AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1229130

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1229130 MtrunA17_Chr8g0335971 99.010 101 1 0 1 101 100 200 7.13e-72 212
Msa1229130 MtrunA17_Chr7g0250121 80.198 101 20 0 1 101 103 203 1.79e-55 171
Msa1229130 MtrunA17_Chr7g0259831 55.556 63 28 0 1 63 124 186 2.57e-19 78.6
Msa1229130 MtrunA17_Chr7g0231431 50.820 61 30 0 1 61 127 187 1.19e-18 77.0
Msa1229130 MtrunA17_Chr2g0322921 43.478 92 51 1 1 92 132 222 8.85e-12 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1229130 AT2G44740.1 62.366 93 30 1 1 93 105 192 2.11e-35 120
Msa1229130 AT5G61650.1 53.333 105 44 2 1 100 113 217 2.16e-32 112
Msa1229130 AT5G07450.1 54.000 100 40 2 1 97 115 211 2.67e-29 104
Msa1229130 AT3G05327.1 51.613 62 30 0 1 62 130 191 1.32e-17 74.3
Msa1229130 AT2G45080.1 37.500 96 59 1 1 96 122 216 1.75e-17 74.3
Msa1229130 AT3G60550.1 39.000 100 60 1 1 100 128 226 2.86e-17 73.9
Msa1229130 AT3G63120.2 51.667 60 29 0 1 60 125 184 2.16e-16 71.6
Msa1229130 AT3G63120.1 51.667 60 29 0 1 60 125 184 2.16e-16 71.6
Msa1229130 AT3G21870.1 49.180 61 31 0 1 61 120 180 1.75e-11 58.2

Find 24 sgRNAs with CRISPR-Local

Find 139 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTGAGTTGGATTTCTTGTT+TGG 0.226808 8_2:+4765147 Msa1229130:CDS
AAGAAAATTCATCTCCGTTT+TGG 0.264352 8_2:-4765127 None:intergenic
AGTTATCAACTTTGCATCAT+TGG 0.277082 8_2:-4763760 None:intergenic
TTGGATTTCTTGTTTGGTTT+AGG 0.294726 8_2:+4765153 Msa1229130:CDS
GCATTTGTAGCATTTCTCTT+TGG 0.372837 8_2:-4765227 None:intergenic
TATGGTTGCTGCTAAATTCA+TGG 0.382597 8_2:+4764035 Msa1229130:exon
ATCAAACAGCTAGTTGTTGT+TGG 0.399140 8_2:-4765341 None:intergenic
AATGCTTATTATGCAAAAGT+TGG 0.413031 8_2:+4765096 Msa1229130:CDS
ATAGCTTTGAATGAGATGTT+TGG 0.420447 8_2:-4763873 None:intergenic
TTCTCTCTTCACTTCTTGAA+AGG 0.431151 8_2:+4763784 Msa1229130:five_prime_UTR
ATCATTGGACTCTCTAACTC+GGG 0.461411 8_2:-4763745 None:intergenic
CATCATTGGACTCTCTAACT+CGG 0.479542 8_2:-4763746 None:intergenic
GTAGTGAATCTGTTACTCAT+TGG 0.495522 8_2:+4765415 Msa1229130:three_prime_UTR
TGAACATTGAAGGAGTTGAT+AGG 0.499691 8_2:-4763991 None:intergenic
CAACAAGCGATGAACATTGA+AGG 0.515637 8_2:-4764001 None:intergenic
AAGGAGTTGATAGGCAAAGA+AGG 0.516713 8_2:-4763982 None:intergenic
CAAAACTTTGTCACTATCCA+TGG 0.518427 8_2:+4763722 Msa1229130:five_prime_UTR
GCTTATTATGCAAAAGTTGG+AGG 0.519013 8_2:+4765099 Msa1229130:CDS
GGACTCTCTAACTCGGGCCA+TGG 0.529793 8_2:-4763739 None:intergenic
GAGTAAGAAAGGAATCCATA+AGG 0.542511 8_2:-4765456 None:intergenic
AAGTTTAGCAAAATCACTAA+AGG 0.550070 8_2:+4765278 Msa1229130:CDS
GAGTTTGAGTGAAACGATCA+AGG 0.564770 8_2:-4763958 None:intergenic
AGTTGGAGGAATCACCAAAA+CGG 0.594734 8_2:+4765113 Msa1229130:CDS
CAATAAGCTTGAAATGTGAC+TGG 0.606542 8_2:-4765195 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATAAAAAAAAAAAAAACAG+AGG - chr8_2:4764266-4764285 None:intergenic 10.0%
!!! TTAAATTTGTTTAGATTTTA+CGG + chr8_2:4764514-4764533 Msa1229130:intron 10.0%
!! TATAAAAAAAAAAAAAACAG+AGG - chr8_2:4764266-4764285 None:intergenic 10.0%
!!! TTAAATTTGTTTAGATTTTA+CGG + chr8_2:4764514-4764533 Msa1229130:intron 10.0%
!! ATCAAATAAAAACAGAATTA+TGG + chr8_2:4764223-4764242 Msa1229130:intron 15.0%
!!! AAATTCAGATCAAAATATTT+TGG - chr8_2:4764303-4764322 None:intergenic 15.0%
!! TTTAAACAAATTTAAGTGTA+TGG - chr8_2:4764486-4764505 None:intergenic 15.0%
!! TAAAAAGAATACAACATTAA+AGG - chr8_2:4764599-4764618 None:intergenic 15.0%
!! ATATTTATAATAACAATTGG+TGG - chr8_2:4764946-4764965 None:intergenic 15.0%
!! ATCAAATAAAAACAGAATTA+TGG + chr8_2:4764223-4764242 Msa1229130:intron 15.0%
!!! AAATTCAGATCAAAATATTT+TGG - chr8_2:4764303-4764322 None:intergenic 15.0%
!! TTTAAACAAATTTAAGTGTA+TGG - chr8_2:4764486-4764505 None:intergenic 15.0%
!! TAAAAAGAATACAACATTAA+AGG - chr8_2:4764599-4764618 None:intergenic 15.0%
!! ATATTTATAATAACAATTGG+TGG - chr8_2:4764946-4764965 None:intergenic 15.0%
!!! TCTTTAGAAAAAATTGTCTT+AGG + chr8_2:4764176-4764195 Msa1229130:intron 20.0%
!!! AATCAGACTTTACTAATTTT+CGG - chr8_2:4764669-4764688 None:intergenic 20.0%
!!! TTTTAAAGTACTTTTCCTTA+TGG + chr8_2:4765441-4765460 Msa1229130:three_prime_UTR 20.0%
!!! TCTTTAGAAAAAATTGTCTT+AGG + chr8_2:4764176-4764195 Msa1229130:intron 20.0%
!!! AATCAGACTTTACTAATTTT+CGG - chr8_2:4764669-4764688 None:intergenic 20.0%
!!! TTTTAAAGTACTTTTCCTTA+TGG + chr8_2:4765441-4765460 Msa1229130:three_prime_UTR 20.0%
! GAAAAATAGAGATCTTATGA+TGG - chr8_2:4763839-4763858 None:intergenic 25.0%
!!! CATAAGATCTCTATTTTTCA+TGG + chr8_2:4763840-4763859 Msa1229130:five_prime_UTR 25.0%
!!! TGCATAAAATTCTGAAACTT+TGG + chr8_2:4764091-4764110 Msa1229130:intron 25.0%
! TCTTAGGAATTCTATGTATT+TGG + chr8_2:4764192-4764211 Msa1229130:intron 25.0%
! CACATCAAAATATAGAAGAA+AGG - chr8_2:4764369-4764388 None:intergenic 25.0%
! CCAAAATTTAGCATATTTGA+GGG - chr8_2:4764453-4764472 None:intergenic 25.0%
! TCCAAAATTTAGCATATTTG+AGG - chr8_2:4764454-4764473 None:intergenic 25.0%
!! TAGATTTTACGGTTAACTTT+TGG + chr8_2:4764525-4764544 Msa1229130:intron 25.0%
!!! GGTTCTATTTTTCTGAAAAT+CGG - chr8_2:4764627-4764646 None:intergenic 25.0%
!! AATAGAACCTTGATAATTCA+AGG + chr8_2:4764638-4764657 Msa1229130:intron 25.0%
!!! AACAATTTTAGTCCAATCTA+TGG + chr8_2:4764749-4764768 Msa1229130:intron 25.0%
!! AAGTCTAAAATACCATAGAT+TGG - chr8_2:4764764-4764783 None:intergenic 25.0%
! CATAGTATTATTCACAAGAA+AGG - chr8_2:4764845-4764864 None:intergenic 25.0%
! GGATTATAAATCATAGACAA+AGG - chr8_2:4765062-4765081 None:intergenic 25.0%
! AATGCTTATTATGCAAAAGT+TGG + chr8_2:4765096-4765115 Msa1229130:CDS 25.0%
! GTAGAATCTTCAAAAATTAG+AGG - chr8_2:4765255-4765274 None:intergenic 25.0%
! AAGTTTAGCAAAATCACTAA+AGG + chr8_2:4765278-4765297 Msa1229130:CDS 25.0%
! GAAAAATAGAGATCTTATGA+TGG - chr8_2:4763839-4763858 None:intergenic 25.0%
!!! CATAAGATCTCTATTTTTCA+TGG + chr8_2:4763840-4763859 Msa1229130:five_prime_UTR 25.0%
!!! TGCATAAAATTCTGAAACTT+TGG + chr8_2:4764091-4764110 Msa1229130:intron 25.0%
! TCTTAGGAATTCTATGTATT+TGG + chr8_2:4764192-4764211 Msa1229130:intron 25.0%
! CACATCAAAATATAGAAGAA+AGG - chr8_2:4764369-4764388 None:intergenic 25.0%
! CCAAAATTTAGCATATTTGA+GGG - chr8_2:4764453-4764472 None:intergenic 25.0%
! TCCAAAATTTAGCATATTTG+AGG - chr8_2:4764454-4764473 None:intergenic 25.0%
!! TAGATTTTACGGTTAACTTT+TGG + chr8_2:4764525-4764544 Msa1229130:intron 25.0%
!!! GGTTCTATTTTTCTGAAAAT+CGG - chr8_2:4764627-4764646 None:intergenic 25.0%
!! AATAGAACCTTGATAATTCA+AGG + chr8_2:4764638-4764657 Msa1229130:intron 25.0%
!!! AACAATTTTAGTCCAATCTA+TGG + chr8_2:4764749-4764768 Msa1229130:intron 25.0%
!! AAGTCTAAAATACCATAGAT+TGG - chr8_2:4764764-4764783 None:intergenic 25.0%
! CATAGTATTATTCACAAGAA+AGG - chr8_2:4764845-4764864 None:intergenic 25.0%
! GGATTATAAATCATAGACAA+AGG - chr8_2:4765062-4765081 None:intergenic 25.0%
! AATGCTTATTATGCAAAAGT+TGG + chr8_2:4765096-4765115 Msa1229130:CDS 25.0%
! GTAGAATCTTCAAAAATTAG+AGG - chr8_2:4765255-4765274 None:intergenic 25.0%
! AAGTTTAGCAAAATCACTAA+AGG + chr8_2:4765278-4765297 Msa1229130:CDS 25.0%
AGTTATCAACTTTGCATCAT+TGG - chr8_2:4763763-4763782 None:intergenic 30.0%
!! ATAGCTTTGAATGAGATGTT+TGG - chr8_2:4763876-4763895 None:intergenic 30.0%
!!! CTTGTTGATCACTAGTTTTA+TGG + chr8_2:4764017-4764036 Msa1229130:exon 30.0%
! GGTCATCATTGATGAATTTT+TGG + chr8_2:4764112-4764131 Msa1229130:intron 30.0%
! CCCTCAAATATGCTAAATTT+TGG + chr8_2:4764450-4764469 Msa1229130:intron 30.0%
!! TCTATTTTTCTGAAAATCGG+AGG - chr8_2:4764624-4764643 None:intergenic 30.0%
! AACCTTGATAATTCAAGGTT+CGG + chr8_2:4764643-4764662 Msa1229130:intron 30.0%
! GAGTTCTAGTGAATGATTAA+TGG - chr8_2:4764726-4764745 None:intergenic 30.0%
TTGTGAATAATACTATGTCC+AGG + chr8_2:4764848-4764867 Msa1229130:intron 30.0%
GACAAAGGAAAAAGAACATT+AGG - chr8_2:4765047-4765066 None:intergenic 30.0%
GTCTATGATTTATAATCCTC+AGG + chr8_2:4765064-4765083 Msa1229130:intron 30.0%
! AAGAAAATTCATCTCCGTTT+TGG - chr8_2:4765130-4765149 None:intergenic 30.0%
! TTGGATTTCTTGTTTGGTTT+AGG + chr8_2:4765153-4765172 Msa1229130:CDS 30.0%
AGTTATCAACTTTGCATCAT+TGG - chr8_2:4763763-4763782 None:intergenic 30.0%
!! ATAGCTTTGAATGAGATGTT+TGG - chr8_2:4763876-4763895 None:intergenic 30.0%
!!! CTTGTTGATCACTAGTTTTA+TGG + chr8_2:4764017-4764036 Msa1229130:exon 30.0%
! GGTCATCATTGATGAATTTT+TGG + chr8_2:4764112-4764131 Msa1229130:intron 30.0%
! CCCTCAAATATGCTAAATTT+TGG + chr8_2:4764450-4764469 Msa1229130:intron 30.0%
!! TCTATTTTTCTGAAAATCGG+AGG - chr8_2:4764624-4764643 None:intergenic 30.0%
! AACCTTGATAATTCAAGGTT+CGG + chr8_2:4764643-4764662 Msa1229130:intron 30.0%
! GAGTTCTAGTGAATGATTAA+TGG - chr8_2:4764726-4764745 None:intergenic 30.0%
TTGTGAATAATACTATGTCC+AGG + chr8_2:4764848-4764867 Msa1229130:intron 30.0%
GACAAAGGAAAAAGAACATT+AGG - chr8_2:4765047-4765066 None:intergenic 30.0%
GTCTATGATTTATAATCCTC+AGG + chr8_2:4765064-4765083 Msa1229130:intron 30.0%
! AAGAAAATTCATCTCCGTTT+TGG - chr8_2:4765130-4765149 None:intergenic 30.0%
! TTGGATTTCTTGTTTGGTTT+AGG + chr8_2:4765153-4765172 Msa1229130:CDS 30.0%
CAAAACTTTGTCACTATCCA+TGG + chr8_2:4763722-4763741 Msa1229130:five_prime_UTR 35.0%
TTCTCTCTTCACTTCTTGAA+AGG + chr8_2:4763784-4763803 Msa1229130:five_prime_UTR 35.0%
! TGAACATTGAAGGAGTTGAT+AGG - chr8_2:4763994-4764013 None:intergenic 35.0%
TATGGTTGCTGCTAAATTCA+TGG + chr8_2:4764035-4764054 Msa1229130:exon 35.0%
CGGATTGATTGTATGTTTGT+TGG - chr8_2:4764882-4764901 None:intergenic 35.0%
GCTTATTATGCAAAAGTTGG+AGG + chr8_2:4765099-4765118 Msa1229130:CDS 35.0%
! GGAGATGAATTTTCTTGAGT+TGG + chr8_2:4765134-4765153 Msa1229130:CDS 35.0%
!! CTTGAGTTGGATTTCTTGTT+TGG + chr8_2:4765147-4765166 Msa1229130:CDS 35.0%
CAATAAGCTTGAAATGTGAC+TGG - chr8_2:4765198-4765217 None:intergenic 35.0%
GCATTTGTAGCATTTCTCTT+TGG - chr8_2:4765230-4765249 None:intergenic 35.0%
ATCAAACAGCTAGTTGTTGT+TGG - chr8_2:4765344-4765363 None:intergenic 35.0%
GTAGTGAATCTGTTACTCAT+TGG + chr8_2:4765415-4765434 Msa1229130:three_prime_UTR 35.0%
! GTGACAAAGTTTTGCTTCAA+CGG - chr8_2:4763716-4763735 None:intergenic 35.0%
CAAAACTTTGTCACTATCCA+TGG + chr8_2:4763722-4763741 Msa1229130:five_prime_UTR 35.0%
TTCTCTCTTCACTTCTTGAA+AGG + chr8_2:4763784-4763803 Msa1229130:five_prime_UTR 35.0%
! TGAACATTGAAGGAGTTGAT+AGG - chr8_2:4763994-4764013 None:intergenic 35.0%
TATGGTTGCTGCTAAATTCA+TGG + chr8_2:4764035-4764054 Msa1229130:exon 35.0%
CGGATTGATTGTATGTTTGT+TGG - chr8_2:4764882-4764901 None:intergenic 35.0%
GCTTATTATGCAAAAGTTGG+AGG + chr8_2:4765099-4765118 Msa1229130:CDS 35.0%
! GGAGATGAATTTTCTTGAGT+TGG + chr8_2:4765134-4765153 Msa1229130:CDS 35.0%
!! CTTGAGTTGGATTTCTTGTT+TGG + chr8_2:4765147-4765166 Msa1229130:CDS 35.0%
CAATAAGCTTGAAATGTGAC+TGG - chr8_2:4765198-4765217 None:intergenic 35.0%
GCATTTGTAGCATTTCTCTT+TGG - chr8_2:4765230-4765249 None:intergenic 35.0%
ATCAAACAGCTAGTTGTTGT+TGG - chr8_2:4765344-4765363 None:intergenic 35.0%
GTAGTGAATCTGTTACTCAT+TGG + chr8_2:4765415-4765434 Msa1229130:three_prime_UTR 35.0%
ATCATTGGACTCTCTAACTC+GGG - chr8_2:4763748-4763767 None:intergenic 40.0%
CATCATTGGACTCTCTAACT+CGG - chr8_2:4763749-4763768 None:intergenic 40.0%
GAGTTTGAGTGAAACGATCA+AGG - chr8_2:4763961-4763980 None:intergenic 40.0%
!! AAGGAGTTGATAGGCAAAGA+AGG - chr8_2:4763985-4764004 None:intergenic 40.0%
CAACAAGCGATGAACATTGA+AGG - chr8_2:4764004-4764023 None:intergenic 40.0%
! TTTTGGCCAAATGCATCGTA+TGG + chr8_2:4764542-4764561 Msa1229130:intron 40.0%
TAGAGACCATACGATGCATT+TGG - chr8_2:4764551-4764570 None:intergenic 40.0%
GAATAATACTATGTCCAGGC+TGG + chr8_2:4764852-4764871 Msa1229130:intron 40.0%
GTTAGCTAGCAAACTCACAT+GGG - chr8_2:4764905-4764924 None:intergenic 40.0%
AGTTAGCTAGCAAACTCACA+TGG - chr8_2:4764906-4764925 None:intergenic 40.0%
AAGCATTATTGTAGCACCTG+AGG - chr8_2:4765083-4765102 None:intergenic 40.0%
AGTTGGAGGAATCACCAAAA+CGG + chr8_2:4765113-4765132 Msa1229130:CDS 40.0%
ATCATTGGACTCTCTAACTC+GGG - chr8_2:4763748-4763767 None:intergenic 40.0%
CATCATTGGACTCTCTAACT+CGG - chr8_2:4763749-4763768 None:intergenic 40.0%
GAGTTTGAGTGAAACGATCA+AGG - chr8_2:4763961-4763980 None:intergenic 40.0%
!! AAGGAGTTGATAGGCAAAGA+AGG - chr8_2:4763985-4764004 None:intergenic 40.0%
CAACAAGCGATGAACATTGA+AGG - chr8_2:4764004-4764023 None:intergenic 40.0%
! TTTTGGCCAAATGCATCGTA+TGG + chr8_2:4764542-4764561 Msa1229130:intron 40.0%
TAGAGACCATACGATGCATT+TGG - chr8_2:4764551-4764570 None:intergenic 40.0%
GAATAATACTATGTCCAGGC+TGG + chr8_2:4764852-4764871 Msa1229130:intron 40.0%
GTTAGCTAGCAAACTCACAT+GGG - chr8_2:4764905-4764924 None:intergenic 40.0%
AGTTAGCTAGCAAACTCACA+TGG - chr8_2:4764906-4764925 None:intergenic 40.0%
AAGCATTATTGTAGCACCTG+AGG - chr8_2:4765083-4765102 None:intergenic 40.0%
AGTTGGAGGAATCACCAAAA+CGG + chr8_2:4765113-4765132 Msa1229130:CDS 40.0%
GGCCGAACCTTGAATTATCA+AGG - chr8_2:4764648-4764667 None:intergenic 45.0%
GGCCGAACCTTGAATTATCA+AGG - chr8_2:4764648-4764667 None:intergenic 45.0%
!! ATTATATTTATAATAACAAT+TGG - chr8_2:4764949-4764968 None:intergenic 5.0%
!! ATTATATTTATAATAACAAT+TGG - chr8_2:4764949-4764968 None:intergenic 5.0%
! TGTTTGTTGGAAAGCCAGCC+TGG - chr8_2:4764869-4764888 None:intergenic 50.0%
AGCTAGCAAACTCACATGGG+CGG - chr8_2:4764902-4764921 None:intergenic 50.0%
! TGTTTGTTGGAAAGCCAGCC+TGG - chr8_2:4764869-4764888 None:intergenic 50.0%
AGCTAGCAAACTCACATGGG+CGG - chr8_2:4764902-4764921 None:intergenic 50.0%
GGACTCTCTAACTCGGGCCA+TGG - chr8_2:4763742-4763761 None:intergenic 60.0%
GGACTCTCTAACTCGGGCCA+TGG - chr8_2:4763742-4763761 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr8_2 gene 4763715 4765468 4763715 ID=Msa1229130;Name=Msa1229130
chr8_2 mRNA 4763715 4765468 4763715 ID=Msa1229130-mRNA-1;Parent=Msa1229130;Name=Msa1229130-mRNA-1;_AED=0.05;_eAED=0.05;_QI=321|1|1|1|0|0|2|106|101
chr8_2 exon 4763715 4764064 4763715 ID=Msa1229130-mRNA-1:exon:1587;Parent=Msa1229130-mRNA-1
chr8_2 exon 4765086 4765468 4765086 ID=Msa1229130-mRNA-1:exon:1588;Parent=Msa1229130-mRNA-1
chr8_2 five_prime_UTR 4763715 4764035 4763715 ID=Msa1229130-mRNA-1:five_prime_utr;Parent=Msa1229130-mRNA-1
chr8_2 CDS 4764036 4764064 4764036 ID=Msa1229130-mRNA-1:cds;Parent=Msa1229130-mRNA-1
chr8_2 CDS 4765086 4765362 4765086 ID=Msa1229130-mRNA-1:cds;Parent=Msa1229130-mRNA-1
chr8_2 three_prime_UTR 4765363 4765468 4765363 ID=Msa1229130-mRNA-1:three_prime_utr;Parent=Msa1229130-mRNA-1
Gene Sequence

>Msa1229130

ATGGTTGCTGCTAAATTCATGGATGATGTGTGCTACAATAATGCTTATTATGCAAAAGTTGGAGGAATCACCAAAACGGAGATGAATTTTCTTGAGTTGGATTTCTTGTTTGGTTTAGGTTTCAATTTAAATGTAACACCAGTCACATTTCAAGCTTATTGTGTTCATCTCCAAAGAGAAATGCTACAAATGCAACCTCTAATTTTTGAAGATTCTACACTAAGTTTAGCAAAATCACTAAAGGCTCATTTATGCTTGAATGAAGATGAATCTTCTCATCAAAACCAACAACAACTAGCTGTTTGA
Protein sequence

>Msa1229130

MVAAKFMDDVCYNNAYYAKVGGITKTEMNFLELDFLFGLGFNLNVTPVTFQAYCVHLQREMLQMQPLIFEDSTLSLAKSLKAHLCLNEDESSHQNQQQLAV*