AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1079080

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1079080 MtrunA17_Chr7g0263831 94.048 84 5 0 1 84 1 84 1.02e-30 103
Msa1079080 MtrunA17_Chr7g0263871 89.474 76 3 1 9 84 3 73 1.30e-17 70.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1079080 AT2G37120.1 77.778 63 14 0 22 84 14 76 2.54e-15 64.7
Msa1079080 AT3G53370.1 78.333 60 13 0 25 84 17 76 6.72e-13 58.5

Find 36 sgRNAs with CRISPR-Local

Find 118 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTAATAGTTCTCCTGGTTAT+TGG 0.281375 7_2:-78098158 Msa1079080:CDS
TTATGTAAGTATAATCAATT+AGG 0.364072 7_2:+78097811 None:intergenic
ACAAACCGTGGTGCAAACTT+TGG 0.386650 7_2:-78098626 Msa1079080:five_prime_UTR
TGGGGAAATGTTTAGAAAGC+TGG 0.417081 7_2:-78098203 Msa1079080:intron
GTCTCTGCACCTGGAGAGTA+GGG 0.431630 7_2:-78098008 Msa1079080:exon
TACTTTAGCAATATATTTCG+TGG 0.434438 7_2:-78097854 Msa1079080:three_prime_UTR
GTCCATTGCCCCTACTCTCC+AGG 0.446840 7_2:+78097999 None:intergenic
ATGGCCGATGACTTTGAATT+CGG 0.448197 7_2:-78098556 Msa1079080:CDS
ACCAGGAGAACTATTAAGCC+TGG 0.450176 7_2:+78098164 None:intergenic
TTGCTGTTGACATTCCTCAT+AGG 0.463310 7_2:-78098131 Msa1079080:CDS
CCCAGGCTTAATAGTTCTCC+TGG 0.470539 7_2:-78098165 Msa1079080:CDS
ATAGTTCTCCTGGTTATTGG+TGG 0.478741 7_2:-78098155 Msa1079080:CDS
GTTTAGAAAGCTGGATCTCA+AGG 0.480415 7_2:-78098194 Msa1079080:intron
TCCTCCTTCCTTTGATCGCA+TGG 0.481901 7_2:-78098524 Msa1079080:intron
TAGTTCTCCTGGTTATTGGT+GGG 0.495632 7_2:-78098154 Msa1079080:CDS
CAATGGACTCAAATGTCCTA+TGG 0.502962 7_2:-78097984 Msa1079080:three_prime_UTR
AAGCAAGGAGTCTCTGCACC+TGG 0.523372 7_2:-78098017 Msa1079080:CDS
AGTCTCTGCACCTGGAGAGT+AGG 0.526480 7_2:-78098009 Msa1079080:exon
GAAGAGTACCATGCGATCAA+AGG 0.548062 7_2:+78098516 None:intergenic
GAATTCAAAGTCATCGGCCA+TGG 0.568004 7_2:+78098558 None:intergenic
ATCATTCACATCTTCAACCA+TGG 0.569977 7_2:-78098575 Msa1079080:exon
CACCTGGAGAGTAGGGGCAA+TGG 0.575695 7_2:-78098001 Msa1079080:exon
AGAGTGCATAATTTCCTATG+AGG 0.578802 7_2:+78098117 None:intergenic
ATCACCGAATTCAAAGTCAT+CGG 0.579370 7_2:+78098552 None:intergenic
CCAGGAGAACTATTAAGCCT+GGG 0.597197 7_2:+78098165 None:intergenic
ACAGCAACCCACCAATAACC+AGG 0.598951 7_2:+78098147 None:intergenic
CTCAAATGTCCTATGGAATG+TGG 0.605574 7_2:-78097977 Msa1079080:three_prime_UTR
CAAGGTAATCCACATTCCAT+AGG 0.609050 7_2:+78097968 None:intergenic
TTTAGAAAGCTGGATCTCAA+GGG 0.612528 7_2:-78098193 Msa1079080:intron
AGTACCATGCGATCAAAGGA+AGG 0.619049 7_2:+78098520 None:intergenic
GGATCTCAAGGGTTCAACCC+AGG 0.620507 7_2:-78098182 Msa1079080:CDS
AATCTATTTAAAACAAACCG+TGG 0.654277 7_2:-78098638 Msa1079080:five_prime_UTR
CTAATCCAAAGTTTGCACCA+CGG 0.680497 7_2:+78098621 None:intergenic
ACCATGCGATCAAAGGAAGG+AGG 0.683503 7_2:+78098523 None:intergenic
TCTCTGCACCTGGAGAGTAG+GGG 0.689358 7_2:-78098007 Msa1079080:exon
ACTTTCTGTCAATAACACAC+AGG 0.703987 7_2:+78097894 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAGATAAAAAACTTGATTA+AGG + chr7_2:78098203-78098222 None:intergenic 15.0%
!! TTATGTAAGTATAATCAATT+AGG + chr7_2:78098630-78098649 None:intergenic 15.0%
!! AAAGATAAAAAACTTGATTA+AGG + chr7_2:78098203-78098222 None:intergenic 15.0%
!! TTATGTAAGTATAATCAATT+AGG + chr7_2:78098630-78098649 None:intergenic 15.0%
!! ATAGTTAAGTTTAGCTATAT+GGG + chr7_2:78098071-78098090 None:intergenic 20.0%
!!! AGAATTGTTTAAAAAGTACA+AGG + chr7_2:78098491-78098510 None:intergenic 20.0%
!! ATAGTTAAGTTTAGCTATAT+GGG + chr7_2:78098071-78098090 None:intergenic 20.0%
!!! AGAATTGTTTAAAAAGTACA+AGG + chr7_2:78098491-78098510 None:intergenic 20.0%
!! AATCTATTTAAAACAAACCG+TGG - chr7_2:78097800-78097819 Msa1079080:three_prime_UTR 25.0%
! ATGAGATGTAAGAAAAGAAA+AGG + chr7_2:78097947-78097966 None:intergenic 25.0%
! CATAGTTAAGTTTAGCTATA+TGG + chr7_2:78098072-78098091 None:intergenic 25.0%
! CTCAAAAAAGAAGATGAAAA+AGG - chr7_2:78098390-78098409 Msa1079080:intron 25.0%
! TACTTTAGCAATATATTTCG+TGG - chr7_2:78098584-78098603 Msa1079080:five_prime_UTR 25.0%
!! AATCTATTTAAAACAAACCG+TGG - chr7_2:78097800-78097819 Msa1079080:three_prime_UTR 25.0%
! ATGAGATGTAAGAAAAGAAA+AGG + chr7_2:78097947-78097966 None:intergenic 25.0%
! CATAGTTAAGTTTAGCTATA+TGG + chr7_2:78098072-78098091 None:intergenic 25.0%
! CTCAAAAAAGAAGATGAAAA+AGG - chr7_2:78098390-78098409 Msa1079080:intron 25.0%
! TACTTTAGCAATATATTTCG+TGG - chr7_2:78098584-78098603 Msa1079080:five_prime_UTR 25.0%
TCTTTAGATTAGACATGTCT+TGG - chr7_2:78098015-78098034 Msa1079080:CDS 30.0%
TTAAGTTTAGCTATATGGGT+TGG + chr7_2:78098067-78098086 None:intergenic 30.0%
!!! TTATCTTTTGTTGTTGCTCT+TGG - chr7_2:78098215-78098234 Msa1079080:intron 30.0%
!!! TATCTTTTGTTGTTGCTCTT+GGG - chr7_2:78098216-78098235 Msa1079080:intron 30.0%
TTAATAGTTCTCCTGGTTAT+TGG - chr7_2:78098280-78098299 Msa1079080:intron 30.0%
!!! TTCATCTTCTTTTTTGAGAG+TGG + chr7_2:78098388-78098407 None:intergenic 30.0%
TCTTTAGATTAGACATGTCT+TGG - chr7_2:78098015-78098034 Msa1079080:CDS 30.0%
TTAAGTTTAGCTATATGGGT+TGG + chr7_2:78098067-78098086 None:intergenic 30.0%
!!! TTATCTTTTGTTGTTGCTCT+TGG - chr7_2:78098215-78098234 Msa1079080:intron 30.0%
!!! TATCTTTTGTTGTTGCTCTT+GGG - chr7_2:78098216-78098235 Msa1079080:intron 30.0%
TTAATAGTTCTCCTGGTTAT+TGG - chr7_2:78098280-78098299 Msa1079080:intron 30.0%
!!! TTCATCTTCTTTTTTGAGAG+TGG + chr7_2:78098388-78098407 None:intergenic 30.0%
ATCATTCACATCTTCAACCA+TGG - chr7_2:78097863-78097882 Msa1079080:three_prime_UTR 35.0%
ATCACCGAATTCAAAGTCAT+CGG + chr7_2:78097889-78097908 None:intergenic 35.0%
ATTATTATGCTAGCTCGATG+TGG - chr7_2:78098104-78098123 Msa1079080:CDS 35.0%
!!! ATCTTTTGTTGTTGCTCTTG+GGG - chr7_2:78098217-78098236 Msa1079080:intron 35.0%
TTTAGAAAGCTGGATCTCAA+GGG - chr7_2:78098245-78098264 Msa1079080:intron 35.0%
AGAGTGCATAATTTCCTATG+AGG + chr7_2:78098324-78098343 None:intergenic 35.0%
ACTTTCTGTCAATAACACAC+AGG + chr7_2:78098547-78098566 None:intergenic 35.0%
ATCATTCACATCTTCAACCA+TGG - chr7_2:78097863-78097882 Msa1079080:three_prime_UTR 35.0%
ATCACCGAATTCAAAGTCAT+CGG + chr7_2:78097889-78097908 None:intergenic 35.0%
ATTATTATGCTAGCTCGATG+TGG - chr7_2:78098104-78098123 Msa1079080:CDS 35.0%
!!! ATCTTTTGTTGTTGCTCTTG+GGG - chr7_2:78098217-78098236 Msa1079080:intron 35.0%
TTTAGAAAGCTGGATCTCAA+GGG - chr7_2:78098245-78098264 Msa1079080:intron 35.0%
AGAGTGCATAATTTCCTATG+AGG + chr7_2:78098324-78098343 None:intergenic 35.0%
ACTTTCTGTCAATAACACAC+AGG + chr7_2:78098547-78098566 None:intergenic 35.0%
CTAATCCAAAGTTTGCACCA+CGG + chr7_2:78097820-78097839 None:intergenic 40.0%
ATGGCCGATGACTTTGAATT+CGG - chr7_2:78097882-78097901 Msa1079080:three_prime_UTR 40.0%
! GATTAGACATGTCTTGGTGT+AGG - chr7_2:78098021-78098040 Msa1079080:CDS 40.0%
!! TTAGCTATATGGGTTGGTGT+CGG + chr7_2:78098061-78098080 None:intergenic 40.0%
TGGGGAAATGTTTAGAAAGC+TGG - chr7_2:78098235-78098254 Msa1079080:intron 40.0%
GTTTAGAAAGCTGGATCTCA+AGG - chr7_2:78098244-78098263 Msa1079080:intron 40.0%
ATAGTTCTCCTGGTTATTGG+TGG - chr7_2:78098283-78098302 Msa1079080:intron 40.0%
TAGTTCTCCTGGTTATTGGT+GGG - chr7_2:78098284-78098303 Msa1079080:intron 40.0%
! TTGCTGTTGACATTCCTCAT+AGG - chr7_2:78098307-78098326 Msa1079080:intron 40.0%
!!! CTTCTTTTTTCTAGGAGGGA+GGG + chr7_2:78098365-78098384 None:intergenic 40.0%
!!! GTGGCTTCTTTTTTCTAGGA+GGG + chr7_2:78098369-78098388 None:intergenic 40.0%
!!! AGTGGCTTCTTTTTTCTAGG+AGG + chr7_2:78098370-78098389 None:intergenic 40.0%
!!! GAGAGTGGCTTCTTTTTTCT+AGG + chr7_2:78098373-78098392 None:intergenic 40.0%
AAAAAGGAGAGACTGAAGCA+AGG - chr7_2:78098406-78098425 Msa1079080:intron 40.0%
! CAATGGACTCAAATGTCCTA+TGG - chr7_2:78098454-78098473 Msa1079080:intron 40.0%
CTCAAATGTCCTATGGAATG+TGG - chr7_2:78098461-78098480 Msa1079080:intron 40.0%
CAAGGTAATCCACATTCCAT+AGG + chr7_2:78098473-78098492 None:intergenic 40.0%
CTAATCCAAAGTTTGCACCA+CGG + chr7_2:78097820-78097839 None:intergenic 40.0%
ATGGCCGATGACTTTGAATT+CGG - chr7_2:78097882-78097901 Msa1079080:three_prime_UTR 40.0%
! GATTAGACATGTCTTGGTGT+AGG - chr7_2:78098021-78098040 Msa1079080:CDS 40.0%
!! TTAGCTATATGGGTTGGTGT+CGG + chr7_2:78098061-78098080 None:intergenic 40.0%
TGGGGAAATGTTTAGAAAGC+TGG - chr7_2:78098235-78098254 Msa1079080:intron 40.0%
GTTTAGAAAGCTGGATCTCA+AGG - chr7_2:78098244-78098263 Msa1079080:intron 40.0%
ATAGTTCTCCTGGTTATTGG+TGG - chr7_2:78098283-78098302 Msa1079080:intron 40.0%
TAGTTCTCCTGGTTATTGGT+GGG - chr7_2:78098284-78098303 Msa1079080:intron 40.0%
! TTGCTGTTGACATTCCTCAT+AGG - chr7_2:78098307-78098326 Msa1079080:intron 40.0%
!!! CTTCTTTTTTCTAGGAGGGA+GGG + chr7_2:78098365-78098384 None:intergenic 40.0%
!!! GTGGCTTCTTTTTTCTAGGA+GGG + chr7_2:78098369-78098388 None:intergenic 40.0%
!!! AGTGGCTTCTTTTTTCTAGG+AGG + chr7_2:78098370-78098389 None:intergenic 40.0%
!!! GAGAGTGGCTTCTTTTTTCT+AGG + chr7_2:78098373-78098392 None:intergenic 40.0%
AAAAAGGAGAGACTGAAGCA+AGG - chr7_2:78098406-78098425 Msa1079080:intron 40.0%
! CAATGGACTCAAATGTCCTA+TGG - chr7_2:78098454-78098473 Msa1079080:intron 40.0%
CTCAAATGTCCTATGGAATG+TGG - chr7_2:78098461-78098480 Msa1079080:intron 40.0%
CAAGGTAATCCACATTCCAT+AGG + chr7_2:78098473-78098492 None:intergenic 40.0%
ACAAACCGTGGTGCAAACTT+TGG - chr7_2:78097812-78097831 Msa1079080:three_prime_UTR 45.0%
GAATTCAAAGTCATCGGCCA+TGG + chr7_2:78097883-78097902 None:intergenic 45.0%
AGTACCATGCGATCAAAGGA+AGG + chr7_2:78097921-78097940 None:intergenic 45.0%
!! GAAGAGTACCATGCGATCAA+AGG + chr7_2:78097925-78097944 None:intergenic 45.0%
CCAGGAGAACTATTAAGCCT+GGG + chr7_2:78098276-78098295 None:intergenic 45.0%
ACCAGGAGAACTATTAAGCC+TGG + chr7_2:78098277-78098296 None:intergenic 45.0%
!!! GCTTCTTTTTTCTAGGAGGG+AGG + chr7_2:78098366-78098385 None:intergenic 45.0%
ACAAACCGTGGTGCAAACTT+TGG - chr7_2:78097812-78097831 Msa1079080:three_prime_UTR 45.0%
GAATTCAAAGTCATCGGCCA+TGG + chr7_2:78097883-78097902 None:intergenic 45.0%
AGTACCATGCGATCAAAGGA+AGG + chr7_2:78097921-78097940 None:intergenic 45.0%
!! GAAGAGTACCATGCGATCAA+AGG + chr7_2:78097925-78097944 None:intergenic 45.0%
CCAGGAGAACTATTAAGCCT+GGG + chr7_2:78098276-78098295 None:intergenic 45.0%
ACCAGGAGAACTATTAAGCC+TGG + chr7_2:78098277-78098296 None:intergenic 45.0%
!!! GCTTCTTTTTTCTAGGAGGG+AGG + chr7_2:78098366-78098385 None:intergenic 45.0%
TCCTCCTTCCTTTGATCGCA+TGG - chr7_2:78097914-78097933 Msa1079080:three_prime_UTR 50.0%
ACCATGCGATCAAAGGAAGG+AGG + chr7_2:78097918-78097937 None:intergenic 50.0%
!! AAGAGTGTCTGCGTGTGAGA+TGG + chr7_2:78097999-78098018 None:intergenic 50.0%
!! CTATATGGGTTGGTGTCGGA+CGG + chr7_2:78098057-78098076 None:intergenic 50.0%
CCCAGGCTTAATAGTTCTCC+TGG - chr7_2:78098273-78098292 Msa1079080:intron 50.0%
ACAGCAACCCACCAATAACC+AGG + chr7_2:78098294-78098313 None:intergenic 50.0%
TCCTCCTTCCTTTGATCGCA+TGG - chr7_2:78097914-78097933 Msa1079080:three_prime_UTR 50.0%
ACCATGCGATCAAAGGAAGG+AGG + chr7_2:78097918-78097937 None:intergenic 50.0%
!! AAGAGTGTCTGCGTGTGAGA+TGG + chr7_2:78097999-78098018 None:intergenic 50.0%
!! CTATATGGGTTGGTGTCGGA+CGG + chr7_2:78098057-78098076 None:intergenic 50.0%
CCCAGGCTTAATAGTTCTCC+TGG - chr7_2:78098273-78098292 Msa1079080:intron 50.0%
ACAGCAACCCACCAATAACC+AGG + chr7_2:78098294-78098313 None:intergenic 50.0%
GGATCTCAAGGGTTCAACCC+AGG - chr7_2:78098256-78098275 Msa1079080:intron 55.0%
AAGCAAGGAGTCTCTGCACC+TGG - chr7_2:78098421-78098440 Msa1079080:intron 55.0%
AGTCTCTGCACCTGGAGAGT+AGG - chr7_2:78098429-78098448 Msa1079080:intron 55.0%
GTCTCTGCACCTGGAGAGTA+GGG - chr7_2:78098430-78098449 Msa1079080:intron 55.0%
TCTCTGCACCTGGAGAGTAG+GGG - chr7_2:78098431-78098450 Msa1079080:intron 55.0%
GGATCTCAAGGGTTCAACCC+AGG - chr7_2:78098256-78098275 Msa1079080:intron 55.0%
AAGCAAGGAGTCTCTGCACC+TGG - chr7_2:78098421-78098440 Msa1079080:intron 55.0%
AGTCTCTGCACCTGGAGAGT+AGG - chr7_2:78098429-78098448 Msa1079080:intron 55.0%
GTCTCTGCACCTGGAGAGTA+GGG - chr7_2:78098430-78098449 Msa1079080:intron 55.0%
TCTCTGCACCTGGAGAGTAG+GGG - chr7_2:78098431-78098450 Msa1079080:intron 55.0%
CACCTGGAGAGTAGGGGCAA+TGG - chr7_2:78098437-78098456 Msa1079080:intron 60.0%
GTCCATTGCCCCTACTCTCC+AGG + chr7_2:78098442-78098461 None:intergenic 60.0%
CACCTGGAGAGTAGGGGCAA+TGG - chr7_2:78098437-78098456 Msa1079080:intron 60.0%
GTCCATTGCCCCTACTCTCC+AGG + chr7_2:78098442-78098461 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 78097791 78098669 78097791 ID=Msa1079080;Name=Msa1079080
chr7_2 mRNA 78097791 78098669 78097791 ID=Msa1079080-mRNA-1;Parent=Msa1079080;Name=Msa1079080-mRNA-1;_AED=0.00;_eAED=0.00;_QI=91|1|1|1|1|1|2|219|84
chr7_2 exon 78097791 78098210 78097791 ID=Msa1079080-mRNA-1:exon:19421;Parent=Msa1079080-mRNA-1
chr7_2 exon 78098525 78098669 78098525 ID=Msa1079080-mRNA-1:exon:19420;Parent=Msa1079080-mRNA-1
chr7_2 five_prime_UTR 78098579 78098669 78098579 ID=Msa1079080-mRNA-1:five_prime_utr;Parent=Msa1079080-mRNA-1
chr7_2 CDS 78098525 78098578 78098525 ID=Msa1079080-mRNA-1:cds;Parent=Msa1079080-mRNA-1
chr7_2 CDS 78098010 78098210 78098010 ID=Msa1079080-mRNA-1:cds;Parent=Msa1079080-mRNA-1
chr7_2 three_prime_UTR 78097791 78098009 78097791 ID=Msa1079080-mRNA-1:three_prime_utr;Parent=Msa1079080-mRNA-1
Gene Sequence

>Msa1079080

ATGGCCGATGACTTTGAATTCGGTGATAAAGTTCCTCCTTCCTTTGATCGCATGAAAGCTGGATCTCAAGGGTTCAACCCAGGCTTAATAGTTCTCCTGGTTATTGGTGGGTTGCTGTTGACATTCCTCATAGGAAATTATGCACTCTACGTTTATGCACAGAAGACCCTCCCTCCTAGAAAAAAGAAGCCACTCTCAAAAAAGAAGATGAAAAAGGAGAGACTGAAGCAAGGAGTCTCTGCACCTGGAGAGTAG
Protein sequence

>Msa1079080

MADDFEFGDKVPPSFDRMKAGSQGFNPGLIVLLVIGGLLLTFLIGNYALYVYAQKTLPPRKKKPLSKKKMKKERLKQGVSAPGE*