AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0089110

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0089110 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
Msa0089110 AT3G49780.1 49.275 69 34 1 15 83 12 79 5.13e-19 73.9
Msa0089110 AT2G22860.1 44.304 79 36 3 11 82 8 85 2.98e-13 59.7
Msa0089110 AT5G65870.1 43.902 82 37 5 4 83 3 77 5.03e-11 53.5

Find 33 sgRNAs with CRISPR-Local

Find 105 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTATACTACATAATAATTA+TGG 0.223016 1_2:+70526678 Msa0089110:three_prime_UTR
TGATTATTGCTTGAAATGAT+AGG 0.250100 1_2:-70526006 None:intergenic
TTTACAGCTTATACTTTGAT+AGG 0.290425 1_2:-70526758 None:intergenic
TGTAAAGTTCATGACTTGTT+TGG 0.355335 1_2:+70526775 Msa0089110:three_prime_UTR
TTGTCTGCAACTACACGAAT+TGG 0.375988 1_2:-70526550 None:intergenic
GATTATTGCTTGAAATGATA+GGG 0.382504 1_2:-70526005 None:intergenic
TTCCTGCATCACAAAGTAAT+AGG 0.397235 1_2:+70525863 None:intergenic
GAAATGATAGGGGAAGAAAC+TGG 0.413968 1_2:-70525994 None:intergenic
CTTTGCAAAAGAACCGACTT+TGG 0.416548 1_2:-70526819 None:intergenic
GAAGAACACTGCCAGGCAAA+GGG 0.420808 1_2:-70525932 None:intergenic
TGCCTATTACTTTGTGATGC+AGG 0.436701 1_2:-70525865 None:intergenic
TTTGATAGGACCATTCAAAC+TGG 0.445080 1_2:-70526744 None:intergenic
AGCAATGTTTCCAGTTTGAA+TGG 0.448153 1_2:+70526734 Msa0089110:three_prime_UTR
TTCTTCACCTTCACATATGC+AGG 0.450291 1_2:+70525961 Msa0089110:CDS
CGACATAGAGGAGAATTGTA+AGG 0.464439 1_2:+70526337 Msa0089110:CDS
TTCAAGCAATAATCAATATG+AGG 0.505839 1_2:+70526014 Msa0089110:CDS
AGAGGAAGAAGAACACTGCC+AGG 0.527252 1_2:-70525939 None:intergenic
AGAAGAACACTGCCAGGCAA+AGG 0.533283 1_2:-70525933 None:intergenic
AGAACACTGCCAGGCAAAGG+GGG 0.545291 1_2:-70525930 None:intergenic
ATTATTGCTTGAAATGATAG+GGG 0.553608 1_2:-70526004 None:intergenic
AAGAACACTGCCAGGCAAAG+GGG 0.559740 1_2:-70525931 None:intergenic
AAATGATAGGGGAAGAAACT+GGG 0.571715 1_2:-70525993 None:intergenic
TTCACATATGCAGGAAGACA+TGG 0.574815 1_2:+70525970 Msa0089110:CDS
AGATGAAAAGGTCGACATAG+AGG 0.578140 1_2:+70526325 Msa0089110:CDS
CAACAAAATGTATCCAAAGT+CGG 0.598594 1_2:+70526806 Msa0089110:three_prime_UTR
GAACACTGCCAGGCAAAGGG+GGG 0.612397 1_2:-70525929 None:intergenic
TAACTAAACTACCTGATCGA+AGG 0.623162 1_2:-70526518 None:intergenic
GACATAGAGGAGAATTGTAA+GGG 0.628135 1_2:+70526338 Msa0089110:CDS
CATATGTGAAGGTGAAGAAG+AGG 0.635282 1_2:-70525957 None:intergenic
GGACTATATCTACACACAGA+AGG 0.637377 1_2:+70526409 Msa0089110:CDS
AAGAACACTTGTAGCTCACA+CGG 0.638996 1_2:+70526388 Msa0089110:CDS
ATGTCTTCCTGCATATGTGA+AGG 0.667872 1_2:-70525968 None:intergenic
TTATACATAAAATTACAACA+AGG 0.776318 1_2:-70526464 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTATACTACATAATAATTA+TGG + chr1_2:70526678-70526697 Msa0089110:three_prime_UTR 10.0%
!! TTTATACTACATAATAATTA+TGG + chr1_2:70526678-70526697 Msa0089110:three_prime_UTR 10.0%
!! TTATACATAAAATTACAACA+AGG - chr1_2:70526467-70526486 None:intergenic 15.0%
!!! TTCTTATTTGTTTTCTTTTT+GGG + chr1_2:70526703-70526722 Msa0089110:three_prime_UTR 15.0%
!! TTATACATAAAATTACAACA+AGG - chr1_2:70526467-70526486 None:intergenic 15.0%
!!! TTCTTATTTGTTTTCTTTTT+GGG + chr1_2:70526703-70526722 Msa0089110:three_prime_UTR 15.0%
!!! GTTCTTATTTGTTTTCTTTT+TGG + chr1_2:70526702-70526721 Msa0089110:three_prime_UTR 20.0%
!!! GTTCTTATTTGTTTTCTTTT+TGG + chr1_2:70526702-70526721 Msa0089110:three_prime_UTR 20.0%
! ATTATTGCTTGAAATGATAG+GGG - chr1_2:70526007-70526026 None:intergenic 25.0%
! GATTATTGCTTGAAATGATA+GGG - chr1_2:70526008-70526027 None:intergenic 25.0%
! TGATTATTGCTTGAAATGAT+AGG - chr1_2:70526009-70526028 None:intergenic 25.0%
! TTCAAGCAATAATCAATATG+AGG + chr1_2:70526014-70526033 Msa0089110:CDS 25.0%
! AATTGAACAATACAAAAGAG+AGG - chr1_2:70526259-70526278 None:intergenic 25.0%
! TTCTTAAACGTGTTAATTGA+AGG + chr1_2:70526295-70526314 Msa0089110:intron 25.0%
! AAAAACCATAGGTTCAAAAA+TGG + chr1_2:70526432-70526451 Msa0089110:exon 25.0%
!!! TATTTGTTTTCTTTTTGGGT+TGG + chr1_2:70526707-70526726 Msa0089110:three_prime_UTR 25.0%
! TTTACAGCTTATACTTTGAT+AGG - chr1_2:70526761-70526780 None:intergenic 25.0%
!! AAGTGAATAATAACTTTTGC+AGG + chr1_2:70526839-70526858 Msa0089110:three_prime_UTR 25.0%
! ATTATTGCTTGAAATGATAG+GGG - chr1_2:70526007-70526026 None:intergenic 25.0%
! GATTATTGCTTGAAATGATA+GGG - chr1_2:70526008-70526027 None:intergenic 25.0%
! TGATTATTGCTTGAAATGAT+AGG - chr1_2:70526009-70526028 None:intergenic 25.0%
! TTCAAGCAATAATCAATATG+AGG + chr1_2:70526014-70526033 Msa0089110:CDS 25.0%
! AATTGAACAATACAAAAGAG+AGG - chr1_2:70526259-70526278 None:intergenic 25.0%
! TTCTTAAACGTGTTAATTGA+AGG + chr1_2:70526295-70526314 Msa0089110:intron 25.0%
! AAAAACCATAGGTTCAAAAA+TGG + chr1_2:70526432-70526451 Msa0089110:exon 25.0%
!!! TATTTGTTTTCTTTTTGGGT+TGG + chr1_2:70526707-70526726 Msa0089110:three_prime_UTR 25.0%
! TTTACAGCTTATACTTTGAT+AGG - chr1_2:70526761-70526780 None:intergenic 25.0%
!! AAGTGAATAATAACTTTTGC+AGG + chr1_2:70526839-70526858 Msa0089110:three_prime_UTR 25.0%
TATATGTAATCTTAACGACG+TGG + chr1_2:70526098-70526117 Msa0089110:intron 30.0%
! AACGTGTTAATTGAAGGTTT+TGG + chr1_2:70526301-70526320 Msa0089110:intron 30.0%
!! GAAAACCATTTTTGAACCTA+TGG - chr1_2:70526440-70526459 None:intergenic 30.0%
! TTAATTTTTGACCTTCGATC+AGG + chr1_2:70526507-70526526 Msa0089110:three_prime_UTR 30.0%
TCAAAAATCAGTATACACAC+TGG - chr1_2:70526630-70526649 None:intergenic 30.0%
!! TGTAAAGTTCATGACTTGTT+TGG + chr1_2:70526775-70526794 Msa0089110:three_prime_UTR 30.0%
CAACAAAATGTATCCAAAGT+CGG + chr1_2:70526806-70526825 Msa0089110:three_prime_UTR 30.0%
! TGAATAATAACTTTTGCAGG+AGG + chr1_2:70526842-70526861 Msa0089110:three_prime_UTR 30.0%
TATATGTAATCTTAACGACG+TGG + chr1_2:70526098-70526117 Msa0089110:intron 30.0%
! AACGTGTTAATTGAAGGTTT+TGG + chr1_2:70526301-70526320 Msa0089110:intron 30.0%
!! GAAAACCATTTTTGAACCTA+TGG - chr1_2:70526440-70526459 None:intergenic 30.0%
! TTAATTTTTGACCTTCGATC+AGG + chr1_2:70526507-70526526 Msa0089110:three_prime_UTR 30.0%
TCAAAAATCAGTATACACAC+TGG - chr1_2:70526630-70526649 None:intergenic 30.0%
!! TGTAAAGTTCATGACTTGTT+TGG + chr1_2:70526775-70526794 Msa0089110:three_prime_UTR 30.0%
CAACAAAATGTATCCAAAGT+CGG + chr1_2:70526806-70526825 Msa0089110:three_prime_UTR 30.0%
AAATGATAGGGGAAGAAACT+GGG - chr1_2:70525996-70526015 None:intergenic 35.0%
! TTGTACTCGAGTTCGATTTT+TGG + chr1_2:70526167-70526186 Msa0089110:intron 35.0%
TGTCTAAGTGATTCGATCTT+CGG - chr1_2:70526220-70526239 None:intergenic 35.0%
!!! GAAGGTTTTGGAAGATGAAA+AGG + chr1_2:70526313-70526332 Msa0089110:intron 35.0%
GACATAGAGGAGAATTGTAA+GGG + chr1_2:70526338-70526357 Msa0089110:CDS 35.0%
TAACTAAACTACCTGATCGA+AGG - chr1_2:70526521-70526540 None:intergenic 35.0%
!!! TTGTTTTCTTTTTGGGTTGG+AGG + chr1_2:70526710-70526729 Msa0089110:three_prime_UTR 35.0%
AGCAATGTTTCCAGTTTGAA+TGG + chr1_2:70526734-70526753 Msa0089110:three_prime_UTR 35.0%
TTTGATAGGACCATTCAAAC+TGG - chr1_2:70526747-70526766 None:intergenic 35.0%
! CGACTTTGGATACATTTTGT+TGG - chr1_2:70526808-70526827 None:intergenic 35.0%
AAATGATAGGGGAAGAAACT+GGG - chr1_2:70525996-70526015 None:intergenic 35.0%
! TTGTACTCGAGTTCGATTTT+TGG + chr1_2:70526167-70526186 Msa0089110:intron 35.0%
TGTCTAAGTGATTCGATCTT+CGG - chr1_2:70526220-70526239 None:intergenic 35.0%
!!! GAAGGTTTTGGAAGATGAAA+AGG + chr1_2:70526313-70526332 Msa0089110:intron 35.0%
GACATAGAGGAGAATTGTAA+GGG + chr1_2:70526338-70526357 Msa0089110:CDS 35.0%
TAACTAAACTACCTGATCGA+AGG - chr1_2:70526521-70526540 None:intergenic 35.0%
!!! TTGTTTTCTTTTTGGGTTGG+AGG + chr1_2:70526710-70526729 Msa0089110:three_prime_UTR 35.0%
AGCAATGTTTCCAGTTTGAA+TGG + chr1_2:70526734-70526753 Msa0089110:three_prime_UTR 35.0%
TTTGATAGGACCATTCAAAC+TGG - chr1_2:70526747-70526766 None:intergenic 35.0%
! CGACTTTGGATACATTTTGT+TGG - chr1_2:70526808-70526827 None:intergenic 35.0%
CATATGTGAAGGTGAAGAAG+AGG - chr1_2:70525960-70525979 None:intergenic 40.0%
TTCTTCACCTTCACATATGC+AGG + chr1_2:70525961-70525980 Msa0089110:CDS 40.0%
ATGTCTTCCTGCATATGTGA+AGG - chr1_2:70525971-70525990 None:intergenic 40.0%
TTCACATATGCAGGAAGACA+TGG + chr1_2:70525970-70525989 Msa0089110:CDS 40.0%
GAAATGATAGGGGAAGAAAC+TGG - chr1_2:70525997-70526016 None:intergenic 40.0%
AGATGAAAAGGTCGACATAG+AGG + chr1_2:70526325-70526344 Msa0089110:CDS 40.0%
CGACATAGAGGAGAATTGTA+AGG + chr1_2:70526337-70526356 Msa0089110:CDS 40.0%
AAGAACACTTGTAGCTCACA+CGG + chr1_2:70526388-70526407 Msa0089110:CDS 40.0%
GGACTATATCTACACACAGA+AGG + chr1_2:70526409-70526428 Msa0089110:CDS 40.0%
CACACAGAAGGAAAAACCAT+AGG + chr1_2:70526421-70526440 Msa0089110:CDS 40.0%
TTGTCTGCAACTACACGAAT+TGG - chr1_2:70526553-70526572 None:intergenic 40.0%
! CTTTGCAAAAGAACCGACTT+TGG - chr1_2:70526822-70526841 None:intergenic 40.0%
CATATGTGAAGGTGAAGAAG+AGG - chr1_2:70525960-70525979 None:intergenic 40.0%
TTCTTCACCTTCACATATGC+AGG + chr1_2:70525961-70525980 Msa0089110:CDS 40.0%
ATGTCTTCCTGCATATGTGA+AGG - chr1_2:70525971-70525990 None:intergenic 40.0%
TTCACATATGCAGGAAGACA+TGG + chr1_2:70525970-70525989 Msa0089110:CDS 40.0%
GAAATGATAGGGGAAGAAAC+TGG - chr1_2:70525997-70526016 None:intergenic 40.0%
AGATGAAAAGGTCGACATAG+AGG + chr1_2:70526325-70526344 Msa0089110:CDS 40.0%
CGACATAGAGGAGAATTGTA+AGG + chr1_2:70526337-70526356 Msa0089110:CDS 40.0%
AAGAACACTTGTAGCTCACA+CGG + chr1_2:70526388-70526407 Msa0089110:CDS 40.0%
GGACTATATCTACACACAGA+AGG + chr1_2:70526409-70526428 Msa0089110:CDS 40.0%
CACACAGAAGGAAAAACCAT+AGG + chr1_2:70526421-70526440 Msa0089110:CDS 40.0%
TTGTCTGCAACTACACGAAT+TGG - chr1_2:70526553-70526572 None:intergenic 40.0%
! CTTTGCAAAAGAACCGACTT+TGG - chr1_2:70526822-70526841 None:intergenic 40.0%
GTGGTTCAGCTAAGTGGTTA+TGG + chr1_2:70526117-70526136 Msa0089110:intron 45.0%
GTGGTTCAGCTAAGTGGTTA+TGG + chr1_2:70526117-70526136 Msa0089110:intron 45.0%
AAGAACACTGCCAGGCAAAG+GGG - chr1_2:70525934-70525953 None:intergenic 50.0%
GAAGAACACTGCCAGGCAAA+GGG - chr1_2:70525935-70525954 None:intergenic 50.0%
AGAAGAACACTGCCAGGCAA+AGG - chr1_2:70525936-70525955 None:intergenic 50.0%
AGAGGAAGAAGAACACTGCC+AGG - chr1_2:70525942-70525961 None:intergenic 50.0%
AACGACGTGGTTCAGCTAAG+TGG + chr1_2:70526111-70526130 Msa0089110:intron 50.0%
AAGAACACTGCCAGGCAAAG+GGG - chr1_2:70525934-70525953 None:intergenic 50.0%
GAAGAACACTGCCAGGCAAA+GGG - chr1_2:70525935-70525954 None:intergenic 50.0%
AGAAGAACACTGCCAGGCAA+AGG - chr1_2:70525936-70525955 None:intergenic 50.0%
AGAGGAAGAAGAACACTGCC+AGG - chr1_2:70525942-70525961 None:intergenic 50.0%
AACGACGTGGTTCAGCTAAG+TGG + chr1_2:70526111-70526130 Msa0089110:intron 50.0%
AGAACACTGCCAGGCAAAGG+GGG - chr1_2:70525933-70525952 None:intergenic 55.0%
AGAACACTGCCAGGCAAAGG+GGG - chr1_2:70525933-70525952 None:intergenic 55.0%
AGTTAGTGCCCCCCTTTGCC+TGG + chr1_2:70525921-70525940 Msa0089110:CDS 60.0%
GAACACTGCCAGGCAAAGGG+GGG - chr1_2:70525932-70525951 None:intergenic 60.0%
AGTTAGTGCCCCCCTTTGCC+TGG + chr1_2:70525921-70525940 Msa0089110:CDS 60.0%
GAACACTGCCAGGCAAAGGG+GGG - chr1_2:70525932-70525951 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 70525868 70526863 70525868 ID=Msa0089110;Name=Msa0089110
chr1_2 mRNA 70525868 70526863 70525868 ID=Msa0089110-mRNA-1;Parent=Msa0089110;Name=Msa0089110-mRNA-1;_AED=0.00;_eAED=0.00;_QI=42|1|1|1|1|1|2|421|83
chr1_2 exon 70525868 70526035 70525868 ID=Msa0089110-mRNA-1:exon:24227;Parent=Msa0089110-mRNA-1
chr1_2 exon 70526317 70526863 70526317 ID=Msa0089110-mRNA-1:exon:24228;Parent=Msa0089110-mRNA-1
chr1_2 five_prime_UTR 70525868 70525909 70525868 ID=Msa0089110-mRNA-1:five_prime_utr;Parent=Msa0089110-mRNA-1
chr1_2 CDS 70525910 70526035 70525910 ID=Msa0089110-mRNA-1:cds;Parent=Msa0089110-mRNA-1
chr1_2 CDS 70526317 70526442 70526317 ID=Msa0089110-mRNA-1:cds;Parent=Msa0089110-mRNA-1
chr1_2 three_prime_UTR 70526443 70526863 70526443 ID=Msa0089110-mRNA-1:three_prime_utr;Parent=Msa0089110-mRNA-1
Gene Sequence

>Msa0089110

ATGTCGTCTAAAGTTAGTGCCCCCCTTTGCCTGGCAGTGTTCTTCTTCCTCTTCTTCACCTTCACATATGCAGGAAGACATGGCCCAGTTTCTTCCCCTATCATTTCAAGCAATAATCAATATGAGGTTTTGGAAGATGAAAAGGTCGACATAGAGGAGAATTGTAAGGGTGTTAGTGAAGAAGATTGTTTGATGAGAAGAACACTTGTAGCTCACACGGACTATATCTACACACAGAAGGAAAAACCATAG
Protein sequence

>Msa0089110

MSSKVSAPLCLAVFFFLFFTFTYAGRHGPVSSPIISSNNQYEVLEDEKVDIEENCKGVSEEDCLMRRTLVAHTDYIYTQKEKP*