AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1127010

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1127010 MtrunA17_Chr7g0270601 61.272 173 21 4 1 127 282 454 1.88e-50 166
Msa1127010 MtrunA17_Chr7g0269191 69.697 99 19 3 40 127 1 99 7.92e-29 101
Msa1127010 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
Msa1127010 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:-78524802 Msa1127010:CDS
GTACATTCCCATCTGCTTAC+TGG 0.214575 7_3:-78524345 Msa1127010:three_prime_UTR
GTACATTTCAATCTGCTTAC+TGG 0.250536 7_3:-78524285 Msa1127010:three_prime_UTR
CAATTCCTTGCTTCATTTAT+CGG 0.255799 7_3:-78524811 Msa1127010:CDS
CGTGGTTCCCAGACGCAATC+TGG 0.270910 7_3:-78524846 Msa1127010:CDS
TTAGCCTCTGTAAGTGAAAA+TGG 0.275804 7_3:+78524536 None:intergenic
GGGTGATGTACTTAAGATTT+TGG 0.277803 7_3:-78524619 Msa1127010:CDS
GATGACACAGATAGTGATTC+TGG 0.347850 7_3:-78524502 Msa1127010:three_prime_UTR
AAGGTGGTTAAACGAGTCTT+TGG 0.382873 7_3:-78524925 Msa1127010:CDS
ATCCTAACCCAGATTGCGTC+TGG 0.396295 7_3:+78524838 None:intergenic
TTATACCTTGTCATTCTAGA+TGG 0.412658 7_3:-78524569 Msa1127010:CDS
GAATACACTGATGAATGAAA+TGG 0.416796 7_3:-78525052 Msa1127010:intron
CTGTAAGTGAAAATGGTAAT+CGG 0.431067 7_3:+78524543 None:intergenic
TTGTTGCAAATGAGAATCTA+TGG 0.442211 7_3:-78524885 Msa1127010:CDS
TTATAATCACAATCAAGAAA+TGG 0.466378 7_3:-78524593 Msa1127010:CDS
CCTCTACATATCTCTAACTA+CGG 0.467900 7_3:+78524419 None:intergenic
TTGCGTCTGGGAACCACGTA+AGG 0.473407 7_3:+78524851 None:intergenic
TCCCAGACGCAATCTGGGTT+AGG 0.483088 7_3:-78524840 Msa1127010:CDS
AGCAGATGGGAATGTACAAA+AGG 0.496986 7_3:+78524351 None:intergenic
TGTCTTGAAGAGCTTGTGTT+GGG 0.501883 7_3:-78524639 Msa1127010:CDS
CATTTCAATCTGCTTACTGG+TGG 0.505776 7_3:-78524282 Msa1127010:three_prime_UTR
ATTCCCATCTGCTTACTGGT+GGG 0.506945 7_3:-78524341 Msa1127010:three_prime_UTR
TGAGAATTTGCAAGGACTTG+TGG 0.513544 7_3:-78525094 Msa1127010:CDS
CATTCCCATCTGCTTACTGG+TGG 0.519665 7_3:-78524342 Msa1127010:three_prime_UTR
TTCCCATCTGCTTACTGGTG+GGG 0.524628 7_3:-78524340 Msa1127010:three_prime_UTR
GTGTCTTGAAGAGCTTGTGT+TGG 0.527052 7_3:-78524640 Msa1127010:CDS
GTGGTTCCCAGACGCAATCT+GGG 0.539558 7_3:-78524845 Msa1127010:CDS
AGTCCCCACCAGTAAGCAGA+TGG 0.550048 7_3:+78524337 None:intergenic
TCCTAACCCAGATTGCGTCT+GGG 0.566146 7_3:+78524839 None:intergenic
GAGATATGTAGAGGAATTCG+TGG 0.572067 7_3:-78524410 Msa1127010:three_prime_UTR
CCGTAGTTAGAGATATGTAG+AGG 0.580945 7_3:-78524419 Msa1127010:three_prime_UTR
TGCGTCTGGGAACCACGTAA+GGG 0.598064 7_3:+78524852 None:intergenic
GTCCCCACCAGTAAGCAGAT+GGG 0.623279 7_3:+78524338 None:intergenic
AATTGCCGATAAATGAAGCA+AGG 0.623661 7_3:+78524806 None:intergenic
AAACTACGTGAGCTTTGACA+TGG 0.629175 7_3:-78524454 Msa1127010:three_prime_UTR
TCAACACATGAGAATTTGCA+AGG 0.634115 7_3:-78525102 Msa1127010:CDS
GCGTCTGGGAACCACGTAAG+GGG 0.647796 7_3:+78524853 None:intergenic
GGAAGTGTGAACCCCTTACG+TGG 0.663822 7_3:-78524864 Msa1127010:CDS
GGCTGCCATCTAGAATGACA+AGG 0.705174 7_3:+78524564 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACATATAATAAAAGACAAA+AGG + chr7_3:78524681-78524700 None:intergenic 15.0%
!! AACATATAATAAAAGACAAA+AGG + chr7_3:78524681-78524700 None:intergenic 15.0%
!! ATATCAAATGTCTCATATTT+GGG + chr7_3:78524399-78524418 None:intergenic 20.0%
!! AATATCAAATGTCTCATATT+TGG + chr7_3:78524400-78524419 None:intergenic 20.0%
!! AATATGAGACATTTGATATT+AGG - chr7_3:78524400-78524419 Msa1127010:three_prime_UTR 20.0%
!! TTATAATCACAATCAAGAAA+TGG - chr7_3:78524785-78524804 Msa1127010:intron 20.0%
!! ATATCAAATGTCTCATATTT+GGG + chr7_3:78524399-78524418 None:intergenic 20.0%
!! AATATCAAATGTCTCATATT+TGG + chr7_3:78524400-78524419 None:intergenic 20.0%
!! AATATGAGACATTTGATATT+AGG - chr7_3:78524400-78524419 Msa1127010:three_prime_UTR 20.0%
!! TTATAATCACAATCAAGAAA+TGG - chr7_3:78524785-78524804 Msa1127010:intron 20.0%
! GCAATCAATTATATTTCCTT+CGG + chr7_3:78524361-78524380 None:intergenic 25.0%
! ATAATTGATTGCATTCGTTA+TGG - chr7_3:78524369-78524388 Msa1127010:three_prime_UTR 25.0%
!!! TATTGTTTTTCTTAGTTCCT+TGG - chr7_3:78524621-78524640 Msa1127010:CDS 25.0%
! GCAATCAATTATATTTCCTT+CGG + chr7_3:78524361-78524380 None:intergenic 25.0%
! ATAATTGATTGCATTCGTTA+TGG - chr7_3:78524369-78524388 Msa1127010:three_prime_UTR 25.0%
!!! TATTGTTTTTCTTAGTTCCT+TGG - chr7_3:78524621-78524640 Msa1127010:CDS 25.0%
GAATACACTGATGAATGAAA+TGG - chr7_3:78524326-78524345 Msa1127010:three_prime_UTR 30.0%
TCAATTATATTTCCTTCGGT+AGG + chr7_3:78524357-78524376 None:intergenic 30.0%
TGAGACATTTGATATTAGGA+AGG - chr7_3:78524404-78524423 Msa1127010:three_prime_UTR 30.0%
GAGACATTTGATATTAGGAA+GGG - chr7_3:78524405-78524424 Msa1127010:three_prime_UTR 30.0%
TTGTTGCAAATGAGAATCTA+TGG - chr7_3:78524493-78524512 Msa1127010:three_prime_UTR 30.0%
CAATTCCTTGCTTCATTTAT+CGG - chr7_3:78524567-78524586 Msa1127010:CDS 30.0%
TAACAAGTAATAAAGCTCCA+AGG + chr7_3:78524641-78524660 None:intergenic 30.0%
TTATACCTTGTCATTCTAGA+TGG - chr7_3:78524809-78524828 Msa1127010:CDS 30.0%
CTGTAAGTGAAAATGGTAAT+CGG + chr7_3:78524838-78524857 None:intergenic 30.0%
! ATTACCATTTTCACTTACAG+AGG - chr7_3:78524838-78524857 Msa1127010:CDS 30.0%
GAATACACTGATGAATGAAA+TGG - chr7_3:78524326-78524345 Msa1127010:three_prime_UTR 30.0%
TCAATTATATTTCCTTCGGT+AGG + chr7_3:78524357-78524376 None:intergenic 30.0%
TGAGACATTTGATATTAGGA+AGG - chr7_3:78524404-78524423 Msa1127010:three_prime_UTR 30.0%
GAGACATTTGATATTAGGAA+GGG - chr7_3:78524405-78524424 Msa1127010:three_prime_UTR 30.0%
TTGTTGCAAATGAGAATCTA+TGG - chr7_3:78524493-78524512 Msa1127010:three_prime_UTR 30.0%
CAATTCCTTGCTTCATTTAT+CGG - chr7_3:78524567-78524586 Msa1127010:CDS 30.0%
TAACAAGTAATAAAGCTCCA+AGG + chr7_3:78524641-78524660 None:intergenic 30.0%
TTATACCTTGTCATTCTAGA+TGG - chr7_3:78524809-78524828 Msa1127010:CDS 30.0%
CTGTAAGTGAAAATGGTAAT+CGG + chr7_3:78524838-78524857 None:intergenic 30.0%
! ATTACCATTTTCACTTACAG+AGG - chr7_3:78524838-78524857 Msa1127010:CDS 30.0%
TCAACACATGAGAATTTGCA+AGG - chr7_3:78524276-78524295 Msa1127010:three_prime_UTR 35.0%
AATTGCCGATAAATGAAGCA+AGG + chr7_3:78524575-78524594 None:intergenic 35.0%
! GCTTCATTTATCGGCAATTT+TGG - chr7_3:78524576-78524595 Msa1127010:CDS 35.0%
! GGGTGATGTACTTAAGATTT+TGG - chr7_3:78524759-78524778 Msa1127010:intron 35.0%
TTAGCCTCTGTAAGTGAAAA+TGG + chr7_3:78524845-78524864 None:intergenic 35.0%
CCTCTACATATCTCTAACTA+CGG + chr7_3:78524962-78524981 None:intergenic 35.0%
GTACATTTCAATCTGCTTAC+TGG - chr7_3:78525093-78525112 Msa1127010:CDS 35.0%
!!! CTTACTGGTGGATTTTTTGA+TGG - chr7_3:78525108-78525127 Msa1127010:CDS 35.0%
TCAACACATGAGAATTTGCA+AGG - chr7_3:78524276-78524295 Msa1127010:three_prime_UTR 35.0%
AATTGCCGATAAATGAAGCA+AGG + chr7_3:78524575-78524594 None:intergenic 35.0%
! GCTTCATTTATCGGCAATTT+TGG - chr7_3:78524576-78524595 Msa1127010:CDS 35.0%
! GGGTGATGTACTTAAGATTT+TGG - chr7_3:78524759-78524778 Msa1127010:intron 35.0%
TTAGCCTCTGTAAGTGAAAA+TGG + chr7_3:78524845-78524864 None:intergenic 35.0%
CCTCTACATATCTCTAACTA+CGG + chr7_3:78524962-78524981 None:intergenic 35.0%
GTACATTTCAATCTGCTTAC+TGG - chr7_3:78525093-78525112 Msa1127010:CDS 35.0%
!!! CTTACTGGTGGATTTTTTGA+TGG - chr7_3:78525108-78525127 Msa1127010:CDS 35.0%
TGAGAATTTGCAAGGACTTG+TGG - chr7_3:78524284-78524303 Msa1127010:three_prime_UTR 40.0%
! GAAATGGTTTTTCCTACCGA+AGG - chr7_3:78524342-78524361 Msa1127010:three_prime_UTR 40.0%
TTGTGCAATTGAGCAACAGA+AGG - chr7_3:78524434-78524453 Msa1127010:three_prime_UTR 40.0%
AAGGTGGTTAAACGAGTCTT+TGG - chr7_3:78524453-78524472 Msa1127010:three_prime_UTR 40.0%
!! CAATTTTGGCGTCTTGTAAC+AGG - chr7_3:78524590-78524609 Msa1127010:CDS 40.0%
TGTCTTGAAGAGCTTGTGTT+GGG - chr7_3:78524739-78524758 Msa1127010:intron 40.0%
GATGACACAGATAGTGATTC+TGG - chr7_3:78524876-78524895 Msa1127010:CDS 40.0%
! AAACTACGTGAGCTTTGACA+TGG - chr7_3:78524924-78524943 Msa1127010:CDS 40.0%
CCGTAGTTAGAGATATGTAG+AGG - chr7_3:78524959-78524978 Msa1127010:intron 40.0%
GAGATATGTAGAGGAATTCG+TGG - chr7_3:78524968-78524987 Msa1127010:intron 40.0%
AGCAGATGGGAATGTACAAA+AGG + chr7_3:78525030-78525049 None:intergenic 40.0%
CATTTCAATCTGCTTACTGG+TGG - chr7_3:78525096-78525115 Msa1127010:CDS 40.0%
TGAGAATTTGCAAGGACTTG+TGG - chr7_3:78524284-78524303 Msa1127010:three_prime_UTR 40.0%
! GAAATGGTTTTTCCTACCGA+AGG - chr7_3:78524342-78524361 Msa1127010:three_prime_UTR 40.0%
TTGTGCAATTGAGCAACAGA+AGG - chr7_3:78524434-78524453 Msa1127010:three_prime_UTR 40.0%
AAGGTGGTTAAACGAGTCTT+TGG - chr7_3:78524453-78524472 Msa1127010:three_prime_UTR 40.0%
!! CAATTTTGGCGTCTTGTAAC+AGG - chr7_3:78524590-78524609 Msa1127010:CDS 40.0%
TGTCTTGAAGAGCTTGTGTT+GGG - chr7_3:78524739-78524758 Msa1127010:intron 40.0%
GATGACACAGATAGTGATTC+TGG - chr7_3:78524876-78524895 Msa1127010:CDS 40.0%
! AAACTACGTGAGCTTTGACA+TGG - chr7_3:78524924-78524943 Msa1127010:CDS 40.0%
CCGTAGTTAGAGATATGTAG+AGG - chr7_3:78524959-78524978 Msa1127010:intron 40.0%
GAGATATGTAGAGGAATTCG+TGG - chr7_3:78524968-78524987 Msa1127010:intron 40.0%
AGCAGATGGGAATGTACAAA+AGG + chr7_3:78525030-78525049 None:intergenic 40.0%
CATTTCAATCTGCTTACTGG+TGG - chr7_3:78525096-78525115 Msa1127010:CDS 40.0%
TGCAATTGAGCAACAGAAGG+TGG - chr7_3:78524437-78524456 Msa1127010:three_prime_UTR 45.0%
GTGTCTTGAAGAGCTTGTGT+TGG - chr7_3:78524738-78524757 Msa1127010:intron 45.0%
GTACATTCCCATCTGCTTAC+TGG - chr7_3:78525033-78525052 Msa1127010:intron 45.0%
ATTCCCATCTGCTTACTGGT+GGG - chr7_3:78525037-78525056 Msa1127010:intron 45.0%
! TACTGGTGGGGACTTTTTGT+TGG - chr7_3:78525050-78525069 Msa1127010:intron 45.0%
TGCAATTGAGCAACAGAAGG+TGG - chr7_3:78524437-78524456 Msa1127010:three_prime_UTR 45.0%
GTGTCTTGAAGAGCTTGTGT+TGG - chr7_3:78524738-78524757 Msa1127010:intron 45.0%
GTACATTCCCATCTGCTTAC+TGG - chr7_3:78525033-78525052 Msa1127010:intron 45.0%
ATTCCCATCTGCTTACTGGT+GGG - chr7_3:78525037-78525056 Msa1127010:intron 45.0%
! TACTGGTGGGGACTTTTTGT+TGG - chr7_3:78525050-78525069 Msa1127010:intron 45.0%
TCCTAACCCAGATTGCGTCT+GGG + chr7_3:78524542-78524561 None:intergenic 50.0%
ATCCTAACCCAGATTGCGTC+TGG + chr7_3:78524543-78524562 None:intergenic 50.0%
! GGCTGCCATCTAGAATGACA+AGG + chr7_3:78524817-78524836 None:intergenic 50.0%
CATTCCCATCTGCTTACTGG+TGG - chr7_3:78525036-78525055 Msa1127010:intron 50.0%
TTCCCATCTGCTTACTGGTG+GGG - chr7_3:78525038-78525057 Msa1127010:intron 50.0%
TCCTAACCCAGATTGCGTCT+GGG + chr7_3:78524542-78524561 None:intergenic 50.0%
ATCCTAACCCAGATTGCGTC+TGG + chr7_3:78524543-78524562 None:intergenic 50.0%
! GGCTGCCATCTAGAATGACA+AGG + chr7_3:78524817-78524836 None:intergenic 50.0%
CATTCCCATCTGCTTACTGG+TGG - chr7_3:78525036-78525055 Msa1127010:intron 50.0%
TTCCCATCTGCTTACTGGTG+GGG - chr7_3:78525038-78525057 Msa1127010:intron 50.0%
! GGAAGTGTGAACCCCTTACG+TGG - chr7_3:78524514-78524533 Msa1127010:three_prime_UTR 55.0%
TGCGTCTGGGAACCACGTAA+GGG + chr7_3:78524529-78524548 None:intergenic 55.0%
TTGCGTCTGGGAACCACGTA+AGG + chr7_3:78524530-78524549 None:intergenic 55.0%
GTGGTTCCCAGACGCAATCT+GGG - chr7_3:78524533-78524552 Msa1127010:exon 55.0%
TCCCAGACGCAATCTGGGTT+AGG - chr7_3:78524538-78524557 Msa1127010:CDS 55.0%
GTCCCCACCAGTAAGCAGAT+GGG + chr7_3:78525043-78525062 None:intergenic 55.0%
AGTCCCCACCAGTAAGCAGA+TGG + chr7_3:78525044-78525063 None:intergenic 55.0%
! GGAAGTGTGAACCCCTTACG+TGG - chr7_3:78524514-78524533 Msa1127010:three_prime_UTR 55.0%
TGCGTCTGGGAACCACGTAA+GGG + chr7_3:78524529-78524548 None:intergenic 55.0%
TTGCGTCTGGGAACCACGTA+AGG + chr7_3:78524530-78524549 None:intergenic 55.0%
GTGGTTCCCAGACGCAATCT+GGG - chr7_3:78524533-78524552 Msa1127010:exon 55.0%
TCCCAGACGCAATCTGGGTT+AGG - chr7_3:78524538-78524557 Msa1127010:CDS 55.0%
GTCCCCACCAGTAAGCAGAT+GGG + chr7_3:78525043-78525062 None:intergenic 55.0%
AGTCCCCACCAGTAAGCAGA+TGG + chr7_3:78525044-78525063 None:intergenic 55.0%
GCGTCTGGGAACCACGTAAG+GGG + chr7_3:78524528-78524547 None:intergenic 60.0%
CGTGGTTCCCAGACGCAATC+TGG - chr7_3:78524532-78524551 Msa1127010:exon 60.0%
GCGTCTGGGAACCACGTAAG+GGG + chr7_3:78524528-78524547 None:intergenic 60.0%
CGTGGTTCCCAGACGCAATC+TGG - chr7_3:78524532-78524551 Msa1127010:exon 60.0%
Chromosome Type Strat End Strand Name
chr7_3 gene 78524255 78525145 78524255 ID=Msa1127010;Name=Msa1127010
chr7_3 mRNA 78524255 78525145 78524255 ID=Msa1127010-mRNA-1;Parent=Msa1127010;Name=Msa1127010-mRNA-1;_AED=0.13;_eAED=0.13;_QI=0|0|0.33|1|0.5|0.33|3|281|132
chr7_3 exon 78524255 78524692 78524255 ID=Msa1127010-mRNA-1:exon:22020;Parent=Msa1127010-mRNA-1
chr7_3 exon 78524796 78524944 78524796 ID=Msa1127010-mRNA-1:exon:22019;Parent=Msa1127010-mRNA-1
chr7_3 exon 78525053 78525145 78525053 ID=Msa1127010-mRNA-1:exon:22018;Parent=Msa1127010-mRNA-1
chr7_3 CDS 78525053 78525145 78525053 ID=Msa1127010-mRNA-1:cds;Parent=Msa1127010-mRNA-1
chr7_3 CDS 78524796 78524944 78524796 ID=Msa1127010-mRNA-1:cds;Parent=Msa1127010-mRNA-1
chr7_3 CDS 78524536 78524692 78524536 ID=Msa1127010-mRNA-1:cds;Parent=Msa1127010-mRNA-1
chr7_3 three_prime_UTR 78524255 78524535 78524255 ID=Msa1127010-mRNA-1:three_prime_utr;Parent=Msa1127010-mRNA-1
Gene Sequence

>Msa1127010

TTAGAGACTTTGAAAACAATATCAACACATGAGAATTTGCAAGGACTTGTGGATATTATTCTAGTCACTTCGAATACACTGATGAATGAAATGGTGGTTAAACGAGTCTTTGGCACATTACGTTTGTATGTTGTTGCAAATGAGAATCTATGGAAGTGTGAACCCCTTACGTGGTTCCCAGACGCAATCTGGGTTAGGATAGAGCAATTCCTTGCTTCATTTATCGGCAATTTTGGCGTCTTATATGAAGCTTCATTAATTCTAAAGAGATTGTGTCTTGAAGAGCTTGTGTTGGGTGATGTACTTAAGATTTTGGAGATTATAATCACAATCAAGAAATGGATTATACCTTGTCATTCTAGATGGCAGCCGATTACCATTTTCACTTACAGAGGCTAA
Protein sequence

>Msa1127010

LETLKTISTHENLQGLVDIILVTSNTLMNEMVVKRVFGTLRLYVVANENLWKCEPLTWFPDAIWVRIEQFLASFIGNFGVLYEASLILKRLCLEELVLGDVLKILEIIITIKKWIIPCHSRWQPITIFTYRG*