AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene22560

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene22560.t1 MTR_5g011750 94.828 116 6 0 1 116 1 116 4.77e-77 223
MS.gene22560.t1 MTR_4g102040 62.385 109 36 1 5 113 41 144 7.48e-40 130
MS.gene22560.t1 MTR_2g084805 53.763 93 43 0 20 112 51 143 2.11e-26 97.4
MS.gene22560.t1 MTR_4g055420 50.562 89 44 0 24 112 67 155 8.39e-26 95.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene22560.t1 AT2G27830 52.128 94 45 0 19 112 61 154 1.16e-30 108

Find 31 sgRNAs with CRISPR-Local

Find 41 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAACCAATGACTCTCCTCTT+AGG 0.375382 5.2:-4304321 MS.gene22560:CDS
TGCATTGATGACTTATGATA+AGG 0.419305 5.2:-4304200 MS.gene22560:CDS
AACGGAAATTTGTCAGTTTG+AGG 0.425120 5.2:+4304355 None:intergenic
TAGTGAGAAATTGAAGAACT+TGG 0.435583 5.2:-4303832 MS.gene22560:CDS
TAATTACTTTCAAGCGTGAA+TGG 0.437696 5.2:+4304118 None:intergenic
ATGAAATGGTGCAGGTTTGA+AGG 0.447179 5.2:-4303856 MS.gene22560:intron
GGATCGGTGTCCTTCAATAA+TGG 0.452970 5.2:+4304166 None:intergenic
AAGTGAAGTTGGTAGCGGTT+TGG 0.461676 5.2:+4304145 None:intergenic
TGGCCTAAGAGGAGAGTCAT+TGG 0.468313 5.2:+4304318 None:intergenic
AGTGAGAAATTGAAGAACTT+GGG 0.475992 5.2:-4303831 MS.gene22560:CDS
TTGGAAGTTCAGATTGAAGA+AGG 0.480987 5.2:+4303780 None:intergenic
TGAATGGAGAGAAGTGAAGT+TGG 0.482669 5.2:+4304134 None:intergenic
GAAGAGAAGGCCATTATTGA+AGG 0.491115 5.2:-4304176 MS.gene22560:CDS
AATTGAAGAACTTGGGGTCA+AGG 0.496307 5.2:-4303824 MS.gene22560:CDS
AGAAGTTTCGATGGCCTAAG+AGG 0.500163 5.2:+4304307 None:intergenic
GAGAGAAGTGAAGTTGGTAG+CGG 0.523441 5.2:+4304140 None:intergenic
TTTGTCTTTGGCTTCATGGG+TGG 0.526303 5.2:-4304391 None:intergenic
TCAAACTGACAAATTTCCGT+TGG 0.528724 5.2:-4304353 MS.gene22560:CDS
GTCAGTTTGAGGAGTAGAAA+CGG 0.529246 5.2:+4304366 None:intergenic
GTGTCCATCGAGAACACGTT+GGG 0.537604 5.2:-4304277 MS.gene22560:CDS
CAAATTTCCGTTGGATACAA+CGG 0.549881 5.2:-4304344 MS.gene22560:CDS
TTGGTTTCCGTTGTATCCAA+CGG 0.551596 5.2:+4304337 None:intergenic
TACCGTTGGCGAATTAGTGA+AGG 0.567706 5.2:-4304224 MS.gene22560:CDS
GTGAGAAATTGAAGAACTTG+GGG 0.585031 5.2:-4303830 MS.gene22560:CDS
CTTATGATAAGGAGAAGAGA+AGG 0.588206 5.2:-4304189 MS.gene22560:CDS
AAGTTGGTAGCGGTTTGGAT+CGG 0.590772 5.2:+4304150 None:intergenic
ATGTCGCCTGAAAATACCGT+TGG 0.599343 5.2:-4304238 MS.gene22560:CDS
TGCACCCAACGTGTTCTCGA+TGG 0.600223 5.2:+4304273 None:intergenic
ACGTTGAGTAGAAGTTTCGA+TGG 0.630336 5.2:+4304298 None:intergenic
AACCTTCACTAATTCGCCAA+CGG 0.655659 5.2:+4304222 None:intergenic
CGTGTCCATCGAGAACACGT+TGG 0.692755 5.2:-4304278 MS.gene22560:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAATGATATGAAAAAACA+AGG + chr5.2:4304117-4304136 None:intergenic 15.0%
!! AGGATATAAATTATGAAAAA+AGG + chr5.2:4304097-4304116 None:intergenic 15.0%
!! GGATATAAATTATGAAAAAA+GGG + chr5.2:4304096-4304115 None:intergenic 15.0%
AGTGAGAAATTGAAGAACTT+GGG - chr5.2:4304333-4304352 MS.gene22560:CDS 30.0%
ATGAAAAAAGGGAACATTGA+AGG + chr5.2:4304085-4304104 None:intergenic 30.0%
TAATCAACCACCAAATGAAA+TGG - chr5.2:4304294-4304313 MS.gene22560:CDS 30.0%
TAATTACTTTCAAGCGTGAA+TGG + chr5.2:4304049-4304068 None:intergenic 30.0%
TAGTGAGAAATTGAAGAACT+TGG - chr5.2:4304332-4304351 MS.gene22560:CDS 30.0%
TATACACGATGCATATGATA+AGG + chr5.2:4304249-4304268 None:intergenic 30.0%
! TGCATTGATGACTTATGATA+AGG - chr5.2:4303964-4303983 MS.gene22560:intron 30.0%
AACGGAAATTTGTCAGTTTG+AGG + chr5.2:4303812-4303831 None:intergenic 35.0%
AAGGGAACATTGAAGGATTA+AGG + chr5.2:4304078-4304097 None:intergenic 35.0%
CAAATTTCCGTTGGATACAA+CGG - chr5.2:4303820-4303839 MS.gene22560:CDS 35.0%
CTTATGATAAGGAGAAGAGA+AGG - chr5.2:4303975-4303994 MS.gene22560:intron 35.0%
GTGAGAAATTGAAGAACTTG+GGG - chr5.2:4304334-4304353 MS.gene22560:CDS 35.0%
TCAAACTGACAAATTTCCGT+TGG - chr5.2:4303811-4303830 MS.gene22560:CDS 35.0%
! CATTTGGTGGTTGATTAACA+TGG + chr5.2:4304291-4304310 None:intergenic 35.0%
AAACCAATGACTCTCCTCTT+AGG - chr5.2:4303843-4303862 MS.gene22560:CDS 40.0%
AACCTTCACTAATTCGCCAA+CGG + chr5.2:4303945-4303964 None:intergenic 40.0%
AATTGAAGAACTTGGGGTCA+AGG - chr5.2:4304340-4304359 MS.gene22560:CDS 40.0%
ACGTTGAGTAGAAGTTTCGA+TGG + chr5.2:4303869-4303888 None:intergenic 40.0%
ATGAAATGGTGCAGGTTTGA+AGG - chr5.2:4304308-4304327 MS.gene22560:CDS 40.0%
CAAACCTGCACCATTTCATT+TGG + chr5.2:4304307-4304326 None:intergenic 40.0%
GAAGAGAAGGCCATTATTGA+AGG - chr5.2:4303988-4304007 MS.gene22560:intron 40.0%
GTCAGTTTGAGGAGTAGAAA+CGG + chr5.2:4303801-4303820 None:intergenic 40.0%
TGAATGGAGAGAAGTGAAGT+TGG + chr5.2:4304033-4304052 None:intergenic 40.0%
TTGGTTTCCGTTGTATCCAA+CGG + chr5.2:4303830-4303849 None:intergenic 40.0%
! AATTCGCCAACGGTATTTTC+AGG + chr5.2:4303935-4303954 None:intergenic 40.0%
ACCACCAAATGAAATGGTGC+AGG - chr5.2:4304300-4304319 MS.gene22560:CDS 45.0%
ACCTGCACCATTTCATTTGG+TGG + chr5.2:4304304-4304323 None:intergenic 45.0%
AGAAGTTTCGATGGCCTAAG+AGG + chr5.2:4303860-4303879 None:intergenic 45.0%
ATGTCGCCTGAAAATACCGT+TGG - chr5.2:4303926-4303945 MS.gene22560:intron 45.0%
TACCGTTGGCGAATTAGTGA+AGG - chr5.2:4303940-4303959 MS.gene22560:intron 45.0%
! GGATCGGTGTCCTTCAATAA+TGG + chr5.2:4304001-4304020 None:intergenic 45.0%
!! AAGTGAAGTTGGTAGCGGTT+TGG + chr5.2:4304022-4304041 None:intergenic 45.0%
!! AAGTTGGTAGCGGTTTGGAT+CGG + chr5.2:4304017-4304036 None:intergenic 45.0%
!! GAGAGAAGTGAAGTTGGTAG+CGG + chr5.2:4304027-4304046 None:intergenic 45.0%
GTGTCCATCGAGAACACGTT+GGG - chr5.2:4303887-4303906 MS.gene22560:intron 50.0%
TGGCCTAAGAGGAGAGTCAT+TGG + chr5.2:4303849-4303868 None:intergenic 50.0%
CGTGTCCATCGAGAACACGT+TGG - chr5.2:4303886-4303905 MS.gene22560:intron 55.0%
TGCACCCAACGTGTTCTCGA+TGG + chr5.2:4303894-4303913 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 4303788 4304398 4303788 ID=MS.gene22560
chr5.2 mRNA 4303788 4304398 4303788 ID=MS.gene22560.t1;Parent=MS.gene22560
chr5.2 exon 4304125 4304398 4304125 ID=MS.gene22560.t1.exon1;Parent=MS.gene22560.t1
chr5.2 CDS 4304125 4304398 4304125 ID=cds.MS.gene22560.t1;Parent=MS.gene22560.t1
chr5.2 exon 4303788 4303864 4303788 ID=MS.gene22560.t1.exon2;Parent=MS.gene22560.t1
chr5.2 CDS 4303788 4303864 4303788 ID=cds.MS.gene22560.t1;Parent=MS.gene22560.t1
Gene Sequence

>MS.gene22560

ATGGGTGGTACCGTTTCTACTCCTCAAACTGACAAATTTCCGTTGGATACAACGGAAACCAATGACTCTCCTCTTAGGCCATCGAAACTTCTACTCAACGTGTCCATCGAGAACACGTTGGGTGCAATACAAGTTTTGATGTCGCCTGAAAATACCGTTGGCGAATTAGTGAAGGTTGCATTGATGACTTATGATAAGGAGAAGAGAAGGCCATTATTGAAGGACACCGATCCAAACCGCTACCAACTTCACTTCTCTCCATTCACGCTTGAAAGTAATTATTTTAACCTTAATCCTTCAATGTTCCCTTTTTTCATAATTTATATCCTTGTTTTTTCATATCATTTTTTAGACTAGTTTTTAGATGTTATAGATCTTTATTATTGCATATTAATGTATAATTAGACTGATCGATGACAACAATATATGAATACGAATTCAATTAATTTTTCTGATGTCCTTATCATATGCATCGTGTATATATGATACAAAAATATTTTCCATGTTAATCAACCACCAAATGAAATGGTGCAGGTTTGAAGGTTAGTGAGAAATTGAAGAACTTGGGGTCAAGGAATTTCTTTCTATGCTCAAAGCCTTCTTCAATCTGA
Protein sequence

>MS.gene22560.t1

MGGTVSTPQTDKFPLDTTETNDSPLRPSKLLLNVSIENTLGAIQVLMSPENTVGELVKVALMTYDKEKRRPLLKDTDPNRYQLHFSPFTLESLKVSEKLKNLGSRNFFLCSKPSSI