AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene55241

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene55241.t1 MTR_5g041290 92.771 166 12 0 1 166 1 166 5.27e-114 320
MS.gene55241.t1 MTR_5g041280 65.152 66 16 1 89 154 11 69 1.29e-22 85.9
MS.gene55241.t1 MTR_2g044920 34.711 121 75 2 46 163 45 164 2.11e-18 77.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene55241.t1 AT1G14205 61.111 162 62 1 5 165 8 169 2.38e-67 202
MS.gene55241.t1 AT1G48350 34.127 126 79 2 41 163 44 168 2.00e-18 78.2

Find 32 sgRNAs with CRISPR-Local

Find 87 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAATAAGCACTTCTTATTT+TGG 0.196854 5.2:+30925012 None:intergenic
GAGATTGCCATTTCCAATTA+TGG 0.211384 5.2:-30924702 MS.gene55241:CDS
TCCTATGATCGCAATGGTTT+TGG 0.281803 5.2:-30924750 MS.gene55241:CDS
TGAAAGGAAATGAATGGTTT+TGG 0.296469 5.2:+30926200 None:intergenic
AATAAGAAGTGCTTATTCTA+TGG 0.305092 5.2:-30925008 MS.gene55241:CDS
TCTAGGCAAGAATCCATAAT+TGG 0.308302 5.2:+30924689 None:intergenic
AAACAGAAAGATGCAGAAAA+AGG 0.318727 5.2:-30925787 MS.gene55241:intron
TTCAATACTTCTTCTTTCTT+CGG 0.345225 5.2:-30926230 MS.gene55241:CDS
TTATGGATTCTTGCCTAGAT+AGG 0.359313 5.2:-30924685 None:intergenic
AGGAAGCTGCTCAACGTGTT+GGG 0.364800 5.2:-30924821 MS.gene55241:CDS
AATAACTTACTTATACTTTG+TGG 0.391351 5.2:+30926176 None:intergenic
GTCTTAAAATATGGTTCTAA+TGG 0.394319 5.2:-30926276 None:intergenic
CAAGAATCCATAATTGGAAA+TGG 0.423178 5.2:+30924695 None:intergenic
AATCAGTTGCATACCTATCT+AGG 0.428417 5.2:+30924672 None:intergenic
ACCAAAACCATTGCGATCAT+AGG 0.452925 5.2:+30924749 None:intergenic
ACTACTTACTGCAGTGCTAC+AGG 0.464722 5.2:+30924950 None:intergenic
TTTAGTTAAGAAACCGTTAG+TGG 0.466736 5.2:-30925853 MS.gene55241:CDS
ACTTATACTTTGTGGTTGAA+AGG 0.484617 5.2:+30926184 None:intergenic
TCAACGTGTTGGGGAGGCAC+TGG 0.498648 5.2:-30924811 MS.gene55241:CDS
TAGGAAGCTGCTCAACGTGT+TGG 0.507260 5.2:-30924822 MS.gene55241:CDS
GAGCAAAATACTGAAAGCCT+TGG 0.512963 5.2:+30925068 None:intergenic
TGTGGTTGAAAGGAAATGAA+TGG 0.515986 5.2:+30926194 None:intergenic
GCCTTGGCTTTAGCCACTAA+CGG 0.538041 5.2:+30925840 None:intergenic
GGAAGCTGCTCAACGTGTTG+GGG 0.551335 5.2:-30924820 MS.gene55241:CDS
CTACTTACTGCAGTGCTACA+GGG 0.557559 5.2:+30924951 None:intergenic
AGCTGCTCAACGTGTTGGGG+AGG 0.565535 5.2:-30924817 MS.gene55241:CDS
ACCGTTAGTGGCTAAAGCCA+AGG 0.574909 5.2:-30925841 MS.gene55241:CDS
ATTGGAAATGGCAATCTCAA+AGG 0.577676 5.2:+30924707 None:intergenic
ATGGTACTGCAACACATCCA+AGG 0.592302 5.2:-30925085 MS.gene55241:CDS
ATTTATGTTTAGATCAACAC+AGG 0.599501 5.2:+30924782 None:intergenic
ATATCATCCTATGATCGCAA+TGG 0.637436 5.2:-30924756 MS.gene55241:CDS
CTTACTGCAGTGCTACAGGG+AGG 0.759661 5.2:+30924954 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACAAAAAAAAAAAACAAATT+GGG + chr5.2:30924820-30924839 None:intergenic 10.0%
!! ACCATTAAACTAAAAAAAAA+GGG + chr5.2:30925852-30925871 None:intergenic 15.0%
!! CACAAAAAAAAAAAACAAAT+TGG + chr5.2:30924821-30924840 None:intergenic 15.0%
!! TAAAATTTGAATTTACTTTC+AGG - chr5.2:30925076-30925095 MS.gene55241:CDS 15.0%
!! TACCATTAAACTAAAAAAAA+AGG + chr5.2:30925853-30925872 None:intergenic 15.0%
!!! ATTCATCATAATATCAATTT+TGG - chr5.2:30925017-30925036 MS.gene55241:CDS 15.0%
!! AATAACTTACTTATACTTTG+TGG + chr5.2:30924779-30924798 None:intergenic 20.0%
!! ACATAATTCAATGAAATCAT+AGG - chr5.2:30924931-30924950 MS.gene55241:intron 20.0%
!! ATGGTATTAATAAAAGATAG+AGG + chr5.2:30925820-30925839 None:intergenic 20.0%
!! TTATAAGGTCTATAATTGAT+TGG - chr5.2:30924866-30924885 MS.gene55241:intron 20.0%
!!! TGATTTTGTAGAATTGATTT+TGG - chr5.2:30925425-30925444 MS.gene55241:intron 20.0%
! ATTGTTTAAATATGCTACAG+TGG - chr5.2:30925708-30925727 MS.gene55241:intron 25.0%
! ATTTATGTTTAGATCAACAC+AGG + chr5.2:30926173-30926192 None:intergenic 25.0%
! TTAAACTAAAAAAAAAGGGC+AGG + chr5.2:30925848-30925867 None:intergenic 25.0%
! TTCAATACTTCTTCTTTCTT+CGG - chr5.2:30924722-30924741 MS.gene55241:CDS 25.0%
!! AAATGGATTTAGTGTATGTT+TGG + chr5.2:30925660-30925679 None:intergenic 25.0%
!! CATGCTTTTCATGTTTTATA+AGG - chr5.2:30924851-30924870 MS.gene55241:intron 25.0%
!!! AATAAGAAGTGCTTATTCTA+TGG - chr5.2:30925944-30925963 MS.gene55241:intron 25.0%
!!! AGAATAAGCACTTCTTATTT+TGG + chr5.2:30925943-30925962 None:intergenic 25.0%
!!! CAATATCTGTCTTTAAAATG+TGG + chr5.2:30926031-30926050 None:intergenic 25.0%
!!! GCCCTTTTTTTTTAGTTTAA+TGG - chr5.2:30925848-30925867 MS.gene55241:CDS 25.0%
!!! TTGGATTTTTTCTTATGCTT+GGG - chr5.2:30926094-30926113 MS.gene55241:intron 25.0%
!!! TTTGGATTTTTTCTTATGCT+TGG - chr5.2:30926093-30926112 MS.gene55241:intron 25.0%
AAACAGAAAGATGCAGAAAA+AGG - chr5.2:30925165-30925184 MS.gene55241:intron 30.0%
ACTTATACTTTGTGGTTGAA+AGG + chr5.2:30924771-30924790 None:intergenic 30.0%
CAAGAATCCATAATTGGAAA+TGG + chr5.2:30926260-30926279 None:intergenic 30.0%
CTATAATTGATTGGATACAC+AGG - chr5.2:30924875-30924894 MS.gene55241:intron 30.0%
GAAATCATAGGTATTAGTGT+CGG - chr5.2:30924943-30924962 MS.gene55241:intron 30.0%
TTTAGTTAAGAAACCGTTAG+TGG - chr5.2:30925099-30925118 MS.gene55241:intron 30.0%
! CTTGGGTGAAATATTGTTTT+AGG - chr5.2:30926111-30926130 MS.gene55241:intron 30.0%
! GAAAGGAAATGAATGGTTTT+GGG + chr5.2:30924754-30924773 None:intergenic 30.0%
! GACTAAAAGTGATTTGTGTT+TGG - chr5.2:30925463-30925482 MS.gene55241:intron 30.0%
! GTTACATTAGACTTTAGCTT+TGG - chr5.2:30926075-30926094 MS.gene55241:intron 30.0%
! TGAAAGGAAATGAATGGTTT+TGG + chr5.2:30924755-30924774 None:intergenic 30.0%
!! TATCTGTCTTTAAAATGTGG+TGG + chr5.2:30926028-30926047 None:intergenic 30.0%
AAAAAAAGGGCAGGATAACA+TGG + chr5.2:30925839-30925858 None:intergenic 35.0%
AAACATGCCAGAATCAATTC+TGG - chr5.2:30925617-30925636 MS.gene55241:intron 35.0%
AAACCAACTACTGCTAACTA+AGG + chr5.2:30925336-30925355 None:intergenic 35.0%
AACTAAGTGTGTGTTTGGTT+GGG - chr5.2:30925374-30925393 MS.gene55241:intron 35.0%
AGACAGATATTGTATGAGAC+TGG - chr5.2:30926039-30926058 MS.gene55241:intron 35.0%
ATATCATCCTATGATCGCAA+TGG - chr5.2:30926196-30926215 MS.gene55241:CDS 35.0%
ATTGGAAATGGCAATCTCAA+AGG + chr5.2:30926248-30926267 None:intergenic 35.0%
CTATGAACTAAGTGTGTGTT+TGG - chr5.2:30925369-30925388 MS.gene55241:intron 35.0%
GACAGATATTGTATGAGACT+GGG - chr5.2:30926040-30926059 MS.gene55241:intron 35.0%
TAGAAGTTTCAGTGTTGCAT+AGG - chr5.2:30925271-30925290 MS.gene55241:intron 35.0%
TCACATATACTCCTCGAATA+AGG + chr5.2:30924998-30925017 None:intergenic 35.0%
TCTAGGCAAGAATCCATAAT+TGG + chr5.2:30926266-30926285 None:intergenic 35.0%
TGTGGTTGAAAGGAAATGAA+TGG + chr5.2:30924761-30924780 None:intergenic 35.0%
TTTCCTTAGTTAGCAGTAGT+TGG - chr5.2:30925330-30925349 MS.gene55241:intron 35.0%
! AATTGATTCTCCTTGAAGCT+AGG + chr5.2:30925563-30925582 None:intergenic 35.0%
! AGAATTGATTCTGGCATGTT+TGG + chr5.2:30925618-30925637 None:intergenic 35.0%
! GAGATTGCCATTTCCAATTA+TGG - chr5.2:30926250-30926269 MS.gene55241:CDS 35.0%
! TGTTAAATGTGCTGGTGTAA+TGG - chr5.2:30925201-30925220 MS.gene55241:intron 35.0%
! TTCTTTTCTTGCATTTGCCT+TGG + chr5.2:30925131-30925150 None:intergenic 35.0%
!! CTTTTGGTTGTTAAATGTGC+TGG - chr5.2:30925193-30925212 MS.gene55241:intron 35.0%
!! GCAGAAAAAGGTATGTCTTT+TGG - chr5.2:30925177-30925196 MS.gene55241:intron 35.0%
ACCAAAACCATTGCGATCAT+AGG + chr5.2:30926206-30926225 None:intergenic 40.0%
AGCTACAAATCCTAGCTTCA+AGG - chr5.2:30925550-30925569 MS.gene55241:intron 40.0%
GAACTAAGTGTGTGTTTGGT+TGG - chr5.2:30925373-30925392 MS.gene55241:intron 40.0%
GAGCAAAATACTGAAAGCCT+TGG + chr5.2:30925887-30925906 None:intergenic 40.0%
GCTTCAAGGAGAATCAATTC+TGG - chr5.2:30925564-30925583 MS.gene55241:intron 40.0%
TCAAGGAGAATCAATTCTGG+AGG - chr5.2:30925567-30925586 MS.gene55241:intron 40.0%
! AATTCTGGTCTCTCTAGAAG+TGG - chr5.2:30925632-30925651 MS.gene55241:intron 40.0%
! AGAGAGACCAGAATTGATTC+TGG + chr5.2:30925627-30925646 None:intergenic 40.0%
! TCCTATGATCGCAATGGTTT+TGG - chr5.2:30926202-30926221 MS.gene55241:CDS 40.0%
! TTCTAACTGAAAAGCGTGTC+TGG + chr5.2:30925256-30925275 None:intergenic 40.0%
ACTACTTACTGCAGTGCTAC+AGG + chr5.2:30926005-30926024 None:intergenic 45.0%
ATGGTACTGCAACACATCCA+AGG - chr5.2:30925867-30925886 MS.gene55241:intron 45.0%
CTACTTACTGCAGTGCTACA+GGG + chr5.2:30926004-30926023 None:intergenic 45.0%
!!! ATGGTTTTGGTCGTGGAGAA+AGG - chr5.2:30926215-30926234 MS.gene55241:CDS 45.0%
!!! ATGTATTTTTATATTTAAAA+TGG + chr5.2:30925677-30925696 None:intergenic 5.0%
AATAAGGCGTGTCTCAGGGT+CGG + chr5.2:30924982-30925001 None:intergenic 50.0%
ACCGTTAGTGGCTAAAGCCA+AGG - chr5.2:30925111-30925130 MS.gene55241:intron 50.0%
AGGAAGCTGCTCAACGTGTT+GGG - chr5.2:30926131-30926150 MS.gene55241:intron 50.0%
CTCGAATAAGGCGTGTCTCA+GGG + chr5.2:30924986-30925005 None:intergenic 50.0%
GTGTGTGTTTGGTTGGGCAA+TGG - chr5.2:30925380-30925399 MS.gene55241:intron 50.0%
TAGGAAGCTGCTCAACGTGT+TGG - chr5.2:30926130-30926149 MS.gene55241:intron 50.0%
!! GCCTTGGCTTTAGCCACTAA+CGG + chr5.2:30925115-30925134 None:intergenic 50.0%
!!! GATCGCAATGGTTTTGGTCG+TGG - chr5.2:30926208-30926227 MS.gene55241:CDS 50.0%
AGCGTGTCTGGTGTTCGATG+CGG + chr5.2:30925244-30925263 None:intergenic 55.0%
CCTCGAATAAGGCGTGTCTC+AGG + chr5.2:30924987-30925006 None:intergenic 55.0%
CTTACTGCAGTGCTACAGGG+AGG + chr5.2:30926001-30926020 None:intergenic 55.0%
GGAAGCTGCTCAACGTGTTG+GGG - chr5.2:30926132-30926151 MS.gene55241:intron 55.0%
! CCTGAGACACGCCTTATTCG+AGG - chr5.2:30924984-30925003 MS.gene55241:CDS 55.0%
AGCTGCTCAACGTGTTGGGG+AGG - chr5.2:30926135-30926154 MS.gene55241:intron 60.0%
GCGTGTCTGGTGTTCGATGC+GGG + chr5.2:30925243-30925262 None:intergenic 60.0%
! TCAACGTGTTGGGGAGGCAC+TGG - chr5.2:30926141-30926160 MS.gene55241:intron 60.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 30924686 30926288 30924686 ID=MS.gene55241
chr5.2 mRNA 30924686 30926288 30924686 ID=MS.gene55241.t1;Parent=MS.gene55241
chr5.2 exon 30926186 30926288 30926186 ID=MS.gene55241.t1.exon1;Parent=MS.gene55241.t1
chr5.2 CDS 30926186 30926288 30926186 ID=cds.MS.gene55241.t1;Parent=MS.gene55241.t1
chr5.2 exon 30925788 30925876 30925788 ID=MS.gene55241.t1.exon2;Parent=MS.gene55241.t1
chr5.2 CDS 30925788 30925876 30925788 ID=cds.MS.gene55241.t1;Parent=MS.gene55241.t1
chr5.2 exon 30924959 30925111 30924959 ID=MS.gene55241.t1.exon3;Parent=MS.gene55241.t1
chr5.2 CDS 30924959 30925111 30924959 ID=cds.MS.gene55241.t1;Parent=MS.gene55241.t1
chr5.2 exon 30924686 30924841 30924686 ID=MS.gene55241.t1.exon4;Parent=MS.gene55241.t1
chr5.2 CDS 30924686 30924841 30924686 ID=cds.MS.gene55241.t1;Parent=MS.gene55241.t1
Gene Sequence

>MS.gene55241

ATGGTTCTAATGGTGAATTCATTTCAACTATTTCAATTCAATACTTCTTCTTTCTTCGGAGTTATCCCAAAACCATTCATTTCCTTTCAACCACAAAGTATAAGTAAGTTATTAAACATAACTTAAATCTTCCCAATTTGTTTTTTTTTTTTGTGTGATGTGTTTCATGCTTTTCATGTTTTATAAGGTCTATAATTGATTGGATACACAGGACACGACAACACAGTCAATAATATGAGAAAATGACATAATTCAATGAAATCATAGGTATTAGTGTCGGACACGATACATATCCGACCCTGAGACACGCCTTATTCGAGGAGTATATGTGATTCATCATAATATCAATTTTGGTATTGTGTTTAATGTGAATTTTGATAATGCTTGTAGTAAAATTTGAATTTACTTTCAGGTTTAGTTAAGAAACCGTTAGTGGCTAAAGCCAAGGCAAATGCAAGAAAAGAAAGTGCTAAAATTCGAAACAGAAAGATGCAGAAAAAGGTATGTCTTTTGGTTGTTAAATGTGCTGGTGTAATGGCACTGTCTGACATTGACCCGCATCGAACACCAGACACGCTTTTCAGTTAGAAGTTTCAGTGTTGCATAGGTTTGTTGTGTCTACAAACAAGTTTATCACTCATTTTTTTCCTTAGTTAGCAGTAGTTGGTTTCAGTACAAAAGTTCTATGAACTAAGTGTGTGTTTGGTTGGGCAATGGAGATAATTGATTTTGATAGAATTGATTTTGTAGAATTGATTTTGGTTAAAAGTAATTTTTGACTAAAAGTGATTTGTGTTTGGATACATTTATATAAAAATGAGTTGAAATATAAATTTGTATGTGAAAATCAATTCTAGAATCAGAAGCTACAAATCCTAGCTTCAAGGAGAATCAATTCTGGAGGCATAATCAATTATATTCGACATCAACCAAACATGCCAGAATCAATTCTGGTCTCTCTAGAAGTGGAACCAAACATACACTAAATCCATTTTAAATATAAAAATACATAATTTTATAGTATTGTTTAAATATGCTACAGTGGACAAGTTGTTGCTGCATTGATAAAGAACAACTAGATAAAGAACAACTAAGTAGTTGAGTACTTGAGTTACTTCAATTAGCGTTTATCCTCTATCTTTTATTAATACCATGTTATCCTGCCCTTTTTTTTTAGTTTAATGGTACTGCAACACATCCAAGGCTTTCAGTATTTTGCTCAGATAAGCAATTGTATGCAATGCTTGTAGATGACCAAAATAAGAAGTGCTTATTCTATGGAAGCACGCTGCAGAAATCGTTTCAAGAAAATCCTCCCTGTAGCACTGCAGTAAGTAGTCCACCACATTTTAAAGACAGATATTGTATGAGACTGGGTAAACAACTTTTGTTACATTAGACTTTAGCTTTGGATTTTTTCTTATGCTTGGGTGAAATATTGTTTTAGGAAGCTGCTCAACGTGTTGGGGAGGCACTGGTGAAAGCCTGTGTTGATCTAAACATAAATGAAATATCATCCTATGATCGCAATGGTTTTGGTCGTGGAGAAAGGTTAAACGCCTTTGAGATTGCCATTTCCAATTATGGATTCTTGCCTAGATAG
Protein sequence

>MS.gene55241.t1

MVLMVNSFQLFQFNTSSFFGVIPKPFISFQPQSISLVKKPLVAKAKANARKESAKIRNRKMQKKFNGTATHPRLSVFCSDKQLYAMLVDDQNKKCLFYGSTLQKSFQENPPCSTAEAAQRVGEALVKACVDLNINEISSYDRNGFGRGERLNAFEIAISNYGFLPR