AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene53484

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene53484.t1 MTR_8g089170 92.308 156 12 0 1 156 1 156 5.35e-100 284
MS.gene53484.t1 MTR_8g089130 84.177 158 23 2 1 156 1 158 1.95e-90 260
MS.gene53484.t1 MTR_8g089145 87.671 73 9 0 1 73 1 73 2.75e-42 135
MS.gene53484.t1 MTR_1g089830 37.500 152 66 4 4 155 3 125 5.59e-22 86.3
MS.gene53484.t1 MTR_4g028990 54.545 77 33 1 81 155 20 96 2.37e-20 80.5
MS.gene53484.t1 MTR_1g045040 39.333 150 65 4 7 155 6 130 2.12e-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 31 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 4.2:-12342957 MS.gene53484:CDS
CTTTGAGGTTTCCCCAGTTT+TGG 0.256311 4.2:+12343407 None:intergenic
CATAAAACTGGCTTGTCTTC+TGG 0.266801 4.2:+12343451 None:intergenic
ATTCTCAAACTACGTCTCTT+TGG 0.299791 4.2:+12343104 None:intergenic
TCAAACAATAAGGCCTCTTC+TGG 0.301830 4.2:+12342993 None:intergenic
TGGCGCCATGCTGGAGTTGC+TGG 0.314815 4.2:+12343478 None:intergenic
GATGTTTCTGATTCAGATAA+TGG 0.318368 4.2:-12343292 MS.gene53484:intron
CTGTTCGTAACAAGTTCTTT+TGG 0.340372 4.2:+12343361 None:intergenic
TCTGGTCCCTGGCGCCATGC+TGG 0.378150 4.2:+12343469 None:intergenic
GAAAACAACGTTTGAGAGAA+TGG 0.387976 4.2:+12343383 None:intergenic
GTGGACTAAGATACCAAAAC+TGG 0.405891 4.2:-12343420 MS.gene53484:CDS
CCACATGCATTGCATAAAAC+TGG 0.410323 4.2:+12343439 None:intergenic
CCTTCAAATGAAATTGGCCT+TGG 0.419265 4.2:-12342951 MS.gene53484:CDS
CCAAGGCCAATTTCATTTGA+AGG 0.421742 4.2:+12342951 None:intergenic
AGCAACTCCAGCATGGCGCC+AGG 0.436034 4.2:-12343476 MS.gene53484:CDS
GTTTGAGAGAATGGTCTTTG+AGG 0.475222 4.2:+12343392 None:intergenic
TCTTCTGGAGATGACTCATC+TGG 0.489997 4.2:+12343008 None:intergenic
CTGGCTTGTCTTCTGGTCCC+TGG 0.494515 4.2:+12343458 None:intergenic
TCTTGTTGAAACTTCTCCAT+CGG 0.530728 4.2:+12343062 None:intergenic
ATCTGAATCAGAAACATCAA+TGG 0.539843 4.2:+12343297 None:intergenic
TTCTACATAGAAGAACCGTC+TGG 0.563851 4.2:+12342912 None:intergenic
GCAACTCCAGCATGGCGCCA+GGG 0.585142 4.2:-12343475 MS.gene53484:CDS
AGATGAGTCATCTCCAGAAG+AGG 0.604525 4.2:-12343006 MS.gene53484:CDS
GCGGTTCTTCTTAAACCAGA+CGG 0.605404 4.2:-12342927 MS.gene53484:CDS
AAATGAAATTGGCCTTGGAG+CGG 0.608265 4.2:-12342946 MS.gene53484:CDS
CAATCAGAAGATGACACCGA+TGG 0.614119 4.2:-12343078 MS.gene53484:CDS
TGGACTAAGATACCAAAACT+GGG 0.618651 4.2:-12343419 MS.gene53484:CDS
GTTTAAGAAGAACCGCTCCA+AGG 0.637380 4.2:+12342934 None:intergenic
AAAGAACTTGTTACGAACAG+TGG 0.644687 4.2:-12343358 MS.gene53484:CDS
CATCACCAGCAACTCCAGCA+TGG 0.651498 4.2:-12343483 MS.gene53484:CDS
GGACTAAGATACCAAAACTG+GGG 0.731002 4.2:-12343418 MS.gene53484:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GATATATATTACTTTTGTGA+GGG - chr4.2:12343182-12343201 MS.gene53484:intron 20.0%
!!! TGATATATATTACTTTTGTG+AGG - chr4.2:12343181-12343200 MS.gene53484:intron 20.0%
! TGTAAAGAAAAGAGTGAAAA+TGG + chr4.2:12343160-12343179 None:intergenic 25.0%
! TTCATACCTTCAAATGAAAT+TGG - chr4.2:12343447-12343466 MS.gene53484:CDS 25.0%
!! GTTCACATTTTCAAACAATA+AGG + chr4.2:12343424-12343443 None:intergenic 25.0%
ATCTGAATCAGAAACATCAA+TGG + chr4.2:12343110-12343129 None:intergenic 30.0%
! GATGTTTCTGATTCAGATAA+TGG - chr4.2:12343112-12343131 MS.gene53484:CDS 30.0%
!! ATATATTACTTTTGTGAGGG+TGG - chr4.2:12343185-12343204 MS.gene53484:intron 30.0%
!! TATATTACTTTTGTGAGGGT+GGG - chr4.2:12343186-12343205 MS.gene53484:intron 30.0%
ATTCTCAAACTACGTCTCTT+TGG + chr4.2:12343303-12343322 None:intergenic 35.0%
GAAAACAACGTTTGAGAGAA+TGG + chr4.2:12343024-12343043 None:intergenic 35.0%
TCTTGTTGAAACTTCTCCAT+CGG + chr4.2:12343345-12343364 None:intergenic 35.0%
TGGACTAAGATACCAAAACT+GGG - chr4.2:12342985-12343004 MS.gene53484:CDS 35.0%
! CTGTTCGTAACAAGTTCTTT+TGG + chr4.2:12343046-12343065 None:intergenic 35.0%
!! AAAGAACTTGTTACGAACAG+TGG - chr4.2:12343046-12343065 MS.gene53484:CDS 35.0%
CCAAGGCCAATTTCATTTGA+AGG + chr4.2:12343456-12343475 None:intergenic 40.0%
CCACATGCATTGCATAAAAC+TGG + chr4.2:12342968-12342987 None:intergenic 40.0%
GGACTAAGATACCAAAACTG+GGG - chr4.2:12342986-12343005 MS.gene53484:CDS 40.0%
GTTTGAGAGAATGGTCTTTG+AGG + chr4.2:12343015-12343034 None:intergenic 40.0%
TCAAACAATAAGGCCTCTTC+TGG + chr4.2:12343414-12343433 None:intergenic 40.0%
! CCTTCAAATGAAATTGGCCT+TGG - chr4.2:12343453-12343472 MS.gene53484:CDS 40.0%
! GTGGACTAAGATACCAAAAC+TGG - chr4.2:12342984-12343003 MS.gene53484:CDS 40.0%
!! AAATGAAATTGGCCTTGGAG+CGG - chr4.2:12343458-12343477 MS.gene53484:CDS 40.0%
!! CATAAAACTGGCTTGTCTTC+TGG + chr4.2:12342956-12342975 None:intergenic 40.0%
!! CCAGTTTTATGCAATGCATG+TGG - chr4.2:12342965-12342984 MS.gene53484:CDS 40.0%
AGATGAGTCATCTCCAGAAG+AGG - chr4.2:12343398-12343417 MS.gene53484:CDS 45.0%
CAATCAGAAGATGACACCGA+TGG - chr4.2:12343326-12343345 MS.gene53484:CDS 45.0%
GCGGTTCTTCTTAAACCAGA+CGG - chr4.2:12343477-12343496 MS.gene53484:CDS 45.0%
GTTTAAGAAGAACCGCTCCA+AGG + chr4.2:12343473-12343492 None:intergenic 45.0%
! TCTTCTGGAGATGACTCATC+TGG + chr4.2:12343399-12343418 None:intergenic 45.0%
!!! CTTTGAGGTTTCCCCAGTTT+TGG + chr4.2:12343000-12343019 None:intergenic 45.0%
CATCACCAGCAACTCCAGCA+TGG - chr4.2:12342921-12342940 MS.gene53484:CDS 55.0%
! CTGGCTTGTCTTCTGGTCCC+TGG + chr4.2:12342949-12342968 None:intergenic 60.0%
AGCAACTCCAGCATGGCGCC+AGG - chr4.2:12342928-12342947 MS.gene53484:CDS 65.0%
GCAACTCCAGCATGGCGCCA+GGG - chr4.2:12342929-12342948 MS.gene53484:CDS 65.0%
TGGCGCCATGCTGGAGTTGC+TGG + chr4.2:12342929-12342948 None:intergenic 65.0%
TCTGGTCCCTGGCGCCATGC+TGG + chr4.2:12342938-12342957 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 12342914 12343512 12342914 ID=MS.gene53484
chr4.2 mRNA 12342914 12343512 12342914 ID=MS.gene53484.t1;Parent=MS.gene53484
chr4.2 exon 12343293 12343512 12343293 ID=MS.gene53484.t1.exon1;Parent=MS.gene53484.t1
chr4.2 CDS 12343293 12343512 12343293 ID=cds.MS.gene53484.t1;Parent=MS.gene53484.t1
chr4.2 exon 12342914 12343164 12342914 ID=MS.gene53484.t1.exon2;Parent=MS.gene53484.t1
chr4.2 CDS 12342914 12343164 12342914 ID=cds.MS.gene53484.t1;Parent=MS.gene53484.t1
Gene Sequence

>MS.gene53484

ATGGATTCATCACCAGCAACTCCAGCATGGCGCCAGGGACCAGAAGACAAGCCAGTTTTATGCAATGCATGTGGACTAAGATACCAAAACTGGGGAAACCTCAAAGACCATTCTCTCAAACGTTGTTTTCCAAAAGAACTTGTTACGAACAGTGGCAACAGTAGCAACAAGAGTCTCAAAGAAAGTTCATCAACCATTGATGTTTCTGATTCAGATAATGGTATGTGTTTATACTAGTACTAGCCATTTTCACTCTTTTCTTTACAATGATATATATTACTTTTGTGAGGGTGGGCGTGCGTGAATACTTCTTTTAAATTGTCAATAAATAAGAGAATTTTTACTCAGATGAAAAAGATTCAGATTCATGCAAGTCTGCAGTCTCTCCAAAGAGACGTAGTTTGAGAATTATCAATCAGAAGATGACACCGATGGAGAAGTTTCAACAAGAACTTCTCGATGAGTTGAAAAATCACGAGATACCAGATGAGTCATCTCCAGAAGAGGCCTTATTGTTTGAAAATGTGAACAACTTCATACCTTCAAATGAAATTGGCCTTGGAGCGGTTCTTCTTAAACCAGACGGTTCTTCTATGTAG
Protein sequence

>MS.gene53484.t1

MDSSPATPAWRQGPEDKPVLCNACGLRYQNWGNLKDHSLKRCFPKELVTNSGNSSNKSLKESSSTIDVSDSDNDEKDSDSCKSAVSPKRRSLRIINQKMTPMEKFQQELLDELKNHEIPDESSPEEALLFENVNNFIPSNEIGLGAVLLKPDGSSM