AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1107160

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1107160 MtrunA17_Chr7g0240411 93.671 79 5 0 1 79 1 79 9.24e-50 150
Msa1107160 MtrunA17_Chr4g0008691 61.728 81 29 2 1 79 1 81 6.74e-32 106
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 102 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTACCTTGATTTGAAATTA+AGG 0.204434 7_3:-48636313 None:intergenic
ATGAATTGTTACACAATTCA+TGG 0.321299 7_3:-48636921 None:intergenic
TTATGAAACCTCAAAGTTAG+AGG 0.325794 7_3:-48636153 None:intergenic
TTTCTCTAAACTTGATATAT+AGG 0.334813 7_3:-48636599 None:intergenic
ATAAAGACATGAGGCTTGTT+AGG 0.338032 7_3:-48636225 None:intergenic
ATGAATTGTGTAACAATTCA+TGG 0.370990 7_3:+48636923 Msa1107160:three_prime_UTR
CTCTTGAACCTCTAACTTTG+AGG 0.371597 7_3:+48636145 Msa1107160:five_prime_UTR
GAGTTGGGAGATATATAAAA+AGG 0.385399 7_3:-48636107 None:intergenic
TTTGTGTCTGCTAGTGCTAA+TGG 0.389664 7_3:+48636653 Msa1107160:three_prime_UTR
ATGATATTGAACTCGCTTAG+AGG 0.390672 7_3:-48637015 None:intergenic
GAGGTACTTGCACTAGTACT+TGG 0.403825 7_3:+48636491 Msa1107160:CDS
CTTTCCTTAATTTCAAATCA+AGG 0.418332 7_3:+48636309 Msa1107160:CDS
TTTGGTTTGAAACAAGTCAA+TGG 0.446404 7_3:+48636720 Msa1107160:three_prime_UTR
CTAAGCGAGTTCAATATCAT+TGG 0.447939 7_3:+48637018 Msa1107160:three_prime_UTR
TGCAAATGTTGTGATGGAAT+TGG 0.452852 7_3:+48636469 Msa1107160:CDS
TTGGTTTGAAACAAGTCAAT+GGG 0.459688 7_3:+48636721 Msa1107160:three_prime_UTR
TGAAATTAAGGAAAGTGTCC+TGG 0.472749 7_3:-48636301 None:intergenic
AGTTAGAGGTTCAAGAGCTA+TGG 0.475561 7_3:-48636139 None:intergenic
TTGTGTCTGCTAGTGCTAAT+GGG 0.495526 7_3:+48636654 Msa1107160:three_prime_UTR
GCTATGGAGCACTGATGAGT+TGG 0.497002 7_3:-48636123 None:intergenic
CTATGGAGCACTGATGAGTT+GGG 0.500776 7_3:-48636122 None:intergenic
AGGATAGGAAACTTGTAGGA+TGG 0.515633 7_3:-48636087 None:intergenic
GGATAGGAAACTTGTAGGAT+GGG 0.533450 7_3:-48636086 None:intergenic
GTTGTTTGCAAATGTTGTGA+TGG 0.534057 7_3:+48636463 Msa1107160:CDS
AACCATCACTTATAGAAGCC+AGG 0.541348 7_3:+48636283 Msa1107160:CDS
AATAACTAGTGTGATTTCCA+AGG 0.557652 7_3:-48636544 None:intergenic
TGATATTGAACTCGCTTAGA+GGG 0.562089 7_3:-48637014 None:intergenic
GTCCTGGCTTCTATAAGTGA+TGG 0.565417 7_3:-48636285 None:intergenic
ATAGGAAACTTGTAGGATGG+GGG 0.578714 7_3:-48636084 None:intergenic
ATAACTTAAAGTGTTCACCT+TGG 0.595348 7_3:+48636527 Msa1107160:CDS
AAATGTTGTGATGGAATTGG+AGG 0.597103 7_3:+48636472 Msa1107160:CDS
GATAGGAAACTTGTAGGATG+GGG 0.605112 7_3:-48636085 None:intergenic
ATTAGTAATATAAAGACATG+AGG 0.651146 7_3:-48636234 None:intergenic
AACAAGTTGCAATAGACATG+TGG 0.663724 7_3:-48636770 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTTTATTTTTTTTATTT+TGG + chr7_3:48636398-48636417 Msa1107160:intron 0.0%
!!! TTTTTTTATTTTTTTTATTT+TGG + chr7_3:48636398-48636417 Msa1107160:intron 0.0%
!! ATAAAAAAAAATAGATCTAG+TGG - chr7_3:48636387-48636406 None:intergenic 15.0%
!! ATAAAAAAAAATAGATCTAG+TGG - chr7_3:48636387-48636406 None:intergenic 15.0%
!! CATCAAAAAATAAGAGATTT+AGG + chr7_3:48636179-48636198 Msa1107160:five_prime_UTR 20.0%
!! ATTAGTAATATAAAGACATG+AGG - chr7_3:48636237-48636256 None:intergenic 20.0%
!!! ATTACCTTGATTTGAAATTA+AGG - chr7_3:48636316-48636335 None:intergenic 20.0%
!!! TTATTTTGGTATGTATTTTC+AGG + chr7_3:48636412-48636431 Msa1107160:intron 20.0%
!!! TATTTTGGTATGTATTTTCA+GGG + chr7_3:48636413-48636432 Msa1107160:intron 20.0%
!!! AGTTATTTTTGTGATTTTTC+TGG + chr7_3:48636560-48636579 Msa1107160:exon 20.0%
!! TTTCTCTAAACTTGATATAT+AGG - chr7_3:48636602-48636621 None:intergenic 20.0%
!!! ATGATTTTTCATTGATGATA+AGG + chr7_3:48636836-48636855 Msa1107160:three_prime_UTR 20.0%
!!! TGATTTTTCATTGATGATAA+GGG + chr7_3:48636837-48636856 Msa1107160:three_prime_UTR 20.0%
!!! ATGAAGCATATTTTAACTTT+TGG + chr7_3:48636953-48636972 Msa1107160:three_prime_UTR 20.0%
!!! TGAAGCATATTTTAACTTTT+GGG + chr7_3:48636954-48636973 Msa1107160:three_prime_UTR 20.0%
!! CATCAAAAAATAAGAGATTT+AGG + chr7_3:48636179-48636198 Msa1107160:five_prime_UTR 20.0%
!! ATTAGTAATATAAAGACATG+AGG - chr7_3:48636237-48636256 None:intergenic 20.0%
!!! ATTACCTTGATTTGAAATTA+AGG - chr7_3:48636316-48636335 None:intergenic 20.0%
!!! TTATTTTGGTATGTATTTTC+AGG + chr7_3:48636412-48636431 Msa1107160:intron 20.0%
!!! TATTTTGGTATGTATTTTCA+GGG + chr7_3:48636413-48636432 Msa1107160:intron 20.0%
!!! AGTTATTTTTGTGATTTTTC+TGG + chr7_3:48636560-48636579 Msa1107160:exon 20.0%
!! TTTCTCTAAACTTGATATAT+AGG - chr7_3:48636602-48636621 None:intergenic 20.0%
!!! ATGATTTTTCATTGATGATA+AGG + chr7_3:48636836-48636855 Msa1107160:three_prime_UTR 20.0%
!!! TGATTTTTCATTGATGATAA+GGG + chr7_3:48636837-48636856 Msa1107160:three_prime_UTR 20.0%
!!! ATGAAGCATATTTTAACTTT+TGG + chr7_3:48636953-48636972 Msa1107160:three_prime_UTR 20.0%
!!! TGAAGCATATTTTAACTTTT+GGG + chr7_3:48636954-48636973 Msa1107160:three_prime_UTR 20.0%
! CTTTCCTTAATTTCAAATCA+AGG + chr7_3:48636309-48636328 Msa1107160:CDS 25.0%
!!! TATATGTGTCCATAGTTTTT+TGG + chr7_3:48636702-48636721 Msa1107160:three_prime_UTR 25.0%
! TGTTTCAAACCAAAAAACTA+TGG - chr7_3:48636714-48636733 None:intergenic 25.0%
! ATGAATTGTTACACAATTCA+TGG - chr7_3:48636924-48636943 None:intergenic 25.0%
! ATGAATTGTGTAACAATTCA+TGG + chr7_3:48636923-48636942 Msa1107160:three_prime_UTR 25.0%
!!! ACATTTTGAAGAGTATGTAT+TGG + chr7_3:48637047-48637066 Msa1107160:three_prime_UTR 25.0%
! CTTTCCTTAATTTCAAATCA+AGG + chr7_3:48636309-48636328 Msa1107160:CDS 25.0%
!!! TATATGTGTCCATAGTTTTT+TGG + chr7_3:48636702-48636721 Msa1107160:three_prime_UTR 25.0%
! TGTTTCAAACCAAAAAACTA+TGG - chr7_3:48636714-48636733 None:intergenic 25.0%
! ATGAATTGTTACACAATTCA+TGG - chr7_3:48636924-48636943 None:intergenic 25.0%
! ATGAATTGTGTAACAATTCA+TGG + chr7_3:48636923-48636942 Msa1107160:three_prime_UTR 25.0%
!!! ACATTTTGAAGAGTATGTAT+TGG + chr7_3:48637047-48637066 Msa1107160:three_prime_UTR 25.0%
AAAAAGGATAGGAAACTTGT+AGG - chr7_3:48636094-48636113 None:intergenic 30.0%
GGGAGATATATAAAAAGGAT+AGG - chr7_3:48636105-48636124 None:intergenic 30.0%
GAGTTGGGAGATATATAAAA+AGG - chr7_3:48636110-48636129 None:intergenic 30.0%
TTATGAAACCTCAAAGTTAG+AGG - chr7_3:48636156-48636175 None:intergenic 30.0%
! TCAAAGATTTTTGCAACACT+TGG + chr7_3:48636439-48636458 Msa1107160:CDS 30.0%
! ATAACTTAAAGTGTTCACCT+TGG + chr7_3:48636527-48636546 Msa1107160:CDS 30.0%
AATAACTAGTGTGATTTCCA+AGG - chr7_3:48636547-48636566 None:intergenic 30.0%
!! TTTGGTTTGAAACAAGTCAA+TGG + chr7_3:48636720-48636739 Msa1107160:three_prime_UTR 30.0%
! TTGGTTTGAAACAAGTCAAT+GGG + chr7_3:48636721-48636740 Msa1107160:three_prime_UTR 30.0%
AAAAAGGATAGGAAACTTGT+AGG - chr7_3:48636094-48636113 None:intergenic 30.0%
GGGAGATATATAAAAAGGAT+AGG - chr7_3:48636105-48636124 None:intergenic 30.0%
GAGTTGGGAGATATATAAAA+AGG - chr7_3:48636110-48636129 None:intergenic 30.0%
TTATGAAACCTCAAAGTTAG+AGG - chr7_3:48636156-48636175 None:intergenic 30.0%
! TCAAAGATTTTTGCAACACT+TGG + chr7_3:48636439-48636458 Msa1107160:CDS 30.0%
! ATAACTTAAAGTGTTCACCT+TGG + chr7_3:48636527-48636546 Msa1107160:CDS 30.0%
AATAACTAGTGTGATTTCCA+AGG - chr7_3:48636547-48636566 None:intergenic 30.0%
!! TTTGGTTTGAAACAAGTCAA+TGG + chr7_3:48636720-48636739 Msa1107160:three_prime_UTR 30.0%
! TTGGTTTGAAACAAGTCAAT+GGG + chr7_3:48636721-48636740 Msa1107160:three_prime_UTR 30.0%
! ATAAAGACATGAGGCTTGTT+AGG - chr7_3:48636228-48636247 None:intergenic 35.0%
!! TGAAATTAAGGAAAGTGTCC+TGG - chr7_3:48636304-48636323 None:intergenic 35.0%
AAATAGATCTAGTGGAAGAG+AGG - chr7_3:48636379-48636398 None:intergenic 35.0%
GTTGTTTGCAAATGTTGTGA+TGG + chr7_3:48636463-48636482 Msa1107160:CDS 35.0%
! TGCAAATGTTGTGATGGAAT+TGG + chr7_3:48636469-48636488 Msa1107160:CDS 35.0%
! AAATGTTGTGATGGAATTGG+AGG + chr7_3:48636472-48636491 Msa1107160:CDS 35.0%
AACAAGTTGCAATAGACATG+TGG - chr7_3:48636773-48636792 None:intergenic 35.0%
TGATATTGAACTCGCTTAGA+GGG - chr7_3:48637017-48637036 None:intergenic 35.0%
ATGATATTGAACTCGCTTAG+AGG - chr7_3:48637018-48637037 None:intergenic 35.0%
CTAAGCGAGTTCAATATCAT+TGG + chr7_3:48637018-48637037 Msa1107160:three_prime_UTR 35.0%
! ATAAAGACATGAGGCTTGTT+AGG - chr7_3:48636228-48636247 None:intergenic 35.0%
!! TGAAATTAAGGAAAGTGTCC+TGG - chr7_3:48636304-48636323 None:intergenic 35.0%
AAATAGATCTAGTGGAAGAG+AGG - chr7_3:48636379-48636398 None:intergenic 35.0%
GTTGTTTGCAAATGTTGTGA+TGG + chr7_3:48636463-48636482 Msa1107160:CDS 35.0%
! TGCAAATGTTGTGATGGAAT+TGG + chr7_3:48636469-48636488 Msa1107160:CDS 35.0%
! AAATGTTGTGATGGAATTGG+AGG + chr7_3:48636472-48636491 Msa1107160:CDS 35.0%
AACAAGTTGCAATAGACATG+TGG - chr7_3:48636773-48636792 None:intergenic 35.0%
TGATATTGAACTCGCTTAGA+GGG - chr7_3:48637017-48637036 None:intergenic 35.0%
ATGATATTGAACTCGCTTAG+AGG - chr7_3:48637018-48637037 None:intergenic 35.0%
CTAAGCGAGTTCAATATCAT+TGG + chr7_3:48637018-48637037 Msa1107160:three_prime_UTR 35.0%
ATAGGAAACTTGTAGGATGG+GGG - chr7_3:48636087-48636106 None:intergenic 40.0%
GATAGGAAACTTGTAGGATG+GGG - chr7_3:48636088-48636107 None:intergenic 40.0%
GGATAGGAAACTTGTAGGAT+GGG - chr7_3:48636089-48636108 None:intergenic 40.0%
AGGATAGGAAACTTGTAGGA+TGG - chr7_3:48636090-48636109 None:intergenic 40.0%
AGTTAGAGGTTCAAGAGCTA+TGG - chr7_3:48636142-48636161 None:intergenic 40.0%
CTCTTGAACCTCTAACTTTG+AGG + chr7_3:48636145-48636164 Msa1107160:five_prime_UTR 40.0%
AACCATCACTTATAGAAGCC+AGG + chr7_3:48636283-48636302 Msa1107160:CDS 40.0%
TTTGTGTCTGCTAGTGCTAA+TGG + chr7_3:48636653-48636672 Msa1107160:three_prime_UTR 40.0%
TTGTGTCTGCTAGTGCTAAT+GGG + chr7_3:48636654-48636673 Msa1107160:three_prime_UTR 40.0%
ATAGGAAACTTGTAGGATGG+GGG - chr7_3:48636087-48636106 None:intergenic 40.0%
GATAGGAAACTTGTAGGATG+GGG - chr7_3:48636088-48636107 None:intergenic 40.0%
GGATAGGAAACTTGTAGGAT+GGG - chr7_3:48636089-48636108 None:intergenic 40.0%
AGGATAGGAAACTTGTAGGA+TGG - chr7_3:48636090-48636109 None:intergenic 40.0%
AGTTAGAGGTTCAAGAGCTA+TGG - chr7_3:48636142-48636161 None:intergenic 40.0%
CTCTTGAACCTCTAACTTTG+AGG + chr7_3:48636145-48636164 Msa1107160:five_prime_UTR 40.0%
AACCATCACTTATAGAAGCC+AGG + chr7_3:48636283-48636302 Msa1107160:CDS 40.0%
TTTGTGTCTGCTAGTGCTAA+TGG + chr7_3:48636653-48636672 Msa1107160:three_prime_UTR 40.0%
TTGTGTCTGCTAGTGCTAAT+GGG + chr7_3:48636654-48636673 Msa1107160:three_prime_UTR 40.0%
!! CTATGGAGCACTGATGAGTT+GGG - chr7_3:48636125-48636144 None:intergenic 45.0%
GTCCTGGCTTCTATAAGTGA+TGG - chr7_3:48636288-48636307 None:intergenic 45.0%
! GAGGTACTTGCACTAGTACT+TGG + chr7_3:48636491-48636510 Msa1107160:CDS 45.0%
!! CTATGGAGCACTGATGAGTT+GGG - chr7_3:48636125-48636144 None:intergenic 45.0%
GTCCTGGCTTCTATAAGTGA+TGG - chr7_3:48636288-48636307 None:intergenic 45.0%
! GAGGTACTTGCACTAGTACT+TGG + chr7_3:48636491-48636510 Msa1107160:CDS 45.0%
!! GCTATGGAGCACTGATGAGT+TGG - chr7_3:48636126-48636145 None:intergenic 50.0%
!! GCTATGGAGCACTGATGAGT+TGG - chr7_3:48636126-48636145 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr7_3 gene 48636084 48637091 48636084 ID=Msa1107160;Name=Msa1107160
chr7_3 mRNA 48636084 48637091 48636084 ID=Msa1107160-mRNA-1;Parent=Msa1107160;Name=Msa1107160-mRNA-1;_AED=0.00;_eAED=0.00;_QI=135|1|1|1|0|0.5|2|530|79
chr7_3 exon 48636084 48636330 48636084 ID=Msa1107160-mRNA-1:exon:9881;Parent=Msa1107160-mRNA-1
chr7_3 exon 48636434 48637091 48636434 ID=Msa1107160-mRNA-1:exon:9882;Parent=Msa1107160-mRNA-1
chr7_3 five_prime_UTR 48636084 48636218 48636084 ID=Msa1107160-mRNA-1:five_prime_utr;Parent=Msa1107160-mRNA-1
chr7_3 CDS 48636219 48636330 48636219 ID=Msa1107160-mRNA-1:cds;Parent=Msa1107160-mRNA-1
chr7_3 CDS 48636434 48636561 48636434 ID=Msa1107160-mRNA-1:cds;Parent=Msa1107160-mRNA-1
chr7_3 three_prime_UTR 48636562 48637091 48636562 ID=Msa1107160-mRNA-1:three_prime_utr;Parent=Msa1107160-mRNA-1
Gene Sequence

>Msa1107160

ATGAGTCCTAACAAGCCTCATGTCTTTATATTACTAATCATCATGCTTGTTTCAGTTTCTAATAAACCATCACTTATAGAAGCCAGGACACTTTCCTTAATTTCAAATCAAGGGTACTCAAAGATTTTTGCAACACTTGGAGTTGTTTGCAAATGTTGTGATGGAATTGGAGGTACTTGCACTAGTACTTGGACACAATCTTGTAATAACTTAAAGTGTTCACCTTGGAAATCACACTAG
Protein sequence

>Msa1107160

MSPNKPHVFILLIIMLVSVSNKPSLIEARTLSLISNQGYSKIFATLGVVCKCCDGIGGTCTSTWTQSCNNLKCSPWKSH*