AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0045140


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0045140 MtrunA17_Chr2g0301881 49.485 97 20 1 1 68 246 342 1.84e-17 77.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 21 sgRNAs with CRISPR-Local

Find 122 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTCTTGGTCGTGCTTATTT+TGG 0.178155 1_1:-76840390 Msa0045140:CDS
TCTTTATTACTGTTTGTTCT+TGG 0.257547 1_1:-76840486 Msa0045140:CDS
CACAAAATTTGTTGAATACA+TGG 0.358653 1_1:-76841618 Msa0045140:CDS
TGCAACATACATTTAACCTT+TGG 0.369964 1_1:-76840344 Msa0045140:CDS
ATGCAGCTGGGAACACGTTC+AGG 0.372158 1_1:+76840301 None:intergenic
GAAGAGGTTGTCCTTCGAAC+TGG 0.406908 1_1:+76841590 None:intergenic
CAAGTCTAAATGTATGCAGC+TGG 0.433392 1_1:+76840288 None:intergenic
ATGAAATCACTTGCAAAAGA+TGG 0.438991 1_1:+76841298 None:intergenic
TAGTCAATGAAGACAGCGTT+TGG 0.456859 1_1:-76840510 Msa0045140:CDS
CACTTGCAAAAGATGGAGAC+AGG 0.478454 1_1:+76841305 None:intergenic
ATGCAGGCGAGGTGCTGTCT+CGG 0.514779 1_1:+76841267 None:intergenic
AGAGCTTGGTGTAGTCCTCT+TGG 0.517761 1_1:-76840405 Msa0045140:CDS
CCTTCATTAGCTCTTCATGC+AGG 0.532164 1_1:+76841251 None:intergenic
ACATGGAAATTCCAGTTCGA+AGG 0.590375 1_1:-76841601 Msa0045140:CDS
AACATAATAAGCTTCTGAAG+AGG 0.600221 1_1:+76841574 None:intergenic
CCTGCATGAAGAGCTAATGA+AGG 0.605404 1_1:-76841251 Msa0045140:intron
ATTAGCTCTTCATGCAGGCG+AGG 0.608084 1_1:+76841256 None:intergenic
CCAAAATAAGCACGACCAAG+AGG 0.622212 1_1:+76840390 None:intergenic
AAGTCTAAATGTATGCAGCT+GGG 0.631360 1_1:+76840289 None:intergenic
ATTCTAGAGTGATATACCAA+AGG 0.636013 1_1:+76840328 None:intergenic
ACTTGCAAAAGATGGAGACA+GGG 0.688727 1_1:+76841306 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTATATGATATGTTTTAAT+AGG - chr1_1:76840892-76840911 Msa0045140:intron 10.0%
!!! TTTATATGATATGTTTTAAT+AGG - chr1_1:76840892-76840911 Msa0045140:intron 10.0%
!! CAAAAAAAGAATACATTATT+TGG + chr1_1:76840483-76840502 None:intergenic 15.0%
!!! TATTTTACTTATTGAAAAAC+TGG - chr1_1:76840791-76840810 Msa0045140:intron 15.0%
!!! ATTTTACTTATTGAAAAACT+GGG - chr1_1:76840792-76840811 Msa0045140:intron 15.0%
!!! AAACTACATAAATTTAAAGT+AGG - chr1_1:76840827-76840846 Msa0045140:intron 15.0%
!! TGATAATCTTAATTTAAATG+TGG + chr1_1:76840986-76841005 None:intergenic 15.0%
!! CAAAAAAAGAATACATTATT+TGG + chr1_1:76840483-76840502 None:intergenic 15.0%
!!! TATTTTACTTATTGAAAAAC+TGG - chr1_1:76840791-76840810 Msa0045140:intron 15.0%
!!! ATTTTACTTATTGAAAAACT+GGG - chr1_1:76840792-76840811 Msa0045140:intron 15.0%
!!! AAACTACATAAATTTAAAGT+AGG - chr1_1:76840827-76840846 Msa0045140:intron 15.0%
!! TGATAATCTTAATTTAAATG+TGG + chr1_1:76840986-76841005 None:intergenic 15.0%
!!! CACAAAATTTGTTGAATACA+TGG - chr1_1:76840304-76840323 Msa0045140:CDS 25.0%
! TCTAAACGAAAATATCATAG+GGG + chr1_1:76840552-76840571 None:intergenic 25.0%
! GTCTAAACGAAAATATCATA+GGG + chr1_1:76840553-76840572 None:intergenic 25.0%
! TGTCTAAACGAAAATATCAT+AGG + chr1_1:76840554-76840573 None:intergenic 25.0%
! ATCGAATCTAATCTATCAAA+AGG + chr1_1:76840722-76840741 None:intergenic 25.0%
! ATACTTAACAGTAAGATGAA+CGG + chr1_1:76840766-76840785 None:intergenic 25.0%
! CATGAAATATATAAAGAGAC+TGG + chr1_1:76841114-76841133 None:intergenic 25.0%
! AAAGAAATTGTTGTAGATGA+AGG + chr1_1:76841225-76841244 None:intergenic 25.0%
!! TATGATTTTTCTCTGAACTT+TGG - chr1_1:76841347-76841366 Msa0045140:CDS 25.0%
!! TCATTGACTAGTAAATTGAA+AGG + chr1_1:76841402-76841421 None:intergenic 25.0%
! TCTTTATTACTGTTTGTTCT+TGG - chr1_1:76841436-76841455 Msa0045140:intron 25.0%
!!! CACAAAATTTGTTGAATACA+TGG - chr1_1:76840304-76840323 Msa0045140:CDS 25.0%
! TCTAAACGAAAATATCATAG+GGG + chr1_1:76840552-76840571 None:intergenic 25.0%
! GTCTAAACGAAAATATCATA+GGG + chr1_1:76840553-76840572 None:intergenic 25.0%
! TGTCTAAACGAAAATATCAT+AGG + chr1_1:76840554-76840573 None:intergenic 25.0%
! ATCGAATCTAATCTATCAAA+AGG + chr1_1:76840722-76840741 None:intergenic 25.0%
! ATACTTAACAGTAAGATGAA+CGG + chr1_1:76840766-76840785 None:intergenic 25.0%
! CATGAAATATATAAAGAGAC+TGG + chr1_1:76841114-76841133 None:intergenic 25.0%
! AAAGAAATTGTTGTAGATGA+AGG + chr1_1:76841225-76841244 None:intergenic 25.0%
!! TATGATTTTTCTCTGAACTT+TGG - chr1_1:76841347-76841366 Msa0045140:CDS 25.0%
!! TCATTGACTAGTAAATTGAA+AGG + chr1_1:76841402-76841421 None:intergenic 25.0%
! TCTTTATTACTGTTTGTTCT+TGG - chr1_1:76841436-76841455 Msa0045140:intron 25.0%
! AACATAATAAGCTTCTGAAG+AGG + chr1_1:76840351-76840370 None:intergenic 30.0%
ATGAAATCACTTGCAAAAGA+TGG + chr1_1:76840627-76840646 None:intergenic 30.0%
! CTTTTGCAAGTGATTTCATA+CGG - chr1_1:76840628-76840647 Msa0045140:intron 30.0%
!! GTGGTTATCATCTTTAGTTT+TGG + chr1_1:76840967-76840986 None:intergenic 30.0%
GTCATCATTATCTTATGTGA+TGG - chr1_1:76841016-76841035 Msa0045140:intron 30.0%
TAAATGCAAGCGATAAGAAA+AGG + chr1_1:76841199-76841218 None:intergenic 30.0%
! ATTTCTTTTCCTATGCAACT+AGG - chr1_1:76841237-76841256 Msa0045140:intron 30.0%
TGTAAATCAATTGTTGTACC+AGG - chr1_1:76841260-76841279 Msa0045140:CDS 30.0%
GTAAATCAATTGTTGTACCA+GGG - chr1_1:76841261-76841280 Msa0045140:CDS 30.0%
! GCACATTTTCTATAACTTCT+TGG + chr1_1:76841561-76841580 None:intergenic 30.0%
TGCAACATACATTTAACCTT+TGG - chr1_1:76841578-76841597 Msa0045140:CDS 30.0%
!! ATTCTAGAGTGATATACCAA+AGG + chr1_1:76841597-76841616 None:intergenic 30.0%
! AACATAATAAGCTTCTGAAG+AGG + chr1_1:76840351-76840370 None:intergenic 30.0%
ATGAAATCACTTGCAAAAGA+TGG + chr1_1:76840627-76840646 None:intergenic 30.0%
! CTTTTGCAAGTGATTTCATA+CGG - chr1_1:76840628-76840647 Msa0045140:intron 30.0%
!! GTGGTTATCATCTTTAGTTT+TGG + chr1_1:76840967-76840986 None:intergenic 30.0%
GTCATCATTATCTTATGTGA+TGG - chr1_1:76841016-76841035 Msa0045140:intron 30.0%
TAAATGCAAGCGATAAGAAA+AGG + chr1_1:76841199-76841218 None:intergenic 30.0%
! ATTTCTTTTCCTATGCAACT+AGG - chr1_1:76841237-76841256 Msa0045140:intron 30.0%
TGTAAATCAATTGTTGTACC+AGG - chr1_1:76841260-76841279 Msa0045140:CDS 30.0%
GTAAATCAATTGTTGTACCA+GGG - chr1_1:76841261-76841280 Msa0045140:CDS 30.0%
! GCACATTTTCTATAACTTCT+TGG + chr1_1:76841561-76841580 None:intergenic 30.0%
TGCAACATACATTTAACCTT+TGG - chr1_1:76841578-76841597 Msa0045140:CDS 30.0%
!! ATTCTAGAGTGATATACCAA+AGG + chr1_1:76841597-76841616 None:intergenic 30.0%
TCAACAGTTGCTAAAGTAAG+AGG - chr1_1:76841153-76841172 Msa0045140:intron 35.0%
CAACAGTTGCTAAAGTAAGA+GGG - chr1_1:76841154-76841173 Msa0045140:intron 35.0%
TGATTTACACCTAGTTGCAT+AGG + chr1_1:76841249-76841268 None:intergenic 35.0%
! TTTTGTTGATACAGAGAGCT+TGG - chr1_1:76841503-76841522 Msa0045140:intron 35.0%
TCAACAGTTGCTAAAGTAAG+AGG - chr1_1:76841153-76841172 Msa0045140:intron 35.0%
CAACAGTTGCTAAAGTAAGA+GGG - chr1_1:76841154-76841173 Msa0045140:intron 35.0%
TGATTTACACCTAGTTGCAT+AGG + chr1_1:76841249-76841268 None:intergenic 35.0%
! TTTTGTTGATACAGAGAGCT+TGG - chr1_1:76841503-76841522 Msa0045140:intron 35.0%
ACATGGAAATTCCAGTTCGA+AGG - chr1_1:76840321-76840340 Msa0045140:CDS 40.0%
GCTCTTGCTTAATGTTCTTG+AGG + chr1_1:76840398-76840417 None:intergenic 40.0%
ACTTGCAAAAGATGGAGACA+GGG + chr1_1:76840619-76840638 None:intergenic 40.0%
TAGTCAATGAAGACAGCGTT+TGG - chr1_1:76841412-76841431 Msa0045140:intron 40.0%
ACATGGAAATTCCAGTTCGA+AGG - chr1_1:76840321-76840340 Msa0045140:CDS 40.0%
GCTCTTGCTTAATGTTCTTG+AGG + chr1_1:76840398-76840417 None:intergenic 40.0%
ACTTGCAAAAGATGGAGACA+GGG + chr1_1:76840619-76840638 None:intergenic 40.0%
TAGTCAATGAAGACAGCGTT+TGG - chr1_1:76841412-76841431 Msa0045140:intron 40.0%
! AGCAAGAGCAGACCAAGTTT+TGG - chr1_1:76840409-76840428 Msa0045140:CDS 45.0%
CACGATGCTCTTCCAAAACT+TGG + chr1_1:76840424-76840443 None:intergenic 45.0%
TCATAGGGGTGAGCACAAAA+AGG + chr1_1:76840538-76840557 None:intergenic 45.0%
CACTTGCAAAAGATGGAGAC+AGG + chr1_1:76840620-76840639 None:intergenic 45.0%
! CCTTCATTAGCTCTTCATGC+AGG + chr1_1:76840674-76840693 None:intergenic 45.0%
CCTGCATGAAGAGCTAATGA+AGG - chr1_1:76840671-76840690 Msa0045140:intron 45.0%
GAAGAGCTAATGAAGGTGAC+TGG - chr1_1:76840678-76840697 Msa0045140:intron 45.0%
ATATAAACCCACACTCCCAC+AGG + chr1_1:76840879-76840898 None:intergenic 45.0%
! GACTGGAGCATTAGACAATG+AGG + chr1_1:76841097-76841116 None:intergenic 45.0%
ATTCGCATTGCTTCAAACCC+TGG + chr1_1:76841281-76841300 None:intergenic 45.0%
CCAAAATAAGCACGACCAAG+AGG + chr1_1:76841535-76841554 None:intergenic 45.0%
! CCTCTTGGTCGTGCTTATTT+TGG - chr1_1:76841532-76841551 Msa0045140:intron 45.0%
!!! CTTGGTCGTGCTTATTTTGG+TGG - chr1_1:76841535-76841554 Msa0045140:intron 45.0%
! AGCAAGAGCAGACCAAGTTT+TGG - chr1_1:76840409-76840428 Msa0045140:CDS 45.0%
CACGATGCTCTTCCAAAACT+TGG + chr1_1:76840424-76840443 None:intergenic 45.0%
TCATAGGGGTGAGCACAAAA+AGG + chr1_1:76840538-76840557 None:intergenic 45.0%
CACTTGCAAAAGATGGAGAC+AGG + chr1_1:76840620-76840639 None:intergenic 45.0%
! CCTTCATTAGCTCTTCATGC+AGG + chr1_1:76840674-76840693 None:intergenic 45.0%
CCTGCATGAAGAGCTAATGA+AGG - chr1_1:76840671-76840690 Msa0045140:intron 45.0%
GAAGAGCTAATGAAGGTGAC+TGG - chr1_1:76840678-76840697 Msa0045140:intron 45.0%
ATATAAACCCACACTCCCAC+AGG + chr1_1:76840879-76840898 None:intergenic 45.0%
! GACTGGAGCATTAGACAATG+AGG + chr1_1:76841097-76841116 None:intergenic 45.0%
ATTCGCATTGCTTCAAACCC+TGG + chr1_1:76841281-76841300 None:intergenic 45.0%
CCAAAATAAGCACGACCAAG+AGG + chr1_1:76841535-76841554 None:intergenic 45.0%
! CCTCTTGGTCGTGCTTATTT+TGG - chr1_1:76841532-76841551 Msa0045140:intron 45.0%
!!! CTTGGTCGTGCTTATTTTGG+TGG - chr1_1:76841535-76841554 Msa0045140:intron 45.0%
GAAGAGGTTGTCCTTCGAAC+TGG + chr1_1:76840335-76840354 None:intergenic 50.0%
!! AGAGCATCGTGTACTAGCAG+AGG - chr1_1:76840433-76840452 Msa0045140:CDS 50.0%
! ATTAGCTCTTCATGCAGGCG+AGG + chr1_1:76840669-76840688 None:intergenic 50.0%
AGTAGGCTGAACTGCACTTG+TGG - chr1_1:76840844-76840863 Msa0045140:intron 50.0%
TTGTGGCAAGCTCTTCCTGT+GGG - chr1_1:76840861-76840880 Msa0045140:intron 50.0%
!! AGAGCTTGGTGTAGTCCTCT+TGG - chr1_1:76841517-76841536 Msa0045140:intron 50.0%
GAAGAGGTTGTCCTTCGAAC+TGG + chr1_1:76840335-76840354 None:intergenic 50.0%
!! AGAGCATCGTGTACTAGCAG+AGG - chr1_1:76840433-76840452 Msa0045140:CDS 50.0%
! ATTAGCTCTTCATGCAGGCG+AGG + chr1_1:76840669-76840688 None:intergenic 50.0%
AGTAGGCTGAACTGCACTTG+TGG - chr1_1:76840844-76840863 Msa0045140:intron 50.0%
TTGTGGCAAGCTCTTCCTGT+GGG - chr1_1:76840861-76840880 Msa0045140:intron 50.0%
!! AGAGCTTGGTGTAGTCCTCT+TGG - chr1_1:76841517-76841536 Msa0045140:intron 50.0%
CTTGTGGCAAGCTCTTCCTG+TGG - chr1_1:76840860-76840879 Msa0045140:intron 55.0%
AAGCTCTTCCTGTGGGAGTG+TGG - chr1_1:76840868-76840887 Msa0045140:intron 55.0%
! AGCTCTTCCTGTGGGAGTGT+GGG - chr1_1:76840869-76840888 Msa0045140:intron 55.0%
ATGCAGCTGGGAACACGTTC+AGG + chr1_1:76841624-76841643 None:intergenic 55.0%
CTTGTGGCAAGCTCTTCCTG+TGG - chr1_1:76840860-76840879 Msa0045140:intron 55.0%
AAGCTCTTCCTGTGGGAGTG+TGG - chr1_1:76840868-76840887 Msa0045140:intron 55.0%
! AGCTCTTCCTGTGGGAGTGT+GGG - chr1_1:76840869-76840888 Msa0045140:intron 55.0%
ATGCAGCTGGGAACACGTTC+AGG + chr1_1:76841624-76841643 None:intergenic 55.0%
!! ATGCAGGCGAGGTGCTGTCT+CGG + chr1_1:76840658-76840677 None:intergenic 60.0%
!! ATGCAGGCGAGGTGCTGTCT+CGG + chr1_1:76840658-76840677 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr1_1 gene 76840293 76841651 76840293 ID=Msa0045140;Name=Msa0045140
chr1_1 mRNA 76840293 76841651 76840293 ID=Msa0045140-mRNA-1;Parent=Msa0045140;Name=Msa0045140-mRNA-1;_AED=0.44;_eAED=0.85;_QI=0|0|0.33|1|1|1|3|0|146
chr1_1 exon 76841566 76841651 76841566 ID=Msa0045140-mRNA-1:exon:26265;Parent=Msa0045140-mRNA-1
chr1_1 exon 76841252 76841369 76841252 ID=Msa0045140-mRNA-1:exon:26264;Parent=Msa0045140-mRNA-1
chr1_1 exon 76840293 76840529 76840293 ID=Msa0045140-mRNA-1:exon:26263;Parent=Msa0045140-mRNA-1
chr1_1 CDS 76841566 76841651 76841566 ID=Msa0045140-mRNA-1:cds;Parent=Msa0045140-mRNA-1
chr1_1 CDS 76841252 76841369 76841252 ID=Msa0045140-mRNA-1:cds;Parent=Msa0045140-mRNA-1
chr1_1 CDS 76840293 76840529 76840293 ID=Msa0045140-mRNA-1:cds;Parent=Msa0045140-mRNA-1
Gene Sequence

>Msa0045140

ATGGATGTTTTCACAAAATTTGTTGAATACATGGAAATTCCAGTTCGAAGGACAACCTCTTCAGAAGCTTATTATGTTGTTAACAAAGAGCTATTAGATCAAGTTCAGTTGACTCGTGCATTTGCATCCCTGTCTCCATCTTTTGCAAGTGATTTCATACGGATTTCCGAGACAGCACCTCGCCTGCATGAAGAGCTAATGAAGTCAATGAAGACAGCGTTTGGTTCTTTATTACTGTTTGTTCTTGGTTACTTGCTTGTTTATGTTGAATATGACTTCACTAATTTAAAGCTTTTGTTGATACAGAGAGCTTGGTGTAGTCCTCTTGGTCGTGCTTATTTTGGTGGCCAAGAAGTTATAGAAAATGTGCAACATACATTTAACCTTTGGTATATCACTCTAGAATTTATCCTGAACGTGTTCCCAGCTGCATACATTTAG

Protein sequence

>Msa0045140

MDVFTKFVEYMEIPVRRTTSSEAYYVVNKELLDQVQLTRAFASLSPSFASDFIRISETAPRLHEELMKSMKTAFGSLLLFVLGYLLVYVEYDFTNLKLLLIQRAWCSPLGRAYFGGQEVIENVQHTFNLWYITLEFILNVFPAAYI*