AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0968310

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0968310 MtrunA17_Chr7g0263831 92.857 84 6 0 1 84 1 84 1.03e-29 100
Msa0968310 MtrunA17_Chr7g0263871 89.474 76 3 1 9 84 3 73 1.59e-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
Msa0968310 AT2G37120.1 78.689 61 13 0 24 84 16 76 6.03e-15 63.5
Msa0968310 AT3G53370.1 80.000 60 12 0 25 84 17 76 7.50e-13 58.2

Find 35 sgRNAs with CRISPR-Local

Find 116 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTAATAGTTCTCCTGGTTAT+TGG 0.281375 6_3:+98642426 Msa0968310:CDS
TTATGTAAGTATAATCAATT+AGG 0.364072 6_3:-98642773 None:intergenic
CAATGGACTCAAATGTTCTA+TGG 0.367098 6_3:+98642600 Msa0968310:three_prime_UTR
ACAAACCGTGGTGCAAACTT+TGG 0.386650 6_3:+98641972 Msa0968310:five_prime_UTR
GTTTAGAAAGCTGGATCTCT+AGG 0.416187 6_3:+98642390 Msa0968310:intron
TGGGGAAATGTTTAGAAAGC+TGG 0.417081 6_3:+98642381 Msa0968310:intron
GTCTCTGCACCTGGAGAGTA+GGG 0.431630 6_3:+98642576 Msa0968310:CDS
TACTTTAGCAATATATTTCG+TGG 0.434438 6_3:+98642730 Msa0968310:three_prime_UTR
GTCCATTGCCCCTACTCTCC+AGG 0.446840 6_3:-98642585 None:intergenic
ATGGCCGATGACTTTGAATT+CGG 0.448197 6_3:+98642042 Msa0968310:CDS
ACCAGGAGAACTATTAAGCC+TGG 0.450176 6_3:-98642420 None:intergenic
TTGCTGTTGACATTCCTCAT+AGG 0.463310 6_3:+98642453 Msa0968310:CDS
CCCAGGCTTAATAGTTCTCC+TGG 0.470539 6_3:+98642419 Msa0968310:CDS
ATAGTTCTCCTGGTTATTGG+TGG 0.478741 6_3:+98642429 Msa0968310:CDS
TCCTCCTTCCTTTGATCGCA+TGG 0.481901 6_3:+98642074 Msa0968310:CDS
TAGTTCTCCTGGTTATTGGT+GGG 0.495632 6_3:+98642430 Msa0968310:CDS
AAGCAAGGAGTCTCTGCACC+TGG 0.523372 6_3:+98642567 Msa0968310:CDS
AGTCTCTGCACCTGGAGAGT+AGG 0.526480 6_3:+98642575 Msa0968310:CDS
GAAGAGTACCATGCGATCAA+AGG 0.548062 6_3:-98642082 None:intergenic
TTTAGAAAGCTGGATCTCTA+GGG 0.566106 6_3:+98642391 Msa0968310:intron
GAATTCAAAGTCATCGGCCA+TGG 0.568004 6_3:-98642040 None:intergenic
CACCTGGAGAGTAGGGGCAA+TGG 0.575695 6_3:+98642583 Msa0968310:exon
ATCACTCACATCTTCAACCA+TGG 0.576797 6_3:+98642023 Msa0968310:exon
AGAGTGCATAATTTCCTATG+AGG 0.578802 6_3:-98642467 None:intergenic
ATCACCGAATTCAAAGTCAT+CGG 0.579370 6_3:-98642046 None:intergenic
CCAGGAGAACTATTAAGCCT+GGG 0.597197 6_3:-98642419 None:intergenic
CTCAAATGTTCTATGGAATG+TGG 0.598269 6_3:+98642607 Msa0968310:three_prime_UTR
ACAGCAACCCACCAATAACC+AGG 0.598951 6_3:-98642437 None:intergenic
AGTACCATGCGATCAAAGGA+AGG 0.619049 6_3:-98642078 None:intergenic
CGAATCCAAAGTTTGCACCA+CGG 0.626371 6_3:-98641977 None:intergenic
AATCTATTTAAAACAAACCG+TGG 0.654277 6_3:+98641960 Msa0968310:five_prime_UTR
GGATCTCTAGGGTTCAACCC+AGG 0.683092 6_3:+98642402 Msa0968310:CDS
ACCATGCGATCAAAGGAAGG+AGG 0.683503 6_3:-98642075 None:intergenic
TCTCTGCACCTGGAGAGTAG+GGG 0.689358 6_3:+98642577 Msa0968310:CDS
ACTTTCTGTCAATAACACAC+AGG 0.703987 6_3:-98642690 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTATGTAAGTATAATCAATT+AGG - chr6_3:98642776-98642795 None:intergenic 15.0%
!! TTATGTAAGTATAATCAATT+AGG - chr6_3:98642776-98642795 None:intergenic 15.0%
!! TTAAGTTTAACTATATGTGT+TGG - chr6_3:98642227-98642246 None:intergenic 20.0%
!!! AGAATTGTTTAAAAAGTACA+AGG - chr6_3:98642637-98642656 None:intergenic 20.0%
!! TTAAGTTTAACTATATGTGT+TGG - chr6_3:98642227-98642246 None:intergenic 20.0%
!!! AGAATTGTTTAAAAAGTACA+AGG - chr6_3:98642637-98642656 None:intergenic 20.0%
!! AATCTATTTAAAACAAACCG+TGG + chr6_3:98641960-98641979 Msa0968310:five_prime_UTR 25.0%
! ATGAGATGTAAGAAAAGAAA+AGG - chr6_3:98642107-98642126 None:intergenic 25.0%
! TTCAAATTATTATGCTAGCT+CGG + chr6_3:98642259-98642278 Msa0968310:intron 25.0%
! ATAACACAGAGCAATTAAAT+CGG - chr6_3:98642331-98642350 None:intergenic 25.0%
!! TTAATCAAGTTTTTGCTCTT+GGG + chr6_3:98642362-98642381 Msa0968310:intron 25.0%
! CTCAAAAAAGAAGATGAAAA+AGG + chr6_3:98642536-98642555 Msa0968310:CDS 25.0%
! TACTTTAGCAATATATTTCG+TGG + chr6_3:98642730-98642749 Msa0968310:three_prime_UTR 25.0%
!! AATCTATTTAAAACAAACCG+TGG + chr6_3:98641960-98641979 Msa0968310:five_prime_UTR 25.0%
! ATGAGATGTAAGAAAAGAAA+AGG - chr6_3:98642107-98642126 None:intergenic 25.0%
! TTCAAATTATTATGCTAGCT+CGG + chr6_3:98642259-98642278 Msa0968310:intron 25.0%
! ATAACACAGAGCAATTAAAT+CGG - chr6_3:98642331-98642350 None:intergenic 25.0%
!! TTAATCAAGTTTTTGCTCTT+GGG + chr6_3:98642362-98642381 Msa0968310:intron 25.0%
! CTCAAAAAAGAAGATGAAAA+AGG + chr6_3:98642536-98642555 Msa0968310:CDS 25.0%
! TACTTTAGCAATATATTTCG+TGG + chr6_3:98642730-98642749 Msa0968310:three_prime_UTR 25.0%
TCTTTAGATTAGACATGTCT+TGG + chr6_3:98642175-98642194 Msa0968310:intron 30.0%
! TTAACTATATGTGTTGGTGT+CGG - chr6_3:98642221-98642240 None:intergenic 30.0%
CAAGAGCAAAAACTTGATTA+AGG - chr6_3:98642363-98642382 None:intergenic 30.0%
! CTTAATCAAGTTTTTGCTCT+TGG + chr6_3:98642361-98642380 Msa0968310:intron 30.0%
! TAATCAAGTTTTTGCTCTTG+GGG + chr6_3:98642363-98642382 Msa0968310:intron 30.0%
TTAATAGTTCTCCTGGTTAT+TGG + chr6_3:98642426-98642445 Msa0968310:CDS 30.0%
!!! TTCATCTTCTTTTTTGAGAC+TGG - chr6_3:98642534-98642553 None:intergenic 30.0%
TCTTTAGATTAGACATGTCT+TGG + chr6_3:98642175-98642194 Msa0968310:intron 30.0%
! TTAACTATATGTGTTGGTGT+CGG - chr6_3:98642221-98642240 None:intergenic 30.0%
CAAGAGCAAAAACTTGATTA+AGG - chr6_3:98642363-98642382 None:intergenic 30.0%
! CTTAATCAAGTTTTTGCTCT+TGG + chr6_3:98642361-98642380 Msa0968310:intron 30.0%
! TAATCAAGTTTTTGCTCTTG+GGG + chr6_3:98642363-98642382 Msa0968310:intron 30.0%
TTAATAGTTCTCCTGGTTAT+TGG + chr6_3:98642426-98642445 Msa0968310:CDS 30.0%
!!! TTCATCTTCTTTTTTGAGAC+TGG - chr6_3:98642534-98642553 None:intergenic 30.0%
ATCACCGAATTCAAAGTCAT+CGG - chr6_3:98642049-98642068 None:intergenic 35.0%
TTTAGAAAGCTGGATCTCTA+GGG + chr6_3:98642391-98642410 Msa0968310:intron 35.0%
AGAGTGCATAATTTCCTATG+AGG - chr6_3:98642470-98642489 None:intergenic 35.0%
! CAATGGACTCAAATGTTCTA+TGG + chr6_3:98642600-98642619 Msa0968310:three_prime_UTR 35.0%
CTCAAATGTTCTATGGAATG+TGG + chr6_3:98642607-98642626 Msa0968310:three_prime_UTR 35.0%
ACTTTCTGTCAATAACACAC+AGG - chr6_3:98642693-98642712 None:intergenic 35.0%
ATCACCGAATTCAAAGTCAT+CGG - chr6_3:98642049-98642068 None:intergenic 35.0%
TTTAGAAAGCTGGATCTCTA+GGG + chr6_3:98642391-98642410 Msa0968310:intron 35.0%
AGAGTGCATAATTTCCTATG+AGG - chr6_3:98642470-98642489 None:intergenic 35.0%
! CAATGGACTCAAATGTTCTA+TGG + chr6_3:98642600-98642619 Msa0968310:three_prime_UTR 35.0%
CTCAAATGTTCTATGGAATG+TGG + chr6_3:98642607-98642626 Msa0968310:three_prime_UTR 35.0%
ACTTTCTGTCAATAACACAC+AGG - chr6_3:98642693-98642712 None:intergenic 35.0%
ATCACTCACATCTTCAACCA+TGG + chr6_3:98642023-98642042 Msa0968310:exon 40.0%
ATGGCCGATGACTTTGAATT+CGG + chr6_3:98642042-98642061 Msa0968310:CDS 40.0%
! GATTAGACATGTCTTGGTGT+AGG + chr6_3:98642181-98642200 Msa0968310:intron 40.0%
! ATTATTATGCTAGCTCGGTG+TGG + chr6_3:98642264-98642283 Msa0968310:intron 40.0%
TGGGGAAATGTTTAGAAAGC+TGG + chr6_3:98642381-98642400 Msa0968310:intron 40.0%
GTTTAGAAAGCTGGATCTCT+AGG + chr6_3:98642390-98642409 Msa0968310:intron 40.0%
ATAGTTCTCCTGGTTATTGG+TGG + chr6_3:98642429-98642448 Msa0968310:CDS 40.0%
TAGTTCTCCTGGTTATTGGT+GGG + chr6_3:98642430-98642449 Msa0968310:CDS 40.0%
! TTGCTGTTGACATTCCTCAT+AGG + chr6_3:98642453-98642472 Msa0968310:CDS 40.0%
!!! CTTCTTTTTTCTAGGAGGGA+GGG - chr6_3:98642511-98642530 None:intergenic 40.0%
!!! CTGGCTTCTTTTTTCTAGGA+GGG - chr6_3:98642515-98642534 None:intergenic 40.0%
!!! ACTGGCTTCTTTTTTCTAGG+AGG - chr6_3:98642516-98642535 None:intergenic 40.0%
!!! GAGACTGGCTTCTTTTTTCT+AGG - chr6_3:98642519-98642538 None:intergenic 40.0%
AAAAAGGAGAGACTGAAGCA+AGG + chr6_3:98642552-98642571 Msa0968310:CDS 40.0%
ATCACTCACATCTTCAACCA+TGG + chr6_3:98642023-98642042 Msa0968310:exon 40.0%
ATGGCCGATGACTTTGAATT+CGG + chr6_3:98642042-98642061 Msa0968310:CDS 40.0%
! GATTAGACATGTCTTGGTGT+AGG + chr6_3:98642181-98642200 Msa0968310:intron 40.0%
! ATTATTATGCTAGCTCGGTG+TGG + chr6_3:98642264-98642283 Msa0968310:intron 40.0%
TGGGGAAATGTTTAGAAAGC+TGG + chr6_3:98642381-98642400 Msa0968310:intron 40.0%
GTTTAGAAAGCTGGATCTCT+AGG + chr6_3:98642390-98642409 Msa0968310:intron 40.0%
ATAGTTCTCCTGGTTATTGG+TGG + chr6_3:98642429-98642448 Msa0968310:CDS 40.0%
TAGTTCTCCTGGTTATTGGT+GGG + chr6_3:98642430-98642449 Msa0968310:CDS 40.0%
! TTGCTGTTGACATTCCTCAT+AGG + chr6_3:98642453-98642472 Msa0968310:CDS 40.0%
!!! CTTCTTTTTTCTAGGAGGGA+GGG - chr6_3:98642511-98642530 None:intergenic 40.0%
!!! CTGGCTTCTTTTTTCTAGGA+GGG - chr6_3:98642515-98642534 None:intergenic 40.0%
!!! ACTGGCTTCTTTTTTCTAGG+AGG - chr6_3:98642516-98642535 None:intergenic 40.0%
!!! GAGACTGGCTTCTTTTTTCT+AGG - chr6_3:98642519-98642538 None:intergenic 40.0%
AAAAAGGAGAGACTGAAGCA+AGG + chr6_3:98642552-98642571 Msa0968310:CDS 40.0%
ACAAACCGTGGTGCAAACTT+TGG + chr6_3:98641972-98641991 Msa0968310:five_prime_UTR 45.0%
CGAATCCAAAGTTTGCACCA+CGG - chr6_3:98641980-98641999 None:intergenic 45.0%
GAATTCAAAGTCATCGGCCA+TGG - chr6_3:98642043-98642062 None:intergenic 45.0%
AGTACCATGCGATCAAAGGA+AGG - chr6_3:98642081-98642100 None:intergenic 45.0%
!! GAAGAGTACCATGCGATCAA+AGG - chr6_3:98642085-98642104 None:intergenic 45.0%
!! CTATATGTGTTGGTGTCGGA+CGG - chr6_3:98642217-98642236 None:intergenic 45.0%
CCAGGAGAACTATTAAGCCT+GGG - chr6_3:98642422-98642441 None:intergenic 45.0%
ACCAGGAGAACTATTAAGCC+TGG - chr6_3:98642423-98642442 None:intergenic 45.0%
!!! GCTTCTTTTTTCTAGGAGGG+AGG - chr6_3:98642512-98642531 None:intergenic 45.0%
ACAAACCGTGGTGCAAACTT+TGG + chr6_3:98641972-98641991 Msa0968310:five_prime_UTR 45.0%
CGAATCCAAAGTTTGCACCA+CGG - chr6_3:98641980-98641999 None:intergenic 45.0%
GAATTCAAAGTCATCGGCCA+TGG - chr6_3:98642043-98642062 None:intergenic 45.0%
AGTACCATGCGATCAAAGGA+AGG - chr6_3:98642081-98642100 None:intergenic 45.0%
!! GAAGAGTACCATGCGATCAA+AGG - chr6_3:98642085-98642104 None:intergenic 45.0%
!! CTATATGTGTTGGTGTCGGA+CGG - chr6_3:98642217-98642236 None:intergenic 45.0%
CCAGGAGAACTATTAAGCCT+GGG - chr6_3:98642422-98642441 None:intergenic 45.0%
ACCAGGAGAACTATTAAGCC+TGG - chr6_3:98642423-98642442 None:intergenic 45.0%
!!! GCTTCTTTTTTCTAGGAGGG+AGG - chr6_3:98642512-98642531 None:intergenic 45.0%
TCCTCCTTCCTTTGATCGCA+TGG + chr6_3:98642074-98642093 Msa0968310:CDS 50.0%
ACCATGCGATCAAAGGAAGG+AGG - chr6_3:98642078-98642097 None:intergenic 50.0%
!! AAGAGTGTCTGCGTGTGAGA+TGG - chr6_3:98642159-98642178 None:intergenic 50.0%
CCCAGGCTTAATAGTTCTCC+TGG + chr6_3:98642419-98642438 Msa0968310:CDS 50.0%
ACAGCAACCCACCAATAACC+AGG - chr6_3:98642440-98642459 None:intergenic 50.0%
TCCTCCTTCCTTTGATCGCA+TGG + chr6_3:98642074-98642093 Msa0968310:CDS 50.0%
ACCATGCGATCAAAGGAAGG+AGG - chr6_3:98642078-98642097 None:intergenic 50.0%
!! AAGAGTGTCTGCGTGTGAGA+TGG - chr6_3:98642159-98642178 None:intergenic 50.0%
CCCAGGCTTAATAGTTCTCC+TGG + chr6_3:98642419-98642438 Msa0968310:CDS 50.0%
ACAGCAACCCACCAATAACC+AGG - chr6_3:98642440-98642459 None:intergenic 50.0%
!! GGATCTCTAGGGTTCAACCC+AGG + chr6_3:98642402-98642421 Msa0968310:CDS 55.0%
AAGCAAGGAGTCTCTGCACC+TGG + chr6_3:98642567-98642586 Msa0968310:CDS 55.0%
AGTCTCTGCACCTGGAGAGT+AGG + chr6_3:98642575-98642594 Msa0968310:CDS 55.0%
GTCTCTGCACCTGGAGAGTA+GGG + chr6_3:98642576-98642595 Msa0968310:CDS 55.0%
TCTCTGCACCTGGAGAGTAG+GGG + chr6_3:98642577-98642596 Msa0968310:CDS 55.0%
!! GGATCTCTAGGGTTCAACCC+AGG + chr6_3:98642402-98642421 Msa0968310:CDS 55.0%
AAGCAAGGAGTCTCTGCACC+TGG + chr6_3:98642567-98642586 Msa0968310:CDS 55.0%
AGTCTCTGCACCTGGAGAGT+AGG + chr6_3:98642575-98642594 Msa0968310:CDS 55.0%
GTCTCTGCACCTGGAGAGTA+GGG + chr6_3:98642576-98642595 Msa0968310:CDS 55.0%
TCTCTGCACCTGGAGAGTAG+GGG + chr6_3:98642577-98642596 Msa0968310:CDS 55.0%
CACCTGGAGAGTAGGGGCAA+TGG + chr6_3:98642583-98642602 Msa0968310:exon 60.0%
GTCCATTGCCCCTACTCTCC+AGG - chr6_3:98642588-98642607 None:intergenic 60.0%
CACCTGGAGAGTAGGGGCAA+TGG + chr6_3:98642583-98642602 Msa0968310:exon 60.0%
GTCCATTGCCCCTACTCTCC+AGG - chr6_3:98642588-98642607 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr6_3 gene 98641951 98642828 98641951 ID=Msa0968310;Name=Msa0968310
chr6_3 mRNA 98641951 98642828 98641951 ID=Msa0968310-mRNA-1;Parent=Msa0968310;Name=Msa0968310-mRNA-1;_AED=0.02;_eAED=0.02;_QI=91|1|1|1|1|1|2|232|84
chr6_3 exon 98641951 98642095 98641951 ID=Msa0968310-mRNA-1:exon:18535;Parent=Msa0968310-mRNA-1
chr6_3 exon 98642396 98642828 98642396 ID=Msa0968310-mRNA-1:exon:18536;Parent=Msa0968310-mRNA-1
chr6_3 five_prime_UTR 98641951 98642041 98641951 ID=Msa0968310-mRNA-1:five_prime_utr;Parent=Msa0968310-mRNA-1
chr6_3 CDS 98642042 98642095 98642042 ID=Msa0968310-mRNA-1:cds;Parent=Msa0968310-mRNA-1
chr6_3 CDS 98642396 98642596 98642396 ID=Msa0968310-mRNA-1:cds;Parent=Msa0968310-mRNA-1
chr6_3 three_prime_UTR 98642597 98642828 98642597 ID=Msa0968310-mRNA-1:three_prime_utr;Parent=Msa0968310-mRNA-1
Gene Sequence

>Msa0968310

ATGGCCGATGACTTTGAATTCGGTGATAAAGTTCCTCCTTCCTTTGATCGCATGAAAGCTGGATCTCTAGGGTTCAACCCAGGCTTAATAGTTCTCCTGGTTATTGGTGGGTTGCTGTTGACATTCCTCATAGGAAATTATGCACTCTACGTTTATGCACAGAAGACCCTCCCTCCTAGAAAAAAGAAGCCAGTCTCAAAAAAGAAGATGAAAAAGGAGAGACTGAAGCAAGGAGTCTCTGCACCTGGAGAGTAG
Protein sequence

>Msa0968310

MADDFEFGDKVPPSFDRMKAGSLGFNPGLIVLLVIGGLLLTFLIGNYALYVYAQKTLPPRKKKPVSKKKMKKERLKQGVSAPGE*