AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380014004.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380014004.01.T01 MTR_3g020730 60.377 53 21 0 58 110 1 53 1.99e-13 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380014004.01.T01 ATCG00220 93.548 31 2 0 80 110 4 34 1.15e-11 55.1

Find 20 sgRNAs with CRISPR-Local

Find 105 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAAGAAAACATAGAGATTA+TGG 0.215607 3:+48627056 MsG0380014004.01.T01:CDS
TACGTAAATTATAAGTAAAA+AGG 0.320012 3:-48627132 None:intergenic
CCCTCATCGTCTAGTGGTTT+AGG 0.347484 3:+48625964 MsG0380014004.01.T01:CDS
CTCTCTTTCAAGGAGGCAAC+GGG 0.349769 3:+48625991 MsG0380014004.01.T01:CDS
AACGGGGATTCGACTTCCCC+TGG 0.367840 3:+48626008 MsG0380014004.01.T01:CDS
TTATTTCTAATAAATACTTC+GGG 0.385730 3:-48627029 None:intergenic
TTTAGGACATCTCTCTTTCA+AGG 0.418451 3:+48625981 MsG0380014004.01.T01:CDS
TTATCTCGATGATATAAAAT+CGG 0.425719 3:-48626951 None:intergenic
AATATCACGAATAACAATAT+CGG 0.432137 3:-48626925 None:intergenic
TTTATTTCTAATAAATACTT+CGG 0.454517 3:-48627030 None:intergenic
ACGGGGATTCGACTTCCCCT+GGG 0.464493 3:+48626009 MsG0380014004.01.T01:CDS
TCTCTCTTTCAAGGAGGCAA+CGG 0.550761 3:+48625990 MsG0380014004.01.T01:CDS
CGGGGATTCGACTTCCCCTG+GGG 0.598264 3:+48626010 MsG0380014004.01.T01:CDS
TCCTAAACCACTAGACGATG+AGG 0.634037 3:-48625965 None:intergenic
AGTATGCCCTCATCGTCTAG+TGG 0.655450 3:+48625958 None:intergenic
TCTTTCGTCAGTAAATTCAG+TGG 0.659250 3:-48626982 None:intergenic
CCTAAACCACTAGACGATGA+GGG 0.665401 3:-48625964 None:intergenic
AGGACATCTCTCTTTCAAGG+AGG 0.674472 3:+48625984 MsG0380014004.01.T01:CDS
GGGGATTCGACTTCCCCTGG+GGG 0.678595 3:+48626011 MsG0380014004.01.T01:CDS
TCTCTTTCAAGGAGGCAACG+GGG 0.717958 3:+48625992 MsG0380014004.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTTTTTTTTATTTGGTA+TGG + Chr3:48626843-48626862 MsG0380014004.01.T01:intron 10.0%
!!! TGATATATTGATATTTTTAT+GGG - Chr3:48626478-48626497 None:intergenic 10.0%
!!! TTGATATATTGATATTTTTA+TGG - Chr3:48626479-48626498 None:intergenic 10.0%
!!! TTTATTTCTAATAAATACTT+CGG - Chr3:48627033-48627052 None:intergenic 10.0%
!! ACTTATAATTTACGTAAAAA+CGG + Chr3:48627139-48627158 MsG0380014004.01.T01:CDS 15.0%
!! AGAATTAAATAGTATAACAT+AGG - Chr3:48626881-48626900 None:intergenic 15.0%
!! CATTATACTAAAAAAGAAAA+AGG - Chr3:48626771-48626790 None:intergenic 15.0%
!! TACGTAAATTATAAGTAAAA+AGG - Chr3:48627135-48627154 None:intergenic 15.0%
!!! AATCTAAAATAGAAAAACAA+AGG + Chr3:48626538-48626557 MsG0380014004.01.T01:intron 15.0%
!!! ATCTAAAATAGAAAAACAAA+GGG + Chr3:48626539-48626558 MsG0380014004.01.T01:intron 15.0%
!!! TCTTTTTTAGTATAATGTAA+AGG + Chr3:48626774-48626793 MsG0380014004.01.T01:intron 15.0%
!!! TTATTTCTAATAAATACTTC+GGG - Chr3:48627032-48627051 None:intergenic 15.0%
!! AAAAAAATCTCATTTCTAAC+AGG + Chr3:48626741-48626760 MsG0380014004.01.T01:intron 20.0%
!! AAAAAATCTCATTTCTAACA+GGG + Chr3:48626742-48626761 MsG0380014004.01.T01:intron 20.0%
!! AATATCACGAATAACAATAT+CGG - Chr3:48626928-48626947 None:intergenic 20.0%
!! ATTGAAAAATCAATGAATCA+AGG - Chr3:48626396-48626415 None:intergenic 20.0%
!! TAAAATATAAGTCTTAGGAA+AGG + Chr3:48626340-48626359 MsG0380014004.01.T01:intron 20.0%
!! TTATCTCGATGATATAAAAT+CGG - Chr3:48626954-48626973 None:intergenic 20.0%
!! TTGTGGAAAAATATGTAATA+TGG - Chr3:48626289-48626308 None:intergenic 20.0%
!! TTTAGTATAATGTAAAGGTT+CGG + Chr3:48626779-48626798 MsG0380014004.01.T01:intron 20.0%
!!! CGAAATCAATTGATATTTTT+TGG - Chr3:48626696-48626715 None:intergenic 20.0%
!!! GAAAGATTTTTCATTTCTAT+GGG + Chr3:48626999-48627018 MsG0380014004.01.T01:CDS 20.0%
!!! GGATTTAAAATATAAGTCTT+AGG + Chr3:48626335-48626354 MsG0380014004.01.T01:intron 20.0%
!!! TACATATTTTTCCACAAATT+CGG + Chr3:48626292-48626311 MsG0380014004.01.T01:intron 20.0%
! ATGAAATGATATAACCCATT+TGG + Chr3:48626198-48626217 MsG0380014004.01.T01:intron 25.0%
! ATTATAAGTAAAAAGGCAGT+AGG - Chr3:48627128-48627147 None:intergenic 25.0%
! GAAAGAAAACATAGAGATTA+TGG + Chr3:48627056-48627075 MsG0380014004.01.T01:CDS 25.0%
! TTTCAATCAAGTTAGCAATA+AGG + Chr3:48626409-48626428 MsG0380014004.01.T01:intron 25.0%
!! AATTGATTTCGTATGTGAAA+GGG + Chr3:48626705-48626724 MsG0380014004.01.T01:intron 25.0%
!! CGAAAGATTTTTCATTTCTA+TGG + Chr3:48626998-48627017 MsG0380014004.01.T01:CDS 25.0%
!! GAGATTTTATTCTTCTGTAT+GGG - Chr3:48626248-48626267 None:intergenic 25.0%
!!! AAATGGGTTATATCATTTCA+TGG - Chr3:48626199-48626218 None:intergenic 25.0%
!!! CTTATATTTTAAATCCCGAT+AGG - Chr3:48626331-48626350 None:intergenic 25.0%
!!! GATTTTGAAAAATTCCTATC+GGG + Chr3:48626314-48626333 MsG0380014004.01.T01:intron 25.0%
!!! GGATTTTGAAAAATTCCTAT+CGG + Chr3:48626313-48626332 MsG0380014004.01.T01:intron 25.0%
!!! TTTTTCAAAATCCGAATTTG+TGG - Chr3:48626306-48626325 None:intergenic 25.0%
!!! TTTTTTGGATTTGTATCCAT+CGG - Chr3:48626681-48626700 None:intergenic 25.0%
ACTACAAAAGGAAATTGATC+AGG + Chr3:48626040-48626059 MsG0380014004.01.T01:intron 30.0%
ATCAAGTTAGCAATAAGGAA+CGG + Chr3:48626414-48626433 MsG0380014004.01.T01:intron 30.0%
CTACAAAAGGAAATTGATCA+GGG + Chr3:48626041-48626060 MsG0380014004.01.T01:intron 30.0%
! AGACTAAAATTGATTCTTCC+TGG + Chr3:48626075-48626094 MsG0380014004.01.T01:intron 30.0%
! ATTTTCAGAGAACACCAAAT+GGG - Chr3:48626215-48626234 None:intergenic 30.0%
! CAATTGATTTCGTATGTGAA+AGG + Chr3:48626704-48626723 MsG0380014004.01.T01:intron 30.0%
! CGAGATTTTATTCTTCTGTA+TGG - Chr3:48626249-48626268 None:intergenic 30.0%
! GACTAAAATTGATTCTTCCT+GGG + Chr3:48626076-48626095 MsG0380014004.01.T01:intron 30.0%
! TTTTTGGATTTGTATCCATC+GGG - Chr3:48626680-48626699 None:intergenic 30.0%
TCTTTCGTCAGTAAATTCAG+TGG - Chr3:48626985-48627004 None:intergenic 35.0%
TGGGTTATATCATTTCATGG+TGG - Chr3:48626196-48626215 None:intergenic 35.0%
! GATTTTCAGAGAACACCAAA+TGG - Chr3:48626216-48626235 None:intergenic 35.0%
! GTTCTCTGAAAATCACCAAT+GGG + Chr3:48626222-48626241 MsG0380014004.01.T01:intron 35.0%
! TGTTCTCTGAAAATCACCAA+TGG + Chr3:48626221-48626240 MsG0380014004.01.T01:intron 35.0%
! TTTAGGACATCTCTCTTTCA+AGG + Chr3:48625981-48626000 MsG0380014004.01.T01:CDS 35.0%
!! ATGCTATACAACTTTTTCCC+TGG + Chr3:48626587-48626606 MsG0380014004.01.T01:intron 35.0%
!! TGCTATACAACTTTTTCCCT+GGG + Chr3:48626588-48626607 MsG0380014004.01.T01:intron 35.0%
!! TGGTGGATCAGCAAATTTTT+GGG - Chr3:48626179-48626198 None:intergenic 35.0%
!!! ATGGTGGATCAGCAAATTTT+TGG - Chr3:48626180-48626199 None:intergenic 35.0%
ACCAATTGACTACAATCCCA+GGG - Chr3:48626607-48626626 None:intergenic 40.0%
CCTCTTTCAGTTACAGTACA+GGG + Chr3:48626511-48626530 MsG0380014004.01.T01:intron 40.0%
GTTCGGACGAAGAAAGAAAA+AGG + Chr3:48626796-48626815 MsG0380014004.01.T01:intron 40.0%
AGGACATCTCTCTTTCAAGG+AGG + Chr3:48625984-48626003 MsG0380014004.01.T01:CDS 45.0%
ATTCTTCTGTATGGGCCCAT+TGG - Chr3:48626240-48626259 None:intergenic 45.0%
CCCTGTACTGTAACTGAAAG+AGG - Chr3:48626514-48626533 None:intergenic 45.0%
CCTAAACCACTAGACGATGA+GGG - Chr3:48625967-48625986 None:intergenic 45.0%
GACCAATTGACTACAATCCC+AGG - Chr3:48626608-48626627 None:intergenic 45.0%
GCACTTTAGCGAAATCGACA+CGG - Chr3:48626452-48626471 None:intergenic 45.0%
GCCTCTTTCAGTTACAGTAC+AGG + Chr3:48626510-48626529 MsG0380014004.01.T01:intron 45.0%
TCCCTGGGATTGTAGTCAAT+TGG + Chr3:48626603-48626622 MsG0380014004.01.T01:intron 45.0%
TCCTAAACCACTAGACGATG+AGG - Chr3:48625968-48625987 None:intergenic 45.0%
TCTCTCTTTCAAGGAGGCAA+CGG + Chr3:48625990-48626009 MsG0380014004.01.T01:CDS 45.0%
TTTGTATCCATCGGGACTGA+CGG - Chr3:48626672-48626691 None:intergenic 45.0%
!!! AAGTAATTTTTTTTTTTATT+TGG + Chr3:48626838-48626857 MsG0380014004.01.T01:intron 5.0%
CCCTCATCGTCTAGTGGTTT+AGG + Chr3:48625964-48625983 MsG0380014004.01.T01:CDS 50.0%
CGTTGGCAATATGTCTACGC+TGG + Chr3:48626137-48626156 MsG0380014004.01.T01:intron 50.0%
CTCTCTTTCAAGGAGGCAAC+GGG + Chr3:48625991-48626010 MsG0380014004.01.T01:CDS 50.0%
TCTCTTTCAAGGAGGCAACG+GGG + Chr3:48625992-48626011 MsG0380014004.01.T01:CDS 50.0%
TTGTATCCATCGGGACTGAC+GGG - Chr3:48626671-48626690 None:intergenic 50.0%
TTTGTAGTACCCTACCCCCA+GGG - Chr3:48626028-48626047 None:intergenic 50.0%
! TGGGGGTAGGGTACTACAAA+AGG + Chr3:48626028-48626047 MsG0380014004.01.T01:intron 50.0%
! TTTTGTAGTACCCTACCCCC+AGG - Chr3:48626029-48626048 None:intergenic 50.0%
!! ACGCTGGTTCAAATCCAGCT+CGG + Chr3:48626153-48626172 MsG0380014004.01.T01:intron 50.0%
!! AGCAAATTTTTGGGCCGAGC+TGG - Chr3:48626170-48626189 None:intergenic 50.0%
!! GGGACGGACTGTAAATTCGT+TGG + Chr3:48626120-48626139 MsG0380014004.01.T01:intron 50.0%
TCGATGCCCGAGCGGTTAAT+GGG + Chr3:48626099-48626118 MsG0380014004.01.T01:intron 55.0%
TTGTAGTACCCTACCCCCAG+GGG - Chr3:48626027-48626046 None:intergenic 55.0%
AACGGGGATTCGACTTCCCC+TGG + Chr3:48626008-48626027 MsG0380014004.01.T01:CDS 60.0%
ACGGGGATTCGACTTCCCCT+GGG + Chr3:48626009-48626028 MsG0380014004.01.T01:CDS 60.0%
ATTCGACTTCCCCTGGGGGT+AGG + Chr3:48626015-48626034 MsG0380014004.01.T01:CDS 60.0%
CGATGCCCGAGCGGTTAATG+GGG + Chr3:48626100-48626119 MsG0380014004.01.T01:intron 60.0%
GTCCGTCCCCATTAACCGCT+CGG - Chr3:48626109-48626128 None:intergenic 60.0%
GTCGATGCCCGAGCGGTTAA+TGG + Chr3:48626098-48626117 MsG0380014004.01.T01:intron 60.0%
TCCGTCCCCATTAACCGCTC+GGG - Chr3:48626108-48626127 None:intergenic 60.0%
TTCGACTTCCCCTGGGGGTA+GGG + Chr3:48626016-48626035 MsG0380014004.01.T01:CDS 60.0%
CAGCTTCCGCCTTGACAGGG+CGG - Chr3:48626637-48626656 None:intergenic 65.0%
CCCTGTCAAGGCGGAAGCTG+CGG + Chr3:48626637-48626656 MsG0380014004.01.T01:intron 65.0%
CCGCAGCTTCCGCCTTGACA+GGG - Chr3:48626640-48626659 None:intergenic 65.0%
CCTGTCAAGGCGGAAGCTGC+GGG + Chr3:48626638-48626657 MsG0380014004.01.T01:intron 65.0%
CGGGGATTCGACTTCCCCTG+GGG + Chr3:48626010-48626029 MsG0380014004.01.T01:CDS 65.0%
GCCCGAGCGGTTAATGGGGA+CGG + Chr3:48626104-48626123 MsG0380014004.01.T01:intron 65.0%
GGGGATTCGACTTCCCCTGG+GGG + Chr3:48626011-48626030 MsG0380014004.01.T01:CDS 65.0%
TCGAGTCCCGTCAGTCCCGA+TGG + Chr3:48626662-48626681 MsG0380014004.01.T01:intron 65.0%
TTCCTGGGTCGATGCCCGAG+CGG + Chr3:48626091-48626110 MsG0380014004.01.T01:intron 65.0%
!! AGAGCACCGCCCTGTCAAGG+CGG + Chr3:48626628-48626647 MsG0380014004.01.T01:intron 65.0%
!! GTCAGAGCACCGCCCTGTCA+AGG + Chr3:48626625-48626644 MsG0380014004.01.T01:intron 65.0%
CCCGCAGCTTCCGCCTTGAC+AGG - Chr3:48626641-48626660 None:intergenic 70.0%
!! AACCGCTCGGGCATCGACCC+AGG - Chr3:48626096-48626115 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
Chr3 gene 48625961 48627178 48625961 ID=MsG0380014004.01;Name=MsG0380014004.01
Chr3 mRNA 48625961 48627178 48625961 ID=MsG0380014004.01.T01;Parent=MsG0380014004.01;Name=MsG0380014004.01.T01;_AED=0.50;_eAED=0.86;_QI=0|0|0|1|0|0|2|0|110
Chr3 exon 48625961 48626037 48625961 ID=MsG0380014004.01.T01:exon:8569;Parent=MsG0380014004.01.T01
Chr3 exon 48626923 48627178 48626923 ID=MsG0380014004.01.T01:exon:8570;Parent=MsG0380014004.01.T01
Chr3 CDS 48625961 48626037 48625961 ID=MsG0380014004.01.T01:cds;Parent=MsG0380014004.01.T01
Chr3 CDS 48626923 48627178 48626923 ID=MsG0380014004.01.T01:cds;Parent=MsG0380014004.01.T01
Gene Sequence

>MsG0380014004.01.T01

ATGCCCTCATCGTCTAGTGGTTTAGGACATCTCTCTTTCAAGGAGGCAACGGGGATTCGACTTCCCCTGGGGGTAGGCTCCGATATTGTTATTCGTGATATTGATCCGATTTTATATCATCGAGATAAAATTTATACCACTGAATTTACTGACGAAAGATTTTTCATTTCTATGGGATTAAATCCCGAAGTATTTATTAGAAATAAAAGAGAAAGAAAACATAGAGATTATGGAAGTCATATTCTCGCATTTATAGCTACTGCACTCTTCATTCTAGTTCCTACTGCCTTTTTACTTATAATTTACGTAAAAACGGTAAGTCAAAGTGACTAA

Protein sequence

>MsG0380014004.01.T01

MPSSSSGLGHLSFKEATGIRLPLGVGSDIVIRDIDPILYHRDKIYTTEFTDERFFISMGLNPEVFIRNKRERKHRDYGSHILAFIATALFILVPTAFLLIIYVKTVSQSD*