AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1385620


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1385620 MtrunA17_Chr1g0155441 95.620 137 3 1 1 134 1 137 7.49e-94 266
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1385620 AT1G75350.1 60.150 133 41 2 1 121 1 133 3.87e-53 164

Find 41 sgRNAs with CRISPR-Local

Find 136 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATCAACCACATACTCTTTC+TGG 0.120517 tig0020764:-50649 None:intergenic
TTAGCATCTTCGTAGAATTT+TGG 0.129378 tig0020764:-50584 None:intergenic
ACTCTGAGCCAATGTGATTT+TGG 0.193088 tig0020764:+51037 Msa1385620:three_prime_UTR
GGAAAACGAAAACTACATTT+TGG 0.218245 tig0020764:+51058 Msa1385620:three_prime_UTR
ATTGCGTAAATGCAGATAAT+AGG 0.242567 tig0020764:-51136 None:intergenic
ATGGAGATTCCTGTGCTTAA+AGG 0.247138 tig0020764:+50779 Msa1385620:CDS
CGGTGAATTGTCGCAGATTA+TGG 0.250630 tig0020764:+50760 Msa1385620:CDS
ATGAGAAACAAATATGGTTT+TGG 0.267437 tig0020764:+51109 Msa1385620:three_prime_UTR
TTCTCATTTAAGTGTATGTT+TGG 0.298488 tig0020764:-51093 None:intergenic
AGGTAACAGGTCTGCTCTTA+TGG 0.321423 tig0020764:+50700 Msa1385620:CDS
GACCTGTTACCTAGGTAAAA+TGG 0.333258 tig0020764:-50689 None:intergenic
GAAGAGATTTAATTCATGTT+TGG 0.358930 tig0020764:+50991 Msa1385620:three_prime_UTR
ACTTAAATGAGAAACAAATA+TGG 0.366380 tig0020764:+51103 Msa1385620:three_prime_UTR
CAATCATGAATCTCGACTAT+TGG 0.367693 tig0020764:+51155 Msa1385620:three_prime_UTR
TTAATCCCTTTACGTCTAGA+AGG 0.369196 tig0020764:-50815 None:intergenic
GGAATTGTAATTTGATTGTA+TGG 0.374281 tig0020764:+50875 Msa1385620:three_prime_UTR
TGTTTGGATTGTTGCAAGAT+TGG 0.408788 tig0020764:+51007 Msa1385620:three_prime_UTR
TTATTCCTTCTAGACGTAAA+GGG 0.415844 tig0020764:+50810 Msa1385620:CDS
ATCAACCACATACTCTTTCT+GGG 0.433365 tig0020764:-50648 None:intergenic
ATAACCAATACCTTTGTTCA+AGG 0.436471 tig0020764:+50145 Msa1385620:CDS
GTTATTCCTTCTAGACGTAA+AGG 0.445368 tig0020764:+50809 Msa1385620:CDS
TTGCGTAAATGCAGATAATA+GGG 0.459388 tig0020764:-51135 None:intergenic
TATGTGGTTGATGTTTGGTC+TGG 0.461863 tig0020764:+50659 Msa1385620:CDS
TCTTATGGTGAGTGATGATC+AGG 0.475882 tig0020764:+50715 Msa1385620:CDS
AAGAGTATGTGGTTGATGTT+TGG 0.479372 tig0020764:+50654 Msa1385620:CDS
GAGAAGTTTCGTAAGAAGTT+CGG 0.485181 tig0020764:+50740 Msa1385620:CDS
ATGAATCTCGACTATTGGAT+TGG 0.494793 tig0020764:+51160 Msa1385620:three_prime_UTR
AACGAGCTTGTGATGACAAC+TGG 0.499125 tig0020764:+50620 Msa1385620:CDS
ATGTGGTTGATGTTTGGTCT+GGG 0.499973 tig0020764:+50660 Msa1385620:CDS
TTTGTGGGAAGTGGAAGGAA+TGG 0.505762 tig0020764:-50172 None:intergenic
TAAGAGCAGACCTGTTACCT+AGG 0.535799 tig0020764:-50697 None:intergenic
AAAGGGATTAAAAGTGGTGG+AGG 0.538533 tig0020764:+50827 Msa1385620:CDS
AAAATTCTACGAAGATGCTA+AGG 0.547901 tig0020764:+50586 Msa1385620:CDS
ACAATCTCACCTTTAAGCAC+AGG 0.575557 tig0020764:-50788 None:intergenic
AGACGTAAAGGGATTAAAAG+TGG 0.579688 tig0020764:+50821 Msa1385620:CDS
CGTAAAGGGATTAAAAGTGG+TGG 0.606986 tig0020764:+50824 Msa1385620:CDS
GTTTGGTTGCAGAATCAACA+AGG 0.616245 tig0020764:+50512 Msa1385620:intron
AAGGGATTAAAAGTGGTGGA+GGG 0.644540 tig0020764:+50828 Msa1385620:CDS
TGTTACCTAGGTAAAATGGA+TGG 0.664203 tig0020764:-50685 None:intergenic
TGGAACCCAGAAAGAGTATG+TGG 0.674951 tig0020764:+50643 Msa1385620:CDS
GAGCTTGTGATGACAACTGG+TGG 0.675964 tig0020764:+50623 Msa1385620:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTATTTAATTTCCTAAAT+AGG + tig0020764:50314-50333 Msa1385620:intron 10.0%
!!! ATTTATTTAATTTCCTAAAT+AGG + tig0020764:50314-50333 Msa1385620:intron 10.0%
!! ATATTCTAATAGAAATGATA+AGG - tig0020764:50224-50243 None:intergenic 15.0%
!! GAAACAATAATATGAATAAT+TGG - tig0020764:50440-50459 None:intergenic 15.0%
!! ATATTCTAATAGAAATGATA+AGG - tig0020764:50224-50243 None:intergenic 15.0%
!! GAAACAATAATATGAATAAT+TGG - tig0020764:50440-50459 None:intergenic 15.0%
!! AAATGATATCAATACAATCA+GGG + tig0020764:50364-50383 Msa1385620:intron 20.0%
!! ATATGTCTATATTAGAATCA+GGG - tig0020764:50406-50425 None:intergenic 20.0%
!! AATATGTCTATATTAGAATC+AGG - tig0020764:50407-50426 None:intergenic 20.0%
!! AACAAAACAAAAAAACATGT+TGG - tig0020764:50476-50495 None:intergenic 20.0%
!! ACTTAAATGAGAAACAAATA+TGG + tig0020764:51103-51122 Msa1385620:three_prime_UTR 20.0%
!! AAATGATATCAATACAATCA+GGG + tig0020764:50364-50383 Msa1385620:intron 20.0%
!! ATATGTCTATATTAGAATCA+GGG - tig0020764:50406-50425 None:intergenic 20.0%
!! AATATGTCTATATTAGAATC+AGG - tig0020764:50407-50426 None:intergenic 20.0%
!! AACAAAACAAAAAAACATGT+TGG - tig0020764:50476-50495 None:intergenic 20.0%
!! ACTTAAATGAGAAACAAATA+TGG + tig0020764:51103-51122 Msa1385620:three_prime_UTR 20.0%
! CTAATCTCATCTGAAAAAAA+TGG + tig0020764:50114-50133 Msa1385620:exon 25.0%
! TAATAGAAATGATAAGGAAG+TGG - tig0020764:50218-50237 None:intergenic 25.0%
! AACTGTTTACAAACCTATTT+AGG - tig0020764:50330-50349 None:intergenic 25.0%
! CAAATGATATCAATACAATC+AGG + tig0020764:50363-50382 Msa1385620:intron 25.0%
! GGAATTGTAATTTGATTGTA+TGG + tig0020764:50875-50894 Msa1385620:three_prime_UTR 25.0%
! GAAGAGATTTAATTCATGTT+TGG + tig0020764:50991-51010 Msa1385620:three_prime_UTR 25.0%
! TTCTCATTTAAGTGTATGTT+TGG - tig0020764:51096-51115 None:intergenic 25.0%
!! ATGAGAAACAAATATGGTTT+TGG + tig0020764:51109-51128 Msa1385620:three_prime_UTR 25.0%
! CTAATCTCATCTGAAAAAAA+TGG + tig0020764:50114-50133 Msa1385620:exon 25.0%
! TAATAGAAATGATAAGGAAG+TGG - tig0020764:50218-50237 None:intergenic 25.0%
! AACTGTTTACAAACCTATTT+AGG - tig0020764:50330-50349 None:intergenic 25.0%
! CAAATGATATCAATACAATC+AGG + tig0020764:50363-50382 Msa1385620:intron 25.0%
! GGAATTGTAATTTGATTGTA+TGG + tig0020764:50875-50894 Msa1385620:three_prime_UTR 25.0%
! GAAGAGATTTAATTCATGTT+TGG + tig0020764:50991-51010 Msa1385620:three_prime_UTR 25.0%
! TTCTCATTTAAGTGTATGTT+TGG - tig0020764:51096-51115 None:intergenic 25.0%
!! ATGAGAAACAAATATGGTTT+TGG + tig0020764:51109-51128 Msa1385620:three_prime_UTR 25.0%
ATAACCAATACCTTTGTTCA+AGG + tig0020764:50145-50164 Msa1385620:CDS 30.0%
!! TTTTCCTTGAACAAAGGTAT+TGG - tig0020764:50152-50171 None:intergenic 30.0%
!!! TACTACAGTACGTTTTTTGT+GGG - tig0020764:50190-50209 None:intergenic 30.0%
!!! TTACTACAGTACGTTTTTTG+TGG - tig0020764:50191-50210 None:intergenic 30.0%
TTCTCATGAATTGTGATTCA+TGG - tig0020764:50295-50314 None:intergenic 30.0%
! TTTTTGTGTGTGTTTGTGTT+TGG + tig0020764:50495-50514 Msa1385620:intron 30.0%
GGAAAAAAAGTGAGCAATTT+CGG + tig0020764:50533-50552 Msa1385620:CDS 30.0%
! TAGCATCTTCGTAGAATTTT+GGG - tig0020764:50586-50605 None:intergenic 30.0%
! TTAGCATCTTCGTAGAATTT+TGG - tig0020764:50587-50606 None:intergenic 30.0%
AAAATTCTACGAAGATGCTA+AGG + tig0020764:50586-50605 Msa1385620:CDS 30.0%
TTATTCCTTCTAGACGTAAA+GGG + tig0020764:50810-50829 Msa1385620:CDS 30.0%
! TTCGTTTTCCAAAATCACAT+TGG - tig0020764:51048-51067 None:intergenic 30.0%
! GGAAAACGAAAACTACATTT+TGG + tig0020764:51058-51077 Msa1385620:three_prime_UTR 30.0%
TTGCGTAAATGCAGATAATA+GGG - tig0020764:51138-51157 None:intergenic 30.0%
ATTGCGTAAATGCAGATAAT+AGG - tig0020764:51139-51158 None:intergenic 30.0%
ATAACCAATACCTTTGTTCA+AGG + tig0020764:50145-50164 Msa1385620:CDS 30.0%
!! TTTTCCTTGAACAAAGGTAT+TGG - tig0020764:50152-50171 None:intergenic 30.0%
!!! TACTACAGTACGTTTTTTGT+GGG - tig0020764:50190-50209 None:intergenic 30.0%
!!! TTACTACAGTACGTTTTTTG+TGG - tig0020764:50191-50210 None:intergenic 30.0%
TTCTCATGAATTGTGATTCA+TGG - tig0020764:50295-50314 None:intergenic 30.0%
! TTTTTGTGTGTGTTTGTGTT+TGG + tig0020764:50495-50514 Msa1385620:intron 30.0%
GGAAAAAAAGTGAGCAATTT+CGG + tig0020764:50533-50552 Msa1385620:CDS 30.0%
! TAGCATCTTCGTAGAATTTT+GGG - tig0020764:50586-50605 None:intergenic 30.0%
! TTAGCATCTTCGTAGAATTT+TGG - tig0020764:50587-50606 None:intergenic 30.0%
AAAATTCTACGAAGATGCTA+AGG + tig0020764:50586-50605 Msa1385620:CDS 30.0%
TTATTCCTTCTAGACGTAAA+GGG + tig0020764:50810-50829 Msa1385620:CDS 30.0%
! TTCGTTTTCCAAAATCACAT+TGG - tig0020764:51048-51067 None:intergenic 30.0%
! GGAAAACGAAAACTACATTT+TGG + tig0020764:51058-51077 Msa1385620:three_prime_UTR 30.0%
TTGCGTAAATGCAGATAATA+GGG - tig0020764:51138-51157 None:intergenic 30.0%
ATTGCGTAAATGCAGATAAT+AGG - tig0020764:51139-51158 None:intergenic 30.0%
! GAATGGTTTTCCTTGAACAA+AGG - tig0020764:50158-50177 None:intergenic 35.0%
AGAAATGATAAGGAAGTGGT+TGG - tig0020764:50214-50233 None:intergenic 35.0%
TGTGATTCATGGCTAATGAA+TGG - tig0020764:50284-50303 None:intergenic 35.0%
ATCAACCACATACTCTTTCT+GGG - tig0020764:50651-50670 None:intergenic 35.0%
! AAGAGTATGTGGTTGATGTT+TGG + tig0020764:50654-50673 Msa1385620:CDS 35.0%
TGTTACCTAGGTAAAATGGA+TGG - tig0020764:50688-50707 None:intergenic 35.0%
! ATCCATTTTACCTAGGTAAC+AGG + tig0020764:50687-50706 Msa1385620:CDS 35.0%
GAGAAGTTTCGTAAGAAGTT+CGG + tig0020764:50740-50759 Msa1385620:CDS 35.0%
GTTATTCCTTCTAGACGTAA+AGG + tig0020764:50809-50828 Msa1385620:CDS 35.0%
TTAATCCCTTTACGTCTAGA+AGG - tig0020764:50818-50837 None:intergenic 35.0%
AGACGTAAAGGGATTAAAAG+TGG + tig0020764:50821-50840 Msa1385620:CDS 35.0%
! AAGAAGTGAGTGTTTTGTGT+TGG + tig0020764:50854-50873 Msa1385620:exon 35.0%
TGTTTGGATTGTTGCAAGAT+TGG + tig0020764:51007-51026 Msa1385620:three_prime_UTR 35.0%
CAATCATGAATCTCGACTAT+TGG + tig0020764:51155-51174 Msa1385620:three_prime_UTR 35.0%
ATGAATCTCGACTATTGGAT+TGG + tig0020764:51160-51179 Msa1385620:three_prime_UTR 35.0%
! GAATGGTTTTCCTTGAACAA+AGG - tig0020764:50158-50177 None:intergenic 35.0%
AGAAATGATAAGGAAGTGGT+TGG - tig0020764:50214-50233 None:intergenic 35.0%
TGTGATTCATGGCTAATGAA+TGG - tig0020764:50284-50303 None:intergenic 35.0%
ATCAACCACATACTCTTTCT+GGG - tig0020764:50651-50670 None:intergenic 35.0%
! AAGAGTATGTGGTTGATGTT+TGG + tig0020764:50654-50673 Msa1385620:CDS 35.0%
TGTTACCTAGGTAAAATGGA+TGG - tig0020764:50688-50707 None:intergenic 35.0%
! ATCCATTTTACCTAGGTAAC+AGG + tig0020764:50687-50706 Msa1385620:CDS 35.0%
GAGAAGTTTCGTAAGAAGTT+CGG + tig0020764:50740-50759 Msa1385620:CDS 35.0%
GTTATTCCTTCTAGACGTAA+AGG + tig0020764:50809-50828 Msa1385620:CDS 35.0%
TTAATCCCTTTACGTCTAGA+AGG - tig0020764:50818-50837 None:intergenic 35.0%
AGACGTAAAGGGATTAAAAG+TGG + tig0020764:50821-50840 Msa1385620:CDS 35.0%
! AAGAAGTGAGTGTTTTGTGT+TGG + tig0020764:50854-50873 Msa1385620:exon 35.0%
TGTTTGGATTGTTGCAAGAT+TGG + tig0020764:51007-51026 Msa1385620:three_prime_UTR 35.0%
CAATCATGAATCTCGACTAT+TGG + tig0020764:51155-51174 Msa1385620:three_prime_UTR 35.0%
ATGAATCTCGACTATTGGAT+TGG + tig0020764:51160-51179 Msa1385620:three_prime_UTR 35.0%
!!! AGTACGTTTTTTGTGGGAAG+TGG - tig0020764:50184-50203 None:intergenic 40.0%
GTTTGGTTGCAGAATCAACA+AGG + tig0020764:50512-50531 Msa1385620:intron 40.0%
CATCAACCACATACTCTTTC+TGG - tig0020764:50652-50671 None:intergenic 40.0%
! TATGTGGTTGATGTTTGGTC+TGG + tig0020764:50659-50678 Msa1385620:CDS 40.0%
! ATGTGGTTGATGTTTGGTCT+GGG + tig0020764:50660-50679 Msa1385620:CDS 40.0%
GACCTGTTACCTAGGTAAAA+TGG - tig0020764:50692-50711 None:intergenic 40.0%
TCTTATGGTGAGTGATGATC+AGG + tig0020764:50715-50734 Msa1385620:CDS 40.0%
ATGGAGATTCCTGTGCTTAA+AGG + tig0020764:50779-50798 Msa1385620:CDS 40.0%
ACAATCTCACCTTTAAGCAC+AGG - tig0020764:50791-50810 None:intergenic 40.0%
CGTAAAGGGATTAAAAGTGG+TGG + tig0020764:50824-50843 Msa1385620:CDS 40.0%
AAAGGGATTAAAAGTGGTGG+AGG + tig0020764:50827-50846 Msa1385620:CDS 40.0%
! AAGGGATTAAAAGTGGTGGA+GGG + tig0020764:50828-50847 Msa1385620:CDS 40.0%
! ACTCTGAGCCAATGTGATTT+TGG + tig0020764:51037-51056 Msa1385620:three_prime_UTR 40.0%
!!! AGTACGTTTTTTGTGGGAAG+TGG - tig0020764:50184-50203 None:intergenic 40.0%
GTTTGGTTGCAGAATCAACA+AGG + tig0020764:50512-50531 Msa1385620:intron 40.0%
CATCAACCACATACTCTTTC+TGG - tig0020764:50652-50671 None:intergenic 40.0%
! TATGTGGTTGATGTTTGGTC+TGG + tig0020764:50659-50678 Msa1385620:CDS 40.0%
! ATGTGGTTGATGTTTGGTCT+GGG + tig0020764:50660-50679 Msa1385620:CDS 40.0%
GACCTGTTACCTAGGTAAAA+TGG - tig0020764:50692-50711 None:intergenic 40.0%
TCTTATGGTGAGTGATGATC+AGG + tig0020764:50715-50734 Msa1385620:CDS 40.0%
ATGGAGATTCCTGTGCTTAA+AGG + tig0020764:50779-50798 Msa1385620:CDS 40.0%
ACAATCTCACCTTTAAGCAC+AGG - tig0020764:50791-50810 None:intergenic 40.0%
CGTAAAGGGATTAAAAGTGG+TGG + tig0020764:50824-50843 Msa1385620:CDS 40.0%
AAAGGGATTAAAAGTGGTGG+AGG + tig0020764:50827-50846 Msa1385620:CDS 40.0%
! AAGGGATTAAAAGTGGTGGA+GGG + tig0020764:50828-50847 Msa1385620:CDS 40.0%
! ACTCTGAGCCAATGTGATTT+TGG + tig0020764:51037-51056 Msa1385620:three_prime_UTR 40.0%
TTTGTGGGAAGTGGAAGGAA+TGG - tig0020764:50175-50194 None:intergenic 45.0%
!!! CGTTTTTTGTGGGAAGTGGA+AGG - tig0020764:50180-50199 None:intergenic 45.0%
AACGAGCTTGTGATGACAAC+TGG + tig0020764:50620-50639 Msa1385620:CDS 45.0%
! TGGAACCCAGAAAGAGTATG+TGG + tig0020764:50643-50662 Msa1385620:CDS 45.0%
! GGGAACCATCCATTTTACCT+AGG + tig0020764:50680-50699 Msa1385620:CDS 45.0%
TAAGAGCAGACCTGTTACCT+AGG - tig0020764:50700-50719 None:intergenic 45.0%
AGGTAACAGGTCTGCTCTTA+TGG + tig0020764:50700-50719 Msa1385620:CDS 45.0%
CGGTGAATTGTCGCAGATTA+TGG + tig0020764:50760-50779 Msa1385620:CDS 45.0%
TTTGTGGGAAGTGGAAGGAA+TGG - tig0020764:50175-50194 None:intergenic 45.0%
!!! CGTTTTTTGTGGGAAGTGGA+AGG - tig0020764:50180-50199 None:intergenic 45.0%
AACGAGCTTGTGATGACAAC+TGG + tig0020764:50620-50639 Msa1385620:CDS 45.0%
! TGGAACCCAGAAAGAGTATG+TGG + tig0020764:50643-50662 Msa1385620:CDS 45.0%
! GGGAACCATCCATTTTACCT+AGG + tig0020764:50680-50699 Msa1385620:CDS 45.0%
TAAGAGCAGACCTGTTACCT+AGG - tig0020764:50700-50719 None:intergenic 45.0%
AGGTAACAGGTCTGCTCTTA+TGG + tig0020764:50700-50719 Msa1385620:CDS 45.0%
CGGTGAATTGTCGCAGATTA+TGG + tig0020764:50760-50779 Msa1385620:CDS 45.0%
GAGCTTGTGATGACAACTGG+TGG + tig0020764:50623-50642 Msa1385620:CDS 50.0%
GAGCTTGTGATGACAACTGG+TGG + tig0020764:50623-50642 Msa1385620:CDS 50.0%
Chromosome Type Strat End Strand Name
tig0020764 gene 50095 51223 50095 ID=Msa1385620;Name=Msa1385620
tig0020764 mRNA 50095 51223 50095 ID=Msa1385620-mRNA-1;Parent=Msa1385620;Name=Msa1385620-mRNA-1;_AED=0.01;_eAED=0.01;_QI=38|1|1|1|1|1|2|361|134
tig0020764 exon 50095 50198 50095 ID=Msa1385620-mRNA-1:exon:9657;Parent=Msa1385620-mRNA-1
tig0020764 exon 50524 51223 50524 ID=Msa1385620-mRNA-1:exon:9658;Parent=Msa1385620-mRNA-1
tig0020764 five_prime_UTR 50095 50132 50095 ID=Msa1385620-mRNA-1:five_prime_utr;Parent=Msa1385620-mRNA-1
tig0020764 CDS 50133 50198 50133 ID=Msa1385620-mRNA-1:cds;Parent=Msa1385620-mRNA-1
tig0020764 CDS 50524 50862 50524 ID=Msa1385620-mRNA-1:cds;Parent=Msa1385620-mRNA-1
tig0020764 three_prime_UTR 50863 51223 50863 ID=Msa1385620-mRNA-1:three_prime_utr;Parent=Msa1385620-mRNA-1
Gene Sequence

>Msa1385620

ATGGCGCAGTGCATAACCAATACCTTTGTTCAAGGAAAACCATTCCTTCCACTTCCCACAAAAAACAATCAACAAGGAAAAAAAGTGAGCAATTTCGGAGTGTATTGCAAGAAGAAAGACATACACCCAAAATTCTACGAAGATGCTAAGGTTTACTGTAACAACGAGCTTGTGATGACAACTGGTGGAACCCAGAAAGAGTATGTGGTTGATGTTTGGTCTGGGAACCATCCATTTTACCTAGGTAACAGGTCTGCTCTTATGGTGAGTGATGATCAGGTAGAGAAGTTTCGTAAGAAGTTCGGTGAATTGTCGCAGATTATGGAGATTCCTGTGCTTAAAGGTGAGATTGTTATTCCTTCTAGACGTAAAGGGATTAAAAGTGGTGGAGGGAAGAAGAAGTGA

Protein sequence

>Msa1385620

MAQCITNTFVQGKPFLPLPTKNNQQGKKVSNFGVYCKKKDIHPKFYEDAKVYCNNELVMTTGGTQKEYVVDVWSGNHPFYLGNRSALMVSDDQVEKFRKKFGELSQIMEIPVLKGEIVIPSRRKGIKSGGGKKK*