Msa1126950:three_prime_UTR 40.0%
CCGTAGTTAGAGATATGTAG+AGG + chr7_3:78483439-78483458 Msa1126950:three_prime_UTR 40.0%
GAGATATGTAGAGGAATTCG+TGG + chr7_3:78483448-78483467 Msa1126950:three_prime_UTR 40.0%
AGCAGATGGGAATGTACAAA+AGG - chr7_3:78483510-78483529 None:intergenic 40.0%
CATTTCAATCTGCTTACTGG+TGG + chr7_3:78483576-78483595 Msa1126950:three_prime_UTR 40.0%
TGCAATTGAGCAACAGAAGG+TGG + chr7_3:78482916-78482935 Msa1126950:intron 45.0%
GTGTCTTGAAGAGCTTGTGT+TGG + chr7_3:78483218-78483237 Msa1126950:CDS 45.0%
GTACATTCCCATCTGCTTAC+TGG + chr7_3:78483513-78483532 Msa1126950:three_prime_UTR 45.0%
ATTCCCATCTGCTTACTGGT+GGG + chr7_3:78483517-78483536 Msa1126950:three_prime_UTR 45.0%
! TACTGGTGGGGACTTTTTGT+TGG + chr7_3:78483530-78483549 Msa1126950:three_prime_UTR 45.0%
TGCAATTGAGCAACAGAAGG+TGG + chr7_3:78482916-78482935 Msa1126950:intron 45.0%
GTGTCTTGAAGAGCTTGTGT+TGG + chr7_3:78483218-78483237 Msa1126950:CDS 45.0%
GTACATTCCCATCTGCTTAC+TGG + chr7_3:78483513-78483532 Msa1126950:three_prime_UTR 45.0%
ATTCCCATCTGCTTACTGGT+GGG + chr7_3:78483517-78483536 Msa1126950:three_prime_UTR 45.0%
! TACTGGTGGGGACTTTTTGT+TGG + chr7_3:78483530-78483549 Msa1126950:three_prime_UTR 45.0%
TCCTAACCCAGATTGCGTCT+GGG - chr7_3:78483021-78483040 None:intergenic 50.0%
ATCCTAACCCAGATTGCGTC+TGG - chr7_3:78483022-78483041 None:intergenic 50.0%
! GGCTGCCATCTAGAATGACA+AGG - chr7_3:78483297-78483316 None:intergenic 50.0%
CATTCCCATCTGCTTACTGG+TGG + chr7_3:78483516-78483535 Msa1126950:three_prime_UTR 50.0%
TTCCCATCTGCTTACTGGTG+GGG + chr7_3:78483518-78483537 Msa1126950:three_prime_UTR 50.0%
TCCTAACCCAGATTGCGTCT+GGG - chr7_3:78483021-78483040 None:intergenic 50.0%
ATCCTAACCCAGATTGCGTC+TGG - chr7_3:78483022-78483041 None:intergenic 50.0%
! GGCTGCCATCTAGAATGACA+AGG - chr7_3:78483297-78483316 None:intergenic 50.0%
CATTCCCATCTGCTTACTGG+TGG + chr7_3:78483516-78483535 Msa1126950:three_prime_UTR 50.0%
TTCCCATCTGCTTACTGGTG+GGG + chr7_3:78483518-78483537 Msa1126950:three_prime_UTR 50.0%
! GGAAGTGTGAACCCCTTACG+TGG + chr7_3:78482993-78483012 Msa1126950:CDS 55.0%
TGCGTCTGGGAACCACGTAA+GGG - chr7_3:78483008-78483027 None:intergenic 55.0%
TTGCGTCTGGGAACCACGTA+AGG - chr7_3:78483009-78483028 None:intergenic 55.0%
GTGGTTCCCAGACGCAATCT+GGG + chr7_3:78483012-78483031 Msa1126950:CDS 55.0%
TCCCAGACGCAATCTGGGTT+AGG + chr7_3:78483017-78483036 Msa1126950:CDS 55.0%
GTCCCCACCAGTAAGCAGAT+GGG - chr7_3:78483523-78483542 None:intergenic 55.0%
AGTCCCCACCAGTAAGCAGA+TGG - chr7_3:78483524-78483543 None:intergenic 55.0%
! GGAAGTGTGAACCCCTTACG+TGG + chr7_3:78482993-78483012 Msa1126950:CDS 55.0%
TGCGTCTGGGAACCACGTAA+GGG - chr7_3:78483008-78483027 None:intergenic 55.0%
TTGCGTCTGGGAACCACGTA+AGG - chr7_3:78483009-78483028 None:intergenic 55.0%
GTGGTTCCCAGACGCAATCT+GGG + chr7_3:78483012-78483031 Msa1126950:CDS 55.0%
TCCCAGACGCAATCTGGGTT+AGG + chr7_3:78483017-78483036 Msa1126950:CDS 55.0%
GTCCCCACCAGTAAGCAGAT+GGG - chr7_3:78483523-78483542 None:intergenic 55.0%
AGTCCCCACCAGTAAGCAGA+TGG - chr7_3:78483524-78483543 None:intergenic 55.0%
GCGTCTGGGAACCACGTAAG+GGG - chr7_3:78483007-78483026 None:intergenic 60.0%
CGTGGTTCCCAGACGCAATC+TGG + chr7_3:78483011-78483030 Msa1126950:CDS 60.0%
GCGTCTGGGAACCACGTAAG+GGG - chr7_3:78483007-78483026 None:intergenic 60.0%
CGTGGTTCCCAGACGCAATC+TGG + chr7_3:78483011-78483030 Msa1126950:CDS 60.0%
Chromosome Type Strat End Strand Name
chr7_3 gene 78482734 78483625 78482734 ID=Msa1126950;Name=Msa1126950
chr7_3 mRNA 78482734 78483625 78482734 ID=Msa1126950-mRNA-1;Parent=Msa1126950;Name=Msa1126950-mRNA-1;_AED=0.13;_eAED=0.18;_QI=0|0|0.33|1|0.5|0.33|3|281|132
chr7_3 exon 78482734 78482826 78482734 ID=Msa1126950-mRNA-1:exon:21896;Parent=Msa1126950-mRNA-1
chr7_3 exon 78482935 78483083 78482935 ID=Msa1126950-mRNA-1:exon:21897;Parent=Msa1126950-mRNA-1
chr7_3 exon 78483188 78483625 78483188 ID=Msa1126950-mRNA-1:exon:21898;Parent=Msa1126950-mRNA-1
chr7_3 CDS 78482734 78482826 78482734 ID=Msa1126950-mRNA-1:cds;Parent=Msa1126950-mRNA-1
chr7_3 CDS 78482935 78483083 78482935 ID=Msa1126950-mRNA-1:cds;Parent=Msa1126950-mRNA-1
chr7_3 CDS 78483188 78483344 78483188 ID=Msa1126950-mRNA-1:cds;Parent=Msa1126950-mRNA-1
chr7_3 three_prime_UTR 78483345 78483625 78483345 ID=Msa1126950-mRNA-1:three_prime_utr;Parent=Msa1126950-mRNA-1
Gene Sequence

>Msa1126950

TTAGAGACTTTGAAAACAATATCAACACATGAGAATTTGCAAGGACTTGTGGATATTATTCTAGTCACTTCGAATACACTGATGAATGAAATGGTGGTTAAACGAGTCTTTGGCACATTACGTTTGTATGTTGTTGCAAATGAGAATCTATGGAAGTGTGAACCCCTTACGTGGTTCCCAGACGCAATCTGGGTTAGGATAGAGCAATTCCTTGCTTCATTTATCGGCAATTTTGGCGTCTTATATGAAGCTTCATTAATTCTAAAGAGATTGTGTCTTGAAGAGCTTGTGTTGGGTGATGTACTTAAGATTTTGGAGATTATAATCACAATCAAGAAATGGATTATACCTTGTCATTCTAGATGGCAGCCGATTACCATTTTCACTTACAGAGGCTAA
Protein sequence

>Msa1126950

LETLKTISTHENLQGLVDIILVTSNTLMNEMVVKRVFGTLRLYVVANENLWKCEPLTWFPDAIWVRIEQFLASFIGNFGVLYEASLILKRLCLEELVLGDVLKILEIIITIKKWIIPCHSRWQPITIFTYRG*