AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0320460

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0320460 MtrunA17_Chr2g0295651 95.139 144 7 0 1 144 1 144 9.28e-89 254
Msa0320460 MtrunA17_Chr4g0067541 57.627 118 36 4 1 112 1 110 2.19e-31 108
Msa0320460 MtrunA17_Chr3g0115551 45.833 72 37 1 37 106 61 132 5.34e-17 72.8
Msa0320460 MtrunA17_Chr5g0400051 50.000 58 28 1 53 110 74 130 5.00e-14 65.5
Msa0320460 MtrunA17_Chr4g0055191 48.276 58 30 0 53 110 62 119 1.84e-13 63.5
Msa0320460 MtrunA17_Chr8g0344991 42.667 75 40 1 64 135 39 113 2.95e-13 62.4
Msa0320460 MtrunA17_Chr3g0124361 38.554 83 42 2 26 106 91 166 3.21e-13 63.9
Msa0320460 MtrunA17_Chr8g0336591 50.000 54 20 1 51 104 32 78 4.87e-12 58.9
Msa0320460 MtrunA17_Chr3g0138651 50.000 58 28 1 58 114 348 405 3.07e-11 59.7
Msa0320460 MtrunA17_Chr4g0070221 57.778 45 18 1 62 106 176 219 5.36e-11 58.5
Msa0320460 MtrunA17_Chr2g0301141 62.791 43 15 1 64 106 186 227 9.37e-11 57.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0320460 AT5G49120.1 40.789 152 80 4 1 144 1 150 6.39e-30 106
Msa0320460 AT1G22160.1 53.704 54 22 1 53 106 70 120 2.49e-14 66.2
Msa0320460 AT1G78020.1 42.623 61 35 0 64 124 89 149 2.52e-14 66.6
Msa0320460 AT5G47060.2 55.769 52 23 0 53 104 86 137 5.48e-14 65.9
Msa0320460 AT5G47060.1 55.769 52 23 0 53 104 86 137 5.48e-14 65.9
Msa0320460 AT4G39795.1 54.167 48 22 0 62 109 71 118 1.55e-13 63.5
Msa0320460 AT4G17670.1 52.000 50 24 0 55 104 67 116 1.23e-11 59.3
Msa0320460 AT1G74940.1 43.902 82 38 3 62 143 148 221 1.54e-11 60.1
Msa0320460 AT2G44670.1 57.778 45 19 0 60 104 12 56 5.28e-11 56.2
Msa0320460 AT5G65040.1 54.545 44 20 0 64 107 57 100 5.80e-11 56.6

Find 27 sgRNAs with CRISPR-Local

Find 94 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTTCTTATCATCATGAAAA+AGG 0.300416 2_4:+20958541 Msa0320460:CDS
TTAATTAAGCAGGGTAAAAC+TGG 0.323409 2_4:-20958693 None:intergenic
GCTCCATTCTCCAACCTCTT+TGG 0.343871 2_4:+20958798 Msa0320460:three_prime_UTR
TTGGTAATGTAGTGTGGTTT+TGG 0.361553 2_4:+20958817 Msa0320460:three_prime_UTR
TTAATTAATGTTGTTAGATA+AGG 0.409759 2_4:+20958708 Msa0320460:three_prime_UTR
TCTAACAACATTAATTAAGC+AGG 0.429786 2_4:-20958703 None:intergenic
AATGAGCAAAACCACCGGTT+TGG 0.436942 2_4:-20958573 None:intergenic
GGCTAGTAGTTACTAGTGAA+TGG 0.502662 2_4:-20957931 None:intergenic
GTAGTGTTAGAATCTCAAAA+AGG 0.513194 2_4:+20957994 Msa0320460:CDS
ACCTCTTTGGTAATGTAGTG+TGG 0.517027 2_4:+20958811 Msa0320460:three_prime_UTR
ATTGATACATGAATGAAGAA+AGG 0.524095 2_4:+20958593 Msa0320460:exon
GGACGTTTCAGCTTCATACA+AGG 0.529104 2_4:-20958754 None:intergenic
CACTACATTACCAAAGAGGT+TGG 0.538254 2_4:-20958808 None:intergenic
TTTGGTTATTATAATTGACT+TGG 0.543260 2_4:+20958835 Msa0320460:three_prime_UTR
TAGTGAATGGAAAATGTATG+AGG 0.546686 2_4:-20957918 None:intergenic
TTACCAAAGAGGTTGGAGAA+TGG 0.552783 2_4:-20958801 None:intergenic
ATGATGGAAATAAGAACTCA+AGG 0.565409 2_4:-20958115 None:intergenic
TATTAACAATAGCAAGAAGA+AGG 0.566617 2_4:+20958023 Msa0320460:CDS
CCTGAAAATGAGATTCATGA+TGG 0.569541 2_4:-20958131 None:intergenic
AAAGGAAGAAGAAACCAAAC+CGG 0.585292 2_4:+20958559 Msa0320460:CDS
CTAACAACATTAATTAAGCA+GGG 0.589637 2_4:-20958702 None:intergenic
GGATAGAGCTTTCTGTAGTG+TGG 0.592385 2_4:+20958420 Msa0320460:CDS
ACCACACTACATTACCAAAG+AGG 0.594824 2_4:-20958812 None:intergenic
TAGATGCAAGCAAATTGTGA+TGG 0.624999 2_4:+20958447 Msa0320460:CDS
GGAAGAAGAAACCAAACCGG+TGG 0.683708 2_4:+20958562 Msa0320460:CDS
GTATCAATGAGCAAAACCAC+CGG 0.685317 2_4:-20958578 None:intergenic
AAGATGAAGAAATTGCAGCA+TGG 0.688850 2_4:-20958510 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATATAAAGTTTCATAACAT+AGG - chr2_4:20958259-20958278 None:intergenic 15.0%
!! AAAAATAAAAACAAAGATCT+AGG - chr2_4:20958320-20958339 None:intergenic 15.0%
!! ATTGTGAGATAAAAAAAAAA+TGG + chr2_4:20958641-20958660 Msa0320460:three_prime_UTR 15.0%
!! TTAATTAATGTTGTTAGATA+AGG + chr2_4:20958708-20958727 Msa0320460:three_prime_UTR 15.0%
!!! CTTTCTACTTTTTATTTTAT+GGG + chr2_4:20958776-20958795 Msa0320460:three_prime_UTR 15.0%
!! AATATAAAGTTTCATAACAT+AGG - chr2_4:20958259-20958278 None:intergenic 15.0%
!! AAAAATAAAAACAAAGATCT+AGG - chr2_4:20958320-20958339 None:intergenic 15.0%
!! ATTGTGAGATAAAAAAAAAA+TGG + chr2_4:20958641-20958660 Msa0320460:three_prime_UTR 15.0%
!! TTAATTAATGTTGTTAGATA+AGG + chr2_4:20958708-20958727 Msa0320460:three_prime_UTR 15.0%
!!! CTTTCTACTTTTTATTTTAT+GGG + chr2_4:20958776-20958795 Msa0320460:three_prime_UTR 15.0%
!! AAAGTGAGAGAATAAAAAAA+TGG + chr2_4:20957960-20957979 Msa0320460:exon 20.0%
!!! ATTGTTTTGTTAATCACTTT+TGG - chr2_4:20958054-20958073 None:intergenic 20.0%
!!! TGTTTATTTTTTTGTGAAGA+GGG + chr2_4:20958398-20958417 Msa0320460:intron 20.0%
!! CCATAAAATAAAAAGTAGAA+AGG - chr2_4:20958778-20958797 None:intergenic 20.0%
!!! CCTTTCTACTTTTTATTTTA+TGG + chr2_4:20958775-20958794 Msa0320460:three_prime_UTR 20.0%
!! TTTGGTTATTATAATTGACT+TGG + chr2_4:20958835-20958854 Msa0320460:three_prime_UTR 20.0%
!! AAAGTGAGAGAATAAAAAAA+TGG + chr2_4:20957960-20957979 Msa0320460:exon 20.0%
!!! ATTGTTTTGTTAATCACTTT+TGG - chr2_4:20958054-20958073 None:intergenic 20.0%
!!! TGTTTATTTTTTTGTGAAGA+GGG + chr2_4:20958398-20958417 Msa0320460:intron 20.0%
!! CCATAAAATAAAAAGTAGAA+AGG - chr2_4:20958778-20958797 None:intergenic 20.0%
!!! CCTTTCTACTTTTTATTTTA+TGG + chr2_4:20958775-20958794 Msa0320460:three_prime_UTR 20.0%
!! TTTGGTTATTATAATTGACT+TGG + chr2_4:20958835-20958854 Msa0320460:three_prime_UTR 20.0%
!!! TTATTCTCTCACTTTTTTTG+TGG - chr2_4:20957955-20957974 None:intergenic 25.0%
! TGAGAGAATAAAAAAATGGT+GGG + chr2_4:20957964-20957983 Msa0320460:exon 25.0%
! TATTAACAATAGCAAGAAGA+AGG + chr2_4:20958023-20958042 Msa0320460:CDS 25.0%
!!! GTGTTTATTTTTTTGTGAAG+AGG + chr2_4:20958397-20958416 Msa0320460:intron 25.0%
!!! GTTTATTTTTTTGTGAAGAG+GGG + chr2_4:20958399-20958418 Msa0320460:intron 25.0%
! ATTGATACATGAATGAAGAA+AGG + chr2_4:20958593-20958612 Msa0320460:exon 25.0%
! CTAACAACATTAATTAAGCA+GGG - chr2_4:20958705-20958724 None:intergenic 25.0%
! TCTAACAACATTAATTAAGC+AGG - chr2_4:20958706-20958725 None:intergenic 25.0%
!!! TTATTCTCTCACTTTTTTTG+TGG - chr2_4:20957955-20957974 None:intergenic 25.0%
! TGAGAGAATAAAAAAATGGT+GGG + chr2_4:20957964-20957983 Msa0320460:exon 25.0%
! TATTAACAATAGCAAGAAGA+AGG + chr2_4:20958023-20958042 Msa0320460:CDS 25.0%
!!! GTGTTTATTTTTTTGTGAAG+AGG + chr2_4:20958397-20958416 Msa0320460:intron 25.0%
!!! GTTTATTTTTTTGTGAAGAG+GGG + chr2_4:20958399-20958418 Msa0320460:intron 25.0%
! ATTGATACATGAATGAAGAA+AGG + chr2_4:20958593-20958612 Msa0320460:exon 25.0%
! CTAACAACATTAATTAAGCA+GGG - chr2_4:20958705-20958724 None:intergenic 25.0%
! TCTAACAACATTAATTAAGC+AGG - chr2_4:20958706-20958725 None:intergenic 25.0%
TAGTGAATGGAAAATGTATG+AGG - chr2_4:20957921-20957940 None:intergenic 30.0%
GTGAGAGAATAAAAAAATGG+TGG + chr2_4:20957963-20957982 Msa0320460:exon 30.0%
GTAGTGTTAGAATCTCAAAA+AGG + chr2_4:20957994-20958013 Msa0320460:CDS 30.0%
! ATGATGGAAATAAGAACTCA+AGG - chr2_4:20958118-20958137 None:intergenic 30.0%
! TACATATAGATGTCTTTTCC+AGG - chr2_4:20958210-20958229 None:intergenic 30.0%
GCTTCTTATCATCATGAAAA+AGG + chr2_4:20958541-20958560 Msa0320460:CDS 30.0%
TTAATTAAGCAGGGTAAAAC+TGG - chr2_4:20958696-20958715 None:intergenic 30.0%
TAGTGAATGGAAAATGTATG+AGG - chr2_4:20957921-20957940 None:intergenic 30.0%
GTGAGAGAATAAAAAAATGG+TGG + chr2_4:20957963-20957982 Msa0320460:exon 30.0%
GTAGTGTTAGAATCTCAAAA+AGG + chr2_4:20957994-20958013 Msa0320460:CDS 30.0%
! ATGATGGAAATAAGAACTCA+AGG - chr2_4:20958118-20958137 None:intergenic 30.0%
! TACATATAGATGTCTTTTCC+AGG - chr2_4:20958210-20958229 None:intergenic 30.0%
GCTTCTTATCATCATGAAAA+AGG + chr2_4:20958541-20958560 Msa0320460:CDS 30.0%
TTAATTAAGCAGGGTAAAAC+TGG - chr2_4:20958696-20958715 None:intergenic 30.0%
GTGTTAGAATCTCAAAAAGG+TGG + chr2_4:20957997-20958016 Msa0320460:CDS 35.0%
TTAGAATCTCAAAAAGGTGG+TGG + chr2_4:20958000-20958019 Msa0320460:CDS 35.0%
CCTGAAAATGAGATTCATGA+TGG - chr2_4:20958134-20958153 None:intergenic 35.0%
! CCATCATGAATCTCATTTTC+AGG + chr2_4:20958131-20958150 Msa0320460:CDS 35.0%
!!! TTGAGCTTTGTTTTCTCTGT+AGG + chr2_4:20958172-20958191 Msa0320460:CDS 35.0%
TGTAGGAAAAAGTTGTTACC+TGG + chr2_4:20958189-20958208 Msa0320460:CDS 35.0%
TAGATGCAAGCAAATTGTGA+TGG + chr2_4:20958447-20958466 Msa0320460:CDS 35.0%
AAGATGAAGAAATTGCAGCA+TGG - chr2_4:20958513-20958532 None:intergenic 35.0%
AAAGGAAGAAGAAACCAAAC+CGG + chr2_4:20958559-20958578 Msa0320460:CDS 35.0%
!!! TTGGTAATGTAGTGTGGTTT+TGG + chr2_4:20958817-20958836 Msa0320460:three_prime_UTR 35.0%
GTGTTAGAATCTCAAAAAGG+TGG + chr2_4:20957997-20958016 Msa0320460:CDS 35.0%
TTAGAATCTCAAAAAGGTGG+TGG + chr2_4:20958000-20958019 Msa0320460:CDS 35.0%
CCTGAAAATGAGATTCATGA+TGG - chr2_4:20958134-20958153 None:intergenic 35.0%
! CCATCATGAATCTCATTTTC+AGG + chr2_4:20958131-20958150 Msa0320460:CDS 35.0%
!!! TTGAGCTTTGTTTTCTCTGT+AGG + chr2_4:20958172-20958191 Msa0320460:CDS 35.0%
TGTAGGAAAAAGTTGTTACC+TGG + chr2_4:20958189-20958208 Msa0320460:CDS 35.0%
TAGATGCAAGCAAATTGTGA+TGG + chr2_4:20958447-20958466 Msa0320460:CDS 35.0%
AAGATGAAGAAATTGCAGCA+TGG - chr2_4:20958513-20958532 None:intergenic 35.0%
AAAGGAAGAAGAAACCAAAC+CGG + chr2_4:20958559-20958578 Msa0320460:CDS 35.0%
!!! TTGGTAATGTAGTGTGGTTT+TGG + chr2_4:20958817-20958836 Msa0320460:three_prime_UTR 35.0%
GGCTAGTAGTTACTAGTGAA+TGG - chr2_4:20957934-20957953 None:intergenic 40.0%
GTATCAATGAGCAAAACCAC+CGG - chr2_4:20958581-20958600 None:intergenic 40.0%
TTACCAAAGAGGTTGGAGAA+TGG - chr2_4:20958804-20958823 None:intergenic 40.0%
CACTACATTACCAAAGAGGT+TGG - chr2_4:20958811-20958830 None:intergenic 40.0%
!! ACCTCTTTGGTAATGTAGTG+TGG + chr2_4:20958811-20958830 Msa0320460:three_prime_UTR 40.0%
ACCACACTACATTACCAAAG+AGG - chr2_4:20958815-20958834 None:intergenic 40.0%
GGCTAGTAGTTACTAGTGAA+TGG - chr2_4:20957934-20957953 None:intergenic 40.0%
GTATCAATGAGCAAAACCAC+CGG - chr2_4:20958581-20958600 None:intergenic 40.0%
TTACCAAAGAGGTTGGAGAA+TGG - chr2_4:20958804-20958823 None:intergenic 40.0%
CACTACATTACCAAAGAGGT+TGG - chr2_4:20958811-20958830 None:intergenic 40.0%
!! ACCTCTTTGGTAATGTAGTG+TGG + chr2_4:20958811-20958830 Msa0320460:three_prime_UTR 40.0%
ACCACACTACATTACCAAAG+AGG - chr2_4:20958815-20958834 None:intergenic 40.0%
GGATAGAGCTTTCTGTAGTG+TGG + chr2_4:20958420-20958439 Msa0320460:CDS 45.0%
! AATGAGCAAAACCACCGGTT+TGG - chr2_4:20958576-20958595 None:intergenic 45.0%
GGACGTTTCAGCTTCATACA+AGG - chr2_4:20958757-20958776 None:intergenic 45.0%
GGATAGAGCTTTCTGTAGTG+TGG + chr2_4:20958420-20958439 Msa0320460:CDS 45.0%
! AATGAGCAAAACCACCGGTT+TGG - chr2_4:20958576-20958595 None:intergenic 45.0%
GGACGTTTCAGCTTCATACA+AGG - chr2_4:20958757-20958776 None:intergenic 45.0%
GGAAGAAGAAACCAAACCGG+TGG + chr2_4:20958562-20958581 Msa0320460:CDS 50.0%
GCTCCATTCTCCAACCTCTT+TGG + chr2_4:20958798-20958817 Msa0320460:three_prime_UTR 50.0%
GGAAGAAGAAACCAAACCGG+TGG + chr2_4:20958562-20958581 Msa0320460:CDS 50.0%
GCTCCATTCTCCAACCTCTT+TGG + chr2_4:20958798-20958817 Msa0320460:three_prime_UTR 50.0%
Chromosome Type Strat End Strand Name
chr2_4 gene 20957912 20958872 20957912 ID=Msa0320460;Name=Msa0320460
chr2_4 mRNA 20957912 20958872 20957912 ID=Msa0320460-mRNA-1;Parent=Msa0320460;Name=Msa0320460-mRNA-1;_AED=0.01;_eAED=0.01;_QI=67|1|1|1|1|1|2|275|144
chr2_4 exon 20957912 20958232 20957912 ID=Msa0320460-mRNA-1:exon:7659;Parent=Msa0320460-mRNA-1
chr2_4 exon 20958417 20958872 20958417 ID=Msa0320460-mRNA-1:exon:7660;Parent=Msa0320460-mRNA-1
chr2_4 five_prime_UTR 20957912 20957978 20957912 ID=Msa0320460-mRNA-1:five_prime_utr;Parent=Msa0320460-mRNA-1
chr2_4 CDS 20957979 20958232 20957979 ID=Msa0320460-mRNA-1:cds;Parent=Msa0320460-mRNA-1
chr2_4 CDS 20958417 20958597 20958417 ID=Msa0320460-mRNA-1:cds;Parent=Msa0320460-mRNA-1
chr2_4 three_prime_UTR 20958598 20958872 20958598 ID=Msa0320460-mRNA-1:three_prime_utr;Parent=Msa0320460-mRNA-1
Gene Sequence

>Msa0320460

ATGGTGGGTTTGAGTGTAGTGTTAGAATCTCAAAAAGGTGGTGGTATTAACAATAGCAAGAAGAAGGAAACTCCAAAAGTGATTAACAAAACAATGATGCTTAGTAGCAACAACAACAAACAATCTTCTATAGTTTCCTTGAGTTCTTATTTCCATCATGAATCTCATTTTCAGGAACAACAAACAACGTTTCTTGAGCTTTGTTTTCTCTGTAGGAAAAAGTTGTTACCTGGAAAAGACATCTATATGTACAAAGGGGATAGAGCTTTCTGTAGTGTGGAATGTAGATGCAAGCAAATTGTGATGGATGAAGAAGAAAGTAACAATATTCAAAATGAGAACTGTTACCATGCTGCAATTTCTTCATCTTCTTCAGAAGCTTCTTATCATCATGAAAAAGGAAGAAGAAACCAAACCGGTGGTTTTGCTCATTGA
Protein sequence

>Msa0320460

MVGLSVVLESQKGGGINNSKKKETPKVINKTMMLSSNNNKQSSIVSLSSYFHHESHFQEQQTTFLELCFLCRKKLLPGKDIYMYKGDRAFCSVECRCKQIVMDEEESNNIQNENCYHAAISSSSSEASYHHEKGRRNQTGGFAH*