AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0200260


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0200260 MtrunA17_Chr2g0295651 97.222 144 4 0 1 144 1 144 9.05e-103 290
Msa0200260 MtrunA17_Chr4g0067541 58.475 118 35 4 1 112 1 110 1.80e-32 111
Msa0200260 MtrunA17_Chr3g0115551 44.444 72 38 1 37 106 61 132 2.59e-16 71.2
Msa0200260 MtrunA17_Chr5g0400051 48.276 58 29 1 53 110 74 130 3.48e-13 63.2
Msa0200260 MtrunA17_Chr4g0055191 46.552 58 31 0 53 110 62 119 1.05e-12 61.6
Msa0200260 MtrunA17_Chr8g0344991 41.333 75 41 1 64 135 39 113 1.09e-12 60.8
Msa0200260 MtrunA17_Chr3g0124361 37.349 83 43 2 26 106 91 166 3.32e-12 61.2
Msa0200260 MtrunA17_Chr8g0336591 48.148 54 21 1 51 104 32 78 2.53e-11 57.0
Msa0200260 MtrunA17_Chr3g0138651 50.000 58 28 1 58 114 348 405 6.90e-11 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0200260 AT5G49120.1 40.789 152 80 4 1 144 1 150 1.29e-29 105
Msa0200260 AT1G78020.1 40.278 72 40 1 64 135 89 157 1.05e-13 64.7
Msa0200260 AT1G22160.1 51.852 54 23 1 53 106 70 120 1.39e-13 64.3
Msa0200260 AT5G47060.2 53.846 52 24 0 53 104 86 137 3.04e-13 63.9
Msa0200260 AT5G47060.1 53.846 52 24 0 53 104 86 137 3.04e-13 63.9
Msa0200260 AT4G39795.1 52.083 48 23 0 62 109 71 118 7.59e-13 61.6
Msa0200260 AT1G74940.1 42.169 83 40 3 62 144 148 222 4.02e-11 58.9
Msa0200260 AT4G17670.1 50.000 50 25 0 55 104 67 116 6.84e-11 57.4
Msa0200260 AT5G20700.1 55.319 47 20 1 60 106 178 223 8.47e-11 58.5

Find 25 sgRNAs with CRISPR-Local

Find 90 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTTCTTATCATCATGAAAA+AGG 0.300416 2_1:-19996576 Msa0200260:CDS
TTAATTAAGCAGGGTAAAAC+TGG 0.323409 2_1:+19996422 None:intergenic
GCTCCATTCTCCAACCTCTT+TGG 0.343871 2_1:-19996317 Msa0200260:three_prime_UTR
AATAAGCAAAACCACCGTTT+TGG 0.352315 2_1:+19996544 None:intergenic
TTGGTAATGTAGTGTGGCTT+TGG 0.366395 2_1:-19996298 Msa0200260:three_prime_UTR
TTAATTAATGTTGTTAGATA+AGG 0.409759 2_1:-19996407 Msa0200260:three_prime_UTR
TCTAACAACATTAATTAAGC+AGG 0.429786 2_1:+19996412 None:intergenic
GGCTAGTAGTTACTAGTGAA+TGG 0.502662 2_1:+19997260 None:intergenic
GTAGTGTTAGAATCTCAAAA+AGG 0.513194 2_1:-19997197 Msa0200260:CDS
ATTGATACATGAATGAAGAA+AGG 0.524095 2_1:-19996524 Msa0200260:exon
ACCTCTTTGGTAATGTAGTG+TGG 0.535072 2_1:-19996304 Msa0200260:three_prime_UTR
CACTACATTACCAAAGAGGT+TGG 0.538254 2_1:+19996307 None:intergenic
TTTGGTTATTATAATTGACT+TGG 0.540976 2_1:-19996280 Msa0200260:three_prime_UTR
TTACCAAAGAGGTTGGAGAA+TGG 0.552783 2_1:+19996314 None:intergenic
GGACGTTTCAGCTTCATACA+AGG 0.556649 2_1:+19996361 None:intergenic
ATGATGAAAATAAGAACTCA+AGG 0.565409 2_1:+19997076 None:intergenic
TATTAACAATAGCAAGAAGA+AGG 0.566617 2_1:-19997168 Msa0200260:CDS
CTAACAACATTAATTAAGCA+GGG 0.589637 2_1:+19996413 None:intergenic
GGATAGAGCTTTCTGTAGTG+TGG 0.592385 2_1:-19996697 Msa0200260:CDS
GCCACACTACATTACCAAAG+AGG 0.595597 2_1:+19996303 None:intergenic
AGTGAATGGAAAGTGTAATG+AGG 0.611727 2_1:+19997274 None:intergenic
AAAGGAAGAAGAAACCAAAA+CGG 0.628233 2_1:-19996558 Msa0200260:CDS
TAGATGCAAGCATATTGTGA+TGG 0.653765 2_1:-19996670 Msa0200260:CDS
GGAAGAAGAAACCAAAACGG+TGG 0.688263 2_1:-19996555 Msa0200260:CDS
AAGATGAAGAAATTGCAGCA+TGG 0.688850 2_1:+19996607 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAGTGATAGAATAAAAAAA+TGG - chr2_1:19996314-19996333 Msa0200260:three_prime_UTR 15.0%
!! AATATAAAGTTTCATAACAT+AGG + chr2_1:19996613-19996632 None:intergenic 15.0%
!! AAAAATAAAAACAAAGATCT+AGG + chr2_1:19996746-19996765 None:intergenic 15.0%
!! TTAATTAATGTTGTTAGATA+AGG - chr2_1:19997138-19997157 Msa0200260:CDS 15.0%
!! AAAGTGATAGAATAAAAAAA+TGG - chr2_1:19996314-19996333 Msa0200260:three_prime_UTR 15.0%
!! AATATAAAGTTTCATAACAT+AGG + chr2_1:19996613-19996632 None:intergenic 15.0%
!! AAAAATAAAAACAAAGATCT+AGG + chr2_1:19996746-19996765 None:intergenic 15.0%
!! TTAATTAATGTTGTTAGATA+AGG - chr2_1:19997138-19997157 Msa0200260:CDS 15.0%
!!! TTATTCTATCACTTTTTTTG+TGG + chr2_1:19996309-19996328 None:intergenic 20.0%
!! TGATAGAATAAAAAAATGGT+GGG - chr2_1:19996318-19996337 Msa0200260:three_prime_UTR 20.0%
!!! ATTGTTTTGTTAATCACTTT+TGG + chr2_1:19996408-19996427 None:intergenic 20.0%
!!! TGTTTATTTTTTTGTGAAGA+GGG - chr2_1:19996826-19996845 Msa0200260:intron 20.0%
!! TATTGCGAGATAAAAAAAAA+TGG - chr2_1:19997068-19997087 Msa0200260:CDS 20.0%
!!! CTCTCTACTTTTTATTTTAT+GGG - chr2_1:19997206-19997225 Msa0200260:CDS 20.0%
!! TTTGGTTATTATAATTGACT+TGG - chr2_1:19997265-19997284 Msa0200260:five_prime_UTR 20.0%
!!! TTATTCTATCACTTTTTTTG+TGG + chr2_1:19996309-19996328 None:intergenic 20.0%
!! TGATAGAATAAAAAAATGGT+GGG - chr2_1:19996318-19996337 Msa0200260:three_prime_UTR 20.0%
!!! ATTGTTTTGTTAATCACTTT+TGG + chr2_1:19996408-19996427 None:intergenic 20.0%
!!! TGTTTATTTTTTTGTGAAGA+GGG - chr2_1:19996826-19996845 Msa0200260:intron 20.0%
!! TATTGCGAGATAAAAAAAAA+TGG - chr2_1:19997068-19997087 Msa0200260:CDS 20.0%
!!! CTCTCTACTTTTTATTTTAT+GGG - chr2_1:19997206-19997225 Msa0200260:CDS 20.0%
!! TTTGGTTATTATAATTGACT+TGG - chr2_1:19997265-19997284 Msa0200260:five_prime_UTR 20.0%
! GTGATAGAATAAAAAAATGG+TGG - chr2_1:19996317-19996336 Msa0200260:three_prime_UTR 25.0%
! TATTAACAATAGCAAGAAGA+AGG - chr2_1:19996377-19996396 Msa0200260:three_prime_UTR 25.0%
! ATGATGAAAATAAGAACTCA+AGG + chr2_1:19996472-19996491 None:intergenic 25.0%
!!! GTGTTTATTTTTTTGTGAAG+AGG - chr2_1:19996825-19996844 Msa0200260:intron 25.0%
!!! GTTTATTTTTTTGTGAAGAG+GGG - chr2_1:19996827-19996846 Msa0200260:intron 25.0%
! ATTGATACATGAATGAAGAA+AGG - chr2_1:19997021-19997040 Msa0200260:CDS 25.0%
! CTAACAACATTAATTAAGCA+GGG + chr2_1:19997135-19997154 None:intergenic 25.0%
! TCTAACAACATTAATTAAGC+AGG + chr2_1:19997136-19997155 None:intergenic 25.0%
! CCATAAAATAAAAAGTAGAG+AGG + chr2_1:19997208-19997227 None:intergenic 25.0%
!!! CCTCTCTACTTTTTATTTTA+TGG - chr2_1:19997205-19997224 Msa0200260:CDS 25.0%
! GTGATAGAATAAAAAAATGG+TGG - chr2_1:19996317-19996336 Msa0200260:three_prime_UTR 25.0%
! TATTAACAATAGCAAGAAGA+AGG - chr2_1:19996377-19996396 Msa0200260:three_prime_UTR 25.0%
! ATGATGAAAATAAGAACTCA+AGG + chr2_1:19996472-19996491 None:intergenic 25.0%
!!! GTGTTTATTTTTTTGTGAAG+AGG - chr2_1:19996825-19996844 Msa0200260:intron 25.0%
!!! GTTTATTTTTTTGTGAAGAG+GGG - chr2_1:19996827-19996846 Msa0200260:intron 25.0%
! ATTGATACATGAATGAAGAA+AGG - chr2_1:19997021-19997040 Msa0200260:CDS 25.0%
! CTAACAACATTAATTAAGCA+GGG + chr2_1:19997135-19997154 None:intergenic 25.0%
! TCTAACAACATTAATTAAGC+AGG + chr2_1:19997136-19997155 None:intergenic 25.0%
! CCATAAAATAAAAAGTAGAG+AGG + chr2_1:19997208-19997227 None:intergenic 25.0%
!!! CCTCTCTACTTTTTATTTTA+TGG - chr2_1:19997205-19997224 Msa0200260:CDS 25.0%
GTAGTGTTAGAATCTCAAAA+AGG - chr2_1:19996348-19996367 Msa0200260:three_prime_UTR 30.0%
! TCATCATGAATCTCATTTTC+AGG - chr2_1:19996485-19996504 Msa0200260:three_prime_UTR 30.0%
! TACATATAGATGTCTTTTCC+AGG + chr2_1:19996564-19996583 None:intergenic 30.0%
GCTTCTTATCATCATGAAAA+AGG - chr2_1:19996969-19996988 Msa0200260:intron 30.0%
AAAGGAAGAAGAAACCAAAA+CGG - chr2_1:19996987-19997006 Msa0200260:CDS 30.0%
TTAATTAAGCAGGGTAAAAC+TGG + chr2_1:19997126-19997145 None:intergenic 30.0%
GTAGTGTTAGAATCTCAAAA+AGG - chr2_1:19996348-19996367 Msa0200260:three_prime_UTR 30.0%
! TCATCATGAATCTCATTTTC+AGG - chr2_1:19996485-19996504 Msa0200260:three_prime_UTR 30.0%
! TACATATAGATGTCTTTTCC+AGG + chr2_1:19996564-19996583 None:intergenic 30.0%
GCTTCTTATCATCATGAAAA+AGG - chr2_1:19996969-19996988 Msa0200260:intron 30.0%
AAAGGAAGAAGAAACCAAAA+CGG - chr2_1:19996987-19997006 Msa0200260:CDS 30.0%
TTAATTAAGCAGGGTAAAAC+TGG + chr2_1:19997126-19997145 None:intergenic 30.0%
! AGTGAATGGAAAGTGTAATG+AGG + chr2_1:19996274-19996293 None:intergenic 35.0%
GTGTTAGAATCTCAAAAAGG+TGG - chr2_1:19996351-19996370 Msa0200260:three_prime_UTR 35.0%
TTAGAATCTCAAAAAGGTGG+TGG - chr2_1:19996354-19996373 Msa0200260:three_prime_UTR 35.0%
!!! TTGAGCTTTGTTTTCTCTGT+AGG - chr2_1:19996526-19996545 Msa0200260:exon 35.0%
TGTAGGAAAAAGTTGTTACC+TGG - chr2_1:19996543-19996562 Msa0200260:CDS 35.0%
TAGATGCAAGCATATTGTGA+TGG - chr2_1:19996875-19996894 Msa0200260:intron 35.0%
AAGATGAAGAAATTGCAGCA+TGG + chr2_1:19996941-19996960 None:intergenic 35.0%
! AATAAGCAAAACCACCGTTT+TGG + chr2_1:19997004-19997023 None:intergenic 35.0%
! AGTGAATGGAAAGTGTAATG+AGG + chr2_1:19996274-19996293 None:intergenic 35.0%
GTGTTAGAATCTCAAAAAGG+TGG - chr2_1:19996351-19996370 Msa0200260:three_prime_UTR 35.0%
TTAGAATCTCAAAAAGGTGG+TGG - chr2_1:19996354-19996373 Msa0200260:three_prime_UTR 35.0%
!!! TTGAGCTTTGTTTTCTCTGT+AGG - chr2_1:19996526-19996545 Msa0200260:exon 35.0%
TGTAGGAAAAAGTTGTTACC+TGG - chr2_1:19996543-19996562 Msa0200260:CDS 35.0%
TAGATGCAAGCATATTGTGA+TGG - chr2_1:19996875-19996894 Msa0200260:intron 35.0%
AAGATGAAGAAATTGCAGCA+TGG + chr2_1:19996941-19996960 None:intergenic 35.0%
! AATAAGCAAAACCACCGTTT+TGG + chr2_1:19997004-19997023 None:intergenic 35.0%
GGCTAGTAGTTACTAGTGAA+TGG + chr2_1:19996288-19996307 None:intergenic 40.0%
TTACCAAAGAGGTTGGAGAA+TGG + chr2_1:19997234-19997253 None:intergenic 40.0%
CACTACATTACCAAAGAGGT+TGG + chr2_1:19997241-19997260 None:intergenic 40.0%
!! ACCTCTTTGGTAATGTAGTG+TGG - chr2_1:19997241-19997260 Msa0200260:five_prime_UTR 40.0%
!! TTGGTAATGTAGTGTGGCTT+TGG - chr2_1:19997247-19997266 Msa0200260:five_prime_UTR 40.0%
GGCTAGTAGTTACTAGTGAA+TGG + chr2_1:19996288-19996307 None:intergenic 40.0%
TTACCAAAGAGGTTGGAGAA+TGG + chr2_1:19997234-19997253 None:intergenic 40.0%
CACTACATTACCAAAGAGGT+TGG + chr2_1:19997241-19997260 None:intergenic 40.0%
!! ACCTCTTTGGTAATGTAGTG+TGG - chr2_1:19997241-19997260 Msa0200260:five_prime_UTR 40.0%
!! TTGGTAATGTAGTGTGGCTT+TGG - chr2_1:19997247-19997266 Msa0200260:five_prime_UTR 40.0%
GGATAGAGCTTTCTGTAGTG+TGG - chr2_1:19996848-19996867 Msa0200260:intron 45.0%
GGAAGAAGAAACCAAAACGG+TGG - chr2_1:19996990-19997009 Msa0200260:CDS 45.0%
GGACGTTTCAGCTTCATACA+AGG + chr2_1:19997187-19997206 None:intergenic 45.0%
GCCACACTACATTACCAAAG+AGG + chr2_1:19997245-19997264 None:intergenic 45.0%
GGATAGAGCTTTCTGTAGTG+TGG - chr2_1:19996848-19996867 Msa0200260:intron 45.0%
GGAAGAAGAAACCAAAACGG+TGG - chr2_1:19996990-19997009 Msa0200260:CDS 45.0%
GGACGTTTCAGCTTCATACA+AGG + chr2_1:19997187-19997206 None:intergenic 45.0%
GCCACACTACATTACCAAAG+AGG + chr2_1:19997245-19997264 None:intergenic 45.0%
GCTCCATTCTCCAACCTCTT+TGG - chr2_1:19997228-19997247 Msa0200260:exon 50.0%
GCTCCATTCTCCAACCTCTT+TGG - chr2_1:19997228-19997247 Msa0200260:exon 50.0%
Chromosome Type Strat End Strand Name
chr2_1 gene 19996265 19997302 19996265 ID=Msa0200260;Name=Msa0200260
chr2_1 mRNA 19996265 19997302 19996265 ID=Msa0200260-mRNA-1;Parent=Msa0200260;Name=Msa0200260-mRNA-1;_AED=0.01;_eAED=0.01;_QI=68|1|1|1|1|1|2|277|144
chr2_1 exon 19996265 19996722 19996265 ID=Msa0200260-mRNA-1:exon:8333;Parent=Msa0200260-mRNA-1
chr2_1 exon 19996981 19997302 19996981 ID=Msa0200260-mRNA-1:exon:8332;Parent=Msa0200260-mRNA-1
chr2_1 five_prime_UTR 19997235 19997302 19997235 ID=Msa0200260-mRNA-1:five_prime_utr;Parent=Msa0200260-mRNA-1
chr2_1 CDS 19996981 19997234 19996981 ID=Msa0200260-mRNA-1:cds;Parent=Msa0200260-mRNA-1
chr2_1 CDS 19996542 19996722 19996542 ID=Msa0200260-mRNA-1:cds;Parent=Msa0200260-mRNA-1
chr2_1 three_prime_UTR 19996265 19996541 19996265 ID=Msa0200260-mRNA-1:three_prime_utr;Parent=Msa0200260-mRNA-1
Gene Sequence

>Msa0200260

ATGGTGGGTTTGAGTGTAGTGTTAGAATCTCAAAAAGGTGGTGGTATTAACAATAGCAAGAAGAAGGAAACTCCAAAAGTGATTAACAAAACAATGATGCTTAGTAGCAACAACAACAAACAATCTTCTATAGTTTCCTTGAGTTCTTATTTTCATCATGAATCTCATTTTCAGGAACAACAAACAACGTTTCTTGAGCTTTGTTTTCTCTGTAGGAAAAAGTTGTTACCTGGAAAAGACATCTATATGTACAAAGGGGATAGAGCTTTCTGTAGTGTGGAATGTAGATGCAAGCATATTGTGATGGATGAAGAAGAAAGTAACAATATTCAGAATGAGAACTGTTACCATGCTGCAATTTCTTCATCTTCTTCAGAAGCTTCTTATCATCATGAAAAAGGAAGAAGAAACCAAAACGGTGGTTTTGCTTATTGA

Protein sequence

>Msa0200260

MVGLSVVLESQKGGGINNSKKKETPKVINKTMMLSSNNNKQSSIVSLSSYFHHESHFQEQQTTFLELCFLCRKKLLPGKDIYMYKGDRAFCSVECRCKHIVMDEEESNNIQNENCYHAAISSSSSEASYHHEKGRRNQNGGFAY*