AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene025586

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene025586.t1 MTR_4g039380 80.800 125 16 2 1 125 1 117 1.36e-59 179
MS.gene025586.t1 MTR_4g039340 79.545 132 19 2 1 125 1 131 3.05e-59 179
MS.gene025586.t1 MTR_4g039640 69.697 132 18 3 1 125 1 117 2.26e-45 143
MS.gene025586.t1 MTR_4g039400 38.462 117 30 1 1 117 1 75 9.07e-14 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 21 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTCACTCATCTGGTGTATA+AGG 0.223072 4.1:-59849426 None:intergenic
TCTGGTTGAGGCTGGTAATT+TGG 0.230425 4.1:-59849198 None:intergenic
GGTGGAGCTGGTGCATTTCT+TGG 0.287826 4.1:-59849321 None:intergenic
CTCGATTCTAATATATAATC+TGG 0.322005 4.1:-59849159 None:intergenic
AGGTCGAAAGCACGAACATT+AGG 0.411724 4.1:-59849393 None:intergenic
CTCACTCATCTGGTGTATAA+GGG 0.433158 4.1:-59849425 None:intergenic
GTGTATAAGGGAGATTATTA+AGG 0.444305 4.1:-59849413 None:intergenic
GGTTGAGGCTGGTAATTTGG+TGG 0.465939 4.1:-59849195 None:intergenic
GGTGCATTTCTTGGTGGAGC+CGG 0.469690 4.1:-59849312 None:intergenic
TGAGGCTGGTAATTTGGTGG+TGG 0.493466 4.1:-59849192 None:intergenic
GGAGGCTGGTTCAAGTCAAA+TGG 0.504409 4.1:-59849372 None:intergenic
AAGTCAAATGGCTGCACATG+TGG 0.521723 4.1:-59849360 None:intergenic
ACTGCTAAAGCTTGTGGAGA+TGG 0.545041 4.1:-59849114 None:intergenic
GGAGCTGGTGCATTTCTTGG+TGG 0.547442 4.1:-59849318 None:intergenic
AATGGCTGCACATGTGGAGG+TGG 0.555990 4.1:-59849354 None:intergenic
AAGCACGAACATTAGGAGGC+TGG 0.567243 4.1:-59849386 None:intergenic
ACATGCACTGCTAAAGCTTG+TGG 0.578207 4.1:-59849120 None:intergenic
TCGAAAGCACGAACATTAGG+AGG 0.607481 4.1:-59849390 None:intergenic
ACATCAACCACAAAATGCAC+CGG 0.623532 4.1:+59849293 MS.gene025586:CDS
ATATTAGAATCGAGTAAACA+TGG 0.652245 4.1:+59849168 MS.gene025586:CDS
TCAAATGGCTGCACATGTGG+AGG 0.671560 4.1:-59849357 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ATATTAGAATCGAGTAAACA+TGG + chr4.1:59849168-59849187 MS.gene025586:CDS 25.0%
! CTCGATTCTAATATATAATC+TGG - chr4.1:59849162-59849181 None:intergenic 25.0%
GTGTATAAGGGAGATTATTA+AGG - chr4.1:59849416-59849435 None:intergenic 30.0%
! TGATGTTCAACATTTTGTGG+TGG - chr4.1:59849237-59849256 None:intergenic 35.0%
!! GGTTGATGTTCAACATTTTG+TGG - chr4.1:59849240-59849259 None:intergenic 35.0%
ACATCAACCACAAAATGCAC+CGG + chr4.1:59849251-59849270 MS.gene025586:CDS 40.0%
! GGTTGAGATTGAGCATTTTC+TGG - chr4.1:59849219-59849238 None:intergenic 40.0%
!!! GATTGAGCATTTTCTGGTTG+AGG - chr4.1:59849213-59849232 None:intergenic 40.0%
AAGTCAAATGGCTGCACATG+TGG - chr4.1:59849363-59849382 None:intergenic 45.0%
ACATGCACTGCTAAAGCTTG+TGG - chr4.1:59849123-59849142 None:intergenic 45.0%
ACTGCTAAAGCTTGTGGAGA+TGG - chr4.1:59849117-59849136 None:intergenic 45.0%
TCTGGTTGAGGCTGGTAATT+TGG - chr4.1:59849201-59849220 None:intergenic 45.0%
! AGGTCGAAAGCACGAACATT+AGG - chr4.1:59849396-59849415 None:intergenic 45.0%
! TCGAAAGCACGAACATTAGG+AGG - chr4.1:59849393-59849412 None:intergenic 45.0%
AAGCACGAACATTAGGAGGC+TGG - chr4.1:59849389-59849408 None:intergenic 50.0%
GGTTGAGGCTGGTAATTTGG+TGG - chr4.1:59849198-59849217 None:intergenic 50.0%
TCAAATGGCTGCACATGTGG+AGG - chr4.1:59849360-59849379 None:intergenic 50.0%
! GGAGGCTGGTTCAAGTCAAA+TGG - chr4.1:59849375-59849394 None:intergenic 50.0%
! GGTGGAGCTAGTGCATTTTG+TGG - chr4.1:59849261-59849280 None:intergenic 50.0%
! TGAGGCTGGTAATTTGGTGG+TGG - chr4.1:59849195-59849214 None:intergenic 50.0%
! TGTGGAGGTGGTGCATTTTG+TGG - chr4.1:59849345-59849364 None:intergenic 50.0%
!!! GAGCATTTTCTGGTTGAGGC+TGG - chr4.1:59849209-59849228 None:intergenic 50.0%
AATGGCTGCACATGTGGAGG+TGG - chr4.1:59849357-59849376 None:intergenic 55.0%
GGAGCTGGTGCATTTCTTGG+TGG - chr4.1:59849321-59849340 None:intergenic 55.0%
GGTGCATTTCTTGGTGGAGC+CGG - chr4.1:59849315-59849334 None:intergenic 55.0%
GGTGGAGCTGGTGCATTTCT+TGG - chr4.1:59849324-59849343 None:intergenic 55.0%
! GGAGGTGGTGCATTTTGTGG+TGG - chr4.1:59849342-59849361 None:intergenic 55.0%
!! GGTGCATTTTGTGGTGGAGC+TGG - chr4.1:59849336-59849355 None:intergenic 55.0%
! GGTGGAGCCGGTGCATTTTG+TGG - chr4.1:59849303-59849322 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 59849069 59849446 59849069 ID=MS.gene025586
chr4.1 mRNA 59849069 59849446 59849069 ID=MS.gene025586.t1;Parent=MS.gene025586
chr4.1 exon 59849069 59849446 59849069 ID=MS.gene025586.t1.exon1;Parent=MS.gene025586.t1
chr4.1 CDS 59849069 59849446 59849069 ID=cds.MS.gene025586.t1;Parent=MS.gene025586.t1
Gene Sequence

>MS.gene025586

ATGTCAAAGCTAGAATTCTTATGCGATGAATGTGACACAAAGTTTCCATCTCCACAAGCTTTAGCAGTGCATGTTGTCGAAGAACATCATCCAGATTATATATTAGAATCGAGTAAACATGGTCCACCACCAAATTACCAGCCTCAACCAGAAAATGCTCAATCTCAACCACAAAATGTTGAACATCAACCACAAAATGCACTAGCTCCACCACAAAATGTTGAACATCAACCACAAAATGCACCGGCTCCACCAAGAAATGCACCAGCTCCACCACAAAATGCACCACCTCCACATGTGCAGCCATTTGACTTGAACCAGCCTCCTAATGTTCGTGCTTTCGACCTTAATAATCTCCCTTATACACCAGATGAGTGA
Protein sequence

>MS.gene025586.t1

MSKLEFLCDECDTKFPSPQALAVHVVEEHHPDYILESSKHGPPPNYQPQPENAQSQPQNVEHQPQNALAPPQNVEHQPQNAPAPPRNAPAPPQNAPPPHVQPFDLNQPPNVRAFDLNNLPYTPDE