AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene96388

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene96388.t1 MTR_1g048720 90.845 142 13 0 1 142 1 142 3.97e-93 268
MS.gene96388.t1 MTR_1g048720 90.845 142 13 0 1 142 1 142 6.54e-93 269
MS.gene96388.t1 MTR_1g048720 90.141 142 13 1 1 142 1 141 1.26e-90 262
MS.gene96388.t1 MTR_1g048720 90.141 142 13 1 1 142 1 141 2.12e-90 263
MS.gene96388.t1 MTR_1g048750 85.816 141 12 1 1 141 1 133 1.10e-82 244
MS.gene96388.t1 MTR_1g048710 83.803 142 14 2 1 142 1 133 2.19e-79 234
MS.gene96388.t1 MTR_7g090410 51.656 151 56 5 1 142 1 143 1.12e-26 100
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene96388.t1 AT3G56970 49.669 151 55 5 1 137 1 144 5.96e-36 124
MS.gene96388.t1 AT3G56980 47.482 139 47 5 1 120 1 132 1.77e-27 102
MS.gene96388.t1 AT5G04150 59.524 84 31 1 60 140 78 161 1.49e-26 100
MS.gene96388.t1 AT2G41240 46.032 126 53 3 1 120 1 117 2.15e-26 99.8
MS.gene96388.t1 AT5G04150 59.524 84 31 1 60 140 78 161 2.80e-26 99.8
MS.gene96388.t1 AT2G41240 45.238 126 53 4 1 120 1 116 6.57e-24 93.2

Find 29 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCACCTGTTTCTGTAATTC+TGG 0.155913 1.3:+30949967 None:intergenic
TGATGCTGGTTATGGGTTAT+TGG 0.230970 1.3:+30950344 None:intergenic
ATGAACTCTGATGCTGGTTA+TGG 0.359283 1.3:+30950336 None:intergenic
AGGACTCTTGAAATTGTTGC+TGG 0.367920 1.3:+30950000 None:intergenic
CTTAGATAACCTCTTCTACT+TGG 0.368095 1.3:+30949899 None:intergenic
GATCGCGTTCACTAGCATTA+TGG 0.375108 1.3:+30950195 None:intergenic
AGTACCATTTGATCTGAAAC+AGG 0.414053 1.3:+30950125 None:intergenic
CATACCAGAATTACAGAAAC+AGG 0.417584 1.3:-30949971 MS.gene96388:CDS
TTAGATAACCTCTTCTACTT+GGG 0.422139 1.3:+30949900 None:intergenic
TCTTCCTGTTTCAGATCAAA+TGG 0.439923 1.3:-30950129 MS.gene96388:intron
ATGGGTTATTGGCTCCTCAA+AGG 0.463079 1.3:+30950355 None:intergenic
AACAATTGGATGGCCCTTTG+AGG 0.464251 1.3:-30950369 MS.gene96388:CDS
TGAACTCTGATGCTGGTTAT+GGG 0.477659 1.3:+30950337 None:intergenic
TGGGTTATTGGCTCCTCAAA+GGG 0.488564 1.3:+30950356 None:intergenic
CATGCCAAGGTCACTGCTTG+TGG 0.499479 1.3:+30950232 None:intergenic
ACAAATTATTGATCTTCTTG+CGG 0.529574 1.3:+30950171 None:intergenic
ACTTTCTCCCCAAGTAGAAG+AGG 0.556979 1.3:-30949908 MS.gene96388:CDS
CATCCAATTGTTGAAAACAT+AGG 0.558093 1.3:+30950380 None:intergenic
TGTAGAATGAACTCTGATGC+TGG 0.560692 1.3:+30950330 None:intergenic
CAATCCACAAGCAGTGACCT+TGG 0.569748 1.3:-30950236 MS.gene96388:CDS
CCAATTGTTGAAAACATAGG+AGG 0.582074 1.3:+30950383 None:intergenic
TAGATAACCTCTTCTACTTG+GGG 0.586846 1.3:+30949901 None:intergenic
ACTAGTTAAGAGAAAAGAAG+AGG 0.589176 1.3:-30949941 MS.gene96388:CDS
GTCACTGCTTGTGGATTGTG+AGG 0.591686 1.3:+30950241 None:intergenic
CACAAGCAGTGACCTTGGCA+TGG 0.602895 1.3:-30950231 MS.gene96388:CDS
CAAGCTTCTTAACCATGCCA+AGG 0.655760 1.3:+30950219 None:intergenic
ACCAGAATTACAGAAACAGG+TGG 0.656125 1.3:-30949968 MS.gene96388:CDS
GAATTACAGAAACAGGTGGA+AGG 0.659206 1.3:-30949964 MS.gene96388:CDS
TCACTGCTTGTGGATTGTGA+GGG 0.698792 1.3:+30950242 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTAACAAAATCATATAGA+AGG + chr1.3:30950208-30950227 None:intergenic 15.0%
!! ATTAACAAAATCATATAGAA+GGG + chr1.3:30950207-30950226 None:intergenic 15.0%
! ACAAATTATTGATCTTCTTG+CGG + chr1.3:30950130-30950149 None:intergenic 25.0%
!! GTAATTCTGGTATGTATTTT+AGG + chr1.3:30950321-30950340 None:intergenic 25.0%
!!! TAATTTTCTTGATCAAGTTG+AGG - chr1.3:30950013-30950032 MS.gene96388:CDS 25.0%
ACTAGTTAAGAGAAAAGAAG+AGG - chr1.3:30950357-30950376 MS.gene96388:CDS 30.0%
CATCCAATTGTTGAAAACAT+AGG + chr1.3:30949921-30949940 None:intergenic 30.0%
TTAGATAACCTCTTCTACTT+GGG + chr1.3:30950401-30950420 None:intergenic 30.0%
! CTATGTTTTCAACAATTGGA+TGG - chr1.3:30949919-30949938 MS.gene96388:CDS 30.0%
CATACCAGAATTACAGAAAC+AGG - chr1.3:30950327-30950346 MS.gene96388:CDS 35.0%
CCAATTGTTGAAAACATAGG+AGG + chr1.3:30949918-30949937 None:intergenic 35.0%
TAGATAACCTCTTCTACTTG+GGG + chr1.3:30950400-30950419 None:intergenic 35.0%
TCTTCCTGTTTCAGATCAAA+TGG - chr1.3:30950169-30950188 MS.gene96388:CDS 35.0%
! AGTACCATTTGATCTGAAAC+AGG + chr1.3:30950176-30950195 None:intergenic 35.0%
! CCTCCTATGTTTTCAACAAT+TGG - chr1.3:30949915-30949934 MS.gene96388:CDS 35.0%
ACCAGAATTACAGAAACAGG+TGG - chr1.3:30950330-30950349 MS.gene96388:CDS 40.0%
AGGACTCTTGAAATTGTTGC+TGG + chr1.3:30950301-30950320 None:intergenic 40.0%
GAATTACAGAAACAGGTGGA+AGG - chr1.3:30950334-30950353 MS.gene96388:CDS 40.0%
TGTAGAATGAACTCTGATGC+TGG + chr1.3:30949971-30949990 None:intergenic 40.0%
! ATGAACTCTGATGCTGGTTA+TGG + chr1.3:30949965-30949984 None:intergenic 40.0%
! TGAACTCTGATGCTGGTTAT+GGG + chr1.3:30949964-30949983 None:intergenic 40.0%
! TGATGCTGGTTATGGGTTAT+TGG + chr1.3:30949957-30949976 None:intergenic 40.0%
!! TCCACCTGTTTCTGTAATTC+TGG + chr1.3:30950334-30950353 None:intergenic 40.0%
AACAATTGGATGGCCCTTTG+AGG - chr1.3:30949929-30949948 MS.gene96388:CDS 45.0%
ACTTTCTCCCCAAGTAGAAG+AGG - chr1.3:30950390-30950409 MS.gene96388:CDS 45.0%
CAAGCTTCTTAACCATGCCA+AGG + chr1.3:30950082-30950101 None:intergenic 45.0%
GATCGCGTTCACTAGCATTA+TGG + chr1.3:30950106-30950125 None:intergenic 45.0%
! TCACTGCTTGTGGATTGTGA+GGG + chr1.3:30950059-30950078 None:intergenic 45.0%
!! ATGGGTTATTGGCTCCTCAA+AGG + chr1.3:30949946-30949965 None:intergenic 45.0%
!! TGGGTTATTGGCTCCTCAAA+GGG + chr1.3:30949945-30949964 None:intergenic 45.0%
CAATCCACAAGCAGTGACCT+TGG - chr1.3:30950062-30950081 MS.gene96388:intron 50.0%
! GTCACTGCTTGTGGATTGTG+AGG + chr1.3:30950060-30950079 None:intergenic 50.0%
CACAAGCAGTGACCTTGGCA+TGG - chr1.3:30950067-30950086 MS.gene96388:intron 55.0%
CATGCCAAGGTCACTGCTTG+TGG + chr1.3:30950069-30950088 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 30949900 30950420 30949900 ID=MS.gene96388
chr1.3 mRNA 30949900 30950420 30949900 ID=MS.gene96388.t1;Parent=MS.gene96388
chr1.3 exon 30950130 30950420 30950130 ID=MS.gene96388.t1.exon1;Parent=MS.gene96388.t1
chr1.3 CDS 30950130 30950420 30950130 ID=cds.MS.gene96388.t1;Parent=MS.gene96388.t1
chr1.3 exon 30949900 30950037 30949900 ID=MS.gene96388.t1.exon2;Parent=MS.gene96388.t1
chr1.3 CDS 30949900 30950037 30949900 ID=cds.MS.gene96388.t1;Parent=MS.gene96388.t1
Gene Sequence

>MS.gene96388

ATGTTAGCGATATCTCCTCCTATGTTTTCAACAATTGGATGGCCCTTTGAGGAGCCAATAACCCATAACCAGCATCAGAGTTCATTCTACAAAGACACTGCTGATCAATTATTTAATTTTCTTGATCAAGTTGAGGCAGAAATTAATTCAAAAGATCCCTCACAATCCACAAGCAGTGACCTTGGCATGGTTAAGAAGCTTGTCCATAATGCTAGTGAACGCGATCGCCGCAAGAAGATCAATAATTTGTATTCATCACTTCGTTCACTTCTTCCTGTTTCAGATCAAATGGTACTTAATTAAACCCTTCTATATGATTTTGTTAATTTGTATCTCTTTTTAATACTATTGTCTTAGTATTAATTTATACATATATGTTGCAGAAGAAATTGAGCATTCCAGCAACAATTTCAAGAGTCCTAAAATACATACCAGAATTACAGAAACAGGTGGAAGGACTAGTTAAGAGAAAAGAAGAGGTCTTATTGAGACTTTCTCCCCAAGTAGAAGAGGTTATCTAA
Protein sequence

>MS.gene96388.t1

MLAISPPMFSTIGWPFEEPITHNQHQSSFYKDTADQLFNFLDQVEAEINSKDPSQSTSSDLGMVKKLVHNASERDRRKKINNLYSSLRSLLPVSDQMKKLSIPATISRVLKYIPELQKQVEGLVKRKEEVLLRLSPQVEEVI