AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1409880


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1409880 MtrunA17_Chr2g0298711 94.348 230 13 0 1 230 84 313 1.75e-140 395
Msa1409880 MtrunA17_Chr4g0071811 36.916 214 101 6 31 228 113 308 4.76e-14 70.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 66 sgRNAs with CRISPR-Local

Find 77 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCTTCTCCGCCACTATTTC+CGG 0.205971 tig0023574:-77828 None:intergenic
GAAGTGGTGGAACGTGATTC+TGG 0.325302 tig0023574:+77719 Msa1409880:CDS
AATCCGTGGTTTGGGCGTTT+TGG 0.332255 tig0023574:+77881 Msa1409880:CDS
GAGAGAGTGAATCCGTGGTT+TGG 0.364752 tig0023574:+77872 Msa1409880:CDS
GGAGAAGAGGAATTCGAGTT+TGG 0.365864 tig0023574:+78072 Msa1409880:CDS
TAGGAATTTGTGGTCGGAAC+GGG 0.371859 tig0023574:+78132 Msa1409880:CDS
ATTTGATTGTAAACCGATCT+TGG 0.376219 tig0023574:+77748 Msa1409880:CDS
CGGCAAAATCACCGGCGAAA+TGG 0.402834 tig0023574:-78160 None:intergenic
GCCGGTTTCTTCTTCAATCC+CGG 0.404939 tig0023574:-77992 None:intergenic
AGAGAGTGAATCCGTGGTTT+GGG 0.414523 tig0023574:+77873 Msa1409880:CDS
CCACAACACTCCGTTACAAC+AGG 0.422127 tig0023574:-77530 None:intergenic
TTGATAGTATCATCGGGAGT+AGG 0.447385 tig0023574:+77792 Msa1409880:CDS
AACTGAACTACGCGGATGTT+AGG 0.451034 tig0023574:+78113 Msa1409880:CDS
GAAAACTACTCCGGAAATAG+TGG 0.458176 tig0023574:+77818 Msa1409880:CDS
GGAGAAGGAGGTTTCTGTTA+CGG 0.464126 tig0023574:+77842 Msa1409880:CDS
ACACTCCGTTACAACAGGTT+TGG 0.470904 tig0023574:-77525 None:intergenic
TTGGAAGATGAGATTGAGGA+AGG 0.473613 tig0023574:+77767 Msa1409880:CDS
GATGTTCTTGAAATCTCGCC+GGG 0.473893 tig0023574:+77974 Msa1409880:CDS
TCAATCTCATCTTCCAAGAT+CGG 0.477220 tig0023574:-77761 None:intergenic
ACGCGGATGTTAGGAATTTG+TGG 0.489666 tig0023574:+78122 Msa1409880:CDS
TGATAGTATCATCGGGAGTA+GGG 0.503072 tig0023574:+77793 Msa1409880:CDS
TGTTCGTGAGAAAGAGAAAG+AGG 0.506328 tig0023574:+77667 Msa1409880:CDS
TCCGGAAATAGTGGCGGAGA+AGG 0.506904 tig0023574:+77827 Msa1409880:CDS
AGAAAGAAAACGTGGAGAAG+AGG 0.513497 tig0023574:+78059 Msa1409880:CDS
CGGGAAAATCGGTATGATGA+AGG 0.520211 tig0023574:+77904 Msa1409880:CDS
TCACTTCCTCTAAAATCAAA+CGG 0.521600 tig0023574:-77581 None:intergenic
GGAGGTTTCTGTTACGGCGG+CGG 0.527254 tig0023574:+77848 Msa1409880:CDS
GGCGGCGGTGATTCCTATGC+CGG 0.527648 tig0023574:+78012 Msa1409880:CDS
TGATGTTCTTGAAATCTCGC+CGG 0.534008 tig0023574:+77973 Msa1409880:CDS
GAAGGGATTGATAGTATCAT+CGG 0.536499 tig0023574:+77785 Msa1409880:CDS
CGAGTTTGGCTTTGCCTCTG+CGG 0.537308 tig0023574:+78086 Msa1409880:CDS
TAAATTTACACGGCGGCGGT+AGG 0.539835 tig0023574:-77502 None:intergenic
GCCGGGATTGAAGAAGAAAC+CGG 0.540089 tig0023574:+77991 Msa1409880:CDS
GAAGGAGGTTTCTGTTACGG+CGG 0.542523 tig0023574:+77845 Msa1409880:CDS
GGTGATTCCTATGCCGGCGG+CGG 0.554261 tig0023574:+78018 Msa1409880:CDS
ATTTACCAAACCTGTTGTAA+CGG 0.559874 tig0023574:+77520 Msa1409880:CDS
TTAGGAATTTGTGGTCGGAA+CGG 0.563469 tig0023574:+78131 Msa1409880:CDS
TGGAAGATGAGATTGAGGAA+GGG 0.564697 tig0023574:+77768 Msa1409880:CDS
GGCATAGGAATCACCGCCGC+CGG 0.565478 tig0023574:-78010 None:intergenic
GATCTTGGAAGATGAGATTG+AGG 0.567004 tig0023574:+77763 Msa1409880:CDS
AGGAATTTGTGGTCGGAACG+GGG 0.568258 tig0023574:+78133 Msa1409880:CDS
AAGGGATTGATAGTATCATC+GGG 0.575119 tig0023574:+77786 Msa1409880:CDS
CCGCCAAAACGCCCAAACCA+CGG 0.586894 tig0023574:-77884 None:intergenic
ACAGGTTTGGTAAATTTACA+CGG 0.593937 tig0023574:-77512 None:intergenic
GGAAATAGTGGCGGAGAAGG+AGG 0.600415 tig0023574:+77830 Msa1409880:CDS
GGCGGTGATTCCTATGCCGG+CGG 0.608446 tig0023574:+78015 Msa1409880:CDS
CAACTTGTTGAATATTGCGA+TGG 0.621725 tig0023574:+77949 Msa1409880:CDS
GGATGTTAGGAATTTGTGGT+CGG 0.629537 tig0023574:+78126 Msa1409880:CDS
ATTGAAGAAGAAACCGGCGG+CGG 0.633812 tig0023574:+77997 Msa1409880:CDS
TTGGTAAATTTACACGGCGG+CGG 0.639344 tig0023574:-77506 None:intergenic
AGTAGGGATGAAAACTACTC+CGG 0.642670 tig0023574:+77809 Msa1409880:CDS
TGTGAATTCGGATGAAGTGG+TGG 0.643177 tig0023574:+77706 Msa1409880:CDS
AAATCAAACGGCAACAACAA+CGG 0.643478 tig0023574:-77569 None:intergenic
AACTACTCCGGAAATAGTGG+CGG 0.644512 tig0023574:+77821 Msa1409880:CDS
TAGTTCAGTTTCAACCGCAG+AGG 0.654507 tig0023574:-78100 None:intergenic
AGTTGTGAATTCGGATGAAG+TGG 0.654704 tig0023574:+77703 Msa1409880:CDS
GCAGAGGAAGAAAGAAAACG+TGG 0.655845 tig0023574:+78051 Msa1409880:CDS
ACAAGTTGACATCGCCTACG+TGG 0.660262 tig0023574:-77934 None:intergenic
GCGGTGAGAGAGTGAATCCG+TGG 0.661590 tig0023574:+77867 Msa1409880:CDS
GGTGGAACGTGATTCTGGAG+AGG 0.667553 tig0023574:+77724 Msa1409880:CDS
ATGAAGGCTCTTCGCCACGT+AGG 0.694737 tig0023574:+77920 Msa1409880:CDS
GGGATTGAAGAAGAAACCGG+CGG 0.714712 tig0023574:+77994 Msa1409880:CDS
GGAAAAGTGATTCTCAAACG+CGG 0.738994 tig0023574:+77636 Msa1409880:CDS
GCGGTTGAAACTGAACTACG+CGG 0.778633 tig0023574:+78105 Msa1409880:CDS
CCTGTTGTAACGGAGTGTTG+TGG 0.784473 tig0023574:+77530 Msa1409880:CDS
GGTTTGGTAAATTTACACGG+CGG 0.831507 tig0023574:-77509 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAATGATTTTTTGCTTGAA+AGG + tig0023574:77615-77634 Msa1409880:CDS 25.0%
! ACAGGTTTGGTAAATTTACA+CGG - tig0023574:77515-77534 None:intergenic 30.0%
ATTTACCAAACCTGTTGTAA+CGG + tig0023574:77520-77539 Msa1409880:CDS 30.0%
!! TCACTTCCTCTAAAATCAAA+CGG - tig0023574:77584-77603 None:intergenic 30.0%
ATTTGATTGTAAACCGATCT+TGG + tig0023574:77748-77767 Msa1409880:CDS 30.0%
AAATCAAACGGCAACAACAA+CGG - tig0023574:77572-77591 None:intergenic 35.0%
!! TTGTTGCCGTTTGATTTTAG+AGG + tig0023574:77575-77594 Msa1409880:CDS 35.0%
!!! GTTTTCTGGAGTTGTGAATT+CGG + tig0023574:77694-77713 Msa1409880:CDS 35.0%
TCAATCTCATCTTCCAAGAT+CGG - tig0023574:77764-77783 None:intergenic 35.0%
! GAAGGGATTGATAGTATCAT+CGG + tig0023574:77785-77804 Msa1409880:CDS 35.0%
! AAGGGATTGATAGTATCATC+GGG + tig0023574:77786-77805 Msa1409880:CDS 35.0%
!! CAACTTGTTGAATATTGCGA+TGG + tig0023574:77949-77968 Msa1409880:CDS 35.0%
! GGTTTGGTAAATTTACACGG+CGG - tig0023574:77512-77531 None:intergenic 40.0%
GGAAAAGTGATTCTCAAACG+CGG + tig0023574:77636-77655 Msa1409880:CDS 40.0%
TGTTCGTGAGAAAGAGAAAG+AGG + tig0023574:77667-77686 Msa1409880:CDS 40.0%
! GAGAAAGAGGAAGAGTTTTC+TGG + tig0023574:77680-77699 Msa1409880:CDS 40.0%
AGTTGTGAATTCGGATGAAG+TGG + tig0023574:77703-77722 Msa1409880:CDS 40.0%
GATCTTGGAAGATGAGATTG+AGG + tig0023574:77763-77782 Msa1409880:CDS 40.0%
TTGGAAGATGAGATTGAGGA+AGG + tig0023574:77767-77786 Msa1409880:CDS 40.0%
TGGAAGATGAGATTGAGGAA+GGG + tig0023574:77768-77787 Msa1409880:CDS 40.0%
! TTGATAGTATCATCGGGAGT+AGG + tig0023574:77792-77811 Msa1409880:CDS 40.0%
TGATAGTATCATCGGGAGTA+GGG + tig0023574:77793-77812 Msa1409880:CDS 40.0%
AGTAGGGATGAAAACTACTC+CGG + tig0023574:77809-77828 Msa1409880:CDS 40.0%
GAAAACTACTCCGGAAATAG+TGG + tig0023574:77818-77837 Msa1409880:CDS 40.0%
TGATGTTCTTGAAATCTCGC+CGG + tig0023574:77973-77992 Msa1409880:CDS 40.0%
AGAAAGAAAACGTGGAGAAG+AGG + tig0023574:78059-78078 Msa1409880:CDS 40.0%
GGATGTTAGGAATTTGTGGT+CGG + tig0023574:78126-78145 Msa1409880:CDS 40.0%
TTAGGAATTTGTGGTCGGAA+CGG + tig0023574:78131-78150 Msa1409880:CDS 40.0%
TTGGTAAATTTACACGGCGG+CGG - tig0023574:77509-77528 None:intergenic 45.0%
ACACTCCGTTACAACAGGTT+TGG - tig0023574:77528-77547 None:intergenic 45.0%
TGTGAATTCGGATGAAGTGG+TGG + tig0023574:77706-77725 Msa1409880:CDS 45.0%
AACTACTCCGGAAATAGTGG+CGG + tig0023574:77821-77840 Msa1409880:CDS 45.0%
GGAGAAGGAGGTTTCTGTTA+CGG + tig0023574:77842-77861 Msa1409880:CDS 45.0%
AGAGAGTGAATCCGTGGTTT+GGG + tig0023574:77873-77892 Msa1409880:CDS 45.0%
CGGGAAAATCGGTATGATGA+AGG + tig0023574:77904-77923 Msa1409880:CDS 45.0%
GATGTTCTTGAAATCTCGCC+GGG + tig0023574:77974-77993 Msa1409880:CDS 45.0%
GCAGAGGAAGAAAGAAAACG+TGG + tig0023574:78051-78070 Msa1409880:CDS 45.0%
! GGAGAAGAGGAATTCGAGTT+TGG + tig0023574:78072-78091 Msa1409880:CDS 45.0%
TAGTTCAGTTTCAACCGCAG+AGG - tig0023574:78103-78122 None:intergenic 45.0%
AACTGAACTACGCGGATGTT+AGG + tig0023574:78113-78132 Msa1409880:CDS 45.0%
ACGCGGATGTTAGGAATTTG+TGG + tig0023574:78122-78141 Msa1409880:CDS 45.0%
TAGGAATTTGTGGTCGGAAC+GGG + tig0023574:78132-78151 Msa1409880:CDS 45.0%
TAAATTTACACGGCGGCGGT+AGG - tig0023574:77505-77524 None:intergenic 50.0%
CCACAACACTCCGTTACAAC+AGG - tig0023574:77533-77552 None:intergenic 50.0%
!! CCTGTTGTAACGGAGTGTTG+TGG + tig0023574:77530-77549 Msa1409880:CDS 50.0%
! GAAGTGGTGGAACGTGATTC+TGG + tig0023574:77719-77738 Msa1409880:CDS 50.0%
TCCTTCTCCGCCACTATTTC+CGG - tig0023574:77831-77850 None:intergenic 50.0%
GAAGGAGGTTTCTGTTACGG+CGG + tig0023574:77845-77864 Msa1409880:CDS 50.0%
GAGAGAGTGAATCCGTGGTT+TGG + tig0023574:77872-77891 Msa1409880:CDS 50.0%
!! AATCCGTGGTTTGGGCGTTT+TGG + tig0023574:77881-77900 Msa1409880:CDS 50.0%
! ACAAGTTGACATCGCCTACG+TGG - tig0023574:77937-77956 None:intergenic 50.0%
GCCGGGATTGAAGAAGAAAC+CGG + tig0023574:77991-78010 Msa1409880:CDS 50.0%
! GCCGGTTTCTTCTTCAATCC+CGG - tig0023574:77995-78014 None:intergenic 50.0%
GGGATTGAAGAAGAAACCGG+CGG + tig0023574:77994-78013 Msa1409880:CDS 50.0%
ATTGAAGAAGAAACCGGCGG+CGG + tig0023574:77997-78016 Msa1409880:CDS 50.0%
GCGGTTGAAACTGAACTACG+CGG + tig0023574:78105-78124 Msa1409880:CDS 50.0%
AGGAATTTGTGGTCGGAACG+GGG + tig0023574:78133-78152 Msa1409880:CDS 50.0%
!!! ACGGCGGCGGTAGGTTTTTT+AGG - tig0023574:77496-77515 None:intergenic 55.0%
! GGTGGAACGTGATTCTGGAG+AGG + tig0023574:77724-77743 Msa1409880:CDS 55.0%
! TCCGGAAATAGTGGCGGAGA+AGG + tig0023574:77827-77846 Msa1409880:CDS 55.0%
! GGAAATAGTGGCGGAGAAGG+AGG + tig0023574:77830-77849 Msa1409880:CDS 55.0%
!! GGGCGTTTTGGCGGGAAAAT+CGG + tig0023574:77893-77912 Msa1409880:CDS 55.0%
ATGAAGGCTCTTCGCCACGT+AGG + tig0023574:77920-77939 Msa1409880:CDS 55.0%
! TGCTTCTTTTTCTCCGCCGC+CGG - tig0023574:78034-78053 None:intergenic 55.0%
CGGCGGAGAAAAAGAAGCAG+AGG + tig0023574:78035-78054 Msa1409880:CDS 55.0%
!! CGAGTTTGGCTTTGCCTCTG+CGG + tig0023574:78086-78105 Msa1409880:CDS 55.0%
! AACGGGGTTTGCCATTTCGC+CGG + tig0023574:78149-78168 Msa1409880:CDS 55.0%
GGAGGTTTCTGTTACGGCGG+CGG + tig0023574:77848-77867 Msa1409880:CDS 60.0%
GCGGTGAGAGAGTGAATCCG+TGG + tig0023574:77867-77886 Msa1409880:CDS 60.0%
CCGCCAAAACGCCCAAACCA+CGG - tig0023574:77887-77906 None:intergenic 60.0%
!! CCGTGGTTTGGGCGTTTTGG+CGG + tig0023574:77884-77903 Msa1409880:CDS 60.0%
!! CGTGGTTTGGGCGTTTTGGC+GGG + tig0023574:77885-77904 Msa1409880:CDS 60.0%
! TTTTTCTCCGCCGCCGGCAT+AGG - tig0023574:78028-78047 None:intergenic 60.0%
GGCATAGGAATCACCGCCGC+CGG - tig0023574:78013-78032 None:intergenic 65.0%
GGCGGCGGTGATTCCTATGC+CGG + tig0023574:78012-78031 Msa1409880:CDS 65.0%
GGCGGTGATTCCTATGCCGG+CGG + tig0023574:78015-78034 Msa1409880:CDS 65.0%
GGTGATTCCTATGCCGGCGG+CGG + tig0023574:78018-78037 Msa1409880:CDS 65.0%
Chromosome Type Strat End Strand Name
tig0023574 gene 77482 78174 77482 ID=Msa1409880;Name=Msa1409880
tig0023574 mRNA 77482 78174 77482 ID=Msa1409880-mRNA-1;Parent=Msa1409880;Name=Msa1409880-mRNA-1;_AED=0.13;_eAED=0.21;_QI=0|-1|0|1|-1|1|1|0|230
tig0023574 exon 77482 78174 77482 ID=Msa1409880-mRNA-1:exon:26265;Parent=Msa1409880-mRNA-1
tig0023574 CDS 77482 78174 77482 ID=Msa1409880-mRNA-1:cds;Parent=Msa1409880-mRNA-1
Gene Sequence

>Msa1409880

CTGTTTCGTAACCTAAAAAACCTACCGCCGCCGTGTAAATTTACCAAACCTGTTGTAACGGAGTGTTGTGGCAATGATTTCTTTGAACCGTTGTTGTTGCCGTTTGATTTTAGAGGAAGTGATTATGATGATGTGAATGATTTTTTGCTTGAAAGGAAAAGTGATTCTCAAACGCGGTATATCAGTGTTCGTGAGAAAGAGAAAGAGGAAGAGTTTTCTGGAGTTGTGAATTCGGATGAAGTGGTGGAACGTGATTCTGGAGAGGAATTTGATTGTAAACCGATCTTGGAAGATGAGATTGAGGAAGGGATTGATAGTATCATCGGGAGTAGGGATGAAAACTACTCCGGAAATAGTGGCGGAGAAGGAGGTTTCTGTTACGGCGGCGGTGAGAGAGTGAATCCGTGGTTTGGGCGTTTTGGCGGGAAAATCGGTATGATGAAGGCTCTTCGCCACGTAGGCGATGTCAACTTGTTGAATATTGCGATGGTTGATGTTCTTGAAATCTCGCCGGGATTGAAGAAGAAACCGGCGGCGGTGATTCCTATGCCGGCGGCGGAGAAAAAGAAGCAGAGGAAGAAAGAAAACGTGGAGAAGAGGAATTCGAGTTTGGCTTTGCCTCTGCGGTTGAAACTGAACTACGCGGATGTTAGGAATTTGTGGTCGGAACGGGGTTTGCCATTTCGCCGGTGA

Protein sequence

>Msa1409880

LFRNLKNLPPPCKFTKPVVTECCGNDFFEPLLLPFDFRGSDYDDVNDFLLERKSDSQTRYISVREKEKEEEFSGVVNSDEVVERDSGEEFDCKPILEDEIEEGIDSIIGSRDENYSGNSGGEGGFCYGGGERVNPWFGRFGGKIGMMKALRHVGDVNLLNIAMVDVLEISPGLKKKPAAVIPMPAAEKKKQRKKENVEKRNSSLALPLRLKLNYADVRNLWSERGLPFRR*