AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0287650


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0287650 MtrunA17_Chr2g0295651 97.222 144 4 0 1 144 1 144 2.25e-102 289
Msa0287650 MtrunA17_Chr4g0067541 56.780 118 37 4 1 112 1 110 2.09e-31 108
Msa0287650 MtrunA17_Chr3g0115551 45.833 72 37 1 37 106 61 132 5.46e-17 72.8
Msa0287650 MtrunA17_Chr5g0400051 50.000 58 28 1 53 110 74 130 5.22e-14 65.5
Msa0287650 MtrunA17_Chr4g0055191 48.276 58 30 0 53 110 62 119 1.73e-13 63.9
Msa0287650 MtrunA17_Chr8g0344991 42.667 75 40 1 64 135 39 113 3.21e-13 62.4
Msa0287650 MtrunA17_Chr3g0124361 38.554 83 42 2 26 106 91 166 3.35e-13 63.9
Msa0287650 MtrunA17_Chr8g0336591 50.000 54 20 1 51 104 32 78 5.36e-12 58.9
Msa0287650 MtrunA17_Chr3g0138651 50.000 58 28 1 58 114 348 405 3.44e-11 59.7
Msa0287650 MtrunA17_Chr4g0070221 57.778 45 18 1 62 106 176 219 5.42e-11 58.5
Msa0287650 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
Msa0287650 AT5G49120.1 40.789 152 80 4 1 144 1 150 2.54e-30 107
Msa0287650 AT1G22160.1 53.704 54 22 1 53 106 70 120 2.77e-14 65.9
Msa0287650 AT1G78020.1 42.623 61 35 0 64 124 89 149 3.07e-14 66.2
Msa0287650 AT5G47060.2 55.769 52 23 0 53 104 86 137 4.94e-14 65.9
Msa0287650 AT5G47060.1 55.769 52 23 0 53 104 86 137 4.94e-14 65.9
Msa0287650 AT4G39795.1 54.167 48 22 0 62 109 71 118 1.55e-13 63.5
Msa0287650 AT1G74940.1 43.373 83 39 3 62 144 148 222 1.07e-11 60.5
Msa0287650 AT4G17670.1 52.000 50 24 0 55 104 67 116 1.17e-11 59.3
Msa0287650 AT2G44670.1 57.778 45 19 0 60 104 12 56 4.75e-11 56.2
Msa0287650 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 2_3:-30695294 Msa0287650:CDS
TTAATTAAGCAGGGTAAAAC+TGG 0.323409 2_3:+30695140 None:intergenic
GCTCCATTCTCCAACCTCTT+TGG 0.343871 2_3:-30695035 Msa0287650:three_prime_UTR
AATAAGCAAAACCACCGTTT+TGG 0.352315 2_3:+30695262 None:intergenic
TTGGTAATGTAGTGTGGTTT+TGG 0.361553 2_3:-30695016 Msa0287650:three_prime_UTR
TTAATTAATGTTGTTAGATA+AGG 0.409759 2_3:-30695125 Msa0287650:three_prime_UTR
TCTAACAACATTAATTAAGC+AGG 0.429786 2_3:+30695130 None:intergenic
GGCTAGTAGTTACTAGTGAA+TGG 0.502662 2_3:+30695890 None:intergenic
GTAGTGTTAGAATCTCAAAA+AGG 0.513194 2_3:-30695827 Msa0287650:CDS
ACCTCTTTGGTAATGTAGTG+TGG 0.517027 2_3:-30695022 Msa0287650:three_prime_UTR
TAGTGAATGGAAAGTGTATG+AGG 0.523850 2_3:+30695903 None:intergenic
ATTGATACATGAATGAAGAA+AGG 0.524095 2_3:-30695242 Msa0287650:exon
GGACGTTTCAGCTTCATACA+AGG 0.529104 2_3:+30695079 None:intergenic
CACTACATTACCAAAGAGGT+TGG 0.538254 2_3:+30695025 None:intergenic
TTTGGTTATTATAATTGACT+TGG 0.543260 2_3:-30694998 Msa0287650:three_prime_UTR
TTACCAAAGAGGTTGGAGAA+TGG 0.552783 2_3:+30695032 None:intergenic
ATGATGAAAATAAGAACTCA+AGG 0.565409 2_3:+30695706 None:intergenic
TATTAGCAATAGCAAGAAGA+AGG 0.566617 2_3:-30695798 Msa0287650:CDS
CTAACAACATTAATTAAGCA+GGG 0.589637 2_3:+30695131 None:intergenic
GGATAGAGCTTTCTGTAGTG+TGG 0.592385 2_3:-30695415 Msa0287650:CDS
ACCACACTACATTACCAAAG+AGG 0.594824 2_3:+30695021 None:intergenic
TAGATGCAAGCAAATTGTGA+TGG 0.624999 2_3:-30695388 Msa0287650:CDS
AAAGGAAGAAGAAACCAAAA+CGG 0.628233 2_3:-30695276 Msa0287650:CDS
GGAAGAAGAAACCAAAACGG+TGG 0.688263 2_3:-30695273 Msa0287650:CDS
AAGATGAAGAAATTGCAGCA+TGG 0.688850 2_3:+30695325 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAGTGATAGAATAAAAAAA+TGG - chr2_3:30695031-30695050 Msa0287650:three_prime_UTR 15.0%
!! AATATAAAGTTTCATAACAT+AGG + chr2_3:30695330-30695349 None:intergenic 15.0%
!! AAAAATAAAAACAAAGATCT+AGG + chr2_3:30695376-30695395 None:intergenic 15.0%
!! ATTGTGAGATAAAAAAAAAA+TGG - chr2_3:30695698-30695717 Msa0287650:CDS 15.0%
!! TTAATTAATGTTGTTAGATA+AGG - chr2_3:30695767-30695786 Msa0287650:CDS 15.0%
!!! CTTTCTACTTTTTATTTTAT+GGG - chr2_3:30695835-30695854 Msa0287650:CDS 15.0%
!! AAAGTGATAGAATAAAAAAA+TGG - chr2_3:30695031-30695050 Msa0287650:three_prime_UTR 15.0%
!! AATATAAAGTTTCATAACAT+AGG + chr2_3:30695330-30695349 None:intergenic 15.0%
!! AAAAATAAAAACAAAGATCT+AGG + chr2_3:30695376-30695395 None:intergenic 15.0%
!! ATTGTGAGATAAAAAAAAAA+TGG - chr2_3:30695698-30695717 Msa0287650:CDS 15.0%
!! TTAATTAATGTTGTTAGATA+AGG - chr2_3:30695767-30695786 Msa0287650:CDS 15.0%
!!! CTTTCTACTTTTTATTTTAT+GGG - chr2_3:30695835-30695854 Msa0287650:CDS 15.0%
!!! TTATTCTATCACTTTTTTTG+TGG + chr2_3:30695026-30695045 None:intergenic 20.0%
!! TGATAGAATAAAAAAATGGT+GGG - chr2_3:30695035-30695054 Msa0287650:three_prime_UTR 20.0%
!!! ATTGTTTTGTTAATCACTTT+TGG + chr2_3:30695125-30695144 None:intergenic 20.0%
!! CATAGGTTATAAAATATAGA+AGG + chr2_3:30695313-30695332 None:intergenic 20.0%
!!! TGTTTATTTTTTTGTGAAGA+GGG - chr2_3:30695455-30695474 Msa0287650:intron 20.0%
!! CCATAAAATAAAAAGTAGAA+AGG + chr2_3:30695837-30695856 None:intergenic 20.0%
!!! CCTTTCTACTTTTTATTTTA+TGG - chr2_3:30695834-30695853 Msa0287650:CDS 20.0%
!! TTTGGTTATTATAATTGACT+TGG - chr2_3:30695894-30695913 Msa0287650:five_prime_UTR 20.0%
!!! TTATTCTATCACTTTTTTTG+TGG + chr2_3:30695026-30695045 None:intergenic 20.0%
!! TGATAGAATAAAAAAATGGT+GGG - chr2_3:30695035-30695054 Msa0287650:three_prime_UTR 20.0%
!!! ATTGTTTTGTTAATCACTTT+TGG + chr2_3:30695125-30695144 None:intergenic 20.0%
!! CATAGGTTATAAAATATAGA+AGG + chr2_3:30695313-30695332 None:intergenic 20.0%
!!! TGTTTATTTTTTTGTGAAGA+GGG - chr2_3:30695455-30695474 Msa0287650:intron 20.0%
!! CCATAAAATAAAAAGTAGAA+AGG + chr2_3:30695837-30695856 None:intergenic 20.0%
!!! CCTTTCTACTTTTTATTTTA+TGG - chr2_3:30695834-30695853 Msa0287650:CDS 20.0%
!! TTTGGTTATTATAATTGACT+TGG - chr2_3:30695894-30695913 Msa0287650:five_prime_UTR 20.0%
! GTGATAGAATAAAAAAATGG+TGG - chr2_3:30695034-30695053 Msa0287650:three_prime_UTR 25.0%
! ATGATGAAAATAAGAACTCA+AGG + chr2_3:30695189-30695208 None:intergenic 25.0%
!!! GTGTTTATTTTTTTGTGAAG+AGG - chr2_3:30695454-30695473 Msa0287650:intron 25.0%
!!! GTTTATTTTTTTGTGAAGAG+GGG - chr2_3:30695456-30695475 Msa0287650:intron 25.0%
! ATTGATACATGAATGAAGAA+AGG - chr2_3:30695650-30695669 Msa0287650:CDS 25.0%
! CTAACAACATTAATTAAGCA+GGG + chr2_3:30695764-30695783 None:intergenic 25.0%
! TCTAACAACATTAATTAAGC+AGG + chr2_3:30695765-30695784 None:intergenic 25.0%
! GTGATAGAATAAAAAAATGG+TGG - chr2_3:30695034-30695053 Msa0287650:three_prime_UTR 25.0%
! ATGATGAAAATAAGAACTCA+AGG + chr2_3:30695189-30695208 None:intergenic 25.0%
!!! GTGTTTATTTTTTTGTGAAG+AGG - chr2_3:30695454-30695473 Msa0287650:intron 25.0%
!!! GTTTATTTTTTTGTGAAGAG+GGG - chr2_3:30695456-30695475 Msa0287650:intron 25.0%
! ATTGATACATGAATGAAGAA+AGG - chr2_3:30695650-30695669 Msa0287650:CDS 25.0%
! CTAACAACATTAATTAAGCA+GGG + chr2_3:30695764-30695783 None:intergenic 25.0%
! TCTAACAACATTAATTAAGC+AGG + chr2_3:30695765-30695784 None:intergenic 25.0%
GTAGTGTTAGAATCTCAAAA+AGG - chr2_3:30695065-30695084 Msa0287650:three_prime_UTR 30.0%
TATTAGCAATAGCAAGAAGA+AGG - chr2_3:30695094-30695113 Msa0287650:three_prime_UTR 30.0%
! TCATCATGAATCTCATTTTC+AGG - chr2_3:30695202-30695221 Msa0287650:three_prime_UTR 30.0%
GCTTCTTATCATCATGAAAA+AGG - chr2_3:30695598-30695617 Msa0287650:intron 30.0%
AAAGGAAGAAGAAACCAAAA+CGG - chr2_3:30695616-30695635 Msa0287650:CDS 30.0%
TTAATTAAGCAGGGTAAAAC+TGG + chr2_3:30695755-30695774 None:intergenic 30.0%
GTAGTGTTAGAATCTCAAAA+AGG - chr2_3:30695065-30695084 Msa0287650:three_prime_UTR 30.0%
TATTAGCAATAGCAAGAAGA+AGG - chr2_3:30695094-30695113 Msa0287650:three_prime_UTR 30.0%
! TCATCATGAATCTCATTTTC+AGG - chr2_3:30695202-30695221 Msa0287650:three_prime_UTR 30.0%
GCTTCTTATCATCATGAAAA+AGG - chr2_3:30695598-30695617 Msa0287650:intron 30.0%
AAAGGAAGAAGAAACCAAAA+CGG - chr2_3:30695616-30695635 Msa0287650:CDS 30.0%
TTAATTAAGCAGGGTAAAAC+TGG + chr2_3:30695755-30695774 None:intergenic 30.0%
! TAGTGAATGGAAAGTGTATG+AGG + chr2_3:30694992-30695011 None:intergenic 35.0%
GTGTTAGAATCTCAAAAAGG+TGG - chr2_3:30695068-30695087 Msa0287650:three_prime_UTR 35.0%
TTAGAATCTCAAAAAGGTGG+TGG - chr2_3:30695071-30695090 Msa0287650:three_prime_UTR 35.0%
!!! TTGAGCTTTGTTTTCTCTGT+AGG - chr2_3:30695243-30695262 Msa0287650:exon 35.0%
TGTAGGAAAAAGTTGTTACC+TGG - chr2_3:30695260-30695279 Msa0287650:CDS 35.0%
! TACATGTAGATGTCTTTTCC+AGG + chr2_3:30695281-30695300 None:intergenic 35.0%
TAGATGCAAGCAAATTGTGA+TGG - chr2_3:30695504-30695523 Msa0287650:intron 35.0%
AAGATGAAGAAATTGCAGCA+TGG + chr2_3:30695570-30695589 None:intergenic 35.0%
! AATAAGCAAAACCACCGTTT+TGG + chr2_3:30695633-30695652 None:intergenic 35.0%
!!! TTGGTAATGTAGTGTGGTTT+TGG - chr2_3:30695876-30695895 Msa0287650:five_prime_UTR 35.0%
! TAGTGAATGGAAAGTGTATG+AGG + chr2_3:30694992-30695011 None:intergenic 35.0%
GTGTTAGAATCTCAAAAAGG+TGG - chr2_3:30695068-30695087 Msa0287650:three_prime_UTR 35.0%
TTAGAATCTCAAAAAGGTGG+TGG - chr2_3:30695071-30695090 Msa0287650:three_prime_UTR 35.0%
!!! TTGAGCTTTGTTTTCTCTGT+AGG - chr2_3:30695243-30695262 Msa0287650:exon 35.0%
TGTAGGAAAAAGTTGTTACC+TGG - chr2_3:30695260-30695279 Msa0287650:CDS 35.0%
! TACATGTAGATGTCTTTTCC+AGG + chr2_3:30695281-30695300 None:intergenic 35.0%
TAGATGCAAGCAAATTGTGA+TGG - chr2_3:30695504-30695523 Msa0287650:intron 35.0%
AAGATGAAGAAATTGCAGCA+TGG + chr2_3:30695570-30695589 None:intergenic 35.0%
! AATAAGCAAAACCACCGTTT+TGG + chr2_3:30695633-30695652 None:intergenic 35.0%
!!! TTGGTAATGTAGTGTGGTTT+TGG - chr2_3:30695876-30695895 Msa0287650:five_prime_UTR 35.0%
GGCTAGTAGTTACTAGTGAA+TGG + chr2_3:30695005-30695024 None:intergenic 40.0%
TTACCAAAGAGGTTGGAGAA+TGG + chr2_3:30695863-30695882 None:intergenic 40.0%
CACTACATTACCAAAGAGGT+TGG + chr2_3:30695870-30695889 None:intergenic 40.0%
!! ACCTCTTTGGTAATGTAGTG+TGG - chr2_3:30695870-30695889 Msa0287650:five_prime_UTR 40.0%
ACCACACTACATTACCAAAG+AGG + chr2_3:30695874-30695893 None:intergenic 40.0%
GGCTAGTAGTTACTAGTGAA+TGG + chr2_3:30695005-30695024 None:intergenic 40.0%
TTACCAAAGAGGTTGGAGAA+TGG + chr2_3:30695863-30695882 None:intergenic 40.0%
CACTACATTACCAAAGAGGT+TGG + chr2_3:30695870-30695889 None:intergenic 40.0%
!! ACCTCTTTGGTAATGTAGTG+TGG - chr2_3:30695870-30695889 Msa0287650:five_prime_UTR 40.0%
ACCACACTACATTACCAAAG+AGG + chr2_3:30695874-30695893 None:intergenic 40.0%
GGATAGAGCTTTCTGTAGTG+TGG - chr2_3:30695477-30695496 Msa0287650:intron 45.0%
GGAAGAAGAAACCAAAACGG+TGG - chr2_3:30695619-30695638 Msa0287650:CDS 45.0%
GGACGTTTCAGCTTCATACA+AGG + chr2_3:30695816-30695835 None:intergenic 45.0%
GGATAGAGCTTTCTGTAGTG+TGG - chr2_3:30695477-30695496 Msa0287650:intron 45.0%
GGAAGAAGAAACCAAAACGG+TGG - chr2_3:30695619-30695638 Msa0287650:CDS 45.0%
GGACGTTTCAGCTTCATACA+AGG + chr2_3:30695816-30695835 None:intergenic 45.0%
GCTCCATTCTCCAACCTCTT+TGG - chr2_3:30695857-30695876 Msa0287650:exon 50.0%
GCTCCATTCTCCAACCTCTT+TGG - chr2_3:30695857-30695876 Msa0287650:exon 50.0%
Chromosome Type Strat End Strand Name
chr2_3 gene 30694983 30695931 30694983 ID=Msa0287650;Name=Msa0287650
chr2_3 mRNA 30694983 30695931 30694983 ID=Msa0287650-mRNA-1;Parent=Msa0287650;Name=Msa0287650-mRNA-1;_AED=0.01;_eAED=0.01;_QI=67|1|1|1|1|1|2|277|144
chr2_3 exon 30694983 30695440 30694983 ID=Msa0287650-mRNA-1:exon:10552;Parent=Msa0287650-mRNA-1
chr2_3 exon 30695611 30695931 30695611 ID=Msa0287650-mRNA-1:exon:10551;Parent=Msa0287650-mRNA-1
chr2_3 five_prime_UTR 30695865 30695931 30695865 ID=Msa0287650-mRNA-1:five_prime_utr;Parent=Msa0287650-mRNA-1
chr2_3 CDS 30695611 30695864 30695611 ID=Msa0287650-mRNA-1:cds;Parent=Msa0287650-mRNA-1
chr2_3 CDS 30695260 30695440 30695260 ID=Msa0287650-mRNA-1:cds;Parent=Msa0287650-mRNA-1
chr2_3 three_prime_UTR 30694983 30695259 30694983 ID=Msa0287650-mRNA-1:three_prime_utr;Parent=Msa0287650-mRNA-1
Gene Sequence

>Msa0287650

ATGGTGGGTTTGAGTGTAGTGTTAGAATCTCAAAAAGGTGGTGGTATTAGCAATAGCAAGAAGAAGGAAACTCCAAAAGTGATTAACAAAACAATGATGCTTAGTAGCAACAACAACAAACAATCTTCTATAGTTTCCTTGAGTTCTTATTTTCATCATGAATCTCATTTTCAGGAACAACAAACAACGTTTCTTGAGCTTTGTTTTCTCTGTAGGAAAAAGTTGTTACCTGGAAAAGACATCTACATGTACAAAGGGGATAGAGCTTTCTGTAGTGTGGAATGTAGATGCAAGCAAATTGTGATGGATGAAGAAGAAAGTAACAATATTCAGAATGAGAACTGTTACCATGCTGCAATTTCTTCATCTTCTTCAGAAGCTTCTTATCATCATGAAAAAGGAAGAAGAAACCAAAACGGTGGTTTTGCTTATTGA

Protein sequence

>Msa0287650

MVGLSVVLESQKGGGISNSKKKETPKVINKTMMLSSNNNKQSSIVSLSSYFHHESHFQEQQTTFLELCFLCRKKLLPGKDIYMYKGDRAFCSVECRCKQIVMDEEESNNIQNENCYHAAISSSSSEASYHHEKGRRNQNGGFAY*