AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene052863


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 33 sgRNAs with CRISPR-Local

Find 63 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCCAGGTTGATTTGCTTAA+AGG 0.222619 4.3:-23576417 MS.gene052863:intron
ACTTGATAAAGAGGCCTTTC+AGG 0.294843 4.3:+23576815 None:intergenic
AAGACAAGTCAGGGGCAAAA+AGG 0.303775 4.3:-23576520 MS.gene052863:CDS
CTTGCTCCTGGAACTTTGCT+TGG 0.355394 4.3:-23576685 MS.gene052863:CDS
GCAAGGGAGGAGAGAAATTA+CGG 0.412571 4.3:-23576220 MS.gene052863:CDS
CACTTTACTGCCAGAGGAGT+TGG 0.419852 4.3:-23576370 MS.gene052863:CDS
ACGGGCACCCAAGACAAGTC+AGG 0.445877 4.3:-23576530 MS.gene052863:CDS
GAAAGACTCACTTGATAAAG+AGG 0.469037 4.3:+23576806 None:intergenic
CTCCAGTTATGTGGTTGGCA+CGG 0.469111 4.3:-23576549 MS.gene052863:intron
GTACAGGTCTATATGATTTG+AGG 0.471177 4.3:+23576145 None:intergenic
GTAGTTCCAAGCAAAGTTCC+AGG 0.471231 4.3:+23576679 None:intergenic
TCCAGTTATGTGGTTGGCAC+GGG 0.478302 4.3:-23576548 MS.gene052863:intron
TTTCTCTCCAGTTATGTGGT+TGG 0.493505 4.3:-23576554 MS.gene052863:intron
TCCATGACATCCAACTCCTC+TGG 0.503135 4.3:+23576360 None:intergenic
GCCAGAGGAGTTGGATGTCA+TGG 0.505402 4.3:-23576361 MS.gene052863:CDS
CGGGCACCCAAGACAAGTCA+GGG 0.533145 4.3:-23576529 MS.gene052863:CDS
TTACGAAGGTCAATAACATC+AGG 0.537927 4.3:+23576854 None:intergenic
CCTTCCTCTGCTCCTTACGA+AGG 0.570728 4.3:+23576840 None:intergenic
TGATGTTATTGACCTTCGTA+AGG 0.573751 4.3:-23576852 MS.gene052863:CDS
GCGTGAGGATTTCAGTGACA+TGG 0.578706 4.3:-23576192 MS.gene052863:CDS
AGGTCAAAAGACAGATAGAG+TGG 0.585081 4.3:-23576397 MS.gene052863:CDS
ATTCCAGGTATAATGAAGCA+AGG 0.588332 4.3:-23576237 MS.gene052863:intron
TTGACCTTCGTAAGGAGCAG+AGG 0.605333 4.3:-23576844 MS.gene052863:CDS
TTTCAGCACACCGACTGGGG+TGG 0.609891 4.3:-23576882 None:intergenic
TTCCAGGTATAATGAAGCAA+GGG 0.612990 4.3:-23576236 MS.gene052863:intron
CCTTCGTAAGGAGCAGAGGA+AGG 0.617282 4.3:-23576840 MS.gene052863:CDS
GGATGTCACTTTACTGCCAG+AGG 0.626847 4.3:-23576376 MS.gene052863:CDS
AGCAGAGGAAGGAACCTGAA+AGG 0.633570 4.3:-23576829 MS.gene052863:CDS
CAGGTATAATGAAGCAAGGG+AGG 0.633629 4.3:-23576233 MS.gene052863:CDS
TTTCAGTGACATGGTTGCTG+AGG 0.651024 4.3:-23576183 MS.gene052863:CDS
TCAGGTGTCTCCACCCCAGT+CGG 0.652819 4.3:+23576872 None:intergenic
GAAATTACGGAGTCAGCGTG+AGG 0.659191 4.3:-23576207 MS.gene052863:CDS
GGGCACCCAAGACAAGTCAG+GGG 0.712783 4.3:-23576528 MS.gene052863:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTATCATATTTTCTGTTA+AGG - chr4.3:23576298-23576317 MS.gene052863:intron 15.0%
! GTATTGTATCTTGATAAACT+CGG - chr4.3:23576444-23576463 MS.gene052863:intron 25.0%
AATACTTGTGAGGGAAAAAA+AGG + chr4.3:23576429-23576448 None:intergenic 30.0%
ACGATGTTAACATCATTAAC+GGG + chr4.3:23576743-23576762 None:intergenic 30.0%
ATCAAGATACAATACTTGTG+AGG + chr4.3:23576439-23576458 None:intergenic 30.0%
CACGATGTTAACATCATTAA+CGG + chr4.3:23576744-23576763 None:intergenic 30.0%
TATAAAACAGAAGTCATACC+TGG + chr4.3:23576709-23576728 None:intergenic 30.0%
TCAAGATACAATACTTGTGA+GGG + chr4.3:23576438-23576457 None:intergenic 30.0%
! AGTTTCTTGCTCCTTTTTAT+GGG - chr4.3:23576544-23576563 MS.gene052863:CDS 30.0%
! GTTTTTCCTCTTTTTCTTCA+AGG + chr4.3:23576325-23576344 None:intergenic 30.0%
!! TAACGTGTTTTATTGTTTCC+AGG - chr4.3:23576596-23576615 MS.gene052863:intron 30.0%
ACATCTGCTAAAACTATTCC+AGG - chr4.3:23576777-23576796 MS.gene052863:intron 35.0%
ATTCCAGGTATAATGAAGCA+AGG - chr4.3:23576792-23576811 MS.gene052863:intron 35.0%
CGTTATCCCACAAGAAAATA+CGG + chr4.3:23576581-23576600 None:intergenic 35.0%
GAAAGACTCACTTGATAAAG+AGG + chr4.3:23576226-23576245 None:intergenic 35.0%
TAAGGTCCTTGAAGAAAAAG+AGG - chr4.3:23576316-23576335 MS.gene052863:intron 35.0%
TGATGTTATTGACCTTCGTA+AGG - chr4.3:23576177-23576196 MS.gene052863:CDS 35.0%
TTACGAAGGTCAATAACATC+AGG + chr4.3:23576178-23576197 None:intergenic 35.0%
TTCCAGGTATAATGAAGCAA+GGG - chr4.3:23576793-23576812 MS.gene052863:intron 35.0%
! AAATGTGCCGTATTTTCTTG+TGG - chr4.3:23576571-23576590 MS.gene052863:intron 35.0%
! AATGTGCCGTATTTTCTTGT+GGG - chr4.3:23576572-23576591 MS.gene052863:intron 35.0%
! GAGTTTCTTGCTCCTTTTTA+TGG - chr4.3:23576543-23576562 MS.gene052863:CDS 35.0%
! GTTTCTTGCTCCTTTTTATG+GGG - chr4.3:23576545-23576564 MS.gene052863:CDS 35.0%
! TTTCTTGCTCCTTTTTATGG+GGG - chr4.3:23576546-23576565 MS.gene052863:CDS 35.0%
!! TTCCAGGTTGATTTGCTTAA+AGG - chr4.3:23576612-23576631 MS.gene052863:intron 35.0%
ACTTGATAAAGAGGCCTTTC+AGG + chr4.3:23576217-23576236 None:intergenic 40.0%
AGGTCAAAAGACAGATAGAG+TGG - chr4.3:23576632-23576651 MS.gene052863:intron 40.0%
CACATTTACCCCCCATAAAA+AGG + chr4.3:23576558-23576577 None:intergenic 40.0%
CCACATAACTGGAGAGAAAA+TGG + chr4.3:23576474-23576493 None:intergenic 40.0%
GACCTTTAAGCAAATCAACC+TGG + chr4.3:23576617-23576636 None:intergenic 40.0%
TTTCTCTCCAGTTATGTGGT+TGG - chr4.3:23576475-23576494 MS.gene052863:intron 40.0%
! AAAGAGGAAAAACTTGCTCC+TGG - chr4.3:23576332-23576351 MS.gene052863:intron 40.0%
! CCATTTTCTCTCCAGTTATG+TGG - chr4.3:23576471-23576490 MS.gene052863:intron 40.0%
! TGGAGAACGTTTTACATACC+AGG - chr4.3:23576688-23576707 MS.gene052863:CDS 40.0%
! TTCTTGCTCCTTTTTATGGG+GGG - chr4.3:23576547-23576566 MS.gene052863:intron 40.0%
AAGACAAGTCAGGGGCAAAA+AGG - chr4.3:23576509-23576528 MS.gene052863:intron 45.0%
AGACAAGTCAGGGGCAAAAA+GGG - chr4.3:23576510-23576529 MS.gene052863:intron 45.0%
CAGGTATAATGAAGCAAGGG+AGG - chr4.3:23576796-23576815 MS.gene052863:intron 45.0%
CTCCCTTGCTTCATTATACC+TGG + chr4.3:23576798-23576817 None:intergenic 45.0%
GCAAGGGAGGAGAGAAATTA+CGG - chr4.3:23576809-23576828 MS.gene052863:intron 45.0%
GTAGTTCCAAGCAAAGTTCC+AGG + chr4.3:23576353-23576372 None:intergenic 45.0%
TTTCAGTGACATGGTTGCTG+AGG - chr4.3:23576846-23576865 MS.gene052863:CDS 45.0%
!! TTTTGCCCCTGACTTGTCTT+GGG + chr4.3:23576509-23576528 None:intergenic 45.0%
!! TTTTTGCCCCTGACTTGTCT+TGG + chr4.3:23576510-23576529 None:intergenic 45.0%
!!! TATAATTTTTTTATAGTATT+TGG - chr4.3:23576393-23576412 MS.gene052863:CDS 5.0%
AGCAGAGGAAGGAACCTGAA+AGG - chr4.3:23576200-23576219 MS.gene052863:CDS 50.0%
CACTTTACTGCCAGAGGAGT+TGG - chr4.3:23576659-23576678 MS.gene052863:intron 50.0%
CTCCAGTTATGTGGTTGGCA+CGG - chr4.3:23576480-23576499 MS.gene052863:intron 50.0%
CTTGCTCCTGGAACTTTGCT+TGG - chr4.3:23576344-23576363 MS.gene052863:CDS 50.0%
GAAATTACGGAGTCAGCGTG+AGG - chr4.3:23576822-23576841 MS.gene052863:CDS 50.0%
GCGTGAGGATTTCAGTGACA+TGG - chr4.3:23576837-23576856 MS.gene052863:CDS 50.0%
TCCAGTTATGTGGTTGGCAC+GGG - chr4.3:23576481-23576500 MS.gene052863:intron 50.0%
TCCATGACATCCAACTCCTC+TGG + chr4.3:23576672-23576691 None:intergenic 50.0%
TTGACCTTCGTAAGGAGCAG+AGG - chr4.3:23576185-23576204 MS.gene052863:CDS 50.0%
!! GGATGTCACTTTACTGCCAG+AGG - chr4.3:23576653-23576672 MS.gene052863:intron 50.0%
CCTTCCTCTGCTCCTTACGA+AGG + chr4.3:23576192-23576211 None:intergenic 55.0%
CCTTCGTAAGGAGCAGAGGA+AGG - chr4.3:23576189-23576208 MS.gene052863:CDS 55.0%
GCCAGAGGAGTTGGATGTCA+TGG - chr4.3:23576668-23576687 MS.gene052863:intron 55.0%
ACGGGCACCCAAGACAAGTC+AGG - chr4.3:23576499-23576518 MS.gene052863:intron 60.0%
CGGGCACCCAAGACAAGTCA+GGG - chr4.3:23576500-23576519 MS.gene052863:intron 60.0%
GCCCGTGCCAACCACATAAC+TGG + chr4.3:23576485-23576504 None:intergenic 60.0%
GGGCACCCAAGACAAGTCAG+GGG - chr4.3:23576501-23576520 MS.gene052863:intron 60.0%
TCAGGTGTCTCCACCCCAGT+CGG + chr4.3:23576160-23576179 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 23576153 23576898 23576153 ID=MS.gene052863
chr4.3 mRNA 23576153 23576898 23576153 ID=MS.gene052863.t1;Parent=MS.gene052863
chr4.3 exon 23576817 23576898 23576817 ID=MS.gene052863.t1.exon1;Parent=MS.gene052863.t1
chr4.3 CDS 23576817 23576898 23576817 ID=cds.MS.gene052863.t1;Parent=MS.gene052863.t1
chr4.3 exon 23576673 23576731 23576673 ID=MS.gene052863.t1.exon2;Parent=MS.gene052863.t1
chr4.3 CDS 23576673 23576731 23576673 ID=cds.MS.gene052863.t1;Parent=MS.gene052863.t1
chr4.3 exon 23576520 23576565 23576520 ID=MS.gene052863.t1.exon3;Parent=MS.gene052863.t1
chr4.3 CDS 23576520 23576565 23576520 ID=cds.MS.gene052863.t1;Parent=MS.gene052863.t1
chr4.3 exon 23576342 23576433 23576342 ID=MS.gene052863.t1.exon4;Parent=MS.gene052863.t1
chr4.3 CDS 23576342 23576433 23576342 ID=cds.MS.gene052863.t1;Parent=MS.gene052863.t1
chr4.3 exon 23576153 23576252 23576153 ID=MS.gene052863.t1.exon5;Parent=MS.gene052863.t1
chr4.3 CDS 23576153 23576252 23576153 ID=cds.MS.gene052863.t1;Parent=MS.gene052863.t1
Gene Sequence

>MS.gene052863

CACACCGACTGGGGTGGAGACACCTGATGTTATTGACCTTCGTAAGGAGCAGAGGAAGGAACCTGAAAGGCCTCTTTATCAAGTGAGTCTTTCTACTGCTGCTCTTCTATCAGCTTTAGCTTCTCTTGATTAGTCTGTTGATGTCTTTTATCATATTTTCTGTTAAGGTCCTTGAAGAAAAAGAGGAAAAACTTGCTCCTGGAACTTTGCTTGGAACTACACACACGTATGCTAAATTTTTATAATTTTTTTATAGTATTTGGTTTTGTTTTTCCTTTTTTTCCCTCACAAGTATTGTATCTTGATAAACTCGGATATCCATTTTCTCTCCAGTTATGTGGTTGGCACGGGCACCCAAGACAAGTCAGGGGCAAAAAGGGTAAGAATGAAGAGTTTCTTGCTCCTTTTTATGGGGGGTAAATGTGCCGTATTTTCTTGTGGGATAACGTGTTTTATTGTTTCCAGGTTGATTTGCTTAAAGGTCAAAAGACAGATAGAGTGGATGTCACTTTACTGCCAGAGGAGTTGGATGTCATGGAGAACGTTTTACATACCAGGTATGACTTCTGTTTTATATGTTTTGTTTGCCCGTTAATGATGTTAACATCGTGTATCTTGTTTCTTACATCTGCTAAAACTATTCCAGGTATAATGAAGCAAGGGAGGAGAGAAATTACGGAGTCAGCGTGAGGATTTCAGTGACATGGTTGCTGAGGTGTGTTGCATTCAATCCTCAAATCATATAG

Protein sequence

>MS.gene052863.t1

HTDWGGDTUCYUPSUGAEEGTUKASLSSPURKRGKTCSWNFAWNYTHLCGWHGHPRQVRGKKGUFAURSKDRUSGCHFTARGVGCHGERFTYQVUUSKGGEKLRSQREDFSDMVAEVCCIQSSNHI