AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0049010

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0049010 MtrunA17_Chr4g0019351 79.798 99 15 2 1 97 1 96 3.23e-49 150
Msa0049010 MtrunA17_Chr4g0019341 76.768 99 18 2 1 97 1 96 1.87e-45 141
Msa0049010 MtrunA17_Chr4g0019361 56.122 98 18 2 1 97 1 74 4.47e-26 92.0
Msa0049010 MtrunA17_Chr4g0018981 46.392 97 33 1 1 97 1 78 4.97e-21 79.3
Msa0049010 MtrunA17_Chr4g0018971 46.875 96 30 2 1 96 1 75 6.63e-19 73.9
Msa0049010 MtrunA17_Chr4g0019021 40.541 111 46 4 1 97 1 105 6.50e-18 72.0
Msa0049010 MtrunA17_Chr8g0368881 38.776 98 45 2 1 97 1 84 2.21e-17 70.1
Msa0049010 MtrunA17_Chr4g0018961 43.299 97 33 1 1 97 1 75 8.53e-16 65.9
Msa0049010 MtrunA17_Chr4g0018931 38.776 98 39 2 1 97 1 78 2.83e-13 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 24 sgRNAs with CRISPR-Local

Find 112 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAGAAGTGCTCTCTTATTT+TGG 0.217478 1_2:+2138740 Msa0049010:CDS
TTGTGGCCACGTGCTTTATC+AGG 0.279751 1_2:-2139009 None:intergenic
CGTTAGGTTGGATCAATTTA+CGG 0.318370 1_2:+2139502 Msa0049010:three_prime_UTR
TGTATAGTTTCAGATGAAAT+AGG 0.330215 1_2:+2138952 Msa0049010:intron
AATAAGAAGAGACTCCTTGC+TGG 0.444927 1_2:+2138979 Msa0049010:CDS
CTATGAATGATATGGGCGTT+AGG 0.451730 1_2:+2139486 Msa0049010:exon
GAATGATATGGGCGTTAGGT+TGG 0.467597 1_2:+2139490 Msa0049010:exon
GACTCCTTGCAGAAAATTGT+GGG 0.487595 1_2:+2139415 Msa0049010:CDS
GATCAATTTACGGATGAAGT+TGG 0.531820 1_2:+2139512 Msa0049010:three_prime_UTR
AGACTCCTTGCAGAAAATTG+TGG 0.531866 1_2:+2139414 Msa0049010:CDS
AAGTAAAACCTGCAAAATTG+TGG 0.541805 1_2:-2139026 None:intergenic
CGAAAGCTCGAGTGTTGCAC+GGG 0.550887 1_2:+2139604 Msa0049010:three_prime_UTR
TTGCAGAAAATTGTGGGAGA+AGG 0.572891 1_2:+2139421 Msa0049010:CDS
TCGAAAGCTCGAGTGTTGCA+CGG 0.581217 1_2:+2139603 Msa0049010:three_prime_UTR
CACATGGTCCTCATGCTGAT+CGG 0.585701 1_2:+2139445 Msa0049010:CDS
TTTCATCAAAGACATTAGCA+AGG 0.595257 1_2:+2138790 Msa0049010:CDS
AACACTCGAGCTTTCGACCT+AGG 0.613127 1_2:-2139597 None:intergenic
ATATCATTCATAGAAAATTG+TGG 0.617375 1_2:-2139476 None:intergenic
AGAAGAGACTCCTTGCTGGT+AGG 0.629830 1_2:+2138983 Msa0049010:CDS
TATCAGGCTTCCTACCAGCA+AGG 0.630061 1_2:-2138993 None:intergenic
CAACGTGGCCGATCAGCATG+AGG 0.638536 1_2:-2139453 None:intergenic
CATAGAAAATTGTGGCAACG+TGG 0.674818 1_2:-2139468 None:intergenic
AATTGTGGGAGAAGGACACA+TGG 0.681375 1_2:+2139429 Msa0049010:CDS
AGGAAGCCTGATAAAGCACG+TGG 0.728123 1_2:+2139003 Msa0049010:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTTCTTGTATTAATATT+TGG + chr1_2:2139349-2139368 Msa0049010:intron 10.0%
!!! TTTTTTCTTGTATTAATATT+TGG + chr1_2:2139349-2139368 Msa0049010:intron 10.0%
!! AATAACAAAATGGATATTAT+GGG - chr1_2:2138860-2138879 None:intergenic 15.0%
!! TATTATTTATGGATATTATG+GGG - chr1_2:2139052-2139071 None:intergenic 15.0%
!! GTATTATTTATGGATATTAT+GGG - chr1_2:2139053-2139072 None:intergenic 15.0%
!! AGTATTATTTATGGATATTA+TGG - chr1_2:2139054-2139073 None:intergenic 15.0%
!!! TATTTTGAGAAAAGAAAAAT+GGG + chr1_2:2139288-2139307 Msa0049010:intron 15.0%
!! TTGGTAGAAAAAATAAATAA+TGG + chr1_2:2139531-2139550 Msa0049010:three_prime_UTR 15.0%
!! TGGTAGAAAAAATAAATAAT+GGG + chr1_2:2139532-2139551 Msa0049010:three_prime_UTR 15.0%
!! AATAACAAAATGGATATTAT+GGG - chr1_2:2138860-2138879 None:intergenic 15.0%
!! TATTATTTATGGATATTATG+GGG - chr1_2:2139052-2139071 None:intergenic 15.0%
!! GTATTATTTATGGATATTAT+GGG - chr1_2:2139053-2139072 None:intergenic 15.0%
!! AGTATTATTTATGGATATTA+TGG - chr1_2:2139054-2139073 None:intergenic 15.0%
!!! TATTTTGAGAAAAGAAAAAT+GGG + chr1_2:2139288-2139307 Msa0049010:intron 15.0%
!! TTGGTAGAAAAAATAAATAA+TGG + chr1_2:2139531-2139550 Msa0049010:three_prime_UTR 15.0%
!! TGGTAGAAAAAATAAATAAT+GGG + chr1_2:2139532-2139551 Msa0049010:three_prime_UTR 15.0%
!! ATAACAAAATGGATATTATG+GGG - chr1_2:2138859-2138878 None:intergenic 20.0%
!! CAATAACAAAATGGATATTA+TGG - chr1_2:2138861-2138880 None:intergenic 20.0%
!! TGGATAAAGTTCAATAAATA+AGG + chr1_2:2139212-2139231 Msa0049010:intron 20.0%
!!! CTATTTTGAGAAAAGAAAAA+TGG + chr1_2:2139287-2139306 Msa0049010:intron 20.0%
!! ATATCATTCATAGAAAATTG+TGG - chr1_2:2139479-2139498 None:intergenic 20.0%
!!! ACAATTTTCTATGAATGATA+TGG + chr1_2:2139478-2139497 Msa0049010:exon 20.0%
!!! CAATTTTCTATGAATGATAT+GGG + chr1_2:2139479-2139498 Msa0049010:exon 20.0%
!!! TTAGTTTGATTTATTTTCCT+AGG + chr1_2:2139580-2139599 Msa0049010:three_prime_UTR 20.0%
!! ATAACAAAATGGATATTATG+GGG - chr1_2:2138859-2138878 None:intergenic 20.0%
!! CAATAACAAAATGGATATTA+TGG - chr1_2:2138861-2138880 None:intergenic 20.0%
!! TGGATAAAGTTCAATAAATA+AGG + chr1_2:2139212-2139231 Msa0049010:intron 20.0%
!!! CTATTTTGAGAAAAGAAAAA+TGG + chr1_2:2139287-2139306 Msa0049010:intron 20.0%
!! ATATCATTCATAGAAAATTG+TGG - chr1_2:2139479-2139498 None:intergenic 20.0%
!!! ACAATTTTCTATGAATGATA+TGG + chr1_2:2139478-2139497 Msa0049010:exon 20.0%
!!! CAATTTTCTATGAATGATAT+GGG + chr1_2:2139479-2139498 Msa0049010:exon 20.0%
!!! TTAGTTTGATTTATTTTCCT+AGG + chr1_2:2139580-2139599 Msa0049010:three_prime_UTR 20.0%
! TGTATAGTTTCAGATGAAAT+AGG + chr1_2:2138952-2138971 Msa0049010:intron 25.0%
! AAACGACTATTATTTAGAGA+CGG - chr1_2:2139081-2139100 None:intergenic 25.0%
! CTCTAAATAATAGTCGTTTA+AGG + chr1_2:2139082-2139101 Msa0049010:intron 25.0%
! CCACTAACTACAATTAATAA+GGG - chr1_2:2139181-2139200 None:intergenic 25.0%
! TCCACTAACTACAATTAATA+AGG - chr1_2:2139182-2139201 None:intergenic 25.0%
! AAAGAAACAATTATTGTGAG+CGG + chr1_2:2139312-2139331 Msa0049010:intron 25.0%
! TGTATAGTTTCAGATGAAAT+AGG + chr1_2:2138952-2138971 Msa0049010:intron 25.0%
! AAACGACTATTATTTAGAGA+CGG - chr1_2:2139081-2139100 None:intergenic 25.0%
! CTCTAAATAATAGTCGTTTA+AGG + chr1_2:2139082-2139101 Msa0049010:intron 25.0%
! CCACTAACTACAATTAATAA+GGG - chr1_2:2139181-2139200 None:intergenic 25.0%
! TCCACTAACTACAATTAATA+AGG - chr1_2:2139182-2139201 None:intergenic 25.0%
! AAAGAAACAATTATTGTGAG+CGG + chr1_2:2139312-2139331 Msa0049010:intron 25.0%
!!! AAAGAAGTGCTCTCTTATTT+TGG + chr1_2:2138740-2138759 Msa0049010:CDS 30.0%
TTTCATCAAAGACATTAGCA+AGG + chr1_2:2138790-2138809 Msa0049010:CDS 30.0%
! GTTGTTCTTGTATTGATGTA+TGG + chr1_2:2138923-2138942 Msa0049010:intron 30.0%
AAGTAAAACCTGCAAAATTG+TGG - chr1_2:2139029-2139048 None:intergenic 30.0%
CCCTTATTAATTGTAGTTAG+TGG + chr1_2:2139178-2139197 Msa0049010:intron 30.0%
!!! AAAGAAGTGCTCTCTTATTT+TGG + chr1_2:2138740-2138759 Msa0049010:CDS 30.0%
TTTCATCAAAGACATTAGCA+AGG + chr1_2:2138790-2138809 Msa0049010:CDS 30.0%
! GTTGTTCTTGTATTGATGTA+TGG + chr1_2:2138923-2138942 Msa0049010:intron 30.0%
AAGTAAAACCTGCAAAATTG+TGG - chr1_2:2139029-2139048 None:intergenic 30.0%
CCCTTATTAATTGTAGTTAG+TGG + chr1_2:2139178-2139197 Msa0049010:intron 30.0%
GCGCAAATGCAATAACAAAA+TGG - chr1_2:2138870-2138889 None:intergenic 35.0%
GACTATTATTTAGAGACGGA+GGG - chr1_2:2139077-2139096 None:intergenic 35.0%
AGTTAGTGGAGTAGTTAAGT+TGG + chr1_2:2139192-2139211 Msa0049010:intron 35.0%
AAACAATTATTGTGAGCGGA+GGG + chr1_2:2139316-2139335 Msa0049010:intron 35.0%
!! CGTTAGGTTGGATCAATTTA+CGG + chr1_2:2139502-2139521 Msa0049010:three_prime_UTR 35.0%
GATCAATTTACGGATGAAGT+TGG + chr1_2:2139512-2139531 Msa0049010:three_prime_UTR 35.0%
GCGCAAATGCAATAACAAAA+TGG - chr1_2:2138870-2138889 None:intergenic 35.0%
GACTATTATTTAGAGACGGA+GGG - chr1_2:2139077-2139096 None:intergenic 35.0%
AGTTAGTGGAGTAGTTAAGT+TGG + chr1_2:2139192-2139211 Msa0049010:intron 35.0%
AAACAATTATTGTGAGCGGA+GGG + chr1_2:2139316-2139335 Msa0049010:intron 35.0%
!! CGTTAGGTTGGATCAATTTA+CGG + chr1_2:2139502-2139521 Msa0049010:three_prime_UTR 35.0%
GATCAATTTACGGATGAAGT+TGG + chr1_2:2139512-2139531 Msa0049010:three_prime_UTR 35.0%
AATAAGAAGAGACTCCTTGC+TGG + chr1_2:2138979-2138998 Msa0049010:CDS 40.0%
!! GACGGAGGGAGTATTATTTA+TGG - chr1_2:2139063-2139082 None:intergenic 40.0%
CGACTATTATTTAGAGACGG+AGG - chr1_2:2139078-2139097 None:intergenic 40.0%
GAAACAATTATTGTGAGCGG+AGG + chr1_2:2139315-2139334 Msa0049010:intron 40.0%
AGACTCCTTGCAGAAAATTG+TGG + chr1_2:2139414-2139433 Msa0049010:CDS 40.0%
GACTCCTTGCAGAAAATTGT+GGG + chr1_2:2139415-2139434 Msa0049010:CDS 40.0%
! TTCTCCCACAATTTTCTGCA+AGG - chr1_2:2139422-2139441 None:intergenic 40.0%
TTGCAGAAAATTGTGGGAGA+AGG + chr1_2:2139421-2139440 Msa0049010:CDS 40.0%
CATAGAAAATTGTGGCAACG+TGG - chr1_2:2139471-2139490 None:intergenic 40.0%
CTATGAATGATATGGGCGTT+AGG + chr1_2:2139486-2139505 Msa0049010:exon 40.0%
AATAAGAAGAGACTCCTTGC+TGG + chr1_2:2138979-2138998 Msa0049010:CDS 40.0%
!! GACGGAGGGAGTATTATTTA+TGG - chr1_2:2139063-2139082 None:intergenic 40.0%
CGACTATTATTTAGAGACGG+AGG - chr1_2:2139078-2139097 None:intergenic 40.0%
GAAACAATTATTGTGAGCGG+AGG + chr1_2:2139315-2139334 Msa0049010:intron 40.0%
AGACTCCTTGCAGAAAATTG+TGG + chr1_2:2139414-2139433 Msa0049010:CDS 40.0%
GACTCCTTGCAGAAAATTGT+GGG + chr1_2:2139415-2139434 Msa0049010:CDS 40.0%
! TTCTCCCACAATTTTCTGCA+AGG - chr1_2:2139422-2139441 None:intergenic 40.0%
TTGCAGAAAATTGTGGGAGA+AGG + chr1_2:2139421-2139440 Msa0049010:CDS 40.0%
CATAGAAAATTGTGGCAACG+TGG - chr1_2:2139471-2139490 None:intergenic 40.0%
CTATGAATGATATGGGCGTT+AGG + chr1_2:2139486-2139505 Msa0049010:exon 40.0%
TATGGGGAAGTTCACGTACT+TGG - chr1_2:2138843-2138862 None:intergenic 45.0%
AATTGTGGGAGAAGGACACA+TGG + chr1_2:2139429-2139448 Msa0049010:CDS 45.0%
GAATGATATGGGCGTTAGGT+TGG + chr1_2:2139490-2139509 Msa0049010:exon 45.0%
TATGGGGAAGTTCACGTACT+TGG - chr1_2:2138843-2138862 None:intergenic 45.0%
AATTGTGGGAGAAGGACACA+TGG + chr1_2:2139429-2139448 Msa0049010:CDS 45.0%
GAATGATATGGGCGTTAGGT+TGG + chr1_2:2139490-2139509 Msa0049010:exon 45.0%
AGAAGAGACTCCTTGCTGGT+AGG + chr1_2:2138983-2139002 Msa0049010:CDS 50.0%
TATCAGGCTTCCTACCAGCA+AGG - chr1_2:2138996-2139015 None:intergenic 50.0%
AGGAAGCCTGATAAAGCACG+TGG + chr1_2:2139003-2139022 Msa0049010:CDS 50.0%
TTGTGGCCACGTGCTTTATC+AGG - chr1_2:2139012-2139031 None:intergenic 50.0%
CACATGGTCCTCATGCTGAT+CGG + chr1_2:2139445-2139464 Msa0049010:CDS 50.0%
AACACTCGAGCTTTCGACCT+AGG - chr1_2:2139600-2139619 None:intergenic 50.0%
! TCGAAAGCTCGAGTGTTGCA+CGG + chr1_2:2139603-2139622 Msa0049010:three_prime_UTR 50.0%
AGAAGAGACTCCTTGCTGGT+AGG + chr1_2:2138983-2139002 Msa0049010:CDS 50.0%
TATCAGGCTTCCTACCAGCA+AGG - chr1_2:2138996-2139015 None:intergenic 50.0%
AGGAAGCCTGATAAAGCACG+TGG + chr1_2:2139003-2139022 Msa0049010:CDS 50.0%
TTGTGGCCACGTGCTTTATC+AGG - chr1_2:2139012-2139031 None:intergenic 50.0%
CACATGGTCCTCATGCTGAT+CGG + chr1_2:2139445-2139464 Msa0049010:CDS 50.0%
AACACTCGAGCTTTCGACCT+AGG - chr1_2:2139600-2139619 None:intergenic 50.0%
! TCGAAAGCTCGAGTGTTGCA+CGG + chr1_2:2139603-2139622 Msa0049010:three_prime_UTR 50.0%
! GCACGTGGCCACAATTTTGC+AGG + chr1_2:2139018-2139037 Msa0049010:CDS 55.0%
! CGAAAGCTCGAGTGTTGCAC+GGG + chr1_2:2139604-2139623 Msa0049010:three_prime_UTR 55.0%
! GCACGTGGCCACAATTTTGC+AGG + chr1_2:2139018-2139037 Msa0049010:CDS 55.0%
! CGAAAGCTCGAGTGTTGCAC+GGG + chr1_2:2139604-2139623 Msa0049010:three_prime_UTR 55.0%
CAACGTGGCCGATCAGCATG+AGG - chr1_2:2139456-2139475 None:intergenic 60.0%
CAACGTGGCCGATCAGCATG+AGG - chr1_2:2139456-2139475 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 2138722 2139673 2138722 ID=Msa0049010;Name=Msa0049010
chr1_2 mRNA 2138722 2139673 2138722 ID=Msa0049010-mRNA-1;Parent=Msa0049010;Name=Msa0049010-mRNA-1;_AED=0.00;_eAED=0.00;_QI=10|1|1|1|1|1|3|182|97
chr1_2 exon 2138722 2138843 2138722 ID=Msa0049010-mRNA-1:exon:391;Parent=Msa0049010-mRNA-1
chr1_2 exon 2138959 2139039 2138959 ID=Msa0049010-mRNA-1:exon:392;Parent=Msa0049010-mRNA-1
chr1_2 exon 2139391 2139673 2139391 ID=Msa0049010-mRNA-1:exon:393;Parent=Msa0049010-mRNA-1
chr1_2 five_prime_UTR 2138722 2138731 2138722 ID=Msa0049010-mRNA-1:five_prime_utr;Parent=Msa0049010-mRNA-1
chr1_2 CDS 2138732 2138843 2138732 ID=Msa0049010-mRNA-1:cds;Parent=Msa0049010-mRNA-1
chr1_2 CDS 2138959 2139039 2138959 ID=Msa0049010-mRNA-1:cds;Parent=Msa0049010-mRNA-1
chr1_2 CDS 2139391 2139491 2139391 ID=Msa0049010-mRNA-1:cds;Parent=Msa0049010-mRNA-1
chr1_2 three_prime_UTR 2139492 2139673 2139492 ID=Msa0049010-mRNA-1:three_prime_utr;Parent=Msa0049010-mRNA-1
Gene Sequence

>Msa0049010

ATGGCTTCAAAGAAGTGCTCTCTTATTTTGGTAGTTCTCTTTCTTTGTCTGTTGAGTTTTTCATCAAAGACATTAGCAAGGAACATTGCGAATGCTTCGAAACTTTATCCAATTTCAGATGAAATAGGTCTGAATAAGAAGAGACTCCTTGCTGGTAGGAAGCCTGATAAAGCACGTGGCCACAATTTTGCAGAAGAAATAAATCTGAATAAGAAGAGACTCCTTGCAGAAAATTGTGGGAGAAGGACACATGGTCCTCATGCTGATCGGCCACGTTGCCACAATTTTCTATGA
Protein sequence

>Msa0049010

MASKKCSLILVVLFLCLLSFSSKTLARNIANASKLYPISDEIGLNKKRLLAGRKPDKARGHNFAEEINLNKKRLLAENCGRRTHGPHADRPRCHNFL*