AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene063356

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene063356.t1 MTR_6g042060 87.500 80 10 0 1 80 1 80 3.82e-47 144
MS.gene063356.t1 MTR_7g111710 92.754 69 5 0 1 69 602 670 7.04e-40 139
MS.gene063356.t1 MTR_1g068945 89.552 67 7 0 14 80 1 67 7.69e-40 125
MS.gene063356.t1 MTR_8g096550 77.586 58 13 0 23 80 5 62 3.15e-28 96.7
MS.gene063356.t1 MTR_1g112310 37.681 69 43 0 1 69 699 767 2.04e-11 58.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene063356.t1 AT3G07100 78.261 69 15 0 1 69 620 688 2.18e-33 120

Find 15 sgRNAs with CRISPR-Local

Find 32 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAAATTGAGTCATGAATTA+AGG 0.308061 2.4:-26276989 MS.gene063356:CDS
CATACACATTTACTGAGATT+TGG 0.310882 2.4:+26277508 None:intergenic
TCCTGTCTGTGTAGGAACTC+TGG 0.429146 2.4:-26277072 MS.gene063356:intron
TCTCCCCATGAGTAGCTGAT+TGG 0.442822 2.4:+26277009 None:intergenic
TGAGTAGCTGATTGGAAAGC+TGG 0.469035 2.4:+26277017 None:intergenic
GAGAGACTGCATGGGAAGCA+TGG 0.524555 2.4:-26276953 MS.gene063356:CDS
GCTTTCCAATCAGCTACTCA+TGG 0.528786 2.4:-26277014 MS.gene063356:CDS
TACACTGACATAGCCTCCTT+AGG 0.536987 2.4:-26277471 MS.gene063356:intron
CTTTCCAATCAGCTACTCAT+GGG 0.542155 2.4:-26277013 MS.gene063356:CDS
GGAAAATAAAACACCTAAGG+AGG 0.554451 2.4:+26277458 None:intergenic
ACCTCACAAGAGAGACTGCA+TGG 0.560035 2.4:-26276962 MS.gene063356:CDS
ACTCTGGCAAAGTACACTGC+TGG 0.591069 2.4:-26277056 MS.gene063356:CDS
CCCATGCAGTCTCTCTTGTG+AGG 0.598716 2.4:+26276961 None:intergenic
TTTCCAATCAGCTACTCATG+GGG 0.686768 2.4:-26277012 MS.gene063356:CDS
CCTCACAAGAGAGACTGCAT+GGG 0.693489 2.4:-26276961 MS.gene063356:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAACAGGTTTAAAAATAGAA+TGG + chr2.4:26277044-26277063 None:intergenic 20.0%
! ACGAAATACATAGAAATTGA+AGG + chr2.4:26277017-26277036 None:intergenic 25.0%
! AGAAATTGAGTCATGAATTA+AGG - chr2.4:26277462-26277481 MS.gene063356:intron 25.0%
! ATCAATTAATCAAGAGTAAC+AGG + chr2.4:26277060-26277079 None:intergenic 25.0%
AAATGCTGACAGAATTACAT+CGG + chr2.4:26277293-26277312 None:intergenic 30.0%
CATACACATTTACTGAGATT+TGG + chr2.4:26276946-26276965 None:intergenic 30.0%
GAAGGAAAATAAAACACCTA+AGG + chr2.4:26276999-26277018 None:intergenic 30.0%
TAAACTGATACTCTAACTCA+TGG - chr2.4:26277163-26277182 MS.gene063356:intron 30.0%
! ACTTGATGACATGAGTTTAT+GGG - chr2.4:26277120-26277139 MS.gene063356:intron 30.0%
! ATTTGATGATTCTTCAGTTG+TGG - chr2.4:26277082-26277101 MS.gene063356:intron 30.0%
AATGCTGACAGAATTACATC+GGG + chr2.4:26277292-26277311 None:intergenic 35.0%
GGAAAATAAAACACCTAAGG+AGG + chr2.4:26276996-26277015 None:intergenic 35.0%
GGATCTATTTGACTATGAAC+TGG - chr2.4:26277184-26277203 MS.gene063356:intron 35.0%
! GACTTGATGACATGAGTTTA+TGG - chr2.4:26277119-26277138 MS.gene063356:intron 35.0%
!!! GTTTTTTTTCCTGTCTGTGT+AGG - chr2.4:26277371-26277390 MS.gene063356:intron 35.0%
CTTTCCAATCAGCTACTCAT+GGG - chr2.4:26277438-26277457 MS.gene063356:intron 40.0%
TTTCCAATCAGCTACTCATG+GGG - chr2.4:26277439-26277458 MS.gene063356:intron 40.0%
ACAGAATTACATCGGGACAC+GGG + chr2.4:26277285-26277304 None:intergenic 45.0%
CATCAGCACGCAAGACTATA+TGG + chr2.4:26277328-26277347 None:intergenic 45.0%
GACAGAATTACATCGGGACA+CGG + chr2.4:26277286-26277305 None:intergenic 45.0%
GCTTTCCAATCAGCTACTCA+TGG - chr2.4:26277437-26277456 MS.gene063356:intron 45.0%
TACACTGACATAGCCTCCTT+AGG - chr2.4:26276980-26276999 MS.gene063356:CDS 45.0%
TGAGTAGCTGATTGGAAAGC+TGG + chr2.4:26277437-26277456 None:intergenic 45.0%
ACCTCACAAGAGAGACTGCA+TGG - chr2.4:26277489-26277508 MS.gene063356:CDS 50.0%
ACTCTGGCAAAGTACACTGC+TGG - chr2.4:26277395-26277414 MS.gene063356:intron 50.0%
CAGAATTACATCGGGACACG+GGG + chr2.4:26277284-26277303 None:intergenic 50.0%
CCTCACAAGAGAGACTGCAT+GGG - chr2.4:26277490-26277509 MS.gene063356:CDS 50.0%
TCCTGTCTGTGTAGGAACTC+TGG - chr2.4:26277379-26277398 MS.gene063356:intron 50.0%
TCTCCCCATGAGTAGCTGAT+TGG + chr2.4:26277445-26277464 None:intergenic 50.0%
CCCATGCAGTCTCTCTTGTG+AGG + chr2.4:26277493-26277512 None:intergenic 55.0%
GAGAGACTGCATGGGAAGCA+TGG - chr2.4:26277498-26277517 MS.gene063356:CDS 55.0%
GCCAGAGTTCCTACACAGAC+AGG + chr2.4:26277383-26277402 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 26276920 26277553 26276920 ID=MS.gene063356
chr2.4 mRNA 26276920 26277553 26276920 ID=MS.gene063356.t1;Parent=MS.gene063356
chr2.4 exon 26277472 26277553 26277472 ID=MS.gene063356.t1.exon1;Parent=MS.gene063356.t1
chr2.4 CDS 26277472 26277553 26277472 ID=cds.MS.gene063356.t1;Parent=MS.gene063356.t1
chr2.4 exon 26276920 26277080 26276920 ID=MS.gene063356.t1.exon2;Parent=MS.gene063356.t1
chr2.4 CDS 26276920 26277080 26276920 ID=cds.MS.gene063356.t1;Parent=MS.gene063356.t1
Gene Sequence

>MS.gene063356

ATGGCTGCTGAGTTTTTCAAGTACCAAATCTCAGTAAATGTGTATGCATTCAGTGATAAGTACACTGACATAGCCTCCTTAGGTGTTTTATTTTCCTTCAATTTCTATGTATTTCGTTATGCCATTCTATTTTTAAACCTGTTACTCTTGATTAATTGATATATTTGATGATTCTTCAGTTGTGGCAGTGTTTTATGATGACTTGATGACATGAGTTTATGGGCTTCAACTATGATTTGATTATAAACTGATACTCTAACTCATGGATCTATTTGACTATGAACTGGTCTGTAGATGCTCAAAAAGAATTCACAAGTTATGTGTTGATTGTTGTAGTTATATCTGTAAACAATCAATGTATCCCCGTGTCCCGATGTAATTCTGTCAGCATTTGCAGTCTTCTAACCATATAGTCTTGCGTGCTGATGATCTTATACTTGAAGTAAATTATGTTTTTTTTCCTGTCTGTGTAGGAACTCTGGCAAAGTACACTGCTGGTCAAGTGTATTACTTTCCAGCTTTCCAATCAGCTACTCATGGGGAGAAATTGAGTCATGAATTAAGGAGATACCTCACAAGAGAGACTGCATGGGAAGCATGGATCATATGCATTGCAGAGATACTTAGTAACTAG
Protein sequence

>MS.gene063356.t1

MAAEFFKYQISVNVYAFSDKYTDIASLGTLAKYTAGQVYYFPAFQSATHGEKLSHELRRYLTRETAWEAWIICIAEILSN