AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1040250

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1040250 MtrunA17_Chr7g0271281 100.000 54 0 0 1 54 1 54 6.61e-33 106
Msa1040250 MtrunA17_Chr7g0271271 87.037 54 7 0 1 54 1 54 1.67e-29 98.2
Msa1040250 MtrunA17_Chr7g0271261 81.481 54 10 0 1 54 1 54 1.79e-26 90.5
Msa1040250 MtrunA17_Chr6g0462381 61.538 52 20 0 1 52 1 52 1.32e-19 73.2
Msa1040250 MtrunA17_Chr4g0073821 62.500 48 17 1 6 52 8 55 1.61e-14 60.8
Msa1040250 MtrunA17_Chr4g0073811 56.522 46 19 1 8 52 10 55 5.86e-12 54.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1040250 AT3G05890.1 81.481 54 10 0 1 54 1 54 1.91e-26 90.9
Msa1040250 AT3G05880.1 75.926 54 13 0 1 54 1 54 3.72e-25 87.4
Msa1040250 AT2G38905.1 62.264 53 20 0 1 53 1 53 2.85e-20 75.1
Msa1040250 AT1G57550.1 50.980 51 25 0 4 54 2 52 1.53e-15 63.2
Msa1040250 AT4G28088.1 57.692 52 21 1 2 52 4 55 1.02e-14 61.6
Msa1040250 AT2G24040.1 64.583 48 16 1 6 52 8 55 1.40e-14 61.2
Msa1040250 AT4G30650.1 65.217 46 15 1 8 52 10 55 4.79e-14 60.1
Msa1040250 AT4G30660.1 67.391 46 14 1 8 52 10 55 3.05e-13 58.2
Msa1040250 AT4G30660.2 67.391 46 14 1 8 52 10 55 3.05e-13 58.2

Find 32 sgRNAs with CRISPR-Local

Find 106 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATAGATAGACATATTATTAT+TGG 0.187773 7_1:+77583668 None:intergenic
TCTCCCCAAAAGATCGAAAA+TGG 0.199118 7_1:-77585691 Msa1040250:exon
CTTATTAATATATTAATTTA+CGG 0.261789 7_1:-77583735 Msa1040250:three_prime_UTR
TGCCATCATCCTCCCTCCTC+TGG 0.264513 7_1:-77585640 Msa1040250:CDS
CGTAAATTAATATATTAATA+AGG 0.271474 7_1:+77583736 None:intergenic
TTCCAGGGAGATAGCCAAAA+AGG 0.293556 7_1:+77585460 None:intergenic
CTGGGTGTCTTCCTCAAGTT+TGG 0.312222 7_1:-77585621 Msa1040250:CDS
TATCGCTTTACATTGTCTTT+AGG 0.348966 7_1:-77585772 Msa1040250:five_prime_UTR
GTATTATATAGGTGGAGTTC+TGG 0.387189 7_1:-77585500 Msa1040250:intron
TAGATAGCATAGAGAATTCC+AGG 0.393214 7_1:+77585444 None:intergenic
GTAAATTAATATATTAATAA+GGG 0.407952 7_1:+77583737 None:intergenic
GGTGGAGTTCTGGCTCTGTT+TGG 0.420945 7_1:-77585490 Msa1040250:CDS
GTGGATCATACATAGTTGTC+AGG 0.428834 7_1:-77584022 Msa1040250:three_prime_UTR
AGTTTACAGAACAGTGTTGT+TGG 0.434777 7_1:+77585738 None:intergenic
GCCATCATCCTCCCTCCTCT+GGG 0.447378 7_1:-77585639 Msa1040250:CDS
GTTTACAGAACAGTGTTGTT+GGG 0.452524 7_1:+77585739 None:intergenic
CAAATGCTAAATTGATCACT+TGG 0.460414 7_1:+77585413 None:intergenic
CTCCCCAAAAGATCGAAAAT+GGG 0.498888 7_1:-77585690 Msa1040250:exon
GAAACCATGTAACATGTATG+AGG 0.530320 7_1:+77583997 None:intergenic
CATGAACAAGATTATTGAGA+AGG 0.531399 7_1:+77583813 None:intergenic
GGGGCCTCATACATGTTACA+TGG 0.555701 7_1:-77584001 Msa1040250:three_prime_UTR
ACCCAGAGGAGGGAGGATGA+TGG 0.561117 7_1:+77585638 None:intergenic
GGGAGATTATAATAAAGTCA+AGG 0.600729 7_1:+77583757 None:intergenic
TGGATCATACATAGTTGTCA+GGG 0.613653 7_1:-77584021 Msa1040250:three_prime_UTR
TGAGGAAGACACCCAGAGGA+GGG 0.623808 7_1:+77585628 None:intergenic
TTACATGGCAGCCAAACTTG+AGG 0.631155 7_1:+77585610 None:intergenic
AAGCTTATGAACTCTAGCAA+TGG 0.636321 7_1:-77583864 Msa1040250:three_prime_UTR
TTGAGGAAGACACCCAGAGG+AGG 0.651577 7_1:+77585627 None:intergenic
AGATAGCATAGAGAATTCCA+GGG 0.676358 7_1:+77585445 None:intergenic
GGAAGACACCCAGAGGAGGG+AGG 0.680794 7_1:+77585631 None:intergenic
GGATCATACATAGTTGTCAG+GGG 0.694128 7_1:-77584020 Msa1040250:three_prime_UTR
AACTTGAGGAAGACACCCAG+AGG 0.724844 7_1:+77585624 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAAAAAAAAAAGAAGAA+AGG + chr7_1:77583882-77583901 None:intergenic 10.0%
!! TAATTAATTAATCAATTGTT+TGG - chr7_1:77583923-77583942 Msa1040250:three_prime_UTR 10.0%
!! TAAACTAATTAATAATCAAT+TGG - chr7_1:77584759-77584778 Msa1040250:intron 10.0%
!! CGTAAATTAATATATTAATA+AGG + chr7_1:77585720-77585739 None:intergenic 10.0%
!!! GATGATTTATTTTATTTGAA+TGG + chr7_1:77584139-77584158 None:intergenic 15.0%
!! AATTAACAATTGAGTATAAT+AGG + chr7_1:77584200-77584219 None:intergenic 15.0%
!! TGTGAATTAGTAAAAAAATA+TGG - chr7_1:77584523-77584542 Msa1040250:intron 15.0%
!!! AATTAGTTTATTACATAGAT+AGG + chr7_1:77584749-77584768 None:intergenic 15.0%
!!! AAATGTAAATTTTTATCAGA+GGG + chr7_1:77584792-77584811 None:intergenic 15.0%
!!! AAAATGTAAATTTTTATCAG+AGG + chr7_1:77584793-77584812 None:intergenic 15.0%
!! AAAACACTTTATGTTAAAAA+GGG - chr7_1:77585159-77585178 Msa1040250:intron 15.0%
!! ACATAAAAAAAGAATAACTT+TGG + chr7_1:77585511-77585530 None:intergenic 15.0%
!!! ATTCTTTTTTTATGTCTTTT+CGG - chr7_1:77585516-77585535 Msa1040250:intron 15.0%
!! TTAATTAATCAATTGTTTGG+TGG - chr7_1:77583926-77583945 Msa1040250:three_prime_UTR 20.0%
!! AATAATGTATATTGTCAACT+AGG - chr7_1:77584563-77584582 Msa1040250:intron 20.0%
!!! CTATTGAGTTATTTTATTAC+CGG - chr7_1:77585096-77585115 Msa1040250:intron 20.0%
!! CAAAACACTTTATGTTAAAA+AGG - chr7_1:77585158-77585177 Msa1040250:intron 20.0%
!! AAACACTTTATGTTAAAAAG+GGG - chr7_1:77585160-77585179 Msa1040250:intron 20.0%
!! TATTTCTCAGTTTCATTATT+TGG - chr7_1:77585206-77585225 Msa1040250:intron 20.0%
!!! TTAATTTTCCTTCAATAACA+AGG - chr7_1:77585352-77585371 Msa1040250:intron 20.0%
!! TCAAAAATAGAGCAAAATAA+AGG + chr7_1:77585552-77585571 None:intergenic 20.0%
!! TTGGTGGTAATGTATTATAT+AGG - chr7_1:77583942-77583961 Msa1040250:three_prime_UTR 25.0%
!! TAGATAGAAAAGGGTATAAT+TGG + chr7_1:77584072-77584091 None:intergenic 25.0%
! AGCAAGAAATAGATAGAAAA+GGG + chr7_1:77584081-77584100 None:intergenic 25.0%
! CATACAATTCATCATATACT+TGG + chr7_1:77584239-77584258 None:intergenic 25.0%
! CAAGTATATGATGAATTGTA+TGG - chr7_1:77584237-77584256 Msa1040250:intron 25.0%
!! TTTGACTTTGCATATACATT+TGG + chr7_1:77584306-77584325 None:intergenic 25.0%
! CAAAGATAAAACAAATGCAT+TGG + chr7_1:77584403-77584422 None:intergenic 25.0%
! AATATCATGTAAGATGTTGT+TGG + chr7_1:77584494-77584513 None:intergenic 25.0%
!!! ATTGCGTTTTAGTTTATGTT+TGG - chr7_1:77584975-77584994 Msa1040250:intron 25.0%
! TAACTCAATAGAAATAACAC+AGG + chr7_1:77585087-77585106 None:intergenic 25.0%
! GATAAGCATCACAATTATTT+AGG + chr7_1:77585317-77585336 None:intergenic 25.0%
!!! AATTAGTTCCTTGTTATTGA+AGG + chr7_1:77585363-77585382 None:intergenic 25.0%
!!! CATTAATTGTTTTTGTTGAC+AGG - chr7_1:77585409-77585428 Msa1040250:intron 25.0%
!!! AACTTTGTTTTGTTTAGTGA+TGG - chr7_1:77585484-77585503 Msa1040250:CDS 25.0%
TATCGCTTTACATTGTCTTT+AGG - chr7_1:77583681-77583700 Msa1040250:three_prime_UTR 30.0%
!!! GGAAGAGAATTTTAGTTACA+TGG + chr7_1:77583861-77583880 None:intergenic 30.0%
! GTGGTAATGTATTATATAGG+TGG - chr7_1:77583945-77583964 Msa1040250:three_prime_UTR 30.0%
CAAATGCTAAATTGATCACT+TGG + chr7_1:77584043-77584062 None:intergenic 30.0%
GAGCAAGAAATAGATAGAAA+AGG + chr7_1:77584082-77584101 None:intergenic 30.0%
TGAGTATAATAGGAAAACCA+GGG + chr7_1:77584190-77584209 None:intergenic 30.0%
TTGAGTATAATAGGAAAACC+AGG + chr7_1:77584191-77584210 None:intergenic 30.0%
GTATATGATGAATTGTATGG+AGG - chr7_1:77584240-77584259 Msa1040250:intron 30.0%
! TCAACTAGGTCATCTAAAAT+GGG + chr7_1:77584366-77584385 None:intergenic 30.0%
TCAACTAGGTCATATATTGA+GGG - chr7_1:77584577-77584596 Msa1040250:intron 30.0%
!! TTTAGACGATCGATTTGTAA+AGG - chr7_1:77584698-77584717 Msa1040250:intron 30.0%
CAATAGAAATAACACAGGTT+TGG + chr7_1:77585082-77585101 None:intergenic 30.0%
AAAGGGGAAAATATGTGAAA+AGG - chr7_1:77585176-77585195 Msa1040250:intron 30.0%
AAGGGGAAAATATGTGAAAA+GGG - chr7_1:77585177-77585196 Msa1040250:intron 30.0%
!!! TAATTGTTTTTGTTGACAGG+TGG - chr7_1:77585412-77585431 Msa1040250:intron 30.0%
CATGAACAAGATTATTGAGA+AGG + chr7_1:77585643-77585662 None:intergenic 30.0%
GGGAGATTATAATAAAGTCA+AGG + chr7_1:77585699-77585718 None:intergenic 30.0%
! GTTTACAGAACAGTGTTGTT+GGG + chr7_1:77583717-77583736 None:intergenic 35.0%
AGTTTACAGAACAGTGTTGT+TGG + chr7_1:77583718-77583737 None:intergenic 35.0%
GTATTATATAGGTGGAGTTC+TGG - chr7_1:77583953-77583972 Msa1040250:three_prime_UTR 35.0%
AGATAGCATAGAGAATTCCA+GGG + chr7_1:77584011-77584030 None:intergenic 35.0%
TAGATAGCATAGAGAATTCC+AGG + chr7_1:77584012-77584031 None:intergenic 35.0%
! CTTTGCATATACATTTGGTG+TGG + chr7_1:77584301-77584320 None:intergenic 35.0%
GTCAACTAGGTCATCTAAAA+TGG + chr7_1:77584367-77584386 None:intergenic 35.0%
GTCAACTAGGTCATATATTG+AGG - chr7_1:77584576-77584595 Msa1040250:intron 35.0%
TCCTCTTGTATTAAATCGCA+AGG - chr7_1:77584723-77584742 Msa1040250:intron 35.0%
!! AATTTTGAGTGTGTTTGAGC+CGG + chr7_1:77585118-77585137 None:intergenic 35.0%
CAGACAGCATATAATGATCT+GGG + chr7_1:77585291-77585310 None:intergenic 35.0%
ACAGACAGCATATAATGATC+TGG + chr7_1:77585292-77585311 None:intergenic 35.0%
TGGATCATACATAGTTGTCA+GGG - chr7_1:77585432-77585451 Msa1040250:CDS 35.0%
GAAACCATGTAACATGTATG+AGG + chr7_1:77585459-77585478 None:intergenic 35.0%
AAGCTTATGAACTCTAGCAA+TGG - chr7_1:77585589-77585608 Msa1040250:intron 35.0%
TCTCCCCAAAAGATCGAAAA+TGG - chr7_1:77583762-77583781 Msa1040250:three_prime_UTR 40.0%
CTCCCCAAAAGATCGAAAAT+GGG - chr7_1:77583763-77583782 Msa1040250:three_prime_UTR 40.0%
! TGCCCATTTTCGATCTTTTG+GGG + chr7_1:77583768-77583787 None:intergenic 40.0%
! GTGCCCATTTTCGATCTTTT+GGG + chr7_1:77583769-77583788 None:intergenic 40.0%
! AGTGCCCATTTTCGATCTTT+TGG + chr7_1:77583770-77583789 None:intergenic 40.0%
!!! TGTTTGGTGCTAACCCTTTT+TGG - chr7_1:77583979-77583998 Msa1040250:three_prime_UTR 40.0%
! GCATAAAAAAGCATGACACG+AGG + chr7_1:77584161-77584180 None:intergenic 40.0%
!!! CTTTTTTATGCACGATACCC+TGG - chr7_1:77584170-77584189 Msa1040250:intron 40.0%
! CTAGGTCATCTAAAATGGGA+CGG + chr7_1:77584362-77584381 None:intergenic 40.0%
! AAATGCATTGGTACGTGTGT+CGG + chr7_1:77584391-77584410 None:intergenic 40.0%
GTCATATATTGAGGGACAGA+GGG - chr7_1:77584585-77584604 Msa1040250:intron 40.0%
GCCTTGCGATTTAATACAAG+AGG + chr7_1:77584727-77584746 None:intergenic 40.0%
! TTTTCGCTCATACTTACGAC+CGG - chr7_1:77584892-77584911 Msa1040250:intron 40.0%
GTGGATCATACATAGTTGTC+AGG - chr7_1:77585431-77585450 Msa1040250:CDS 40.0%
GGATCATACATAGTTGTCAG+GGG - chr7_1:77585433-77585452 Msa1040250:CDS 40.0%
TTACATGGCAGCCAAACTTG+AGG + chr7_1:77583846-77583865 None:intergenic 45.0%
TCCAGGGAGATAGCCAAAAA+GGG + chr7_1:77583995-77584014 None:intergenic 45.0%
TTCCAGGGAGATAGCCAAAA+AGG + chr7_1:77583996-77584015 None:intergenic 45.0%
! GTCATCTAAAATGGGACGGA+GGG + chr7_1:77584358-77584377 None:intergenic 45.0%
GGTCATATATTGAGGGACAG+AGG - chr7_1:77584584-77584603 Msa1040250:intron 45.0%
CGTGAAAAGAAGAAGACGTG+TGG - chr7_1:77585247-77585266 Msa1040250:intron 45.0%
!! GTAAATTAATATATTAATAA+GGG + chr7_1:77585719-77585738 None:intergenic 5.0%
!! CTTATTAATATATTAATTTA+CGG - chr7_1:77585718-77585737 Msa1040250:five_prime_UTR 5.0%
AACTTGAGGAAGACACCCAG+AGG + chr7_1:77583832-77583851 None:intergenic 50.0%
CTGGGTGTCTTCCTCAAGTT+TGG - chr7_1:77583832-77583851 Msa1040250:three_prime_UTR 50.0%
!!! ACCCTTTTTGGCTATCTCCC+TGG - chr7_1:77583991-77584010 Msa1040250:three_prime_UTR 50.0%
! GGTCATCTAAAATGGGACGG+AGG + chr7_1:77584359-77584378 None:intergenic 50.0%
TACGTGTGTCGGAGTCAACT+AGG + chr7_1:77584380-77584399 None:intergenic 50.0%
ACTTAGCTCGTTGTACCCTC+CGG + chr7_1:77584914-77584933 None:intergenic 50.0%
GGGGCCTCATACATGTTACA+TGG - chr7_1:77585452-77585471 Msa1040250:CDS 50.0%
TGAGGAAGACACCCAGAGGA+GGG + chr7_1:77583828-77583847 None:intergenic 55.0%
TTGAGGAAGACACCCAGAGG+AGG + chr7_1:77583829-77583848 None:intergenic 55.0%
!! GGTGGAGTTCTGGCTCTGTT+TGG - chr7_1:77583963-77583982 Msa1040250:three_prime_UTR 55.0%
TCGCTCATACTTACGACCGG+AGG - chr7_1:77584895-77584914 Msa1040250:intron 55.0%
CGCTCATACTTACGACCGGA+GGG - chr7_1:77584896-77584915 Msa1040250:intron 55.0%
TGCCATCATCCTCCCTCCTC+TGG - chr7_1:77583813-77583832 Msa1040250:three_prime_UTR 60.0%
GCCATCATCCTCCCTCCTCT+GGG - chr7_1:77583814-77583833 Msa1040250:three_prime_UTR 60.0%
ACCCAGAGGAGGGAGGATGA+TGG + chr7_1:77583818-77583837 None:intergenic 60.0%
GGAAGACACCCAGAGGAGGG+AGG + chr7_1:77583825-77583844 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr7_1 gene 77583676 77585799 77583676 ID=Msa1040250;Name=Msa1040250
chr7_1 mRNA 77583676 77585799 77583676 ID=Msa1040250-mRNA-1;Parent=Msa1040250;Name=Msa1040250-mRNA-1;_AED=0.07;_eAED=0.07;_QI=105|1|1|1|0.5|0.33|3|383|54
chr7_1 exon 77583676 77584044 77583676 ID=Msa1040250-mRNA-1:exon:20464;Parent=Msa1040250-mRNA-1
chr7_1 exon 77585414 77585511 77585414 ID=Msa1040250-mRNA-1:exon:20463;Parent=Msa1040250-mRNA-1
chr7_1 exon 77585614 77585799 77585614 ID=Msa1040250-mRNA-1:exon:20462;Parent=Msa1040250-mRNA-1
chr7_1 five_prime_UTR 77585695 77585799 77585695 ID=Msa1040250-mRNA-1:five_prime_utr;Parent=Msa1040250-mRNA-1
chr7_1 CDS 77585614 77585694 77585614 ID=Msa1040250-mRNA-1:cds;Parent=Msa1040250-mRNA-1
chr7_1 CDS 77585428 77585511 77585428 ID=Msa1040250-mRNA-1:cds;Parent=Msa1040250-mRNA-1
chr7_1 three_prime_UTR 77585414 77585427 77585414 ID=Msa1040250-mRNA-1:three_prime_utr;Parent=Msa1040250-mRNA-1
chr7_1 three_prime_UTR 77583676 77584044 77583676 ID=Msa1040250-mRNA-1:three_prime_utr;Parent=Msa1040250-mRNA-1
Gene Sequence

>Msa1040250

ATGGGCACTGCTACATGCATCGATATCATTGTTGCCATCATCCTCCCTCCTCTGGGTGTCTTCCTCAAGTTTGGCTGCCATGTGGAGTTCTGGCTCTGTTTGGTGCTAACCCTTTTTGGCTATCTCCCTGGAATTCTCTATGCTATCTATGCTATTACCAAGTGA
Protein sequence

>Msa1040250

MGTATCIDIIVAIILPPLGVFLKFGCHVEFWLCLVLTLFGYLPGILYAIYAITK*