AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene044766

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene044766.t1 MTR_4g052060 93.956 182 6 2 1 177 1 182 9.83e-121 338
MS.gene044766.t1 MTR_4g052040 71.111 180 39 4 1 170 1 177 5.02e-74 220
MS.gene044766.t1 MTR_5g079710 44.516 155 80 4 6 159 12 161 6.18e-31 113
MS.gene044766.t1 MTR_0907s0020 59.701 67 27 0 91 157 104 170 7.10e-22 87.4
MS.gene044766.t1 MTR_7g105790 66.667 60 20 0 91 150 112 171 8.85e-22 87.8
MS.gene044766.t1 MTR_8g103520 41.558 77 45 0 82 158 217 293 8.54e-13 65.1
MS.gene044766.t1 MTR_5g075210 49.180 61 31 0 92 152 283 343 7.26e-11 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene044766.t1 AT3G52525 59.091 66 26 1 85 149 61 126 2.13e-20 83.2
MS.gene044766.t1 AT2G36026 59.016 61 25 0 94 154 91 151 7.73e-19 79.7
MS.gene044766.t1 AT5G22240 37.864 103 60 2 54 155 63 162 1.51e-12 63.5
MS.gene044766.t1 AT5G19650 44.776 67 37 0 88 154 153 219 1.89e-12 63.5

Find 33 sgRNAs with CRISPR-Local

Find 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATTTGGCTAATGGAAATTT+TGG 0.176660 4.1:-45867947 None:intergenic
TGGATGAAGCCTTGCTAATT+TGG 0.245892 4.1:-45867963 None:intergenic
GCTTCATCCAACACAACTTT+AGG 0.315005 4.1:+45867976 MS.gene044766:CDS
AGAGTGTTCTCAACAAATAT+TGG 0.353041 4.1:+45867868 MS.gene044766:CDS
AGCCTTGCTAATTTGGCTAA+TGG 0.359333 4.1:-45867956 None:intergenic
TCATAAACATGTATATTAGA+AGG 0.359929 4.1:-45868351 None:intergenic
AAACACTGTGGTTGTTGAAA+AGG 0.406424 4.1:+45868113 MS.gene044766:CDS
GAGTGCTTGAAATCATGATA+TGG 0.426047 4.1:-45868147 None:intergenic
ATGATCTTCGAGTTCTTCTT+CGG 0.426591 4.1:+45868211 MS.gene044766:CDS
ACAACCACAGTGTTTGATAG+AGG 0.460583 4.1:-45868105 None:intergenic
CACAACTTTAGGTGAAAGAA+AGG 0.468235 4.1:+45867987 MS.gene044766:CDS
TCTTTCACCTAAAGTTGTGT+TGG 0.468817 4.1:-45867983 None:intergenic
GCTGTGGTCGACGCTACAAC+CGG 0.476684 4.1:-45868013 None:intergenic
AGCTTCAGAGAAAGTGGTGG+TGG 0.499280 4.1:-45868046 None:intergenic
TATGCTTCAAATGATCTTCG+AGG 0.503327 4.1:+45868170 MS.gene044766:CDS
TCAACAAATATTGGAAGTTG+TGG 0.506051 4.1:+45867877 MS.gene044766:CDS
GTAGTAGTACAAACCTTGTC+GGG 0.514681 4.1:-45868312 None:intergenic
TGTTTCAGCTTCAGAGAAAG+TGG 0.518295 4.1:-45868052 None:intergenic
GTTTGATAGAGGGCTATGCT+TGG 0.522411 4.1:-45868094 None:intergenic
TTCCATTAGCCAAATTAGCA+AGG 0.533087 4.1:+45867954 MS.gene044766:CDS
TTTGATAGAGGGCTATGCTT+GGG 0.544333 4.1:-45868093 None:intergenic
AGTACACGAGCCTATTCAAA+AGG 0.546512 4.1:+45867924 MS.gene044766:CDS
CTTCGAGGATGAGATCGATT+CGG 0.564919 4.1:+45868185 MS.gene044766:CDS
GATAGAGGGCTATGCTTGGG+TGG 0.581428 4.1:-45868090 None:intergenic
AGTAGTAGTACAAACCTTGT+CGG 0.598934 4.1:-45868313 None:intergenic
CAACCACAGTGTTTGATAGA+GGG 0.606410 4.1:-45868104 None:intergenic
TTAGGTGAAAGAAAGGGTGC+CGG 0.615123 4.1:+45867994 MS.gene044766:CDS
ACAACTTTAGGTGAAAGAAA+GGG 0.626599 4.1:+45867988 MS.gene044766:CDS
TTCAGCTTCAGAGAAAGTGG+TGG 0.661349 4.1:-45868049 None:intergenic
CGAGGATGAGATCGATTCGG+AGG 0.665085 4.1:+45868188 MS.gene044766:CDS
TAAAGACTTTAACGATGACA+AGG 0.672661 4.1:-45868266 None:intergenic
TGGTGGAGAAATCGTCGCTG+TGG 0.708398 4.1:-45868029 None:intergenic
TAGCCCTCTATCAAACACTG+TGG 0.798981 4.1:+45868101 MS.gene044766:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TCATAAACATGTATATTAGA+AGG - chr4.1:45868354-45868373 None:intergenic 20.0%
!! AATTTGGCTAATGGAAATTT+TGG - chr4.1:45867950-45867969 None:intergenic 25.0%
ACAACTTTAGGTGAAAGAAA+GGG + chr4.1:45867988-45868007 MS.gene044766:CDS 30.0%
TAAAGACTTTAACGATGACA+AGG - chr4.1:45868269-45868288 None:intergenic 30.0%
TCAACAAATATTGGAAGTTG+TGG + chr4.1:45867877-45867896 MS.gene044766:CDS 30.0%
! AGAGTGTTCTCAACAAATAT+TGG + chr4.1:45867868-45867887 MS.gene044766:CDS 30.0%
!! GAAATTTTGGCCTTTTGAAT+AGG - chr4.1:45867937-45867956 None:intergenic 30.0%
AAACACTGTGGTTGTTGAAA+AGG + chr4.1:45868113-45868132 MS.gene044766:CDS 35.0%
AGTAGTAGTACAAACCTTGT+CGG - chr4.1:45868316-45868335 None:intergenic 35.0%
CACAACTTTAGGTGAAAGAA+AGG + chr4.1:45867987-45868006 MS.gene044766:CDS 35.0%
GAGTGCTTGAAATCATGATA+TGG - chr4.1:45868150-45868169 None:intergenic 35.0%
TATGCTTCAAATGATCTTCG+AGG + chr4.1:45868170-45868189 MS.gene044766:CDS 35.0%
TCTTTCACCTAAAGTTGTGT+TGG - chr4.1:45867986-45868005 None:intergenic 35.0%
TTCCATTAGCCAAATTAGCA+AGG + chr4.1:45867954-45867973 MS.gene044766:CDS 35.0%
! ATGATCTTCGAGTTCTTCTT+CGG + chr4.1:45868211-45868230 MS.gene044766:CDS 35.0%
! TGAGAACACTCTTTTCTTGT+TGG - chr4.1:45867860-45867879 None:intergenic 35.0%
ACAACCACAGTGTTTGATAG+AGG - chr4.1:45868108-45868127 None:intergenic 40.0%
AGCCTTGCTAATTTGGCTAA+TGG - chr4.1:45867959-45867978 None:intergenic 40.0%
AGTACACGAGCCTATTCAAA+AGG + chr4.1:45867924-45867943 MS.gene044766:CDS 40.0%
CAACCACAGTGTTTGATAGA+GGG - chr4.1:45868107-45868126 None:intergenic 40.0%
GCTTCATCCAACACAACTTT+AGG + chr4.1:45867976-45867995 MS.gene044766:CDS 40.0%
GTAGTAGTACAAACCTTGTC+GGG - chr4.1:45868315-45868334 None:intergenic 40.0%
TGGATGAAGCCTTGCTAATT+TGG - chr4.1:45867966-45867985 None:intergenic 40.0%
TGTTTCAGCTTCAGAGAAAG+TGG - chr4.1:45868055-45868074 None:intergenic 40.0%
TTTGATAGAGGGCTATGCTT+GGG - chr4.1:45868096-45868115 None:intergenic 40.0%
CTTCGAGGATGAGATCGATT+CGG + chr4.1:45868185-45868204 MS.gene044766:CDS 45.0%
GTTTGATAGAGGGCTATGCT+TGG - chr4.1:45868097-45868116 None:intergenic 45.0%
TAGCCCTCTATCAAACACTG+TGG + chr4.1:45868101-45868120 MS.gene044766:CDS 45.0%
TTCAGCTTCAGAGAAAGTGG+TGG - chr4.1:45868052-45868071 None:intergenic 45.0%
! TCATGAAGCTTTTCCCGACA+AGG + chr4.1:45868299-45868318 MS.gene044766:CDS 45.0%
! TTAGGTGAAAGAAAGGGTGC+CGG + chr4.1:45867994-45868013 MS.gene044766:CDS 45.0%
AGCTTCAGAGAAAGTGGTGG+TGG - chr4.1:45868049-45868068 None:intergenic 50.0%
GATAGAGGGCTATGCTTGGG+TGG - chr4.1:45868093-45868112 None:intergenic 55.0%
TGGTGGAGAAATCGTCGCTG+TGG - chr4.1:45868032-45868051 None:intergenic 55.0%
!! CGAGGATGAGATCGATTCGG+AGG + chr4.1:45868188-45868207 MS.gene044766:CDS 55.0%
GCTGTGGTCGACGCTACAAC+CGG - chr4.1:45868016-45868035 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 45867850 45868383 45867850 ID=MS.gene044766
chr4.1 mRNA 45867850 45868383 45867850 ID=MS.gene044766.t1;Parent=MS.gene044766
chr4.1 exon 45867850 45868383 45867850 ID=MS.gene044766.t1.exon1;Parent=MS.gene044766.t1
chr4.1 CDS 45867850 45868383 45867850 ID=cds.MS.gene044766.t1;Parent=MS.gene044766.t1
Gene Sequence

>MS.gene044766

ATGTCTTCCAACAAGAAAAGAGTGTTCTCAACAAATATTGGAAGTTGTGGCTGTGCAAAAAAGAAAGCAATTGAAGTACACGAGCCTATTCAAAAGGCCAAAATTTCCATTAGCCAAATTAGCAAGGCTTCATCCAACACAACTTTAGGTGAAAGAAAGGGTGCCGGTTGTAGCGTCGACCACAGCGACGATTTCTCCACCACCACTTTCTCTGAAGCTGAAACAACTCAAAACTATTCTCCACCCAAGCATAGCCCTCTATCAAACACTGTGGTTGTTGAAAAGGATTCTGACGATCCATATCATGATTTCAAGCACTCTATGCTTCAAATGATCTTCGAGGATGAGATCGATTCGGAGGATGATCTTCGAGTTCTTCTTCGGTGTTTTCTTCATCTCAATGATACTTATTATCACCTTGTCATCGTTAAAGTCTTTAATGATATATGTCATGAAGCTTTTCCCGACAAGGTTTGTACTACTACTTCGTCTGCTATCAAACCTTCTAATATACATGTTTATGAAAATGAATAA
Protein sequence

>MS.gene044766.t1

MSSNKKRVFSTNIGSCGCAKKKAIEVHEPIQKAKISISQISKASSNTTLGERKGAGCSVDHSDDFSTTTFSEAETTQNYSPPKHSPLSNTVVVEKDSDDPYHDFKHSMLQMIFEDEIDSEDDLRVLLRCFLHLNDTYYHLVIVKVFNDICHEAFPDKVCTTTSSAIKPSNIHVYENE