AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0064350


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0064350 MtrunA17_Chr1g0166111 100.000 77 0 0 1 77 1 77 2.79e-53 159
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0064350 AT4G14615.1 66.667 75 24 1 1 75 1 74 3.82e-32 106
Msa0064350 AT1G52825.2 68.182 66 20 1 1 66 1 65 3.26e-26 92.0
Msa0064350 AT1G52825.1 68.182 66 20 1 1 66 1 65 3.26e-26 92.0

Find 35 sgRNAs with CRISPR-Local

Find 138 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATCAAATCTCTCTCTTAAA+TGG 0.118498 1_2:-25405036 None:intergenic
TCTAAACTACTCTAAATAAA+AGG 0.240104 1_2:+25407611 Msa0064350:three_prime_UTR
AAGCATCAAACGAATGAAAT+TGG 0.276298 1_2:+25405007 Msa0064350:five_prime_UTR
ATTCTAGAAATTGCAAAGTT+TGG 0.311771 1_2:+25405135 Msa0064350:CDS
CGGTGGCGTATTTGTATCCT+TGG 0.314633 1_2:-25407394 None:intergenic
GAGATTTGATCTGAGTTGTT+TGG 0.379171 1_2:+25405048 Msa0064350:five_prime_UTR
CACCGCCACCAGAGGAACTT+AGG 0.405202 1_2:+25407412 Msa0064350:CDS
GAGTTCATCTTGTTTCTTCA+AGG 0.411033 1_2:+25405076 Msa0064350:five_prime_UTR
GTGGGTCGATTGTGCTTTAG+TGG 0.429882 1_2:+25407485 Msa0064350:three_prime_UTR
AATCTCTCTCTTAAATGGGC+TGG 0.433079 1_2:-25405031 None:intergenic
ATCAAATCTCTCTCTTAAAT+GGG 0.438583 1_2:-25405035 None:intergenic
ATCTCTCTCTTAAATGGGCT+GGG 0.449260 1_2:-25405030 None:intergenic
GCCATTTCCCTAAGTTCCTC+TGG 0.453339 1_2:-25407420 None:intergenic
ACCAGAGGAACTTAGGGAAA+TGG 0.455027 1_2:+25407419 Msa0064350:CDS
CTAAGTTCCTCTGGTGGCGG+TGG 0.488476 1_2:-25407411 None:intergenic
GAATTTGTGGAGGGAGTTGT+CGG 0.502242 1_2:-25405208 None:intergenic
CGAGGGAGCTAGCTCGCAAA+AGG 0.515998 1_2:+25407442 Msa0064350:CDS
CAATCACTGATGCTCCTTGT+GGG 0.517735 1_2:+25407467 Msa0064350:exon
GGTGGCGTATTTGTATCCTT+GGG 0.519575 1_2:-25407393 None:intergenic
TCCCTAAGTTCCTCTGGTGG+CGG 0.519584 1_2:-25407414 None:intergenic
AACTCCCTCCACAAATTCAT+CGG 0.541704 1_2:+25405213 Msa0064350:CDS
ACCGCCACCAGAGGAACTTA+GGG 0.541856 1_2:+25407413 Msa0064350:CDS
ATTTGATCTGAGTTGTTTGG+TGG 0.546522 1_2:+25405051 Msa0064350:five_prime_UTR
TCATCACTGGGAACATCGAA+GGG 0.547643 1_2:+25405111 Msa0064350:CDS
GTCATCACTGGGAACATCGA+AGG 0.550820 1_2:+25405110 Msa0064350:CDS
TAAACGTACATAAGAACGAT+TGG 0.555395 1_2:-25405174 None:intergenic
ACTTGAGAATTTCGCAAACA+AGG 0.566635 1_2:-25407647 None:intergenic
ACAATCACTGATGCTCCTTG+TGG 0.568209 1_2:+25407466 Msa0064350:exon
GTCATACATTGAATATCCCA+AGG 0.616788 1_2:+25407377 Msa0064350:CDS
AGGAACTTAGGGAAATGGCG+AGG 0.624927 1_2:+25407424 Msa0064350:CDS
GGAACTTAGGGAAATGGCGA+GGG 0.630297 1_2:+25407425 Msa0064350:CDS
ATTTCCCTAAGTTCCTCTGG+TGG 0.642092 1_2:-25407417 None:intergenic
AAATACGCCACCGCCACCAG+AGG 0.666326 1_2:+25407404 Msa0064350:CDS
TAAAGCACAATCGACCCACA+AGG 0.677666 1_2:-25407481 None:intergenic
CATCACTGGGAACATCGAAG+GGG 0.716260 1_2:+25405112 Msa0064350:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAAATTTCTTCTATTTTATT+TGG + chr1_2:25406485-25406504 Msa0064350:intron 10.0%
!! AAGAATAAATCTAAGAAAAA+AGG - chr1_2:25405266-25405285 None:intergenic 15.0%
!!! ATTTTATTTTGATGTACTAT+CGG - chr1_2:25405824-25405843 None:intergenic 15.0%
!! AAAAAAAAAAAAACTCCTAA+TGG - chr1_2:25407166-25407185 None:intergenic 15.0%
!! TAACATAATTGCATTTATTT+GGG - chr1_2:25407297-25407316 None:intergenic 15.0%
!! TTAACATAATTGCATTTATT+TGG - chr1_2:25407298-25407317 None:intergenic 15.0%
!!! TAGTTTTTTTTTTTTTGTTG+AGG + chr1_2:25407516-25407535 Msa0064350:three_prime_UTR 15.0%
!!! AGTTTTTTTTTTTTTGTTGA+GGG + chr1_2:25407517-25407536 Msa0064350:three_prime_UTR 15.0%
!!! TTTTTCAATTAAGAAGACAA+GGG - chr1_2:25405458-25405477 None:intergenic 20.0%
!!! TTTTTTCAATTAAGAAGACA+AGG - chr1_2:25405459-25405478 None:intergenic 20.0%
!!! ATATTTATACTCTAGTTCAA+TGG + chr1_2:25405517-25405536 Msa0064350:intron 20.0%
!!! TTTTAATCTTTTGAGAAACA+GGG + chr1_2:25405896-25405915 Msa0064350:intron 20.0%
!!! GAATTAGGTATATTTTTCTT+GGG - chr1_2:25406116-25406135 None:intergenic 20.0%
!!! TGAATTAGGTATATTTTTCT+TGG - chr1_2:25406117-25406136 None:intergenic 20.0%
!!! ATTAGATTCTTCATTTTCTT+TGG + chr1_2:25406271-25406290 Msa0064350:intron 20.0%
!!! TTTTAATCTTTTGAGAAACA+GGG - chr1_2:25405896-25405915 None:intergenic 20.0%
!!! TGTAACCAATTTATTTTACA+CGG - chr1_2:25405801-25405820 None:intergenic 20.0%
!! GAAACCAAATACATTAATAA+TGG + chr1_2:25406816-25406835 Msa0064350:intron 20.0%
!! AAGTTATAACTTAATCCATT+AGG + chr1_2:25407148-25407167 Msa0064350:intron 20.0%
!! TCTAAACTACTCTAAATAAA+AGG + chr1_2:25407611-25407630 Msa0064350:three_prime_UTR 20.0%
! ATCAAATCTCTCTCTTAAAT+GGG - chr1_2:25405038-25405057 None:intergenic 25.0%
! AAAGTAAAAATGTCATCACT+GGG + chr1_2:25405099-25405118 Msa0064350:exon 25.0%
!! ATTCTAGAAATTGCAAAGTT+TGG + chr1_2:25405135-25405154 Msa0064350:CDS 25.0%
! TTAACTAAAACAGACATGTT+TGG + chr1_2:25405331-25405350 Msa0064350:intron 25.0%
! TTATCTCTATTAGTGTGATT+AGG + chr1_2:25405596-25405615 Msa0064350:intron 25.0%
!! CATCATTTTATATTTCGATC+AGG - chr1_2:25405632-25405651 None:intergenic 25.0%
! GTGTAAAATAAATTGGTTAC+AGG - chr1_2:25406519-25406538 None:intergenic 25.0%
! ACTATCGGTGTAAAATAAAT+TGG - chr1_2:25405809-25405828 None:intergenic 25.0%
! AAGATTAAAACTCAGCTTAT+AGG - chr1_2:25405886-25405905 None:intergenic 25.0%
!!! GTTTTAATCTTTTGAGAAAC+AGG + chr1_2:25405895-25405914 Msa0064350:intron 25.0%
!! CGAAGAATAAAAGCATAAAA+TGG + chr1_2:25406026-25406045 Msa0064350:intron 25.0%
! TTCAAATCGTTAATAGAATG+AGG + chr1_2:25406086-25406105 Msa0064350:intron 25.0%
! TCAAATCGTTAATAGAATGA+GGG + chr1_2:25406087-25406106 Msa0064350:intron 25.0%
!!! GTTTTAATCTTTTGAGAAAC+AGG - chr1_2:25405895-25405914 None:intergenic 25.0%
! AAGATTAAAACTCAACTTGT+AGG + chr1_2:25406437-25406456 Msa0064350:intron 25.0%
! ACTATCCGTGTAAAATAAAT+TGG + chr1_2:25406512-25406531 Msa0064350:intron 25.0%
! ATTTACATGTCACTAAAAGA+GGG + chr1_2:25406567-25406586 Msa0064350:intron 25.0%
!! CAACATTTTATATTTCGATC+AGG + chr1_2:25406699-25406718 Msa0064350:intron 25.0%
! ACCAAATACATTAATAATGG+TGG + chr1_2:25406819-25406838 Msa0064350:intron 25.0%
! TCCACCATTATTAATGTATT+TGG - chr1_2:25406823-25406842 None:intergenic 25.0%
!!! CATAATACTTTTTTGGTACT+AGG + chr1_2:25406874-25406893 Msa0064350:intron 25.0%
! TCAAATCTTGCTACATTATA+GGG - chr1_2:25406909-25406928 None:intergenic 25.0%
! TTCAAATCTTGCTACATTAT+AGG - chr1_2:25406910-25406929 None:intergenic 25.0%
! ATTGACAATACTATTGTTAC+TGG + chr1_2:25407055-25407074 Msa0064350:intron 25.0%
! GAAATCTATCTACATATTCT+TGG - chr1_2:25407093-25407112 None:intergenic 25.0%
!! TTTTTACAATAATCCAGTCT+GGG + chr1_2:25407202-25407221 Msa0064350:intron 25.0%
AAGCATCAAACGAATGAAAT+TGG + chr1_2:25405007-25405026 Msa0064350:five_prime_UTR 30.0%
GATCAAATCTCTCTCTTAAA+TGG - chr1_2:25405039-25405058 None:intergenic 30.0%
GAAAGTAAAAATGTCATCAC+TGG + chr1_2:25405098-25405117 Msa0064350:exon 30.0%
TAAACGTACATAAGAACGAT+TGG - chr1_2:25405177-25405196 None:intergenic 30.0%
!! TTACTTTTCCGATGAATTTG+TGG - chr1_2:25405224-25405243 None:intergenic 30.0%
CTGATTGAATTTGTAGAGTT+TGG - chr1_2:25405552-25405571 None:intergenic 30.0%
AGAAGAAATTTACCTTTGAG+TGG + chr1_2:25405844-25405863 Msa0064350:intron 30.0%
AAATGTGAAGAAGCTGAATT+AGG - chr1_2:25406131-25406150 None:intergenic 30.0%
TCAACAAACATACGAAGTTA+TGG - chr1_2:25406243-25406262 None:intergenic 30.0%
! AGTAGAGATCAGAATTTGTT+TGG - chr1_2:25406385-25406404 None:intergenic 30.0%
ATAGAAGAAATTTACCTGAG+TGG - chr1_2:25406479-25406498 None:intergenic 30.0%
CATTTACATGTCACTAAAAG+AGG + chr1_2:25406566-25406585 Msa0064350:intron 30.0%
! TAAAAGAGGGTAACTTTTTG+AGG + chr1_2:25406580-25406599 Msa0064350:intron 30.0%
TTACATTAGTGTGACATGTT+AGG - chr1_2:25406735-25406754 None:intergenic 30.0%
TTGTGATAGATGATCAAGAA+AGG + chr1_2:25406763-25406782 Msa0064350:intron 30.0%
!! GTATACAAGCTCTATTTTTC+CGG + chr1_2:25406845-25406864 Msa0064350:intron 30.0%
!! TATACAAGCTCTATTTTTCC+GGG + chr1_2:25406846-25406865 Msa0064350:intron 30.0%
!! AAAAAGTATTATGACAGTCC+CGG - chr1_2:25406867-25406886 None:intergenic 30.0%
!!! GGACTGTCATAATACTTTTT+TGG + chr1_2:25406867-25406886 Msa0064350:intron 30.0%
ATTATATCACTGTGAAGTAG+CGG + chr1_2:25407004-25407023 Msa0064350:intron 30.0%
TGTCAATCACAAATAACTAG+CGG - chr1_2:25407042-25407061 None:intergenic 30.0%
ACAATACTATTGTTACTGGA+GGG + chr1_2:25407059-25407078 Msa0064350:intron 30.0%
! GTTTTTACAATAATCCAGTC+TGG + chr1_2:25407201-25407220 Msa0064350:intron 30.0%
ACAAGCAATGACATTCAATT+TGG - chr1_2:25407248-25407267 None:intergenic 30.0%
AATTGAATGTCATTGCTTGT+TGG + chr1_2:25407248-25407267 Msa0064350:intron 30.0%
!!! TTTTTTTTTGTTGAGGGAAG+TGG + chr1_2:25407523-25407542 Msa0064350:three_prime_UTR 30.0%
GAGATTTGATCTGAGTTGTT+TGG + chr1_2:25405048-25405067 Msa0064350:five_prime_UTR 35.0%
ATTTGATCTGAGTTGTTTGG+TGG + chr1_2:25405051-25405070 Msa0064350:five_prime_UTR 35.0%
! GAGTTCATCTTGTTTCTTCA+AGG + chr1_2:25405076-25405095 Msa0064350:five_prime_UTR 35.0%
! TTTTCCGATGAATTTGTGGA+GGG - chr1_2:25405220-25405239 None:intergenic 35.0%
TAAGCTATAAGCTCATGAGA+AGG - chr1_2:25405366-25405385 None:intergenic 35.0%
CTCTACAAATTCAATCAGCT+AGG + chr1_2:25405554-25405573 Msa0064350:intron 35.0%
! TCAAAGAGGGTAACTTTTTG+AGG - chr1_2:25405741-25405760 None:intergenic 35.0%
ATTTCCATGTCACTCAAAGA+GGG - chr1_2:25405754-25405773 None:intergenic 35.0%
ACATGGAAATGCATGATTGA+GGG + chr1_2:25405764-25405783 Msa0064350:intron 35.0%
CATGTTCATTCGCAAACTAA+CGG - chr1_2:25406167-25406186 None:intergenic 35.0%
! TCGTATGTTTGTTGAGCATA+AGG + chr1_2:25406248-25406267 Msa0064350:intron 35.0%
AGTAATGCTCCAAATAACCA+GGG - chr1_2:25406320-25406339 None:intergenic 35.0%
TAGTAATGCTCCAAATAACC+AGG - chr1_2:25406321-25406340 None:intergenic 35.0%
TGCATGATTGAGTGATAGAA+GGG - chr1_2:25406548-25406567 None:intergenic 35.0%
ATGCATGATTGAGTGATAGA+AGG - chr1_2:25406549-25406568 None:intergenic 35.0%
GACAATACTATTGTTACTGG+AGG + chr1_2:25407058-25407077 Msa0064350:intron 35.0%
TGAGCTTCTGTTACAAGTAA+TGG - chr1_2:25407125-25407144 None:intergenic 35.0%
CAATGACATTCAATTTGGCA+AGG - chr1_2:25407243-25407262 None:intergenic 35.0%
GTCATACATTGAATATCCCA+AGG + chr1_2:25407377-25407396 Msa0064350:CDS 35.0%
ACTTGAGAATTTCGCAAACA+AGG - chr1_2:25407650-25407669 None:intergenic 35.0%
! ATCTCTCTCTTAAATGGGCT+GGG - chr1_2:25405033-25405052 None:intergenic 40.0%
AATCTCTCTCTTAAATGGGC+TGG - chr1_2:25405034-25405053 None:intergenic 40.0%
AACTCCCTCCACAAATTCAT+CGG + chr1_2:25405213-25405232 Msa0064350:CDS 40.0%
! CTTTTCCGATGAATTTGTGG+AGG - chr1_2:25405221-25405240 None:intergenic 40.0%
TAAGCTCATGAGAAGGTCAA+GGG - chr1_2:25405359-25405378 None:intergenic 40.0%
ATAAGCTCATGAGAAGGTCA+AGG - chr1_2:25405360-25405379 None:intergenic 40.0%
CATTTCCATGTCACTCAAAG+AGG - chr1_2:25405755-25405774 None:intergenic 40.0%
GACATGGAAATGCATGATTG+AGG + chr1_2:25405763-25405782 Msa0064350:intron 40.0%
ATGCATGATTGAGGGATAGA+AGG + chr1_2:25405772-25405791 Msa0064350:intron 40.0%
AACTGTTCTCTACCACTCAA+AGG - chr1_2:25405859-25405878 None:intergenic 40.0%
!! CGTTAGTTTGCGAATGAACA+TGG + chr1_2:25406165-25406184 Msa0064350:intron 40.0%
GAATGAACATGGTAGCTATG+TGG + chr1_2:25406176-25406195 Msa0064350:intron 40.0%
AGTTATGGCAAACACAGAGA+TGG - chr1_2:25406228-25406247 None:intergenic 40.0%
TGAGTGGTAGAGAACAGTTA+GGG - chr1_2:25405860-25405879 None:intergenic 40.0%
TCATCACTGGGAACATCGAA+GGG + chr1_2:25405111-25405130 Msa0064350:CDS 45.0%
GAATTTGTGGAGGGAGTTGT+CGG - chr1_2:25405211-25405230 None:intergenic 45.0%
GTTACCCTCTTTGAGTGACA+TGG + chr1_2:25405747-25405766 Msa0064350:intron 45.0%
TTAAACTTGCCTTCGTTCCC+TGG + chr1_2:25406300-25406319 Msa0064350:intron 45.0%
TCCAAATAACCAGGGAACGA+AGG - chr1_2:25406312-25406331 None:intergenic 45.0%
CTGAGTGGTAGAGAACAGTT+AGG - chr1_2:25406464-25406483 None:intergenic 45.0%
CTAACTGTTCTCTACCACTC+AGG + chr1_2:25406462-25406481 Msa0064350:intron 45.0%
GTGACGTAGCAATGCATGAT+TGG + chr1_2:25406627-25406646 Msa0064350:intron 45.0%
TTAGCTACTAAGACCCAGAC+TGG - chr1_2:25407218-25407237 None:intergenic 45.0%
GGTGGCGTATTTGTATCCTT+GGG - chr1_2:25407396-25407415 None:intergenic 45.0%
ATTTCCCTAAGTTCCTCTGG+TGG - chr1_2:25407420-25407439 None:intergenic 45.0%
ACCAGAGGAACTTAGGGAAA+TGG + chr1_2:25407419-25407438 Msa0064350:CDS 45.0%
ACAATCACTGATGCTCCTTG+TGG + chr1_2:25407466-25407485 Msa0064350:exon 45.0%
CAATCACTGATGCTCCTTGT+GGG + chr1_2:25407467-25407486 Msa0064350:exon 45.0%
TAAAGCACAATCGACCCACA+AGG - chr1_2:25407484-25407503 None:intergenic 45.0%
GTCATCACTGGGAACATCGA+AGG + chr1_2:25405110-25405129 Msa0064350:CDS 50.0%
CATCACTGGGAACATCGAAG+GGG + chr1_2:25405112-25405131 Msa0064350:CDS 50.0%
GCCTTCGTTCCCTGGTTATT+TGG + chr1_2:25406308-25406327 Msa0064350:intron 50.0%
GCTTGACTGAGACGAAAGAC+AGG - chr1_2:25406792-25406811 None:intergenic 50.0%
CGGTGGCGTATTTGTATCCT+TGG - chr1_2:25407397-25407416 None:intergenic 50.0%
GCCATTTCCCTAAGTTCCTC+TGG - chr1_2:25407423-25407442 None:intergenic 50.0%
AGGAACTTAGGGAAATGGCG+AGG + chr1_2:25407424-25407443 Msa0064350:CDS 50.0%
GGAACTTAGGGAAATGGCGA+GGG + chr1_2:25407425-25407444 Msa0064350:CDS 50.0%
GTGGGTCGATTGTGCTTTAG+TGG + chr1_2:25407485-25407504 Msa0064350:three_prime_UTR 50.0%
!! GAAACAGGGTATCGCAGCTC+AGG + chr1_2:25405910-25405929 Msa0064350:intron 55.0%
!! GAAACAGGGTATCGCAGCTC+AGG - chr1_2:25405910-25405929 None:intergenic 55.0%
ACCGCCACCAGAGGAACTTA+GGG + chr1_2:25407413-25407432 Msa0064350:CDS 55.0%
TCCCTAAGTTCCTCTGGTGG+CGG - chr1_2:25407417-25407436 None:intergenic 55.0%
AAATACGCCACCGCCACCAG+AGG + chr1_2:25407404-25407423 Msa0064350:CDS 60.0%
!! CTAAGTTCCTCTGGTGGCGG+TGG - chr1_2:25407414-25407433 None:intergenic 60.0%
CACCGCCACCAGAGGAACTT+AGG + chr1_2:25407412-25407431 Msa0064350:CDS 60.0%
CGAGGGAGCTAGCTCGCAAA+AGG + chr1_2:25407442-25407461 Msa0064350:CDS 60.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 25404999 25407710 25404999 ID=Msa0064350;Name=Msa0064350
chr1_2 mRNA 25404999 25407710 25404999 ID=Msa0064350-mRNA-1;Parent=Msa0064350;Name=Msa0064350-mRNA-1;_AED=0.01;_eAED=0.01;_QI=109|1|1|1|0|0|2|234|77
chr1_2 exon 25404999 25405239 25404999 ID=Msa0064350-mRNA-1:exon:9078;Parent=Msa0064350-mRNA-1
chr1_2 exon 25407375 25407710 25407375 ID=Msa0064350-mRNA-1:exon:9079;Parent=Msa0064350-mRNA-1
chr1_2 five_prime_UTR 25404999 25405107 25404999 ID=Msa0064350-mRNA-1:five_prime_utr;Parent=Msa0064350-mRNA-1
chr1_2 CDS 25405108 25405239 25405108 ID=Msa0064350-mRNA-1:cds;Parent=Msa0064350-mRNA-1
chr1_2 CDS 25407375 25407476 25407375 ID=Msa0064350-mRNA-1:cds;Parent=Msa0064350-mRNA-1
chr1_2 three_prime_UTR 25407477 25407710 25407477 ID=Msa0064350-mRNA-1:three_prime_utr;Parent=Msa0064350-mRNA-1
Gene Sequence

>Msa0064350

ATGTCATCACTGGGAACATCGAAGGGGATTCTAGAAATTGCAAAGTTTGGTGTATACGTAACTGTACCAATCGTTCTTATGTACGTTTATGCTAGCAATACCGACAACTCCCTCCACAAATTCATCGGAAAAAAGTCATACATTGAATATCCCAAGGATACAAATACGCCACCGCCACCAGAGGAACTTAGGGAAATGGCGAGGGAGCTAGCTCGCAAAAGGAACAATCACTGA

Protein sequence

>Msa0064350

MSSLGTSKGILEIAKFGVYVTVPIVLMYVYASNTDNSLHKFIGKKSYIEYPKDTNTPPPPEELREMARELARKRNNH*