AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1361980


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1361980 MtrunA17_Chr7g0269881 94.924 197 10 0 1 197 1 197 1.55e-141 392
Msa1361980 MtrunA17_Chr1g0194831 52.792 197 68 5 1 192 1 177 1.33e-64 197
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1361980 AT4G02090.1 38.579 197 83 9 9 183 16 196 4.30e-28 105

Find 38 sgRNAs with CRISPR-Local

Find 48 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTCTTTCCTCCATCATTTC+TGG 0.096966 tig0017690:-104410 None:intergenic
ATAAGCTCTGCTACTGTTAT+TGG 0.153548 tig0017690:-104050 None:intergenic
ACCATCATAGTAAATGATTT+TGG 0.206418 tig0017690:-104006 None:intergenic
AGAGCTCGATAGATAATTAT+TGG 0.225759 tig0017690:-104270 None:intergenic
AACTCAACAACAACATGTTT+TGG 0.228014 tig0017690:-104083 None:intergenic
TTGTACCAATCAAACTTCTA+AGG 0.282032 tig0017690:-104538 None:intergenic
AATTTGAGTAGGCAATTATC+AGG 0.284221 tig0017690:+104443 Msa1361980:CDS
GCCTAGCTTGGATACTATTA+AGG 0.302250 tig0017690:+104478 Msa1361980:CDS
GCTCTCAAGGCTTTGTTCCT+TGG 0.316149 tig0017690:+104288 Msa1361980:CDS
GCTTTGTTCCTTGGCTTGTA+AGG 0.325698 tig0017690:+104297 Msa1361980:CDS
ACGGGCTTCCCTGGTTTCAT+TGG 0.343712 tig0017690:-104188 None:intergenic
ACCAAAATCATTTACTATGA+TGG 0.388071 tig0017690:+104005 Msa1361980:CDS
AAGAATTCGACGACAATCTT+CGG 0.416240 tig0017690:-104222 None:intergenic
ATTTCTAGGTTCTTGTCAGC+TGG 0.436018 tig0017690:-104143 None:intergenic
TTGTGGCATGAAATGAGATA+TGG 0.438798 tig0017690:-103983 None:intergenic
AGGTTCTTGTCAGCTGGTAG+TGG 0.455725 tig0017690:-104137 None:intergenic
TTGTCAGCTGGTAGTGGTGT+TGG 0.459537 tig0017690:-104131 None:intergenic
GTATTCCTTAGAAGTTTGAT+TGG 0.462601 tig0017690:+104533 Msa1361980:CDS
AAGGTTAAGAGAAAGATATC+TGG 0.480587 tig0017690:+104506 Msa1361980:CDS
GGATACTATTAAGGAAAAGA+AGG 0.488586 tig0017690:+104487 Msa1361980:CDS
CAGAGTATTTGAATTTGAGT+AGG 0.490159 tig0017690:+104432 Msa1361980:CDS
GAAAGGGTGGAAGCCTAGCT+TGG 0.506451 tig0017690:+104466 Msa1361980:CDS
TAAGAGAAAGATATCTGGTT+GGG 0.509583 tig0017690:+104511 Msa1361980:CDS
AGTAGGCAATTATCAGGGAA+AGG 0.530002 tig0017690:+104449 Msa1361980:CDS
TGCAGATAAATGAAGAAGAG+AGG 0.538383 tig0017690:+104366 Msa1361980:CDS
TCCTTAATAGTATCCAAGCT+AGG 0.540949 tig0017690:-104479 None:intergenic
GGCAATTATCAGGGAAAGGG+TGG 0.561848 tig0017690:+104453 Msa1361980:CDS
AATTATCTATCGAGCTCTCA+AGG 0.562278 tig0017690:+104275 Msa1361980:CDS
AAAGAAAGTTGAAATTGGAG+AGG 0.565965 tig0017690:+104331 Msa1361980:CDS
GTCATGGTTCCAATGAAACC+AGG 0.568862 tig0017690:+104179 Msa1361980:CDS
TTAAGAGAAAGATATCTGGT+TGG 0.583864 tig0017690:+104510 Msa1361980:CDS
ATCTTCGGCACTTAATCCGA+CGG 0.584491 tig0017690:-104207 None:intergenic
GTAGGCAATTATCAGGGAAA+GGG 0.585684 tig0017690:+104450 Msa1361980:CDS
ATTAAAAGATGAATTAACGA+TGG 0.589712 tig0017690:-104246 None:intergenic
TCTTCGGCACTTAATCCGAC+GGG 0.598400 tig0017690:-104206 None:intergenic
ATTTGAGTAGGCAATTATCA+GGG 0.600835 tig0017690:+104444 Msa1361980:CDS
TCATGGTTCCAATGAAACCA+GGG 0.644756 tig0017690:+104180 Msa1361980:CDS
ATGAAACCAGGGAAGCCCGT+CGG 0.678146 tig0017690:+104191 Msa1361980:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CATATTTTTTGTTCATTTCT+AGG - tig0017690:104160-104179 None:intergenic 20.0%
!! AATGAACAAAAAATATGTCA+TGG + tig0017690:104163-104182 Msa1361980:CDS 20.0%
!! ATTAAAAGATGAATTAACGA+TGG - tig0017690:104249-104268 None:intergenic 20.0%
!! AAGAAAAAGAAAGTTGAAAT+TGG + tig0017690:104326-104345 Msa1361980:CDS 20.0%
!!! ATAGTAAATGATTTTGGTTG+TGG - tig0017690:104003-104022 None:intergenic 25.0%
! ACCAAAATCATTTACTATGA+TGG + tig0017690:104005-104024 Msa1361980:CDS 25.0%
!! ACCATCATAGTAAATGATTT+TGG - tig0017690:104009-104028 None:intergenic 25.0%
! ACTCAACAACAACATGTTTT+GGG - tig0017690:104085-104104 None:intergenic 30.0%
! AACTCAACAACAACATGTTT+TGG - tig0017690:104086-104105 None:intergenic 30.0%
AGAGCTCGATAGATAATTAT+TGG - tig0017690:104273-104292 None:intergenic 30.0%
AAAGAAAGTTGAAATTGGAG+AGG + tig0017690:104331-104350 Msa1361980:CDS 30.0%
! CAGAGTATTTGAATTTGAGT+AGG + tig0017690:104432-104451 Msa1361980:CDS 30.0%
AATTTGAGTAGGCAATTATC+AGG + tig0017690:104443-104462 Msa1361980:CDS 30.0%
ATTTGAGTAGGCAATTATCA+GGG + tig0017690:104444-104463 Msa1361980:CDS 30.0%
GGATACTATTAAGGAAAAGA+AGG + tig0017690:104487-104506 Msa1361980:CDS 30.0%
AAGGTTAAGAGAAAGATATC+TGG + tig0017690:104506-104525 Msa1361980:CDS 30.0%
TTAAGAGAAAGATATCTGGT+TGG + tig0017690:104510-104529 Msa1361980:CDS 30.0%
TAAGAGAAAGATATCTGGTT+GGG + tig0017690:104511-104530 Msa1361980:CDS 30.0%
GTATTCCTTAGAAGTTTGAT+TGG + tig0017690:104533-104552 Msa1361980:CDS 30.0%
TTGTACCAATCAAACTTCTA+AGG - tig0017690:104541-104560 None:intergenic 30.0%
TTGTGGCATGAAATGAGATA+TGG - tig0017690:103986-104005 None:intergenic 35.0%
ATAAGCTCTGCTACTGTTAT+TGG - tig0017690:104053-104072 None:intergenic 35.0%
AAGAATTCGACGACAATCTT+CGG - tig0017690:104225-104244 None:intergenic 35.0%
AATTATCTATCGAGCTCTCA+AGG + tig0017690:104275-104294 Msa1361980:CDS 35.0%
TTCAAAAACCTTACAAGCCA+AGG - tig0017690:104308-104327 None:intergenic 35.0%
TGCAGATAAATGAAGAAGAG+AGG + tig0017690:104366-104385 Msa1361980:CDS 35.0%
! TGAGTTTTTGCCAGAAATGA+TGG + tig0017690:104400-104419 Msa1361980:CDS 35.0%
TCCTTAATAGTATCCAAGCT+AGG - tig0017690:104482-104501 None:intergenic 35.0%
!!! GTAGTGGTGTTGGTTTTTTC+TGG - tig0017690:104124-104143 None:intergenic 40.0%
! ATTTCTAGGTTCTTGTCAGC+TGG - tig0017690:104146-104165 None:intergenic 40.0%
TCATGGTTCCAATGAAACCA+GGG + tig0017690:104180-104199 Msa1361980:CDS 40.0%
! GTTTTTGCCAGAAATGATGG+AGG + tig0017690:104403-104422 Msa1361980:CDS 40.0%
AGTAGGCAATTATCAGGGAA+AGG + tig0017690:104449-104468 Msa1361980:CDS 40.0%
GTAGGCAATTATCAGGGAAA+GGG + tig0017690:104450-104469 Msa1361980:CDS 40.0%
GCCTAGCTTGGATACTATTA+AGG + tig0017690:104478-104497 Msa1361980:CDS 40.0%
GTCATGGTTCCAATGAAACC+AGG + tig0017690:104179-104198 Msa1361980:CDS 45.0%
ATCTTCGGCACTTAATCCGA+CGG - tig0017690:104210-104229 None:intergenic 45.0%
!! GCTTTGTTCCTTGGCTTGTA+AGG + tig0017690:104297-104316 Msa1361980:CDS 45.0%
GCTCTTTCCTCCATCATTTC+TGG - tig0017690:104413-104432 None:intergenic 45.0%
!! TTGTCAGCTGGTAGTGGTGT+TGG - tig0017690:104134-104153 None:intergenic 50.0%
AGGTTCTTGTCAGCTGGTAG+TGG - tig0017690:104140-104159 None:intergenic 50.0%
TCTTCGGCACTTAATCCGAC+GGG - tig0017690:104209-104228 None:intergenic 50.0%
!! GCTCTCAAGGCTTTGTTCCT+TGG + tig0017690:104288-104307 Msa1361980:CDS 50.0%
GGCAATTATCAGGGAAAGGG+TGG + tig0017690:104453-104472 Msa1361980:CDS 50.0%
ACGGGCTTCCCTGGTTTCAT+TGG - tig0017690:104191-104210 None:intergenic 55.0%
ATGAAACCAGGGAAGCCCGT+CGG + tig0017690:104191-104210 Msa1361980:CDS 55.0%
GAAAGGGTGGAAGCCTAGCT+TGG + tig0017690:104466-104485 Msa1361980:CDS 55.0%
! CTTAATCCGACGGGCTTCCC+TGG - tig0017690:104200-104219 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
tig0017690 gene 103975 104568 103975 ID=Msa1361980;Name=Msa1361980
tig0017690 mRNA 103975 104568 103975 ID=Msa1361980-mRNA-1;Parent=Msa1361980;Name=Msa1361980-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|197
tig0017690 exon 103975 104568 103975 ID=Msa1361980-mRNA-1:exon:12766;Parent=Msa1361980-mRNA-1
tig0017690 CDS 103975 104568 103975 ID=Msa1361980-mRNA-1:cds;Parent=Msa1361980-mRNA-1
Gene Sequence

>Msa1361980

ATGGGAAACCATATCTCATTTCATGCCACAACCAAAATCATTTACTATGATGGTTCTGTTCAAGAATTTGATCAACCAATAACAGTAGCAGAGCTTATGTTAGATCACCCAAAACATGTTGTTGTTGAGTTTCATTCAGCAATGAACCAGAAAAAACCAACACCACTACCAGCTGACAAGAACCTAGAAATGAACAAAAAATATGTCATGGTTCCAATGAAACCAGGGAAGCCCGTCGGATTAAGTGCCGAAGATTGTCGTCGAATTCTTTCCATCGTTAATTCATCTTTTAATACCAATAATTATCTATCGAGCTCTCAAGGCTTTGTTCCTTGGCTTGTAAGGTTTTTGAAGAAAAAGAAAGTTGAAATTGGAGAGGTTGAAACAAGTATGCAGATAAATGAAGAAGAGAGGTTTAATTTTTGTGAGTTTTTGCCAGAAATGATGGAGGAAAGAGCAGAGTATTTGAATTTGAGTAGGCAATTATCAGGGAAAGGGTGGAAGCCTAGCTTGGATACTATTAAGGAAAAGAAGGTTAAGAGAAAGATATCTGGTTGGGTATTCCTTAGAAGTTTGATTGGTACAAAGATTTGA

Protein sequence

>Msa1361980

MGNHISFHATTKIIYYDGSVQEFDQPITVAELMLDHPKHVVVEFHSAMNQKKPTPLPADKNLEMNKKYVMVPMKPGKPVGLSAEDCRRILSIVNSSFNTNNYLSSSQGFVPWLVRFLKKKKVEIGEVETSMQINEEERFNFCEFLPEMMEERAEYLNLSRQLSGKGWKPSLDTIKEKKVKRKISGWVFLRSLIGTKI*