AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0269830


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0269830 MtrunA17_Chr2g0319461 98.684 152 2 0 1 152 64 215 2.24e-107 305
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0269830 AT1G51100.1 76.821 151 34 1 2 152 62 211 8.31e-78 230

Find 26 sgRNAs with CRISPR-Local

Find 37 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCCAACCTATTTCAAAATT+TGG 0.094353 2_3:+878906 None:intergenic
TTCTCTATAGGAAATGTTTC+TGG 0.167892 2_3:+878993 None:intergenic
GAGGTTGATGGAAATGGATT+TGG 0.355148 2_3:-878667 Msa0269830:CDS
GAACTTATGAAGAAGGAATA+TGG 0.383069 2_3:-878813 Msa0269830:CDS
GTTGGAGGAACTTATGAAGA+AGG 0.476939 2_3:-878820 Msa0269830:CDS
TGGCTCGGCATTTGCAAGGT+CGG 0.477066 2_3:+878929 None:intergenic
CAACCTATTTCAAAATTTGG+TGG 0.478009 2_3:+878909 None:intergenic
AGGAAAAGTTGAGGAGAGAA+TGG 0.490855 2_3:-878712 Msa0269830:CDS
ATGAAGAGTTAAAATTCAAA+AGG 0.492536 2_3:+878551 None:intergenic
GAGAGATGAAGGAAAAGTTG+AGG 0.497620 2_3:-878721 Msa0269830:CDS
ACAGAACTGTTGGCAAAAGT+TGG 0.501386 2_3:-878786 Msa0269830:CDS
TATTTCAAAATTTGGTGGCT+CGG 0.505623 2_3:+878914 None:intergenic
TATGGTGAAAGCTTCTGTTA+AGG 0.539994 2_3:-878643 Msa0269830:CDS
AGGAAGATACTTTGAATGAG+AGG 0.541636 2_3:-878623 Msa0269830:CDS
ATATGGTTCAACAGAACTGT+TGG 0.553725 2_3:-878796 Msa0269830:CDS
GATGGAAATGGATTTGGCTA+TGG 0.555092 2_3:-878661 Msa0269830:CDS
CAGAGATAATCAGACAAAGA+AGG 0.559049 2_3:-878959 Msa0269830:CDS
TCAGCTACCACATACCCTAC+TGG 0.567101 2_3:+878855 None:intergenic
TGAGAAGCCAGTAGGGTATG+TGG 0.573091 2_3:-878862 Msa0269830:CDS
TTGGTGGCTCGGCATTTGCA+AGG 0.573166 2_3:+878925 None:intergenic
ATCAAGCTAAGGCTAGGTGC+AGG 0.575411 2_3:-878596 Msa0269830:CDS
ATTAACCTTGAGAAGCCAGT+AGG 0.578990 2_3:-878870 Msa0269830:CDS
TGAGAGGCTTGATCAAGCTA+AGG 0.591500 2_3:-878607 Msa0269830:CDS
GGCTTGATCAAGCTAAGGCT+AGG 0.619994 2_3:-878602 Msa0269830:CDS
TTAACCTTGAGAAGCCAGTA+GGG 0.629422 2_3:-878869 Msa0269830:CDS
CATACCCTACTGGCTTCTCA+AGG 0.644603 2_3:+878865 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TTCCAACCTATTTCAAAATT+TGG + chr2_3:878665-878684 None:intergenic 25.0%
!!! ATTTTGAAATAGGTTGGAAA+AGG - chr2_3:878666-878685 Msa0269830:CDS 25.0%
TTCTCTATAGGAAATGTTTC+TGG + chr2_3:878578-878597 None:intergenic 30.0%
! GATCTTCTTCTTTTCTCTAT+AGG + chr2_3:878590-878609 None:intergenic 30.0%
! TATTTCAAAATTTGGTGGCT+CGG + chr2_3:878657-878676 None:intergenic 30.0%
CAACCTATTTCAAAATTTGG+TGG + chr2_3:878662-878681 None:intergenic 30.0%
!!! CACCAAATTTTGAAATAGGT+TGG - chr2_3:878660-878679 Msa0269830:CDS 30.0%
GAACTTATGAAGAAGGAATA+TGG - chr2_3:878755-878774 Msa0269830:CDS 30.0%
!!! TTGAACTCTTTAGAGTTTTG+AGG - chr2_3:878882-878901 Msa0269830:CDS 30.0%
CAGAGATAATCAGACAAAGA+AGG - chr2_3:878609-878628 Msa0269830:CDS 35.0%
!!! GAGCCACCAAATTTTGAAAT+AGG - chr2_3:878656-878675 Msa0269830:CDS 35.0%
!!! GTATGTGGTAGCTGATTTTT+TGG - chr2_3:878721-878740 Msa0269830:CDS 35.0%
!!! AGCTGATTTTTTGGAGAAGT+TGG - chr2_3:878730-878749 Msa0269830:CDS 35.0%
!!! TGATTTTTTGGAGAAGTTGG+AGG - chr2_3:878733-878752 Msa0269830:CDS 35.0%
ATATGGTTCAACAGAACTGT+TGG - chr2_3:878772-878791 Msa0269830:CDS 35.0%
!! GCAGAAATTTTGAGAGATGA+AGG - chr2_3:878836-878855 Msa0269830:CDS 35.0%
!!! CTTTAGAGTTTTGAGGTTGA+TGG - chr2_3:878889-878908 Msa0269830:CDS 35.0%
!!! AGTTTTGAGGTTGATGGAAA+TGG - chr2_3:878895-878914 Msa0269830:CDS 35.0%
TATGGTGAAAGCTTCTGTTA+AGG - chr2_3:878925-878944 Msa0269830:CDS 35.0%
AGGAAGATACTTTGAATGAG+AGG - chr2_3:878945-878964 Msa0269830:CDS 35.0%
ATTAACCTTGAGAAGCCAGT+AGG - chr2_3:878698-878717 Msa0269830:CDS 40.0%
TTAACCTTGAGAAGCCAGTA+GGG - chr2_3:878699-878718 Msa0269830:CDS 40.0%
GTTGGAGGAACTTATGAAGA+AGG - chr2_3:878748-878767 Msa0269830:CDS 40.0%
ACAGAACTGTTGGCAAAAGT+TGG - chr2_3:878782-878801 Msa0269830:CDS 40.0%
GAGAGATGAAGGAAAAGTTG+AGG - chr2_3:878847-878866 Msa0269830:CDS 40.0%
AGGAAAAGTTGAGGAGAGAA+TGG - chr2_3:878856-878875 Msa0269830:CDS 40.0%
!! GAGGTTGATGGAAATGGATT+TGG - chr2_3:878901-878920 Msa0269830:CDS 40.0%
! GATGGAAATGGATTTGGCTA+TGG - chr2_3:878907-878926 Msa0269830:CDS 40.0%
!! GCATTTGCAAGGTCGGTTTT+CGG + chr2_3:878635-878654 None:intergenic 45.0%
TGAGAGGCTTGATCAAGCTA+AGG - chr2_3:878961-878980 Msa0269830:CDS 45.0%
!! CATACCCTACTGGCTTCTCA+AGG + chr2_3:878706-878725 None:intergenic 50.0%
TGAGAAGCCAGTAGGGTATG+TGG - chr2_3:878706-878725 Msa0269830:CDS 50.0%
TCAGCTACCACATACCCTAC+TGG + chr2_3:878716-878735 None:intergenic 50.0%
GGCTTGATCAAGCTAAGGCT+AGG - chr2_3:878966-878985 Msa0269830:CDS 50.0%
ATCAAGCTAAGGCTAGGTGC+AGG - chr2_3:878972-878991 Msa0269830:CDS 50.0%
! TGGCTCGGCATTTGCAAGGT+CGG + chr2_3:878642-878661 None:intergenic 55.0%
! TTGGTGGCTCGGCATTTGCA+AGG + chr2_3:878646-878665 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr2_3 gene 878566 879024 878566 ID=Msa0269830;Name=Msa0269830
chr2_3 mRNA 878566 879024 878566 ID=Msa0269830-mRNA-1;Parent=Msa0269830;Name=Msa0269830-mRNA-1;_AED=0.15;_eAED=0.15;_QI=0|-1|0|1|-1|1|1|0|152
chr2_3 exon 878566 879024 878566 ID=Msa0269830-mRNA-1:exon:461;Parent=Msa0269830-mRNA-1
chr2_3 CDS 878566 879024 878566 ID=Msa0269830-mRNA-1:cds;Parent=Msa0269830-mRNA-1
Gene Sequence

>Msa0269830

ATGAACAGTCCAGAAACATTTCCTATAGAGAAAAGAAGAAGATCAGAGATAATCAGACAAAGAAGGCCGAAAACCGACCTTGCAAATGCCGAGCCACCAAATTTTGAAATAGGTTGGAAAAGGACAAAAGAGATTAACCTTGAGAAGCCAGTAGGGTATGTGGTAGCTGATTTTTTGGAGAAGTTGGAGGAACTTATGAAGAAGGAATATGGTTCAACAGAACTGTTGGCAAAAGTTGGTGAAATTGTTGCTGAAAGAGCAAGAGAAGAAGCAGAAATTTTGAGAGATGAAGGAAAAGTTGAGGAGAGAATGGTTGTTGAACTCTTTAGAGTTTTGAGGTTGATGGAAATGGATTTGGCTATGGTGAAAGCTTCTGTTAAGGAAGATACTTTGAATGAGAGGCTTGATCAAGCTAAGGCTAGGTGCAGGCAAGCTATACTTGTTTGTTATTCCTTTTGA

Protein sequence

>Msa0269830

MNSPETFPIEKRRRSEIIRQRRPKTDLANAEPPNFEIGWKRTKEINLEKPVGYVVADFLEKLEELMKKEYGSTELLAKVGEIVAERAREEAEILRDEGKVEERMVVELFRVLRLMEMDLAMVKASVKEDTLNERLDQAKARCRQAILVCYSF*