AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1170030

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1170030 MtrunA17_Chr7g0263831 92.857 84 6 0 1 84 1 84 1.03e-29 100
Msa1170030 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
Msa1170030 AT2G37120.1 78.689 61 13 0 24 84 16 76 6.03e-15 63.5
Msa1170030 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 7_4:+63134807 Msa1170030:CDS
TTATGTAAGTATAATCAATT+AGG 0.364072 7_4:-63135154 None:intergenic
CAATGGACTCAAATGTTCTA+TGG 0.367098 7_4:+63134981 Msa1170030:three_prime_UTR
ACAAACCGTGGTGCAAACTT+TGG 0.386650 7_4:+63134353 Msa1170030:five_prime_UTR
GTTTAGAAAGCTGGATCTCT+AGG 0.416187 7_4:+63134771 Msa1170030:intron
TGGGGAAATGTTTAGAAAGC+TGG 0.417081 7_4:+63134762 Msa1170030:intron
GTCTCTGCACCTGGAGAGTA+GGG 0.431630 7_4:+63134957 Msa1170030:CDS
TACTTTAGCAATATATTTCG+TGG 0.434438 7_4:+63135111 Msa1170030:three_prime_UTR
GTCCATTGCCCCTACTCTCC+AGG 0.446840 7_4:-63134966 None:intergenic
ATGGCCGATGACTTTGAATT+CGG 0.448197 7_4:+63134423 Msa1170030:CDS
ACCAGGAGAACTATTAAGCC+TGG 0.450176 7_4:-63134801 None:intergenic
TTGCTGTTGACATTCCTCAT+AGG 0.463310 7_4:+63134834 Msa1170030:CDS
CCCAGGCTTAATAGTTCTCC+TGG 0.470539 7_4:+63134800 Msa1170030:CDS
ATAGTTCTCCTGGTTATTGG+TGG 0.478741 7_4:+63134810 Msa1170030:CDS
TCCTCCTTCCTTTGATCGCA+TGG 0.481901 7_4:+63134455 Msa1170030:CDS
TAGTTCTCCTGGTTATTGGT+GGG 0.495632 7_4:+63134811 Msa1170030:CDS
AAGCAAGGAGTCTCTGCACC+TGG 0.523372 7_4:+63134948 Msa1170030:CDS
AGTCTCTGCACCTGGAGAGT+AGG 0.526480 7_4:+63134956 Msa1170030:CDS
GAAGAGTACCATGCGATCAA+AGG 0.548062 7_4:-63134463 None:intergenic
TTTAGAAAGCTGGATCTCTA+GGG 0.566106 7_4:+63134772 Msa1170030:intron
GAATTCAAAGTCATCGGCCA+TGG 0.568004 7_4:-63134421 None:intergenic
CACCTGGAGAGTAGGGGCAA+TGG 0.575695 7_4:+63134964 Msa1170030:exon
ATCACTCACATCTTCAACCA+TGG 0.576797 7_4:+63134404 Msa1170030:exon
AGAGTGCATAATTTCCTATG+AGG 0.578802 7_4:-63134848 None:intergenic
ATCACCGAATTCAAAGTCAT+CGG 0.579370 7_4:-63134427 None:intergenic
CCAGGAGAACTATTAAGCCT+GGG 0.597197 7_4:-63134800 None:intergenic
CTCAAATGTTCTATGGAATG+TGG 0.598269 7_4:+63134988 Msa1170030:three_prime_UTR
ACAGCAACCCACCAATAACC+AGG 0.598951 7_4:-63134818 None:intergenic
AGTACCATGCGATCAAAGGA+AGG 0.619049 7_4:-63134459 None:intergenic
CGAATCCAAAGTTTGCACCA+CGG 0.626371 7_4:-63134358 None:intergenic
AATCTATTTAAAACAAACCG+TGG 0.654277 7_4:+63134341 Msa1170030:five_prime_UTR
GGATCTCTAGGGTTCAACCC+AGG 0.683092 7_4:+63134783 Msa1170030:CDS
ACCATGCGATCAAAGGAAGG+AGG 0.683503 7_4:-63134456 None:intergenic
TCTCTGCACCTGGAGAGTAG+GGG 0.689358 7_4:+63134958 Msa1170030:CDS
ACTTTCTGTCAATAACACAC+AGG 0.703987 7_4:-63135071 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTATGTAAGTATAATCAATT+AGG - chr7_4:63135157-63135176 None:intergenic 15.0%
!! TTATGTAAGTATAATCAATT+AGG - chr7_4:63135157-63135176 None:intergenic 15.0%
!! TTAAGTTTAACTATATGTGT+TGG - chr7_4:63134608-63134627 None:intergenic 20.0%
!!! AGAATTGTTTAAAAAGTACA+AGG - chr7_4:63135018-63135037 None:intergenic 20.0%
!! TTAAGTTTAACTATATGTGT+TGG - chr7_4:63134608-63134627 None:intergenic 20.0%
!!! AGAATTGTTTAAAAAGTACA+AGG - chr7_4:63135018-63135037 None:intergenic 20.0%
!! AATCTATTTAAAACAAACCG+TGG + chr7_4:63134341-63134360 Msa1170030:five_prime_UTR 25.0%
! ATGAGATGTAAGAAAAGAAA+AGG - chr7_4:63134488-63134507 None:intergenic 25.0%
! TTCAAATTATTATGCTAGCT+CGG + chr7_4:63134640-63134659 Msa1170030:intron 25.0%
! ATAACACAGAGCAATTAAAT+CGG - chr7_4:63134712-63134731 None:intergenic 25.0%
!! TTAATCAAGTTTTTGCTCTT+GGG + chr7_4:63134743-63134762 Msa1170030:intron 25.0%
! CTCAAAAAAGAAGATGAAAA+AGG + chr7_4:63134917-63134936 Msa1170030:CDS 25.0%
! TACTTTAGCAATATATTTCG+TGG + chr7_4:63135111-63135130 Msa1170030:three_prime_UTR 25.0%
!! AATCTATTTAAAACAAACCG+TGG + chr7_4:63134341-63134360 Msa1170030:five_prime_UTR 25.0%
! ATGAGATGTAAGAAAAGAAA+AGG - chr7_4:63134488-63134507 None:intergenic 25.0%
! TTCAAATTATTATGCTAGCT+CGG + chr7_4:63134640-63134659 Msa1170030:intron 25.0%
! ATAACACAGAGCAATTAAAT+CGG - chr7_4:63134712-63134731 None:intergenic 25.0%
!! TTAATCAAGTTTTTGCTCTT+GGG + chr7_4:63134743-63134762 Msa1170030:intron 25.0%
! CTCAAAAAAGAAGATGAAAA+AGG + chr7_4:63134917-63134936 Msa1170030:CDS 25.0%
! TACTTTAGCAATATATTTCG+TGG + chr7_4:63135111-63135130 Msa1170030:three_prime_UTR 25.0%
TCTTTAGATTAGACATGTCT+TGG + chr7_4:63134556-63134575 Msa1170030:intron 30.0%
! TTAACTATATGTGTTGGTGT+CGG - chr7_4:63134602-63134621 None:intergenic 30.0%
CAAGAGCAAAAACTTGATTA+AGG - chr7_4:63134744-63134763 None:intergenic 30.0%
! CTTAATCAAGTTTTTGCTCT+TGG + chr7_4:63134742-63134761 Msa1170030:intron 30.0%
! TAATCAAGTTTTTGCTCTTG+GGG + chr7_4:63134744-63134763 Msa1170030:intron 30.0%
TTAATAGTTCTCCTGGTTAT+TGG + chr7_4:63134807-63134826 Msa1170030:CDS 30.0%
!!! TTCATCTTCTTTTTTGAGAC+TGG - chr7_4:63134915-63134934 None:intergenic 30.0%
TCTTTAGATTAGACATGTCT+TGG + chr7_4:63134556-63134575 Msa1170030:intron 30.0%
! TTAACTATATGTGTTGGTGT+CGG - chr7_4:63134602-63134621 None:intergenic 30.0%
CAAGAGCAAAAACTTGATTA+AGG - chr7_4:63134744-63134763 None:intergenic 30.0%
! CTTAATCAAGTTTTTGCTCT+TGG + chr7_4:63134742-63134761 Msa1170030:intron 30.0%
! TAATCAAGTTTTTGCTCTTG+GGG + chr7_4:63134744-63134763 Msa1170030:intron 30.0%
TTAATAGTTCTCCTGGTTAT+TGG + chr7_4:63134807-63134826 Msa1170030:CDS 30.0%
!!! TTCATCTTCTTTTTTGAGAC+TGG - chr7_4:63134915-63134934 None:intergenic 30.0%
ATCACCGAATTCAAAGTCAT+CGG - chr7_4:63134430-63134449 None:intergenic 35.0%
TTTAGAAAGCTGGATCTCTA+GGG + chr7_4:63134772-63134791 Msa1170030:intron 35.0%
AGAGTGCATAATTTCCTATG+AGG - chr7_4:63134851-63134870 None:intergenic 35.0%
! CAATGGACTCAAATGTTCTA+TGG + chr7_4:63134981-63135000 Msa1170030:three_prime_UTR 35.0%
CTCAAATGTTCTATGGAATG+TGG + chr7_4:63134988-63135007 Msa1170030:three_prime_UTR 35.0%
ACTTTCTGTCAATAACACAC+AGG - chr7_4:63135074-63135093 None:intergenic 35.0%
ATCACCGAATTCAAAGTCAT+CGG - chr7_4:63134430-63134449 None:intergenic 35.0%
TTTAGAAAGCTGGATCTCTA+GGG + chr7_4:63134772-63134791 Msa1170030:intron 35.0%
AGAGTGCATAATTTCCTATG+AGG - chr7_4:63134851-63134870 None:intergenic 35.0%
! CAATGGACTCAAATGTTCTA+TGG + chr7_4:63134981-63135000 Msa1170030:three_prime_UTR 35.0%
CTCAAATGTTCTATGGAATG+TGG + chr7_4:63134988-63135007 Msa1170030:three_prime_UTR 35.0%
ACTTTCTGTCAATAACACAC+AGG - chr7_4:63135074-63135093 None:intergenic 35.0%
ATCACTCACATCTTCAACCA+TGG + chr7_4:63134404-63134423 Msa1170030:exon 40.0%
ATGGCCGATGACTTTGAATT+CGG + chr7_4:63134423-63134442 Msa1170030:CDS 40.0%
! GATTAGACATGTCTTGGTGT+AGG + chr7_4:63134562-63134581 Msa1170030:intron 40.0%
! ATTATTATGCTAGCTCGGTG+TGG + chr7_4:63134645-63134664 Msa1170030:intron 40.0%
TGGGGAAATGTTTAGAAAGC+TGG + chr7_4:63134762-63134781 Msa1170030:intron 40.0%
GTTTAGAAAGCTGGATCTCT+AGG + chr7_4:63134771-63134790 Msa1170030:intron 40.0%
ATAGTTCTCCTGGTTATTGG+TGG + chr7_4:63134810-63134829 Msa1170030:CDS 40.0%
TAGTTCTCCTGGTTATTGGT+GGG + chr7_4:63134811-63134830 Msa1170030:CDS 40.0%
! TTGCTGTTGACATTCCTCAT+AGG + chr7_4:63134834-63134853 Msa1170030:CDS 40.0%
!!! CTTCTTTTTTCTAGGAGGGA+GGG - chr7_4:63134892-63134911 None:intergenic 40.0%
!!! CTGGCTTCTTTTTTCTAGGA+GGG - chr7_4:63134896-63134915 None:intergenic 40.0%
!!! ACTGGCTTCTTTTTTCTAGG+AGG - chr7_4:63134897-63134916 None:intergenic 40.0%
!!! GAGACTGGCTTCTTTTTTCT+AGG - chr7_4:63134900-63134919 None:intergenic 40.0%
AAAAAGGAGAGACTGAAGCA+AGG + chr7_4:63134933-63134952 Msa1170030:CDS 40.0%
ATCACTCACATCTTCAACCA+TGG + chr7_4:63134404-63134423 Msa1170030:exon 40.0%
ATGGCCGATGACTTTGAATT+CGG + chr7_4:63134423-63134442 Msa1170030:CDS 40.0%
! GATTAGACATGTCTTGGTGT+AGG + chr7_4:63134562-63134581 Msa1170030:intron 40.0%
! ATTATTATGCTAGCTCGGTG+TGG + chr7_4:63134645-63134664 Msa1170030:intron 40.0%
TGGGGAAATGTTTAGAAAGC+TGG + chr7_4:63134762-63134781 Msa1170030:intron 40.0%
GTTTAGAAAGCTGGATCTCT+AGG + chr7_4:63134771-63134790 Msa1170030:intron 40.0%
ATAGTTCTCCTGGTTATTGG+TGG + chr7_4:63134810-63134829 Msa1170030:CDS 40.0%
TAGTTCTCCTGGTTATTGGT+GGG + chr7_4:63134811-63134830 Msa1170030:CDS 40.0%
! TTGCTGTTGACATTCCTCAT+AGG + chr7_4:63134834-63134853 Msa1170030:CDS 40.0%
!!! CTTCTTTTTTCTAGGAGGGA+GGG - chr7_4:63134892-63134911 None:intergenic 40.0%
!!! CTGGCTTCTTTTTTCTAGGA+GGG - chr7_4:63134896-63134915 None:intergenic 40.0%
!!! ACTGGCTTCTTTTTTCTAGG+AGG - chr7_4:63134897-63134916 None:intergenic 40.0%
!!! GAGACTGGCTTCTTTTTTCT+AGG - chr7_4:63134900-63134919 None:intergenic 40.0%
AAAAAGGAGAGACTGAAGCA+AGG + chr7_4:63134933-63134952 Msa1170030:CDS 40.0%
ACAAACCGTGGTGCAAACTT+TGG + chr7_4:63134353-63134372 Msa1170030:five_prime_UTR 45.0%
CGAATCCAAAGTTTGCACCA+CGG - chr7_4:63134361-63134380 None:intergenic 45.0%
GAATTCAAAGTCATCGGCCA+TGG - chr7_4:63134424-63134443 None:intergenic 45.0%
AGTACCATGCGATCAAAGGA+AGG - chr7_4:63134462-63134481 None:intergenic 45.0%
!! GAAGAGTACCATGCGATCAA+AGG - chr7_4:63134466-63134485 None:intergenic 45.0%
!! CTATATGTGTTGGTGTCGGA+CGG - chr7_4:63134598-63134617 None:intergenic 45.0%
CCAGGAGAACTATTAAGCCT+GGG - chr7_4:63134803-63134822 None:intergenic 45.0%
ACCAGGAGAACTATTAAGCC+TGG - chr7_4:63134804-63134823 None:intergenic 45.0%
!!! GCTTCTTTTTTCTAGGAGGG+AGG - chr7_4:63134893-63134912 None:intergenic 45.0%
ACAAACCGTGGTGCAAACTT+TGG + chr7_4:63134353-63134372 Msa1170030:five_prime_UTR 45.0%
CGAATCCAAAGTTTGCACCA+CGG - chr7_4:63134361-63134380 None:intergenic 45.0%
GAATTCAAAGTCATCGGCCA+TGG - chr7_4:63134424-63134443 None:intergenic 45.0%
AGTACCATGCGATCAAAGGA+AGG - chr7_4:63134462-63134481 None:intergenic 45.0%
!! GAAGAGTACCATGCGATCAA+AGG - chr7_4:63134466-63134485 None:intergenic 45.0%
!! CTATATGTGTTGGTGTCGGA+CGG - chr7_4:63134598-63134617 None:intergenic 45.0%
CCAGGAGAACTATTAAGCCT+GGG - chr7_4:63134803-63134822 None:intergenic 45.0%
ACCAGGAGAACTATTAAGCC+TGG - chr7_4:63134804-63134823 None:intergenic 45.0%
!!! GCTTCTTTTTTCTAGGAGGG+AGG - chr7_4:63134893-63134912 None:intergenic 45.0%
TCCTCCTTCCTTTGATCGCA+TGG + chr7_4:63134455-63134474 Msa1170030:CDS 50.0%
ACCATGCGATCAAAGGAAGG+AGG - chr7_4:63134459-63134478 None:intergenic 50.0%
!! AAGAGTGTCTGCGTGTGAGA+TGG - chr7_4:63134540-63134559 None:intergenic 50.0%
CCCAGGCTTAATAGTTCTCC+TGG + chr7_4:63134800-63134819 Msa1170030:CDS 50.0%
ACAGCAACCCACCAATAACC+AGG - chr7_4:63134821-63134840 None:intergenic 50.0%
TCCTCCTTCCTTTGATCGCA+TGG + chr7_4:63134455-63134474 Msa1170030:CDS 50.0%
ACCATGCGATCAAAGGAAGG+AGG - chr7_4:63134459-63134478 None:intergenic 50.0%
!! AAGAGTGTCTGCGTGTGAGA+TGG - chr7_4:63134540-63134559 None:intergenic 50.0%
CCCAGGCTTAATAGTTCTCC+TGG + chr7_4:63134800-63134819 Msa1170030:CDS 50.0%
ACAGCAACCCACCAATAACC+AGG - chr7_4:63134821-63134840 None:intergenic 50.0%
!! GGATCTCTAGGGTTCAACCC+AGG + chr7_4:63134783-63134802 Msa1170030:CDS 55.0%
AAGCAAGGAGTCTCTGCACC+TGG + chr7_4:63134948-63134967 Msa1170030:CDS 55.0%
AGTCTCTGCACCTGGAGAGT+AGG + chr7_4:63134956-63134975 Msa1170030:CDS 55.0%
GTCTCTGCACCTGGAGAGTA+GGG + chr7_4:63134957-63134976 Msa1170030:CDS 55.0%
TCTCTGCACCTGGAGAGTAG+GGG + chr7_4:63134958-63134977 Msa1170030:CDS 55.0%
!! GGATCTCTAGGGTTCAACCC+AGG + chr7_4:63134783-63134802 Msa1170030:CDS 55.0%
AAGCAAGGAGTCTCTGCACC+TGG + chr7_4:63134948-63134967 Msa1170030:CDS 55.0%
AGTCTCTGCACCTGGAGAGT+AGG + chr7_4:63134956-63134975 Msa1170030:CDS 55.0%
GTCTCTGCACCTGGAGAGTA+GGG + chr7_4:63134957-63134976 Msa1170030:CDS 55.0%
TCTCTGCACCTGGAGAGTAG+GGG + chr7_4:63134958-63134977 Msa1170030:CDS 55.0%
CACCTGGAGAGTAGGGGCAA+TGG + chr7_4:63134964-63134983 Msa1170030:exon 60.0%
GTCCATTGCCCCTACTCTCC+AGG - chr7_4:63134969-63134988 None:intergenic 60.0%
CACCTGGAGAGTAGGGGCAA+TGG + chr7_4:63134964-63134983 Msa1170030:exon 60.0%
GTCCATTGCCCCTACTCTCC+AGG - chr7_4:63134969-63134988 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr7_4 gene 63134332 63135209 63134332 ID=Msa1170030;Name=Msa1170030
chr7_4 mRNA 63134332 63135209 63134332 ID=Msa1170030-mRNA-1;Parent=Msa1170030;Name=Msa1170030-mRNA-1;_AED=0.02;_eAED=0.02;_QI=91|1|1|1|1|1|2|232|84
chr7_4 exon 63134332 63134476 63134332 ID=Msa1170030-mRNA-1:exon:20145;Parent=Msa1170030-mRNA-1
chr7_4 exon 63134777 63135209 63134777 ID=Msa1170030-mRNA-1:exon:20146;Parent=Msa1170030-mRNA-1
chr7_4 five_prime_UTR 63134332 63134422 63134332 ID=Msa1170030-mRNA-1:five_prime_utr;Parent=Msa1170030-mRNA-1
chr7_4 CDS 63134423 63134476 63134423 ID=Msa1170030-mRNA-1:cds;Parent=Msa1170030-mRNA-1
chr7_4 CDS 63134777 63134977 63134777 ID=Msa1170030-mRNA-1:cds;Parent=Msa1170030-mRNA-1
chr7_4 three_prime_UTR 63134978 63135209 63134978 ID=Msa1170030-mRNA-1:three_prime_utr;Parent=Msa1170030-mRNA-1
Gene Sequence

>Msa1170030

ATGGCCGATGACTTTGAATTCGGTGATAAAGTTCCTCCTTCCTTTGATCGCATGAAAGCTGGATCTCTAGGGTTCAACCCAGGCTTAATAGTTCTCCTGGTTATTGGTGGGTTGCTGTTGACATTCCTCATAGGAAATTATGCACTCTACGTTTATGCACAGAAGACCCTCCCTCCTAGAAAAAAGAAGCCAGTCTCAAAAAAGAAGATGAAAAAGGAGAGACTGAAGCAAGGAGTCTCTGCACCTGGAGAGTAG
Protein sequence

>Msa1170030

MADDFEFGDKVPPSFDRMKAGSLGFNPGLIVLLVIGGLLLTFLIGNYALYVYAQKTLPPRKKKPVSKKKMKKERLKQGVSAPGE*