AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0618520


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0618520 MtrunA17_Chr8g0383481 93.506 77 4 1 1 76 36 112 2.70e-48 148
Msa0618520 MtrunA17_Chr3g0129411 50.588 85 33 3 1 76 35 119 1.34e-19 75.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 34 sgRNAs with CRISPR-Local

Find 86 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTTGTCTGCCTAGAAAATA+TGG 0.191697 4_2:+69468732 None:intergenic
AAATATTTGTAGCTCCTTCT+AGG 0.236923 4_2:+69468597 None:intergenic
ACCTCTACTATACGTGTATT+TGG 0.243926 4_2:+69468810 None:intergenic
AAAATATGGGTATGTGCTAT+TGG 0.285709 4_2:+69468746 None:intergenic
ATCGGTGGCTTCCTTCTTGC+TGG 0.286574 4_2:+69468106 None:intergenic
TAAGGTAGATCATATGTTTA+AGG 0.311443 4_2:-69468179 Msa0618520:CDS
AAATATGGGTATGTGCTATT+GGG 0.333544 4_2:+69468747 None:intergenic
AATGAGTAATACTCATAATA+AGG 0.356818 4_2:-69468197 Msa0618520:CDS
GCATTAAACTTCGTGGCAAT+TGG 0.368027 4_2:-69468637 Msa0618520:five_prime_UTR
ATAGTAGAGGTTGACATTCA+TGG 0.371098 4_2:-69468798 Msa0618520:five_prime_UTR
AAAAGTCGAATTATTTAAGA+TGG 0.436642 4_2:-69468471 Msa0618520:exon
CCTCTACTATACGTGTATTT+GGG 0.444033 4_2:+69468811 None:intergenic
ACAATATTTCAATTGTGAAT+CGG 0.450645 4_2:+69468088 None:intergenic
TGCATAATACCACAATCATA+TGG 0.494409 4_2:-69468662 Msa0618520:five_prime_UTR
ATAACTTAATACCTCTAGCT+TGG 0.497100 4_2:+69468387 None:intergenic
TATGGTTGCATTAAACTTCG+TGG 0.508843 4_2:-69468644 Msa0618520:five_prime_UTR
TAACTTAATACCTCTAGCTT+GGG 0.523329 4_2:+69468388 None:intergenic
GAAGGAATAGAACCACTACT+AGG 0.529646 4_2:+69468426 None:intergenic
CTTGTCTGCCTAGAAAATAT+GGG 0.530731 4_2:+69468733 None:intergenic
AATATGGGTATGTGCTATTG+GGG 0.541039 4_2:+69468748 None:intergenic
GGCAAAAGAAGAACATAATG+TGG 0.544421 4_2:-69468158 Msa0618520:CDS
AAACAAACGTTTCCTAGTAG+TGG 0.554374 4_2:-69468438 Msa0618520:CDS
TGGGTATGTGCTATTGGGGA+AGG 0.558645 4_2:+69468752 None:intergenic
TGGTGCAGCACGAACTCTGA+AGG 0.582207 4_2:-69468236 Msa0618520:intron
GGGTATGTGCTATTGGGGAA+GGG 0.584361 4_2:+69468753 None:intergenic
ATATTTCAATTGTGAATCGG+TGG 0.587562 4_2:+69468091 None:intergenic
TTAATGCAACCATATGATTG+TGG 0.591100 4_2:+69468653 None:intergenic
CCCAAATACACGTATAGTAG+AGG 0.592182 4_2:-69468811 Msa0618520:five_prime_UTR
TGGATTACACTCCAGCAAGA+AGG 0.596499 4_2:-69468117 Msa0618520:CDS
GCAAAAGAAGAACATAATGT+GGG 0.604097 4_2:-69468157 Msa0618520:CDS
GGGTAGATATGAAACAGAGA+AGG 0.633587 4_2:+69468408 None:intergenic
TTCATATCTACCCAAGCTAG+AGG 0.668712 4_2:-69468398 Msa0618520:intron
TGCACAATAAGAGAGAGTAA+TGG 0.674857 4_2:+69468681 None:intergenic
ATACATATTGATATGATACA+CGG 0.690316 4_2:-69467945 Msa0618520:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TACAAATATTTTTCTATATA+AGG - chr4_2:69468157-69468176 Msa0618520:CDS 10.0%
!!! ACAAATATTTTTCTATATAA+GGG - chr4_2:69468158-69468177 Msa0618520:CDS 10.0%
!!! GATTATGATTTTATTAAAAA+AGG + chr4_2:69468435-69468454 None:intergenic 10.0%
!!! TACAAATATTTTTCTATATA+AGG - chr4_2:69468157-69468176 Msa0618520:CDS 10.0%
!!! ACAAATATTTTTCTATATAA+GGG - chr4_2:69468158-69468177 Msa0618520:CDS 10.0%
!!! GATTATGATTTTATTAAAAA+AGG + chr4_2:69468435-69468454 None:intergenic 10.0%
!! GATTATGTTCTTAATTATAT+TGG - chr4_2:69468383-69468402 Msa0618520:intron 15.0%
!! TCTAACATGATTTATATATA+TGG - chr4_2:69468486-69468505 Msa0618520:five_prime_UTR 15.0%
!! GATTATGTTCTTAATTATAT+TGG - chr4_2:69468383-69468402 Msa0618520:intron 15.0%
!! TCTAACATGATTTATATATA+TGG - chr4_2:69468486-69468505 Msa0618520:five_prime_UTR 15.0%
!! AAAAGTCGAATTATTTAAGA+TGG - chr4_2:69468271-69468290 Msa0618520:intron 20.0%
!! AATGAGTAATACTCATAATA+AGG - chr4_2:69468545-69468564 Msa0618520:five_prime_UTR 20.0%
!! ACAATATTTCAATTGTGAAT+CGG + chr4_2:69468657-69468676 None:intergenic 20.0%
!! ATACATATTGATATGATACA+CGG - chr4_2:69468797-69468816 Msa0618520:five_prime_UTR 20.0%
!! AAAAGTCGAATTATTTAAGA+TGG - chr4_2:69468271-69468290 Msa0618520:intron 20.0%
!! AATGAGTAATACTCATAATA+AGG - chr4_2:69468545-69468564 Msa0618520:five_prime_UTR 20.0%
!! ACAATATTTCAATTGTGAAT+CGG + chr4_2:69468657-69468676 None:intergenic 20.0%
!! ATACATATTGATATGATACA+CGG - chr4_2:69468797-69468816 Msa0618520:five_prime_UTR 20.0%
! TAAGGTAGATCATATGTTTA+AGG - chr4_2:69468563-69468582 Msa0618520:five_prime_UTR 25.0%
! TAAGGTAGATCATATGTTTA+AGG - chr4_2:69468563-69468582 Msa0618520:five_prime_UTR 25.0%
! AAATATGGGTATGTGCTATT+GGG + chr4_2:69467998-69468017 None:intergenic 30.0%
AAAATATGGGTATGTGCTAT+TGG + chr4_2:69467999-69468018 None:intergenic 30.0%
TGCATAATACCACAATCATA+TGG - chr4_2:69468080-69468099 Msa0618520:exon 30.0%
TTAATGCAACCATATGATTG+TGG + chr4_2:69468092-69468111 None:intergenic 30.0%
! CTAGTAATTTTCAACCTAGA+AGG - chr4_2:69468131-69468150 Msa0618520:CDS 30.0%
AAATATTTGTAGCTCCTTCT+AGG + chr4_2:69468148-69468167 None:intergenic 30.0%
! TAACTTAATACCTCTAGCTT+GGG + chr4_2:69468357-69468376 None:intergenic 30.0%
ATAACTTAATACCTCTAGCT+TGG + chr4_2:69468358-69468377 None:intergenic 30.0%
GCAAAAGAAGAACATAATGT+GGG - chr4_2:69468585-69468604 Msa0618520:five_prime_UTR 30.0%
ATATTTCAATTGTGAATCGG+TGG + chr4_2:69468654-69468673 None:intergenic 30.0%
! AAATATGGGTATGTGCTATT+GGG + chr4_2:69467998-69468017 None:intergenic 30.0%
AAAATATGGGTATGTGCTAT+TGG + chr4_2:69467999-69468018 None:intergenic 30.0%
TGCATAATACCACAATCATA+TGG - chr4_2:69468080-69468099 Msa0618520:exon 30.0%
TTAATGCAACCATATGATTG+TGG + chr4_2:69468092-69468111 None:intergenic 30.0%
! CTAGTAATTTTCAACCTAGA+AGG - chr4_2:69468131-69468150 Msa0618520:CDS 30.0%
AAATATTTGTAGCTCCTTCT+AGG + chr4_2:69468148-69468167 None:intergenic 30.0%
! TAACTTAATACCTCTAGCTT+GGG + chr4_2:69468357-69468376 None:intergenic 30.0%
ATAACTTAATACCTCTAGCT+TGG + chr4_2:69468358-69468377 None:intergenic 30.0%
GCAAAAGAAGAACATAATGT+GGG - chr4_2:69468585-69468604 Msa0618520:five_prime_UTR 30.0%
ATATTTCAATTGTGAATCGG+TGG + chr4_2:69468654-69468673 None:intergenic 30.0%
CCTCTACTATACGTGTATTT+GGG + chr4_2:69467934-69467953 None:intergenic 35.0%
ACCTCTACTATACGTGTATT+TGG + chr4_2:69467935-69467954 None:intergenic 35.0%
ATAGTAGAGGTTGACATTCA+TGG - chr4_2:69467944-69467963 Msa0618520:three_prime_UTR 35.0%
! AATATGGGTATGTGCTATTG+GGG + chr4_2:69467997-69468016 None:intergenic 35.0%
! AGCACATACCCATATTTTCT+AGG - chr4_2:69468001-69468020 Msa0618520:three_prime_UTR 35.0%
CTTGTCTGCCTAGAAAATAT+GGG + chr4_2:69468012-69468031 None:intergenic 35.0%
ACTTGTCTGCCTAGAAAATA+TGG + chr4_2:69468013-69468032 None:intergenic 35.0%
! TATTTTCTAGGCAGACAAGT+AGG - chr4_2:69468013-69468032 Msa0618520:three_prime_UTR 35.0%
TGCACAATAAGAGAGAGTAA+TGG + chr4_2:69468064-69468083 None:intergenic 35.0%
TATGGTTGCATTAAACTTCG+TGG - chr4_2:69468098-69468117 Msa0618520:CDS 35.0%
AAACAAACGTTTCCTAGTAG+TGG - chr4_2:69468304-69468323 Msa0618520:intron 35.0%
GGCAAAAGAAGAACATAATG+TGG - chr4_2:69468584-69468603 Msa0618520:five_prime_UTR 35.0%
!! GGGAGATGAAGTATTTTCAA+TGG - chr4_2:69468605-69468624 Msa0618520:five_prime_UTR 35.0%
CCTCTACTATACGTGTATTT+GGG + chr4_2:69467934-69467953 None:intergenic 35.0%
ACCTCTACTATACGTGTATT+TGG + chr4_2:69467935-69467954 None:intergenic 35.0%
ATAGTAGAGGTTGACATTCA+TGG - chr4_2:69467944-69467963 Msa0618520:three_prime_UTR 35.0%
! AATATGGGTATGTGCTATTG+GGG + chr4_2:69467997-69468016 None:intergenic 35.0%
! AGCACATACCCATATTTTCT+AGG - chr4_2:69468001-69468020 Msa0618520:three_prime_UTR 35.0%
CTTGTCTGCCTAGAAAATAT+GGG + chr4_2:69468012-69468031 None:intergenic 35.0%
ACTTGTCTGCCTAGAAAATA+TGG + chr4_2:69468013-69468032 None:intergenic 35.0%
! TATTTTCTAGGCAGACAAGT+AGG - chr4_2:69468013-69468032 Msa0618520:three_prime_UTR 35.0%
TGCACAATAAGAGAGAGTAA+TGG + chr4_2:69468064-69468083 None:intergenic 35.0%
TATGGTTGCATTAAACTTCG+TGG - chr4_2:69468098-69468117 Msa0618520:CDS 35.0%
AAACAAACGTTTCCTAGTAG+TGG - chr4_2:69468304-69468323 Msa0618520:intron 35.0%
GGCAAAAGAAGAACATAATG+TGG - chr4_2:69468584-69468603 Msa0618520:five_prime_UTR 35.0%
!! GGGAGATGAAGTATTTTCAA+TGG - chr4_2:69468605-69468624 Msa0618520:five_prime_UTR 35.0%
CCCAAATACACGTATAGTAG+AGG - chr4_2:69467931-69467950 Msa0618520:three_prime_UTR 40.0%
GCATTAAACTTCGTGGCAAT+TGG - chr4_2:69468105-69468124 Msa0618520:CDS 40.0%
GAAGGAATAGAACCACTACT+AGG + chr4_2:69468319-69468338 None:intergenic 40.0%
GGGTAGATATGAAACAGAGA+AGG + chr4_2:69468337-69468356 None:intergenic 40.0%
TTCATATCTACCCAAGCTAG+AGG - chr4_2:69468344-69468363 Msa0618520:intron 40.0%
CCCAAATACACGTATAGTAG+AGG - chr4_2:69467931-69467950 Msa0618520:three_prime_UTR 40.0%
GCATTAAACTTCGTGGCAAT+TGG - chr4_2:69468105-69468124 Msa0618520:CDS 40.0%
GAAGGAATAGAACCACTACT+AGG + chr4_2:69468319-69468338 None:intergenic 40.0%
GGGTAGATATGAAACAGAGA+AGG + chr4_2:69468337-69468356 None:intergenic 40.0%
TTCATATCTACCCAAGCTAG+AGG - chr4_2:69468344-69468363 Msa0618520:intron 40.0%
TGGATTACACTCCAGCAAGA+AGG - chr4_2:69468625-69468644 Msa0618520:five_prime_UTR 45.0%
TGGATTACACTCCAGCAAGA+AGG - chr4_2:69468625-69468644 Msa0618520:five_prime_UTR 45.0%
! GGGTATGTGCTATTGGGGAA+GGG + chr4_2:69467992-69468011 None:intergenic 50.0%
! TGGGTATGTGCTATTGGGGA+AGG + chr4_2:69467993-69468012 None:intergenic 50.0%
! GGGTATGTGCTATTGGGGAA+GGG + chr4_2:69467992-69468011 None:intergenic 50.0%
! TGGGTATGTGCTATTGGGGA+AGG + chr4_2:69467993-69468012 None:intergenic 50.0%
TGGTGCAGCACGAACTCTGA+AGG - chr4_2:69468506-69468525 Msa0618520:five_prime_UTR 55.0%
ATCGGTGGCTTCCTTCTTGC+TGG + chr4_2:69468639-69468658 None:intergenic 55.0%
TGGTGCAGCACGAACTCTGA+AGG - chr4_2:69468506-69468525 Msa0618520:five_prime_UTR 55.0%
ATCGGTGGCTTCCTTCTTGC+TGG + chr4_2:69468639-69468658 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 69467912 69468852 69467912 ID=Msa0618520;Name=Msa0618520
chr4_2 mRNA 69467912 69468852 69467912 ID=Msa0618520-mRNA-1;Parent=Msa0618520;Name=Msa0618520-mRNA-1;_AED=0.03;_eAED=0.03;_QI=378|1|1|1|1|1|2|184|76
chr4_2 exon 69467912 69468250 69467912 ID=Msa0618520-mRNA-1:exon:20079;Parent=Msa0618520-mRNA-1
chr4_2 exon 69468399 69468852 69468399 ID=Msa0618520-mRNA-1:exon:20078;Parent=Msa0618520-mRNA-1
chr4_2 five_prime_UTR 69468475 69468852 69468475 ID=Msa0618520-mRNA-1:five_prime_utr;Parent=Msa0618520-mRNA-1
chr4_2 CDS 69468399 69468474 69468399 ID=Msa0618520-mRNA-1:cds;Parent=Msa0618520-mRNA-1
chr4_2 CDS 69468096 69468250 69468096 ID=Msa0618520-mRNA-1:cds;Parent=Msa0618520-mRNA-1
chr4_2 three_prime_UTR 69467912 69468095 69467912 ID=Msa0618520-mRNA-1:three_prime_utr;Parent=Msa0618520-mRNA-1
Gene Sequence

>Msa0618520

ATGGCTATTGCACAAAACAAACGTTTCCTAGTAGTGGTTCTATTCCTTCTCTGTTTCATATCTACCCAAGCTAGAGCACGAACTCTGAAGGAAAAAAGCAATGATGTAATGAGTAATACTCATAATAAGGTAGATCATATGTTTAAGGCAAAAGAAGAACATAATGTGGGAGATGAAGTATTTTCAATGGATTACACTCCAGCAAGAAGGAAGCCACCGATTCACAATTGA

Protein sequence

>Msa0618520

MAIAQNKRFLVVVLFLLCFISTQARARTLKEKSNDVMSNTHNKVDHMFKAKEEHNVGDEVFSMDYTPARRKPPIHN*