AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene27955

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene27955.t1 MTR_8g089170 92.308 156 12 0 1 156 1 156 2.25e-99 283
MS.gene27955.t1 MTR_8g089130 84.177 158 23 2 1 156 1 158 1.08e-90 261
MS.gene27955.t1 MTR_8g089145 87.671 73 9 0 1 73 1 73 1.81e-42 136
MS.gene27955.t1 MTR_1g089830 36.842 152 67 4 4 155 3 125 4.61e-22 86.3
MS.gene27955.t1 MTR_4g028990 54.545 77 33 1 81 155 20 96 2.62e-20 80.5
MS.gene27955.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 38 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCATACCTTCAAATGAAAT+TGG 0.214941 4.4:-12012738 MS.gene27955:CDS
CATAAAACTGGCTTGTCTTT+TGG 0.254968 4.4:+12013232 None:intergenic
CTTTGAGGTTTCCCCAGTTT+TGG 0.256311 4.4:+12013188 None:intergenic
ATTCTCAAACTACGTCTCTT+TGG 0.299791 4.4:+12012885 None:intergenic
TCAAACAATAAGGCCTCTTC+TGG 0.301830 4.4:+12012774 None:intergenic
TGGCGCCATGCTGGAGTTGC+TGG 0.314815 4.4:+12013259 None:intergenic
GATGTTTCTGATTCAGATAA+TGG 0.318368 4.4:-12013073 MS.gene27955:intron
CTGTTCGTAACAAGTTCTTT+TGG 0.340372 4.4:+12013142 None:intergenic
TTTGGTCCCTGGCGCCATGC+TGG 0.374123 4.4:+12013250 None:intergenic
GAAAACAACGTTTGAGAGAA+TGG 0.387976 4.4:+12013164 None:intergenic
GTGGACTAAGATACCAAAAC+TGG 0.405891 4.4:-12013201 MS.gene27955:CDS
CCACATGCATTGCATAAAAC+TGG 0.410323 4.4:+12013220 None:intergenic
CCTTCAAATGAAATTGGCCT+TGG 0.419265 4.4:-12012732 MS.gene27955:CDS
CCAAGGCCAATTTCATTTGA+AGG 0.421742 4.4:+12012732 None:intergenic
AGCAACTCCAGCATGGCGCC+AGG 0.436034 4.4:-12013257 MS.gene27955:CDS
GTTTGAGAGAATGGTCTTTG+AGG 0.475222 4.4:+12013173 None:intergenic
TCTTCTGGAGATGACTCATC+TGG 0.489997 4.4:+12012789 None:intergenic
TCTTGTTGAAACTTCTCCAT+CGG 0.530728 4.4:+12012843 None:intergenic
ATCTGAATCAGAAACATCAA+TGG 0.539843 4.4:+12013078 None:intergenic
TTCTACATAGAAGATCCGTC+TGG 0.554465 4.4:+12012693 None:intergenic
GCAACTCCAGCATGGCGCCA+GGG 0.585142 4.4:-12013256 MS.gene27955:CDS
AGATGAGTCATCTCCAGAAG+AGG 0.604525 4.4:-12012787 MS.gene27955:CDS
AAATGAAATTGGCCTTGGAG+CGG 0.608265 4.4:-12012727 MS.gene27955:CDS
CAATCAGAAGATGACACCGA+TGG 0.614119 4.4:-12012859 MS.gene27955:CDS
TGGACTAAGATACCAAAACT+GGG 0.618651 4.4:-12013200 MS.gene27955:CDS
GCGGTTCTTCTTAAACCAGA+CGG 0.625463 4.4:-12012708 MS.gene27955:CDS
GTTTAAGAAGAACCGCTCCA+AGG 0.637380 4.4:+12012715 None:intergenic
AAAGAACTTGTTACGAACAG+TGG 0.644687 4.4:-12013139 MS.gene27955:CDS
CATCACCAGCAACTCCAGCA+TGG 0.651498 4.4:-12013264 MS.gene27955:CDS
GGACTAAGATACCAAAACTG+GGG 0.731002 4.4:-12013199 MS.gene27955:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACAAAAGTAGTATATATCAT+TGG + chr4.4:12012961-12012980 None:intergenic 20.0%
! TTCATACCTTCAAATGAAAT+TGG - chr4.4:12013228-12013247 MS.gene27955:CDS 25.0%
!! GTTCACATTTTCAAACAATA+AGG + chr4.4:12013205-12013224 None:intergenic 25.0%
!!! GATATATACTACTTTTGTGA+GGG - chr4.4:12012963-12012982 MS.gene27955:intron 25.0%
!!! TGATATATACTACTTTTGTG+AGG - chr4.4:12012962-12012981 MS.gene27955:intron 25.0%
ATCTGAATCAGAAACATCAA+TGG + chr4.4:12012891-12012910 None:intergenic 30.0%
TGGAAAGAAAAGAGTGAAAA+TGG + chr4.4:12012941-12012960 None:intergenic 30.0%
! GATGTTTCTGATTCAGATAA+TGG - chr4.4:12012893-12012912 MS.gene27955:CDS 30.0%
ATTCTCAAACTACGTCTCTT+TGG + chr4.4:12013084-12013103 None:intergenic 35.0%
GAAAACAACGTTTGAGAGAA+TGG + chr4.4:12012805-12012824 None:intergenic 35.0%
TCTTGTTGAAACTTCTCCAT+CGG + chr4.4:12013126-12013145 None:intergenic 35.0%
TGGACTAAGATACCAAAACT+GGG - chr4.4:12012766-12012785 MS.gene27955:CDS 35.0%
! CTGTTCGTAACAAGTTCTTT+TGG + chr4.4:12012827-12012846 None:intergenic 35.0%
!! AAAGAACTTGTTACGAACAG+TGG - chr4.4:12012827-12012846 MS.gene27955:CDS 35.0%
!! ATATACTACTTTTGTGAGGG+TGG - chr4.4:12012966-12012985 MS.gene27955:intron 35.0%
!! TATACTACTTTTGTGAGGGT+GGG - chr4.4:12012967-12012986 MS.gene27955:intron 35.0%
!!! CATAAAACTGGCTTGTCTTT+TGG + chr4.4:12012737-12012756 None:intergenic 35.0%
CCAAGGCCAATTTCATTTGA+AGG + chr4.4:12013237-12013256 None:intergenic 40.0%
CCACATGCATTGCATAAAAC+TGG + chr4.4:12012749-12012768 None:intergenic 40.0%
GGACTAAGATACCAAAACTG+GGG - chr4.4:12012767-12012786 MS.gene27955:CDS 40.0%
GTTTGAGAGAATGGTCTTTG+AGG + chr4.4:12012796-12012815 None:intergenic 40.0%
TCAAACAATAAGGCCTCTTC+TGG + chr4.4:12013195-12013214 None:intergenic 40.0%
! CCTTCAAATGAAATTGGCCT+TGG - chr4.4:12013234-12013253 MS.gene27955:CDS 40.0%
! GTGGACTAAGATACCAAAAC+TGG - chr4.4:12012765-12012784 MS.gene27955:CDS 40.0%
!! AAATGAAATTGGCCTTGGAG+CGG - chr4.4:12013239-12013258 MS.gene27955:CDS 40.0%
!! CCAGTTTTATGCAATGCATG+TGG - chr4.4:12012746-12012765 MS.gene27955:CDS 40.0%
AGATGAGTCATCTCCAGAAG+AGG - chr4.4:12013179-12013198 MS.gene27955:CDS 45.0%
CAATCAGAAGATGACACCGA+TGG - chr4.4:12013107-12013126 MS.gene27955:CDS 45.0%
GCGGTTCTTCTTAAACCAGA+CGG - chr4.4:12013258-12013277 MS.gene27955:CDS 45.0%
GTTTAAGAAGAACCGCTCCA+AGG + chr4.4:12013254-12013273 None:intergenic 45.0%
! TCTTCTGGAGATGACTCATC+TGG + chr4.4:12013180-12013199 None:intergenic 45.0%
!!! CTTTGAGGTTTCCCCAGTTT+TGG + chr4.4:12012781-12012800 None:intergenic 45.0%
CATCACCAGCAACTCCAGCA+TGG - chr4.4:12012702-12012721 MS.gene27955:CDS 55.0%
!! CTGGCTTGTCTTTTGGTCCC+TGG + chr4.4:12012730-12012749 None:intergenic 55.0%
AGCAACTCCAGCATGGCGCC+AGG - chr4.4:12012709-12012728 MS.gene27955:CDS 65.0%
GCAACTCCAGCATGGCGCCA+GGG - chr4.4:12012710-12012729 MS.gene27955:CDS 65.0%
TGGCGCCATGCTGGAGTTGC+TGG + chr4.4:12012710-12012729 None:intergenic 65.0%
TTTGGTCCCTGGCGCCATGC+TGG + chr4.4:12012719-12012738 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr4.4 gene 12012695 12013293 12012695 ID=MS.gene27955
chr4.4 mRNA 12012695 12013293 12012695 ID=MS.gene27955.t1;Parent=MS.gene27955
chr4.4 exon 12013074 12013293 12013074 ID=MS.gene27955.t1.exon1;Parent=MS.gene27955.t1
chr4.4 CDS 12013074 12013293 12013074 ID=cds.MS.gene27955.t1;Parent=MS.gene27955.t1
chr4.4 exon 12012695 12012945 12012695 ID=MS.gene27955.t1.exon2;Parent=MS.gene27955.t1
chr4.4 CDS 12012695 12012945 12012695 ID=cds.MS.gene27955.t1;Parent=MS.gene27955.t1
Gene Sequence

>MS.gene27955

ATGGATTCATCACCAGCAACTCCAGCATGGCGCCAGGGACCAAAAGACAAGCCAGTTTTATGCAATGCATGTGGACTAAGATACCAAAACTGGGGAAACCTCAAAGACCATTCTCTCAAACGTTGTTTTCCAAAAGAACTTGTTACGAACAGTGGCAACAGTAGCAACAACAGTCTCAAAGAAAGTTCATCAACCATTGATGTTTCTGATTCAGATAATGGTATGTGTTTATACTAGTACTAGCCATTTTCACTCTTTTCTTTCCAATGATATATACTACTTTTGTGAGGGTGGGCGTGCGTGAATACTTCTTTTAAATTGTTAATAAATAAGAGAATTTTTACTCAGATGAAAAAGATTCAGATTCATGCAAGTCTGCAGTCTCTCCAAAGAGACGTAGTTTGAGAATTATCAATCAGAAGATGACACCGATGGAGAAGTTTCAACAAGAACTTCTCGATGAGTTGAAAAATCACGAGATACCAGATGAGTCATCTCCAGAAGAGGCCTTATTGTTTGAAAATGTGAACAACTTCATACCTTCAAATGAAATTGGCCTTGGAGCGGTTCTTCTTAAACCAGACGGATCTTCTATGTAG
Protein sequence

>MS.gene27955.t1

MDSSPATPAWRQGPKDKPVLCNACGLRYQNWGNLKDHSLKRCFPKELVTNSGNSSNNSLKESSSTIDVSDSDNDEKDSDSCKSAVSPKRRSLRIINQKMTPMEKFQQELLDELKNHEIPDESSPEEALLFENVNNFIPSNEIGLGAVLLKPDGSSM