AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0580024329.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0580024329.01.T01 MTR_5g009110 92.233 103 5 2 1 101 1 102 3.15e-43 148
MsG0580024329.01.T01 MTR_5g009110 92.233 103 5 2 1 101 1 102 2.27e-42 147
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0580024329.01.T01 AT4G15110 56.098 82 29 2 21 101 34 109 5.39e-23 94.4

Find 38 sgRNAs with CRISPR-Local

Find 55 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGTTAAGCGGCGGAAGTTT+AGG 0.231351 5:-3472156 MsG0580024329.01.T01:CDS
ATTACATTACACTGAATAAA+AGG 0.273336 5:+3472547 None:intergenic
ACTATATGATTGGTTCTTAG+AGG 0.322038 5:-3472073 MsG0580024329.01.T01:intron
TGTTAAGCGGCGGAAGTTTA+GGG 0.323526 5:-3472155 MsG0580024329.01.T01:CDS
CAAGTTTGTTAAAAGATTGC+TGG 0.347825 5:+3472176 None:intergenic
ACGTTCAATAATATCCTCAT+AGG 0.420134 5:+3471580 None:intergenic
AGATACAACGACAAATGCTT+TGG 0.422931 5:+3471521 None:intergenic
AAAGGAAAAGGAAAATGTTA+AGG 0.429638 5:+3472565 None:intergenic
ATTTACCTTGTCATAAGAAA+AGG 0.447689 5:+3471461 None:intergenic
CAGAATATGTCTTGCAACAA+TGG 0.449614 5:+3471494 None:intergenic
GGTGACAGCACCTTCAGCTA+TGG 0.474224 5:+3472125 None:intergenic
AACGCCTTTCTTCTACCATC+AGG 0.483384 5:-3472361 MsG0580024329.01.T01:intron
GCGAGAGGGATGAAGAAATC+TGG 0.484231 5:+3472400 None:intergenic
GATGGTAGAAGAAAGGCGTT+TGG 0.486828 5:+3472364 None:intergenic
AGAATATGTCTTGCAACAAT+GGG 0.502788 5:+3471495 None:intergenic
GATACAACGACAAATGCTTT+GGG 0.505782 5:+3471522 None:intergenic
TTACACTGAATAAAAGGAAA+AGG 0.510728 5:+3472553 None:intergenic
TCTGTGTATAAACTTGCGTT+TGG 0.519155 5:-3471546 MsG0580024329.01.T01:CDS
GAGAGGTCGATCAAACAAAT+CGG 0.535600 5:+3472104 None:intergenic
ATCTCCACCGTCACACTCAC+CGG 0.540695 5:-3472437 MsG0580024329.01.T01:CDS
GTGACAGCACCTTCAGCTAT+GGG 0.549521 5:+3472126 None:intergenic
AAGACCTGATGGTAGAAGAA+AGG 0.558346 5:+3472357 None:intergenic
TTTCCACTAGTATCTTTCAA+CGG 0.569415 5:-3472516 MsG0580024329.01.T01:five_prime_UTR
GGGAATATGCCCATAGCTGA+AGG 0.570938 5:-3472135 MsG0580024329.01.T01:CDS
GTTCCGTTGAAAGATACTAG+TGG 0.581818 5:+3472513 None:intergenic
GGAGATAGCGACGGCAACCA+TGG 0.585840 5:+3472454 None:intergenic
ATAATAATGTAGATGTCAAG+CGG 0.609412 5:-3472253 MsG0580024329.01.T01:intron
TATTATTGAACGTGACAGCA+TGG 0.619127 5:-3471570 MsG0580024329.01.T01:CDS
TCACACTGTCGTCAACGCCA+TGG 0.628094 5:-3472471 MsG0580024329.01.T01:exon
TTAACAAACTTGTTAAGCGG+CGG 0.642481 5:-3472165 MsG0580024329.01.T01:CDS
GAATGAGAAGAAAAGCGAGA+GGG 0.644279 5:+3472386 None:intergenic
GGCGTTGACGACAGTGTGAG+TGG 0.646147 5:+3472475 None:intergenic
GGAATGAGAAGAAAAGCGAG+AGG 0.652809 5:+3472385 None:intergenic
TCTGGTGTGAAGATTTGCAC+CGG 0.661413 5:+3472418 None:intergenic
ATTTGCACCGGTGAGTGTGA+CGG 0.682239 5:+3472430 None:intergenic
TGCACCGGTGAGTGTGACGG+TGG 0.696349 5:+3472433 None:intergenic
TGTGACGGTGGAGATAGCGA+CGG 0.719430 5:+3472445 None:intergenic
GTTGACGACAGTGTGAGTGG+TGG 0.731713 5:+3472478 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTATTAAAATAAGCTAAAAC+AGG + Chr5:3472104-3472123 None:intergenic 15.0%
!! ATTACATTACACTGAATAAA+AGG + Chr5:3471501-3471520 None:intergenic 20.0%
!! ATTCAAAATCCAAATGAAAA+AGG + Chr5:3472005-3472024 None:intergenic 20.0%
!!! TATAATAACATTTTCCCTTT+TGG + Chr5:3472328-3472347 None:intergenic 20.0%
! AAAGGAAAAGGAAAATGTTA+AGG + Chr5:3471483-3471502 None:intergenic 25.0%
! ATAATAATGTAGATGTCAAG+CGG - Chr5:3471792-3471811 MsG0580024329.01.T01:intron 25.0%
! TTACACTGAATAAAAGGAAA+AGG + Chr5:3471495-3471514 None:intergenic 25.0%
!! GGATTTTGAATTTCAACTTA+CGG - Chr5:3472014-3472033 MsG0580024329.01.T01:intron 25.0%
!! TCTTTTTCTCACTATATGAT+TGG - Chr5:3471962-3471981 MsG0580024329.01.T01:intron 25.0%
!!! AACTAAACTGTTTTTCCAAA+AGG - Chr5:3472310-3472329 MsG0580024329.01.T01:intron 25.0%
!!! ACTAAACTGTTTTTCCAAAA+GGG - Chr5:3472311-3472330 MsG0580024329.01.T01:intron 25.0%
!!! CTTTTAACAAACTTGTTAAG+CGG - Chr5:3471877-3471896 MsG0580024329.01.T01:intron 25.0%
ACGTTCAATAATATCCTCAT+AGG + Chr5:3472468-3472487 None:intergenic 30.0%
AGAATATGTCTTGCAACAAT+GGG + Chr5:3472553-3472572 None:intergenic 30.0%
TCATATAGTGAGAAAAAGAG+AGG + Chr5:3471961-3471980 None:intergenic 30.0%
TTGTGTTCATAAGCTCTATT+TGG + Chr5:3472243-3472262 None:intergenic 30.0%
TTTCCACTAGTATCTTTCAA+CGG - Chr5:3471529-3471548 MsG0580024329.01.T01:CDS 30.0%
! AAATGCCTTTTCTTATGACA+AGG - Chr5:3472579-3472598 MsG0580024329.01.T01:five_prime_UTR 30.0%
! ACTATATGATTGGTTCTTAG+AGG - Chr5:3471972-3471991 MsG0580024329.01.T01:intron 30.0%
! GTTTTCTTACATTGTCGAAT+TGG - Chr5:3472375-3472394 MsG0580024329.01.T01:CDS 30.0%
!! CAAGTTTGTTAAAAGATTGC+TGG + Chr5:3471872-3471891 None:intergenic 30.0%
!! TCACTTTTAGTTATCCTATG+AGG - Chr5:3472451-3472470 MsG0580024329.01.T01:CDS 30.0%
AGATACAACGACAAATGCTT+TGG + Chr5:3472527-3472546 None:intergenic 35.0%
ATTTCAACTTACGGTCTGTT+TGG - Chr5:3472023-3472042 MsG0580024329.01.T01:intron 35.0%
CAGAATATGTCTTGCAACAA+TGG + Chr5:3472554-3472573 None:intergenic 35.0%
GATACAACGACAAATGCTTT+GGG + Chr5:3472526-3472545 None:intergenic 35.0%
TATTATTGAACGTGACAGCA+TGG - Chr5:3472475-3472494 MsG0580024329.01.T01:five_prime_UTR 35.0%
TCTGTGTATAAACTTGCGTT+TGG - Chr5:3472499-3472518 MsG0580024329.01.T01:five_prime_UTR 35.0%
TGCAGCTTATAGCATAATTG+TGG + Chr5:3472205-3472224 None:intergenic 35.0%
TTAACCAGAAAAAGACCTGA+TGG + Chr5:3471702-3471721 None:intergenic 35.0%
!! GGTATTCGACCTTTTTCATT+TGG - Chr5:3471993-3472012 MsG0580024329.01.T01:intron 35.0%
!! TTAACAAACTTGTTAAGCGG+CGG - Chr5:3471880-3471899 MsG0580024329.01.T01:intron 35.0%
AAGACCTGATGGTAGAAGAA+AGG + Chr5:3471691-3471710 None:intergenic 40.0%
GAATGAGAAGAAAAGCGAGA+GGG + Chr5:3471662-3471681 None:intergenic 40.0%
GAGAGGTCGATCAAACAAAT+CGG + Chr5:3471944-3471963 None:intergenic 40.0%
GTTCCGTTGAAAGATACTAG+TGG + Chr5:3471535-3471554 None:intergenic 40.0%
! TCTACCATCAGGTCTTTTTC+TGG - Chr5:3471695-3471714 MsG0580024329.01.T01:intron 40.0%
AACGCCTTTCTTCTACCATC+AGG - Chr5:3471684-3471703 MsG0580024329.01.T01:intron 45.0%
GGAATGAGAAGAAAAGCGAG+AGG + Chr5:3471663-3471682 None:intergenic 45.0%
TCTGGTGTGAAGATTTGCAC+CGG + Chr5:3471630-3471649 None:intergenic 45.0%
TGTTAAGCGGCGGAAGTTTA+GGG - Chr5:3471890-3471909 MsG0580024329.01.T01:intron 45.0%
TTGTTAAGCGGCGGAAGTTT+AGG - Chr5:3471889-3471908 MsG0580024329.01.T01:intron 45.0%
!! GATGGTAGAAGAAAGGCGTT+TGG + Chr5:3471684-3471703 None:intergenic 45.0%
GCGAGAGGGATGAAGAAATC+TGG + Chr5:3471648-3471667 None:intergenic 50.0%
GGGAATATGCCCATAGCTGA+AGG - Chr5:3471910-3471929 MsG0580024329.01.T01:intron 50.0%
GTGACAGCACCTTCAGCTAT+GGG + Chr5:3471922-3471941 None:intergenic 50.0%
! ATTTGCACCGGTGAGTGTGA+CGG + Chr5:3471618-3471637 None:intergenic 50.0%
ATCTCCACCGTCACACTCAC+CGG - Chr5:3471608-3471627 MsG0580024329.01.T01:intron 55.0%
GGTGACAGCACCTTCAGCTA+TGG + Chr5:3471923-3471942 None:intergenic 55.0%
GTTGACGACAGTGTGAGTGG+TGG + Chr5:3471570-3471589 None:intergenic 55.0%
TCACACTGTCGTCAACGCCA+TGG - Chr5:3471574-3471593 MsG0580024329.01.T01:CDS 55.0%
TGTGACGGTGGAGATAGCGA+CGG + Chr5:3471603-3471622 None:intergenic 55.0%
GGAGATAGCGACGGCAACCA+TGG + Chr5:3471594-3471613 None:intergenic 60.0%
!! GGCGTTGACGACAGTGTGAG+TGG + Chr5:3471573-3471592 None:intergenic 60.0%
! TGCACCGGTGAGTGTGACGG+TGG + Chr5:3471615-3471634 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
Chr5 gene 3471463 3472604 3471463 ID=MsG0580024329.01;Name=MsG0580024329.01
Chr5 mRNA 3471463 3472604 3471463 ID=MsG0580024329.01.T01;Parent=MsG0580024329.01;Name=MsG0580024329.01.T01;_AED=0.48;_eAED=0.61;_QI=130|0.5|0.66|1|0|0|3|0|148
Chr5 exon 3471463 3471606 3471463 ID=MsG0580024329.01.T01:exon:1128;Parent=MsG0580024329.01.T01
Chr5 exon 3472074 3472263 3472074 ID=MsG0580024329.01.T01:exon:1127;Parent=MsG0580024329.01.T01
Chr5 exon 3472362 3472604 3472362 ID=MsG0580024329.01.T01:exon:1126;Parent=MsG0580024329.01.T01
Chr5 five_prime_UTR 3472475 3472604 3472475 ID=MsG0580024329.01.T01:five_prime_utr;Parent=MsG0580024329.01.T01
Chr5 CDS 3472362 3472474 3472362 ID=MsG0580024329.01.T01:cds;Parent=MsG0580024329.01.T01
Chr5 CDS 3472074 3472263 3472074 ID=MsG0580024329.01.T01:cds;Parent=MsG0580024329.01.T01
Chr5 CDS 3471463 3471606 3471463 ID=MsG0580024329.01.T01:cds;Parent=MsG0580024329.01.T01
Gene Sequence

>MsG0580024329.01.T01

ATGGTTGCCGTCGCTATCTCCACCGTCACACTCACCGGTGCAAATCTTCACACCAGATTTCTTCATCCCTCTCGCTTTTCTTCTCATTCCAAACGCCTTTCTTCTACCATCAGATGTCAAGCGGTTAACAGTGATAAGAAGAAACAAAGTAGCAGTAGTCGAAATGTGTTTGACAACGCCAGCAATCTTTTAACAAACTTGTTAAGCGGCGGAAGTTTAGGGAATATGCCCATAGCTGAAGGTGCTGTCACCGATTTGTTTGATCGACCTCTCTTTTTCTCACTATATGATTGGTTCTTAGAGTTATCCTATGAGGATATTATTGAACGTGACAGCATGGCTCTGTGTATAAACTTGCGTTTGGTCCCAAAGCATTTGTCGTTGTATCTGATCCCATTGTTGCAAGACATATTCTGCGAGAAAATGCCTTTTCTTATGACAAGGTAA

Protein sequence

>MsG0580024329.01.T01

MVAVAISTVTLTGANLHTRFLHPSRFSSHSKRLSSTIRCQAVNSDKKKQSSSSRNVFDNASNLLTNLLSGGSLGNMPIAEGAVTDLFDRPLFFSLYDWFLELSYEDIIERDSMALCINLRLVPKHLSLYLIPLLQDIFCEKMPFLMTR*