AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene65059

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene65059.t1 MTR_7g057160 95.906 171 7 0 1 171 1 171 1.66e-98 281
MS.gene65059.t1 MTR_3g436010 46.154 156 78 1 16 171 169 318 3.22e-33 120
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene65059.t1 AT3G17609 60.000 130 47 2 39 167 22 147 9.79e-44 142
MS.gene65059.t1 AT3G17609 61.157 121 42 2 48 167 2 118 6.45e-41 134
MS.gene65059.t1 AT3G17609 74.444 90 22 1 79 167 44 133 6.76e-40 132
MS.gene65059.t1 AT3G17609 74.444 90 22 1 79 167 43 132 8.07e-40 132
MS.gene65059.t1 AT5G11260 47.445 137 55 3 31 161 26 151 3.19e-32 113
MS.gene65059.t1 AT5G11260 47.368 133 53 3 31 157 26 147 1.71e-29 107

Find 39 sgRNAs with CRISPR-Local

Find 87 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGAGATATGTTCTTCTAAAT+TGG 0.194375 7.1:+43916720 None:intergenic
CTTCATCTTCATCTTCTTCA+TGG 0.213050 7.1:-43918420 MS.gene65059:CDS
TCTTCCACGGCGGCGCTTGC+CGG 0.245919 7.1:+43917246 None:intergenic
CTTCCACGGCGGCGCTTGCC+GGG 0.275869 7.1:+43917247 None:intergenic
CAAATAGGTTGCTAAGGAAT+AGG 0.306771 7.1:-43916828 MS.gene65059:intron
TCATTGCTCTCATCAACTTT+GGG 0.320674 7.1:+43916527 None:intergenic
TTCATTGCTCTCATCAACTT+TGG 0.343653 7.1:+43916526 None:intergenic
TTCCTTCATCTCAGTATCAT+TGG 0.395557 7.1:+43918462 None:intergenic
TCGGAGCATGGCGTTCTCAT+TGG 0.400151 7.1:+43916690 None:intergenic
ATGAAGGAAGCTGCAACAAC+TGG 0.409191 7.1:-43918448 MS.gene65059:CDS
TTTGATTTGTTAACTCAGAA+TGG 0.409238 7.1:+43917323 None:intergenic
CGTCTATGTTCCTTGTCTGC+AGG 0.409298 7.1:+43917220 None:intergenic
CCTATGCCTCCACATAGATT+TGG 0.415132 7.1:-43918385 MS.gene65059:intron
CATTGTGTACCTTCCACGTC+TGG 0.416640 7.1:+43917355 None:intergenic
AAATAGGTTGCTAAGGAATA+GGG 0.428080 7.1:-43916827 MS.gene65059:intron
CTTCATCTTCTTCATGGAGT+AGG 0.466765 7.1:-43918414 MS.gene65059:CDS
CAACTTCAAGCAGGCTTCCC+CGG 0.470731 7.1:-43917265 MS.gene65059:CDS
GTCTATGTTCCTTGTCTGCA+GGG 0.478530 7.1:+43917221 None:intergenic
CAGTTACATTGCTTTGATTG+TGG 0.494434 7.1:+43917293 None:intergenic
AGCCAATGATACTGAGATGA+AGG 0.496590 7.1:-43918464 MS.gene65059:CDS
TGTCTGCAGGGTTTCTTCCA+CGG 0.500164 7.1:+43917233 None:intergenic
AAAGTTGATGAGAGCAATGA+AGG 0.515891 7.1:-43916524 MS.gene65059:CDS
TTATGTTACCTTTCGGAGCA+TGG 0.517776 7.1:+43916678 None:intergenic
TTCCACGGCGGCGCTTGCCG+GGG 0.522944 7.1:+43917248 None:intergenic
CCAAATCTATGTGGAGGCAT+AGG 0.526031 7.1:+43918385 None:intergenic
AGGAACATAGACGTCTCAAA+AGG 0.535376 7.1:-43917210 MS.gene65059:intron
GTGTTACAAATAGGTTGCTA+AGG 0.552163 7.1:-43916834 MS.gene65059:intron
TGGAAGAAACCCTGCAGACA+AGG 0.552255 7.1:-43917230 MS.gene65059:CDS
CATGAAGAAGATGAAGATGA+AGG 0.570746 7.1:+43918421 None:intergenic
GTTGCTAAGGAATAGGGTCT+CGG 0.571634 7.1:-43916821 MS.gene65059:CDS
AATCTATGTGGAGGCATAGG+AGG 0.581180 7.1:+43918388 None:intergenic
ACTGATGCTCAACTTCAAGC+AGG 0.591244 7.1:-43917274 MS.gene65059:CDS
TTCCCCGGCAAGCGCCGCCG+TGG 0.608180 7.1:-43917250 MS.gene65059:CDS
TGAGAACGCCATGCTCCGAA+AGG 0.615500 7.1:-43916686 MS.gene65059:intron
CACTTACCAAATCTATGTGG+AGG 0.634191 7.1:+43918379 None:intergenic
TGACACTTACCAAATCTATG+TGG 0.640404 7.1:+43918376 None:intergenic
CTGCAGGGTTTCTTCCACGG+CGG 0.647406 7.1:+43917236 None:intergenic
TTCGAAGTTCCAGACGTGGA+AGG 0.651516 7.1:-43917364 MS.gene65059:CDS
TCTGTTCGAAGTTCCAGACG+TGG 0.701702 7.1:-43917368 MS.gene65059:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTATAATTGTAATATGTAT+CGG + chr7.1:43917987-43918006 None:intergenic 10.0%
!! TTGTTAAATAAAAATTTAAC+GGG + chr7.1:43917031-43917050 None:intergenic 10.0%
!! AAGAATATTAAGTATATTGT+TGG - chr7.1:43916881-43916900 MS.gene65059:intron 15.0%
!! AATGTCAAATTAAAATTTGA+AGG + chr7.1:43917493-43917512 None:intergenic 15.0%
!! ATGTCAAATTAAAATTTGAA+GGG + chr7.1:43917492-43917511 None:intergenic 15.0%
!! CAAAATTGTTACTATATATT+AGG - chr7.1:43917431-43917450 MS.gene65059:intron 15.0%
!! GGTATATATATAATATAAGT+TGG - chr7.1:43916945-43916964 MS.gene65059:intron 15.0%
!! TCAAAATTTGCATTGAATTT+CGG - chr7.1:43917246-43917265 MS.gene65059:CDS 20.0%
!! TCAAATTGTTGATGTAAAAA+CGG + chr7.1:43917106-43917125 None:intergenic 20.0%
!!! ACAAGTTGTTTTTAAATGAT+CGG + chr7.1:43916910-43916929 None:intergenic 20.0%
!!! TAATATGGACTAAATTGAAT+TGG + chr7.1:43917521-43917540 None:intergenic 20.0%
! AAAACAAGTCACGTTTAATA+TGG + chr7.1:43917536-43917555 None:intergenic 25.0%
! AACTACAGACAATTCAAATT+TGG - chr7.1:43917322-43917341 MS.gene65059:CDS 25.0%
! AACTTTGTGATATGATATTG+TGG + chr7.1:43917143-43917162 None:intergenic 25.0%
! ACTTGTTTCATGAAAAGTAA+AGG - chr7.1:43916924-43916943 MS.gene65059:intron 25.0%
! ATAACATCATGTTGATCAAA+TGG - chr7.1:43918401-43918420 MS.gene65059:CDS 25.0%
! ATATGCGTGTGTATATTATA+AGG + chr7.1:43916986-43917005 None:intergenic 25.0%
! TACACACGCATATATTAAAT+TGG - chr7.1:43916993-43917012 MS.gene65059:intron 25.0%
! TATGAAGAATCTTGTAAGTT+TGG + chr7.1:43916807-43916826 None:intergenic 25.0%
! TATGCGTGTGTATATTATAA+GGG + chr7.1:43916985-43917004 None:intergenic 25.0%
! TCAAATGGAAATTTATTCGA+TGG - chr7.1:43918416-43918435 MS.gene65059:CDS 25.0%
! TGAGATATGTTCTTCTAAAT+TGG + chr7.1:43918281-43918300 None:intergenic 25.0%
!! AAATAAAAGACCTTAACTTG+AGG + chr7.1:43916707-43916726 None:intergenic 25.0%
!! AAATGACTTGTGTTACAAAT+AGG - chr7.1:43918155-43918174 MS.gene65059:intron 25.0%
!! CATATTTTATCCTCAAGTTA+AGG - chr7.1:43916694-43916713 MS.gene65059:CDS 25.0%
!!! ATATAAGTTGGTCCATATTA+AGG - chr7.1:43916957-43916976 MS.gene65059:intron 25.0%
!!! TTTGATTTGTTAACTCAGAA+TGG + chr7.1:43917678-43917697 None:intergenic 25.0%
AAATAGGTTGCTAAGGAATA+GGG - chr7.1:43918171-43918190 MS.gene65059:intron 30.0%
AATAGTGACTATAGAGTGTA+AGG + chr7.1:43917848-43917867 None:intergenic 30.0%
AATCTTGTAAGTTTGGACTT+TGG + chr7.1:43916800-43916819 None:intergenic 30.0%
ACATTAACATGTGCTAACAT+TGG + chr7.1:43917348-43917367 None:intergenic 30.0%
ATGATTATCGATCATTGTGA+AGG + chr7.1:43917172-43917191 None:intergenic 30.0%
GTCTGACTTTACTTATCTTT+CGG - chr7.1:43918100-43918119 MS.gene65059:intron 30.0%
GTTCAGATTATGTTACCTTT+CGG + chr7.1:43918330-43918349 None:intergenic 30.0%
!! ATTATAAGGGCACCTTAATA+TGG + chr7.1:43916972-43916991 None:intergenic 30.0%
ATAGACGTCTCAAAAGGTAA+GGG - chr7.1:43917794-43917813 MS.gene65059:intron 35.0%
ATTATCGATCATTGTGAAGG+TGG + chr7.1:43917169-43917188 None:intergenic 35.0%
CAAATAGGTTGCTAAGGAAT+AGG - chr7.1:43918170-43918189 MS.gene65059:intron 35.0%
CAGTTACATTGCTTTGATTG+TGG + chr7.1:43917708-43917727 None:intergenic 35.0%
CATGAAGAAGATGAAGATGA+AGG + chr7.1:43916580-43916599 None:intergenic 35.0%
CTCAAACGATTGTTGAACTT+CGG - chr7.1:43918035-43918054 MS.gene65059:intron 35.0%
CTTCATCTTCATCTTCTTCA+TGG - chr7.1:43916578-43916597 MS.gene65059:intron 35.0%
GTGTTACAAATAGGTTGCTA+AGG - chr7.1:43918164-43918183 MS.gene65059:intron 35.0%
TATTGATAGGCTCTTGACTT+AGG + chr7.1:43916750-43916769 None:intergenic 35.0%
TCATTGCTCTCATCAACTTT+GGG + chr7.1:43918474-43918493 None:intergenic 35.0%
TGACACTTACCAAATCTATG+TGG + chr7.1:43916625-43916644 None:intergenic 35.0%
TTCATTGCTCTCATCAACTT+TGG + chr7.1:43918475-43918494 None:intergenic 35.0%
TTCCTTCATCTCAGTATCAT+TGG + chr7.1:43916539-43916558 None:intergenic 35.0%
! TTTTTCTTTCACGAGCTTGT+TGG + chr7.1:43918204-43918223 None:intergenic 35.0%
!! AAAGTTGATGAGAGCAATGA+AGG - chr7.1:43918474-43918493 MS.gene65059:CDS 35.0%
!! TTCGATGGTTTTACTTGTAC+AGG - chr7.1:43918431-43918450 MS.gene65059:CDS 35.0%
!! TTTTCTTTCACGAGCTTGTT+GGG + chr7.1:43918203-43918222 None:intergenic 35.0%
AGCCAATGATACTGAGATGA+AGG - chr7.1:43916534-43916553 MS.gene65059:CDS 40.0%
AGGAACATAGACGTCTCAAA+AGG - chr7.1:43917788-43917807 MS.gene65059:intron 40.0%
CACTTACCAAATCTATGTGG+AGG + chr7.1:43916622-43916641 None:intergenic 40.0%
CATAGACGTCTCAAAAGGTA+AGG - chr7.1:43917793-43917812 MS.gene65059:intron 40.0%
CTTCATCTTCTTCATGGAGT+AGG - chr7.1:43916584-43916603 MS.gene65059:intron 40.0%
TTATGTTACCTTTCGGAGCA+TGG + chr7.1:43918323-43918342 None:intergenic 40.0%
ACTGATGCTCAACTTCAAGC+AGG - chr7.1:43917724-43917743 MS.gene65059:intron 45.0%
AGATCTTCATCGCTATCGTC+TGG + chr7.1:43917613-43917632 None:intergenic 45.0%
ATGAAGGAAGCTGCAACAAC+TGG - chr7.1:43916550-43916569 MS.gene65059:intron 45.0%
CCTATGCCTCCACATAGATT+TGG - chr7.1:43916613-43916632 MS.gene65059:intron 45.0%
GGTGACAGTTGGATCTAGAT+TGG + chr7.1:43917276-43917295 None:intergenic 45.0%
GTCTATGTTCCTTGTCTGCA+GGG + chr7.1:43917780-43917799 None:intergenic 45.0%
GTTGCTAAGGAATAGGGTCT+CGG - chr7.1:43918177-43918196 MS.gene65059:intron 45.0%
TAGATCCAACTGTCACCTGA+GGG - chr7.1:43917279-43917298 MS.gene65059:CDS 45.0%
! AATCTATGTGGAGGCATAGG+AGG + chr7.1:43916613-43916632 None:intergenic 45.0%
! CCAAATCTATGTGGAGGCAT+AGG + chr7.1:43916616-43916635 None:intergenic 45.0%
!! ATTGTTAAATAAAAATTTAA+CGG + chr7.1:43917032-43917051 None:intergenic 5.0%
!!! TTTTTAAATTAAATATTGAT+AGG + chr7.1:43916763-43916782 None:intergenic 5.0%
CATTGTGTACCTTCCACGTC+TGG + chr7.1:43917646-43917665 None:intergenic 50.0%
CGTCTATGTTCCTTGTCTGC+AGG + chr7.1:43917781-43917800 None:intergenic 50.0%
CTAGATCCAACTGTCACCTG+AGG - chr7.1:43917278-43917297 MS.gene65059:CDS 50.0%
TCTGTTCGAAGTTCCAGACG+TGG - chr7.1:43917630-43917649 MS.gene65059:intron 50.0%
TGGAAGAAACCCTGCAGACA+AGG - chr7.1:43917768-43917787 MS.gene65059:intron 50.0%
TGTCTGCAGGGTTTCTTCCA+CGG + chr7.1:43917768-43917787 None:intergenic 50.0%
TTCGAAGTTCCAGACGTGGA+AGG - chr7.1:43917634-43917653 MS.gene65059:intron 50.0%
CAACTTCAAGCAGGCTTCCC+CGG - chr7.1:43917733-43917752 MS.gene65059:intron 55.0%
TCACTCCCTCAGGTGACAGT+TGG + chr7.1:43917287-43917306 None:intergenic 55.0%
TCGGAGCATGGCGTTCTCAT+TGG + chr7.1:43918311-43918330 None:intergenic 55.0%
TCTCGTGCATTCACTCCCTC+AGG + chr7.1:43917297-43917316 None:intergenic 55.0%
TGAGAACGCCATGCTCCGAA+AGG - chr7.1:43918312-43918331 MS.gene65059:intron 55.0%
CTGCAGGGTTTCTTCCACGG+CGG + chr7.1:43917765-43917784 None:intergenic 60.0%
TCTTCCACGGCGGCGCTTGC+CGG + chr7.1:43917755-43917774 None:intergenic 70.0%
CTTCCACGGCGGCGCTTGCC+GGG + chr7.1:43917754-43917773 None:intergenic 75.0%
TTCCACGGCGGCGCTTGCCG+GGG + chr7.1:43917753-43917772 None:intergenic 75.0%
!! TTCCCCGGCAAGCGCCGCCG+TGG - chr7.1:43917748-43917767 MS.gene65059:intron 80.0%


Chromosome Type Strat End Strand Name
chr7.1 gene 43916520 43918500 43916520 ID=MS.gene65059
chr7.1 mRNA 43916520 43918500 43916520 ID=MS.gene65059.t1;Parent=MS.gene65059
chr7.1 exon 43918386 43918500 43918386 ID=MS.gene65059.t1.exon1;Parent=MS.gene65059.t1
chr7.1 CDS 43918386 43918500 43918386 ID=cds.MS.gene65059.t1;Parent=MS.gene65059.t1
chr7.1 exon 43917211 43917406 43917211 ID=MS.gene65059.t1.exon2;Parent=MS.gene65059.t1
chr7.1 CDS 43917211 43917406 43917211 ID=cds.MS.gene65059.t1;Parent=MS.gene65059.t1
chr7.1 exon 43916687 43916843 43916687 ID=MS.gene65059.t1.exon3;Parent=MS.gene65059.t1
chr7.1 CDS 43916687 43916843 43916687 ID=cds.MS.gene65059.t1;Parent=MS.gene65059.t1
chr7.1 exon 43916520 43916567 43916520 ID=MS.gene65059.t1.exon4;Parent=MS.gene65059.t1
chr7.1 CDS 43916520 43916567 43916520 ID=cds.MS.gene65059.t1;Parent=MS.gene65059.t1
Gene Sequence

>MS.gene65059

ATGTCTCTTTCAAGAGCCAATGATACTGAGATGAAGGAAGCTGCAACAACTGGAGCACCTTCATCTTCATCTTCTTCATGGAGTAGGTTACCTCCTATGCCTCCACATAGATTTGGTAAGTGTCATTTTCAATTTTTTTTTAATTAGTTTATTTTATGCTGAAGTTTTTTGACTCATATTTTATCCTCAAGTTAAGGTCTTTTATTTTATTTTATTTTTGACATAATCCTAAGTCAAGAGCCTATCAATATTTAATTTAAAAAAATGATTAACTAATCCAAAGTCCAAACTTACAAGATTCTTCATAAAGTTTGTCAAAACAAAAAAAATATATTAAGTATATTGTTTTTTTTTTTTTTTTAAGAATATTAAGTATATTGTTGGATTCCGATCATTTAAAAACAACTTGTTTCATGAAAAGTAAAGGTATATATATAATATAAGTTGGTCCATATTAAGGTGCCCTTATAATATACACACGCATATATTAAATTGGTCTAACATTCTACCCGTTAAATTTTTATTTAACAATTATACTTACACAGCATCATTCTTTTTAGATATGATTGAATGCATGTATAAACCGTTTTTACATCAACAATTTGACAAATTTAGATTATCCACAATATCATATCACAAAGTTTATCCACCTTCACAATGATCGATAATCATTAGATTGAGATCGAACGATCTAGATTTCAAACTTATTTTAACTTAAAAAAATAATCAAAATTTGCATTGAATTTCGGAGCTCCAATCTAGATCCAACTGTCACCTGAGGGAGTGAATGCACGAGATTGCGAACTACAGACAATTCAAATTTGGCCAATGTTAGCACATGTTAATGTACTCGAAATATAAAAATTCGTATGTTCAACTTTTTAAAATTCAAAATATTGTTTTTATCAATGCAAAATTGTTACTATATATTAGGTTCTTTAACATTAGTACACAAGTTAGTTATAATGACCCTTCAAATTTTAATTTGACATTGTATGCCAATTCAATTTAGTCCATATTAAACGTGACTTGTTTTGTTTTGACAATACTAAATATGTCATGTTAATAAGTCATGATTTTTTTACAAATTCCAGACGATAGCGATGAAGATCTGTTCGAAGTTCCAGACGTGGAAGGTACACAATGTCAAAGTGTCCATTCTGAGTTAACAAATCAAAATAGTAACCACAATCAAAGCAATGTAACTGATGCTCAACTTCAAGCAGGCTTCCCCGGCAAGCGCCGCCGTGGAAGAAACCCTGCAGACAAGGAACATAGACGTCTCAAAAGGTAAGGGACACAAGTTAACACAAATTTTAGCTATACCTTACACTCTATAGTCACTATTATAAACAAACAACTATTTTTTAAATTCATTGAATAACTGATGTATTTTGTATATAATATAGACTATTGTATTAATTTCTACATTAAATTATCAAACTTTGTCACTTTAAGAAGATTCCGATACATATTACAATTATAATGTTATTCAAGAGTAATTAAGTTATTGAACTCAAACGATTGTTGAACTTCGGTCAAAGACGAATCATTCAGAATACTTAATGAGAACAATTTTAGTCTGACTTTACTTATCTTTCGGCAGAACTTCAGATTAAACTATCTAAAACTAATAAATGACTTGTGTTACAAATAGGTTGCTAAGGAATAGGGTCTCGGCCCAACAAGCTCGTGAAAGAAAAAAAGTGTACGTGAATGACTTAGAATCAAGAGCTAAAGAGTTTGAAGATAAGAACTCCAATTTAGAAGAACATATCTCAACTTTGACCAATGAGAACGCCATGCTCCGAAAGGTAACATAATCTGAACTAAATATGTTTTAACAAATTGTTTGTCACTTACTATTTACTATAGAATTATATAACATCATGTTGATCAAATGGAAATTTATTCGATGGTTTTACTTGTACAGGTTCTTATGAACACTAGACCCAAAGTTGATGAGAGCAATGAAGGTTAG
Protein sequence

>MS.gene65059.t1

MSLSRANDTEMKEAATTGAPSSSSSSWSRLPPMPPHRFDDSDEDLFEVPDVEGTQCQSVHSELTNQNSNHNQSNVTDAQLQAGFPGKRRRGRNPADKEHRRLKRLLRNRVSAQQARERKKVYVNDLESRAKEFEDKNSNLEEHISTLTNENAMLRKVLMNTRPKVDESNEG