AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene52952

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene52952.t1 MTR_1g075990 97.512 201 0 2 1 200 1 197 4.87e-142 394
MS.gene52952.t1 MTR_1g442860 72.487 189 43 2 1 180 1 189 4.70e-91 266
MS.gene52952.t1 MTR_4g094428 81.119 143 22 1 44 186 39 176 3.26e-86 254
MS.gene52952.t1 MTR_5g072510 78.571 140 30 0 50 189 31 170 4.04e-84 248
MS.gene52952.t1 MTR_7g097030 93.333 135 9 0 52 186 60 194 1.05e-82 244
MS.gene52952.t1 MTR_1g069825 94.656 131 7 0 56 186 52 182 1.27e-81 242
MS.gene52952.t1 MTR_2g016110 71.622 148 42 0 43 190 22 169 1.74e-74 223
MS.gene52952.t1 MTR_3g031830 80.597 134 26 0 56 189 42 175 3.17e-74 223
MS.gene52952.t1 MTR_2g092950 68.212 151 42 1 29 179 2 146 1.23e-73 219
MS.gene52952.t1 MTR_4g079930 68.707 147 41 1 33 179 11 152 2.43e-73 219
MS.gene52952.t1 MTR_2g076400 75.182 137 34 0 54 190 31 167 9.85e-73 218
MS.gene52952.t1 MTR_7g115700 65.839 161 48 3 28 187 4 158 1.26e-71 215
MS.gene52952.t1 MTR_1g080210 83.200 125 21 0 56 180 40 164 1.10e-68 207
MS.gene52952.t1 MTR_8g086350 73.016 126 34 0 54 179 29 154 1.69e-57 179
MS.gene52952.t1 MTR_1g114020 74.510 51 13 0 49 99 64 114 3.39e-21 86.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene52952.t1 AT2G31160 81.595 163 20 1 35 187 23 185 4.27e-84 248
MS.gene52952.t1 AT1G07090 78.723 141 27 1 47 187 25 162 1.55e-83 246
MS.gene52952.t1 AT3G23290 78.235 170 29 1 19 180 3 172 7.29e-82 241
MS.gene52952.t1 AT5G58500 76.596 141 32 1 55 194 18 158 4.48e-80 236
MS.gene52952.t1 AT5G28490 81.379 145 23 1 41 185 14 154 9.95e-74 221
MS.gene52952.t1 AT3G04510 82.308 130 23 0 56 185 33 162 1.05e-70 214
MS.gene52952.t1 AT2G42610 71.233 146 39 1 42 187 14 156 1.84e-70 212
MS.gene52952.t1 AT2G42610 71.233 146 39 1 42 187 14 156 1.84e-70 212
MS.gene52952.t1 AT1G78815 70.079 127 38 0 53 179 37 163 5.44e-66 201
MS.gene52952.t1 AT4G18610 69.841 126 37 1 55 179 36 161 4.20e-63 194
MS.gene52952.t1 AT1G16910 65.909 132 45 0 53 184 20 151 2.04e-62 191

Find 33 sgRNAs with CRISPR-Local

Find 41 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGACAAGGTGCAGGTGGATT+TGG 0.285867 1.1:+56847055 None:intergenic
CTTAGAGTGTTTGTCGTTGC+TGG 0.294103 1.1:+56847256 None:intergenic
AGAAGAGACTGGAACACTTT+TGG 0.322091 1.1:-56847214 MS.gene52952:CDS
GACTCTTTCTTCGTGAAGTT+AGG 0.348358 1.1:-56846916 MS.gene52952:CDS
TTAAGGTATCTTGATCAGTT+TGG 0.366705 1.1:-56847121 MS.gene52952:CDS
TTGTCCTCTCAGACAAGCTT+GGG 0.367576 1.1:-56847032 MS.gene52952:CDS
GTGGTGGTCTATGGTTTCTT+AGG 0.368488 1.1:+56847185 None:intergenic
AAACCTGAAGATAACCCTTT+TGG 0.390636 1.1:-56846953 MS.gene52952:CDS
GGTGGTGGAGGTTGAATTTG+AGG 0.396468 1.1:+56846839 None:intergenic
ACTTAATTAGTTGCATTTGA+TGG 0.399489 1.1:+56846815 None:intergenic
GCACCAAAAGGGTTATCTTC+AGG 0.403413 1.1:+56846950 None:intergenic
ACTCTTTCTTCGTGAAGTTA+GGG 0.427767 1.1:-56846915 MS.gene52952:CDS
GTCTTCTGAGGTTGTTGTGT+TGG 0.429348 1.1:+56847327 None:intergenic
CTTGTCCTCTCAGACAAGCT+TGG 0.437451 1.1:-56847033 MS.gene52952:CDS
GCATTTGATGGTGGTGGTGG+AGG 0.439596 1.1:+56846827 None:intergenic
GTTGCATTTGATGGTGGTGG+TGG 0.444483 1.1:+56846824 None:intergenic
GGAAGTCTTGATGCATTGAT+TGG 0.461550 1.1:-56847010 MS.gene52952:CDS
CTAACAGCACGAGCACCAAA+AGG 0.492363 1.1:+56846938 None:intergenic
AGAGTGAAAGTGGTGGTCTA+TGG 0.493036 1.1:+56847176 None:intergenic
TTAGTTGCATTTGATGGTGG+TGG 0.493298 1.1:+56846821 None:intergenic
CTTTCACTCTCACGTTGTAG+TGG 0.531680 1.1:-56847163 MS.gene52952:CDS
AGAGGACAAGGACAAGGTGC+AGG 0.565916 1.1:+56847046 None:intergenic
CAAGCTTGTCTGAGAGGACA+AGG 0.577230 1.1:+56847034 None:intergenic
CTACAACGTGAGAGTGAAAG+TGG 0.580478 1.1:+56847166 None:intergenic
CTTCCCCAAGCTTGTCTGAG+AGG 0.586547 1.1:+56847028 None:intergenic
TAACAGCACGAGCACCAAAA+GGG 0.587993 1.1:+56846939 None:intergenic
GGACAAGGACAAGGTGCAGG+TGG 0.600667 1.1:+56847049 None:intergenic
GACTCTCAATCTAAAGCTAG+AGG 0.600860 1.1:-56846893 MS.gene52952:CDS
TAATTAGTTGCATTTGATGG+TGG 0.602526 1.1:+56846818 None:intergenic
AGAGTGTTTGTCGTTGCTGG+TGG 0.637477 1.1:+56847259 None:intergenic
TGTCCTCTCAGACAAGCTTG+GGG 0.658773 1.1:-56847031 MS.gene52952:CDS
TGTCTGAGAGGACAAGGACA+AGG 0.664143 1.1:+56847040 None:intergenic
CAACGTGAGAGTGAAAGTGG+TGG 0.746060 1.1:+56847169 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CACATGTTCTTGAATTTTTA+AGG - chr1.1:56847076-56847095 MS.gene52952:CDS 25.0%
AGAATCAAAAAAGAAGAGAC+TGG - chr1.1:56846989-56847008 MS.gene52952:CDS 30.0%
TAATTAGTTGCATTTGATGG+TGG + chr1.1:56847399-56847418 None:intergenic 30.0%
TGATCAGTTTGGAAAAACTA+AGG - chr1.1:56847104-56847123 MS.gene52952:CDS 30.0%
! TTAAGGTATCTTGATCAGTT+TGG - chr1.1:56847093-56847112 MS.gene52952:CDS 30.0%
!!! TCACAGATTTGTCCTTTTTT+TGG - chr1.1:56847132-56847151 MS.gene52952:CDS 30.0%
ACTCTTTCTTCGTGAAGTTA+GGG - chr1.1:56847299-56847318 MS.gene52952:CDS 35.0%
GGATTTGGATGACCAAAAAA+AGG + chr1.1:56847147-56847166 None:intergenic 35.0%
! AAACCTGAAGATAACCCTTT+TGG - chr1.1:56847261-56847280 MS.gene52952:CDS 35.0%
!! GATGTTTTTGTTGTCTTCTG+AGG + chr1.1:56846902-56846921 None:intergenic 35.0%
GACTCTTTCTTCGTGAAGTT+AGG - chr1.1:56847298-56847317 MS.gene52952:CDS 40.0%
! AGAAGAGACTGGAACACTTT+TGG - chr1.1:56847000-56847019 MS.gene52952:CDS 40.0%
! GACTCTCAATCTAAAGCTAG+AGG - chr1.1:56847321-56847340 MS.gene52952:CDS 40.0%
! GGAAGTCTTGATGCATTGAT+TGG - chr1.1:56847204-56847223 MS.gene52952:CDS 40.0%
!! CTGCTTTTGAAGAGAATGGT+GGG - chr1.1:56847238-56847257 MS.gene52952:CDS 40.0%
!! TTAGTTGCATTTGATGGTGG+TGG + chr1.1:56847396-56847415 None:intergenic 40.0%
!!! AGAGCTGCTTTTGAAGAGAA+TGG - chr1.1:56847234-56847253 MS.gene52952:CDS 40.0%
AGAGTGAAAGTGGTGGTCTA+TGG + chr1.1:56847041-56847060 None:intergenic 45.0%
CTACAACGTGAGAGTGAAAG+TGG + chr1.1:56847051-56847070 None:intergenic 45.0%
CTTTCACTCTCACGTTGTAG+TGG - chr1.1:56847051-56847070 MS.gene52952:CDS 45.0%
GCACCAAAAGGGTTATCTTC+AGG + chr1.1:56847267-56847286 None:intergenic 45.0%
GTGGTGGTCTATGGTTTCTT+AGG + chr1.1:56847032-56847051 None:intergenic 45.0%
TAACAGCACGAGCACCAAAA+GGG + chr1.1:56847278-56847297 None:intergenic 45.0%
TTGTCCTCTCAGACAAGCTT+GGG - chr1.1:56847182-56847201 MS.gene52952:CDS 45.0%
! CTTAGAGTGTTTGTCGTTGC+TGG + chr1.1:56846961-56846980 None:intergenic 45.0%
!! GTCTTCTGAGGTTGTTGTGT+TGG + chr1.1:56846890-56846909 None:intergenic 45.0%
!!! GCTGCTTTTGAAGAGAATGG+TGG - chr1.1:56847237-56847256 MS.gene52952:CDS 45.0%
CAACGTGAGAGTGAAAGTGG+TGG + chr1.1:56847048-56847067 None:intergenic 50.0%
CAAGCTTGTCTGAGAGGACA+AGG + chr1.1:56847183-56847202 None:intergenic 50.0%
CTAACAGCACGAGCACCAAA+AGG + chr1.1:56847279-56847298 None:intergenic 50.0%
CTTGTCCTCTCAGACAAGCT+TGG - chr1.1:56847181-56847200 MS.gene52952:CDS 50.0%
TGTCCTCTCAGACAAGCTTG+GGG - chr1.1:56847183-56847202 MS.gene52952:CDS 50.0%
TGTCTGAGAGGACAAGGACA+AGG + chr1.1:56847177-56847196 None:intergenic 50.0%
! AGAGTGTTTGTCGTTGCTGG+TGG + chr1.1:56846958-56846977 None:intergenic 50.0%
!! GGTGGTGGAGGTTGAATTTG+AGG + chr1.1:56847378-56847397 None:intergenic 50.0%
!! GTTGCATTTGATGGTGGTGG+TGG + chr1.1:56847393-56847412 None:intergenic 50.0%
AGAGGACAAGGACAAGGTGC+AGG + chr1.1:56847171-56847190 None:intergenic 55.0%
CTTCCCCAAGCTTGTCTGAG+AGG + chr1.1:56847189-56847208 None:intergenic 55.0%
! GGACAAGGTGCAGGTGGATT+TGG + chr1.1:56847162-56847181 None:intergenic 55.0%
!! GCATTTGATGGTGGTGGTGG+AGG + chr1.1:56847390-56847409 None:intergenic 55.0%
GGACAAGGACAAGGTGCAGG+TGG + chr1.1:56847168-56847187 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 56846817 56847419 56846817 ID=MS.gene52952
chr1.1 mRNA 56846817 56847419 56846817 ID=MS.gene52952.t1;Parent=MS.gene52952
chr1.1 exon 56846817 56847419 56846817 ID=MS.gene52952.t1.exon1;Parent=MS.gene52952.t1
chr1.1 CDS 56846817 56847419 56846817 ID=cds.MS.gene52952.t1;Parent=MS.gene52952.t1
Gene Sequence

>MS.gene52952

ATGAATTCATTTGAAGAATTCAACTCATCATCATCAACAAACACACAAACAAAAAACATCATCAACTTCACCAACACAACAACCTCAGAAGACAACAAAAACATCTCAAATTTCACATCTTCTTCTTCTTCAGCAGTACCACCAGCAACGACAAACACTCTAAGTCGCTATGAGAATCAAAAAAGAAGAGACTGGAACACTTTTGGTCAATACCTAAGAAACCATAGACCACCACTTTCACTCTCACGTTGTAGTGGAGCACATGTTCTTGAATTTTTAAGGTATCTTGATCAGTTTGGAAAAACTAAGGTTCACTCACAGATTTGTCCTTTTTTTGGTCATCCAAATCCACCTGCACCTTGTCCTTGTCCTCTCAGACAAGCTTGGGGAAGTCTTGATGCATTGATTGGAAGACTAAGAGCTGCTTTTGAAGAGAATGGTGGGAAACCTGAAGATAACCCTTTTGGTGCTCGTGCTGTTAGACTCTTTCTTCGTGAAGTTAGGGACTCTCAATCTAAAGCTAGAGGTATTAGCTATGAGAAAAAGAAGCGTAAAAGACCTCAAATTCAACCTCCACCACCACCATCAAATGCAACTAATTAA
Protein sequence

>MS.gene52952.t1

MNSFEEFNSSSSTNTQTKNIINFTNTTTSEDNKNISNFTSSSSSAVPPATTNTLSRYENQKRRDWNTFGQYLRNHRPPLSLSRCSGAHVLEFLRYLDQFGKTKVHSQICPFFGHPNPPAPCPCPLRQAWGSLDALIGRLRAAFEENGGKPEDNPFGARAVRLFLREVRDSQSKARGISYEKKKRKRPQIQPPPPPSNATN