AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene028405

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene028405.t1 MTR_4g094332 95.982 224 9 0 1 224 1 224 4.60e-138 386
MS.gene028405.t1 MTR_4g094328 94.196 224 13 0 1 224 1 224 7.53e-134 375
MS.gene028405.t1 MTR_4g094330 94.196 224 13 0 1 224 1 224 7.53e-134 375
MS.gene028405.t1 MTR_1g099010 66.667 201 63 1 24 224 21 217 1.33e-91 268
MS.gene028405.t1 MTR_6g034975 66.986 209 66 2 16 224 5 210 8.67e-89 261
MS.gene028405.t1 MTR_4g094325 61.792 212 77 2 13 224 32 239 1.07e-84 251
MS.gene028405.t1 MTR_2g008110 61.053 190 65 1 30 219 27 207 6.11e-73 221
MS.gene028405.t1 MTR_0119s0010 61.053 190 65 1 30 219 27 207 6.60e-73 220
MS.gene028405.t1 MTR_0119s0020 61.053 190 65 1 30 219 27 207 6.60e-73 220
MS.gene028405.t1 MTR_4g094335 57.073 205 79 2 18 219 27 225 5.73e-70 214
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene028405.t1 AT3G43660 63.000 200 65 2 26 224 7 198 5.39e-92 268
MS.gene028405.t1 AT1G21140 62.312 199 66 2 26 224 11 200 4.37e-82 243
MS.gene028405.t1 AT3G43630 61.809 199 67 2 24 221 4 194 5.52e-81 241
MS.gene028405.t1 AT1G76800 62.000 200 67 1 25 224 6 196 4.65e-80 238
MS.gene028405.t1 AT3G25190 63.033 211 72 2 18 224 9 217 5.31e-74 223

Find 51 sgRNAs with CRISPR-Local

Find 55 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGGCTATGGCCATTACTTT+TGG 0.296297 4.2:-18624300 MS.gene028405:CDS
ACCAAATTGATTGGCACTAC+TGG 0.296615 4.2:-18624273 MS.gene028405:CDS
TCTTGTGTTAGAGTTCTTAT+TGG 0.297338 4.2:-18624330 MS.gene028405:CDS
TGTGGTTAGCTTTGCTTTGT+TGG 0.303507 4.2:-18624400 MS.gene028405:CDS
TTCAACTTTGAGAGTACTAT+TGG 0.313072 4.2:+18624845 None:intergenic
TCCAGTAGTGCCAATCAATT+TGG 0.330163 4.2:+18624272 None:intergenic
TTTGGTTTCACCAAATTGAT+TGG 0.341339 4.2:-18624282 MS.gene028405:CDS
AGCTTTGCTTTGTTGGTGTT+CGG 0.375879 4.2:-18624393 MS.gene028405:CDS
CTGCATTTATAAAGAATCAT+AGG 0.383563 4.2:-18624446 MS.gene028405:CDS
ATCTCAACCTCAAAATTGTT+TGG 0.384795 4.2:+18624879 None:intergenic
ATCAAAGTAATGCTCCTTGC+TGG 0.393708 4.2:-18624696 MS.gene028405:CDS
AATGCTGCTTGAAATGGATT+TGG 0.394757 4.2:+18624519 None:intergenic
TCCTTCATGGCCTCACAACT+TGG 0.407619 4.2:-18624924 None:intergenic
GAAGCTAATGCTGCTTGAAA+TGG 0.414506 4.2:+18624513 None:intergenic
ATGCTCCTTGCTGGTTTCGC+TGG 0.425505 4.2:-18624687 MS.gene028405:CDS
TGGCTTAGAGCAGCAATGTT+AGG 0.431906 4.2:-18624783 MS.gene028405:CDS
TATTGGAGGTTGGATGGCTA+TGG 0.439649 4.2:-18624313 MS.gene028405:CDS
TGTGTTAGAGTTCTTATTGG+AGG 0.446628 4.2:-18624327 MS.gene028405:CDS
TTAGAGTTCTTATTGGAGGT+TGG 0.455085 4.2:-18624323 MS.gene028405:CDS
AAAGAATCATAGGATTAGAA+TGG 0.457336 4.2:-18624436 MS.gene028405:CDS
AACAGTGATTAGTCCATCAT+TGG 0.469248 4.2:+18624758 None:intergenic
GGTTTCGCTGGTTTAGTAGC+CGG 0.470478 4.2:-18624675 MS.gene028405:CDS
CAGCATTGATTACTTTCAAA+GGG 0.487104 4.2:-18624811 MS.gene028405:CDS
TGATGATGAAAGTACTGAAA+AGG 0.488855 4.2:-18624550 MS.gene028405:CDS
ACAGCATTGATTACTTTCAA+AGG 0.499048 4.2:-18624812 MS.gene028405:CDS
AAGAATCATAGGATTAGAAT+GGG 0.503124 4.2:-18624435 MS.gene028405:CDS
GGAGGAGTGGGTGCATTGGT+TGG 0.503269 4.2:-18624372 MS.gene028405:CDS
AGAGTACTATTGGCATGGAT+AGG 0.503952 4.2:+18624855 None:intergenic
AGTTCTTATTGGAGGTTGGA+TGG 0.512108 4.2:-18624319 MS.gene028405:CDS
GTTCGGAGGAGTGGGTGCAT+TGG 0.514286 4.2:-18624376 MS.gene028405:CDS
GCCTCATTGATGATCGGCGT+TGG 0.515998 4.2:-18624735 MS.gene028405:CDS
AATGGGAGTTGTTGCTGCTG+TGG 0.525549 4.2:-18624418 MS.gene028405:CDS
GAGTACTATTGGCATGGATA+GGG 0.527712 4.2:+18624856 None:intergenic
AACCTCAAAATTGTTTGGTG+AGG 0.527938 4.2:+18624884 None:intergenic
CTTTGAGAGTACTATTGGCA+TGG 0.540482 4.2:+18624850 None:intergenic
TTGTTGGTGTTCGGAGGAGT+GGG 0.540620 4.2:-18624384 MS.gene028405:CDS
TTTGGTGAAACCAAAAGTAA+TGG 0.542621 4.2:+18624290 None:intergenic
AGCAGCATTAGCTTCCGCAC+TGG 0.542923 4.2:-18624505 MS.gene028405:CDS
ATAAATGCAGCTGCTAGTAA+TGG 0.554872 4.2:+18624459 None:intergenic
TTTGTTGGTGTTCGGAGGAG+TGG 0.555153 4.2:-18624385 MS.gene028405:CDS
GGTGCTTGTAGCATGGCAAT+TGG 0.557712 4.2:-18624654 MS.gene028405:CDS
AATTGCCATGCTACAAGCAC+CGG 0.567135 4.2:+18624656 None:intergenic
AGTAGCCGGTGCTTGTAGCA+TGG 0.572629 4.2:-18624661 MS.gene028405:CDS
TTTGCTTTGTTGGTGTTCGG+AGG 0.573531 4.2:-18624390 MS.gene028405:CDS
GCAATGTTAGGAGCCAATGA+TGG 0.586770 4.2:-18624771 MS.gene028405:CDS
ACTGTTGCCTCATTGATGAT+CGG 0.595345 4.2:-18624741 MS.gene028405:CDS
CTAACACAAGACCTCATCAA+AGG 0.604425 4.2:+18624342 None:intergenic
ATTACTTTCAAAGGGCACAA+TGG 0.615521 4.2:-18624803 MS.gene028405:CDS
CTAAACCAGCGAAACCAGCA+AGG 0.672858 4.2:+18624682 None:intergenic
TCCAACGCCGATCATCAATG+AGG 0.683388 4.2:+18624734 None:intergenic
TCCAATAGAAAATGCCAGTG+CGG 0.690209 4.2:+18624491 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAGAATCATAGGATTAGAA+TGG - chr4.2:18624748-18624767 MS.gene028405:CDS 25.0%
! AAGAATCATAGGATTAGAAT+GGG - chr4.2:18624749-18624768 MS.gene028405:CDS 25.0%
! CTGCATTTATAAAGAATCAT+AGG - chr4.2:18624738-18624757 MS.gene028405:CDS 25.0%
ATCTCAACCTCAAAATTGTT+TGG + chr4.2:18624308-18624327 None:intergenic 30.0%
TCTTGTGTTAGAGTTCTTAT+TGG - chr4.2:18624854-18624873 MS.gene028405:CDS 30.0%
TTTGGTGAAACCAAAAGTAA+TGG + chr4.2:18624897-18624916 None:intergenic 30.0%
! TTTGGTTTCACCAAATTGAT+TGG - chr4.2:18624902-18624921 MS.gene028405:CDS 30.0%
!! ACAGCATTGATTACTTTCAA+AGG - chr4.2:18624372-18624391 MS.gene028405:CDS 30.0%
!! CAGCATTGATTACTTTCAAA+GGG - chr4.2:18624373-18624392 MS.gene028405:CDS 30.0%
!! TGATGATGAAAGTACTGAAA+AGG - chr4.2:18624634-18624653 MS.gene028405:CDS 30.0%
!! TTCAACTTTGAGAGTACTAT+TGG + chr4.2:18624342-18624361 None:intergenic 30.0%
ATAAATGCAGCTGCTAGTAA+TGG + chr4.2:18624728-18624747 None:intergenic 35.0%
CAACTTGGAGCAAAAACTAA+TGG - chr4.2:18624275-18624294 MS.gene028405:CDS 35.0%
TGTGTTAGAGTTCTTATTGG+AGG - chr4.2:18624857-18624876 MS.gene028405:CDS 35.0%
TTAGAGTTCTTATTGGAGGT+TGG - chr4.2:18624861-18624880 MS.gene028405:CDS 35.0%
TTGGAAAAACTCCTTTGATG+AGG - chr4.2:18624831-18624850 MS.gene028405:CDS 35.0%
! AACAGTGATTAGTCCATCAT+TGG + chr4.2:18624429-18624448 None:intergenic 35.0%
! AACCTCAAAATTGTTTGGTG+AGG + chr4.2:18624303-18624322 None:intergenic 35.0%
! AACCTCACCAAACAATTTTG+AGG - chr4.2:18624298-18624317 MS.gene028405:CDS 35.0%
! AATGCTGCTTGAAATGGATT+TGG + chr4.2:18624668-18624687 None:intergenic 35.0%
! ATTACTTTCAAAGGGCACAA+TGG - chr4.2:18624381-18624400 MS.gene028405:CDS 35.0%
ACCAAATTGATTGGCACTAC+TGG - chr4.2:18624911-18624930 MS.gene028405:CDS 40.0%
AGTTCTTATTGGAGGTTGGA+TGG - chr4.2:18624865-18624884 MS.gene028405:CDS 40.0%
ATCAAAGTAATGCTCCTTGC+TGG - chr4.2:18624488-18624507 MS.gene028405:CDS 40.0%
CTAACACAAGACCTCATCAA+AGG + chr4.2:18624845-18624864 None:intergenic 40.0%
GAGTACTATTGGCATGGATA+GGG + chr4.2:18624331-18624350 None:intergenic 40.0%
TCCAATAGAAAATGCCAGTG+CGG + chr4.2:18624696-18624715 None:intergenic 40.0%
TCCAGTAGTGCCAATCAATT+TGG + chr4.2:18624915-18624934 None:intergenic 40.0%
! ACTGTTGCCTCATTGATGAT+CGG - chr4.2:18624443-18624462 MS.gene028405:CDS 40.0%
! AGAGTACTATTGGCATGGAT+AGG + chr4.2:18624332-18624351 None:intergenic 40.0%
! AGCTTTGCTTTGTTGGTGTT+CGG - chr4.2:18624791-18624810 MS.gene028405:CDS 40.0%
! AGTTTTTGCTCCAAGTTGTG+AGG + chr4.2:18624273-18624292 None:intergenic 40.0%
! ATGGCTATGGCCATTACTTT+TGG - chr4.2:18624884-18624903 MS.gene028405:CDS 40.0%
! GAAGCTAATGCTGCTTGAAA+TGG + chr4.2:18624674-18624693 None:intergenic 40.0%
!! CTTTGAGAGTACTATTGGCA+TGG + chr4.2:18624337-18624356 None:intergenic 40.0%
!! TGTGGTTAGCTTTGCTTTGT+TGG - chr4.2:18624784-18624803 MS.gene028405:CDS 40.0%
AATTGCCATGCTACAAGCAC+CGG + chr4.2:18624531-18624550 None:intergenic 45.0%
GCAATGTTAGGAGCCAATGA+TGG - chr4.2:18624413-18624432 MS.gene028405:CDS 45.0%
TATTGGAGGTTGGATGGCTA+TGG - chr4.2:18624871-18624890 MS.gene028405:CDS 45.0%
TGGCTTAGAGCAGCAATGTT+AGG - chr4.2:18624401-18624420 MS.gene028405:CDS 45.0%
! TTTGCTTTGTTGGTGTTCGG+AGG - chr4.2:18624794-18624813 MS.gene028405:CDS 45.0%
!! TCCGCACTGGCATTTTCTAT+TGG - chr4.2:18624692-18624711 MS.gene028405:CDS 45.0%
AATGGGAGTTGTTGCTGCTG+TGG - chr4.2:18624766-18624785 MS.gene028405:CDS 50.0%
CTAAACCAGCGAAACCAGCA+AGG + chr4.2:18624505-18624524 None:intergenic 50.0%
GGTGCTTGTAGCATGGCAAT+TGG - chr4.2:18624530-18624549 MS.gene028405:CDS 50.0%
TCCAACGCCGATCATCAATG+AGG + chr4.2:18624453-18624472 None:intergenic 50.0%
! TTGTTGGTGTTCGGAGGAGT+GGG - chr4.2:18624800-18624819 MS.gene028405:CDS 50.0%
! TTTGTTGGTGTTCGGAGGAG+TGG - chr4.2:18624799-18624818 MS.gene028405:CDS 50.0%
!! GGTTTCGCTGGTTTAGTAGC+CGG - chr4.2:18624509-18624528 MS.gene028405:CDS 50.0%
AGTAGCCGGTGCTTGTAGCA+TGG - chr4.2:18624523-18624542 MS.gene028405:CDS 55.0%
! AGCAGCATTAGCTTCCGCAC+TGG - chr4.2:18624679-18624698 MS.gene028405:CDS 55.0%
! GCCTCATTGATGATCGGCGT+TGG - chr4.2:18624449-18624468 MS.gene028405:CDS 55.0%
!! ATGCTCCTTGCTGGTTTCGC+TGG - chr4.2:18624497-18624516 MS.gene028405:CDS 55.0%
GTTCGGAGGAGTGGGTGCAT+TGG - chr4.2:18624808-18624827 MS.gene028405:CDS 60.0%
! GGAGGAGTGGGTGCATTGGT+TGG - chr4.2:18624812-18624831 MS.gene028405:CDS 60.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 18624266 18624940 18624266 ID=MS.gene028405
chr4.2 mRNA 18624266 18624940 18624266 ID=MS.gene028405.t1;Parent=MS.gene028405
chr4.2 exon 18624266 18624940 18624266 ID=MS.gene028405.t1.exon1;Parent=MS.gene028405.t1
chr4.2 CDS 18624266 18624940 18624266 ID=cds.MS.gene028405.t1;Parent=MS.gene028405.t1
Gene Sequence

>MS.gene028405

ATGGCCTCACAACTTGGAGCAAAAACTAATGGAACCTCACCAAACAATTTTGAGGTTGAGATCCCTATCCATGCCAATAGTACTCTCAAAGTTGAAAAAGAGAGCAACAGCATTGATTACTTTCAAAGGGCACAATGGCTTAGAGCAGCAATGTTAGGAGCCAATGATGGACTAATCACTGTTGCCTCATTGATGATCGGCGTTGGAGCTATTAAAGAAGACATCAAAGTAATGCTCCTTGCTGGTTTCGCTGGTTTAGTAGCCGGTGCTTGTAGCATGGCAATTGGTGAGTTTGTTTCTGTTTATACTCAATATGATATTGAGATAGCTCAGATAAAAAGAGAAAGAGAAGCTAATAATAATAACAATGATGATGAAAGTACTGAAAAGGAGAAATTGCCAAATCCATTTCAAGCAGCATTAGCTTCCGCACTGGCATTTTCTATTGGAGCTGTTATGCCATTACTAGCAGCTGCATTTATAAAGAATCATAGGATTAGAATGGGAGTTGTTGCTGCTGTGGTTAGCTTTGCTTTGTTGGTGTTCGGAGGAGTGGGTGCATTGGTTGGAAAAACTCCTTTGATGAGGTCTTGTGTTAGAGTTCTTATTGGAGGTTGGATGGCTATGGCCATTACTTTTGGTTTCACCAAATTGATTGGCACTACTGGACTTTGA
Protein sequence

>MS.gene028405.t1

MASQLGAKTNGTSPNNFEVEIPIHANSTLKVEKESNSIDYFQRAQWLRAAMLGANDGLITVASLMIGVGAIKEDIKVMLLAGFAGLVAGACSMAIGEFVSVYTQYDIEIAQIKREREANNNNNDDESTEKEKLPNPFQAALASALAFSIGAVMPLLAAAFIKNHRIRMGVVAAVVSFALLVFGGVGALVGKTPLMRSCVRVLIGGWMAMAITFGFTKLIGTTGL