AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1165990

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1165990 MtrunA17_Chr7g0270601 88.356 146 10 3 1 139 309 454 1.82e-79 242
Msa1165990 MtrunA17_Chr7g0271391 46.897 145 70 3 2 139 479 623 6.77e-38 135
Msa1165990 MtrunA17_Chr7g0269191 77.778 99 14 3 49 139 1 99 1.64e-34 116
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1165990 AT3G62200.1 46.528 144 70 3 3 139 508 651 6.43e-37 133

Find 47 sgRNAs with CRISPR-Local

Find 114 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATATCAAATGTCTCATATT+TGG 0.127212 7_4:-58023689 None:intergenic
GTACATTCCCATCTGCTTAC+TGG 0.214575 7_4:+58024328 Msa1165990:three_prime_UTR
AATATGAGACATTTGATATT+AGG 0.240226 7_4:+58023692 Msa1165990:CDS
GTACATTTCAATCTGCTTAC+TGG 0.250536 7_4:+58024388 Msa1165990:three_prime_UTR
CGTGGTTCCCAGACGCAATC+TGG 0.270910 7_4:+58023824 Msa1165990:CDS
TTAGCCTCTGTAAGTGAAAA+TGG 0.275804 7_4:-58024137 None:intergenic
GGGTGATGTACTTAAGATTT+TGG 0.277803 7_4:+58024054 Msa1165990:CDS
GATGACACAGATAGTGATTC+TGG 0.347850 7_4:+58024171 Msa1165990:three_prime_UTR
ATATCAAATGTCTCATATTT+GGG 0.356802 7_4:-58023688 None:intergenic
ATAATTGATTGCATTCGTTA+TGG 0.373706 7_4:+58023661 Msa1165990:CDS
AAGGTGGTTAAACGAGTCTT+TGG 0.382873 7_4:+58023745 Msa1165990:CDS
ATCCTAACCCAGATTGCGTC+TGG 0.396295 7_4:-58023832 None:intergenic
TTATACCTTGTCATTCTAGA+TGG 0.412658 7_4:+58024104 Msa1165990:CDS
GAATACACTGATGAATGAAA+TGG 0.416796 7_4:+58023618 Msa1165990:exon
CTGTAAGTGAAAATGGTAAT+CGG 0.431067 7_4:-58024130 None:intergenic
TTGTTGCAAATGAGAATCTA+TGG 0.442211 7_4:+58023785 Msa1165990:CDS
GCAATCAATTATATTTCCTT+CGG 0.464377 7_4:-58023650 None:intergenic
TTATAATCACAATCAAGAAA+TGG 0.466378 7_4:+58024080 Msa1165990:CDS
CCTCTACATATCTCTAACTA+CGG 0.467900 7_4:-58024254 None:intergenic
TTGCGTCTGGGAACCACGTA+AGG 0.473407 7_4:-58023819 None:intergenic
TGAGACATTTGATATTAGGA+AGG 0.482985 7_4:+58023696 Msa1165990:CDS
TCCCAGACGCAATCTGGGTT+AGG 0.483088 7_4:+58023830 Msa1165990:CDS
AGCAGATGGGAATGTACAAA+AGG 0.496986 7_4:-58024322 None:intergenic
TGTCTTGAAGAGCTTGTGTT+GGG 0.501883 7_4:+58024034 Msa1165990:CDS
CATTTCAATCTGCTTACTGG+TGG 0.505776 7_4:+58024391 Msa1165990:three_prime_UTR
ATTCCCATCTGCTTACTGGT+GGG 0.506945 7_4:+58024332 Msa1165990:three_prime_UTR
TGAGAATTTGCAAGGACTTG+TGG 0.513544 7_4:+58023576 Msa1165990:five_prime_UTR
CATTCCCATCTGCTTACTGG+TGG 0.519665 7_4:+58024331 Msa1165990:three_prime_UTR
TTCCCATCTGCTTACTGGTG+GGG 0.524628 7_4:+58024333 Msa1165990:three_prime_UTR
GTGTCTTGAAGAGCTTGTGT+TGG 0.527052 7_4:+58024033 Msa1165990:CDS
GTGGTTCCCAGACGCAATCT+GGG 0.539558 7_4:+58023825 Msa1165990:CDS
GAGACATTTGATATTAGGAA+GGG 0.542549 7_4:+58023697 Msa1165990:CDS
AGTCCCCACCAGTAAGCAGA+TGG 0.550048 7_4:-58024336 None:intergenic
TCAATTATATTTCCTTCGGT+AGG 0.561721 7_4:-58023646 None:intergenic
TCCTAACCCAGATTGCGTCT+GGG 0.566146 7_4:-58023831 None:intergenic
GAGATATGTAGAGGAATTCG+TGG 0.572067 7_4:+58024263 Msa1165990:three_prime_UTR
TGCAATTGAGCAACAGAAGG+TGG 0.573790 7_4:+58023729 Msa1165990:CDS
CCGTAGTTAGAGATATGTAG+AGG 0.580945 7_4:+58024254 Msa1165990:three_prime_UTR
TGCGTCTGGGAACCACGTAA+GGG 0.598064 7_4:-58023818 None:intergenic
GTCCCCACCAGTAAGCAGAT+GGG 0.623279 7_4:-58024335 None:intergenic
AAACTACGTGAGCTTTGACA+TGG 0.629175 7_4:+58024219 Msa1165990:three_prime_UTR
TTGCCGATGAAAATGAAGCA+AGG 0.631727 7_4:-58023864 None:intergenic
TCAACACATGAGAATTTGCA+AGG 0.634115 7_4:+58023568 Msa1165990:five_prime_UTR
TTGTGCAATTGAGCAACAGA+AGG 0.644017 7_4:+58023726 Msa1165990:CDS
GCGTCTGGGAACCACGTAAG+GGG 0.647796 7_4:-58023817 None:intergenic
GGAAGTGTGAACCCCTTACG+TGG 0.663822 7_4:+58023806 Msa1165990:CDS
GGCTGCCATCTAGAATGACA+AGG 0.705174 7_4:-58024109 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACATATAATAAAAGACAAA+AGG - chr7_4:58023975-58023994 None:intergenic 15.0%
!! AACATATAATAAAAGACAAA+AGG - chr7_4:58023975-58023994 None:intergenic 15.0%
!! ATATCAAATGTCTCATATTT+GGG - chr7_4:58023691-58023710 None:intergenic 20.0%
!! AATATCAAATGTCTCATATT+TGG - chr7_4:58023692-58023711 None:intergenic 20.0%
!! AATATGAGACATTTGATATT+AGG + chr7_4:58023692-58023711 Msa1165990:CDS 20.0%
!! TTATAATCACAATCAAGAAA+TGG + chr7_4:58024080-58024099 Msa1165990:CDS 20.0%
!! ATATCAAATGTCTCATATTT+GGG - chr7_4:58023691-58023710 None:intergenic 20.0%
!! AATATCAAATGTCTCATATT+TGG - chr7_4:58023692-58023711 None:intergenic 20.0%
!! AATATGAGACATTTGATATT+AGG + chr7_4:58023692-58023711 Msa1165990:CDS 20.0%
!! TTATAATCACAATCAAGAAA+TGG + chr7_4:58024080-58024099 Msa1165990:CDS 20.0%
! GCAATCAATTATATTTCCTT+CGG - chr7_4:58023653-58023672 None:intergenic 25.0%
! ATAATTGATTGCATTCGTTA+TGG + chr7_4:58023661-58023680 Msa1165990:CDS 25.0%
!!! TATTGTTTTTCTTAGTTCCT+TGG + chr7_4:58023915-58023934 Msa1165990:intron 25.0%
! GCAATCAATTATATTTCCTT+CGG - chr7_4:58023653-58023672 None:intergenic 25.0%
! ATAATTGATTGCATTCGTTA+TGG + chr7_4:58023661-58023680 Msa1165990:CDS 25.0%
!!! TATTGTTTTTCTTAGTTCCT+TGG + chr7_4:58023915-58023934 Msa1165990:intron 25.0%
GAATACACTGATGAATGAAA+TGG + chr7_4:58023618-58023637 Msa1165990:exon 30.0%
TCAATTATATTTCCTTCGGT+AGG - chr7_4:58023649-58023668 None:intergenic 30.0%
TGAGACATTTGATATTAGGA+AGG + chr7_4:58023696-58023715 Msa1165990:CDS 30.0%
GAGACATTTGATATTAGGAA+GGG + chr7_4:58023697-58023716 Msa1165990:CDS 30.0%
TTGTTGCAAATGAGAATCTA+TGG + chr7_4:58023785-58023804 Msa1165990:CDS 30.0%
! ATTCCTTGCTTCATTTTCAT+CGG + chr7_4:58023861-58023880 Msa1165990:CDS 30.0%
! TTCATTTTCATCGGCAATTT+TGG + chr7_4:58023870-58023889 Msa1165990:CDS 30.0%
TAACAAGTAATAAAGCTCCA+AGG - chr7_4:58023935-58023954 None:intergenic 30.0%
TTATACCTTGTCATTCTAGA+TGG + chr7_4:58024104-58024123 Msa1165990:CDS 30.0%
CTGTAAGTGAAAATGGTAAT+CGG - chr7_4:58024133-58024152 None:intergenic 30.0%
! ATTACCATTTTCACTTACAG+AGG + chr7_4:58024133-58024152 Msa1165990:CDS 30.0%
GAATACACTGATGAATGAAA+TGG + chr7_4:58023618-58023637 Msa1165990:exon 30.0%
TCAATTATATTTCCTTCGGT+AGG - chr7_4:58023649-58023668 None:intergenic 30.0%
TGAGACATTTGATATTAGGA+AGG + chr7_4:58023696-58023715 Msa1165990:CDS 30.0%
GAGACATTTGATATTAGGAA+GGG + chr7_4:58023697-58023716 Msa1165990:CDS 30.0%
TTGTTGCAAATGAGAATCTA+TGG + chr7_4:58023785-58023804 Msa1165990:CDS 30.0%
! ATTCCTTGCTTCATTTTCAT+CGG + chr7_4:58023861-58023880 Msa1165990:CDS 30.0%
! TTCATTTTCATCGGCAATTT+TGG + chr7_4:58023870-58023889 Msa1165990:CDS 30.0%
TAACAAGTAATAAAGCTCCA+AGG - chr7_4:58023935-58023954 None:intergenic 30.0%
TTATACCTTGTCATTCTAGA+TGG + chr7_4:58024104-58024123 Msa1165990:CDS 30.0%
CTGTAAGTGAAAATGGTAAT+CGG - chr7_4:58024133-58024152 None:intergenic 30.0%
! ATTACCATTTTCACTTACAG+AGG + chr7_4:58024133-58024152 Msa1165990:CDS 30.0%
TCAACACATGAGAATTTGCA+AGG + chr7_4:58023568-58023587 Msa1165990:five_prime_UTR 35.0%
! GGGTGATGTACTTAAGATTT+TGG + chr7_4:58024054-58024073 Msa1165990:CDS 35.0%
TTAGCCTCTGTAAGTGAAAA+TGG - chr7_4:58024140-58024159 None:intergenic 35.0%
CCTCTACATATCTCTAACTA+CGG - chr7_4:58024257-58024276 None:intergenic 35.0%
GTACATTTCAATCTGCTTAC+TGG + chr7_4:58024388-58024407 Msa1165990:three_prime_UTR 35.0%
!!! CTTACTGGTGGATTTTTTGA+TGG + chr7_4:58024403-58024422 Msa1165990:three_prime_UTR 35.0%
TCAACACATGAGAATTTGCA+AGG + chr7_4:58023568-58023587 Msa1165990:five_prime_UTR 35.0%
! GGGTGATGTACTTAAGATTT+TGG + chr7_4:58024054-58024073 Msa1165990:CDS 35.0%
TTAGCCTCTGTAAGTGAAAA+TGG - chr7_4:58024140-58024159 None:intergenic 35.0%
CCTCTACATATCTCTAACTA+CGG - chr7_4:58024257-58024276 None:intergenic 35.0%
GTACATTTCAATCTGCTTAC+TGG + chr7_4:58024388-58024407 Msa1165990:three_prime_UTR 35.0%
!!! CTTACTGGTGGATTTTTTGA+TGG + chr7_4:58024403-58024422 Msa1165990:three_prime_UTR 35.0%
TGAGAATTTGCAAGGACTTG+TGG + chr7_4:58023576-58023595 Msa1165990:five_prime_UTR 40.0%
! GAAATGGTTTTTCCTACCGA+AGG + chr7_4:58023634-58023653 Msa1165990:CDS 40.0%
TTGTGCAATTGAGCAACAGA+AGG + chr7_4:58023726-58023745 Msa1165990:CDS 40.0%
AAGGTGGTTAAACGAGTCTT+TGG + chr7_4:58023745-58023764 Msa1165990:CDS 40.0%
TTGCCGATGAAAATGAAGCA+AGG - chr7_4:58023867-58023886 None:intergenic 40.0%
!! CAATTTTGGCGTCTTGTAAC+AGG + chr7_4:58023884-58023903 Msa1165990:CDS 40.0%
TGTCTTGAAGAGCTTGTGTT+GGG + chr7_4:58024034-58024053 Msa1165990:CDS 40.0%
GATGACACAGATAGTGATTC+TGG + chr7_4:58024171-58024190 Msa1165990:three_prime_UTR 40.0%
! AAACTACGTGAGCTTTGACA+TGG + chr7_4:58024219-58024238 Msa1165990:three_prime_UTR 40.0%
CCGTAGTTAGAGATATGTAG+AGG + chr7_4:58024254-58024273 Msa1165990:three_prime_UTR 40.0%
GAGATATGTAGAGGAATTCG+TGG + chr7_4:58024263-58024282 Msa1165990:three_prime_UTR 40.0%
AGCAGATGGGAATGTACAAA+AGG - chr7_4:58024325-58024344 None:intergenic 40.0%
CATTTCAATCTGCTTACTGG+TGG + chr7_4:58024391-58024410 Msa1165990:three_prime_UTR 40.0%
TGAGAATTTGCAAGGACTTG+TGG + chr7_4:58023576-58023595 Msa1165990:five_prime_UTR 40.0%
! GAAATGGTTTTTCCTACCGA+AGG + chr7_4:58023634-58023653 Msa1165990:CDS 40.0%
TTGTGCAATTGAGCAACAGA+AGG + chr7_4:58023726-58023745 Msa1165990:CDS 40.0%
AAGGTGGTTAAACGAGTCTT+TGG + chr7_4:58023745-58023764 Msa1165990:CDS 40.0%
TTGCCGATGAAAATGAAGCA+AGG - chr7_4:58023867-58023886 None:intergenic 40.0%
!! CAATTTTGGCGTCTTGTAAC+AGG + chr7_4:58023884-58023903 Msa1165990:CDS 40.0%
TGTCTTGAAGAGCTTGTGTT+GGG + chr7_4:58024034-58024053 Msa1165990:CDS 40.0%
GATGACACAGATAGTGATTC+TGG + chr7_4:58024171-58024190 Msa1165990:three_prime_UTR 40.0%
! AAACTACGTGAGCTTTGACA+TGG + chr7_4:58024219-58024238 Msa1165990:three_prime_UTR 40.0%
CCGTAGTTAGAGATATGTAG+AGG + chr7_4:58024254-58024273 Msa1165990:three_prime_UTR 40.0%
GAGATATGTAGAGGAATTCG+TGG + chr7_4:58024263-58024282 Msa1165990:three_prime_UTR 40.0%
AGCAGATGGGAATGTACAAA+AGG - chr7_4:58024325-58024344 None:intergenic 40.0%
CATTTCAATCTGCTTACTGG+TGG + chr7_4:58024391-58024410 Msa1165990:three_prime_UTR 40.0%
TGCAATTGAGCAACAGAAGG+TGG + chr7_4:58023729-58023748 Msa1165990:CDS 45.0%
GTGTCTTGAAGAGCTTGTGT+TGG + chr7_4:58024033-58024052 Msa1165990:CDS 45.0%
GTACATTCCCATCTGCTTAC+TGG + chr7_4:58024328-58024347 Msa1165990:three_prime_UTR 45.0%
ATTCCCATCTGCTTACTGGT+GGG + chr7_4:58024332-58024351 Msa1165990:three_prime_UTR 45.0%
! TACTGGTGGGGACTTTTTGT+TGG + chr7_4:58024345-58024364 Msa1165990:three_prime_UTR 45.0%
TGCAATTGAGCAACAGAAGG+TGG + chr7_4:58023729-58023748 Msa1165990:CDS 45.0%
GTGTCTTGAAGAGCTTGTGT+TGG + chr7_4:58024033-58024052 Msa1165990:CDS 45.0%
GTACATTCCCATCTGCTTAC+TGG + chr7_4:58024328-58024347 Msa1165990:three_prime_UTR 45.0%
ATTCCCATCTGCTTACTGGT+GGG + chr7_4:58024332-58024351 Msa1165990:three_prime_UTR 45.0%
! TACTGGTGGGGACTTTTTGT+TGG + chr7_4:58024345-58024364 Msa1165990:three_prime_UTR 45.0%
TCCTAACCCAGATTGCGTCT+GGG - chr7_4:58023834-58023853 None:intergenic 50.0%
ATCCTAACCCAGATTGCGTC+TGG - chr7_4:58023835-58023854 None:intergenic 50.0%
! GGCTGCCATCTAGAATGACA+AGG - chr7_4:58024112-58024131 None:intergenic 50.0%
CATTCCCATCTGCTTACTGG+TGG + chr7_4:58024331-58024350 Msa1165990:three_prime_UTR 50.0%
TTCCCATCTGCTTACTGGTG+GGG + chr7_4:58024333-58024352 Msa1165990:three_prime_UTR 50.0%
TCCTAACCCAGATTGCGTCT+GGG - chr7_4:58023834-58023853 None:intergenic 50.0%
ATCCTAACCCAGATTGCGTC+TGG - chr7_4:58023835-58023854 None:intergenic 50.0%
! GGCTGCCATCTAGAATGACA+AGG - chr7_4:58024112-58024131 None:intergenic 50.0%
CATTCCCATCTGCTTACTGG+TGG + chr7_4:58024331-58024350 Msa1165990:three_prime_UTR 50.0%
TTCCCATCTGCTTACTGGTG+GGG + chr7_4:58024333-58024352 Msa1165990:three_prime_UTR 50.0%
! GGAAGTGTGAACCCCTTACG+TGG + chr7_4:58023806-58023825 Msa1165990:CDS 55.0%
TGCGTCTGGGAACCACGTAA+GGG - chr7_4:58023821-58023840 None:intergenic 55.0%
TTGCGTCTGGGAACCACGTA+AGG - chr7_4:58023822-58023841 None:intergenic 55.0%
GTGGTTCCCAGACGCAATCT+GGG + chr7_4:58023825-58023844 Msa1165990:CDS 55.0%
TCCCAGACGCAATCTGGGTT+AGG + chr7_4:58023830-58023849 Msa1165990:CDS 55.0%
GTCCCCACCAGTAAGCAGAT+GGG - chr7_4:58024338-58024357 None:intergenic 55.0%
AGTCCCCACCAGTAAGCAGA+TGG - chr7_4:58024339-58024358 None:intergenic 55.0%
! GGAAGTGTGAACCCCTTACG+TGG + chr7_4:58023806-58023825 Msa1165990:CDS 55.0%
TGCGTCTGGGAACCACGTAA+GGG - chr7_4:58023821-58023840 None:intergenic 55.0%
TTGCGTCTGGGAACCACGTA+AGG - chr7_4:58023822-58023841 None:intergenic 55.0%
GTGGTTCCCAGACGCAATCT+GGG + chr7_4:58023825-58023844 Msa1165990:CDS 55.0%
TCCCAGACGCAATCTGGGTT+AGG + chr7_4:58023830-58023849 Msa1165990:CDS 55.0%
GTCCCCACCAGTAAGCAGAT+GGG - chr7_4:58024338-58024357 None:intergenic 55.0%
AGTCCCCACCAGTAAGCAGA+TGG - chr7_4:58024339-58024358 None:intergenic 55.0%
GCGTCTGGGAACCACGTAAG+GGG - chr7_4:58023820-58023839 None:intergenic 60.0%
CGTGGTTCCCAGACGCAATC+TGG + chr7_4:58023824-58023843 Msa1165990:CDS 60.0%
GCGTCTGGGAACCACGTAAG+GGG - chr7_4:58023820-58023839 None:intergenic 60.0%
CGTGGTTCCCAGACGCAATC+TGG + chr7_4:58023824-58023843 Msa1165990:CDS 60.0%
Chromosome Type Strat End Strand Name
chr7_4 gene 58023527 58024440 58023527 ID=Msa1165990;Name=Msa1165990
chr7_4 mRNA 58023527 58024440 58023527 ID=Msa1165990-mRNA-1;Parent=Msa1165990;Name=Msa1165990-mRNA-1;_AED=0.06;_eAED=0.06;_QI=101|1|1|1|1|1|2|281|144
chr7_4 exon 58023527 58023905 58023527 ID=Msa1165990-mRNA-1:exon:17637;Parent=Msa1165990-mRNA-1
chr7_4 exon 58024003 58024440 58024003 ID=Msa1165990-mRNA-1:exon:17638;Parent=Msa1165990-mRNA-1
chr7_4 five_prime_UTR 58023527 58023627 58023527 ID=Msa1165990-mRNA-1:five_prime_utr;Parent=Msa1165990-mRNA-1
chr7_4 CDS 58023628 58023905 58023628 ID=Msa1165990-mRNA-1:cds;Parent=Msa1165990-mRNA-1
chr7_4 CDS 58024003 58024159 58024003 ID=Msa1165990-mRNA-1:cds;Parent=Msa1165990-mRNA-1
chr7_4 three_prime_UTR 58024160 58024440 58024160 ID=Msa1165990-mRNA-1:three_prime_utr;Parent=Msa1165990-mRNA-1
Gene Sequence

>Msa1165990

ATGAATGAAATGGTTTTTCCTACCGAAGGAAATATAATTGATTGCATTCGTTATGGTGATCCCAAATATGAGACATTTGATATTAGGAAGGGTTTACATTGTGCAATTGAGCAACAGAAGGTGGTTAAACGAGTCTTTGGCACATTACGTTTGTATGTTGTTGCAAATGAGAATCTATGGAAGTGTGAACCCCTTACGTGGTTCCCAGACGCAATCTGGGTTAGGATAGAGCAATTCCTTGCTTCATTTTCATCGGCAATTTTGGCGTCTTGTAACAGATATGAAGCTTCATTAATTCTAAAGAGATTGTGTCTTGAAGAGCTTGTGTTGGGTGATGTACTTAAGATTTTGGAGATTATAATCACAATCAAGAAATGGATTATACCTTGTCATTCTAGATGGCAGCCGATTACCATTTTCACTTACAGAGGCTAA
Protein sequence

>Msa1165990

MNEMVFPTEGNIIDCIRYGDPKYETFDIRKGLHCAIEQQKVVKRVFGTLRLYVVANENLWKCEPLTWFPDAIWVRIEQFLASFSSAILASCNRYEASLILKRLCLEELVLGDVLKILEIIITIKKWIIPCHSRWQPITIFTYRG*