AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene47915

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene47915.t1 MTR_8g089170 92.308 156 12 0 1 156 1 156 2.25e-99 283
MS.gene47915.t1 MTR_8g089130 84.177 158 23 2 1 156 1 158 1.08e-90 261
MS.gene47915.t1 MTR_8g089145 87.671 73 9 0 1 73 1 73 1.81e-42 136
MS.gene47915.t1 MTR_1g089830 36.842 152 67 4 4 155 3 125 4.61e-22 86.3
MS.gene47915.t1 MTR_4g028990 54.545 77 33 1 81 155 20 96 2.62e-20 80.5
MS.gene47915.t1 MTR_1g045040 39.333 150 65 4 7 155 6 130 1.97e-19 79.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 30 sgRNAs with CRISPR-Local

Find 37 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCATACCTTCAAATGAAAT+TGG 0.214941 4.1:-11569378 MS.gene47915:CDS
CATAAAACTGGCTTGTCTTT+TGG 0.254968 4.1:+11569872 None:intergenic
CTTTGAGGTTTCCCCAGTTT+TGG 0.256311 4.1:+11569828 None:intergenic
ATTCTCAAACTACGTCTCTT+TGG 0.299791 4.1:+11569525 None:intergenic
TCAAACAATAAGGCCTCTTC+TGG 0.301830 4.1:+11569414 None:intergenic
TGGCGCCATGCTGGAGTTGC+TGG 0.314815 4.1:+11569899 None:intergenic
GATGTTTCTGATTCAGATAA+TGG 0.318368 4.1:-11569713 MS.gene47915:intron
CTGTTCGTAACAAGTTCTTT+TGG 0.340372 4.1:+11569782 None:intergenic
TTTGGTCCCTGGCGCCATGC+TGG 0.374123 4.1:+11569890 None:intergenic
GAAAACAACGTTTGAGAGAA+TGG 0.387976 4.1:+11569804 None:intergenic
GTGGACTAAGATACCAAAAC+TGG 0.405891 4.1:-11569841 MS.gene47915:CDS
CCACATGCATTGCATAAAAC+TGG 0.410323 4.1:+11569860 None:intergenic
CCTTCAAATGAAATTGGCCT+TGG 0.419265 4.1:-11569372 MS.gene47915:CDS
CCAAGGCCAATTTCATTTGA+AGG 0.421742 4.1:+11569372 None:intergenic
AGCAACTCCAGCATGGCGCC+AGG 0.436034 4.1:-11569897 MS.gene47915:CDS
GTTTGAGAGAATGGTCTTTG+AGG 0.475222 4.1:+11569813 None:intergenic
TCTTCTGGAGATGACTCATC+TGG 0.489997 4.1:+11569429 None:intergenic
TCTTGTTGAAACTTCTCCAT+CGG 0.530728 4.1:+11569483 None:intergenic
ATCTGAATCAGAAACATCAA+TGG 0.539843 4.1:+11569718 None:intergenic
TTCTACATAGAAGAACCGTC+TGG 0.563851 4.1:+11569333 None:intergenic
GCAACTCCAGCATGGCGCCA+GGG 0.585142 4.1:-11569896 MS.gene47915:CDS
AGATGAGTCATCTCCAGAAG+AGG 0.604525 4.1:-11569427 MS.gene47915:CDS
GCGGTTCTTCTTAAACCAGA+CGG 0.605404 4.1:-11569348 MS.gene47915:CDS
AAATGAAATTGGCCTTGGAG+CGG 0.608265 4.1:-11569367 MS.gene47915:CDS
CAATCAGAAGATGACACCGA+TGG 0.614119 4.1:-11569499 MS.gene47915:CDS
TGGACTAAGATACCAAAACT+GGG 0.618651 4.1:-11569840 MS.gene47915:CDS
GTTTAAGAAGAACCGCTCCA+AGG 0.637380 4.1:+11569355 None:intergenic
AAAGAACTTGTTACGAACAG+TGG 0.644687 4.1:-11569779 MS.gene47915:CDS
CATCACCAGCAACTCCAGCA+TGG 0.651498 4.1:-11569904 MS.gene47915:CDS
GGACTAAGATACCAAAACTG+GGG 0.731002 4.1:-11569839 MS.gene47915:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GATATATATTACTTTTGTGA+GGG - chr4.1:11569603-11569622 MS.gene47915:intron 20.0%
!!! TGATATATATTACTTTTGTG+AGG - chr4.1:11569602-11569621 MS.gene47915:intron 20.0%
! TGTAAAGAAAAGAGTGAAAA+TGG + chr4.1:11569581-11569600 None:intergenic 25.0%
! TTCATACCTTCAAATGAAAT+TGG - chr4.1:11569868-11569887 MS.gene47915:CDS 25.0%
!! GTTCACATTTTCAAACAATA+AGG + chr4.1:11569845-11569864 None:intergenic 25.0%
ATCTGAATCAGAAACATCAA+TGG + chr4.1:11569531-11569550 None:intergenic 30.0%
! GATGTTTCTGATTCAGATAA+TGG - chr4.1:11569533-11569552 MS.gene47915:CDS 30.0%
!! ATATATTACTTTTGTGAGGG+TGG - chr4.1:11569606-11569625 MS.gene47915:intron 30.0%
!! TATATTACTTTTGTGAGGGT+GGG - chr4.1:11569607-11569626 MS.gene47915:intron 30.0%
ATTCTCAAACTACGTCTCTT+TGG + chr4.1:11569724-11569743 None:intergenic 35.0%
GAAAACAACGTTTGAGAGAA+TGG + chr4.1:11569445-11569464 None:intergenic 35.0%
TCTTGTTGAAACTTCTCCAT+CGG + chr4.1:11569766-11569785 None:intergenic 35.0%
TGGACTAAGATACCAAAACT+GGG - chr4.1:11569406-11569425 MS.gene47915:CDS 35.0%
! CTGTTCGTAACAAGTTCTTT+TGG + chr4.1:11569467-11569486 None:intergenic 35.0%
!! AAAGAACTTGTTACGAACAG+TGG - chr4.1:11569467-11569486 MS.gene47915:CDS 35.0%
!!! CATAAAACTGGCTTGTCTTT+TGG + chr4.1:11569377-11569396 None:intergenic 35.0%
CCAAGGCCAATTTCATTTGA+AGG + chr4.1:11569877-11569896 None:intergenic 40.0%
CCACATGCATTGCATAAAAC+TGG + chr4.1:11569389-11569408 None:intergenic 40.0%
GGACTAAGATACCAAAACTG+GGG - chr4.1:11569407-11569426 MS.gene47915:CDS 40.0%
GTTTGAGAGAATGGTCTTTG+AGG + chr4.1:11569436-11569455 None:intergenic 40.0%
TCAAACAATAAGGCCTCTTC+TGG + chr4.1:11569835-11569854 None:intergenic 40.0%
! CCTTCAAATGAAATTGGCCT+TGG - chr4.1:11569874-11569893 MS.gene47915:CDS 40.0%
! GTGGACTAAGATACCAAAAC+TGG - chr4.1:11569405-11569424 MS.gene47915:CDS 40.0%
!! AAATGAAATTGGCCTTGGAG+CGG - chr4.1:11569879-11569898 MS.gene47915:CDS 40.0%
!! CCAGTTTTATGCAATGCATG+TGG - chr4.1:11569386-11569405 MS.gene47915:CDS 40.0%
AGATGAGTCATCTCCAGAAG+AGG - chr4.1:11569819-11569838 MS.gene47915:CDS 45.0%
CAATCAGAAGATGACACCGA+TGG - chr4.1:11569747-11569766 MS.gene47915:CDS 45.0%
GCGGTTCTTCTTAAACCAGA+CGG - chr4.1:11569898-11569917 MS.gene47915:CDS 45.0%
GTTTAAGAAGAACCGCTCCA+AGG + chr4.1:11569894-11569913 None:intergenic 45.0%
! TCTTCTGGAGATGACTCATC+TGG + chr4.1:11569820-11569839 None:intergenic 45.0%
!!! CTTTGAGGTTTCCCCAGTTT+TGG + chr4.1:11569421-11569440 None:intergenic 45.0%
CATCACCAGCAACTCCAGCA+TGG - chr4.1:11569342-11569361 MS.gene47915:CDS 55.0%
!! CTGGCTTGTCTTTTGGTCCC+TGG + chr4.1:11569370-11569389 None:intergenic 55.0%
AGCAACTCCAGCATGGCGCC+AGG - chr4.1:11569349-11569368 MS.gene47915:CDS 65.0%
GCAACTCCAGCATGGCGCCA+GGG - chr4.1:11569350-11569369 MS.gene47915:CDS 65.0%
TGGCGCCATGCTGGAGTTGC+TGG + chr4.1:11569350-11569369 None:intergenic 65.0%
TTTGGTCCCTGGCGCCATGC+TGG + chr4.1:11569359-11569378 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 11569335 11569933 11569335 ID=MS.gene47915
chr4.1 mRNA 11569335 11569933 11569335 ID=MS.gene47915.t1;Parent=MS.gene47915
chr4.1 exon 11569714 11569933 11569714 ID=MS.gene47915.t1.exon1;Parent=MS.gene47915.t1
chr4.1 CDS 11569714 11569933 11569714 ID=cds.MS.gene47915.t1;Parent=MS.gene47915.t1
chr4.1 exon 11569335 11569585 11569335 ID=MS.gene47915.t1.exon2;Parent=MS.gene47915.t1
chr4.1 CDS 11569335 11569585 11569335 ID=cds.MS.gene47915.t1;Parent=MS.gene47915.t1
Gene Sequence

>MS.gene47915

ATGGATTCATCACCAGCAACTCCAGCATGGCGCCAGGGACCAAAAGACAAGCCAGTTTTATGCAATGCATGTGGACTAAGATACCAAAACTGGGGAAACCTCAAAGACCATTCTCTCAAACGTTGTTTTCCAAAAGAACTTGTTACGAACAGTGGCAACAGTAGCAACAACAGTCTCAAAGAAAGTTCATCAACCATTGATGTTTCTGATTCAGATAATGGTATGTGTTTATACTAGTACTAGCCATTTTCACTCTTTTCTTTACAATGATATATATTACTTTTGTGAGGGTGGGCGTGCGTGAATACTTCTTTTAAATTGTCAATAAATAAGAGAATTTTTACTCAGATGAAAAAGATTCAGATTCATGCAAGTCTGCAGTCTCTCCAAAGAGACGTAGTTTGAGAATTATCAATCAGAAGATGACACCGATGGAGAAGTTTCAACAAGAACTTCTTGATGAGTTGAAAAATCACGAGATACCAGATGAGTCATCTCCAGAAGAGGCCTTATTGTTTGAAAATGTGAACAACTTCATACCTTCAAATGAAATTGGCCTTGGAGCGGTTCTTCTTAAACCAGACGGTTCTTCTATGTAG
Protein sequence

>MS.gene47915.t1

MDSSPATPAWRQGPKDKPVLCNACGLRYQNWGNLKDHSLKRCFPKELVTNSGNSSNNSLKESSSTIDVSDSDNDEKDSDSCKSAVSPKRRSLRIINQKMTPMEKFQQELLDELKNHEIPDESSPEEALLFENVNNFIPSNEIGLGAVLLKPDGSSM