AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene47811


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene47811.t1 MTR_2g101820 97.279 147 3 1 1 146 1 147 5.34e-99 281
MS.gene47811.t1 MTR_2g101820 95.455 88 3 1 1 87 1 88 3.48e-55 169
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene47811.t1 AT1G52230 79.452 146 29 1 1 146 1 145 2.10e-81 236
MS.gene47811.t1 AT3G16140 78.082 146 31 1 1 146 1 145 7.76e-80 232

Find 45 sgRNAs with CRISPR-Local

Find 75 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTTCAAATCCAAGAATTTA+AGG 0.134528 2.1:-3387455 MS.gene47811:intron
GTGAAAGTACCTTAAATTCT+TGG 0.244082 2.1:+3387446 None:intergenic
CTTGCTGGCAGTTCCATTAC+TGG 0.265222 2.1:-3387510 MS.gene47811:CDS
TACTTCAGTGCCACAGCTTC+AGG 0.317013 2.1:-3386191 MS.gene47811:CDS
TACTTTGATTTGGAGGATAT+TGG 0.323961 2.1:-3387122 MS.gene47811:CDS
CAAGAGTGTGTACTTTGATT+TGG 0.336220 2.1:-3387132 MS.gene47811:CDS
TTGCCACGGGGACCGAGCTT+TGG 0.360365 2.1:+3386131 None:intergenic
CTCAATGTTAAGGGTCTTGC+TGG 0.365303 2.1:-3387525 MS.gene47811:CDS
CTCACCATACAACCCTCTTC+AGG 0.381984 2.1:-3387057 MS.gene47811:intron
ACCAGCTGGTCTCAATGTTA+AGG 0.384673 2.1:-3387535 MS.gene47811:CDS
CCACGGGGACCGAGCTTTGG+TGG 0.404075 2.1:+3386134 None:intergenic
GGCTCTGTGGTAGCAAAGTA+TGG 0.420308 2.1:-3387158 MS.gene47811:CDS
AGCTGTGGACCTTTCTTGAT+TGG 0.426964 2.1:+3386158 None:intergenic
CCAGCTGGTCTCAATGTTAA+GGG 0.447321 2.1:-3387534 MS.gene47811:CDS
GAGTGTGTACTTTGATTTGG+AGG 0.467087 2.1:-3387129 MS.gene47811:CDS
GAGGATATTGGCAACACTAC+AGG 0.483887 2.1:-3387110 MS.gene47811:CDS
AATTCTTGGATTTGAAACTC+TGG 0.485960 2.1:+3387460 None:intergenic
CAAACCTGAAGAGGGTTGTA+TGG 0.501808 2.1:+3387053 None:intergenic
CAAGAGTTGAACCACCTCCT+AGG 0.515089 2.1:+3386216 None:intergenic
AATAATCCTCTCTTTGTGAA+TGG 0.515909 2.1:+3386254 None:intergenic
CCCTTAACATTGAGACCAGC+TGG 0.523582 2.1:+3387534 None:intergenic
CCGAGCTTTGGTGGAAGCTG+TGG 0.524654 2.1:+3386143 None:intergenic
GACATTCTACCAATCAAGAA+AGG 0.540823 2.1:-3386167 MS.gene47811:CDS
AGATAGCTTAGTTCCAGTAA+TGG 0.548416 2.1:+3387497 None:intergenic
AGCTGGTTGTACACAAGCTA+AGG 0.551993 2.1:+3387551 None:intergenic
GCAGCTCCATTCACAAAGAG+AGG 0.555627 2.1:-3386260 MS.gene47811:CDS
TCCAGTAGACAAACCTGAAG+AGG 0.558714 2.1:+3387044 None:intergenic
ACAGGTCAGTGGGATTTGTA+CGG 0.573529 2.1:-3387092 MS.gene47811:CDS
TTAGCTTGTGTACAACCAGC+TGG 0.579471 2.1:-3387549 MS.gene47811:CDS
GTACACAAGCTAAGGTAGCA+AGG 0.579499 2.1:+3387559 None:intergenic
GATTTGAAACTCTGGCGAGA+GGG 0.583566 2.1:+3387468 None:intergenic
CCACAGCTTCCACCAAAGCT+CGG 0.583979 2.1:-3386143 MS.gene47811:CDS
AACTAAATTAGATCTTGCCA+CGG 0.594009 2.1:+3386117 None:intergenic
TGGCAACACTACAGGTCAGT+GGG 0.596869 2.1:-3387102 MS.gene47811:CDS
ACTAAATTAGATCTTGCCAC+GGG 0.597169 2.1:+3386118 None:intergenic
GGATTTGAAACTCTGGCGAG+AGG 0.599558 2.1:+3387467 None:intergenic
CCAGTAGACAAACCTGAAGA+GGG 0.614925 2.1:+3387045 None:intergenic
TACACAAGCTAAGGTAGCAA+GGG 0.622521 2.1:+3387560 None:intergenic
TGAAGAGGGTTGTATGGTGA+GGG 0.652580 2.1:+3387059 None:intergenic
AACTTGCAGGAGTGGCTCTG+TGG 0.654086 2.1:-3387171 MS.gene47811:intron
CCACCAAAGCTCGGTCCCCG+TGG 0.657534 2.1:-3386134 MS.gene47811:CDS
TTGGCAACACTACAGGTCAG+TGG 0.661910 2.1:-3387103 MS.gene47811:CDS
TAGAATGTCACCTGAAGCTG+TGG 0.676047 2.1:+3386181 None:intergenic
CTGAAGAGGGTTGTATGGTG+AGG 0.677728 2.1:+3387058 None:intergenic
CTAAATTAGATCTTGCCACG+GGG 0.688209 2.1:+3386119 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAACTTATCTAATCTAAAT+AGG + chr2.1:3386418-3386437 None:intergenic 15.0%
!! ATCAAATAAACCAATTAATT+TGG + chr2.1:3387337-3387356 None:intergenic 15.0%
!! TTATATTAAGTGTCTTTATA+AGG - chr2.1:3386998-3387017 MS.gene47811:intron 15.0%
!!! TTTTTTCATACCAAATTAAT+TGG - chr2.1:3387324-3387343 MS.gene47811:intron 15.0%
!! AATAAGCTGAAAATAACTTA+TGG - chr2.1:3386901-3386920 MS.gene47811:intron 20.0%
!! ACATTAGCGTAATAAAAAAA+CGG + chr2.1:3386324-3386343 None:intergenic 20.0%
!! TAGATCAACAAAATAATCTA+TGG + chr2.1:3386763-3386782 None:intergenic 20.0%
!!! AAATGTAATTAGTTCTTCAT+TGG - chr2.1:3387174-3387193 MS.gene47811:intron 20.0%
!!! CTTCTTGTTTTCTTATAATA+AGG + chr2.1:3387115-3387134 None:intergenic 20.0%
! AGACATTTAATATGAGAATG+AGG - chr2.1:3387244-3387263 MS.gene47811:intron 25.0%
! GACATTTAATATGAGAATGA+GGG - chr2.1:3387245-3387264 MS.gene47811:intron 25.0%
! GTTTCAAATCCAAGAATTTA+AGG - chr2.1:3386236-3386255 MS.gene47811:CDS 25.0%
!! AGTGATTTTTATATGTGTCT+AGG - chr2.1:3386727-3386746 MS.gene47811:intron 25.0%
!! CTCATTAGTTGATATAAACT+TGG - chr2.1:3387379-3387398 MS.gene47811:intron 25.0%
!! TAAAGTATTCGTATTAGTAC+TGG - chr2.1:3387082-3387101 MS.gene47811:CDS 25.0%
!! TGTTTTCTTATAATAAGGAC+TGG + chr2.1:3387110-3387129 None:intergenic 25.0%
!!! ACATAACATAATTAACTTGC+AGG - chr2.1:3386507-3386526 MS.gene47811:intron 25.0%
!!! CTTATTTTCATAAGTTTTCC+AGG + chr2.1:3386887-3386906 None:intergenic 25.0%
AATAATCCTCTCTTTGTGAA+TGG + chr2.1:3387440-3387459 None:intergenic 30.0%
AGACACTTAATATAACACAG+AGG + chr2.1:3386993-3387012 None:intergenic 30.0%
GACACTTAATATAACACAGA+GGG + chr2.1:3386992-3387011 None:intergenic 30.0%
! AATTCTTGGATTTGAAACTC+TGG + chr2.1:3386234-3386253 None:intergenic 30.0%
! TTTTATATGTGTCTAGGCTT+AGG - chr2.1:3386733-3386752 MS.gene47811:intron 30.0%
!! GTGAAAGTACCTTAAATTCT+TGG + chr2.1:3386248-3386267 None:intergenic 30.0%
!! TACTTTGATTTGGAGGATAT+TGG - chr2.1:3386569-3386588 MS.gene47811:intron 30.0%
!!! GTATTCGATGCATTGATTTT+TGG - chr2.1:3387282-3387301 MS.gene47811:intron 30.0%
AGATAGCTTAGTTCCAGTAA+TGG + chr2.1:3386197-3386216 None:intergenic 35.0%
GACATTCTACCAATCAAGAA+AGG - chr2.1:3387524-3387543 MS.gene47811:CDS 35.0%
TATAGTCTATAGGACAGCAA+AGG + chr2.1:3386967-3386986 None:intergenic 35.0%
! CAAGAGTGTGTACTTTGATT+TGG - chr2.1:3386559-3386578 MS.gene47811:intron 35.0%
! TTGCTCAAGTTTTTGATCCT+AGG - chr2.1:3387458-3387477 MS.gene47811:CDS 35.0%
!! ACATAATTAACTTGCAGGAG+TGG - chr2.1:3386512-3386531 MS.gene47811:intron 35.0%
AAAAAACGGACAGACGAGTA+TGG + chr2.1:3386310-3386329 None:intergenic 40.0%
ATATGTGTCTAGGCTTAGGA+AGG - chr2.1:3386737-3386756 MS.gene47811:intron 40.0%
CACTAGCTACTACTTTAGCA+AGG + chr2.1:3387141-3387160 None:intergenic 40.0%
TACACAAGCTAAGGTAGCAA+GGG + chr2.1:3386134-3386153 None:intergenic 40.0%
! AAGTTTTTGATCCTAGGAGG+TGG - chr2.1:3387464-3387483 MS.gene47811:CDS 40.0%
! ACAGAGGGAGTATAGTCTAT+AGG + chr2.1:3386977-3386996 None:intergenic 40.0%
! CTCAAGTTTTTGATCCTAGG+AGG - chr2.1:3387461-3387480 MS.gene47811:CDS 40.0%
!! GAGTGTGTACTTTGATTTGG+AGG - chr2.1:3386562-3386581 MS.gene47811:intron 40.0%
!! GCTGTTTCTATAAGCTAACC+TGG - chr2.1:3386866-3386885 MS.gene47811:intron 40.0%
ACAGGTCAGTGGGATTTGTA+CGG - chr2.1:3386599-3386618 MS.gene47811:intron 45.0%
AGCTGGTTGTACACAAGCTA+AGG + chr2.1:3386143-3386162 None:intergenic 45.0%
AGCTGTGGACCTTTCTTGAT+TGG + chr2.1:3387536-3387555 None:intergenic 45.0%
AGTCTATAGGACAGCAAAGG+AGG + chr2.1:3386964-3386983 None:intergenic 45.0%
CAAACCTGAAGAGGGTTGTA+TGG + chr2.1:3386641-3386660 None:intergenic 45.0%
CCAGTAGACAAACCTGAAGA+GGG + chr2.1:3386649-3386668 None:intergenic 45.0%
CTCAATGTTAAGGGTCTTGC+TGG - chr2.1:3386166-3386185 MS.gene47811:CDS 45.0%
GAGGATATTGGCAACACTAC+AGG - chr2.1:3386581-3386600 MS.gene47811:intron 45.0%
GTACACAAGCTAAGGTAGCA+AGG + chr2.1:3386135-3386154 None:intergenic 45.0%
TAGAATGTCACCTGAAGCTG+TGG + chr2.1:3387513-3387532 None:intergenic 45.0%
TCCAGTAGACAAACCTGAAG+AGG + chr2.1:3386650-3386669 None:intergenic 45.0%
TGAAGAGGGTTGTATGGTGA+GGG + chr2.1:3386635-3386654 None:intergenic 45.0%
! ACCAGCTGGTCTCAATGTTA+AGG - chr2.1:3386156-3386175 MS.gene47811:CDS 45.0%
! CCAGCTGGTCTCAATGTTAA+GGG - chr2.1:3386157-3386176 MS.gene47811:CDS 45.0%
! GATTTGAAACTCTGGCGAGA+GGG + chr2.1:3386226-3386245 None:intergenic 45.0%
!! TTAGCTTGTGTACAACCAGC+TGG - chr2.1:3386142-3386161 MS.gene47811:CDS 45.0%
CAAGAGTTGAACCACCTCCT+AGG + chr2.1:3387478-3387497 None:intergenic 50.0%
CCCTTAACATTGAGACCAGC+TGG + chr2.1:3386160-3386179 None:intergenic 50.0%
CTCACCATACAACCCTCTTC+AGG - chr2.1:3386634-3386653 MS.gene47811:intron 50.0%
CTGAAGAGGGTTGTATGGTG+AGG + chr2.1:3386636-3386655 None:intergenic 50.0%
CTTGCTGGCAGTTCCATTAC+TGG - chr2.1:3386181-3386200 MS.gene47811:CDS 50.0%
GCAGCTCCATTCACAAAGAG+AGG - chr2.1:3387431-3387450 MS.gene47811:intron 50.0%
GGCTCTGTGGTAGCAAAGTA+TGG - chr2.1:3386533-3386552 MS.gene47811:intron 50.0%
TACTTCAGTGCCACAGCTTC+AGG - chr2.1:3387500-3387519 MS.gene47811:CDS 50.0%
TGGCAACACTACAGGTCAGT+GGG - chr2.1:3386589-3386608 MS.gene47811:intron 50.0%
TTGGCAACACTACAGGTCAG+TGG - chr2.1:3386588-3386607 MS.gene47811:intron 50.0%
! CCCTCTTCAGGTTTGTCTAC+TGG - chr2.1:3386646-3386665 MS.gene47811:intron 50.0%
! GGATTTGAAACTCTGGCGAG+AGG + chr2.1:3386227-3386246 None:intergenic 50.0%
CCACAGCTTCCACCAAAGCT+CGG - chr2.1:3387548-3387567 MS.gene47811:CDS 55.0%
! AACTTGCAGGAGTGGCTCTG+TGG - chr2.1:3386520-3386539 MS.gene47811:intron 55.0%
! CCGAGCTTTGGTGGAAGCTG+TGG + chr2.1:3387551-3387570 None:intergenic 60.0%
TTGCCACGGGGACCGAGCTT+TGG + chr2.1:3387563-3387582 None:intergenic 65.0%
CCACCAAAGCTCGGTCCCCG+TGG - chr2.1:3387557-3387576 MS.gene47811:CDS 70.0%
! CCACGGGGACCGAGCTTTGG+TGG + chr2.1:3387560-3387579 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 3386124 3387589 3386124 ID=MS.gene47811
chr2.1 mRNA 3386124 3387589 3386124 ID=MS.gene47811.t1;Parent=MS.gene47811
chr2.1 exon 3387456 3387589 3387456 ID=MS.gene47811.t1.exon1;Parent=MS.gene47811.t1
chr2.1 CDS 3387456 3387589 3387456 ID=cds.MS.gene47811.t1;Parent=MS.gene47811.t1
chr2.1 exon 3387058 3387184 3387058 ID=MS.gene47811.t1.exon2;Parent=MS.gene47811.t1
chr2.1 CDS 3387058 3387184 3387058 ID=cds.MS.gene47811.t1;Parent=MS.gene47811.t1
chr2.1 exon 3386124 3386303 3386124 ID=MS.gene47811.t1.exon3;Parent=MS.gene47811.t1
chr2.1 CDS 3386124 3386303 3386124 ID=cds.MS.gene47811.t1;Parent=MS.gene47811.t1
Gene Sequence

>MS.gene47811

ATGGCTTCCCTTGCTACCTTAGCTTGTGTACAACCAGCTGGTCTCAATGTTAAGGGTCTTGCTGGCAGTTCCATTACTGGAACTAAGCTATCTTTCAAGCCCTCTCGCCAGAGTTTCAAATCCAAGAATTTAAGGTACTTTCACAACTTTGAACTAATTATTTCAATTAATATAACTAGCATGCCATACTCGTCTGTCCGTTTTTTTATTACGCTAATGTTTATGTTTTTAAAGTATAAAGTGTTTGTAGTGCAATTTTTATTTAAGTAAACTTCTTAAGTTATATGAGATCCTATTTAGATTAGATAAGTTATTTGCAGTTTATAACACAAACACTTATTTAAATTAAATCAACTCATATTATATGTGTATGTGTAAGCTTAACATAACATAATTAACTTGCAGGAGTGGCTCTGTGGTAGCAAAGTATGGTGACAAGAGTGTGTACTTTGATTTGGAGGATATTGGCAACACTACAGGTCAGTGGGATTTGTACGGCTCAGATGCACCCTCACCATACAACCCTCTTCAGGTTTGTCTACTGGATTTTAGATCACTTTACTTTGTTTTGTGCATTCATTTAGTAGTGAGTAATGAACACAAAGTGATTTTTATATGTGTCTAGGCTTAGGAAGGCCATAGATTATTTTGTTGATCTAGCATAAGCACATATCATATAAGTGTTTCTGTATAAGCTATTTTTATAACAAAAATTAAATAAAGTTAAACTATTTTCATATAAGCTGTTTCTATAAGCTAACCTGGAAAACTTATGAAAATAAGCTGAAAATAACTTATGGACAATCAAACATGTTTTCATTATAAGTTCGCTTTAAGCCTCCTTTGCTGTCCTATAGACTATACTCCCTCTGTGTTATATTAAGTGTCTTTATAAGGTTATGCACACTTCTTAAGAAAATCATTGAGTGTAGTTATTCATAAAATGAGTTTTACTTACTAAAGTATTCGTATTAGTACTGGCTCCAGTCCTTATTATAAGAAAACAAGAAGTATCCTTGCTAAAGTAGTAGCTAGTGTATATTAGTAGAAAAATGTAATTAGTTCTTCATTGGTATTCTAAAACGACAAAAAAATGTGAGACAAACAAATATTTCAATTGAGACATTTAATATGAGAATGAGGGAGTAGTATATTCGTGTATTCGATGCATTGATTTTTGGCAGTAAAATGTTTTTTTTTTTTTTTCATACCAAATTAATTGGTTTATTTGATTGAAAATGCACAAACTTGATCTCTCATTAGTTGATATAAACTTGGCATTGCAGAGCAAGTTCTTTGAGACATTTGCAGCTCCATTCACAAAGAGAGGATTATTGCTCAAGTTTTTGATCCTAGGAGGTGGTTCAACTCTTGCATACTTCAGTGCCACAGCTTCAGGTGACATTCTACCAATCAAGAAAGGTCCACAGCTTCCACCAAAGCTCGGTCCCCGTGGCAAGATCTAA

Protein sequence

>MS.gene47811.t1

MASLATLACVQPAGLNVKGLAGSSITGTKLSFKPSRQSFKSKNLRSGSVVAKYGDKSVYFDLEDIGNTTGQWDLYGSDAPSPYNPLQSKFFETFAAPFTKRGLLLKFLILGGGSTLAYFSATASGDILPIKKGPQLPPKLGPRGKI