AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1120990

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1120990 MtrunA17_Chr1g0197421 59.231 130 21 2 1 98 1 130 3.50e-43 137
Msa1120990 MtrunA17_Chr3g0116441 100.000 47 0 0 52 98 219 265 4.01e-28 106
Msa1120990 MtrunA17_Chr3g0116441 84.783 46 7 0 1 46 15 60 4.43e-23 92.0
Msa1120990 MtrunA17_Chr1g0199511 60.417 48 19 0 52 99 338 385 4.57e-17 74.7
Msa1120990 MtrunA17_Chr1g0199511 64.444 45 15 1 1 44 13 57 5.44e-15 68.9
Msa1120990 MtrunA17_Chr5g0410721 63.636 44 16 0 52 95 280 323 2.05e-12 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1120990 AT3G48430.1 87.234 47 6 0 52 98 247 293 1.22e-24 96.7
Msa1120990 AT3G48430.1 62.162 37 14 0 1 37 17 53 4.38e-11 58.2
Msa1120990 AT5G04240.1 58.333 48 20 0 52 99 306 353 5.19e-14 66.6
Msa1120990 AT5G04240.1 62.222 45 16 1 1 44 13 57 3.40e-13 64.3
Msa1120990 AT5G46910.1 59.091 44 18 0 52 95 294 337 6.88e-11 57.8
Msa1120990 AT5G46910.2 59.091 44 18 0 52 95 294 337 8.00e-11 57.4

Find 33 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GACCCTTTGGCCCTTGAATT+TGG 0.187974 7_3:+70898727 None:intergenic
AGCTGGAGTGGCTCGGTATT+CGG 0.220666 7_3:+70898841 None:intergenic
GAGGATGTTGTTAGAGTTCA+TGG 0.296735 7_3:-70898523 Msa1120990:CDS
TAGCTTGAATTATCTTCATA+TGG 0.324265 7_3:-70898596 Msa1120990:CDS
GCTGGAGTGGCTCGGTATTC+GGG 0.341847 7_3:+70898842 None:intergenic
GTTGTTAGAGTTCATGGTTA+TGG 0.343745 7_3:-70898517 Msa1120990:CDS
GAAAACCAAGCTTCCAAATT+CGG 0.373255 7_3:-70898782 Msa1120990:CDS
GCTCGGTATTCGGGTGCTAC+TGG 0.432221 7_3:+70898851 None:intergenic
ATCTTGAAAATGTATTCGAT+TGG 0.441436 7_3:+70898806 None:intergenic
CTTTGGCCCTTGAATTTGGA+AGG 0.452571 7_3:+70898731 None:intergenic
TTGAATTTGGAAGGTGGAAA+AGG 0.454957 7_3:+70898740 None:intergenic
ATTGGATCTTCGAATTCAGC+TGG 0.456740 7_3:+70898824 None:intergenic
AGCTTGAATTATCTTCATAT+GGG 0.462001 7_3:-70898595 Msa1120990:CDS
AGAGTCCGAATTTGGAAGCT+TGG 0.462536 7_3:+70898777 None:intergenic
AAACCTCAACAAAGACCCTT+TGG 0.483798 7_3:+70898714 None:intergenic
GGTGGAGAGATTAACCCTCT+TGG 0.496887 7_3:-70898496 Msa1120990:CDS
GGTGCTTCTAAGACCTGGTA+TGG 0.509028 7_3:-70898574 Msa1120990:CDS
ATTTGGAAGGTGGAAAAGGA+GGG 0.511614 7_3:+70898744 None:intergenic
ATCTCTAGGAACACCATACC+AGG 0.515561 7_3:+70898561 None:intergenic
TTCCAAATTCAAGGGCCAAA+GGG 0.528642 7_3:-70898729 Msa1120990:CDS
GGGCCAAAGGGTCTTTGTTG+AGG 0.534359 7_3:-70898717 Msa1120990:intron
AAAGCAACAGCAGCATCTCT+AGG 0.535968 7_3:+70898547 None:intergenic
AATTTGGAAGGTGGAAAAGG+AGG 0.540672 7_3:+70898743 None:intergenic
CGAATTCAGCTGGAGTGGCT+CGG 0.550842 7_3:+70898834 None:intergenic
GTATTCGGGTGCTACTGGCA+TGG 0.552289 7_3:+70898856 None:intergenic
GTTAGAGTTCATGGTTATGG+TGG 0.562896 7_3:-70898514 Msa1120990:CDS
TTTCCACCTTCCAAATTCAA+GGG 0.562964 7_3:-70898737 Msa1120990:CDS
CTTCCAAATTCAAGGGCCAA+AGG 0.564784 7_3:-70898730 Msa1120990:CDS
ATCTTCGAATTCAGCTGGAG+TGG 0.570450 7_3:+70898829 None:intergenic
ATATGGGTGCTTCTAAGACC+TGG 0.590963 7_3:-70898579 Msa1120990:CDS
TCCATGAACTCTAACCAAGA+GGG 0.604035 7_3:+70898482 None:intergenic
TGGCCCTTGAATTTGGAAGG+TGG 0.617375 7_3:+70898734 None:intergenic
ATCCATGAACTCTAACCAAG+AGG 0.634497 7_3:+70898481 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ATCTTGAAAATGTATTCGAT+TGG + chr7_3:70898543-70898562 None:intergenic 25.0%
!!! AATCGAATACATTTTCAAGA+TGG - chr7_3:70898542-70898561 Msa1120990:CDS 25.0%
! TAGCTTGAATTATCTTCATA+TGG - chr7_3:70898750-70898769 Msa1120990:CDS 25.0%
! AGCTTGAATTATCTTCATAT+GGG - chr7_3:70898751-70898770 Msa1120990:CDS 25.0%
!! TTTATCTTGCCATGCTTTTT+AGG - chr7_3:70898692-70898711 Msa1120990:intron 30.0%
GAAAACCAAGCTTCCAAATT+CGG - chr7_3:70898564-70898583 Msa1120990:CDS 35.0%
TTGAATTTGGAAGGTGGAAA+AGG + chr7_3:70898609-70898628 None:intergenic 35.0%
! TTTTCCACCTTCCAAATTCA+AGG - chr7_3:70898608-70898627 Msa1120990:CDS 35.0%
TTTCCACCTTCCAAATTCAA+GGG - chr7_3:70898609-70898628 Msa1120990:CDS 35.0%
GTCTTTGTTGAGGTTTATGA+AGG - chr7_3:70898639-70898658 Msa1120990:intron 35.0%
TTTGTTGAGGTTTATGAAGG+AGG - chr7_3:70898642-70898661 Msa1120990:intron 35.0%
GTTGTTAGAGTTCATGGTTA+TGG - chr7_3:70898829-70898848 Msa1120990:CDS 35.0%
ATTGGATCTTCGAATTCAGC+TGG + chr7_3:70898525-70898544 None:intergenic 40.0%
! GATTTTGCAGAGTCCGAATT+TGG + chr7_3:70898580-70898599 None:intergenic 40.0%
ATTTGGAAGGTGGAAAAGGA+GGG + chr7_3:70898605-70898624 None:intergenic 40.0%
AATTTGGAAGGTGGAAAAGG+AGG + chr7_3:70898606-70898625 None:intergenic 40.0%
TTCCAAATTCAAGGGCCAAA+GGG - chr7_3:70898617-70898636 Msa1120990:intron 40.0%
AAACCTCAACAAAGACCCTT+TGG + chr7_3:70898635-70898654 None:intergenic 40.0%
GTTTATGAAGGAGGAGATAC+CGG - chr7_3:70898651-70898670 Msa1120990:intron 40.0%
TTTATGAAGGAGGAGATACC+GGG - chr7_3:70898652-70898671 Msa1120990:intron 40.0%
AGCATGGCAAGATAAACCAT+AGG + chr7_3:70898688-70898707 None:intergenic 40.0%
!! ATCTTGCCATGCTTTTTAGG+TGG - chr7_3:70898695-70898714 Msa1120990:intron 40.0%
AGCAAACCACCTAAAAAGCA+TGG + chr7_3:70898704-70898723 None:intergenic 40.0%
GAGGATGTTGTTAGAGTTCA+TGG - chr7_3:70898823-70898842 Msa1120990:CDS 40.0%
GTTAGAGTTCATGGTTATGG+TGG - chr7_3:70898832-70898851 Msa1120990:CDS 40.0%
ATCTTCGAATTCAGCTGGAG+TGG + chr7_3:70898520-70898539 None:intergenic 45.0%
AGAGTCCGAATTTGGAAGCT+TGG + chr7_3:70898572-70898591 None:intergenic 45.0%
CTTTGGCCCTTGAATTTGGA+AGG + chr7_3:70898618-70898637 None:intergenic 45.0%
CTTCCAAATTCAAGGGCCAA+AGG - chr7_3:70898616-70898635 Msa1120990:intron 45.0%
!! TAGGTGGTTTGCTTGACATG+TGG - chr7_3:70898711-70898730 Msa1120990:intron 45.0%
!! ATATGGGTGCTTCTAAGACC+TGG - chr7_3:70898767-70898786 Msa1120990:CDS 45.0%
! ATCTCTAGGAACACCATACC+AGG + chr7_3:70898788-70898807 None:intergenic 45.0%
AAAGCAACAGCAGCATCTCT+AGG + chr7_3:70898802-70898821 None:intergenic 45.0%
!!! AGATGCTGCTGTTGCTTTTG+AGG - chr7_3:70898804-70898823 Msa1120990:CDS 45.0%
TGGCCCTTGAATTTGGAAGG+TGG + chr7_3:70898615-70898634 None:intergenic 50.0%
GACCCTTTGGCCCTTGAATT+TGG + chr7_3:70898622-70898641 None:intergenic 50.0%
ACCATAGGCGAAGTAACTCC+CGG + chr7_3:70898673-70898692 None:intergenic 50.0%
!! GTGGTTTGCTTGACATGTGG+AGG - chr7_3:70898714-70898733 Msa1120990:intron 50.0%
!! GGTGCTTCTAAGACCTGGTA+TGG - chr7_3:70898772-70898791 Msa1120990:CDS 50.0%
GGTGGAGAGATTAACCCTCT+TGG - chr7_3:70898850-70898869 Msa1120990:CDS 50.0%
!! AGCTGGAGTGGCTCGGTATT+CGG + chr7_3:70898508-70898527 None:intergenic 55.0%
CGAATTCAGCTGGAGTGGCT+CGG + chr7_3:70898515-70898534 None:intergenic 55.0%
GGGCCAAAGGGTCTTTGTTG+AGG - chr7_3:70898629-70898648 Msa1120990:intron 55.0%
ACCGGGAGTTACTTCGCCTA+TGG - chr7_3:70898669-70898688 Msa1120990:intron 55.0%
! GCTCGGTATTCGGGTGCTAC+TGG + chr7_3:70898498-70898517 None:intergenic 60.0%
!! GCTGGAGTGGCTCGGTATTC+GGG + chr7_3:70898507-70898526 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr7_3 gene 70898492 70898876 70898492 ID=Msa1120990;Name=Msa1120990
chr7_3 mRNA 70898492 70898876 70898492 ID=Msa1120990-mRNA-1;Parent=Msa1120990;Name=Msa1120990-mRNA-1;_AED=0.08;_eAED=0.08;_QI=0|0|0|1|1|1|2|0|99
chr7_3 exon 70898718 70898876 70898718 ID=Msa1120990-mRNA-1:exon:18065;Parent=Msa1120990-mRNA-1
chr7_3 exon 70898492 70898632 70898492 ID=Msa1120990-mRNA-1:exon:18064;Parent=Msa1120990-mRNA-1
chr7_3 CDS 70898718 70898876 70898718 ID=Msa1120990-mRNA-1:cds;Parent=Msa1120990-mRNA-1
chr7_3 CDS 70898492 70898632 70898492 ID=Msa1120990-mRNA-1:cds;Parent=Msa1120990-mRNA-1
Gene Sequence

>Msa1120990

ATGCCAGTAGCACCCGAATACCGAGCCACTCCAGCTGAATTCGAAGATCCAATCGAATACATTTTCAAGATGGAAAACCAAGCTTCCAAATTCGGACTCTGCAAAATCATCCCTCCTTTTCCACCTTCCAAATTCAAGGGCCAAAGGGTCTTTGTTGAGGATCATGATTTGCATAGCTTGAATTATCTTCATATGGGTGCTTCTAAGACCTGGTATGGTGTTCCTAGAGATGCTGCTGTTGCTTTTGAGGATGTTGTTAGAGTTCATGGTTATGGTGGAGAGATTAACCCTCTTGGTTAG
Protein sequence

>Msa1120990

MPVAPEYRATPAEFEDPIEYIFKMENQASKFGLCKIIPPFPPSKFKGQRVFVEDHDLHSLNYLHMGASKTWYGVPRDAAVAFEDVVRVHGYGGEINPLG*