AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1150710


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1150710 MtrunA17_Chr7g0240411 92.405 79 6 0 1 79 1 79 5.24e-49 149
Msa1150710 MtrunA17_Chr4g0008691 62.963 81 28 2 1 79 1 81 2.30e-32 107
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 38 sgRNAs with CRISPR-Local

Find 117 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTACCTTGGTTTGAAATTA+AGG 0.129246 7_4:-34505113 None:intergenic
GAGTTCGATATTATGTTAAA+TGG 0.198013 7_4:-34505923 None:intergenic
CACTTTGATTTACAAAATTA+TGG 0.210495 7_4:+34505826 Msa1150710:three_prime_UTR
TTCTCTAAACTTTGATATAT+AGG 0.300426 7_4:-34505406 None:intergenic
ATGAGAACATGAGGCTTGTT+TGG 0.314452 7_4:-34505025 None:intergenic
ATGAATTGTTACACAATTCA+TGG 0.321299 7_4:+34505856 Msa1150710:three_prime_UTR
CTAAAGAGTTTAGAAGGATA+AGG 0.353995 7_4:+34505692 Msa1150710:three_prime_UTR
CTTGAACCTCTCTAACTTTG+AGG 0.354710 7_4:+34504944 Msa1150710:five_prime_UTR
AGTTGACTAAAGAGTTTAGA+AGG 0.373568 7_4:+34505686 Msa1150710:three_prime_UTR
GAGTTGGGAGATATATAAAA+AGG 0.385399 7_4:-34504904 None:intergenic
TTTGTGTCTGCTAGTGCTAA+TGG 0.389664 7_4:+34505458 Msa1150710:three_prime_UTR
GAGGTACTTGCACTAGTACT+TGG 0.403825 7_4:+34505298 Msa1150710:CDS
CTTTAGTCAACTTTAGTTGA+AGG 0.419390 7_4:-34505675 None:intergenic
TAAAGAGTTTAGAAGGATAA+GGG 0.425247 7_4:+34505693 Msa1150710:three_prime_UTR
ATGAATTGTGTAACAATTCA+TGG 0.427262 7_4:-34505854 None:intergenic
AAGGATAAGGGATGGATATC+CGG 0.440238 7_4:+34505705 Msa1150710:three_prime_UTR
TTTGGTTTGAAACAAGTCAA+TGG 0.446404 7_4:+34505525 Msa1150710:three_prime_UTR
TGCAAATGTTGTGATGGAAT+TGG 0.452852 7_4:+34505276 Msa1150710:CDS
TTGGTTTGAAACAAGTCAAT+GGG 0.459688 7_4:+34505526 Msa1150710:three_prime_UTR
TTAGAGAGGTTCAAGAGCTA+TGG 0.483018 7_4:-34504936 None:intergenic
TTGTGTCTGCTAGTGCTAAT+GGG 0.495526 7_4:+34505459 Msa1150710:three_prime_UTR
GCTATGGAGCACTGATGAGT+TGG 0.497002 7_4:-34504920 None:intergenic
CTATGGAGCACTGATGAGTT+GGG 0.500776 7_4:-34504919 None:intergenic
GTCCTTGCTTCTATAAGTGA+TGG 0.503145 7_4:-34505085 None:intergenic
AGGATAGGAAACTTGAAGGA+TGG 0.532616 7_4:-34504884 None:intergenic
GGATAGGAAACTTGAAGGAT+GGG 0.533040 7_4:-34504883 None:intergenic
GTTGTTTGCAAATGTTGTGA+TGG 0.534057 7_4:+34505270 Msa1150710:CDS
AATAACTAGTGTGATTTCCA+AGG 0.557652 7_4:-34505351 None:intergenic
GAGTTTAGAAGGATAAGGGA+TGG 0.574430 7_4:+34505697 Msa1150710:three_prime_UTR
CTTTCCTTAATTTCAAACCA+AGG 0.576150 7_4:+34505109 Msa1150710:CDS
ATAGGAAACTTGAAGGATGG+GGG 0.578304 7_4:-34504881 None:intergenic
AACCATCACTTATAGAAGCA+AGG 0.587548 7_4:+34505083 Msa1150710:CDS
ATAACTTAAAGTGTTCACCT+TGG 0.595348 7_4:+34505334 Msa1150710:CDS
ATGAAACCTCAAAGTTAGAG+AGG 0.596758 7_4:-34504950 None:intergenic
AAATGTTGTGATGGAATTGG+AGG 0.597103 7_4:+34505279 Msa1150710:CDS
ATTAGTAATATGAGAACATG+AGG 0.602881 7_4:-34505034 None:intergenic
GATAGGAAACTTGAAGGATG+GGG 0.624815 7_4:-34504882 None:intergenic
AACAAGTTGCAATAGACATG+TGG 0.663724 7_4:-34505575 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTATTATAATTAATTACCT+TGG - chr7_4:34505129-34505148 None:intergenic 10.0%
!! ATTATTATAATTAATTACCT+TGG - chr7_4:34505129-34505148 None:intergenic 10.0%
!! AAATAAAAAATTAGATCTAG+TGG - chr7_4:34505193-34505212 None:intergenic 15.0%
!!! TTATTTTGTTATGTATTTTC+AGG + chr7_4:34505219-34505238 Msa1150710:intron 15.0%
!!! TATTTTGTTATGTATTTTCA+GGG + chr7_4:34505220-34505239 Msa1150710:intron 15.0%
!!! TGTGTAATTTTATTTTGTTT+TGG + chr7_4:34505750-34505769 Msa1150710:three_prime_UTR 15.0%
!!! GTGTAATTTTATTTTGTTTT+GGG + chr7_4:34505751-34505770 Msa1150710:three_prime_UTR 15.0%
!! AAATAAAAAATTAGATCTAG+TGG - chr7_4:34505193-34505212 None:intergenic 15.0%
!!! TTATTTTGTTATGTATTTTC+AGG + chr7_4:34505219-34505238 Msa1150710:intron 15.0%
!!! TATTTTGTTATGTATTTTCA+GGG + chr7_4:34505220-34505239 Msa1150710:intron 15.0%
!!! TGTGTAATTTTATTTTGTTT+TGG + chr7_4:34505750-34505769 Msa1150710:three_prime_UTR 15.0%
!!! GTGTAATTTTATTTTGTTTT+GGG + chr7_4:34505751-34505770 Msa1150710:three_prime_UTR 15.0%
!! ATATAAAAACATCAATCATG+TGG + chr7_4:34504836-34504855 Msa1150710:five_prime_UTR 20.0%
!!! AGTTATTTTTGTGATTTTTC+TGG + chr7_4:34505367-34505386 Msa1150710:exon 20.0%
!! TTCTCTAAACTTTGATATAT+AGG - chr7_4:34505409-34505428 None:intergenic 20.0%
!!! ATGATTTTTCATTGATGATA+AGG + chr7_4:34505641-34505660 Msa1150710:three_prime_UTR 20.0%
!!! TGATTTTTCATTGATGATAA+GGG + chr7_4:34505642-34505661 Msa1150710:three_prime_UTR 20.0%
!!! CACTTTGATTTACAAAATTA+TGG + chr7_4:34505826-34505845 Msa1150710:three_prime_UTR 20.0%
!!! ATGAAGCATATTTTAACTTT+TGG + chr7_4:34505886-34505905 Msa1150710:three_prime_UTR 20.0%
!!! TGAAGCATATTTTAACTTTT+GGG + chr7_4:34505887-34505906 Msa1150710:three_prime_UTR 20.0%
!! ATATAAAAACATCAATCATG+TGG + chr7_4:34504836-34504855 Msa1150710:five_prime_UTR 20.0%
!!! AGTTATTTTTGTGATTTTTC+TGG + chr7_4:34505367-34505386 Msa1150710:exon 20.0%
!! TTCTCTAAACTTTGATATAT+AGG - chr7_4:34505409-34505428 None:intergenic 20.0%
!!! ATGATTTTTCATTGATGATA+AGG + chr7_4:34505641-34505660 Msa1150710:three_prime_UTR 20.0%
!!! TGATTTTTCATTGATGATAA+GGG + chr7_4:34505642-34505661 Msa1150710:three_prime_UTR 20.0%
!!! CACTTTGATTTACAAAATTA+TGG + chr7_4:34505826-34505845 Msa1150710:three_prime_UTR 20.0%
!!! ATGAAGCATATTTTAACTTT+TGG + chr7_4:34505886-34505905 Msa1150710:three_prime_UTR 20.0%
!!! TGAAGCATATTTTAACTTTT+GGG + chr7_4:34505887-34505906 Msa1150710:three_prime_UTR 20.0%
! ATTAGTAATATGAGAACATG+AGG - chr7_4:34505037-34505056 None:intergenic 25.0%
!! ATTACCTTGGTTTGAAATTA+AGG - chr7_4:34505116-34505135 None:intergenic 25.0%
!!! TATATGTGTCCATAGTTTTT+TGG + chr7_4:34505507-34505526 Msa1150710:three_prime_UTR 25.0%
! TGTTTCAAACCAAAAAACTA+TGG - chr7_4:34505519-34505538 None:intergenic 25.0%
! TAAAGAGTTTAGAAGGATAA+GGG + chr7_4:34505693-34505712 Msa1150710:three_prime_UTR 25.0%
! ATGAATTGTGTAACAATTCA+TGG - chr7_4:34505857-34505876 None:intergenic 25.0%
! ATGAATTGTTACACAATTCA+TGG + chr7_4:34505856-34505875 Msa1150710:three_prime_UTR 25.0%
! GAGTTCGATATTATGTTAAA+TGG - chr7_4:34505926-34505945 None:intergenic 25.0%
! ATTAGTAATATGAGAACATG+AGG - chr7_4:34505037-34505056 None:intergenic 25.0%
!! ATTACCTTGGTTTGAAATTA+AGG - chr7_4:34505116-34505135 None:intergenic 25.0%
!!! TATATGTGTCCATAGTTTTT+TGG + chr7_4:34505507-34505526 Msa1150710:three_prime_UTR 25.0%
! TGTTTCAAACCAAAAAACTA+TGG - chr7_4:34505519-34505538 None:intergenic 25.0%
! TAAAGAGTTTAGAAGGATAA+GGG + chr7_4:34505693-34505712 Msa1150710:three_prime_UTR 25.0%
! ATGAATTGTGTAACAATTCA+TGG - chr7_4:34505857-34505876 None:intergenic 25.0%
! ATGAATTGTTACACAATTCA+TGG + chr7_4:34505856-34505875 Msa1150710:three_prime_UTR 25.0%
! GAGTTCGATATTATGTTAAA+TGG - chr7_4:34505926-34505945 None:intergenic 25.0%
AAAAAGGATAGGAAACTTGA+AGG - chr7_4:34504891-34504910 None:intergenic 30.0%
GGGAGATATATAAAAAGGAT+AGG - chr7_4:34504902-34504921 None:intergenic 30.0%
GAGTTGGGAGATATATAAAA+AGG - chr7_4:34504907-34504926 None:intergenic 30.0%
CTTTCCTTAATTTCAAACCA+AGG + chr7_4:34505109-34505128 Msa1150710:CDS 30.0%
! TCAAAGATTTTTGCAACACT+TGG + chr7_4:34505246-34505265 Msa1150710:CDS 30.0%
! ATAACTTAAAGTGTTCACCT+TGG + chr7_4:34505334-34505353 Msa1150710:CDS 30.0%
AATAACTAGTGTGATTTCCA+AGG - chr7_4:34505354-34505373 None:intergenic 30.0%
!! TTTGGTTTGAAACAAGTCAA+TGG + chr7_4:34505525-34505544 Msa1150710:three_prime_UTR 30.0%
! TTGGTTTGAAACAAGTCAAT+GGG + chr7_4:34505526-34505545 Msa1150710:three_prime_UTR 30.0%
CTTTAGTCAACTTTAGTTGA+AGG - chr7_4:34505678-34505697 None:intergenic 30.0%
AGTTGACTAAAGAGTTTAGA+AGG + chr7_4:34505686-34505705 Msa1150710:three_prime_UTR 30.0%
CTAAAGAGTTTAGAAGGATA+AGG + chr7_4:34505692-34505711 Msa1150710:three_prime_UTR 30.0%
AAAAAGGATAGGAAACTTGA+AGG - chr7_4:34504891-34504910 None:intergenic 30.0%
GGGAGATATATAAAAAGGAT+AGG - chr7_4:34504902-34504921 None:intergenic 30.0%
GAGTTGGGAGATATATAAAA+AGG - chr7_4:34504907-34504926 None:intergenic 30.0%
CTTTCCTTAATTTCAAACCA+AGG + chr7_4:34505109-34505128 Msa1150710:CDS 30.0%
! TCAAAGATTTTTGCAACACT+TGG + chr7_4:34505246-34505265 Msa1150710:CDS 30.0%
! ATAACTTAAAGTGTTCACCT+TGG + chr7_4:34505334-34505353 Msa1150710:CDS 30.0%
AATAACTAGTGTGATTTCCA+AGG - chr7_4:34505354-34505373 None:intergenic 30.0%
!! TTTGGTTTGAAACAAGTCAA+TGG + chr7_4:34505525-34505544 Msa1150710:three_prime_UTR 30.0%
! TTGGTTTGAAACAAGTCAAT+GGG + chr7_4:34505526-34505545 Msa1150710:three_prime_UTR 30.0%
CTTTAGTCAACTTTAGTTGA+AGG - chr7_4:34505678-34505697 None:intergenic 30.0%
AGTTGACTAAAGAGTTTAGA+AGG + chr7_4:34505686-34505705 Msa1150710:three_prime_UTR 30.0%
CTAAAGAGTTTAGAAGGATA+AGG + chr7_4:34505692-34505711 Msa1150710:three_prime_UTR 30.0%
ATGAAACCTCAAAGTTAGAG+AGG - chr7_4:34504953-34504972 None:intergenic 35.0%
AACCATCACTTATAGAAGCA+AGG + chr7_4:34505083-34505102 Msa1150710:CDS 35.0%
AATTAGATCTAGTGGAAGAG+AGG - chr7_4:34505185-34505204 None:intergenic 35.0%
GTTGTTTGCAAATGTTGTGA+TGG + chr7_4:34505270-34505289 Msa1150710:CDS 35.0%
! TGCAAATGTTGTGATGGAAT+TGG + chr7_4:34505276-34505295 Msa1150710:CDS 35.0%
! AAATGTTGTGATGGAATTGG+AGG + chr7_4:34505279-34505298 Msa1150710:CDS 35.0%
AACAAGTTGCAATAGACATG+TGG - chr7_4:34505578-34505597 None:intergenic 35.0%
! AGCATCTTTTGAGCTAAAAC+CGG - chr7_4:34505727-34505746 None:intergenic 35.0%
ATGAAACCTCAAAGTTAGAG+AGG - chr7_4:34504953-34504972 None:intergenic 35.0%
AACCATCACTTATAGAAGCA+AGG + chr7_4:34505083-34505102 Msa1150710:CDS 35.0%
AATTAGATCTAGTGGAAGAG+AGG - chr7_4:34505185-34505204 None:intergenic 35.0%
GTTGTTTGCAAATGTTGTGA+TGG + chr7_4:34505270-34505289 Msa1150710:CDS 35.0%
! TGCAAATGTTGTGATGGAAT+TGG + chr7_4:34505276-34505295 Msa1150710:CDS 35.0%
! AAATGTTGTGATGGAATTGG+AGG + chr7_4:34505279-34505298 Msa1150710:CDS 35.0%
AACAAGTTGCAATAGACATG+TGG - chr7_4:34505578-34505597 None:intergenic 35.0%
! AGCATCTTTTGAGCTAAAAC+CGG - chr7_4:34505727-34505746 None:intergenic 35.0%
ATAGGAAACTTGAAGGATGG+GGG - chr7_4:34504884-34504903 None:intergenic 40.0%
GATAGGAAACTTGAAGGATG+GGG - chr7_4:34504885-34504904 None:intergenic 40.0%
GGATAGGAAACTTGAAGGAT+GGG - chr7_4:34504886-34504905 None:intergenic 40.0%
AGGATAGGAAACTTGAAGGA+TGG - chr7_4:34504887-34504906 None:intergenic 40.0%
TTAGAGAGGTTCAAGAGCTA+TGG - chr7_4:34504939-34504958 None:intergenic 40.0%
CTTGAACCTCTCTAACTTTG+AGG + chr7_4:34504944-34504963 Msa1150710:five_prime_UTR 40.0%
! ATGAGAACATGAGGCTTGTT+TGG - chr7_4:34505028-34505047 None:intergenic 40.0%
GTCCTTGCTTCTATAAGTGA+TGG - chr7_4:34505088-34505107 None:intergenic 40.0%
TTTGTGTCTGCTAGTGCTAA+TGG + chr7_4:34505458-34505477 Msa1150710:three_prime_UTR 40.0%
TTGTGTCTGCTAGTGCTAAT+GGG + chr7_4:34505459-34505478 Msa1150710:three_prime_UTR 40.0%
GAGTTTAGAAGGATAAGGGA+TGG + chr7_4:34505697-34505716 Msa1150710:three_prime_UTR 40.0%
AAGGATAAGGGATGGATATC+CGG + chr7_4:34505705-34505724 Msa1150710:three_prime_UTR 40.0%
ATAGGAAACTTGAAGGATGG+GGG - chr7_4:34504884-34504903 None:intergenic 40.0%
GATAGGAAACTTGAAGGATG+GGG - chr7_4:34504885-34504904 None:intergenic 40.0%
GGATAGGAAACTTGAAGGAT+GGG - chr7_4:34504886-34504905 None:intergenic 40.0%
AGGATAGGAAACTTGAAGGA+TGG - chr7_4:34504887-34504906 None:intergenic 40.0%
TTAGAGAGGTTCAAGAGCTA+TGG - chr7_4:34504939-34504958 None:intergenic 40.0%
CTTGAACCTCTCTAACTTTG+AGG + chr7_4:34504944-34504963 Msa1150710:five_prime_UTR 40.0%
! ATGAGAACATGAGGCTTGTT+TGG - chr7_4:34505028-34505047 None:intergenic 40.0%
GTCCTTGCTTCTATAAGTGA+TGG - chr7_4:34505088-34505107 None:intergenic 40.0%
TTTGTGTCTGCTAGTGCTAA+TGG + chr7_4:34505458-34505477 Msa1150710:three_prime_UTR 40.0%
TTGTGTCTGCTAGTGCTAAT+GGG + chr7_4:34505459-34505478 Msa1150710:three_prime_UTR 40.0%
GAGTTTAGAAGGATAAGGGA+TGG + chr7_4:34505697-34505716 Msa1150710:three_prime_UTR 40.0%
AAGGATAAGGGATGGATATC+CGG + chr7_4:34505705-34505724 Msa1150710:three_prime_UTR 40.0%
!! CTATGGAGCACTGATGAGTT+GGG - chr7_4:34504922-34504941 None:intergenic 45.0%
! GAGGTACTTGCACTAGTACT+TGG + chr7_4:34505298-34505317 Msa1150710:CDS 45.0%
!! CTATGGAGCACTGATGAGTT+GGG - chr7_4:34504922-34504941 None:intergenic 45.0%
! GAGGTACTTGCACTAGTACT+TGG + chr7_4:34505298-34505317 Msa1150710:CDS 45.0%
!!! ATGTTTTTATATTATTAATT+AGG - chr7_4:34504828-34504847 None:intergenic 5.0%
!! GCTATGGAGCACTGATGAGT+TGG - chr7_4:34504923-34504942 None:intergenic 50.0%
!! GCTATGGAGCACTGATGAGT+TGG - chr7_4:34504923-34504942 None:intergenic 50.0%
GAAGGATGGGGGATGCTGCT+TGG - chr7_4:34504873-34504892 None:intergenic 60.0%
GAAGGATGGGGGATGCTGCT+TGG - chr7_4:34504873-34504892 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr7_4 gene 34504828 34505977 34504828 ID=Msa1150710;Name=Msa1150710
chr7_4 mRNA 34504828 34505977 34504828 ID=Msa1150710-mRNA-1;Parent=Msa1150710;Name=Msa1150710-mRNA-1;_AED=0.04;_eAED=0.04;_QI=191|1|1|1|1|1|2|609|79
chr7_4 exon 34504828 34505130 34504828 ID=Msa1150710-mRNA-1:exon:8187;Parent=Msa1150710-mRNA-1
chr7_4 exon 34505241 34505977 34505241 ID=Msa1150710-mRNA-1:exon:8188;Parent=Msa1150710-mRNA-1
chr7_4 five_prime_UTR 34504828 34505018 34504828 ID=Msa1150710-mRNA-1:five_prime_utr;Parent=Msa1150710-mRNA-1
chr7_4 CDS 34505019 34505130 34505019 ID=Msa1150710-mRNA-1:cds;Parent=Msa1150710-mRNA-1
chr7_4 CDS 34505241 34505368 34505241 ID=Msa1150710-mRNA-1:cds;Parent=Msa1150710-mRNA-1
chr7_4 three_prime_UTR 34505369 34505977 34505369 ID=Msa1150710-mRNA-1:three_prime_utr;Parent=Msa1150710-mRNA-1
Gene Sequence

>Msa1150710

ATGAGTCCAAACAAGCCTCATGTTCTCATATTACTAATCATCATGCTTGTTTCAGTTTCTAATAAACCATCACTTATAGAAGCAAGGACACTTTCCTTAATTTCAAACCAAGGGTACTCAAAGATTTTTGCAACACTTGGAGTTGTTTGCAAATGTTGTGATGGAATTGGAGGTACTTGCACTAGTACTTGGACACAATCTTGTAATAACTTAAAGTGTTCACCTTGGAAATCACACTAG

Protein sequence

>Msa1150710

MSPNKPHVLILLIIMLVSVSNKPSLIEARTLSLISNQGYSKIFATLGVVCKCCDGIGGTCTSTWTQSCNNLKCSPWKSH*