AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1118600


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1118600 MtrunA17_Chr7g0253661 90.594 202 18 1 1 201 1 202 1.34e-115 327
Msa1118600 MtrunA17_Chr6g0481571 42.000 100 55 1 1 97 1 100 1.46e-22 89.4
Msa1118600 MtrunA17_Chr5g0440291 40.816 98 55 1 8 105 11 105 9.28e-20 84.0
Msa1118600 MtrunA17_Chr5g0440311 34.921 126 73 3 2 118 4 129 5.00e-19 82.4
Msa1118600 MtrunA17_Chr5g0440321 31.538 130 81 3 8 131 10 137 6.07e-14 68.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1118600 AT1G54400.1 42.157 102 56 2 1 101 5 104 7.02e-22 88.6
Msa1118600 AT2G27140.1 35.849 106 67 1 3 107 5 110 5.86e-19 81.6
Msa1118600 AT5G20970.1 36.364 99 63 0 9 107 8 106 2.69e-17 77.8
Msa1118600 AT5G04890.1 34.343 99 60 2 11 104 16 114 4.53e-16 75.9

Find 29 sgRNAs with CRISPR-Local

Find 96 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCATCTTCATTGCAATATTT+TGG 0.150093 7_3:+67345902 Msa1118590:intron
TCTGGCATTTGTTCTTCTTC+TGG 0.224256 7_3:+67345803 Msa1118590:intron
ACATATCAGAGTTTGGAATT+TGG 0.240193 7_3:-67345746 Msa1118600:CDS
ACCATTGAGCTTCATCTTCC+AGG 0.313069 7_3:-67346327 Msa1118600:intron
TACACAACAGACAACAAGTT+TGG 0.336570 7_3:-67345677 Msa1118600:CDS
AGAGGTTGCTCTTAAATTCA+TGG 0.354880 7_3:-67345630 Msa1118600:CDS
GTCCATTTGATGGAACTAAA+TGG 0.359566 7_3:-67345952 Msa1118600:CDS
ATATCCTCATCTTCAAGTTC+TGG 0.365913 7_3:+67345785 Msa1118590:intron
CGAATTCAAATCAACCATCT+TGG 0.372715 7_3:-67345998 Msa1118600:CDS
TTCCATTTAGTTCCATCAAA+TGG 0.385038 7_3:+67345950 Msa1118590:intron
AGTGGAGAGCGTCCATTTGA+TGG 0.411520 7_3:-67345962 Msa1118600:CDS
GAATTCAAATCAACCATCTT+GGG 0.419246 7_3:-67345997 Msa1118600:CDS
GGTTGTGATAATTGTTGTAA+TGG 0.450646 7_3:-67345609 Msa1118600:CDS
TCTTCTTCTGGTTCCTCTTG+AGG 0.457813 7_3:+67345815 Msa1118590:intron
AAAGCAAACATGCACATAAC+CGG 0.483167 7_3:-67346404 Msa1118600:CDS
TGCACATAACCGGTCTTATG+AGG 0.489902 7_3:-67346394 Msa1118600:CDS
GGTTATTGTAAATTATCTTG+TGG 0.496692 7_3:-67345588 Msa1118600:CDS
TGCAATGAAGATGCCATTCG+TGG 0.501501 7_3:-67345893 Msa1118600:CDS
TATCAGAGTTTGGAATTTGG+AGG 0.521412 7_3:-67345743 Msa1118600:CDS
TTGCATGAAATTGCCACGAA+TGG 0.562966 7_3:+67345880 Msa1118590:intron
AGCAAAACCGTCATGGCTCA+AGG 0.573165 7_3:-67345560 Msa1118600:CDS
GATCAAAATCCTCATAAGAC+CGG 0.581928 7_3:+67346385 Msa1118590:intron
AATGCCAGAACTTGAAGATG+AGG 0.591611 7_3:-67345789 Msa1118600:CDS
AGTTGATCTGATACCTCAAG+AGG 0.599832 7_3:-67345828 Msa1118600:CDS
TGATTGACCTTGAGCCATGA+CGG 0.602155 7_3:+67345553 Msa1118590:intron
GCCTGGAAGATGAAGCTCAA+TGG 0.602686 7_3:+67346326 Msa1118590:intron
GGATATGAGCAAAACCGTCA+TGG 0.621622 7_3:-67345567 Msa1118600:CDS
GATGAAGCTCAATGGTGTCA+CGG 0.630838 7_3:+67346334 Msa1118590:intron
TGATGTAGAAACTACTAGAG+AGG 0.643103 7_3:-67345648 Msa1118600:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TCATGTATCTAAATTATATA+TGG - chr7_3:67345652-67345671 Msa1118600:CDS 15.0%
!! AAATGAAATTGAATTAAACA+AGG + chr7_3:67345679-67345698 Msa1118590:intron 15.0%
!!! CATTGTTTTTGTTAAATTTA+GGG + chr7_3:67345838-67345857 Msa1118590:intron 15.0%
!!! ACATTGTTTTTGTTAAATTT+AGG + chr7_3:67345839-67345858 Msa1118590:intron 15.0%
!! TCATGTATCTAAATTATATA+TGG - chr7_3:67345652-67345671 Msa1118600:CDS 15.0%
!! AAATGAAATTGAATTAAACA+AGG + chr7_3:67345679-67345698 Msa1118590:intron 15.0%
!!! CATTGTTTTTGTTAAATTTA+GGG + chr7_3:67345838-67345857 Msa1118590:intron 15.0%
!!! ACATTGTTTTTGTTAAATTT+AGG + chr7_3:67345839-67345858 Msa1118590:intron 15.0%
!! AATAACACTACAACTAAATA+AGG + chr7_3:67345753-67345772 Msa1118590:intron 20.0%
!! AATAACACTACAACTAAATA+AGG + chr7_3:67345753-67345772 Msa1118590:intron 20.0%
!!! ATTTTGATCCTGTTTTTAAG+TGG - chr7_3:67345575-67345594 Msa1118600:CDS 25.0%
! GAAAAATACATATCAGAGTT+TGG - chr7_3:67346193-67346212 Msa1118600:intron 25.0%
! GGTTATTGTAAATTATCTTG+TGG - chr7_3:67346358-67346377 Msa1118600:CDS 25.0%
!!! ATTTTGATCCTGTTTTTAAG+TGG - chr7_3:67345575-67345594 Msa1118600:CDS 25.0%
! GAAAAATACATATCAGAGTT+TGG - chr7_3:67346193-67346212 Msa1118600:intron 25.0%
! GGTTATTGTAAATTATCTTG+TGG - chr7_3:67346358-67346377 Msa1118600:CDS 25.0%
!!! ATAGACTTTTTTCACAGACT+AGG - chr7_3:67345863-67345882 Msa1118600:CDS 30.0%
!!! TAGACTTTTTTCACAGACTA+GGG - chr7_3:67345864-67345883 Msa1118600:CDS 30.0%
!! GCTTTATTTGAGAGTTATGA+GGG - chr7_3:67345886-67345905 Msa1118600:CDS 30.0%
! CTTTATTTGAGAGTTATGAG+GGG - chr7_3:67345887-67345906 Msa1118600:CDS 30.0%
!!! GGGGTTATTAATTTGTTTTC+AGG - chr7_3:67345906-67345925 Msa1118600:CDS 30.0%
GAATTCAAATCAACCATCTT+GGG - chr7_3:67345949-67345968 Msa1118600:CDS 30.0%
! TTCCATTTAGTTCCATCAAA+TGG + chr7_3:67345999-67346018 Msa1118590:intron 30.0%
! GCATCTTCATTGCAATATTT+TGG + chr7_3:67346047-67346066 Msa1118590:intron 30.0%
!!! GGTATCAGATCAACTTTTTT+TGG + chr7_3:67346113-67346132 Msa1118590:intron 30.0%
! ACATATCAGAGTTTGGAATT+TGG - chr7_3:67346200-67346219 Msa1118600:intron 30.0%
GGTTGTGATAATTGTTGTAA+TGG - chr7_3:67346337-67346356 Msa1118600:CDS 30.0%
!!! ATAGACTTTTTTCACAGACT+AGG - chr7_3:67345863-67345882 Msa1118600:CDS 30.0%
!!! TAGACTTTTTTCACAGACTA+GGG - chr7_3:67345864-67345883 Msa1118600:CDS 30.0%
!! GCTTTATTTGAGAGTTATGA+GGG - chr7_3:67345886-67345905 Msa1118600:CDS 30.0%
! CTTTATTTGAGAGTTATGAG+GGG - chr7_3:67345887-67345906 Msa1118600:CDS 30.0%
!!! GGGGTTATTAATTTGTTTTC+AGG - chr7_3:67345906-67345925 Msa1118600:CDS 30.0%
GAATTCAAATCAACCATCTT+GGG - chr7_3:67345949-67345968 Msa1118600:CDS 30.0%
! TTCCATTTAGTTCCATCAAA+TGG + chr7_3:67345999-67346018 Msa1118590:intron 30.0%
! GCATCTTCATTGCAATATTT+TGG + chr7_3:67346047-67346066 Msa1118590:intron 30.0%
!!! GGTATCAGATCAACTTTTTT+TGG + chr7_3:67346113-67346132 Msa1118590:intron 30.0%
! ACATATCAGAGTTTGGAATT+TGG - chr7_3:67346200-67346219 Msa1118600:intron 30.0%
GGTTGTGATAATTGTTGTAA+TGG - chr7_3:67346337-67346356 Msa1118600:CDS 30.0%
AAAGCAAACATGCACATAAC+CGG - chr7_3:67345542-67345561 Msa1118600:CDS 35.0%
GATCAAAATCCTCATAAGAC+CGG + chr7_3:67345564-67345583 Msa1118590:intron 35.0%
ATACATGAAATTCACATGCC+TGG + chr7_3:67345640-67345659 Msa1118590:intron 35.0%
!! GGCTTTATTTGAGAGTTATG+AGG - chr7_3:67345885-67345904 Msa1118600:CDS 35.0%
CGAATTCAAATCAACCATCT+TGG - chr7_3:67345948-67345967 Msa1118600:CDS 35.0%
! AATCAACCATCTTGGGTTTT+TGG - chr7_3:67345956-67345975 Msa1118600:CDS 35.0%
TTATCACCAAAAACCCAAGA+TGG + chr7_3:67345965-67345984 Msa1118590:intron 35.0%
GTCCATTTGATGGAACTAAA+TGG - chr7_3:67345994-67346013 Msa1118600:CDS 35.0%
! ATATCCTCATCTTCAAGTTC+TGG + chr7_3:67346164-67346183 Msa1118590:intron 35.0%
! TATCAGAGTTTGGAATTTGG+AGG - chr7_3:67346203-67346222 Msa1118600:intron 35.0%
TACACAACAGACAACAAGTT+TGG - chr7_3:67346269-67346288 Msa1118600:intron 35.0%
TGATGTAGAAACTACTAGAG+AGG - chr7_3:67346298-67346317 Msa1118600:intron 35.0%
AGAGGTTGCTCTTAAATTCA+TGG - chr7_3:67346316-67346335 Msa1118600:intron 35.0%
AAAGCAAACATGCACATAAC+CGG - chr7_3:67345542-67345561 Msa1118600:CDS 35.0%
GATCAAAATCCTCATAAGAC+CGG + chr7_3:67345564-67345583 Msa1118590:intron 35.0%
ATACATGAAATTCACATGCC+TGG + chr7_3:67345640-67345659 Msa1118590:intron 35.0%
!! GGCTTTATTTGAGAGTTATG+AGG - chr7_3:67345885-67345904 Msa1118600:CDS 35.0%
CGAATTCAAATCAACCATCT+TGG - chr7_3:67345948-67345967 Msa1118600:CDS 35.0%
! AATCAACCATCTTGGGTTTT+TGG - chr7_3:67345956-67345975 Msa1118600:CDS 35.0%
TTATCACCAAAAACCCAAGA+TGG + chr7_3:67345965-67345984 Msa1118590:intron 35.0%
GTCCATTTGATGGAACTAAA+TGG - chr7_3:67345994-67346013 Msa1118600:CDS 35.0%
! ATATCCTCATCTTCAAGTTC+TGG + chr7_3:67346164-67346183 Msa1118590:intron 35.0%
! TATCAGAGTTTGGAATTTGG+AGG - chr7_3:67346203-67346222 Msa1118600:intron 35.0%
TACACAACAGACAACAAGTT+TGG - chr7_3:67346269-67346288 Msa1118600:intron 35.0%
TGATGTAGAAACTACTAGAG+AGG - chr7_3:67346298-67346317 Msa1118600:intron 35.0%
AGAGGTTGCTCTTAAATTCA+TGG - chr7_3:67346316-67346335 Msa1118600:intron 35.0%
TCTCTACGCCACTTAAAAAC+AGG + chr7_3:67345586-67345605 Msa1118590:intron 40.0%
!!! CTTGGGTTTTTGGTGATAAG+TGG - chr7_3:67345966-67345985 Msa1118600:CDS 40.0%
TTGCATGAAATTGCCACGAA+TGG + chr7_3:67346069-67346088 Msa1118590:intron 40.0%
AGTTGATCTGATACCTCAAG+AGG - chr7_3:67346118-67346137 Msa1118600:intron 40.0%
TCTGGCATTTGTTCTTCTTC+TGG + chr7_3:67346146-67346165 Msa1118590:intron 40.0%
AATGCCAGAACTTGAAGATG+AGG - chr7_3:67346157-67346176 Msa1118600:intron 40.0%
TCTCTACGCCACTTAAAAAC+AGG + chr7_3:67345586-67345605 Msa1118590:intron 40.0%
!!! CTTGGGTTTTTGGTGATAAG+TGG - chr7_3:67345966-67345985 Msa1118600:CDS 40.0%
TTGCATGAAATTGCCACGAA+TGG + chr7_3:67346069-67346088 Msa1118590:intron 40.0%
AGTTGATCTGATACCTCAAG+AGG - chr7_3:67346118-67346137 Msa1118600:intron 40.0%
TCTGGCATTTGTTCTTCTTC+TGG + chr7_3:67346146-67346165 Msa1118590:intron 40.0%
AATGCCAGAACTTGAAGATG+AGG - chr7_3:67346157-67346176 Msa1118600:intron 40.0%
! TGCACATAACCGGTCTTATG+AGG - chr7_3:67345552-67345571 Msa1118600:CDS 45.0%
! GATGAAGCTCAATGGTGTCA+CGG + chr7_3:67345615-67345634 Msa1118590:intron 45.0%
ACCATTGAGCTTCATCTTCC+AGG - chr7_3:67345619-67345638 Msa1118600:CDS 45.0%
TGCAATGAAGATGCCATTCG+TGG - chr7_3:67346053-67346072 Msa1118600:intron 45.0%
!! TCTTCTTCTGGTTCCTCTTG+AGG + chr7_3:67346134-67346153 Msa1118590:intron 45.0%
GGATATGAGCAAAACCGTCA+TGG - chr7_3:67346379-67346398 Msa1118600:CDS 45.0%
TGATTGACCTTGAGCCATGA+CGG + chr7_3:67346396-67346415 Msa1118590:intron 45.0%
! TGCACATAACCGGTCTTATG+AGG - chr7_3:67345552-67345571 Msa1118600:CDS 45.0%
! GATGAAGCTCAATGGTGTCA+CGG + chr7_3:67345615-67345634 Msa1118590:intron 45.0%
ACCATTGAGCTTCATCTTCC+AGG - chr7_3:67345619-67345638 Msa1118600:CDS 45.0%
TGCAATGAAGATGCCATTCG+TGG - chr7_3:67346053-67346072 Msa1118600:intron 45.0%
!! TCTTCTTCTGGTTCCTCTTG+AGG + chr7_3:67346134-67346153 Msa1118590:intron 45.0%
GGATATGAGCAAAACCGTCA+TGG - chr7_3:67346379-67346398 Msa1118600:CDS 45.0%
TGATTGACCTTGAGCCATGA+CGG + chr7_3:67346396-67346415 Msa1118590:intron 45.0%
GCCTGGAAGATGAAGCTCAA+TGG + chr7_3:67345623-67345642 Msa1118590:intron 50.0%
!! AGTGGAGAGCGTCCATTTGA+TGG - chr7_3:67345984-67346003 Msa1118600:CDS 50.0%
AGCAAAACCGTCATGGCTCA+AGG - chr7_3:67346386-67346405 Msa1118600:CDS 50.0%
GCCTGGAAGATGAAGCTCAA+TGG + chr7_3:67345623-67345642 Msa1118590:intron 50.0%
!! AGTGGAGAGCGTCCATTTGA+TGG - chr7_3:67345984-67346003 Msa1118600:CDS 50.0%
AGCAAAACCGTCATGGCTCA+AGG - chr7_3:67346386-67346405 Msa1118600:CDS 50.0%
Chromosome Type Strat End Strand Name
chr7_3 gene 67345538 67346430 67345538 ID=Msa1118600;Name=Msa1118600
chr7_3 mRNA 67345538 67346430 67345538 ID=Msa1118600-mRNA-1;Parent=Msa1118600;Name=Msa1118600-mRNA-1;_AED=0.02;_eAED=0.02;_QI=0|0|0|1|1|1|2|0|201
chr7_3 exon 67346328 67346430 67346328 ID=Msa1118600-mRNA-1:exon:16543;Parent=Msa1118600-mRNA-1
chr7_3 exon 67345538 67346040 67345538 ID=Msa1118600-mRNA-1:exon:16542;Parent=Msa1118600-mRNA-1
chr7_3 CDS 67346328 67346430 67346328 ID=Msa1118600-mRNA-1:cds;Parent=Msa1118600-mRNA-1
chr7_3 CDS 67345538 67346040 67345538 ID=Msa1118600-mRNA-1:cds;Parent=Msa1118600-mRNA-1
Gene Sequence

>Msa1118600

ATGGAAAGCAAACATGCACATAACCGGTCTTATGAGGATTTTGATCCTGTTTTTAAGTGGCGTAGAGAACAAGACCGTGACACCATTGAGCTTCATCTTCCAGGTTTTAAGAGAGAGCAAATACGAATTCAAATCAACCATCTTGGGTTTTTGGTGATAAGTGGAGAGCGTCCATTTGATGGAACTAAATGGAAACGTTTCAAGAAAGAATTTGAACTTCCAAAATATTGCAATGAAGATGCCATTCGTGGCAATTTCATGCAAAACATTCTTTCAGTAGTATTGCCAAAAAAAGTTGATCTGATACCTCAAGAGGAACCAGAAGAAGAACAAATGCCAGAACTTGAAGATGAGGATATATATCAAGAGAAAAATACATATCAGAGTTTGGAATTTGGAGGAAGAAATAGAGAAGCAGAGATTGAAAAACTATCAGAATATAATTACACAACAGACAACAAGTTTGGAGAAAATGATGTAGAAACTACTAGAGAGGTTGCTCTTAAATTCATGGTTGTGATAATTGTTGTAATGGTTATTGTAAATTATCTTGTGGATATGAGCAAAACCGTCATGGCTCAAGGTCAATCATATTTTCAAAATTAG

Protein sequence

>Msa1118600

MESKHAHNRSYEDFDPVFKWRREQDRDTIELHLPGFKREQIRIQINHLGFLVISGERPFDGTKWKRFKKEFELPKYCNEDAIRGNFMQNILSVVLPKKVDLIPQEEPEEEQMPELEDEDIYQEKNTYQSLEFGGRNREAEIEKLSEYNYTTDNKFGENDVETTREVALKFMVVIIVVMVIVNYLVDMSKTVMAQGQSYFQN*