AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1210230

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1210230 MtrunA17_Chr5g0393501 31.928 166 110 1 2 164 76 241 1.15e-24 95.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 44 sgRNAs with CRISPR-Local

Find 98 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAGTTCCTATCGTTGGATA+TGG 0.258835 8_1:+69045675 Msa1210230:CDS
AATCGTGATGTTTCACTCTA+AGG 0.341127 8_1:-69045841 None:intergenic
AGGAATTTGCCAAAAGTATC+AGG 0.344083 8_1:-69045821 None:intergenic
TAGGAACTACCTGATACTTT+TGG 0.356273 8_1:+69045812 Msa1210230:intron
CACAGTGCATGTATAAAATC+AGG 0.359207 8_1:+69045249 None:intergenic
CGATTATTCTACGAGTTTAG+TGG 0.386306 8_1:+69045519 Msa1210230:CDS
TCCGAACATCACATTTGGTA+TGG 0.417548 8_1:-69045927 None:intergenic
ATCTACTTCCACCAAGGTAC+TGG 0.428620 8_1:-69045560 None:intergenic
ACCTTTGAAGTTCCTATCGT+TGG 0.439777 8_1:+69045669 Msa1210230:CDS
CCGAACATCACATTTGGTAT+GGG 0.451435 8_1:-69045926 None:intergenic
TTGTGCTGCCAATGGTATTG+AGG 0.463000 8_1:+69045967 Msa1210230:CDS
GAGCAATGTCACTTGCTAGA+TGG 0.472188 8_1:+69045420 Msa1210230:five_prime_UTR
CCAAATGTGATGTTCGGAAA+AGG 0.475440 8_1:+69045932 Msa1210230:CDS
CCCATACCAAATGTGATGTT+CGG 0.477035 8_1:+69045926 Msa1210230:CDS
AAATATTTAGCAACGAAGAA+TGG 0.478005 8_1:-69045384 None:intergenic
GTCATGTGTTTATCAACGCT+TGG 0.483566 8_1:-69046050 None:intergenic
ACACGATGCTGCCGCACTCA+TGG 0.487735 8_1:-69045640 None:intergenic
TTCTATTTAAATAAGATGAA+CGG 0.497916 8_1:+69045299 Msa1210230:five_prime_UTR
TGTGCTGCCAATGGTATTGA+GGG 0.501205 8_1:+69045968 Msa1210230:CDS
ATTATTGCTTTCCAGTACCT+TGG 0.503165 8_1:+69045549 Msa1210230:CDS
TAAATATTTCTACGAGCTAC+CGG 0.507354 8_1:+69045398 Msa1210230:five_prime_UTR
CTGCCTAACTTCTAGGATGT+CGG 0.510869 8_1:+69045351 Msa1210230:five_prime_UTR
GCACTCATGGAATGATATAG+TGG 0.517894 8_1:-69045627 None:intergenic
TCTCCGACATCCTAGAAGTT+AGG 0.525775 8_1:-69045354 None:intergenic
ACAGGAATGATATTGTCATA+AGG 0.528831 8_1:-69045881 None:intergenic
AGTCGGCCGTTGTTGACAGA+TGG 0.531450 8_1:+69045483 Msa1210230:CDS
ATTGCTTTCCAGTACCTTGG+TGG 0.549152 8_1:+69045552 Msa1210230:CDS
CGAACATCACATTTGGTATG+GGG 0.552019 8_1:-69045925 None:intergenic
TCTGTATATTTGAGTCTCAC+AGG 0.555272 8_1:-69045899 None:intergenic
TTTCAAGTGCAAGTGCGTCA+TGG 0.567746 8_1:+69046006 Msa1210230:CDS
GTCTCCGCCCTCAATACCAT+TGG 0.581950 8_1:-69045975 None:intergenic
TCTAGCAAGTGACATTGCTC+CGG 0.590324 8_1:-69045417 None:intergenic
CACGATTACGTCATGTTGTG+CGG 0.590860 8_1:+69045857 Msa1210230:CDS
TGTCACTTGCTAGATGGTGA+TGG 0.596408 8_1:+69045426 Msa1210230:five_prime_UTR
ATGTGATGTTCGGAAAAGGT+TGG 0.606400 8_1:+69045936 Msa1210230:CDS
TGTTCAACAAATCAGTTAGT+CGG 0.609582 8_1:+69045466 Msa1210230:CDS
TCCAACGATAGGAACTTCAA+AGG 0.611311 8_1:-69045670 None:intergenic
GTCACTTGCTAGATGGTGAT+GGG 0.619857 8_1:+69045427 Msa1210230:five_prime_UTR
GTCGATCCATATCCAACGAT+AGG 0.629633 8_1:-69045681 None:intergenic
ACTATATCATTCCATGAGTG+CGG 0.659839 8_1:+69045629 Msa1210230:CDS
TTTGAAATCTACTTCCACCA+AGG 0.681040 8_1:-69045566 None:intergenic
CTACAACCATCTGTCAACAA+CGG 0.697912 8_1:-69045489 None:intergenic
TGGATCGACGAAATCACCGA+AGG 0.700849 8_1:+69045695 Msa1210230:CDS
GCTGCCAATGGTATTGAGGG+CGG 0.739556 8_1:+69045971 Msa1210230:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTCTATTTAAATAAGATGAA+CGG + chr8_1:69045299-69045318 Msa1210230:five_prime_UTR 15.0%
!! TTAGATATATGCTATAATAA+AGG + chr8_1:69045749-69045768 Msa1210230:intron 15.0%
!! TTCTATTTAAATAAGATGAA+CGG + chr8_1:69045299-69045318 Msa1210230:five_prime_UTR 15.0%
!! TTAGATATATGCTATAATAA+AGG + chr8_1:69045749-69045768 Msa1210230:intron 15.0%
! AAATATTTAGCAACGAAGAA+TGG - chr8_1:69045387-69045406 None:intergenic 25.0%
! AAAAAACAATAGACAACCTT+CGG - chr8_1:69045714-69045733 None:intergenic 25.0%
! AAATATTTAGCAACGAAGAA+TGG - chr8_1:69045387-69045406 None:intergenic 25.0%
! AAAAAACAATAGACAACCTT+CGG - chr8_1:69045714-69045733 None:intergenic 25.0%
AGTTAGGCAGAAAAAGTTTA+CGG - chr8_1:69045341-69045360 None:intergenic 30.0%
! TAAATATTTCTACGAGCTAC+CGG + chr8_1:69045398-69045417 Msa1210230:five_prime_UTR 30.0%
TGTTCAACAAATCAGTTAGT+CGG + chr8_1:69045466-69045485 Msa1210230:CDS 30.0%
ACAGGAATGATATTGTCATA+AGG - chr8_1:69045884-69045903 None:intergenic 30.0%
AGTTAGGCAGAAAAAGTTTA+CGG - chr8_1:69045341-69045360 None:intergenic 30.0%
! TAAATATTTCTACGAGCTAC+CGG + chr8_1:69045398-69045417 Msa1210230:five_prime_UTR 30.0%
TGTTCAACAAATCAGTTAGT+CGG + chr8_1:69045466-69045485 Msa1210230:CDS 30.0%
ACAGGAATGATATTGTCATA+AGG - chr8_1:69045884-69045903 None:intergenic 30.0%
!! ACTTTTTCTGCCTAACTTCT+AGG + chr8_1:69045344-69045363 Msa1210230:five_prime_UTR 35.0%
CGATTATTCTACGAGTTTAG+TGG + chr8_1:69045519-69045538 Msa1210230:CDS 35.0%
ATTATTGCTTTCCAGTACCT+TGG + chr8_1:69045549-69045568 Msa1210230:CDS 35.0%
! TTTGAAATCTACTTCCACCA+AGG - chr8_1:69045569-69045588 None:intergenic 35.0%
ACTATATCATTCCATGAGTG+CGG + chr8_1:69045629-69045648 Msa1210230:CDS 35.0%
! TAGGAACTACCTGATACTTT+TGG + chr8_1:69045812-69045831 Msa1210230:intron 35.0%
!! AGGAATTTGCCAAAAGTATC+AGG - chr8_1:69045824-69045843 None:intergenic 35.0%
AATCGTGATGTTTCACTCTA+AGG - chr8_1:69045844-69045863 None:intergenic 35.0%
TCTGTATATTTGAGTCTCAC+AGG - chr8_1:69045902-69045921 None:intergenic 35.0%
!! ACTTTTTCTGCCTAACTTCT+AGG + chr8_1:69045344-69045363 Msa1210230:five_prime_UTR 35.0%
CGATTATTCTACGAGTTTAG+TGG + chr8_1:69045519-69045538 Msa1210230:CDS 35.0%
ATTATTGCTTTCCAGTACCT+TGG + chr8_1:69045549-69045568 Msa1210230:CDS 35.0%
! TTTGAAATCTACTTCCACCA+AGG - chr8_1:69045569-69045588 None:intergenic 35.0%
ACTATATCATTCCATGAGTG+CGG + chr8_1:69045629-69045648 Msa1210230:CDS 35.0%
! TAGGAACTACCTGATACTTT+TGG + chr8_1:69045812-69045831 Msa1210230:intron 35.0%
!! AGGAATTTGCCAAAAGTATC+AGG - chr8_1:69045824-69045843 None:intergenic 35.0%
AATCGTGATGTTTCACTCTA+AGG - chr8_1:69045844-69045863 None:intergenic 35.0%
TCTGTATATTTGAGTCTCAC+AGG - chr8_1:69045902-69045921 None:intergenic 35.0%
CTACAACCATCTGTCAACAA+CGG - chr8_1:69045492-69045511 None:intergenic 40.0%
GCACTCATGGAATGATATAG+TGG - chr8_1:69045630-69045649 None:intergenic 40.0%
!! ACCTTTGAAGTTCCTATCGT+TGG + chr8_1:69045669-69045688 Msa1210230:CDS 40.0%
TCCAACGATAGGAACTTCAA+AGG - chr8_1:69045673-69045692 None:intergenic 40.0%
GAAGTTCCTATCGTTGGATA+TGG + chr8_1:69045675-69045694 Msa1210230:CDS 40.0%
CGAACATCACATTTGGTATG+GGG - chr8_1:69045928-69045947 None:intergenic 40.0%
CCGAACATCACATTTGGTAT+GGG - chr8_1:69045929-69045948 None:intergenic 40.0%
CCCATACCAAATGTGATGTT+CGG + chr8_1:69045926-69045945 Msa1210230:CDS 40.0%
TCCGAACATCACATTTGGTA+TGG - chr8_1:69045930-69045949 None:intergenic 40.0%
! CCTTTTCCGAACATCACATT+TGG - chr8_1:69045935-69045954 None:intergenic 40.0%
CCAAATGTGATGTTCGGAAA+AGG + chr8_1:69045932-69045951 Msa1210230:CDS 40.0%
ATGTGATGTTCGGAAAAGGT+TGG + chr8_1:69045936-69045955 Msa1210230:CDS 40.0%
CTACAACCATCTGTCAACAA+CGG - chr8_1:69045492-69045511 None:intergenic 40.0%
GCACTCATGGAATGATATAG+TGG - chr8_1:69045630-69045649 None:intergenic 40.0%
!! ACCTTTGAAGTTCCTATCGT+TGG + chr8_1:69045669-69045688 Msa1210230:CDS 40.0%
TCCAACGATAGGAACTTCAA+AGG - chr8_1:69045673-69045692 None:intergenic 40.0%
GAAGTTCCTATCGTTGGATA+TGG + chr8_1:69045675-69045694 Msa1210230:CDS 40.0%
CGAACATCACATTTGGTATG+GGG - chr8_1:69045928-69045947 None:intergenic 40.0%
CCGAACATCACATTTGGTAT+GGG - chr8_1:69045929-69045948 None:intergenic 40.0%
CCCATACCAAATGTGATGTT+CGG + chr8_1:69045926-69045945 Msa1210230:CDS 40.0%
TCCGAACATCACATTTGGTA+TGG - chr8_1:69045930-69045949 None:intergenic 40.0%
! CCTTTTCCGAACATCACATT+TGG - chr8_1:69045935-69045954 None:intergenic 40.0%
CCAAATGTGATGTTCGGAAA+AGG + chr8_1:69045932-69045951 Msa1210230:CDS 40.0%
ATGTGATGTTCGGAAAAGGT+TGG + chr8_1:69045936-69045955 Msa1210230:CDS 40.0%
!! CTGCCTAACTTCTAGGATGT+CGG + chr8_1:69045351-69045370 Msa1210230:five_prime_UTR 45.0%
TCTCCGACATCCTAGAAGTT+AGG - chr8_1:69045357-69045376 None:intergenic 45.0%
TCTAGCAAGTGACATTGCTC+CGG - chr8_1:69045420-69045439 None:intergenic 45.0%
! GAGCAATGTCACTTGCTAGA+TGG + chr8_1:69045420-69045439 Msa1210230:five_prime_UTR 45.0%
! TGTCACTTGCTAGATGGTGA+TGG + chr8_1:69045426-69045445 Msa1210230:five_prime_UTR 45.0%
! GTCACTTGCTAGATGGTGAT+GGG + chr8_1:69045427-69045446 Msa1210230:five_prime_UTR 45.0%
ATTGCTTTCCAGTACCTTGG+TGG + chr8_1:69045552-69045571 Msa1210230:CDS 45.0%
ATCTACTTCCACCAAGGTAC+TGG - chr8_1:69045563-69045582 None:intergenic 45.0%
GTCGATCCATATCCAACGAT+AGG - chr8_1:69045684-69045703 None:intergenic 45.0%
CACGATTACGTCATGTTGTG+CGG + chr8_1:69045857-69045876 Msa1210230:CDS 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG + chr8_1:69045959-69045978 Msa1210230:CDS 45.0%
TTGTGCTGCCAATGGTATTG+AGG + chr8_1:69045967-69045986 Msa1210230:CDS 45.0%
! TGTGCTGCCAATGGTATTGA+GGG + chr8_1:69045968-69045987 Msa1210230:CDS 45.0%
! TTTCAAGTGCAAGTGCGTCA+TGG + chr8_1:69046006-69046025 Msa1210230:CDS 45.0%
!! CTGCCTAACTTCTAGGATGT+CGG + chr8_1:69045351-69045370 Msa1210230:five_prime_UTR 45.0%
TCTCCGACATCCTAGAAGTT+AGG - chr8_1:69045357-69045376 None:intergenic 45.0%
TCTAGCAAGTGACATTGCTC+CGG - chr8_1:69045420-69045439 None:intergenic 45.0%
! GAGCAATGTCACTTGCTAGA+TGG + chr8_1:69045420-69045439 Msa1210230:five_prime_UTR 45.0%
! TGTCACTTGCTAGATGGTGA+TGG + chr8_1:69045426-69045445 Msa1210230:five_prime_UTR 45.0%
! GTCACTTGCTAGATGGTGAT+GGG + chr8_1:69045427-69045446 Msa1210230:five_prime_UTR 45.0%
ATTGCTTTCCAGTACCTTGG+TGG + chr8_1:69045552-69045571 Msa1210230:CDS 45.0%
ATCTACTTCCACCAAGGTAC+TGG - chr8_1:69045563-69045582 None:intergenic 45.0%
GTCGATCCATATCCAACGAT+AGG - chr8_1:69045684-69045703 None:intergenic 45.0%
CACGATTACGTCATGTTGTG+CGG + chr8_1:69045857-69045876 Msa1210230:CDS 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG + chr8_1:69045959-69045978 Msa1210230:CDS 45.0%
TTGTGCTGCCAATGGTATTG+AGG + chr8_1:69045967-69045986 Msa1210230:CDS 45.0%
! TGTGCTGCCAATGGTATTGA+GGG + chr8_1:69045968-69045987 Msa1210230:CDS 45.0%
! TTTCAAGTGCAAGTGCGTCA+TGG + chr8_1:69046006-69046025 Msa1210230:CDS 45.0%
!!! TTTTTTTTTTCTTTTTTTTT+AGG + chr8_1:69045793-69045812 Msa1210230:intron 5.0%
!!! TTTTTTTTTTCTTTTTTTTT+AGG + chr8_1:69045793-69045812 Msa1210230:intron 5.0%
TGGATCGACGAAATCACCGA+AGG + chr8_1:69045695-69045714 Msa1210230:CDS 50.0%
TGGATCGACGAAATCACCGA+AGG + chr8_1:69045695-69045714 Msa1210230:CDS 50.0%
AGTCGGCCGTTGTTGACAGA+TGG + chr8_1:69045483-69045502 Msa1210230:CDS 55.0%
! GCTGCCAATGGTATTGAGGG+CGG + chr8_1:69045971-69045990 Msa1210230:CDS 55.0%
GTCTCCGCCCTCAATACCAT+TGG - chr8_1:69045978-69045997 None:intergenic 55.0%
AGTCGGCCGTTGTTGACAGA+TGG + chr8_1:69045483-69045502 Msa1210230:CDS 55.0%
! GCTGCCAATGGTATTGAGGG+CGG + chr8_1:69045971-69045990 Msa1210230:CDS 55.0%
GTCTCCGCCCTCAATACCAT+TGG - chr8_1:69045978-69045997 None:intergenic 55.0%
ACACGATGCTGCCGCACTCA+TGG - chr8_1:69045643-69045662 None:intergenic 60.0%
ACACGATGCTGCCGCACTCA+TGG - chr8_1:69045643-69045662 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 69045253 69046060 69045253 ID=Msa1210230;Name=Msa1210230
chr8_1 mRNA 69045253 69046060 69045253 ID=Msa1210230-mRNA-1;Parent=Msa1210230;Name=Msa1210230-mRNA-1;_AED=0.04;_eAED=0.04;_QI=212|1|0.5|1|1|1|2|0|165
chr8_1 exon 69045253 69045716 69045253 ID=Msa1210230-mRNA-1:exon:23066;Parent=Msa1210230-mRNA-1
chr8_1 exon 69045815 69046060 69045815 ID=Msa1210230-mRNA-1:exon:23067;Parent=Msa1210230-mRNA-1
chr8_1 five_prime_UTR 69045253 69045464 69045253 ID=Msa1210230-mRNA-1:five_prime_utr;Parent=Msa1210230-mRNA-1
chr8_1 CDS 69045465 69045716 69045465 ID=Msa1210230-mRNA-1:cds;Parent=Msa1210230-mRNA-1
chr8_1 CDS 69045815 69046060 69045815 ID=Msa1210230-mRNA-1:cds;Parent=Msa1210230-mRNA-1
Gene Sequence

>Msa1210230

ATGTTCAACAAATCAGTTAGTCGGCCGTTGTTGACAGATGGTTGTAGTGCATTGCGATTATTCTACGAGTTTAGTGGAAGTAAGATTATTGCTTTCCAGTACCTTGGTGGAAGTAGATTTCAAATCTTTGTTTTTGCTCATAACATTACTCTAGCTGATTATCCACTATATCATTCCATGAGTGCGGCAGCATCGTGTTATTGTACCTTTGAAGTTCCTATCGTTGGATATGGATCGACGAAATCACCGAAGGAACTACCTGATACTTTTGGCAAATTCCTTAGAGTGAAACATCACGATTACGTCATGTTGTGCGGACCTTATGACAATATCATTCCTGTGAGACTCAAATATACAGACGACCCCATACCAAATGTGATGTTCGGAAAAGGTTGGACGAGTTTTTGTGCTGCCAATGGTATTGAGGGCGGAGACGTGTTGATTTTCAAGTGCAAGTGCGTCATGGACAAAAAATATGTTATCGTATCCAAGCGTTGA
Protein sequence

>Msa1210230

MFNKSVSRPLLTDGCSALRLFYEFSGSKIIAFQYLGGSRFQIFVFAHNITLADYPLYHSMSAAASCYCTFEVPIVGYGSTKSPKELPDTFGKFLRVKHHDYVMLCGPYDNIIPVRLKYTDDPIPNVMFGKGWTSFCAANGIEGGDVLIFKCKCVMDKKYVIVSKR*