AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0140780


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0140780 MtrunA17_Chr2g0295651 97.222 144 4 0 1 144 1 144 2.25e-102 289
Msa0140780 MtrunA17_Chr4g0067541 56.780 118 37 4 1 112 1 110 2.09e-31 108
Msa0140780 MtrunA17_Chr3g0115551 45.833 72 37 1 37 106 61 132 5.46e-17 72.8
Msa0140780 MtrunA17_Chr5g0400051 50.000 58 28 1 53 110 74 130 5.22e-14 65.5
Msa0140780 MtrunA17_Chr4g0055191 48.276 58 30 0 53 110 62 119 1.73e-13 63.9
Msa0140780 MtrunA17_Chr8g0344991 42.667 75 40 1 64 135 39 113 3.21e-13 62.4
Msa0140780 MtrunA17_Chr3g0124361 38.554 83 42 2 26 106 91 166 3.35e-13 63.9
Msa0140780 MtrunA17_Chr8g0336591 50.000 54 20 1 51 104 32 78 5.36e-12 58.9
Msa0140780 MtrunA17_Chr3g0138651 50.000 58 28 1 58 114 348 405 3.44e-11 59.7
Msa0140780 MtrunA17_Chr4g0070221 57.778 45 18 1 62 106 176 219 5.42e-11 58.5
Msa0140780 MtrunA17_Chr2g0301141 62.791 43 15 1 64 106 186 227 8.74e-11 58.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0140780 AT5G49120.1 40.789 152 80 4 1 144 1 150 2.54e-30 107
Msa0140780 AT1G22160.1 53.704 54 22 1 53 106 70 120 2.77e-14 65.9
Msa0140780 AT1G78020.1 42.623 61 35 0 64 124 89 149 3.07e-14 66.2
Msa0140780 AT5G47060.2 55.769 52 23 0 53 104 86 137 4.94e-14 65.9
Msa0140780 AT5G47060.1 55.769 52 23 0 53 104 86 137 4.94e-14 65.9
Msa0140780 AT4G39795.1 54.167 48 22 0 62 109 71 118 1.55e-13 63.5
Msa0140780 AT1G74940.1 43.373 83 39 3 62 144 148 222 1.07e-11 60.5
Msa0140780 AT4G17670.1 52.000 50 24 0 55 104 67 116 1.17e-11 59.3
Msa0140780 AT2G44670.1 57.778 45 19 0 60 104 12 56 4.75e-11 56.2
Msa0140780 AT5G65040.1 54.545 44 20 0 64 107 57 100 5.86e-11 56.6

Find 25 sgRNAs with CRISPR-Local

Find 92 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTTCTTATCATCATGAAAA+AGG 0.300416 1_3:-75096306 Msa0140780:CDS
TTAATTAAGCAGGGTAAAAC+TGG 0.323409 1_3:+75096152 None:intergenic
GCTCCATTCTCCAACCTCTT+TGG 0.343871 1_3:-75096047 Msa0140780:three_prime_UTR
AATAAGCAAAACCACCGTTT+TGG 0.352315 1_3:+75096274 None:intergenic
TTGGTAATGTAGTGTGGTTT+TGG 0.361553 1_3:-75096028 Msa0140780:three_prime_UTR
TTAATTAATGTTGTTAGATA+AGG 0.409759 1_3:-75096137 Msa0140780:three_prime_UTR
TCTAACAACATTAATTAAGC+AGG 0.429786 1_3:+75096142 None:intergenic
GGCTAGTAGTTACTAGTGAA+TGG 0.502662 1_3:+75096902 None:intergenic
GTAGTGTTAGAATCTCAAAA+AGG 0.513194 1_3:-75096839 Msa0140780:CDS
ACCTCTTTGGTAATGTAGTG+TGG 0.517027 1_3:-75096034 Msa0140780:three_prime_UTR
TAGTGAATGGAAAGTGTATG+AGG 0.523850 1_3:+75096915 None:intergenic
ATTGATACATGAATGAAGAA+AGG 0.524095 1_3:-75096254 Msa0140780:exon
GGACGTTTCAGCTTCATACA+AGG 0.529104 1_3:+75096091 None:intergenic
CACTACATTACCAAAGAGGT+TGG 0.538254 1_3:+75096037 None:intergenic
TTTGGTTATTATAATTGACT+TGG 0.543260 1_3:-75096010 Msa0140780:three_prime_UTR
TTACCAAAGAGGTTGGAGAA+TGG 0.552783 1_3:+75096044 None:intergenic
ATGATGAAAATAAGAACTCA+AGG 0.565409 1_3:+75096718 None:intergenic
TATTAGCAATAGCAAGAAGA+AGG 0.566617 1_3:-75096810 Msa0140780:CDS
CTAACAACATTAATTAAGCA+GGG 0.589637 1_3:+75096143 None:intergenic
GGATAGAGCTTTCTGTAGTG+TGG 0.592385 1_3:-75096427 Msa0140780:CDS
ACCACACTACATTACCAAAG+AGG 0.594824 1_3:+75096033 None:intergenic
TAGATGCAAGCAAATTGTGA+TGG 0.624999 1_3:-75096400 Msa0140780:CDS
AAAGGAAGAAGAAACCAAAA+CGG 0.628233 1_3:-75096288 Msa0140780:CDS
GGAAGAAGAAACCAAAACGG+TGG 0.688263 1_3:-75096285 Msa0140780:CDS
AAGATGAAGAAATTGCAGCA+TGG 0.688850 1_3:+75096337 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAGTGATAGAATAAAAAAA+TGG - chr1_3:75096043-75096062 Msa0140780:three_prime_UTR 15.0%
!! AATATAAAGTTTCATAACAT+AGG + chr1_3:75096342-75096361 None:intergenic 15.0%
!! AAAAATAAAAACAAAGATCT+AGG + chr1_3:75096388-75096407 None:intergenic 15.0%
!! ATTGTGAGATAAAAAAAAAA+TGG - chr1_3:75096710-75096729 Msa0140780:CDS 15.0%
!! TTAATTAATGTTGTTAGATA+AGG - chr1_3:75096779-75096798 Msa0140780:CDS 15.0%
!!! CTTTCTACTTTTTATTTTAT+GGG - chr1_3:75096847-75096866 Msa0140780:CDS 15.0%
!! AAAGTGATAGAATAAAAAAA+TGG - chr1_3:75096043-75096062 Msa0140780:three_prime_UTR 15.0%
!! AATATAAAGTTTCATAACAT+AGG + chr1_3:75096342-75096361 None:intergenic 15.0%
!! AAAAATAAAAACAAAGATCT+AGG + chr1_3:75096388-75096407 None:intergenic 15.0%
!! ATTGTGAGATAAAAAAAAAA+TGG - chr1_3:75096710-75096729 Msa0140780:CDS 15.0%
!! TTAATTAATGTTGTTAGATA+AGG - chr1_3:75096779-75096798 Msa0140780:CDS 15.0%
!!! CTTTCTACTTTTTATTTTAT+GGG - chr1_3:75096847-75096866 Msa0140780:CDS 15.0%
!!! TTATTCTATCACTTTTTTTG+TGG + chr1_3:75096038-75096057 None:intergenic 20.0%
!! TGATAGAATAAAAAAATGGT+GGG - chr1_3:75096047-75096066 Msa0140780:three_prime_UTR 20.0%
!!! ATTGTTTTGTTAATCACTTT+TGG + chr1_3:75096137-75096156 None:intergenic 20.0%
!! CATAGGTTATAAAATATAGA+AGG + chr1_3:75096325-75096344 None:intergenic 20.0%
!!! TGTTTATTTTTTTGTGAAGA+GGG - chr1_3:75096467-75096486 Msa0140780:intron 20.0%
!! CCATAAAATAAAAAGTAGAA+AGG + chr1_3:75096849-75096868 None:intergenic 20.0%
!!! CCTTTCTACTTTTTATTTTA+TGG - chr1_3:75096846-75096865 Msa0140780:CDS 20.0%
!! TTTGGTTATTATAATTGACT+TGG - chr1_3:75096906-75096925 Msa0140780:five_prime_UTR 20.0%
!!! TTATTCTATCACTTTTTTTG+TGG + chr1_3:75096038-75096057 None:intergenic 20.0%
!! TGATAGAATAAAAAAATGGT+GGG - chr1_3:75096047-75096066 Msa0140780:three_prime_UTR 20.0%
!!! ATTGTTTTGTTAATCACTTT+TGG + chr1_3:75096137-75096156 None:intergenic 20.0%
!! CATAGGTTATAAAATATAGA+AGG + chr1_3:75096325-75096344 None:intergenic 20.0%
!!! TGTTTATTTTTTTGTGAAGA+GGG - chr1_3:75096467-75096486 Msa0140780:intron 20.0%
!! CCATAAAATAAAAAGTAGAA+AGG + chr1_3:75096849-75096868 None:intergenic 20.0%
!!! CCTTTCTACTTTTTATTTTA+TGG - chr1_3:75096846-75096865 Msa0140780:CDS 20.0%
!! TTTGGTTATTATAATTGACT+TGG - chr1_3:75096906-75096925 Msa0140780:five_prime_UTR 20.0%
! GTGATAGAATAAAAAAATGG+TGG - chr1_3:75096046-75096065 Msa0140780:three_prime_UTR 25.0%
! ATGATGAAAATAAGAACTCA+AGG + chr1_3:75096201-75096220 None:intergenic 25.0%
!!! GTGTTTATTTTTTTGTGAAG+AGG - chr1_3:75096466-75096485 Msa0140780:intron 25.0%
!!! GTTTATTTTTTTGTGAAGAG+GGG - chr1_3:75096468-75096487 Msa0140780:intron 25.0%
! ATTGATACATGAATGAAGAA+AGG - chr1_3:75096662-75096681 Msa0140780:CDS 25.0%
! CTAACAACATTAATTAAGCA+GGG + chr1_3:75096776-75096795 None:intergenic 25.0%
! TCTAACAACATTAATTAAGC+AGG + chr1_3:75096777-75096796 None:intergenic 25.0%
! GTGATAGAATAAAAAAATGG+TGG - chr1_3:75096046-75096065 Msa0140780:three_prime_UTR 25.0%
! ATGATGAAAATAAGAACTCA+AGG + chr1_3:75096201-75096220 None:intergenic 25.0%
!!! GTGTTTATTTTTTTGTGAAG+AGG - chr1_3:75096466-75096485 Msa0140780:intron 25.0%
!!! GTTTATTTTTTTGTGAAGAG+GGG - chr1_3:75096468-75096487 Msa0140780:intron 25.0%
! ATTGATACATGAATGAAGAA+AGG - chr1_3:75096662-75096681 Msa0140780:CDS 25.0%
! CTAACAACATTAATTAAGCA+GGG + chr1_3:75096776-75096795 None:intergenic 25.0%
! TCTAACAACATTAATTAAGC+AGG + chr1_3:75096777-75096796 None:intergenic 25.0%
GTAGTGTTAGAATCTCAAAA+AGG - chr1_3:75096077-75096096 Msa0140780:three_prime_UTR 30.0%
TATTAGCAATAGCAAGAAGA+AGG - chr1_3:75096106-75096125 Msa0140780:three_prime_UTR 30.0%
! TCATCATGAATCTCATTTTC+AGG - chr1_3:75096214-75096233 Msa0140780:three_prime_UTR 30.0%
GCTTCTTATCATCATGAAAA+AGG - chr1_3:75096610-75096629 Msa0140780:intron 30.0%
AAAGGAAGAAGAAACCAAAA+CGG - chr1_3:75096628-75096647 Msa0140780:CDS 30.0%
TTAATTAAGCAGGGTAAAAC+TGG + chr1_3:75096767-75096786 None:intergenic 30.0%
GTAGTGTTAGAATCTCAAAA+AGG - chr1_3:75096077-75096096 Msa0140780:three_prime_UTR 30.0%
TATTAGCAATAGCAAGAAGA+AGG - chr1_3:75096106-75096125 Msa0140780:three_prime_UTR 30.0%
! TCATCATGAATCTCATTTTC+AGG - chr1_3:75096214-75096233 Msa0140780:three_prime_UTR 30.0%
GCTTCTTATCATCATGAAAA+AGG - chr1_3:75096610-75096629 Msa0140780:intron 30.0%
AAAGGAAGAAGAAACCAAAA+CGG - chr1_3:75096628-75096647 Msa0140780:CDS 30.0%
TTAATTAAGCAGGGTAAAAC+TGG + chr1_3:75096767-75096786 None:intergenic 30.0%
! TAGTGAATGGAAAGTGTATG+AGG + chr1_3:75096004-75096023 None:intergenic 35.0%
GTGTTAGAATCTCAAAAAGG+TGG - chr1_3:75096080-75096099 Msa0140780:three_prime_UTR 35.0%
TTAGAATCTCAAAAAGGTGG+TGG - chr1_3:75096083-75096102 Msa0140780:three_prime_UTR 35.0%
!!! TTGAGCTTTGTTTTCTCTGT+AGG - chr1_3:75096255-75096274 Msa0140780:exon 35.0%
TGTAGGAAAAAGTTGTTACC+TGG - chr1_3:75096272-75096291 Msa0140780:CDS 35.0%
! TACATGTAGATGTCTTTTCC+AGG + chr1_3:75096293-75096312 None:intergenic 35.0%
TAGATGCAAGCAAATTGTGA+TGG - chr1_3:75096516-75096535 Msa0140780:intron 35.0%
AAGATGAAGAAATTGCAGCA+TGG + chr1_3:75096582-75096601 None:intergenic 35.0%
! AATAAGCAAAACCACCGTTT+TGG + chr1_3:75096645-75096664 None:intergenic 35.0%
!!! TTGGTAATGTAGTGTGGTTT+TGG - chr1_3:75096888-75096907 Msa0140780:five_prime_UTR 35.0%
! TAGTGAATGGAAAGTGTATG+AGG + chr1_3:75096004-75096023 None:intergenic 35.0%
GTGTTAGAATCTCAAAAAGG+TGG - chr1_3:75096080-75096099 Msa0140780:three_prime_UTR 35.0%
TTAGAATCTCAAAAAGGTGG+TGG - chr1_3:75096083-75096102 Msa0140780:three_prime_UTR 35.0%
!!! TTGAGCTTTGTTTTCTCTGT+AGG - chr1_3:75096255-75096274 Msa0140780:exon 35.0%
TGTAGGAAAAAGTTGTTACC+TGG - chr1_3:75096272-75096291 Msa0140780:CDS 35.0%
! TACATGTAGATGTCTTTTCC+AGG + chr1_3:75096293-75096312 None:intergenic 35.0%
TAGATGCAAGCAAATTGTGA+TGG - chr1_3:75096516-75096535 Msa0140780:intron 35.0%
AAGATGAAGAAATTGCAGCA+TGG + chr1_3:75096582-75096601 None:intergenic 35.0%
! AATAAGCAAAACCACCGTTT+TGG + chr1_3:75096645-75096664 None:intergenic 35.0%
!!! TTGGTAATGTAGTGTGGTTT+TGG - chr1_3:75096888-75096907 Msa0140780:five_prime_UTR 35.0%
GGCTAGTAGTTACTAGTGAA+TGG + chr1_3:75096017-75096036 None:intergenic 40.0%
TTACCAAAGAGGTTGGAGAA+TGG + chr1_3:75096875-75096894 None:intergenic 40.0%
CACTACATTACCAAAGAGGT+TGG + chr1_3:75096882-75096901 None:intergenic 40.0%
!! ACCTCTTTGGTAATGTAGTG+TGG - chr1_3:75096882-75096901 Msa0140780:five_prime_UTR 40.0%
ACCACACTACATTACCAAAG+AGG + chr1_3:75096886-75096905 None:intergenic 40.0%
GGCTAGTAGTTACTAGTGAA+TGG + chr1_3:75096017-75096036 None:intergenic 40.0%
TTACCAAAGAGGTTGGAGAA+TGG + chr1_3:75096875-75096894 None:intergenic 40.0%
CACTACATTACCAAAGAGGT+TGG + chr1_3:75096882-75096901 None:intergenic 40.0%
!! ACCTCTTTGGTAATGTAGTG+TGG - chr1_3:75096882-75096901 Msa0140780:five_prime_UTR 40.0%
ACCACACTACATTACCAAAG+AGG + chr1_3:75096886-75096905 None:intergenic 40.0%
GGATAGAGCTTTCTGTAGTG+TGG - chr1_3:75096489-75096508 Msa0140780:intron 45.0%
GGAAGAAGAAACCAAAACGG+TGG - chr1_3:75096631-75096650 Msa0140780:CDS 45.0%
GGACGTTTCAGCTTCATACA+AGG + chr1_3:75096828-75096847 None:intergenic 45.0%
GGATAGAGCTTTCTGTAGTG+TGG - chr1_3:75096489-75096508 Msa0140780:intron 45.0%
GGAAGAAGAAACCAAAACGG+TGG - chr1_3:75096631-75096650 Msa0140780:CDS 45.0%
GGACGTTTCAGCTTCATACA+AGG + chr1_3:75096828-75096847 None:intergenic 45.0%
GCTCCATTCTCCAACCTCTT+TGG - chr1_3:75096869-75096888 Msa0140780:exon 50.0%
GCTCCATTCTCCAACCTCTT+TGG - chr1_3:75096869-75096888 Msa0140780:exon 50.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 75095995 75096943 75095995 ID=Msa0140780;Name=Msa0140780
chr1_3 mRNA 75095995 75096943 75095995 ID=Msa0140780-mRNA-1;Parent=Msa0140780;Name=Msa0140780-mRNA-1;_AED=0.01;_eAED=0.01;_QI=67|1|1|1|1|1|2|277|144
chr1_3 exon 75095995 75096452 75095995 ID=Msa0140780-mRNA-1:exon:26290;Parent=Msa0140780-mRNA-1
chr1_3 exon 75096623 75096943 75096623 ID=Msa0140780-mRNA-1:exon:26289;Parent=Msa0140780-mRNA-1
chr1_3 five_prime_UTR 75096877 75096943 75096877 ID=Msa0140780-mRNA-1:five_prime_utr;Parent=Msa0140780-mRNA-1
chr1_3 CDS 75096623 75096876 75096623 ID=Msa0140780-mRNA-1:cds;Parent=Msa0140780-mRNA-1
chr1_3 CDS 75096272 75096452 75096272 ID=Msa0140780-mRNA-1:cds;Parent=Msa0140780-mRNA-1
chr1_3 three_prime_UTR 75095995 75096271 75095995 ID=Msa0140780-mRNA-1:three_prime_utr;Parent=Msa0140780-mRNA-1
Gene Sequence

>Msa0140780

ATGGTGGGTTTGAGTGTAGTGTTAGAATCTCAAAAAGGTGGTGGTATTAGCAATAGCAAGAAGAAGGAAACTCCAAAAGTGATTAACAAAACAATGATGCTTAGTAGCAACAACAACAAACAATCTTCTATAGTTTCCTTGAGTTCTTATTTTCATCATGAATCTCATTTTCAGGAACAACAAACAACGTTTCTTGAGCTTTGTTTTCTCTGTAGGAAAAAGTTGTTACCTGGAAAAGACATCTACATGTACAAAGGGGATAGAGCTTTCTGTAGTGTGGAATGTAGATGCAAGCAAATTGTGATGGATGAAGAAGAAAGTAACAATATTCAGAATGAGAACTGTTACCATGCTGCAATTTCTTCATCTTCTTCAGAAGCTTCTTATCATCATGAAAAAGGAAGAAGAAACCAAAACGGTGGTTTTGCTTATTGA

Protein sequence

>Msa0140780

MVGLSVVLESQKGGGISNSKKKETPKVINKTMMLSSNNNKQSSIVSLSSYFHHESHFQEQQTTFLELCFLCRKKLLPGKDIYMYKGDRAFCSVECRCKQIVMDEEESNNIQNENCYHAAISSSSSEASYHHEKGRRNQNGGFAY*