AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0041480

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0041480 MtrunA17_Chr1g0206931 95.181 83 4 0 1 83 1 83 1.10e-48 148
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0041480 AT3G49780.1 49.275 69 34 1 15 83 12 79 5.13e-19 73.9
Msa0041480 AT2G22860.1 44.304 79 36 3 11 82 8 85 2.98e-13 59.7
Msa0041480 AT5G65870.1 43.902 82 37 5 4 83 3 77 5.03e-11 53.5

Find 33 sgRNAs with CRISPR-Local

Find 109 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAATTTATATATAATAATTA+TGG 0.219026 1_1:+71898883 Msa0041480:three_prime_UTR
TGATTATTGCTTGAAATGAT+AGG 0.250100 1_1:-71898214 None:intergenic
TTTACAGCTTATACTTTGAT+AGG 0.290425 1_1:-71898963 None:intergenic
TGTAAAGTTCATGACTTGTT+TGG 0.355335 1_1:+71898980 Msa0041480:three_prime_UTR
CTGTCTGCAACTACACGAAT+TGG 0.375259 1_1:-71898758 None:intergenic
GATTATTGCTTGAAATGATA+GGG 0.382504 1_1:-71898213 None:intergenic
TTCCTGCATCACAAAGTAAT+AGG 0.397235 1_1:+71898071 None:intergenic
GAAATGATAGGGGAAGAAAC+TGG 0.413968 1_1:-71898202 None:intergenic
CTTTGCAAAAGAACCGACTT+TGG 0.416548 1_1:-71899024 None:intergenic
GAAGAACACTGCCAGGCAAA+GGG 0.420808 1_1:-71898140 None:intergenic
TGCCTATTACTTTGTGATGC+AGG 0.436701 1_1:-71898073 None:intergenic
AGCAATGTTTCCAGTTTGAA+TGG 0.440718 1_1:+71898939 Msa0041480:three_prime_UTR
TTTGATAGGACCATTCAAAC+TGG 0.445080 1_1:-71898949 None:intergenic
TTCTTCACCTTCACATATGC+AGG 0.450291 1_1:+71898169 Msa0041480:CDS
CGACATAGAGGAGAATTGTA+AGG 0.464439 1_1:+71898545 Msa0041480:CDS
TTCAAGCAATAATCAATATG+AGG 0.505839 1_1:+71898222 Msa0041480:CDS
AGAGGAAGAAGAACACTGCC+AGG 0.527252 1_1:-71898147 None:intergenic
AGAAGAACACTGCCAGGCAA+AGG 0.533283 1_1:-71898141 None:intergenic
AGAACACTGCCAGGCAAAGG+GGG 0.545291 1_1:-71898138 None:intergenic
ATTATTGCTTGAAATGATAG+GGG 0.553608 1_1:-71898212 None:intergenic
AAGAACACTGCCAGGCAAAG+GGG 0.559740 1_1:-71898139 None:intergenic
AAATGATAGGGGAAGAAACT+GGG 0.571715 1_1:-71898201 None:intergenic
TTCACATATGCAGGAAGACA+TGG 0.574815 1_1:+71898178 Msa0041480:CDS
AGATGAAAAGGTCGACATAG+AGG 0.578140 1_1:+71898533 Msa0041480:CDS
CAACAAAATGTATCCAAAGT+CGG 0.598594 1_1:+71899011 Msa0041480:three_prime_UTR
GAACACTGCCAGGCAAAGGG+GGG 0.612397 1_1:-71898137 None:intergenic
TAACTAAACTACCTGATCGA+AGG 0.623162 1_1:-71898726 None:intergenic
GACATAGAGGAGAATTGTAA+GGG 0.628135 1_1:+71898546 Msa0041480:CDS
CATATGTGAAGGTGAAGAAG+AGG 0.635282 1_1:-71898165 None:intergenic
GGACTATATCTACACACAGA+AGG 0.637377 1_1:+71898617 Msa0041480:CDS
AAGAACACTTGTAGCTCACA+CGG 0.638996 1_1:+71898596 Msa0041480:CDS
ATGTCTTCCTGCATATGTGA+AGG 0.667872 1_1:-71898176 None:intergenic
TTATACATAAAATTACAACA+AGG 0.776318 1_1:-71898672 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAATTTATATATAATAATTA+TGG + chr1_1:71898883-71898902 Msa0041480:three_prime_UTR 0.0%
!! TAATTTATATATAATAATTA+TGG + chr1_1:71898883-71898902 Msa0041480:three_prime_UTR 0.0%
!! TTATACATAAAATTACAACA+AGG - chr1_1:71898675-71898694 None:intergenic 15.0%
!!! TTCTTATTTGTTTTCTTTTT+GGG + chr1_1:71898908-71898927 Msa0041480:three_prime_UTR 15.0%
!! TTATACATAAAATTACAACA+AGG - chr1_1:71898675-71898694 None:intergenic 15.0%
!!! TTCTTATTTGTTTTCTTTTT+GGG + chr1_1:71898908-71898927 Msa0041480:three_prime_UTR 15.0%
!!! GTTCTTATTTGTTTTCTTTT+TGG + chr1_1:71898907-71898926 Msa0041480:three_prime_UTR 20.0%
!!! GTTCTTATTTGTTTTCTTTT+TGG + chr1_1:71898907-71898926 Msa0041480:three_prime_UTR 20.0%
! ATTATTGCTTGAAATGATAG+GGG - chr1_1:71898215-71898234 None:intergenic 25.0%
! GATTATTGCTTGAAATGATA+GGG - chr1_1:71898216-71898235 None:intergenic 25.0%
! TGATTATTGCTTGAAATGAT+AGG - chr1_1:71898217-71898236 None:intergenic 25.0%
! TTCAAGCAATAATCAATATG+AGG + chr1_1:71898222-71898241 Msa0041480:CDS 25.0%
! AATTGAACAATACAAAAGAG+AGG - chr1_1:71898467-71898486 None:intergenic 25.0%
! TTCTTAAACGTGTTAATTGA+AGG + chr1_1:71898503-71898522 Msa0041480:intron 25.0%
! AAAAACCATAGGTTCAAAAA+TGG + chr1_1:71898640-71898659 Msa0041480:exon 25.0%
!!! TATTTGTTTTCTTTTTGGGT+TGG + chr1_1:71898912-71898931 Msa0041480:three_prime_UTR 25.0%
!!! ATTTGTTTTCTTTTTGGGTT+GGG + chr1_1:71898913-71898932 Msa0041480:three_prime_UTR 25.0%
! TTTACAGCTTATACTTTGAT+AGG - chr1_1:71898966-71898985 None:intergenic 25.0%
!! AAGTGAATAATAACTTTTCC+AGG + chr1_1:71899044-71899063 Msa0041480:three_prime_UTR 25.0%
! ATTATTGCTTGAAATGATAG+GGG - chr1_1:71898215-71898234 None:intergenic 25.0%
! GATTATTGCTTGAAATGATA+GGG - chr1_1:71898216-71898235 None:intergenic 25.0%
! TGATTATTGCTTGAAATGAT+AGG - chr1_1:71898217-71898236 None:intergenic 25.0%
! TTCAAGCAATAATCAATATG+AGG + chr1_1:71898222-71898241 Msa0041480:CDS 25.0%
! AATTGAACAATACAAAAGAG+AGG - chr1_1:71898467-71898486 None:intergenic 25.0%
! TTCTTAAACGTGTTAATTGA+AGG + chr1_1:71898503-71898522 Msa0041480:intron 25.0%
! AAAAACCATAGGTTCAAAAA+TGG + chr1_1:71898640-71898659 Msa0041480:exon 25.0%
!!! TATTTGTTTTCTTTTTGGGT+TGG + chr1_1:71898912-71898931 Msa0041480:three_prime_UTR 25.0%
!!! ATTTGTTTTCTTTTTGGGTT+GGG + chr1_1:71898913-71898932 Msa0041480:three_prime_UTR 25.0%
! TTTACAGCTTATACTTTGAT+AGG - chr1_1:71898966-71898985 None:intergenic 25.0%
!! AAGTGAATAATAACTTTTCC+AGG + chr1_1:71899044-71899063 Msa0041480:three_prime_UTR 25.0%
TATATGTAATCTTAACGACG+TGG + chr1_1:71898306-71898325 Msa0041480:intron 30.0%
! AACGTGTTAATTGAAGGTTT+TGG + chr1_1:71898509-71898528 Msa0041480:intron 30.0%
!! GAAAACCATTTTTGAACCTA+TGG - chr1_1:71898648-71898667 None:intergenic 30.0%
! TTAATTTTTGACCTTCGATC+AGG + chr1_1:71898715-71898734 Msa0041480:three_prime_UTR 30.0%
TCAAAAATCAGTATACACAC+TGG - chr1_1:71898838-71898857 None:intergenic 30.0%
!!! TTTGTTTTCTTTTTGGGTTG+GGG + chr1_1:71898914-71898933 Msa0041480:three_prime_UTR 30.0%
!! TGTAAAGTTCATGACTTGTT+TGG + chr1_1:71898980-71898999 Msa0041480:three_prime_UTR 30.0%
CAACAAAATGTATCCAAAGT+CGG + chr1_1:71899011-71899030 Msa0041480:three_prime_UTR 30.0%
! TGAATAATAACTTTTCCAGG+AGG + chr1_1:71899047-71899066 Msa0041480:three_prime_UTR 30.0%
TATATGTAATCTTAACGACG+TGG + chr1_1:71898306-71898325 Msa0041480:intron 30.0%
! AACGTGTTAATTGAAGGTTT+TGG + chr1_1:71898509-71898528 Msa0041480:intron 30.0%
!! GAAAACCATTTTTGAACCTA+TGG - chr1_1:71898648-71898667 None:intergenic 30.0%
! TTAATTTTTGACCTTCGATC+AGG + chr1_1:71898715-71898734 Msa0041480:three_prime_UTR 30.0%
TCAAAAATCAGTATACACAC+TGG - chr1_1:71898838-71898857 None:intergenic 30.0%
!!! TTTGTTTTCTTTTTGGGTTG+GGG + chr1_1:71898914-71898933 Msa0041480:three_prime_UTR 30.0%
!! TGTAAAGTTCATGACTTGTT+TGG + chr1_1:71898980-71898999 Msa0041480:three_prime_UTR 30.0%
CAACAAAATGTATCCAAAGT+CGG + chr1_1:71899011-71899030 Msa0041480:three_prime_UTR 30.0%
AAATGATAGGGGAAGAAACT+GGG - chr1_1:71898204-71898223 None:intergenic 35.0%
! TTGTACTCGAGTTCGATTTT+TGG + chr1_1:71898375-71898394 Msa0041480:intron 35.0%
TGTCTAAGTGATTCGATCTT+CGG - chr1_1:71898428-71898447 None:intergenic 35.0%
!!! GAAGGTTTTGGAAGATGAAA+AGG + chr1_1:71898521-71898540 Msa0041480:intron 35.0%
GACATAGAGGAGAATTGTAA+GGG + chr1_1:71898546-71898565 Msa0041480:CDS 35.0%
TAACTAAACTACCTGATCGA+AGG - chr1_1:71898729-71898748 None:intergenic 35.0%
!!! TTGTTTTCTTTTTGGGTTGG+GGG + chr1_1:71898915-71898934 Msa0041480:three_prime_UTR 35.0%
AGCAATGTTTCCAGTTTGAA+TGG + chr1_1:71898939-71898958 Msa0041480:three_prime_UTR 35.0%
TTTGATAGGACCATTCAAAC+TGG - chr1_1:71898952-71898971 None:intergenic 35.0%
! CGACTTTGGATACATTTTGT+TGG - chr1_1:71899013-71899032 None:intergenic 35.0%
AAATGATAGGGGAAGAAACT+GGG - chr1_1:71898204-71898223 None:intergenic 35.0%
! TTGTACTCGAGTTCGATTTT+TGG + chr1_1:71898375-71898394 Msa0041480:intron 35.0%
TGTCTAAGTGATTCGATCTT+CGG - chr1_1:71898428-71898447 None:intergenic 35.0%
!!! GAAGGTTTTGGAAGATGAAA+AGG + chr1_1:71898521-71898540 Msa0041480:intron 35.0%
GACATAGAGGAGAATTGTAA+GGG + chr1_1:71898546-71898565 Msa0041480:CDS 35.0%
TAACTAAACTACCTGATCGA+AGG - chr1_1:71898729-71898748 None:intergenic 35.0%
!!! TTGTTTTCTTTTTGGGTTGG+GGG + chr1_1:71898915-71898934 Msa0041480:three_prime_UTR 35.0%
AGCAATGTTTCCAGTTTGAA+TGG + chr1_1:71898939-71898958 Msa0041480:three_prime_UTR 35.0%
TTTGATAGGACCATTCAAAC+TGG - chr1_1:71898952-71898971 None:intergenic 35.0%
! CGACTTTGGATACATTTTGT+TGG - chr1_1:71899013-71899032 None:intergenic 35.0%
CATATGTGAAGGTGAAGAAG+AGG - chr1_1:71898168-71898187 None:intergenic 40.0%
TTCTTCACCTTCACATATGC+AGG + chr1_1:71898169-71898188 Msa0041480:CDS 40.0%
ATGTCTTCCTGCATATGTGA+AGG - chr1_1:71898179-71898198 None:intergenic 40.0%
TTCACATATGCAGGAAGACA+TGG + chr1_1:71898178-71898197 Msa0041480:CDS 40.0%
GAAATGATAGGGGAAGAAAC+TGG - chr1_1:71898205-71898224 None:intergenic 40.0%
AGATGAAAAGGTCGACATAG+AGG + chr1_1:71898533-71898552 Msa0041480:CDS 40.0%
CGACATAGAGGAGAATTGTA+AGG + chr1_1:71898545-71898564 Msa0041480:CDS 40.0%
AAGAACACTTGTAGCTCACA+CGG + chr1_1:71898596-71898615 Msa0041480:CDS 40.0%
GGACTATATCTACACACAGA+AGG + chr1_1:71898617-71898636 Msa0041480:CDS 40.0%
CACACAGAAGGAAAAACCAT+AGG + chr1_1:71898629-71898648 Msa0041480:CDS 40.0%
! CTTTGCAAAAGAACCGACTT+TGG - chr1_1:71899027-71899046 None:intergenic 40.0%
CATATGTGAAGGTGAAGAAG+AGG - chr1_1:71898168-71898187 None:intergenic 40.0%
TTCTTCACCTTCACATATGC+AGG + chr1_1:71898169-71898188 Msa0041480:CDS 40.0%
ATGTCTTCCTGCATATGTGA+AGG - chr1_1:71898179-71898198 None:intergenic 40.0%
TTCACATATGCAGGAAGACA+TGG + chr1_1:71898178-71898197 Msa0041480:CDS 40.0%
GAAATGATAGGGGAAGAAAC+TGG - chr1_1:71898205-71898224 None:intergenic 40.0%
AGATGAAAAGGTCGACATAG+AGG + chr1_1:71898533-71898552 Msa0041480:CDS 40.0%
CGACATAGAGGAGAATTGTA+AGG + chr1_1:71898545-71898564 Msa0041480:CDS 40.0%
AAGAACACTTGTAGCTCACA+CGG + chr1_1:71898596-71898615 Msa0041480:CDS 40.0%
GGACTATATCTACACACAGA+AGG + chr1_1:71898617-71898636 Msa0041480:CDS 40.0%
CACACAGAAGGAAAAACCAT+AGG + chr1_1:71898629-71898648 Msa0041480:CDS 40.0%
! CTTTGCAAAAGAACCGACTT+TGG - chr1_1:71899027-71899046 None:intergenic 40.0%
GTGGTTCAGCTAAGTGGTTA+TGG + chr1_1:71898325-71898344 Msa0041480:intron 45.0%
CTGTCTGCAACTACACGAAT+TGG - chr1_1:71898761-71898780 None:intergenic 45.0%
GTGGTTCAGCTAAGTGGTTA+TGG + chr1_1:71898325-71898344 Msa0041480:intron 45.0%
CTGTCTGCAACTACACGAAT+TGG - chr1_1:71898761-71898780 None:intergenic 45.0%
AAGAACACTGCCAGGCAAAG+GGG - chr1_1:71898142-71898161 None:intergenic 50.0%
GAAGAACACTGCCAGGCAAA+GGG - chr1_1:71898143-71898162 None:intergenic 50.0%
AGAAGAACACTGCCAGGCAA+AGG - chr1_1:71898144-71898163 None:intergenic 50.0%
AGAGGAAGAAGAACACTGCC+AGG - chr1_1:71898150-71898169 None:intergenic 50.0%
AACGACGTGGTTCAGCTAAG+TGG + chr1_1:71898319-71898338 Msa0041480:intron 50.0%
AAGAACACTGCCAGGCAAAG+GGG - chr1_1:71898142-71898161 None:intergenic 50.0%
GAAGAACACTGCCAGGCAAA+GGG - chr1_1:71898143-71898162 None:intergenic 50.0%
AGAAGAACACTGCCAGGCAA+AGG - chr1_1:71898144-71898163 None:intergenic 50.0%
AGAGGAAGAAGAACACTGCC+AGG - chr1_1:71898150-71898169 None:intergenic 50.0%
AACGACGTGGTTCAGCTAAG+TGG + chr1_1:71898319-71898338 Msa0041480:intron 50.0%
AGAACACTGCCAGGCAAAGG+GGG - chr1_1:71898141-71898160 None:intergenic 55.0%
AGAACACTGCCAGGCAAAGG+GGG - chr1_1:71898141-71898160 None:intergenic 55.0%
AGTTAGTGCCCCCCTTTGCC+TGG + chr1_1:71898129-71898148 Msa0041480:CDS 60.0%
GAACACTGCCAGGCAAAGGG+GGG - chr1_1:71898140-71898159 None:intergenic 60.0%
AGTTAGTGCCCCCCTTTGCC+TGG + chr1_1:71898129-71898148 Msa0041480:CDS 60.0%
GAACACTGCCAGGCAAAGGG+GGG - chr1_1:71898140-71898159 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr1_1 gene 71898076 71899068 71898076 ID=Msa0041480;Name=Msa0041480
chr1_1 mRNA 71898076 71899068 71898076 ID=Msa0041480-mRNA-1;Parent=Msa0041480;Name=Msa0041480-mRNA-1;_AED=0.00;_eAED=0.00;_QI=42|1|1|1|1|1|2|418|83
chr1_1 exon 71898076 71898243 71898076 ID=Msa0041480-mRNA-1:exon:23829;Parent=Msa0041480-mRNA-1
chr1_1 exon 71898525 71899068 71898525 ID=Msa0041480-mRNA-1:exon:23830;Parent=Msa0041480-mRNA-1
chr1_1 five_prime_UTR 71898076 71898117 71898076 ID=Msa0041480-mRNA-1:five_prime_utr;Parent=Msa0041480-mRNA-1
chr1_1 CDS 71898118 71898243 71898118 ID=Msa0041480-mRNA-1:cds;Parent=Msa0041480-mRNA-1
chr1_1 CDS 71898525 71898650 71898525 ID=Msa0041480-mRNA-1:cds;Parent=Msa0041480-mRNA-1
chr1_1 three_prime_UTR 71898651 71899068 71898651 ID=Msa0041480-mRNA-1:three_prime_utr;Parent=Msa0041480-mRNA-1
Gene Sequence

>Msa0041480

ATGTCGTCTAAAGTTAGTGCCCCCCTTTGCCTGGCAGTGTTCTTCTTCCTCTTCTTCACCTTCACATATGCAGGAAGACATGGCCCAGTTTCTTCCCCTATCATTTCAAGCAATAATCAATATGAGGTTTTGGAAGATGAAAAGGTCGACATAGAGGAGAATTGTAAGGGTGTTAGTGAAGAAGATTGTTTGATGAGAAGAACACTTGTAGCTCACACGGACTATATCTACACACAGAAGGAAAAACCATAG
Protein sequence

>Msa0041480

MSSKVSAPLCLAVFFFLFFTFTYAGRHGPVSSPIISSNNQYEVLEDEKVDIEENCKGVSEEDCLMRRTLVAHTDYIYTQKEKP*