AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene63716

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene63716.t1 MTR_7g117040 94.521 146 8 0 1 146 29 174 2.10e-101 288
MS.gene63716.t1 MTR_7g117040 91.781 146 8 1 1 146 29 170 6.65e-96 274
MS.gene63716.t1 MTR_7g117040 89.726 146 8 1 1 146 29 167 1.45e-93 268
MS.gene63716.t1 MTR_3g034200 35.772 123 78 1 1 122 29 151 8.37e-23 89.0
MS.gene63716.t1 MTR_3g030055 27.679 112 76 2 11 122 42 148 1.11e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene63716.t1 AT1G03150 90.411 146 14 0 1 146 29 174 4.46e-99 282
MS.gene63716.t1 AT5G13780 36.585 123 77 1 1 122 29 151 2.76e-22 87.8

Find 37 sgRNAs with CRISPR-Local

Find 81 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGAGTGCTACGTTATTATTC+TGG 0.239936 2.1:-23863110 MS.gene63716:CDS
GTAACCCATGATTCGATTTC+CGG 0.242250 2.1:+23863863 None:intergenic
TGATTCGATTTCCGGGGCCT+TGG 0.300853 2.1:+23863871 None:intergenic
GATTCGATTTCCGGGGCCTT+GGG 0.386942 2.1:+23863872 None:intergenic
TAACCCATGATTCGATTTCC+GGG 0.408074 2.1:+23863864 None:intergenic
TAGTCGTATTCTAATTCATC+AGG 0.411545 2.1:+23862901 None:intergenic
TTCTGGGGAAGAAGATGGAT+TGG 0.420903 2.1:-23863093 MS.gene63716:CDS
GATTTCCGGGGCCTTGGGCG+AGG 0.425235 2.1:+23863877 None:intergenic
TATTATTCTGGGGAAGAAGA+TGG 0.447212 2.1:-23863098 MS.gene63716:CDS
AGTCCGTCAGCCCTCTTAAA+CGG 0.466234 2.1:-23862933 MS.gene63716:CDS
GAGTGCTACGTTATTATTCT+GGG 0.470429 2.1:-23863109 MS.gene63716:CDS
TCTGGGGAAGAAGATGGATT+GGG 0.475034 2.1:-23863092 MS.gene63716:intron
TTCCACCTCGCCCAAGGCCC+CGG 0.478626 2.1:-23863882 MS.gene63716:CDS
TTCCGGGGCCTTGGGCGAGG+TGG 0.483135 2.1:+23863880 None:intergenic
GACTATTTCCACCTCGCCCA+AGG 0.483842 2.1:-23863888 MS.gene63716:CDS
TGCTAGATAGGTCATGTAGA+AGG 0.496071 2.1:+23863920 None:intergenic
GGAGTGACATGCCGTTTAAG+AGG 0.496131 2.1:+23862922 None:intergenic
TAGAGGGGCAAGGAGAATCT+TGG 0.499019 2.1:-23863742 MS.gene63716:CDS
TGGGCGAGGTGGAAATAGTC+AGG 0.501782 2.1:+23863891 None:intergenic
AGCCATCAAGATGTATGAAA+AGG 0.514376 2.1:-23863504 MS.gene63716:intron
GTCAGGCCATCGTGCTAGAT+AGG 0.514429 2.1:+23863908 None:intergenic
AGGCCCCGGAAATCGAATCA+TGG 0.515528 2.1:-23863868 MS.gene63716:CDS
GCAGTTATGGGTAAAGTAGA+GGG 0.544970 2.1:-23863758 MS.gene63716:intron
GGCCCCGGAAATCGAATCAT+GGG 0.555258 2.1:-23863867 MS.gene63716:CDS
AACTGCAGTAACCGTTGCTA+CGG 0.572799 2.1:-23863708 MS.gene63716:CDS
ATGGGTAAAGTAGAGGGGCA+AGG 0.572891 2.1:-23863752 MS.gene63716:CDS
TGCAGTTATGGGTAAAGTAG+AGG 0.579669 2.1:-23863759 MS.gene63716:intron
GAGTGACATGCCGTTTAAGA+GGG 0.585815 2.1:+23862923 None:intergenic
CCGTTGCTACGGAGTATCGC+AGG 0.596977 2.1:-23863697 MS.gene63716:CDS
AATAATAACGTAGCACTCGT+CGG 0.603392 2.1:+23863114 None:intergenic
AACCCATGATTCGATTTCCG+GGG 0.619081 2.1:+23863865 None:intergenic
ATGCCGTTTAAGAGGGCTGA+CGG 0.621153 2.1:+23862930 None:intergenic
GGGCAAGGAGAATCTTGGCA+TGG 0.661266 2.1:-23863737 MS.gene63716:CDS
AGTGCTACGTTATTATTCTG+GGG 0.665106 2.1:-23863108 MS.gene63716:CDS
CAGTTATGGGTAAAGTAGAG+GGG 0.668038 2.1:-23863757 MS.gene63716:CDS
CCTGCGATACTCCGTAGCAA+CGG 0.679156 2.1:+23863697 None:intergenic
ACATGACCTATCTAGCACGA+TGG 0.757874 2.1:-23863914 MS.gene63716:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAATGTATAACTTAATCAT+TGG - chr2.1:23863561-23863580 MS.gene63716:intron 15.0%
!! AAAAAACCCTATTAGAATTT+GGG + chr2.1:23863502-23863521 None:intergenic 20.0%
!! AGATTACTTATCAATAGTTT+AGG - chr2.1:23863535-23863554 MS.gene63716:CDS 20.0%
!! TAAAAAACCCTATTAGAATT+TGG + chr2.1:23863503-23863522 None:intergenic 20.0%
!! TATAACTTAATCATTGGATA+TGG - chr2.1:23863567-23863586 MS.gene63716:intron 20.0%
!!! GATATGTTTTCTTTTAGATT+AGG - chr2.1:23863610-23863629 MS.gene63716:intron 20.0%
! AATATCATTCATGCAGTTAT+GGG - chr2.1:23863054-23863073 MS.gene63716:intron 25.0%
! ACAGCAAATAAATAGTGATA+CGG + chr2.1:23863814-23863833 None:intergenic 25.0%
! CAAAAAAGATGAAGAAAAAG+GGG + chr2.1:23863002-23863021 None:intergenic 25.0%
! GCAAAAAAGATGAAGAAAAA+GGG + chr2.1:23863003-23863022 None:intergenic 25.0%
! TCCTCATATCTGAAAATAAA+GGG + chr2.1:23863844-23863863 None:intergenic 25.0%
! TTCCTCATATCTGAAAATAA+AGG + chr2.1:23863845-23863864 None:intergenic 25.0%
!!! ACACAAGGTTTGTTTTAAAT+CGG - chr2.1:23863402-23863421 MS.gene63716:intron 25.0%
!!! TTTATTTTCAGATATGAGGA+AGG - chr2.1:23863844-23863863 MS.gene63716:intron 25.0%
ACATATCCTAATCCAACAAA+TGG + chr2.1:23863597-23863616 None:intergenic 30.0%
ATCCAACCCAAATTCTAATA+GGG - chr2.1:23863493-23863512 MS.gene63716:intron 30.0%
CAAGCTATAAGATGTCAAAA+AGG + chr2.1:23863677-23863696 None:intergenic 30.0%
CAATATCATTCATGCAGTTA+TGG - chr2.1:23863053-23863072 MS.gene63716:intron 30.0%
CATAACTGCATGAATGATAT+TGG + chr2.1:23863055-23863074 None:intergenic 30.0%
CGCAAAAAAGATGAAGAAAA+AGG + chr2.1:23863004-23863023 None:intergenic 30.0%
TAGTCGTATTCTAATTCATC+AGG + chr2.1:23863926-23863945 None:intergenic 30.0%
TGCGTAAAAGACTATACTAT+GGG - chr2.1:23863020-23863039 MS.gene63716:intron 30.0%
TTGCGTAAAAGACTATACTA+TGG - chr2.1:23863019-23863038 MS.gene63716:intron 30.0%
! CTTTTTGACATCTTATAGCT+TGG - chr2.1:23863675-23863694 MS.gene63716:CDS 30.0%
! TACCTTTTCATACATCTTGA+TGG + chr2.1:23863325-23863344 None:intergenic 30.0%
!!! TCCCTTTATTTTCAGATATG+AGG - chr2.1:23863840-23863859 MS.gene63716:intron 30.0%
AAAGATGAAGAAAAAGGGGA+AGG + chr2.1:23862998-23863017 None:intergenic 35.0%
AACCCTATTAGAATTTGGGT+TGG + chr2.1:23863498-23863517 None:intergenic 35.0%
AATAATAACGTAGCACTCGT+CGG + chr2.1:23863713-23863732 None:intergenic 35.0%
AGCCATCAAGATGTATGAAA+AGG - chr2.1:23863320-23863339 MS.gene63716:intron 35.0%
AGTGCTACGTTATTATTCTG+GGG - chr2.1:23863716-23863735 MS.gene63716:CDS 35.0%
AGTGGAAGGTTTAATCTGAA+AGG + chr2.1:23863364-23863383 None:intergenic 35.0%
GAGTGCTACGTTATTATTCT+GGG - chr2.1:23863715-23863734 MS.gene63716:CDS 35.0%
GATCCAACCCAAATTCTAAT+AGG - chr2.1:23863492-23863511 MS.gene63716:intron 35.0%
! TATTATTCTGGGGAAGAAGA+TGG - chr2.1:23863726-23863745 MS.gene63716:CDS 35.0%
!! TTTTCATACATCTTGATGGC+TGG + chr2.1:23863321-23863340 None:intergenic 35.0%
ACCTTGTGTACAAACCTACA+AGG + chr2.1:23863391-23863410 None:intergenic 40.0%
AGCGACAATATGTAAGGCAT+CGG - chr2.1:23863192-23863211 MS.gene63716:intron 40.0%
CAGTTATGGGTAAAGTAGAG+GGG - chr2.1:23863067-23863086 MS.gene63716:intron 40.0%
CGAGTGCTACGTTATTATTC+TGG - chr2.1:23863714-23863733 MS.gene63716:CDS 40.0%
GACATCAGCGACAATATGTA+AGG - chr2.1:23863186-23863205 MS.gene63716:intron 40.0%
GCAGTTATGGGTAAAGTAGA+GGG - chr2.1:23863066-23863085 MS.gene63716:intron 40.0%
GGATATGGACTTCCATTTGT+TGG - chr2.1:23863582-23863601 MS.gene63716:intron 40.0%
GTAACCCATGATTCGATTTC+CGG + chr2.1:23862964-23862983 None:intergenic 40.0%
TAACCCATGATTCGATTTCC+GGG + chr2.1:23862963-23862982 None:intergenic 40.0%
TATGTGTGTTTGTCTCTGTG+TGG - chr2.1:23863215-23863234 MS.gene63716:intron 40.0%
TCCTACAAAATCAGCTTGTG+CGG + chr2.1:23863464-23863483 None:intergenic 40.0%
TCCTTGTAGGTTTGTACACA+AGG - chr2.1:23863387-23863406 MS.gene63716:intron 40.0%
TGCAGTTATGGGTAAAGTAG+AGG - chr2.1:23863065-23863084 MS.gene63716:intron 40.0%
TGCTAGATAGGTCATGTAGA+AGG + chr2.1:23862907-23862926 None:intergenic 40.0%
! GGACTTCCATTTGTTGGATT+AGG - chr2.1:23863588-23863607 MS.gene63716:intron 40.0%
AACCCATGATTCGATTTCCG+GGG + chr2.1:23862962-23862981 None:intergenic 45.0%
AACTGCAGTAACCGTTGCTA+CGG - chr2.1:23863116-23863135 MS.gene63716:CDS 45.0%
ACAAACCTACAAGGAAGCAG+TGG + chr2.1:23863382-23863401 None:intergenic 45.0%
ACATGACCTATCTAGCACGA+TGG - chr2.1:23862910-23862929 MS.gene63716:CDS 45.0%
! GAGTGACATGCCGTTTAAGA+GGG + chr2.1:23863904-23863923 None:intergenic 45.0%
! TCTGGGGAAGAAGATGGATT+GGG - chr2.1:23863732-23863751 MS.gene63716:CDS 45.0%
! TTCTGGGGAAGAAGATGGAT+TGG - chr2.1:23863731-23863750 MS.gene63716:CDS 45.0%
!! ACCGCACAAGCTGATTTTGT+AGG - chr2.1:23863460-23863479 MS.gene63716:intron 45.0%
!! GGAAGAAGATGGATTGGGTA+TGG - chr2.1:23863737-23863756 MS.gene63716:CDS 45.0%
ACCTACAAGGAAGCAGTGGA+AGG + chr2.1:23863378-23863397 None:intergenic 50.0%
ACCTTCCACTGCTTCCTTGT+AGG - chr2.1:23863374-23863393 MS.gene63716:intron 50.0%
AGTCCGTCAGCCCTCTTAAA+CGG - chr2.1:23863891-23863910 MS.gene63716:CDS 50.0%
ATGGGTAAAGTAGAGGGGCA+AGG - chr2.1:23863072-23863091 MS.gene63716:intron 50.0%
GTGTGTTTGTCTCTGTGTGG+AGG - chr2.1:23863218-23863237 MS.gene63716:intron 50.0%
TAGAGGGGCAAGGAGAATCT+TGG - chr2.1:23863082-23863101 MS.gene63716:intron 50.0%
! ATGCCGTTTAAGAGGGCTGA+CGG + chr2.1:23863897-23863916 None:intergenic 50.0%
! GGAGTGACATGCCGTTTAAG+AGG + chr2.1:23863905-23863924 None:intergenic 50.0%
AGGCCCCGGAAATCGAATCA+TGG - chr2.1:23862956-23862975 MS.gene63716:CDS 55.0%
CCTGCGATACTCCGTAGCAA+CGG + chr2.1:23863130-23863149 None:intergenic 55.0%
GACTATTTCCACCTCGCCCA+AGG - chr2.1:23862936-23862955 MS.gene63716:CDS 55.0%
GATTCGATTTCCGGGGCCTT+GGG + chr2.1:23862955-23862974 None:intergenic 55.0%
GGCCCCGGAAATCGAATCAT+GGG - chr2.1:23862957-23862976 MS.gene63716:CDS 55.0%
GGGCAAGGAGAATCTTGGCA+TGG - chr2.1:23863087-23863106 MS.gene63716:intron 55.0%
GTCAGGCCATCGTGCTAGAT+AGG + chr2.1:23862919-23862938 None:intergenic 55.0%
TGATTCGATTTCCGGGGCCT+TGG + chr2.1:23862956-23862975 None:intergenic 55.0%
TGGGCGAGGTGGAAATAGTC+AGG + chr2.1:23862936-23862955 None:intergenic 55.0%
!! CCGTTGCTACGGAGTATCGC+AGG - chr2.1:23863127-23863146 MS.gene63716:CDS 60.0%
GATTTCCGGGGCCTTGGGCG+AGG + chr2.1:23862950-23862969 None:intergenic 70.0%
TTCCACCTCGCCCAAGGCCC+CGG - chr2.1:23862942-23862961 MS.gene63716:CDS 70.0%
TTCCGGGGCCTTGGGCGAGG+TGG + chr2.1:23862947-23862966 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 23862900 23863946 23862900 ID=MS.gene63716
chr2.1 mRNA 23862900 23863946 23862900 ID=MS.gene63716.t1;Parent=MS.gene63716
chr2.1 exon 23863862 23863946 23863862 ID=MS.gene63716.t1.exon1;Parent=MS.gene63716.t1
chr2.1 CDS 23863862 23863946 23863862 ID=cds.MS.gene63716.t1;Parent=MS.gene63716.t1
chr2.1 exon 23863644 23863776 23863644 ID=MS.gene63716.t1.exon2;Parent=MS.gene63716.t1
chr2.1 CDS 23863644 23863776 23863644 ID=cds.MS.gene63716.t1;Parent=MS.gene63716.t1
chr2.1 exon 23863505 23863574 23863505 ID=MS.gene63716.t1.exon3;Parent=MS.gene63716.t1
chr2.1 CDS 23863505 23863574 23863505 ID=cds.MS.gene63716.t1;Parent=MS.gene63716.t1
chr2.1 exon 23863093 23863153 23863093 ID=MS.gene63716.t1.exon4;Parent=MS.gene63716.t1
chr2.1 CDS 23863093 23863153 23863093 ID=cds.MS.gene63716.t1;Parent=MS.gene63716.t1
chr2.1 exon 23862900 23862991 23862900 ID=MS.gene63716.t1.exon5;Parent=MS.gene63716.t1
chr2.1 CDS 23862900 23862991 23862900 ID=cds.MS.gene63716.t1;Parent=MS.gene63716.t1
Gene Sequence

>MS.gene63716

ATGTCCTTCTACATGACCTATCTAGCACGATGGCCTGACTATTTCCACCTCGCCCAAGGCCCCGGAAATCGAATCATGGGTTACAGTAAGTCTTTCCTTCCCCTTTTTCTTCATCTTTTTTGCGTAAAAGACTATACTATGGGATATTAACACCAATATCATTCATGCAGTTATGGGTAAAGTAGAGGGGCAAGGAGAATCTTGGCATGGTCATGTAACTGCAGTAACCGTTGCTACGGAGTATCGCAGGCAACAGTTAGCAAACAAACTAATGAATATTCTCGAAGACATCAGCGACAATATGTAAGGCATCGGTATGTGTGTTTGTCTCTGTGTGGAGGTTTTGATATAATTTAGAATTGAATTTTGCAGTGACAAAGCATACTTTGTTGATCTATTTGTGAGAGCATCAAATGCACCAGCCATCAAGATGTATGAAAAGGTAATCATTTTGTACTTTTCCTTTCAGATTAAACCTTCCACTGCTTCCTTGTAGGTTTGTACACAAGGTTTGTTTTAAATCGGTTTCTTTGTTAGACATCTGTGAAATTAAATAAGACACCGCACAAGCTGATTTTGTAGGATTGAGTTAGATCCAACCCAAATTCTAATAGGGTTTTTTATCAAGAATTTACAGATTACTTATCAATAGTTTAGGAATTTAATGTATAACTTAATCATTGGATATGGACTTCCATTTGTTGGATTAGGATATGTTTTCTTTTAGATTAGGTTTTTCTGATTTTCAAGCTTAAATTGCTAACTAATTATTTTCCTTTTTGACATCTTATAGCTTGGATATGTGATTTACCGACGAGTGCTACGTTATTATTCTGGGGAAGAAGATGGATTGGGTATGGTTTCTTTTTTTTCTTTTTTTTTTTGTACTTCTCTAACTCTTTGAACAAAGTCCGTATCACTATTTATTTGCTGTCGTTTTTCCCTTTATTTTCAGATATGAGGAAGGCGTTATCTCGTGATGTTAATAAGAAGTCCGTCAGCCCTCTTAAACGGCATGTCACTCCTGATGAATTAGAATACGACTAA
Protein sequence

>MS.gene63716.t1

MSFYMTYLARWPDYFHLAQGPGNRIMGYIMGKVEGQGESWHGHVTAVTVATEYRRQQLANKLMNILEDISDNIDKAYFVDLFVRASNAPAIKMYEKLGYVIYRRVLRYYSGEEDGLDMRKALSRDVNKKSVSPLKRHVTPDELEYD