AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1388490


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1388490 MtrunA17_Chr6g0485491 56.579 152 66 0 62 213 4 155 2.79e-56 176
Msa1388490 MtrunA17_Chr6g0485481 63.910 133 47 1 20 151 1 133 3.91e-56 174
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1388490 AT1G79310.1 26.966 178 115 5 5 169 2 177 1.06e-12 66.6

Find 46 sgRNAs with CRISPR-Local

Find 112 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATGCTGACCATATAATATT+TGG 0.148969 tig0021124:-26591 None:intergenic
AAGATGAAAATATTGATTAT+TGG 0.166905 tig0021124:+26040 Msa1388490:CDS
GACTGACTCTTCATCCCTTT+TGG 0.233722 tig0021124:-26476 None:intergenic
ACTATTAAAGCTCTCTTTGT+AGG 0.282700 tig0021124:-25934 None:intergenic
AGAGTCAGTCAAAGGTTCTT+TGG 0.292750 tig0021124:+26489 Msa1388490:CDS
AGTATCACCTGGCTTTGATA+TGG 0.372210 tig0021124:-26139 None:intergenic
GAGTCAGTCAAAGGTTCTTT+GGG 0.376370 tig0021124:+26490 Msa1388490:CDS
AATTCATCATGCGTTATTCC+AGG 0.382392 tig0021124:-26556 None:intergenic
CAAAGGATCCAAATATTATA+TGG 0.383489 tig0021124:+26583 Msa1388490:CDS
TTCTATTCACATCTTCCAAA+AGG 0.390556 tig0021124:+26461 Msa1388490:CDS
TCTTGACGCCGTCAGCCATT+TGG 0.395579 tig0021124:-26375 None:intergenic
GCCAATGGAACTCCTTTACT+TGG 0.433502 tig0021124:+26225 Msa1388490:CDS
TTCATGATTGATGCTTGTTA+CGG 0.446394 tig0021124:+26403 Msa1388490:CDS
CTCATCAGTGGCACAAAGGT+CGG 0.466093 tig0021124:-26629 None:intergenic
ATTGATGCTTGTTACGGAGG+GGG 0.492034 tig0021124:+26409 Msa1388490:CDS
TCATCAGTGGCACAAAGGTC+GGG 0.493995 tig0021124:-26628 None:intergenic
TGATTGATGCTTGTTACGGA+GGG 0.498805 tig0021124:+26407 Msa1388490:CDS
AGTTACCTTGTTGCAGCCAA+TGG 0.499386 tig0021124:+26210 Msa1388490:CDS
TCTATTCACATCTTCCAAAA+GGG 0.515999 tig0021124:+26462 Msa1388490:CDS
TTGAGGAAGTTACCAAGTAA+AGG 0.533780 tig0021124:-26237 None:intergenic
ACCAAGTAAAGGAGTTCCAT+TGG 0.537259 tig0021124:-26226 None:intergenic
TTAATTACCATATCAAAGCC+AGG 0.542624 tig0021124:+26132 Msa1388490:CDS
GACAGAAACGATGGAGGACC+TGG 0.548548 tig0021124:+26066 Msa1388490:CDS
ATGATTGATGCTTGTTACGG+AGG 0.558998 tig0021124:+26406 Msa1388490:CDS
ATGTGAATAGAACAACTTTG+TGG 0.564614 tig0021124:-26450 None:intergenic
CAAATATTATATGGTCAGCA+TGG 0.570578 tig0021124:+26592 Msa1388490:CDS
GTGGCACAAAGGTCGGGTAG+TGG 0.571496 tig0021124:-26622 None:intergenic
CGCATGATGAATTGATACAA+AGG 0.574943 tig0021124:+26566 Msa1388490:CDS
TTGATGCTTGTTACGGAGGG+GGG 0.576592 tig0021124:+26410 Msa1388490:CDS
AAAAGTTTGCTAATAAATCG+TGG 0.578152 tig0021124:+26012 Msa1388490:CDS
ATTCATCATGCGTTATTCCA+GGG 0.587040 tig0021124:-26555 None:intergenic
TCGGAATATGTATTGAGTGT+AGG 0.587606 tig0021124:-25976 None:intergenic
GATTGATGCTTGTTACGGAG+GGG 0.589936 tig0021124:+26408 Msa1388490:CDS
TAGAATCAAGTTAAGAGAGT+GGG 0.593682 tig0021124:+26676 Msa1388490:exon
AGGGATGAAGAGTCAGTCAA+AGG 0.601689 tig0021124:+26481 Msa1388490:CDS
GATTGTGTTAATGATTACCC+TGG 0.604085 tig0021124:+26538 Msa1388490:CDS
CATGGTAACTATCAACAAAG+AGG 0.608307 tig0021124:+26183 Msa1388490:CDS
ATAGAATCAAGTTAAGAGAG+TGG 0.627109 tig0021124:+26675 Msa1388490:exon
ATGGTAACTATCAACAAAGA+GGG 0.636257 tig0021124:+26184 Msa1388490:CDS
GAGTTCCATTGGCTGCAACA+AGG 0.637602 tig0021124:-26215 None:intergenic
ACACTCAATACATATTCCGA+TGG 0.646069 tig0021124:+25979 Msa1388490:CDS
GTGTTAGACCAAATGGCTGA+CGG 0.654978 tig0021124:+26367 Msa1388490:CDS
TATTGGCAAGACAGAAACGA+TGG 0.655578 tig0021124:+26057 Msa1388490:CDS
TCAGCATCAATAAGGAAACC+AGG 0.656233 tig0021124:-26084 None:intergenic
TTATCTCATCAGTGGCACAA+AGG 0.659996 tig0021124:-26633 None:intergenic
TGGCAAGACAGAAACGATGG+AGG 0.703781 tig0021124:+26060 Msa1388490:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAGATGAAAATATTGATTAT+TGG + tig0021124:26040-26059 Msa1388490:CDS 15.0%
!!! AAGATGAAAATATTGATTAT+TGG + tig0021124:26040-26059 Msa1388490:CDS 15.0%
!!! AAAAGTTTGCTAATAAATCG+TGG + tig0021124:26012-26031 Msa1388490:CDS 25.0%
!! TGAAAAAATAAAGTATCACC+TGG - tig0021124:26153-26172 None:intergenic 25.0%
!!! ACTTTATTTTTTCACTTCAG+TGG + tig0021124:26159-26178 Msa1388490:CDS 25.0%
!!! TAAAAAAGTGTTAGACCAAA+TGG + tig0021124:26360-26379 Msa1388490:CDS 25.0%
! CAAAGGATCCAAATATTATA+TGG + tig0021124:26583-26602 Msa1388490:CDS 25.0%
!!! AGAATTTTTTATCTCATCAG+TGG - tig0021124:26644-26663 None:intergenic 25.0%
!!! AAAAGTTTGCTAATAAATCG+TGG + tig0021124:26012-26031 Msa1388490:CDS 25.0%
!! TGAAAAAATAAAGTATCACC+TGG - tig0021124:26153-26172 None:intergenic 25.0%
!!! ACTTTATTTTTTCACTTCAG+TGG + tig0021124:26159-26178 Msa1388490:CDS 25.0%
!!! TAAAAAAGTGTTAGACCAAA+TGG + tig0021124:26360-26379 Msa1388490:CDS 25.0%
! CAAAGGATCCAAATATTATA+TGG + tig0021124:26583-26602 Msa1388490:CDS 25.0%
!!! AGAATTTTTTATCTCATCAG+TGG - tig0021124:26644-26663 None:intergenic 25.0%
ACTATTAAAGCTCTCTTTGT+AGG - tig0021124:25937-25956 None:intergenic 30.0%
! GTATTTTGTCAGCATCAATA+AGG - tig0021124:26095-26114 None:intergenic 30.0%
TTAATTACCATATCAAAGCC+AGG + tig0021124:26132-26151 Msa1388490:CDS 30.0%
ATGGTAACTATCAACAAAGA+GGG + tig0021124:26184-26203 Msa1388490:CDS 30.0%
TATTTGTGATTCTCAATGCA+TGG + tig0021124:26288-26307 Msa1388490:intron 30.0%
! TTCATGATTGATGCTTGTTA+CGG + tig0021124:26403-26422 Msa1388490:CDS 30.0%
ATGTGAATAGAACAACTTTG+TGG - tig0021124:26453-26472 None:intergenic 30.0%
TTCTATTCACATCTTCCAAA+AGG + tig0021124:26461-26480 Msa1388490:CDS 30.0%
TCTATTCACATCTTCCAAAA+GGG + tig0021124:26462-26481 Msa1388490:CDS 30.0%
CATGCTGACCATATAATATT+TGG - tig0021124:26594-26613 None:intergenic 30.0%
CAAATATTATATGGTCAGCA+TGG + tig0021124:26592-26611 Msa1388490:CDS 30.0%
ATAGAATCAAGTTAAGAGAG+TGG + tig0021124:26675-26694 Msa1388490:exon 30.0%
TAGAATCAAGTTAAGAGAGT+GGG + tig0021124:26676-26695 Msa1388490:exon 30.0%
ACTATTAAAGCTCTCTTTGT+AGG - tig0021124:25937-25956 None:intergenic 30.0%
! GTATTTTGTCAGCATCAATA+AGG - tig0021124:26095-26114 None:intergenic 30.0%
TTAATTACCATATCAAAGCC+AGG + tig0021124:26132-26151 Msa1388490:CDS 30.0%
ATGGTAACTATCAACAAAGA+GGG + tig0021124:26184-26203 Msa1388490:CDS 30.0%
TATTTGTGATTCTCAATGCA+TGG + tig0021124:26288-26307 Msa1388490:intron 30.0%
! TTCATGATTGATGCTTGTTA+CGG + tig0021124:26403-26422 Msa1388490:CDS 30.0%
ATGTGAATAGAACAACTTTG+TGG - tig0021124:26453-26472 None:intergenic 30.0%
TTCTATTCACATCTTCCAAA+AGG + tig0021124:26461-26480 Msa1388490:CDS 30.0%
TCTATTCACATCTTCCAAAA+GGG + tig0021124:26462-26481 Msa1388490:CDS 30.0%
CATGCTGACCATATAATATT+TGG - tig0021124:26594-26613 None:intergenic 30.0%
CAAATATTATATGGTCAGCA+TGG + tig0021124:26592-26611 Msa1388490:CDS 30.0%
ATAGAATCAAGTTAAGAGAG+TGG + tig0021124:26675-26694 Msa1388490:exon 30.0%
TAGAATCAAGTTAAGAGAGT+GGG + tig0021124:26676-26695 Msa1388490:exon 30.0%
TCGGAATATGTATTGAGTGT+AGG - tig0021124:25979-25998 None:intergenic 35.0%
ACACTCAATACATATTCCGA+TGG + tig0021124:25979-25998 Msa1388490:CDS 35.0%
! ACTTTTTATCTTCGCACCAT+CGG - tig0021124:25998-26017 None:intergenic 35.0%
!!! TTTTTTCACTTCAGTGGACA+TGG + tig0021124:26165-26184 Msa1388490:CDS 35.0%
CATGGTAACTATCAACAAAG+AGG + tig0021124:26183-26202 Msa1388490:CDS 35.0%
TTGAGGAAGTTACCAAGTAA+AGG - tig0021124:26240-26259 None:intergenic 35.0%
TATTAGCATGAGATGTGTTG+AGG - tig0021124:26257-26276 None:intergenic 35.0%
GATTGTGTTAATGATTACCC+TGG + tig0021124:26538-26557 Msa1388490:CDS 35.0%
ATTCATCATGCGTTATTCCA+GGG - tig0021124:26558-26577 None:intergenic 35.0%
AATTCATCATGCGTTATTCC+AGG - tig0021124:26559-26578 None:intergenic 35.0%
CGCATGATGAATTGATACAA+AGG + tig0021124:26566-26585 Msa1388490:CDS 35.0%
TCGGAATATGTATTGAGTGT+AGG - tig0021124:25979-25998 None:intergenic 35.0%
ACACTCAATACATATTCCGA+TGG + tig0021124:25979-25998 Msa1388490:CDS 35.0%
! ACTTTTTATCTTCGCACCAT+CGG - tig0021124:25998-26017 None:intergenic 35.0%
!!! TTTTTTCACTTCAGTGGACA+TGG + tig0021124:26165-26184 Msa1388490:CDS 35.0%
CATGGTAACTATCAACAAAG+AGG + tig0021124:26183-26202 Msa1388490:CDS 35.0%
TTGAGGAAGTTACCAAGTAA+AGG - tig0021124:26240-26259 None:intergenic 35.0%
TATTAGCATGAGATGTGTTG+AGG - tig0021124:26257-26276 None:intergenic 35.0%
GATTGTGTTAATGATTACCC+TGG + tig0021124:26538-26557 Msa1388490:CDS 35.0%
ATTCATCATGCGTTATTCCA+GGG - tig0021124:26558-26577 None:intergenic 35.0%
AATTCATCATGCGTTATTCC+AGG - tig0021124:26559-26578 None:intergenic 35.0%
CGCATGATGAATTGATACAA+AGG + tig0021124:26566-26585 Msa1388490:CDS 35.0%
TATTGGCAAGACAGAAACGA+TGG + tig0021124:26057-26076 Msa1388490:CDS 40.0%
TCAGCATCAATAAGGAAACC+AGG - tig0021124:26087-26106 None:intergenic 40.0%
!! AGTATCACCTGGCTTTGATA+TGG - tig0021124:26142-26161 None:intergenic 40.0%
ACCAAGTAAAGGAGTTCCAT+TGG - tig0021124:26229-26248 None:intergenic 40.0%
! ATGATTGATGCTTGTTACGG+AGG + tig0021124:26406-26425 Msa1388490:CDS 40.0%
! TGATTGATGCTTGTTACGGA+GGG + tig0021124:26407-26426 Msa1388490:CDS 40.0%
AGAGTCAGTCAAAGGTTCTT+TGG + tig0021124:26489-26508 Msa1388490:CDS 40.0%
GAGTCAGTCAAAGGTTCTTT+GGG + tig0021124:26490-26509 Msa1388490:CDS 40.0%
TTATCTCATCAGTGGCACAA+AGG - tig0021124:26636-26655 None:intergenic 40.0%
TATTGGCAAGACAGAAACGA+TGG + tig0021124:26057-26076 Msa1388490:CDS 40.0%
TCAGCATCAATAAGGAAACC+AGG - tig0021124:26087-26106 None:intergenic 40.0%
!! AGTATCACCTGGCTTTGATA+TGG - tig0021124:26142-26161 None:intergenic 40.0%
ACCAAGTAAAGGAGTTCCAT+TGG - tig0021124:26229-26248 None:intergenic 40.0%
! ATGATTGATGCTTGTTACGG+AGG + tig0021124:26406-26425 Msa1388490:CDS 40.0%
! TGATTGATGCTTGTTACGGA+GGG + tig0021124:26407-26426 Msa1388490:CDS 40.0%
AGAGTCAGTCAAAGGTTCTT+TGG + tig0021124:26489-26508 Msa1388490:CDS 40.0%
GAGTCAGTCAAAGGTTCTTT+GGG + tig0021124:26490-26509 Msa1388490:CDS 40.0%
TTATCTCATCAGTGGCACAA+AGG - tig0021124:26636-26655 None:intergenic 40.0%
AGTTACCTTGTTGCAGCCAA+TGG + tig0021124:26210-26229 Msa1388490:CDS 45.0%
GCCAATGGAACTCCTTTACT+TGG + tig0021124:26225-26244 Msa1388490:CDS 45.0%
! ATTTGCTACGTGACTTGTGC+AGG + tig0021124:26328-26347 Msa1388490:intron 45.0%
GTGTTAGACCAAATGGCTGA+CGG + tig0021124:26367-26386 Msa1388490:CDS 45.0%
! GATTGATGCTTGTTACGGAG+GGG + tig0021124:26408-26427 Msa1388490:CDS 45.0%
! ATTGATGCTTGTTACGGAGG+GGG + tig0021124:26409-26428 Msa1388490:CDS 45.0%
!! GACTGACTCTTCATCCCTTT+TGG - tig0021124:26479-26498 None:intergenic 45.0%
AGGGATGAAGAGTCAGTCAA+AGG + tig0021124:26481-26500 Msa1388490:CDS 45.0%
AGTTACCTTGTTGCAGCCAA+TGG + tig0021124:26210-26229 Msa1388490:CDS 45.0%
GCCAATGGAACTCCTTTACT+TGG + tig0021124:26225-26244 Msa1388490:CDS 45.0%
! ATTTGCTACGTGACTTGTGC+AGG + tig0021124:26328-26347 Msa1388490:intron 45.0%
GTGTTAGACCAAATGGCTGA+CGG + tig0021124:26367-26386 Msa1388490:CDS 45.0%
! GATTGATGCTTGTTACGGAG+GGG + tig0021124:26408-26427 Msa1388490:CDS 45.0%
! ATTGATGCTTGTTACGGAGG+GGG + tig0021124:26409-26428 Msa1388490:CDS 45.0%
!! GACTGACTCTTCATCCCTTT+TGG - tig0021124:26479-26498 None:intergenic 45.0%
AGGGATGAAGAGTCAGTCAA+AGG + tig0021124:26481-26500 Msa1388490:CDS 45.0%
TGGCAAGACAGAAACGATGG+AGG + tig0021124:26060-26079 Msa1388490:CDS 50.0%
! GAGTTCCATTGGCTGCAACA+AGG - tig0021124:26218-26237 None:intergenic 50.0%
! TTGATGCTTGTTACGGAGGG+GGG + tig0021124:26410-26429 Msa1388490:CDS 50.0%
TCATCAGTGGCACAAAGGTC+GGG - tig0021124:26631-26650 None:intergenic 50.0%
CTCATCAGTGGCACAAAGGT+CGG - tig0021124:26632-26651 None:intergenic 50.0%
TGGCAAGACAGAAACGATGG+AGG + tig0021124:26060-26079 Msa1388490:CDS 50.0%
! GAGTTCCATTGGCTGCAACA+AGG - tig0021124:26218-26237 None:intergenic 50.0%
! TTGATGCTTGTTACGGAGGG+GGG + tig0021124:26410-26429 Msa1388490:CDS 50.0%
TCATCAGTGGCACAAAGGTC+GGG - tig0021124:26631-26650 None:intergenic 50.0%
CTCATCAGTGGCACAAAGGT+CGG - tig0021124:26632-26651 None:intergenic 50.0%
GACAGAAACGATGGAGGACC+TGG + tig0021124:26066-26085 Msa1388490:CDS 55.0%
TCTTGACGCCGTCAGCCATT+TGG - tig0021124:26378-26397 None:intergenic 55.0%
GACAGAAACGATGGAGGACC+TGG + tig0021124:26066-26085 Msa1388490:CDS 55.0%
TCTTGACGCCGTCAGCCATT+TGG - tig0021124:26378-26397 None:intergenic 55.0%
GTGGCACAAAGGTCGGGTAG+TGG - tig0021124:26625-26644 None:intergenic 60.0%
GTGGCACAAAGGTCGGGTAG+TGG - tig0021124:26625-26644 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
tig0021124 gene 25925 26738 25925 ID=Msa1388490;Name=Msa1388490
tig0021124 mRNA 25925 26738 25925 ID=Msa1388490-mRNA-1;Parent=Msa1388490;Name=Msa1388490-mRNA-1;_AED=0.04;_eAED=0.04;_QI=0|1|0.5|1|1|0.5|2|60|216
tig0021124 exon 25925 26246 25925 ID=Msa1388490-mRNA-1:exon:11129;Parent=Msa1388490-mRNA-1
tig0021124 exon 26350 26738 26350 ID=Msa1388490-mRNA-1:exon:11130;Parent=Msa1388490-mRNA-1
tig0021124 CDS 25925 26246 25925 ID=Msa1388490-mRNA-1:cds;Parent=Msa1388490-mRNA-1
tig0021124 CDS 26350 26678 26350 ID=Msa1388490-mRNA-1:cds;Parent=Msa1388490-mRNA-1
tig0021124 three_prime_UTR 26679 26738 26679 ID=Msa1388490-mRNA-1:three_prime_utr;Parent=Msa1388490-mRNA-1
Gene Sequence

>Msa1388490

AATAATTCTCCTACAAAGAGAGCTTTAATAGTCAATTTACAATTTCGAGAACCTACACTCAATACATATTCCGATGGTGCGAAGATAAAAAGTTTGCTAATAAATCGTGGATTTAAAGATGAAAATATTGATTATTGGCAAGACAGAAACGATGGAGGACCTGGTTTCCTTATTGATGCTGACAAAATACGTAATAGATTACATGATTTAATTACCATATCAAAGCCAGGTGATACTTTATTTTTTCACTTCAGTGGACATGGTAACTATCAACAAAGAGGGAGAAGTTACCTTGTTGCAGCCAATGGAACTCCTTTACTTGGTTGTGAATTTAAAAAAGTGTTAGACCAAATGGCTGACGGCGTCAAGATAATTTTCATGATTGATGCTTGTTACGGAGGGGGGTTTATTGAACTAGCTCACCACAAAGTTGTTCTATTCACATCTTCCAAAAGGGATGAAGAGTCAGTCAAAGGTTCTTTGGGTTCTGTGTTTACGAATGCGTTTGTTGATTGTGTTAATGATTACCCTGGAATAACGCATGATGAATTGATACAAAGGATCCAAATATTATATGGTCAGCATGGAAGCAAACCACTACCCGACCTTTGTGCCACTGATGAGATAAAAAATTCTATTTTTATTCTATAG

Protein sequence

>Msa1388490

NNSPTKRALIVNLQFREPTLNTYSDGAKIKSLLINRGFKDENIDYWQDRNDGGPGFLIDADKIRNRLHDLITISKPGDTLFFHFSGHGNYQQRGRSYLVAANGTPLLGCEFKKVLDQMADGVKIIFMIDACYGGGFIELAHHKVVLFTSSKRDEESVKGSLGSVFTNAFVDCVNDYPGITHDELIQRIQILYGQHGSKPLPDLCATDEIKNSIFIL*