AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0636510


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0636510 MtrunA17_Chr1g0201251 79.070 43 9 0 1 43 86 128 8.18e-19 76.3
Msa0636510 MtrunA17_Chr6g0466891 72.093 43 12 0 1 43 86 128 2.29e-17 72.4
Msa0636510 MtrunA17_Chr3g0090241 74.419 43 11 0 1 43 86 128 6.44e-16 67.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0636510 AT1G07140.1 56.452 62 24 1 1 59 89 150 6.11e-16 68.9
Msa0636510 AT2G30060.1 53.226 62 26 1 1 59 91 152 1.24e-14 65.5
Msa0636510 AT5G58590.1 53.226 62 26 1 1 59 88 149 5.41e-14 63.9

Find 26 sgRNAs with CRISPR-Local

Find 112 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACAACCGAGCCGTACTAAAT+TGG 0.252478 4_3:+27051065 None:intergenic
TGGGAGCTTCTATGTTGTTT+TGG 0.283216 4_3:-27050256 Msa0636510:CDS
AGCGCAGATCTTGAGGGTTT+TGG 0.290367 4_3:+27050939 None:intergenic
TTAACAGAGTTTCAAGGTTC+TGG 0.300728 4_3:-27050291 Msa0636510:CDS
TGTGGGTGCAGCTGCACTTT+TGG 0.304625 4_3:-27050325 Msa0636510:intron
ATAAGGTTACTTGAAAAGTT+AGG 0.336456 4_3:-27050978 Msa0636510:five_prime_UTR
CGATGGAGTTCTTAAGCATA+AGG 0.412330 4_3:-27050995 Msa0636510:five_prime_UTR
GGTTCTGGTGTGTTTATGCT+TGG 0.433702 4_3:-27050276 Msa0636510:CDS
GAATTGAGAAATCGTGTGTT+TGG 0.437554 4_3:-27050773 Msa0636510:CDS
GAAAAGTTAGGCTTCTTATG+AGG 0.446917 4_3:-27050966 Msa0636510:exon
TAACTTTATGAGTTCTTGAC+TGG 0.460076 4_3:-27051020 Msa0636510:five_prime_UTR
AATCGTGTGTTTGGCATGCT+AGG 0.466273 4_3:-27050764 Msa0636510:CDS
GTTCTGGTGTGTTTATGCTT+GGG 0.479825 4_3:-27050275 Msa0636510:CDS
ACGATTAGCGCAGATCTTGA+GGG 0.489998 4_3:+27050933 None:intergenic
TTCTCTTGCATACTCATCAT+AGG 0.492591 4_3:+27050801 None:intergenic
CAGCGGTTAACAGAGTTTCA+AGG 0.502174 4_3:-27050297 Msa0636510:CDS
GACGATTAGCGCAGATCTTG+AGG 0.502484 4_3:+27050932 None:intergenic
CATGCTAGGGATTCTGCTGA+TGG 0.533927 4_3:-27050750 Msa0636510:intron
ATCGTGTGTTTGGCATGCTA+GGG 0.537370 4_3:-27050763 Msa0636510:CDS
ATGAGTATGCAAGAGAATGT+TGG 0.553283 4_3:-27050795 Msa0636510:CDS
TGAGTTCTTGACTGGTACGA+TGG 0.554894 4_3:-27051012 Msa0636510:five_prime_UTR
AGCAAAGATATTAGCTGCGG+AGG 0.590198 4_3:-27051090 None:intergenic
GCGGAGGATCCAATTTAGTA+CGG 0.590877 4_3:-27051074 Msa0636510:five_prime_UTR
GGATCCAATTTAGTACGGCT+CGG 0.591535 4_3:-27051069 Msa0636510:five_prime_UTR
AGCAGCAAAGATATTAGCTG+CGG 0.638123 4_3:-27051093 None:intergenic
CCAAGAGGTAGGCATCAGCA+CGG 0.700637 4_3:+27050231 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGTTAGATGATGTTTTATTT+TGG - chr4_3:27050726-27050745 Msa0636510:intron 20.0%
!!! GTTAGATGATGTTTTATTTT+GGG - chr4_3:27050727-27050746 Msa0636510:intron 20.0%
!!! TTAGATGATGTTTTATTTTG+GGG - chr4_3:27050728-27050747 Msa0636510:intron 20.0%
!!! TGTTAGATGATGTTTTATTT+TGG - chr4_3:27050726-27050745 Msa0636510:intron 20.0%
!!! GTTAGATGATGTTTTATTTT+GGG - chr4_3:27050727-27050746 Msa0636510:intron 20.0%
!!! TTAGATGATGTTTTATTTTG+GGG - chr4_3:27050728-27050747 Msa0636510:intron 20.0%
! ATAAGGTTACTTGAAAAGTT+AGG - chr4_3:27050351-27050370 Msa0636510:intron 25.0%
!!! TTTTGTGATTTTGATTGTTG+TGG - chr4_3:27050482-27050501 Msa0636510:intron 25.0%
!!! CAGATTTTTTGTAGTTAGAT+TGG - chr4_3:27050680-27050699 Msa0636510:intron 25.0%
!! ATTGGTTTAGATGAATATTG+TGG - chr4_3:27050698-27050717 Msa0636510:intron 25.0%
! TTGGTTTAGATGAATATTGT+GGG - chr4_3:27050699-27050718 Msa0636510:intron 25.0%
!!! TAGATGATGTTTTATTTTGG+GGG - chr4_3:27050729-27050748 Msa0636510:intron 25.0%
!! TATTTGGTAATCAAAGAGTT+AGG - chr4_3:27050900-27050919 Msa0636510:intron 25.0%
! ATAAGGTTACTTGAAAAGTT+AGG - chr4_3:27050351-27050370 Msa0636510:intron 25.0%
!!! TTTTGTGATTTTGATTGTTG+TGG - chr4_3:27050482-27050501 Msa0636510:intron 25.0%
!!! CAGATTTTTTGTAGTTAGAT+TGG - chr4_3:27050680-27050699 Msa0636510:intron 25.0%
!! ATTGGTTTAGATGAATATTG+TGG - chr4_3:27050698-27050717 Msa0636510:intron 25.0%
! TTGGTTTAGATGAATATTGT+GGG - chr4_3:27050699-27050718 Msa0636510:intron 25.0%
!!! TAGATGATGTTTTATTTTGG+GGG - chr4_3:27050729-27050748 Msa0636510:intron 25.0%
!! TATTTGGTAATCAAAGAGTT+AGG - chr4_3:27050900-27050919 Msa0636510:intron 25.0%
TAACTTTATGAGTTCTTGAC+TGG - chr4_3:27050309-27050328 Msa0636510:CDS 30.0%
TGATAACTATCTTGTTAGAG+TGG - chr4_3:27050852-27050871 Msa0636510:intron 30.0%
TAACTTTATGAGTTCTTGAC+TGG - chr4_3:27050309-27050328 Msa0636510:CDS 30.0%
TGATAACTATCTTGTTAGAG+TGG - chr4_3:27050852-27050871 Msa0636510:intron 30.0%
GAAAAGTTAGGCTTCTTATG+AGG - chr4_3:27050363-27050382 Msa0636510:intron 35.0%
TTCTCTTGCATACTCATCAT+AGG + chr4_3:27050531-27050550 None:intergenic 35.0%
ATGAGTATGCAAGAGAATGT+TGG - chr4_3:27050534-27050553 Msa0636510:intron 35.0%
GAATTGAGAAATCGTGTGTT+TGG - chr4_3:27050556-27050575 Msa0636510:intron 35.0%
! AGGATGCACTTTTCTGTTTT+CGG - chr4_3:27050611-27050630 Msa0636510:intron 35.0%
ACTCAACAACTATTGACATG+TGG - chr4_3:27050797-27050816 Msa0636510:CDS 35.0%
! TTGGTAATCAAAGAGTTAGG+TGG - chr4_3:27050903-27050922 Msa0636510:intron 35.0%
!!! TGTTAGAGTTTTTGCTGTTG+TGG - chr4_3:27050986-27051005 Msa0636510:five_prime_UTR 35.0%
!!! GTTAGAGTTTTTGCTGTTGT+GGG - chr4_3:27050987-27051006 Msa0636510:five_prime_UTR 35.0%
TTAACAGAGTTTCAAGGTTC+TGG - chr4_3:27051038-27051057 Msa0636510:five_prime_UTR 35.0%
GAAAAGTTAGGCTTCTTATG+AGG - chr4_3:27050363-27050382 Msa0636510:intron 35.0%
TTCTCTTGCATACTCATCAT+AGG + chr4_3:27050531-27050550 None:intergenic 35.0%
ATGAGTATGCAAGAGAATGT+TGG - chr4_3:27050534-27050553 Msa0636510:intron 35.0%
GAATTGAGAAATCGTGTGTT+TGG - chr4_3:27050556-27050575 Msa0636510:intron 35.0%
! AGGATGCACTTTTCTGTTTT+CGG - chr4_3:27050611-27050630 Msa0636510:intron 35.0%
ACTCAACAACTATTGACATG+TGG - chr4_3:27050797-27050816 Msa0636510:CDS 35.0%
! TTGGTAATCAAAGAGTTAGG+TGG - chr4_3:27050903-27050922 Msa0636510:intron 35.0%
!!! TGTTAGAGTTTTTGCTGTTG+TGG - chr4_3:27050986-27051005 Msa0636510:five_prime_UTR 35.0%
!!! GTTAGAGTTTTTGCTGTTGT+GGG - chr4_3:27050987-27051006 Msa0636510:five_prime_UTR 35.0%
TTAACAGAGTTTCAAGGTTC+TGG - chr4_3:27051038-27051057 Msa0636510:five_prime_UTR 35.0%
CGATGGAGTTCTTAAGCATA+AGG - chr4_3:27050334-27050353 Msa0636510:intron 40.0%
CTATCTTGTTAGAGTGGTGT+TGG - chr4_3:27050858-27050877 Msa0636510:intron 40.0%
AATCAAAGAGTTAGGTGGTG+CGG - chr4_3:27050908-27050927 Msa0636510:intron 40.0%
GTTCTGGTGTGTTTATGCTT+GGG - chr4_3:27051054-27051073 Msa0636510:five_prime_UTR 40.0%
!! TGGGAGCTTCTATGTTGTTT+TGG - chr4_3:27051073-27051092 Msa0636510:five_prime_UTR 40.0%
CGATGGAGTTCTTAAGCATA+AGG - chr4_3:27050334-27050353 Msa0636510:intron 40.0%
CTATCTTGTTAGAGTGGTGT+TGG - chr4_3:27050858-27050877 Msa0636510:intron 40.0%
AATCAAAGAGTTAGGTGGTG+CGG - chr4_3:27050908-27050927 Msa0636510:intron 40.0%
GTTCTGGTGTGTTTATGCTT+GGG - chr4_3:27051054-27051073 Msa0636510:five_prime_UTR 40.0%
!! TGGGAGCTTCTATGTTGTTT+TGG - chr4_3:27051073-27051092 Msa0636510:five_prime_UTR 40.0%
GCGGAGGATCCAATTTAGTA+CGG - chr4_3:27050255-27050274 Msa0636510:CDS 45.0%
GGATCCAATTTAGTACGGCT+CGG - chr4_3:27050260-27050279 Msa0636510:CDS 45.0%
ACAACCGAGCCGTACTAAAT+TGG + chr4_3:27050267-27050286 None:intergenic 45.0%
TGAGTTCTTGACTGGTACGA+TGG - chr4_3:27050317-27050336 Msa0636510:CDS 45.0%
ACGATTAGCGCAGATCTTGA+GGG + chr4_3:27050399-27050418 None:intergenic 45.0%
AATCGTGTGTTTGGCATGCT+AGG - chr4_3:27050565-27050584 Msa0636510:intron 45.0%
ATCGTGTGTTTGGCATGCTA+GGG - chr4_3:27050566-27050585 Msa0636510:intron 45.0%
! TCTGCTGATGGTGAGCTTAA+AGG - chr4_3:27050591-27050610 Msa0636510:intron 45.0%
ATCAAAGAGTTAGGTGGTGC+GGG - chr4_3:27050909-27050928 Msa0636510:intron 45.0%
AGACTAGTGTTGTAGCTGCA+TGG - chr4_3:27050947-27050966 Msa0636510:CDS 45.0%
CAGCGGTTAACAGAGTTTCA+AGG - chr4_3:27051032-27051051 Msa0636510:five_prime_UTR 45.0%
! GGTTCTGGTGTGTTTATGCT+TGG - chr4_3:27051053-27051072 Msa0636510:five_prime_UTR 45.0%
GCGGAGGATCCAATTTAGTA+CGG - chr4_3:27050255-27050274 Msa0636510:CDS 45.0%
GGATCCAATTTAGTACGGCT+CGG - chr4_3:27050260-27050279 Msa0636510:CDS 45.0%
ACAACCGAGCCGTACTAAAT+TGG + chr4_3:27050267-27050286 None:intergenic 45.0%
TGAGTTCTTGACTGGTACGA+TGG - chr4_3:27050317-27050336 Msa0636510:CDS 45.0%
ACGATTAGCGCAGATCTTGA+GGG + chr4_3:27050399-27050418 None:intergenic 45.0%
AATCGTGTGTTTGGCATGCT+AGG - chr4_3:27050565-27050584 Msa0636510:intron 45.0%
ATCGTGTGTTTGGCATGCTA+GGG - chr4_3:27050566-27050585 Msa0636510:intron 45.0%
! TCTGCTGATGGTGAGCTTAA+AGG - chr4_3:27050591-27050610 Msa0636510:intron 45.0%
ATCAAAGAGTTAGGTGGTGC+GGG - chr4_3:27050909-27050928 Msa0636510:intron 45.0%
AGACTAGTGTTGTAGCTGCA+TGG - chr4_3:27050947-27050966 Msa0636510:CDS 45.0%
CAGCGGTTAACAGAGTTTCA+AGG - chr4_3:27051032-27051051 Msa0636510:five_prime_UTR 45.0%
! GGTTCTGGTGTGTTTATGCT+TGG - chr4_3:27051053-27051072 Msa0636510:five_prime_UTR 45.0%
! AGCGCAGATCTTGAGGGTTT+TGG + chr4_3:27050393-27050412 None:intergenic 50.0%
GACGATTAGCGCAGATCTTG+AGG + chr4_3:27050400-27050419 None:intergenic 50.0%
CATGCTAGGGATTCTGCTGA+TGG - chr4_3:27050579-27050598 Msa0636510:intron 50.0%
! TAGAGTGGTGTTGGAATCCG+AGG - chr4_3:27050867-27050886 Msa0636510:intron 50.0%
! AGAGTGGTGTTGGAATCCGA+GGG - chr4_3:27050868-27050887 Msa0636510:intron 50.0%
TGTTGGAATCCGAGGGAGTA+GGG - chr4_3:27050875-27050894 Msa0636510:intron 50.0%
CCAAATACACCCTACTCCCT+CGG + chr4_3:27050887-27050906 None:intergenic 50.0%
!! GTGCAGCTGCACTTTTGGTT+TGG - chr4_3:27051009-27051028 Msa0636510:five_prime_UTR 50.0%
!!! CTGCACTTTTGGTTTGGCAG+CGG - chr4_3:27051015-27051034 Msa0636510:five_prime_UTR 50.0%
! AGCGCAGATCTTGAGGGTTT+TGG + chr4_3:27050393-27050412 None:intergenic 50.0%
GACGATTAGCGCAGATCTTG+AGG + chr4_3:27050400-27050419 None:intergenic 50.0%
CATGCTAGGGATTCTGCTGA+TGG - chr4_3:27050579-27050598 Msa0636510:intron 50.0%
! TAGAGTGGTGTTGGAATCCG+AGG - chr4_3:27050867-27050886 Msa0636510:intron 50.0%
! AGAGTGGTGTTGGAATCCGA+GGG - chr4_3:27050868-27050887 Msa0636510:intron 50.0%
TGTTGGAATCCGAGGGAGTA+GGG - chr4_3:27050875-27050894 Msa0636510:intron 50.0%
CCAAATACACCCTACTCCCT+CGG + chr4_3:27050887-27050906 None:intergenic 50.0%
!! GTGCAGCTGCACTTTTGGTT+TGG - chr4_3:27051009-27051028 Msa0636510:five_prime_UTR 50.0%
!!! CTGCACTTTTGGTTTGGCAG+CGG - chr4_3:27051015-27051034 Msa0636510:five_prime_UTR 50.0%
GTGTTGGAATCCGAGGGAGT+AGG - chr4_3:27050874-27050893 Msa0636510:intron 55.0%
CCGAGGGAGTAGGGTGTATT+TGG - chr4_3:27050884-27050903 Msa0636510:intron 55.0%
AAGAGTTAGGTGGTGCGGGA+AGG - chr4_3:27050913-27050932 Msa0636510:intron 55.0%
AGAGTTAGGTGGTGCGGGAA+GGG - chr4_3:27050914-27050933 Msa0636510:intron 55.0%
! TGTGGGTGCAGCTGCACTTT+TGG - chr4_3:27051004-27051023 Msa0636510:five_prime_UTR 55.0%
GTGTTGGAATCCGAGGGAGT+AGG - chr4_3:27050874-27050893 Msa0636510:intron 55.0%
CCGAGGGAGTAGGGTGTATT+TGG - chr4_3:27050884-27050903 Msa0636510:intron 55.0%
AAGAGTTAGGTGGTGCGGGA+AGG - chr4_3:27050913-27050932 Msa0636510:intron 55.0%
AGAGTTAGGTGGTGCGGGAA+GGG - chr4_3:27050914-27050933 Msa0636510:intron 55.0%
! TGTGGGTGCAGCTGCACTTT+TGG - chr4_3:27051004-27051023 Msa0636510:five_prime_UTR 55.0%
GAGTTAGGTGGTGCGGGAAG+GGG - chr4_3:27050915-27050934 Msa0636510:intron 60.0%
AGTTAGGTGGTGCGGGAAGG+GGG - chr4_3:27050916-27050935 Msa0636510:intron 60.0%
GAGTTAGGTGGTGCGGGAAG+GGG - chr4_3:27050915-27050934 Msa0636510:intron 60.0%
AGTTAGGTGGTGCGGGAAGG+GGG - chr4_3:27050916-27050935 Msa0636510:intron 60.0%
GTTAGGTGGTGCGGGAAGGG+GGG - chr4_3:27050917-27050936 Msa0636510:intron 65.0%
GTTAGGTGGTGCGGGAAGGG+GGG - chr4_3:27050917-27050936 Msa0636510:intron 65.0%
Chromosome Type Strat End Strand Name
chr4_3 gene 27050245 27051106 27050245 ID=Msa0636510;Name=Msa0636510
chr4_3 mRNA 27050245 27051106 27050245 ID=Msa0636510-mRNA-1;Parent=Msa0636510;Name=Msa0636510-mRNA-1;_AED=0.44;_eAED=0.44;_QI=135|0.5|0.33|0.66|1|1|3|0|70
chr4_3 exon 27050245 27050336 27050245 ID=Msa0636510-mRNA-1:exon:6742;Parent=Msa0636510-mRNA-1
chr4_3 exon 27050751 27050828 27050751 ID=Msa0636510-mRNA-1:exon:6741;Parent=Msa0636510-mRNA-1
chr4_3 exon 27050929 27051106 27050929 ID=Msa0636510-mRNA-1:exon:6740;Parent=Msa0636510-mRNA-1
chr4_3 five_prime_UTR 27050972 27051106 27050972 ID=Msa0636510-mRNA-1:five_prime_utr;Parent=Msa0636510-mRNA-1
chr4_3 CDS 27050929 27050971 27050929 ID=Msa0636510-mRNA-1:cds;Parent=Msa0636510-mRNA-1
chr4_3 CDS 27050751 27050828 27050751 ID=Msa0636510-mRNA-1:cds;Parent=Msa0636510-mRNA-1
chr4_3 CDS 27050245 27050336 27050245 ID=Msa0636510-mRNA-1:cds;Parent=Msa0636510-mRNA-1
Gene Sequence

>Msa0636510

ATGAGGCAATCCAAAACCCTCAAGATCTGCGCTAATCGTCTTATTATACCTATGATGAGTATGCAAGAGAATGTTGGAATTGAGAAATCGTGTGTTTGGCATGCTAGGGATTCTGCTGATGCTGCACTTTTGGTTTGGCAGCGGTTAACAGAGTTTCAAGGTTCTGGTGTGTTTATGCTTGGGAGCTTCTATGTTGTTTTGGTTCCGTGCTGA

Protein sequence

>Msa0636510

MRQSKTLKICANRLIIPMMSMQENVGIEKSCVWHARDSADAALLVWQRLTEFQGSGVFMLGSFYVVLVPC*