AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0880040


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0880040 MtrunA17_Chr7g0265751 84.049 163 11 2 1 162 1 149 2.07e-77 233
Msa0880040 MtrunA17_Chr2g0320801 60.736 163 35 4 1 162 1 135 6.22e-61 191
Msa0880040 MtrunA17_Chr1g0162821 59.259 162 37 5 1 161 1 134 4.54e-59 185
Msa0880040 MtrunA17_Chr2g0276891 55.102 49 22 0 9 57 184 232 6.83e-13 64.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0880040 AT1G27650.1 73.984 123 18 2 1 123 1 109 4.61e-60 188
Msa0880040 AT5G42820.1 61.963 163 33 5 1 162 1 135 6.24e-60 187
Msa0880040 AT5G42820.2 61.963 163 33 5 1 162 1 135 6.24e-60 187
Msa0880040 AT3G44785.1 65.753 73 24 1 1 73 1 72 3.51e-31 107
Msa0880040 AT1G27650.2 60.274 73 15 2 51 123 1 59 9.40e-21 85.9
Msa0880040 AT1G10320.2 35.345 116 55 2 9 122 228 325 1.02e-18 82.8
Msa0880040 AT1G10320.1 35.345 116 55 2 9 122 237 334 1.05e-18 82.4

Find 38 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGCTCCGCCATCGATTATT+AGG 0.132506 6_1:+26105904 None:intergenic
AAGTGTTCTTGGAGTTTATC+AGG 0.235787 6_1:+26105641 None:intergenic
CTTGAATATTTGTGACAATT+TGG 0.267256 6_1:-26105479 Msa0880040:CDS
TTATCAGGGTCAAGAGATTC+AGG 0.286148 6_1:+26105656 None:intergenic
TACATACATCGAAGTGTTCT+TGG 0.310686 6_1:+26105630 None:intergenic
TGAGGTTGTTGAGGTTGATT+AGG 0.344172 6_1:+26105698 None:intergenic
GAGCATTTAGCATCGATATT+CGG 0.354185 6_1:-26105887 Msa0880040:CDS
TGAGGTGGTTGAGGAGGTTG+AGG 0.362652 6_1:+26105680 None:intergenic
TGCTCCGCCATCGATTATTA+GGG 0.367053 6_1:+26105905 None:intergenic
GATTCAGGTTGAGGTGGTTG+AGG 0.376296 6_1:+26105671 None:intergenic
ATAAAGTTAAGGTTCATATC+AGG 0.384960 6_1:+26105731 None:intergenic
TTTGAGGAGCTGAGCAAGTA+TGG 0.394906 6_1:-26105514 Msa0880040:CDS
GAGTAGGATTGATAAAGTTA+AGG 0.396234 6_1:+26105720 None:intergenic
TGACAATTTGGCTGATCATA+TGG 0.424836 6_1:-26105467 Msa0880040:CDS
AGTAGGACTAATGGTGGGTT+TGG 0.429071 6_1:+26105781 None:intergenic
AACATAAATAAATCTCGAAA+GGG 0.429853 6_1:-26105949 Msa0880040:five_prime_UTR
TGTTGAGGTTGATTAGGAGT+AGG 0.451883 6_1:+26105704 None:intergenic
TCAGGTTGAGGTGGTTGAGG+AGG 0.483616 6_1:+26105674 None:intergenic
GCTCCGATCTTGAAGTAGAA+TGG 0.500982 6_1:+26105839 None:intergenic
TGAGGAGGTTGAGGTTGTTG+AGG 0.510776 6_1:+26105689 None:intergenic
GGGTCAAGAGATTCAGGTTG+AGG 0.514083 6_1:+26105662 None:intergenic
GAGAACAAGAGTAGGACTAA+TGG 0.530039 6_1:+26105772 None:intergenic
ATCAGGACGTTGATACATGT+TGG 0.531267 6_1:+26105748 None:intergenic
AATGTATATGTTCAGTATAG+AGG 0.537246 6_1:-26105328 Msa0880040:CDS
CAACATAAATAAATCTCGAA+AGG 0.544906 6_1:-26105950 Msa0880040:five_prime_UTR
AGTGTTCTTGGAGTTTATCA+GGG 0.562952 6_1:+26105642 None:intergenic
TGTCCATTCTACTTCAAGAT+CGG 0.570630 6_1:-26105842 Msa0880040:CDS
GAAAGGGGTTCGTGAGAGAG+TGG 0.603769 6_1:-26105933 Msa0880040:five_prime_UTR
GGCGAAACCCTAATAATCGA+TGG 0.614459 6_1:-26105912 Msa0880040:exon
AACAAGAGTAGGACTAATGG+TGG 0.614682 6_1:+26105775 None:intergenic
TCAAGAGATTCAGGTTGAGG+TGG 0.615585 6_1:+26105665 None:intergenic
AAGATCGGAGCTTGTAGACA+TGG 0.618937 6_1:-26105827 Msa0880040:CDS
TTATAAGAGCATTAGCAGCA+TGG 0.629715 6_1:+26105301 None:intergenic
ACATAAATAAATCTCGAAAG+GGG 0.642552 6_1:-26105948 Msa0880040:five_prime_UTR
ATGTTGGAGAGAACAAGAGT+AGG 0.650220 6_1:+26105764 None:intergenic
ACAAGAGTAGGACTAATGGT+GGG 0.704223 6_1:+26105776 None:intergenic
GAAACCCTAATAATCGATGG+CGG 0.712302 6_1:-26105909 Msa0880040:exon
TGGTATGAAGACGAGAACAG+CGG 0.740225 6_1:+26105801 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATCAAAATAAAAAATTGAA+GGG + chr6_1:26105657-26105676 None:intergenic 10.0%
!! AAATCAAAATAAAAAATTGA+AGG + chr6_1:26105658-26105677 None:intergenic 10.0%
!!! TTATGATTTTGTTTTTTTAT+AGG - chr6_1:26105889-26105908 Msa0880040:CDS 10.0%
!! ATCAAAATAAAAAATTGAAG+GGG + chr6_1:26105656-26105675 None:intergenic 15.0%
!! AAAACAAAATCATAAAAATG+AGG + chr6_1:26105884-26105903 None:intergenic 15.0%
!! AACATAAATAAATCTCGAAA+GGG - chr6_1:26105296-26105315 Msa0880040:CDS 20.0%
!!! TTTTTATGAAGATCTATTTG+AGG - chr6_1:26105715-26105734 Msa0880040:CDS 20.0%
!! AAAACAAAAGAAAAAGAGAA+AGG + chr6_1:26105818-26105837 None:intergenic 20.0%
!!! GATTTTGTTTTTTTATAGGT+TGG - chr6_1:26105893-26105912 Msa0880040:CDS 20.0%
! CAACATAAATAAATCTCGAA+AGG - chr6_1:26105295-26105314 Msa0880040:CDS 25.0%
! ACATAAATAAATCTCGAAAG+GGG - chr6_1:26105297-26105316 Msa0880040:CDS 25.0%
! ATAAAGTTAAGGTTCATATC+AGG + chr6_1:26105517-26105536 None:intergenic 25.0%
! CTTGAATATTTGTGACAATT+TGG - chr6_1:26105766-26105785 Msa0880040:CDS 25.0%
! AATGTATATGTTCAGTATAG+AGG - chr6_1:26105917-26105936 Msa0880040:five_prime_UTR 25.0%
GAGTAGGATTGATAAAGTTA+AGG + chr6_1:26105528-26105547 None:intergenic 30.0%
!! GAGCATTTAGCATCGATATT+CGG - chr6_1:26105358-26105377 Msa0880040:intron 35.0%
TGTCCATTCTACTTCAAGAT+CGG - chr6_1:26105403-26105422 Msa0880040:intron 35.0%
AGTGTTCTTGGAGTTTATCA+GGG + chr6_1:26105606-26105625 None:intergenic 35.0%
AAGTGTTCTTGGAGTTTATC+AGG + chr6_1:26105607-26105626 None:intergenic 35.0%
! TACATACATCGAAGTGTTCT+TGG + chr6_1:26105618-26105637 None:intergenic 35.0%
TGACAATTTGGCTGATCATA+TGG - chr6_1:26105778-26105797 Msa0880040:CDS 35.0%
!! TTATAAGAGCATTAGCAGCA+TGG + chr6_1:26105947-26105966 None:intergenic 35.0%
GAAACCCTAATAATCGATGG+CGG - chr6_1:26105336-26105355 Msa0880040:CDS 40.0%
ACAAGAGTAGGACTAATGGT+GGG + chr6_1:26105472-26105491 None:intergenic 40.0%
AACAAGAGTAGGACTAATGG+TGG + chr6_1:26105473-26105492 None:intergenic 40.0%
GAGAACAAGAGTAGGACTAA+TGG + chr6_1:26105476-26105495 None:intergenic 40.0%
ATGTTGGAGAGAACAAGAGT+AGG + chr6_1:26105484-26105503 None:intergenic 40.0%
ATCAGGACGTTGATACATGT+TGG + chr6_1:26105500-26105519 None:intergenic 40.0%
! TGTTGAGGTTGATTAGGAGT+AGG + chr6_1:26105544-26105563 None:intergenic 40.0%
! TGAGGTTGTTGAGGTTGATT+AGG + chr6_1:26105550-26105569 None:intergenic 40.0%
TTATCAGGGTCAAGAGATTC+AGG + chr6_1:26105592-26105611 None:intergenic 40.0%
GGCGAAACCCTAATAATCGA+TGG - chr6_1:26105333-26105352 Msa0880040:CDS 45.0%
! TGCTCCGCCATCGATTATTA+GGG + chr6_1:26105343-26105362 None:intergenic 45.0%
! ATGCTCCGCCATCGATTATT+AGG + chr6_1:26105344-26105363 None:intergenic 45.0%
GCTCCGATCTTGAAGTAGAA+TGG + chr6_1:26105409-26105428 None:intergenic 45.0%
AAGATCGGAGCTTGTAGACA+TGG - chr6_1:26105418-26105437 Msa0880040:intron 45.0%
TGGTATGAAGACGAGAACAG+CGG + chr6_1:26105447-26105466 None:intergenic 45.0%
!! AGTAGGACTAATGGTGGGTT+TGG + chr6_1:26105467-26105486 None:intergenic 45.0%
!! TCAAGAGATTCAGGTTGAGG+TGG + chr6_1:26105583-26105602 None:intergenic 45.0%
TTTGAGGAGCTGAGCAAGTA+TGG - chr6_1:26105731-26105750 Msa0880040:CDS 45.0%
!!! GATTTTTTTTTTTTTTTTTT+AGG - chr6_1:26105691-26105710 Msa0880040:CDS 5.0%
TGAGGAGGTTGAGGTTGTTG+AGG + chr6_1:26105559-26105578 None:intergenic 50.0%
!! GATTCAGGTTGAGGTGGTTG+AGG + chr6_1:26105577-26105596 None:intergenic 50.0%
!! GGGTCAAGAGATTCAGGTTG+AGG + chr6_1:26105586-26105605 None:intergenic 50.0%
GAAAGGGGTTCGTGAGAGAG+TGG - chr6_1:26105312-26105331 Msa0880040:CDS 55.0%
TGAGGTGGTTGAGGAGGTTG+AGG + chr6_1:26105568-26105587 None:intergenic 55.0%
!! TCAGGTTGAGGTGGTTGAGG+AGG + chr6_1:26105574-26105593 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr6_1 gene 26105265 26106002 26105265 ID=Msa0880040;Name=Msa0880040
chr6_1 mRNA 26105265 26106002 26105265 ID=Msa0880040-mRNA-1;Parent=Msa0880040;Name=Msa0880040-mRNA-1;_AED=0.41;_eAED=0.41;_QI=87|0.5|0.66|1|0.5|0.66|3|10|163
chr6_1 exon 26105265 26105356 26105265 ID=Msa0880040-mRNA-1:exon:6406;Parent=Msa0880040-mRNA-1
chr6_1 exon 26105424 26105554 26105424 ID=Msa0880040-mRNA-1:exon:6405;Parent=Msa0880040-mRNA-1
chr6_1 exon 26105637 26106002 26105637 ID=Msa0880040-mRNA-1:exon:6404;Parent=Msa0880040-mRNA-1
chr6_1 five_prime_UTR 26105916 26106002 26105916 ID=Msa0880040-mRNA-1:five_prime_utr;Parent=Msa0880040-mRNA-1
chr6_1 CDS 26105637 26105915 26105637 ID=Msa0880040-mRNA-1:cds;Parent=Msa0880040-mRNA-1
chr6_1 CDS 26105424 26105554 26105424 ID=Msa0880040-mRNA-1:cds;Parent=Msa0880040-mRNA-1
chr6_1 CDS 26105275 26105356 26105275 ID=Msa0880040-mRNA-1:cds;Parent=Msa0880040-mRNA-1
chr6_1 three_prime_UTR 26105265 26105274 26105265 ID=Msa0880040-mRNA-1:three_prime_utr;Parent=Msa0880040-mRNA-1
Gene Sequence

>Msa0880040

ATGGCGGAGCATTTAGCATCGATATTCGGAACAGAGAAAGACAGAGTTAACTGTCCATTCTACTTCAAGATCGGAGCTTGTAGACATGGTGACCGCTGTTCTCGTCTTCATACCAAACCCACCATTAGTCCTACTCTTGTTCTCTCCAACATGTATCAACGTCCTGATATGAACCTTAACTTTATCAATCCTACTCCTAATCAACCTCAACAACCTCAACCTCCTCAACCACCTCAACCTGAATCTCTTGACCCTGATAAACTCCAAGAACACTTCGATGATTTTTATGAAGATCTATTTGAGGAGCTGAGCAAGTATGGTCAAATTCAGAGCTTGAATATTTGTGACAATTTGGCTGATCATATGGTTTGTATTTTAATTCCTTTCTCTTTTTCTTTTGTTTTTATTTTGTTGGCAATGTATATGTTCAGTATAGAGGAAGACCATGCTGCTAATGCTCTTATAATCTATATAAGATTTTATTCATTCTGA

Protein sequence

>Msa0880040

MAEHLASIFGTEKDRVNCPFYFKIGACRHGDRCSRLHTKPTISPTLVLSNMYQRPDMNLNFINPTPNQPQQPQPPQPPQPESLDPDKLQEHFDDFYEDLFEELSKYGQIQSLNICDNLADHMVCILIPFSFSFVFILLAMYMFSIEEDHAANALIIYIRFYSF*