AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene77469

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene77469.t1 MTR_3g083150 75.904 83 17 1 8 90 133 212 4.32e-37 124
MS.gene77469.t1 MTR_3g083100 52.222 90 31 2 9 90 89 174 5.03e-22 84.3
MS.gene77469.t1 MTR_3g083080 47.368 95 36 5 1 89 119 205 2.29e-15 68.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 24 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGGGTAGCATCTTCTGGTTT+TGG 0.308463 3.2:-71985489 None:intergenic
TGAACATGGGTAGCATCTTC+TGG 0.357963 3.2:-71985495 None:intergenic
TCGCCTCTCCAAGCTTGCTT+TGG 0.392937 3.2:+71985258 MS.gene77469:CDS
GAAGTACAATGCTGACAATC+AGG 0.431538 3.2:+71985282 MS.gene77469:CDS
CACGACTTGATCACAGGTTC+AGG 0.456720 3.2:-71985570 None:intergenic
GTACTTCTCCAAAGCAAGCT+TGG 0.468678 3.2:-71985266 None:intergenic
ATCATCATCGGTAATGTCCA+TGG 0.485528 3.2:-71985236 None:intergenic
CGGGCCTGAAAAGTTATAGC+AGG 0.514776 3.2:-71985531 None:intergenic
ACCCGTGTGCATATTCCTCT+TGG 0.518195 3.2:+71985438 MS.gene77469:CDS
AAAAGTTATAGCAGGGCAGT+TGG 0.545343 3.2:-71985523 None:intergenic
TGAATTTGATGTGCTCATCA+AGG 0.546727 3.2:+71985413 MS.gene77469:CDS
CTTGGAGAGGCGATCATCAT+CGG 0.553632 3.2:-71985248 None:intergenic
ATGGAACACGACTTGATCAC+AGG 0.555050 3.2:-71985576 None:intergenic
GTTATAGCAGGGCAGTTGGA+AGG 0.582712 3.2:-71985519 None:intergenic
CAGGCATACTGTCACAGACA+CGG 0.585144 3.2:-71985551 None:intergenic
GGCAGTTGGAAGGATGAACA+TGG 0.590763 3.2:-71985509 None:intergenic
TCATCATCGGTAATGTCCAT+GGG 0.608264 3.2:-71985235 None:intergenic
AGGCATACTGTCACAGACAC+GGG 0.620581 3.2:-71985550 None:intergenic
TCTCCAAAGCAAGCTTGGAG+AGG 0.642137 3.2:-71985261 None:intergenic
GGGCCTGAAAAGTTATAGCA+GGG 0.658880 3.2:-71985530 None:intergenic
TACCAAGAGGAATATGCACA+CGG 0.664367 3.2:-71985440 None:intergenic
GTAATATAATAAGTACCAAG+AGG 0.676156 3.2:-71985453 None:intergenic
GCAGTTGGAAGGATGAACAT+GGG 0.704484 3.2:-71985508 None:intergenic
ACCAAGAGGAATATGCACAC+GGG 0.718548 3.2:-71985439 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAATTTTGTTTCTCTTATTT+AGG + chr3.2:71985380-71985399 MS.gene77469:intron 15.0%
! ACATGGATATAATATAACAG+TGG - chr3.2:71985326-71985345 None:intergenic 25.0%
! GTAATATAATAAGTACCAAG+AGG - chr3.2:71985456-71985475 None:intergenic 25.0%
GATGAGTGAAAGAATAAACA+TGG - chr3.2:71985343-71985362 None:intergenic 30.0%
TGGATATAATATAACAGTGG+TGG - chr3.2:71985323-71985342 None:intergenic 30.0%
!!! TGGTTTTGGTTTTGCTTTAA+AGG - chr3.2:71985478-71985497 None:intergenic 30.0%
TGAATTTGATGTGCTCATCA+AGG + chr3.2:71985413-71985432 MS.gene77469:CDS 35.0%
AAAAGTTATAGCAGGGCAGT+TGG - chr3.2:71985526-71985545 None:intergenic 40.0%
GAAGTACAATGCTGACAATC+AGG + chr3.2:71985282-71985301 MS.gene77469:CDS 40.0%
TACCAAGAGGAATATGCACA+CGG - chr3.2:71985443-71985462 None:intergenic 40.0%
ACCAAGAGGAATATGCACAC+GGG - chr3.2:71985442-71985461 None:intergenic 45.0%
ATGGAACACGACTTGATCAC+AGG - chr3.2:71985579-71985598 None:intergenic 45.0%
GCAGTTGGAAGGATGAACAT+GGG - chr3.2:71985511-71985530 None:intergenic 45.0%
GGGCCTGAAAAGTTATAGCA+GGG - chr3.2:71985533-71985552 None:intergenic 45.0%
GTACTTCTCCAAAGCAAGCT+TGG - chr3.2:71985269-71985288 None:intergenic 45.0%
TGAACATGGGTAGCATCTTC+TGG - chr3.2:71985498-71985517 None:intergenic 45.0%
! ACAGTGGTGGTGAACTAGTT+TGG - chr3.2:71985310-71985329 None:intergenic 45.0%
! CTGCCCTGCTATAACTTTTC+AGG + chr3.2:71985527-71985546 MS.gene77469:CDS 45.0%
!!! TGGGTAGCATCTTCTGGTTT+TGG - chr3.2:71985492-71985511 None:intergenic 45.0%
ACCCGTGTGCATATTCCTCT+TGG + chr3.2:71985438-71985457 MS.gene77469:CDS 50.0%
AGGCATACTGTCACAGACAC+GGG - chr3.2:71985553-71985572 None:intergenic 50.0%
CACGACTTGATCACAGGTTC+AGG - chr3.2:71985573-71985592 None:intergenic 50.0%
CAGGCATACTGTCACAGACA+CGG - chr3.2:71985554-71985573 None:intergenic 50.0%
CGGGCCTGAAAAGTTATAGC+AGG - chr3.2:71985534-71985553 None:intergenic 50.0%
CTTGGAGAGGCGATCATCAT+CGG - chr3.2:71985251-71985270 None:intergenic 50.0%
GGCAGTTGGAAGGATGAACA+TGG - chr3.2:71985512-71985531 None:intergenic 50.0%
GTTATAGCAGGGCAGTTGGA+AGG - chr3.2:71985522-71985541 None:intergenic 50.0%
TCTCCAAAGCAAGCTTGGAG+AGG - chr3.2:71985264-71985283 None:intergenic 50.0%
! TCGCCTCTCCAAGCTTGCTT+TGG + chr3.2:71985258-71985277 MS.gene77469:CDS 55.0%


Chromosome Type Strat End Strand Name
chr3.2 gene 71985238 71985608 71985238 ID=MS.gene77469
chr3.2 mRNA 71985238 71985608 71985238 ID=MS.gene77469.t1;Parent=MS.gene77469
chr3.2 exon 71985238 71985303 71985238 ID=MS.gene77469.t1.exon1;Parent=MS.gene77469.t1
chr3.2 CDS 71985238 71985303 71985238 ID=cds.MS.gene77469.t1;Parent=MS.gene77469.t1
chr3.2 exon 71985402 71985608 71985402 ID=MS.gene77469.t1.exon2;Parent=MS.gene77469.t1
chr3.2 CDS 71985402 71985608 71985402 ID=cds.MS.gene77469.t1;Parent=MS.gene77469.t1
Gene Sequence

>MS.gene77469

ATGGACATTACCGATGATGATCGCCTCTCCAAGCTTGCTTTGGAGAAGTACAATGCTGACAATCAGGTTCCAAACTAGTTCACCACCACTGTTATATTATATCCATGTTTATTCTTTCACTCATCAGCTTCAATATTCTTCTAAATTTTGTTTCTCTTATTTAGGATGTCAAATATGAATTTGATGTGCTCATCAAGGCAACCCGTGTGCATATTCCTCTTGGTACTTATTATATTACCTTTAAAGCAAAACCAAAACCAGAAGATGCTACCCATGTTCATCCTTCCAACTGCCCTGCTATAACTTTTCAGGCCCGTGTCTGTGACAGTATGCCTGAACCTGTGATCAAGTCGTGTTCCATTAAAACCTAA
Protein sequence

>MS.gene77469.t1

MDITDDDRLSKLALEKYNADNQDVKYEFDVLIKATRVHIPLGTYYITFKAKPKPEDATHVHPSNCPAITFQARVCDSMPEPVIKSCSIKT