AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene029536

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene029536.t1 MTR_5g036670 46.512 86 37 2 4 80 31 116 9.53e-16 70.5
MS.gene029536.t1 MTR_1g105955 50.769 65 32 0 10 74 98 162 4.53e-15 66.6
MS.gene029536.t1 MTR_1g105955 47.692 65 31 1 9 70 15 79 2.74e-11 56.6
MS.gene029536.t1 MTR_1g105960 52.239 67 30 1 10 74 2 68 1.07e-14 63.9
MS.gene029536.t1 MTR_8g062700 46.250 80 41 1 8 85 41 120 2.20e-14 66.6
MS.gene029536.t1 MTR_8g062700 46.250 80 41 1 8 85 41 120 2.35e-14 66.6
MS.gene029536.t1 MTR_4g133300 50.000 74 37 0 9 82 174 247 3.18e-14 65.5
MS.gene029536.t1 MTR_4g133470 50.000 74 37 0 9 82 174 247 3.31e-14 65.5
MS.gene029536.t1 MTR_1g105010 45.070 71 39 0 10 80 19 89 1.12e-13 61.6
MS.gene029536.t1 MTR_8g062350 44.444 72 38 1 7 76 12 83 2.47e-13 62.4
MS.gene029536.t1 MTR_6g008970 46.667 75 38 1 8 80 62 136 2.77e-13 63.5
MS.gene029536.t1 MTR_3g006150 55.224 67 27 2 9 72 90 156 6.73e-13 60.5
MS.gene029536.t1 MTR_3g006185 59.184 49 20 0 26 74 118 166 1.02e-12 60.1
MS.gene029536.t1 MTR_3g006065 55.224 67 27 2 9 72 90 156 1.03e-12 60.5
MS.gene029536.t1 MTR_1g109550 47.541 61 31 1 15 75 24 83 1.41e-12 59.3
MS.gene029536.t1 MTR_6g008995 43.243 74 40 1 9 80 37 110 1.50e-12 61.6
MS.gene029536.t1 MTR_3g006010 51.786 56 27 0 21 76 23 78 1.86e-12 61.2
MS.gene029536.t1 MTR_1g104940 48.571 70 34 1 9 76 14 83 2.97e-12 57.8
MS.gene029536.t1 MTR_1g093310 46.154 78 34 2 1 76 1 72 4.36e-12 56.6
MS.gene029536.t1 MTR_1g104960 50.704 71 33 1 8 76 12 82 6.91e-12 58.2
MS.gene029536.t1 MTR_3g006125 47.826 69 33 2 9 74 180 248 2.03e-11 57.8
MS.gene029536.t1 MTR_3g006105 45.455 66 36 0 11 76 13 78 7.10e-11 55.5
MS.gene029536.t1 MTR_1g100260 53.448 58 22 2 26 80 46 101 7.30e-11 54.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene029536.t1 AT1G24190 51.389 72 33 1 8 77 13 84 1.19e-15 70.5
MS.gene029536.t1 AT1G24190 51.389 72 33 1 8 77 13 84 1.30e-15 70.5
MS.gene029536.t1 AT1G24190 51.389 72 33 1 8 77 13 84 1.33e-15 70.5
MS.gene029536.t1 AT5G15020 48.000 75 37 1 8 80 51 125 4.64e-14 65.9
MS.gene029536.t1 AT5G15020 48.000 75 37 1 8 80 51 125 4.69e-14 65.9
MS.gene029536.t1 AT1G70060 52.113 71 32 1 8 76 13 83 5.48e-14 65.9
MS.gene029536.t1 AT1G70060 52.113 71 32 1 8 76 13 83 5.48e-14 65.9
MS.gene029536.t1 AT3G01320 49.296 71 34 1 8 76 56 126 1.72e-13 64.3
MS.gene029536.t1 AT3G01320 49.296 71 34 1 8 76 56 126 1.89e-13 64.3
MS.gene029536.t1 AT1G59890 47.887 71 35 1 9 77 45 115 1.81e-12 61.2
MS.gene029536.t1 AT1G59890 47.887 71 35 1 9 77 45 115 1.85e-12 61.2
MS.gene029536.t1 AT1G59890 47.887 71 35 1 9 77 45 115 1.86e-12 61.2
MS.gene029536.t1 AT1G59890 47.887 71 35 1 9 77 45 115 1.96e-12 61.2
MS.gene029536.t1 AT1G10450 45.946 74 38 1 9 80 84 157 1.49e-11 58.9
MS.gene029536.t1 AT4G12020 46.774 62 32 1 15 76 316 376 1.85e-11 58.5
MS.gene029536.t1 AT4G12020 46.774 62 32 1 15 76 316 376 2.00e-11 58.5
MS.gene029536.t1 AT4G12020 46.774 62 32 1 15 76 316 376 2.10e-11 58.5
MS.gene029536.t1 AT4G12020 46.774 62 32 1 15 76 316 376 2.14e-11 58.5
MS.gene029536.t1 AT4G12020 46.774 62 32 1 15 76 316 376 2.14e-11 58.5
MS.gene029536.t1 AT4G12020 46.774 62 32 1 15 76 249 309 2.14e-11 58.5
MS.gene029536.t1 AT1G10450 45.946 74 38 1 9 80 33 106 2.16e-11 58.2
MS.gene029536.t1 AT1G10450 45.946 74 38 1 9 80 33 106 2.16e-11 58.2
MS.gene029536.t1 AT4G12020 46.774 62 32 1 15 76 316 376 2.16e-11 58.5
MS.gene029536.t1 AT4G12020 46.774 62 32 1 15 76 316 376 2.18e-11 58.2
MS.gene029536.t1 AT4G12020 46.774 62 32 1 15 76 316 376 2.31e-11 58.2
MS.gene029536.t1 AT4G12020 46.774 62 32 1 15 76 316 376 2.57e-11 58.2
MS.gene029536.t1 AT4G12020 46.774 62 32 1 15 76 316 376 2.57e-11 58.2
MS.gene029536.t1 AT1G70030 40.299 67 40 0 14 80 29 95 3.11e-11 55.5
MS.gene029536.t1 AT1G70030 40.299 67 40 0 14 80 29 95 5.69e-11 55.1
MS.gene029536.t1 AT1G70030 40.299 67 40 0 14 80 18 84 9.57e-11 54.7

Find 17 sgRNAs with CRISPR-Local

Find 44 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGGGCATACTGATTTAATTT+TGG 0.112441 1.3:-73996220 MS.gene029536:CDS
AGAGTCAAGCAGCTGCTTAA+AGG 0.323406 1.3:-73996240 MS.gene029536:CDS
AGTTTGATTTGATGTTCCTT+TGG 0.399942 1.3:+73996180 None:intergenic
GAGTCAAGCAGCTGCTTAAA+GGG 0.418662 1.3:-73996239 MS.gene029536:CDS
TGATTTGATGTTCCTTTGGC+AGG 0.443659 1.3:+73996184 None:intergenic
TTGGCAGCGATTGTACAAGC+TGG 0.463810 1.3:-73996354 MS.gene029536:CDS
AAGCTGGGTTTCAAGATAAG+AGG 0.471098 1.3:-73996338 MS.gene029536:CDS
TGGCAGCGATTGTACAAGCT+GGG 0.511829 1.3:-73996353 MS.gene029536:CDS
AGCTGGGTTTCAAGATAAGA+GGG 0.518029 1.3:-73996337 MS.gene029536:CDS
AAAACTCCTAAAAGATGTCA+AGG 0.541090 1.3:-73996295 MS.gene029536:CDS
TTGATGTTCCTTTGGCAGGA+AGG 0.546048 1.3:+73996188 None:intergenic
CAAATCAAACTTGAGACCAC+TGG 0.570634 1.3:-73996168 MS.gene029536:intron
AATTTATACAAGACGTTCTG+CGG 0.581560 1.3:-73996265 MS.gene029536:CDS
ATTCAACACCTTCCTGCCAA+AGG 0.618562 1.3:-73996196 MS.gene029536:CDS
GCTGGGTTTCAAGATAAGAG+GGG 0.722942 1.3:-73996336 MS.gene029536:CDS
TCGCTGCCAACGCATCATCG+CGG 0.747815 1.3:+73996367 None:intergenic
TTGTGGTGGAAAAGAACACG+TGG 0.759088 1.3:-73995694 MS.gene029536:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ACTTATGTGTTTTTTTTTTA+AGG - chr1.3:73996002-73996021 MS.gene029536:intron 15.0%
! AATGATAAATTACTAACCAG+TGG + chr1.3:73995918-73995937 None:intergenic 25.0%
! GTTAATGTTATGATTGTTTG+TGG - chr1.3:73996356-73996375 MS.gene029536:CDS 25.0%
!!! ATTGATTTCACTTTTCTACT+TGG - chr1.3:73995942-73995961 MS.gene029536:intron 25.0%
!!! TTGATTTCACTTTTCTACTT+GGG - chr1.3:73995943-73995962 MS.gene029536:intron 25.0%
AAAACTCCTAAAAGATGTCA+AGG - chr1.3:73995772-73995791 MS.gene029536:intron 30.0%
AATGTTATGATTGTTTGTGG+TGG - chr1.3:73996359-73996378 MS.gene029536:CDS 30.0%
AATTTATACAAGACGTTCTG+CGG - chr1.3:73995802-73995821 MS.gene029536:intron 30.0%
ACAAAAATAGAGTCTTAGTG+TGG + chr1.3:73996216-73996235 None:intergenic 30.0%
! TTTGATCCTTGACATCTTTT+AGG + chr1.3:73995781-73995800 None:intergenic 30.0%
!! AGTTTGATTTGATGTTCCTT+TGG + chr1.3:73995890-73995909 None:intergenic 30.0%
!! TGATTTCACTTTTCTACTTG+GGG - chr1.3:73995944-73995963 MS.gene029536:intron 30.0%
!!! AGGGCATACTGATTTAATTT+TGG - chr1.3:73995847-73995866 MS.gene029536:intron 30.0%
!!! GGGCATACTGATTTAATTTT+GGG - chr1.3:73995848-73995867 MS.gene029536:intron 30.0%
ATAAGTCAAGATGACGACAA+GGG + chr1.3:73995988-73996007 None:intergenic 35.0%
!!! ACTCTATTTTTGTCTGAGCT+GGG - chr1.3:73996223-73996242 MS.gene029536:CDS 35.0%
AAGCTGGGTTTCAAGATAAG+AGG - chr1.3:73995729-73995748 MS.gene029536:intron 40.0%
AGCTGGGTTTCAAGATAAGA+GGG - chr1.3:73995730-73995749 MS.gene029536:intron 40.0%
CAAATCAAACTTGAGACCAC+TGG - chr1.3:73995899-73995918 MS.gene029536:intron 40.0%
CATAAGTCAAGATGACGACA+AGG + chr1.3:73995989-73996008 None:intergenic 40.0%
CGAAACGAAATCACAAGTGT+CGG + chr1.3:73996118-73996137 None:intergenic 40.0%
TGATTTGATGTTCCTTTGGC+AGG + chr1.3:73995886-73995905 None:intergenic 40.0%
! GCACTGACACTTCTGATTAA+AGG - chr1.3:73996059-73996078 MS.gene029536:intron 40.0%
! TTTTGTGTCTGTGTTGTGTC+CGG - chr1.3:73996154-73996173 MS.gene029536:intron 40.0%
!! ATGAAGCACTGACACACATA+CGG + chr1.3:73996187-73996206 None:intergenic 40.0%
!!! GACTCTATTTTTGTCTGAGC+TGG - chr1.3:73996222-73996241 MS.gene029536:CDS 40.0%
AAAAAACCGCGATGATGCGT+TGG - chr1.3:73995694-73995713 MS.gene029536:intron 45.0%
AGAGTCAAGCAGCTGCTTAA+AGG - chr1.3:73995827-73995846 MS.gene029536:intron 45.0%
ATTCAACACCTTCCTGCCAA+AGG - chr1.3:73995871-73995890 MS.gene029536:intron 45.0%
GAGTCAAGCAGCTGCTTAAA+GGG - chr1.3:73995828-73995847 MS.gene029536:intron 45.0%
GCTGGGTTTCAAGATAAGAG+GGG - chr1.3:73995731-73995750 MS.gene029536:intron 45.0%
GTGTCAGACACTACACATGT+CGG + chr1.3:73996096-73996115 None:intergenic 45.0%
TTGATGTTCCTTTGGCAGGA+AGG + chr1.3:73995882-73995901 None:intergenic 45.0%
! TTGTGGTGGAAAAGAACACG+TGG - chr1.3:73996373-73996392 MS.gene029536:CDS 45.0%
!!! AACGCATCATCGCGGTTTTT+TGG + chr1.3:73995695-73995714 None:intergenic 45.0%
!!! ACGCATCATCGCGGTTTTTT+GGG + chr1.3:73995694-73995713 None:intergenic 45.0%
TGGCAGCGATTGTACAAGCT+GGG - chr1.3:73995714-73995733 MS.gene029536:intron 50.0%
TTGGCAGCGATTGTACAAGC+TGG - chr1.3:73995713-73995732 MS.gene029536:intron 50.0%
!! CAGAAGTGTCAGTGCAACGT+AGG + chr1.3:73996054-73996073 None:intergenic 50.0%
ACACACATACGGACAGGCAC+CGG + chr1.3:73996176-73996195 None:intergenic 55.0%
GTCTGAGCTGGGCTATTGAC+AGG - chr1.3:73996234-73996253 MS.gene029536:CDS 55.0%
TGAGCTGGGCTATTGACAGG+AGG - chr1.3:73996237-73996256 MS.gene029536:CDS 55.0%
! GCACTGACACACATACGGAC+AGG + chr1.3:73996182-73996201 None:intergenic 55.0%
TCGCTGCCAACGCATCATCG+CGG + chr1.3:73995703-73995722 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 73995683 73996406 73995683 ID=MS.gene029536
chr1.3 mRNA 73995683 73996406 73995683 ID=MS.gene029536.t1;Parent=MS.gene029536
chr1.3 exon 73996169 73996406 73996169 ID=MS.gene029536.t1.exon1;Parent=MS.gene029536.t1
chr1.3 CDS 73996169 73996406 73996169 ID=cds.MS.gene029536.t1;Parent=MS.gene029536.t1
chr1.3 exon 73995683 73995702 73995683 ID=MS.gene029536.t1.exon2;Parent=MS.gene029536.t1
chr1.3 CDS 73995683 73995702 73995683 ID=cds.MS.gene029536.t1;Parent=MS.gene029536.t1
Gene Sequence

>MS.gene029536

ATGGAGATCCCAAAAAACCGCGATGATGCGTTGGCAGCGATTGTACAAGCTGGGTTTCAAGATAAGAGGGGAGATTATAATGAGCTTTTAAAACTCCTAAAAGATGTCAAGGATCAAACAATTTATACAAGACGTTCTGCGGCAAGAGTCAAGCAGCTGCTTAAAGGGCATACTGATTTAATTTTGGGATTCAACACCTTCCTGCCAAAGGAACATCAAATCAAACTTGAGACCACTGGTTAGTAATTTATCATTATCGATTGATTTCACTTTTCTACTTGGGGTTGATGTCTGTGTTAAAACCCTTGTCGTCATCTTGACTTATGTGTTTTTTTTTTAAGGAATCTTGACTTATGTTTTTTTTTTAACCTACGTTGCACTGACACTTCTGATTAAAGGCGTGTTGTTGTCCGACATGTGTAGTGTCTGACACCGACACTTGTGATTTCGTTTCGTGTCATTTTCTCAGAATTTTGTGTCTGTGTTGTGTCCGGTGCCTGTCCGTATGTGTGTCAGTGCTTCATAACTGTCCACACTAAGACTCTATTTTTGTCTGAGCTGGGCTATTGACAGGAGGCACACAAATATGATTTTAAACTATATTTATCTCTGCAGTCAGAAAGTCTGTTGTTGATTGTAAATGTAGCAGTTCAATTTTTAGAGAACTCTATTAGTTAATGTTATGATTGTTTGTGGTGGAAAAGAACACGTGGTTATTCAATAG
Protein sequence

>MS.gene029536.t1

MEIPKNRDDALAAIVQAGFQDKRGDYNELLKLLKDVKDQTIYTRRSAARVKQLLKGHTDLILGFNTFLPKEHQIKLETTEHVVIQ