AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene95943

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene95943.t1 MTR_6g048860 82.692 52 9 0 39 90 266 317 3.42e-24 94.0
MS.gene95943.t1 MTR_3g037670 80.952 42 8 0 39 80 224 265 8.42e-18 76.3
MS.gene95943.t1 MTR_4g007610 78.947 57 12 0 39 95 294 350 1.07e-17 76.6
MS.gene95943.t1 MTR_8g107350 76.190 42 10 0 39 80 192 233 1.10e-16 73.2
MS.gene95943.t1 MTR_5g038770 50.847 59 28 1 11 68 6 64 9.00e-12 57.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 18 sgRNAs with CRISPR-Local

Find 28 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAGGATAAACAACATTATT+TGG 0.112137 6.2:+76306499 MS.gene95943:intron
AAATTATGATGTTAATAAAA+TGG 0.232813 6.2:+76306361 MS.gene95943:CDS
TCTATCTGCAACTGTGAAAT+TGG 0.248781 6.2:-76305927 None:intergenic
TTATATTTCAGGGATAAGTT+TGG 0.382899 6.2:+76306314 MS.gene95943:intron
GTGTTACCTGTGAGCGAAAG+AGG 0.447507 6.2:-76305964 None:intergenic
GTGAAGCATTCCACCATTCT+CGG 0.464051 6.2:-76306679 None:intergenic
AGGATGAAGTTCAATAGATC+CGG 0.465533 6.2:-76305904 None:intergenic
AACATGAGAAACTTAAGAAA+AGG 0.495000 6.2:+76306546 MS.gene95943:CDS
AGGACTTACTTCATTACTCA+TGG 0.496503 6.2:-76306402 None:intergenic
ATAAAATGGTTGTTAAAGCA+TGG 0.505549 6.2:+76306375 MS.gene95943:CDS
CCGGGACTGTGAAGCTCGAT+CGG 0.546676 6.2:-76305885 None:intergenic
GAATAGGGTGACTCCGAGAA+TGG 0.550110 6.2:+76306666 MS.gene95943:intron
CCGATCGAGCTTCACAGTCC+CGG 0.552827 6.2:+76305885 MS.gene95943:CDS
CGGTGAAGTGTGAAGCTCCA+TGG 0.558822 6.2:-76305865 None:intergenic
ATCTGCAACTGTGAAATTGG+AGG 0.566506 6.2:-76305924 None:intergenic
GGATGAAGTTCAATAGATCC+GGG 0.594180 6.2:-76305903 None:intergenic
GGATAAAGCATCTAAGCGCA+AGG 0.626619 6.2:+76306520 MS.gene95943:CDS
TAGGGTGACTCCGAGAATGG+TGG 0.628698 6.2:+76306669 MS.gene95943:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATTATGATGTTAATAAAA+TGG + chr6.2:76306361-76306380 MS.gene95943:CDS 10.0%
!! AAGTATAAAATTTATATTTC+AGG + chr6.2:76306303-76306322 MS.gene95943:intron 10.0%
!! AGTATAAAATTTATATTTCA+GGG + chr6.2:76306304-76306323 MS.gene95943:intron 10.0%
!! ATTGATTATATTATTTAATC+AGG + chr6.2:76306481-76306500 MS.gene95943:intron 10.0%
!! AACACAAAATCAATTAAATT+TGG - chr6.2:76306585-76306604 None:intergenic 15.0%
!! ACACAAAATCAATTAAATTT+GGG - chr6.2:76306584-76306603 None:intergenic 15.0%
!! AAAGAAGATTTCTTATTCTT+TGG - chr6.2:76306246-76306265 None:intergenic 20.0%
! AACATGAGAAACTTAAGAAA+AGG + chr6.2:76306546-76306565 MS.gene95943:CDS 25.0%
! ATAAAATGGTTGTTAAAGCA+TGG + chr6.2:76306375-76306394 MS.gene95943:CDS 25.0%
! TCAGGATAAACAACATTATT+TGG + chr6.2:76306499-76306518 MS.gene95943:intron 25.0%
! TTATATTTCAGGGATAAGTT+TGG + chr6.2:76306314-76306333 MS.gene95943:intron 25.0%
! TTTGTGTGTTTGATTGAATA+GGG + chr6.2:76306651-76306670 MS.gene95943:intron 25.0%
CATGTGTTGTAATATACTAG+AGG - chr6.2:76306425-76306444 None:intergenic 30.0%
CTTTGTGTGTTTGATTGAAT+AGG + chr6.2:76306650-76306669 MS.gene95943:intron 30.0%
AGGACTTACTTCATTACTCA+TGG - chr6.2:76306405-76306424 None:intergenic 35.0%
AGGATGAAGTTCAATAGATC+CGG - chr6.2:76305907-76305926 None:intergenic 35.0%
TCTATCTGCAACTGTGAAAT+TGG - chr6.2:76305930-76305949 None:intergenic 35.0%
ATCTGCAACTGTGAAATTGG+AGG - chr6.2:76305927-76305946 None:intergenic 40.0%
CTTTGGCAACATCAAACACA+TGG - chr6.2:76306229-76306248 None:intergenic 40.0%
GGATGAAGTTCAATAGATCC+GGG - chr6.2:76305906-76305925 None:intergenic 40.0%
!!! TTTTTTCCTCTTTCGCTCAC+AGG + chr6.2:76305958-76305977 MS.gene95943:CDS 40.0%
! GGATAAAGCATCTAAGCGCA+AGG + chr6.2:76306520-76306539 MS.gene95943:CDS 45.0%
! GTGAAGCATTCCACCATTCT+CGG - chr6.2:76306682-76306701 None:intergenic 45.0%
GAATAGGGTGACTCCGAGAA+TGG + chr6.2:76306666-76306685 MS.gene95943:intron 50.0%
GTGTTACCTGTGAGCGAAAG+AGG - chr6.2:76305967-76305986 None:intergenic 50.0%
TAGGGTGACTCCGAGAATGG+TGG + chr6.2:76306669-76306688 MS.gene95943:intron 55.0%
CCGATCGAGCTTCACAGTCC+CGG + chr6.2:76305885-76305904 MS.gene95943:CDS 60.0%
CCGGGACTGTGAAGCTCGAT+CGG - chr6.2:76305888-76305907 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 76305867 76306708 76305867 ID=MS.gene95943
chr6.2 mRNA 76305867 76306708 76305867 ID=MS.gene95943.t1;Parent=MS.gene95943
chr6.2 exon 76305867 76305979 76305867 ID=MS.gene95943.t1.exon1;Parent=MS.gene95943.t1
chr6.2 CDS 76305867 76305979 76305867 ID=cds.MS.gene95943.t1;Parent=MS.gene95943.t1
chr6.2 exon 76306325 76306415 76306325 ID=MS.gene95943.t1.exon2;Parent=MS.gene95943.t1
chr6.2 CDS 76306325 76306415 76306325 ID=cds.MS.gene95943.t1;Parent=MS.gene95943.t1
chr6.2 exon 76306503 76306567 76306503 ID=MS.gene95943.t1.exon3;Parent=MS.gene95943.t1
chr6.2 CDS 76306503 76306567 76306503 ID=cds.MS.gene95943.t1;Parent=MS.gene95943.t1
chr6.2 exon 76306672 76306708 76306672 ID=MS.gene95943.t1.exon4;Parent=MS.gene95943.t1
chr6.2 CDS 76306672 76306708 76306672 ID=cds.MS.gene95943.t1;Parent=MS.gene95943.t1
Gene Sequence

>MS.gene95943

ATGGAGCTTCACACTTCACCGATCGAGCTTCACAGTCCCGGATCTATTGAACTTCATCCTCCAATTTCACAGTTGCAGATAGAAACAAATCTTTTTTCCTCTTTCGCTCACAGGTAACACTTCTCGAATTCTTCTTATGTTTTGCATTTTTCGCGCTTTCAATTTTGATTTCTCTTAGATTTCAGCGCAATTATCTTCGATTCATGCTTTTTCTATATTATGAATCACAATTTTGATCTATTTCGCTCACATTGTTTAATTTTCGTTTTGAAATTCTATGTGTTTAATTTTCGTTTCACAATTTAACTCAAATTCTTCTTGTTCTGTTTCACATTTGTGATTTATGTTTTCTTTGAAATCCATGTGTTTGATGTTGCCAAAGAATAAGAAATCTTCTTTGTTTAATATATTTTTTAATTTTGCGTTATTTATTAATAAGTATAAAATTTATATTTCAGGGATAAGTTTGGCAATTTTTTTAAAGAATTAGATCAAAATTATGATGTTAATAAAATGGTTGTTAAAGCATGGAACTCCATGAGTAATGAAGTAAGTCCTCTAGTATATTACAACACATGCAATTTGATGAACATAAATAATGTTTGTCTTTTAAAATTGATTATATTATTTAATCAGGATAAACAACATTATTTGGATAAAGCATCTAAGCGCAAGGCAAAACATGAGAAACTTAAGAAAAGGTACTATGTTTATCCCAAATTTAATTGATTTTGTGTTACTGAACTCAATTTCTAATAATATTCTTATAATTGTGTGAATTATCTTTGTGTGTTTGATTGAATAGGGTGACTCCGAGAATGGTGGAATGCTTCACAATTTGA
Protein sequence

>MS.gene95943.t1

MELHTSPIELHSPGSIELHPPISQLQIETNLFSSFAHRDKFGNFFKELDQNYDVNKMVVKAWNSMSNEDKQHYLDKASKRKAKHEKLKKRVTPRMVECFTI