AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene76500


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene76500.t1 MTR_2g101820 97.279 147 3 1 1 146 1 147 5.34e-99 281
MS.gene76500.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.gene76500.t1 AT1G52230 79.452 146 29 1 1 146 1 145 2.10e-81 236
MS.gene76500.t1 AT3G16140 78.082 146 31 1 1 146 1 145 7.76e-80 232

Find 45 sgRNAs with CRISPR-Local

Find 69 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTTCAAATCCAAGAATTTA+AGG 0.134528 2.3:-2343118 MS.gene76500:intron
GTGAAAGTACCTTAAATTCT+TGG 0.244082 2.3:+2343109 None:intergenic
CTTGCTGGCAGTTCCATTAC+TGG 0.265222 2.3:-2343173 MS.gene76500:CDS
TACTTCAGTGCCACAGCTTC+AGG 0.317013 2.3:-2341846 MS.gene76500:CDS
TACTTTGATTTGGAGGATAT+TGG 0.323961 2.3:-2342785 MS.gene76500:CDS
CAAGAGTGTGTACTTTGATT+TGG 0.336220 2.3:-2342795 MS.gene76500:CDS
TTGCCACGGGGACCGAGCTT+TGG 0.360365 2.3:+2341786 None:intergenic
CTCAATGTTAAGGGTCTTGC+TGG 0.365303 2.3:-2343188 MS.gene76500:CDS
CTCACCATACAACCCTCTTC+AGG 0.381984 2.3:-2342720 MS.gene76500:intron
ACCAGCTGGTCTCAATGTTA+AGG 0.384673 2.3:-2343198 MS.gene76500:CDS
CCACGGGGACCGAGCTTTGG+TGG 0.404075 2.3:+2341789 None:intergenic
GGCTCTGTGGTAGCAAAGTA+TGG 0.420308 2.3:-2342821 MS.gene76500:CDS
AGCTGTGGACCTTTCTTGAT+TGG 0.426964 2.3:+2341813 None:intergenic
CCAGCTGGTCTCAATGTTAA+GGG 0.447321 2.3:-2343197 MS.gene76500:CDS
GAGTGTGTACTTTGATTTGG+AGG 0.467087 2.3:-2342792 MS.gene76500:CDS
GAGGATATTGGCAACACTAC+AGG 0.483887 2.3:-2342773 MS.gene76500:CDS
AATTCTTGGATTTGAAACTC+TGG 0.485960 2.3:+2343123 None:intergenic
CAAACCTGAAGAGGGTTGTA+TGG 0.501808 2.3:+2342716 None:intergenic
CAAGAGTTGAACCACCTCCT+AGG 0.515089 2.3:+2341871 None:intergenic
AATAATCCTCTCTTTGTGAA+TGG 0.515909 2.3:+2341909 None:intergenic
CCCTTAACATTGAGACCAGC+TGG 0.523582 2.3:+2343197 None:intergenic
CCGAGCTTTGGTGGAAGCTG+TGG 0.524654 2.3:+2341798 None:intergenic
GACATTCTACCAATCAAGAA+AGG 0.540823 2.3:-2341822 MS.gene76500:CDS
AGATAGCTTAGTTCCAGTAA+TGG 0.548416 2.3:+2343160 None:intergenic
AGCTGGTTGTACACAAGCTA+AGG 0.551993 2.3:+2343214 None:intergenic
GCAGCTCCATTCACAAAGAG+AGG 0.555627 2.3:-2341915 MS.gene76500:CDS
TCCAGTAGACAAACCTGAAG+AGG 0.558714 2.3:+2342707 None:intergenic
ACAGGTCAGTGGGATTTGTA+CGG 0.573529 2.3:-2342755 MS.gene76500:CDS
TTAGCTTGTGTACAACCAGC+TGG 0.579471 2.3:-2343212 MS.gene76500:CDS
GTACACAAGCTAAGGTAGCA+AGG 0.579499 2.3:+2343222 None:intergenic
GATTTGAAACTCTGGCGAGA+GGG 0.583566 2.3:+2343131 None:intergenic
CCACAGCTTCCACCAAAGCT+CGG 0.583979 2.3:-2341798 MS.gene76500:CDS
AACTAAATTAGATCTTGCCA+CGG 0.594009 2.3:+2341772 None:intergenic
TGGCAACACTACAGGTCAGT+GGG 0.596869 2.3:-2342765 MS.gene76500:CDS
ACTAAATTAGATCTTGCCAC+GGG 0.597169 2.3:+2341773 None:intergenic
GGATTTGAAACTCTGGCGAG+AGG 0.599558 2.3:+2343130 None:intergenic
CCAGTAGACAAACCTGAAGA+GGG 0.614925 2.3:+2342708 None:intergenic
TACACAAGCTAAGGTAGCAA+GGG 0.622521 2.3:+2343223 None:intergenic
TGAAGAGGGTTGTATGGTGA+GGG 0.652580 2.3:+2342722 None:intergenic
AACTTGCAGGAGTGGCTCTG+TGG 0.654086 2.3:-2342834 MS.gene76500:intron
CCACCAAAGCTCGGTCCCCG+TGG 0.657534 2.3:-2341789 MS.gene76500:CDS
TTGGCAACACTACAGGTCAG+TGG 0.661910 2.3:-2342766 MS.gene76500:CDS
TAGAATGTCACCTGAAGCTG+TGG 0.676047 2.3:+2341836 None:intergenic
CTGAAGAGGGTTGTATGGTG+AGG 0.677728 2.3:+2342721 None:intergenic
CTAAATTAGATCTTGCCACG+GGG 0.688209 2.3:+2341774 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAACTTATCTAATCTAAAT+AGG + chr2.3:2342073-2342092 None:intergenic 15.0%
!! ATCAAAGAAATCAATTAATT+TGG + chr2.3:2342955-2342974 None:intergenic 15.0%
!! TTATATTAAGTGTCTTTATA+AGG - chr2.3:2342653-2342672 MS.gene76500:intron 15.0%
!! TTTAATATGAGAATGATTTA+TGG - chr2.3:2342904-2342923 MS.gene76500:intron 15.0%
!! AATAAGCTGAAAATAACTTA+TGG - chr2.3:2342556-2342575 MS.gene76500:intron 20.0%
!! ACATTAGCGTAATAAAAAAA+CGG + chr2.3:2341979-2341998 None:intergenic 20.0%
!! TAGATCAACAAAATAATCTA+TGG + chr2.3:2342418-2342437 None:intergenic 20.0%
!!! AAATGTAATTAGTTCTTCAT+TGG - chr2.3:2342829-2342848 MS.gene76500:intron 20.0%
!!! CTTATTTTCATAAGTTTTTC+AGG + chr2.3:2342542-2342561 None:intergenic 20.0%
!!! CTTCTTGTTTTCTTATAATA+AGG + chr2.3:2342770-2342789 None:intergenic 20.0%
! GTTTCAAATCCAAGAATTTA+AGG - chr2.3:2341891-2341910 MS.gene76500:CDS 25.0%
!! TGTTTTCTTATAATAAGGAC+TGG + chr2.3:2342765-2342784 None:intergenic 25.0%
!!! ACATAACATAATTAACTTGC+AGG - chr2.3:2342162-2342181 MS.gene76500:intron 25.0%
AATAATCCTCTCTTTGTGAA+TGG + chr2.3:2343103-2343122 None:intergenic 30.0%
AGACACTTAATATAACACAG+AGG + chr2.3:2342648-2342667 None:intergenic 30.0%
AGTGATGTTTATATGTGTCT+AGG - chr2.3:2342382-2342401 MS.gene76500:intron 30.0%
GACACTTAATATAACACAGA+GGG + chr2.3:2342647-2342666 None:intergenic 30.0%
! AATTCTTGGATTTGAAACTC+TGG + chr2.3:2341889-2341908 None:intergenic 30.0%
!! GTGAAAGTACCTTAAATTCT+TGG + chr2.3:2341903-2341922 None:intergenic 30.0%
!! TACTTTGATTTGGAGGATAT+TGG - chr2.3:2342224-2342243 MS.gene76500:intron 30.0%
AGATAGCTTAGTTCCAGTAA+TGG + chr2.3:2341852-2341871 None:intergenic 35.0%
GACATTCTACCAATCAAGAA+AGG - chr2.3:2343187-2343206 MS.gene76500:CDS 35.0%
GTTTATATGTGTCTAGGCTT+AGG - chr2.3:2342388-2342407 MS.gene76500:intron 35.0%
TATAGTCTATAGGACAGCAA+AGG + chr2.3:2342622-2342641 None:intergenic 35.0%
! CAAGAGTGTGTACTTTGATT+TGG - chr2.3:2342214-2342233 MS.gene76500:intron 35.0%
! TTGCTCAAGTTTTTGATCCT+AGG - chr2.3:2343121-2343140 MS.gene76500:CDS 35.0%
!! ACATAATTAACTTGCAGGAG+TGG - chr2.3:2342167-2342186 MS.gene76500:intron 35.0%
AAAAAACGGACAGACGAGTA+TGG + chr2.3:2341965-2341984 None:intergenic 40.0%
ATATGTGTCTAGGCTTAGGA+AGG - chr2.3:2342392-2342411 MS.gene76500:intron 40.0%
CACTAGCTACTACTTTAGCA+AGG + chr2.3:2342796-2342815 None:intergenic 40.0%
TACACAAGCTAAGGTAGCAA+GGG + chr2.3:2341789-2341808 None:intergenic 40.0%
! AAGTTTTTGATCCTAGGAGG+TGG - chr2.3:2343127-2343146 MS.gene76500:CDS 40.0%
! ACAGAGGGAGTATAGTCTAT+AGG + chr2.3:2342632-2342651 None:intergenic 40.0%
! CTCAAGTTTTTGATCCTAGG+AGG - chr2.3:2343124-2343143 MS.gene76500:CDS 40.0%
!! GAGTGTGTACTTTGATTTGG+AGG - chr2.3:2342217-2342236 MS.gene76500:intron 40.0%
ACAGGTCAGTGGGATTTGTA+CGG - chr2.3:2342254-2342273 MS.gene76500:intron 45.0%
AGCTGGTTGTACACAAGCTA+AGG + chr2.3:2341798-2341817 None:intergenic 45.0%
AGCTGTGGACCTTTCTTGAT+TGG + chr2.3:2343199-2343218 None:intergenic 45.0%
AGTCTATAGGACAGCAAAGG+AGG + chr2.3:2342619-2342638 None:intergenic 45.0%
CAAACCTGAAGAGGGTTGTA+TGG + chr2.3:2342296-2342315 None:intergenic 45.0%
CCAGTAGACAAACCTGAAGA+GGG + chr2.3:2342304-2342323 None:intergenic 45.0%
CTCAATGTTAAGGGTCTTGC+TGG - chr2.3:2341821-2341840 MS.gene76500:CDS 45.0%
GAGGATATTGGCAACACTAC+AGG - chr2.3:2342236-2342255 MS.gene76500:intron 45.0%
GTACACAAGCTAAGGTAGCA+AGG + chr2.3:2341790-2341809 None:intergenic 45.0%
TAGAATGTCACCTGAAGCTG+TGG + chr2.3:2343176-2343195 None:intergenic 45.0%
TCCAGTAGACAAACCTGAAG+AGG + chr2.3:2342305-2342324 None:intergenic 45.0%
TGAAGAGGGTTGTATGGTGA+GGG + chr2.3:2342290-2342309 None:intergenic 45.0%
! ACCAGCTGGTCTCAATGTTA+AGG - chr2.3:2341811-2341830 MS.gene76500:CDS 45.0%
! CCAGCTGGTCTCAATGTTAA+GGG - chr2.3:2341812-2341831 MS.gene76500:CDS 45.0%
! GATTTGAAACTCTGGCGAGA+GGG + chr2.3:2341881-2341900 None:intergenic 45.0%
!! TTAGCTTGTGTACAACCAGC+TGG - chr2.3:2341797-2341816 MS.gene76500:CDS 45.0%
CAAGAGTTGAACCACCTCCT+AGG + chr2.3:2343141-2343160 None:intergenic 50.0%
CCCTTAACATTGAGACCAGC+TGG + chr2.3:2341815-2341834 None:intergenic 50.0%
CTCACCATACAACCCTCTTC+AGG - chr2.3:2342289-2342308 MS.gene76500:intron 50.0%
CTGAAGAGGGTTGTATGGTG+AGG + chr2.3:2342291-2342310 None:intergenic 50.0%
CTTGCTGGCAGTTCCATTAC+TGG - chr2.3:2341836-2341855 MS.gene76500:CDS 50.0%
GCAGCTCCATTCACAAAGAG+AGG - chr2.3:2343094-2343113 MS.gene76500:intron 50.0%
GGCTCTGTGGTAGCAAAGTA+TGG - chr2.3:2342188-2342207 MS.gene76500:intron 50.0%
TACTTCAGTGCCACAGCTTC+AGG - chr2.3:2343163-2343182 MS.gene76500:CDS 50.0%
TGGCAACACTACAGGTCAGT+GGG - chr2.3:2342244-2342263 MS.gene76500:intron 50.0%
TTGGCAACACTACAGGTCAG+TGG - chr2.3:2342243-2342262 MS.gene76500:intron 50.0%
! CCCTCTTCAGGTTTGTCTAC+TGG - chr2.3:2342301-2342320 MS.gene76500:intron 50.0%
! GGATTTGAAACTCTGGCGAG+AGG + chr2.3:2341882-2341901 None:intergenic 50.0%
CCACAGCTTCCACCAAAGCT+CGG - chr2.3:2343211-2343230 MS.gene76500:CDS 55.0%
! AACTTGCAGGAGTGGCTCTG+TGG - chr2.3:2342175-2342194 MS.gene76500:intron 55.0%
! CCGAGCTTTGGTGGAAGCTG+TGG + chr2.3:2343214-2343233 None:intergenic 60.0%
TTGCCACGGGGACCGAGCTT+TGG + chr2.3:2343226-2343245 None:intergenic 65.0%
CCACCAAAGCTCGGTCCCCG+TGG - chr2.3:2343220-2343239 MS.gene76500:CDS 70.0%
! CCACGGGGACCGAGCTTTGG+TGG + chr2.3:2343223-2343242 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 2341779 2343252 2341779 ID=MS.gene76500
chr2.3 mRNA 2341779 2343252 2341779 ID=MS.gene76500.t1;Parent=MS.gene76500
chr2.3 exon 2343119 2343252 2343119 ID=MS.gene76500.t1.exon1;Parent=MS.gene76500.t1
chr2.3 CDS 2343119 2343252 2343119 ID=cds.MS.gene76500.t1;Parent=MS.gene76500.t1
chr2.3 exon 2342721 2342847 2342721 ID=MS.gene76500.t1.exon2;Parent=MS.gene76500.t1
chr2.3 CDS 2342721 2342847 2342721 ID=cds.MS.gene76500.t1;Parent=MS.gene76500.t1
chr2.3 exon 2341779 2341958 2341779 ID=MS.gene76500.t1.exon3;Parent=MS.gene76500.t1
chr2.3 CDS 2341779 2341958 2341779 ID=cds.MS.gene76500.t1;Parent=MS.gene76500.t1
Gene Sequence

>MS.gene76500

ATGGCTTCCCTTGCTACCTTAGCTTGTGTACAACCAGCTGGTCTCAATGTTAAGGGTCTTGCTGGCAGTTCCATTACTGGAACTAAGCTATCTTTCAAGCCCTCTCGCCAGAGTTTCAAATCCAAGAATTTAAGGTACTTTCACAACTTTGAACTAATTATTTCAATTAATATAACTAGCATGCCATACTCGTCTGTCCGTTTTTTTATTACGCTAATGTTTATGTTTTTAAAGTATAAAGTGTTTGTAGTGCAATTTTTATTTAAGTAAACTTCTTAAGTTATATGAGATCCTATTTAGATTAGATAAGTTATTTGCAGTTTATAACACAAACACTTATTTAAATTAAATCAACTCATATTATATGTGTATGTGTAAGCTTAACATAACATAATTAACTTGCAGGAGTGGCTCTGTGGTAGCAAAGTATGGTGACAAGAGTGTGTACTTTGATTTGGAGGATATTGGCAACACTACAGGTCAGTGGGATTTGTACGGCTCAGATGCACCCTCACCATACAACCCTCTTCAGGTTTGTCTACTGGATTTTAGATCACTTTACTTTGTTTTGTGCATTCATTTAGTAGTGAGTAATGAACACAAAGTGATGTTTATATGTGTCTAGGCTTAGGAAGGCCATAGATTATTTTGTTGATCTAGCATAAGCACATATCATATAAGTGTTTCTGTATAAGCTATTTTTATAACAAAAATTAAATAAAGTTAAACTATTTTCATATAAGCTGTTTCTATAAGCTAACCTGAAAAACTTATGAAAATAAGCTGAAAATAACTTATGGACAATCAAACATGTTTTCATTATAAGTTCGCTTTAAGCCTCCTTTGCTGTCCTATAGACTATACTCCCTCTGTGTTATATTAAGTGTCTTTATAAGGTTATGCACACTTCTTAAGAAAATCATTGAGTGTACTTATTGATAAAATGAGTTTTACTTACTAAAGTATTCGTATTAGTACTCGCTCCAGTCCTTATTATAAGAAAACAAGAAGTATCCTTGCTAAAGTAGTAGCTAGTGTATATTAGTAGAAAAATGTAATTAGTTCTTCATTGGTATTCTAAAACGACAAAAAAATGTGAGACAAACAAATATTTCAATTGAGACATTTAATATGAGAATGATTTATGGCAGCAAAATGTTTTTTTTTTTCATACCAAATTAATTGATTTCTTTGATTGAAAAGTTTTTTTTTTTCATACCAAATTAATTGATTTCTTTGATTGAAAATGCACAAACTTGATCTCTCATTTGTTGATATAAACTTGTCATTGCAGAGCAAGTTCTTTGAGACATTTGCAGCTCCATTCACAAAGAGAGGATTATTGCTCAAGTTTTTGATCCTAGGAGGTGGTTCAACTCTTGCATACTTCAGTGCCACAGCTTCAGGTGACATTCTACCAATCAAGAAAGGTCCACAGCTTCCACCAAAGCTCGGTCCCCGTGGCAAGATCTAA

Protein sequence

>MS.gene76500.t1

MASLATLACVQPAGLNVKGLAGSSITGTKLSFKPSRQSFKSKNLRSGSVVAKYGDKSVYFDLEDIGNTTGQWDLYGSDAPSPYNPLQSKFFETFAAPFTKRGLLLKFLILGGGSTLAYFSATASGDILPIKKGPQLPPKLGPRGKI