AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1218450


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1218450 MtrunA17_Chr4g0068031 96.528 144 1 1 1 140 1 144 1.40e-97 276
Msa1218450 MtrunA17_Chr7g0271861 51.754 114 48 4 29 140 21 129 6.57e-30 105
Msa1218450 MtrunA17_Chr1g0151461 63.265 49 18 0 26 74 183 231 4.01e-17 75.9
Msa1218450 MtrunA17_Chr5g0404131 58.000 50 18 1 20 66 179 228 1.52e-13 65.9
Msa1218450 MtrunA17_Chr4g0071301 68.421 38 12 0 22 59 184 221 4.72e-13 64.7
Msa1218450 MtrunA17_Chr2g0299081 76.667 30 7 0 30 59 169 198 3.79e-12 62.0
Msa1218450 MtrunA17_Chr8g0373231 64.865 37 13 0 30 66 125 161 3.82e-12 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1218450 AT3G06740.1 57.857 140 41 6 7 140 22 149 8.57e-42 136
Msa1218450 AT5G49300.1 53.691 149 49 6 2 140 1 139 1.66e-40 132
Msa1218450 AT3G16870.1 42.949 156 43 4 27 140 39 190 2.56e-29 105
Msa1218450 AT4G16141.1 44.444 162 36 6 29 136 36 197 5.32e-27 100
Msa1218450 AT5G26930.1 67.442 43 13 1 30 71 26 68 1.71e-16 70.9
Msa1218450 AT5G56860.1 70.732 41 12 0 23 63 223 263 4.08e-15 71.2
Msa1218450 AT2G18380.1 67.568 37 12 0 30 66 92 128 5.33e-13 63.5
Msa1218450 AT4G26150.1 77.419 31 7 0 30 60 199 229 5.42e-13 65.1
Msa1218450 AT4G36620.1 67.568 37 12 0 30 66 75 111 7.12e-13 63.5
Msa1218450 AT3G50870.1 67.568 37 12 0 30 66 152 188 2.86e-12 62.8

Find 46 sgRNAs with CRISPR-Local

Find 112 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAAGACAATAATAATTTATT+AGG 0.116466 8_1:+81120134 None:intergenic
AATGAATTTCGGTTCAATTT+TGG 0.152831 8_1:-81119942 Msa1218450:three_prime_UTR
AAGCAGAGATTATTGAATTT+AGG 0.186034 8_1:-81120270 Msa1218450:CDS
TTGTTGATGTCTCTTTCTTA+TGG 0.189410 8_1:-81120183 Msa1218450:CDS
TCGATCACATTGGAAGAAAT+TGG 0.220158 8_1:-81120229 Msa1218450:CDS
AGCAGAGATTATTGAATTTA+GGG 0.227823 8_1:-81120269 Msa1218450:CDS
AAGAAGAAGAGAGCGATATT+AGG 0.241089 8_1:-81120381 Msa1218450:CDS
CACTCATACTGATTTGGATT+TGG 0.243753 8_1:+81120064 None:intergenic
ATCAATGAATGAATGAATTT+CGG 0.313341 8_1:-81119953 Msa1218450:three_prime_UTR
ACCGCGCCATAGAGGAGTTT+TGG 0.319064 8_1:+81120540 None:intergenic
TAGGCTCACTCATACTGATT+TGG 0.324802 8_1:+81120058 None:intergenic
ATCAAAATCAGAATCGAAAA+TGG 0.329882 8_1:-81120788 Msa1218450:exon
TCTGATGAAACGGCGGCGTT+AGG 0.333300 8_1:+81120604 None:intergenic
AAGACAATAATAATTTATTA+GGG 0.342562 8_1:+81120135 None:intergenic
AGAAGAAGAGAGCGATATTA+GGG 0.353234 8_1:-81120380 Msa1218450:CDS
CTGATGAAACGGCGGCGTTA+GGG 0.382761 8_1:+81120605 None:intergenic
GAACTTCCAAAACTCCTCTA+TGG 0.382769 8_1:-81120546 Msa1218450:CDS
AACGAAGAAGGAACAAGAAA+GGG 0.398579 8_1:-81120342 Msa1218450:CDS
TTTACACTTATGAAAAGGTT+AGG 0.409265 8_1:+81120039 None:intergenic
TGTGCAATGCTTGCGGGATC+AGG 0.415666 8_1:-81120410 Msa1218450:CDS
CTATGGCGCGGTGGTCCTGC+AGG 0.423095 8_1:-81120529 Msa1218450:CDS
CGATCACATTGGAAGAAATT+GGG 0.429367 8_1:-81120228 Msa1218450:CDS
CAACGAAGAAGGAACAAGAA+AGG 0.448446 8_1:-81120343 Msa1218450:CDS
TTAATTACCTTTGGTCCTGC+AGG 0.462097 8_1:+81120514 None:intergenic
AGTCACTGTGCAATGCTTGC+GGG 0.486682 8_1:-81120416 Msa1218450:CDS
AACAGTGGCGGAAGCAAAGT+TGG 0.487872 8_1:-81120309 Msa1218450:CDS
ATGCTTGCGGGATCAGGAGC+AGG 0.490836 8_1:-81120404 Msa1218450:CDS
TCTGATCACAGAAACAAGAT+TGG 0.493846 8_1:+81120811 None:intergenic
GAGAGAGAAGAGAATGAAAG+AGG 0.520382 8_1:+81120963 None:intergenic
GGTGGTTGATCACAGTGATA+AGG 0.521811 8_1:-81120767 Msa1218450:intron
AGCAAAGGAAACAACGAAGA+AGG 0.525059 8_1:-81120354 Msa1218450:CDS
GGAAGTTCCGCAATCAGCAC+AGG 0.530457 8_1:+81120561 None:intergenic
ATTGTTGTTATCTGATGAAA+CGG 0.531824 8_1:+81120594 None:intergenic
GCAGGACCACCGCGCCATAG+AGG 0.566004 8_1:+81120532 None:intergenic
CGGTGGTCCTGCAGGACCAA+AGG 0.568522 8_1:-81120521 Msa1218450:intron
CAGTCACTGTGCAATGCTTG+CGG 0.579698 8_1:-81120417 Msa1218450:CDS
AAGAAAACCTGTGCTGATTG+CGG 0.600272 8_1:-81120568 Msa1218450:CDS
GAAGAGAATGATGATGATGA+TGG 0.610112 8_1:+81120882 None:intergenic
TGTTTATGAATCGATCACAT+TGG 0.615171 8_1:-81120239 Msa1218450:CDS
ACGAAGAAGGAACAAGAAAG+GGG 0.621165 8_1:-81120341 Msa1218450:CDS
CATTGATTGATTTCTTACAA+CGG 0.630728 8_1:+81119969 None:intergenic
AAAATCAGAATCGAAAATGG+TGG 0.631988 8_1:-81120785 Msa1218450:exon
TCCAAAACTCCTCTATGGCG+CGG 0.651082 8_1:-81120541 Msa1218450:CDS
GCGATATTAGGGATAAGCAA+AGG 0.653138 8_1:-81120369 Msa1218450:CDS
AAAACTCCTCTATGGCGCGG+TGG 0.659999 8_1:-81120538 Msa1218450:CDS
GTTGTTATCTGATGAAACGG+CGG 0.695776 8_1:+81120597 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAGACAATAATAATTTATTA+GGG + chr8_1:81120792-81120811 None:intergenic 10.0%
!! TAAGACAATAATAATTTATT+AGG + chr8_1:81120793-81120812 None:intergenic 10.0%
!! AAGACAATAATAATTTATTA+GGG + chr8_1:81120792-81120811 None:intergenic 10.0%
!! TAAGACAATAATAATTTATT+AGG + chr8_1:81120793-81120812 None:intergenic 10.0%
!!! TTATTAGGGTTTTTTAATTT+AGG + chr8_1:81120778-81120797 None:intergenic 15.0%
!!! ATTTAGTAGATTATTGTTTT+AGG - chr8_1:81120835-81120854 Msa1218450:five_prime_UTR 15.0%
!! AAAAATTTACACTTATGAAA+AGG + chr8_1:81120893-81120912 None:intergenic 15.0%
!!! TTATTAGGGTTTTTTAATTT+AGG + chr8_1:81120778-81120797 None:intergenic 15.0%
!!! ATTTAGTAGATTATTGTTTT+AGG - chr8_1:81120835-81120854 Msa1218450:five_prime_UTR 15.0%
!! AAAAATTTACACTTATGAAA+AGG + chr8_1:81120893-81120912 None:intergenic 15.0%
!!! TTTGTTCATTTTTCATTTTC+AGG - chr8_1:81120274-81120293 Msa1218450:CDS 20.0%
!! ATCAATGAATGAATGAATTT+CGG - chr8_1:81120971-81120990 Msa1218450:five_prime_UTR 20.0%
!!! TTTGTTCATTTTTCATTTTC+AGG - chr8_1:81120274-81120293 Msa1218450:CDS 20.0%
!! ATCAATGAATGAATGAATTT+CGG - chr8_1:81120971-81120990 Msa1218450:five_prime_UTR 20.0%
! ATCAAAATCAGAATCGAAAA+TGG - chr8_1:81120136-81120155 Msa1218450:three_prime_UTR 25.0%
!! ATTGTTGTTATCTGATGAAA+CGG + chr8_1:81120333-81120352 None:intergenic 25.0%
! GATTAGTGATTAATTACCTT+TGG + chr8_1:81120422-81120441 None:intergenic 25.0%
! AAGCAGAGATTATTGAATTT+AGG - chr8_1:81120654-81120673 Msa1218450:intron 25.0%
! AGCAGAGATTATTGAATTTA+GGG - chr8_1:81120655-81120674 Msa1218450:intron 25.0%
! TTTACACTTATGAAAAGGTT+AGG + chr8_1:81120888-81120907 None:intergenic 25.0%
!! CATTGATTGATTTCTTACAA+CGG + chr8_1:81120958-81120977 None:intergenic 25.0%
!! AATGAATTTCGGTTCAATTT+TGG - chr8_1:81120982-81121001 Msa1218450:five_prime_UTR 25.0%
! ATCAAAATCAGAATCGAAAA+TGG - chr8_1:81120136-81120155 Msa1218450:three_prime_UTR 25.0%
!! ATTGTTGTTATCTGATGAAA+CGG + chr8_1:81120333-81120352 None:intergenic 25.0%
! GATTAGTGATTAATTACCTT+TGG + chr8_1:81120422-81120441 None:intergenic 25.0%
! AAGCAGAGATTATTGAATTT+AGG - chr8_1:81120654-81120673 Msa1218450:intron 25.0%
! AGCAGAGATTATTGAATTTA+GGG - chr8_1:81120655-81120674 Msa1218450:intron 25.0%
! TTTACACTTATGAAAAGGTT+AGG + chr8_1:81120888-81120907 None:intergenic 25.0%
!! CATTGATTGATTTCTTACAA+CGG + chr8_1:81120958-81120977 None:intergenic 25.0%
!! AATGAATTTCGGTTCAATTT+TGG - chr8_1:81120982-81121001 Msa1218450:five_prime_UTR 25.0%
AAAATCAGAATCGAAAATGG+TGG - chr8_1:81120139-81120158 Msa1218450:three_prime_UTR 30.0%
!!! TTTCATTTTCAGGTATCAGA+AGG - chr8_1:81120284-81120303 Msa1218450:CDS 30.0%
TGTTTATGAATCGATCACAT+TGG - chr8_1:81120685-81120704 Msa1218450:intron 30.0%
TTGTTGATGTCTCTTTCTTA+TGG - chr8_1:81120741-81120760 Msa1218450:intron 30.0%
AAAATCAGAATCGAAAATGG+TGG - chr8_1:81120139-81120158 Msa1218450:three_prime_UTR 30.0%
!!! TTTCATTTTCAGGTATCAGA+AGG - chr8_1:81120284-81120303 Msa1218450:CDS 30.0%
TGTTTATGAATCGATCACAT+TGG - chr8_1:81120685-81120704 Msa1218450:intron 30.0%
TTGTTGATGTCTCTTTCTTA+TGG - chr8_1:81120741-81120760 Msa1218450:intron 30.0%
! GAAGAGAATGATGATGATGA+TGG + chr8_1:81120045-81120064 None:intergenic 35.0%
TCTGATCACAGAAACAAGAT+TGG + chr8_1:81120116-81120135 None:intergenic 35.0%
TTGAAGTGAAGTGTGTGATT+AGG + chr8_1:81120213-81120232 None:intergenic 35.0%
AAGAAGAAGAGAGCGATATT+AGG - chr8_1:81120543-81120562 Msa1218450:CDS 35.0%
AGAAGAAGAGAGCGATATTA+GGG - chr8_1:81120544-81120563 Msa1218450:CDS 35.0%
AACGAAGAAGGAACAAGAAA+GGG - chr8_1:81120582-81120601 Msa1218450:CDS 35.0%
TCGATCACATTGGAAGAAAT+TGG - chr8_1:81120695-81120714 Msa1218450:intron 35.0%
CGATCACATTGGAAGAAATT+GGG - chr8_1:81120696-81120715 Msa1218450:intron 35.0%
!! CACTCATACTGATTTGGATT+TGG + chr8_1:81120863-81120882 None:intergenic 35.0%
! GAAGAGAATGATGATGATGA+TGG + chr8_1:81120045-81120064 None:intergenic 35.0%
TCTGATCACAGAAACAAGAT+TGG + chr8_1:81120116-81120135 None:intergenic 35.0%
TTGAAGTGAAGTGTGTGATT+AGG + chr8_1:81120213-81120232 None:intergenic 35.0%
AAGAAGAAGAGAGCGATATT+AGG - chr8_1:81120543-81120562 Msa1218450:CDS 35.0%
AGAAGAAGAGAGCGATATTA+GGG - chr8_1:81120544-81120563 Msa1218450:CDS 35.0%
AACGAAGAAGGAACAAGAAA+GGG - chr8_1:81120582-81120601 Msa1218450:CDS 35.0%
TCGATCACATTGGAAGAAAT+TGG - chr8_1:81120695-81120714 Msa1218450:intron 35.0%
CGATCACATTGGAAGAAATT+GGG - chr8_1:81120696-81120715 Msa1218450:intron 35.0%
!! CACTCATACTGATTTGGATT+TGG + chr8_1:81120863-81120882 None:intergenic 35.0%
GAGAGAGAAGAGAATGAAAG+AGG + chr8_1:81119964-81119983 None:intergenic 40.0%
GTTGTTATCTGATGAAACGG+CGG + chr8_1:81120330-81120349 None:intergenic 40.0%
! CAATCAGCACAGGTTTTCTT+TGG + chr8_1:81120356-81120375 None:intergenic 40.0%
!! AAGAAAACCTGTGCTGATTG+CGG - chr8_1:81120356-81120375 Msa1218450:CDS 40.0%
GAACTTCCAAAACTCCTCTA+TGG - chr8_1:81120378-81120397 Msa1218450:CDS 40.0%
TTAATTACCTTTGGTCCTGC+AGG + chr8_1:81120413-81120432 None:intergenic 40.0%
GCGATATTAGGGATAAGCAA+AGG - chr8_1:81120555-81120574 Msa1218450:CDS 40.0%
AGCAAAGGAAACAACGAAGA+AGG - chr8_1:81120570-81120589 Msa1218450:CDS 40.0%
CAACGAAGAAGGAACAAGAA+AGG - chr8_1:81120581-81120600 Msa1218450:CDS 40.0%
ACGAAGAAGGAACAAGAAAG+GGG - chr8_1:81120583-81120602 Msa1218450:CDS 40.0%
AAGGGGAAAAAGAGTAACAG+TGG - chr8_1:81120600-81120619 Msa1218450:CDS 40.0%
! TAGGCTCACTCATACTGATT+TGG + chr8_1:81120869-81120888 None:intergenic 40.0%
GAGAGAGAAGAGAATGAAAG+AGG + chr8_1:81119964-81119983 None:intergenic 40.0%
GTTGTTATCTGATGAAACGG+CGG + chr8_1:81120330-81120349 None:intergenic 40.0%
! CAATCAGCACAGGTTTTCTT+TGG + chr8_1:81120356-81120375 None:intergenic 40.0%
!! AAGAAAACCTGTGCTGATTG+CGG - chr8_1:81120356-81120375 Msa1218450:CDS 40.0%
GAACTTCCAAAACTCCTCTA+TGG - chr8_1:81120378-81120397 Msa1218450:CDS 40.0%
TTAATTACCTTTGGTCCTGC+AGG + chr8_1:81120413-81120432 None:intergenic 40.0%
GCGATATTAGGGATAAGCAA+AGG - chr8_1:81120555-81120574 Msa1218450:CDS 40.0%
AGCAAAGGAAACAACGAAGA+AGG - chr8_1:81120570-81120589 Msa1218450:CDS 40.0%
CAACGAAGAAGGAACAAGAA+AGG - chr8_1:81120581-81120600 Msa1218450:CDS 40.0%
ACGAAGAAGGAACAAGAAAG+GGG - chr8_1:81120583-81120602 Msa1218450:CDS 40.0%
AAGGGGAAAAAGAGTAACAG+TGG - chr8_1:81120600-81120619 Msa1218450:CDS 40.0%
! TAGGCTCACTCATACTGATT+TGG + chr8_1:81120869-81120888 None:intergenic 40.0%
GGTGGTTGATCACAGTGATA+AGG - chr8_1:81120157-81120176 Msa1218450:exon 45.0%
GGGAAAAAGAGTAACAGTGG+CGG - chr8_1:81120603-81120622 Msa1218450:CDS 45.0%
GGTGGTTGATCACAGTGATA+AGG - chr8_1:81120157-81120176 Msa1218450:exon 45.0%
GGGAAAAAGAGTAACAGTGG+CGG - chr8_1:81120603-81120622 Msa1218450:CDS 45.0%
TCCAAAACTCCTCTATGGCG+CGG - chr8_1:81120383-81120402 Msa1218450:CDS 50.0%
CAGTCACTGTGCAATGCTTG+CGG - chr8_1:81120507-81120526 Msa1218450:intron 50.0%
AGTCACTGTGCAATGCTTGC+GGG - chr8_1:81120508-81120527 Msa1218450:intron 50.0%
! AACAGTGGCGGAAGCAAAGT+TGG - chr8_1:81120615-81120634 Msa1218450:CDS 50.0%
TCCAAAACTCCTCTATGGCG+CGG - chr8_1:81120383-81120402 Msa1218450:CDS 50.0%
CAGTCACTGTGCAATGCTTG+CGG - chr8_1:81120507-81120526 Msa1218450:intron 50.0%
AGTCACTGTGCAATGCTTGC+GGG - chr8_1:81120508-81120527 Msa1218450:intron 50.0%
! AACAGTGGCGGAAGCAAAGT+TGG - chr8_1:81120615-81120634 Msa1218450:CDS 50.0%
CTGATGAAACGGCGGCGTTA+GGG + chr8_1:81120322-81120341 None:intergenic 55.0%
TCTGATGAAACGGCGGCGTT+AGG + chr8_1:81120323-81120342 None:intergenic 55.0%
GGAAGTTCCGCAATCAGCAC+AGG + chr8_1:81120366-81120385 None:intergenic 55.0%
! ACCGCGCCATAGAGGAGTTT+TGG + chr8_1:81120387-81120406 None:intergenic 55.0%
AAAACTCCTCTATGGCGCGG+TGG - chr8_1:81120386-81120405 Msa1218450:CDS 55.0%
TGTGCAATGCTTGCGGGATC+AGG - chr8_1:81120514-81120533 Msa1218450:intron 55.0%
CTGATGAAACGGCGGCGTTA+GGG + chr8_1:81120322-81120341 None:intergenic 55.0%
TCTGATGAAACGGCGGCGTT+AGG + chr8_1:81120323-81120342 None:intergenic 55.0%
GGAAGTTCCGCAATCAGCAC+AGG + chr8_1:81120366-81120385 None:intergenic 55.0%
! ACCGCGCCATAGAGGAGTTT+TGG + chr8_1:81120387-81120406 None:intergenic 55.0%
AAAACTCCTCTATGGCGCGG+TGG - chr8_1:81120386-81120405 Msa1218450:CDS 55.0%
TGTGCAATGCTTGCGGGATC+AGG - chr8_1:81120514-81120533 Msa1218450:intron 55.0%
ATGCTTGCGGGATCAGGAGC+AGG - chr8_1:81120520-81120539 Msa1218450:intron 60.0%
ATGCTTGCGGGATCAGGAGC+AGG - chr8_1:81120520-81120539 Msa1218450:intron 60.0%
CGGTGGTCCTGCAGGACCAA+AGG - chr8_1:81120403-81120422 Msa1218450:CDS 65.0%
CGGTGGTCCTGCAGGACCAA+AGG - chr8_1:81120403-81120422 Msa1218450:CDS 65.0%
GCAGGACCACCGCGCCATAG+AGG + chr8_1:81120395-81120414 None:intergenic 70.0%
CTATGGCGCGGTGGTCCTGC+AGG - chr8_1:81120395-81120414 Msa1218450:CDS 70.0%
GCAGGACCACCGCGCCATAG+AGG + chr8_1:81120395-81120414 None:intergenic 70.0%
CTATGGCGCGGTGGTCCTGC+AGG - chr8_1:81120395-81120414 Msa1218450:CDS 70.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 81119930 81121016 81119930 ID=Msa1218450;Name=Msa1218450
chr8_1 mRNA 81119930 81121016 81119930 ID=Msa1218450-mRNA-1;Parent=Msa1218450;Name=Msa1218450-mRNA-1;_AED=0.01;_eAED=0.01;_QI=225|1|1|1|1|1|3|237|140
chr8_1 exon 81119930 81120436 81119930 ID=Msa1218450-mRNA-1:exon:28613;Parent=Msa1218450-mRNA-1
chr8_1 exon 81120522 81120650 81120522 ID=Msa1218450-mRNA-1:exon:28612;Parent=Msa1218450-mRNA-1
chr8_1 exon 81120768 81121016 81120768 ID=Msa1218450-mRNA-1:exon:28611;Parent=Msa1218450-mRNA-1
chr8_1 five_prime_UTR 81120792 81121016 81120792 ID=Msa1218450-mRNA-1:five_prime_utr;Parent=Msa1218450-mRNA-1
chr8_1 CDS 81120768 81120791 81120768 ID=Msa1218450-mRNA-1:cds;Parent=Msa1218450-mRNA-1
chr8_1 CDS 81120522 81120650 81120522 ID=Msa1218450-mRNA-1:cds;Parent=Msa1218450-mRNA-1
chr8_1 CDS 81120167 81120436 81120167 ID=Msa1218450-mRNA-1:cds;Parent=Msa1218450-mRNA-1
chr8_1 three_prime_UTR 81119930 81120166 81119930 ID=Msa1218450-mRNA-1:three_prime_utr;Parent=Msa1218450-mRNA-1
Gene Sequence

>Msa1218450

ATGGTGGTTGATCACAGTGATAAGGTATCAGAAGGTGAAGATTCAAACCCTAACGCCGCCGTTTCATCAGATAACAACAATCCAAAGAAAACCTGTGCTGATTGCGGAACTTCCAAAACTCCTCTATGGCGCGGTGGTCCTGCAGGACCAAAGTCACTGTGCAATGCTTGCGGGATCAGGAGCAGGAAGAAGAAGAGAGCGATATTAGGGATAAGCAAAGGAAACAACGAAGAAGGAACAAGAAAGGGGAAAAAGAGTAACAGTGGCGGAAGCAAAGTTGGTGATAATTTGAACATGAAGCAGAGATTATTGAATTTAGGGAAAGAAGTGTTTATGAATCGATCACATTGGAAGAAATTGGGAGAAGATGAACAAGCTGCTGTGTTGTTGATGTCTCTTTCTTATGGATCTGTTTATGCCTAA

Protein sequence

>Msa1218450

MVVDHSDKVSEGEDSNPNAAVSSDNNNPKKTCADCGTSKTPLWRGGPAGPKSLCNACGIRSRKKKRAILGISKGNNEEGTRKGKKSNSGGSKVGDNLNMKQRLLNLGKEVFMNRSHWKKLGEDEQAAVLLMSLSYGSVYA*