AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene023404

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene023404.t1 MTR_8g080380 93.548 93 6 0 1 93 92 184 1.18e-60 183
MS.gene023404.t1 MTR_3g085510 76.344 93 22 0 1 93 1 93 2.99e-49 151
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene023404.t1 AT4G40042 77.215 79 18 0 1 79 1 79 9.09e-42 132
MS.gene023404.t1 AT2G22425 72.043 93 25 1 1 93 1 92 1.70e-41 131
MS.gene023404.t1 AT2G22425 72.043 93 25 1 1 93 1 92 1.70e-41 131

Find 27 sgRNAs with CRISPR-Local

Find 27 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCACAGATGGTTCTGGCTT+TGG 0.242295 4.4:-15792053 None:intergenic
GCATTTGCTGTGATTGCATT+TGG 0.297854 4.4:+15791882 MS.gene023404:CDS
GCCCCATTCACAGATGGTTC+TGG 0.371797 4.4:-15792059 None:intergenic
CATATGTGAGGATCATTGTT+TGG 0.377646 4.4:-15791929 None:intergenic
GTGGTTGAAGAAGGGCCAAT+TGG 0.421141 4.4:-15791988 None:intergenic
AGCCAGAACCATCTGTGAAT+GGG 0.421365 4.4:+15792057 MS.gene023404:CDS
GTTTGCTTGATTAGATGGAT+TGG 0.432453 4.4:+15791814 None:intergenic
TCAACCACCATCCTCTTAAG+TGG 0.461213 4.4:+15792003 MS.gene023404:CDS
AAGAGGATGGTGGTTGAAGA+AGG 0.473842 4.4:-15791997 None:intergenic
CATTAGTCACTATTCCCAAT+TGG 0.473943 4.4:+15791973 MS.gene023404:CDS
CTCGGGTCCAACCACTTAAG+AGG 0.481325 4.4:-15792014 None:intergenic
TGGTTGAAGAAGGGCCAATT+GGG 0.491266 4.4:-15791987 None:intergenic
AAGCCAGAACCATCTGTGAA+TGG 0.493580 4.4:+15792056 MS.gene023404:CDS
TTTGCTTGATTAGATGGATT+GGG 0.508127 4.4:+15791815 None:intergenic
GCTGTGATTGCATTTGGAGC+TGG 0.523448 4.4:+15791888 MS.gene023404:CDS
TTTGTAGCCCCATTCACAGA+TGG 0.525901 4.4:-15792065 None:intergenic
ACAATGATCCTCACATATGC+TGG 0.532761 4.4:+15791933 MS.gene023404:CDS
CCACCATCCTCTTAAGTGGT+TGG 0.557168 4.4:+15792007 MS.gene023404:CDS
ATTTGGAGCTGGATATCTCA+CGG 0.563264 4.4:+15791899 MS.gene023404:CDS
CTTGATTAGATGGATTGGGA+AGG 0.597000 4.4:+15791819 None:intergenic
AGAGGATGGTGGTTGAAGAA+GGG 0.597108 4.4:-15791996 None:intergenic
GGTCCAACCACTTAAGAGGA+TGG 0.613558 4.4:-15792010 None:intergenic
GCCAGAACCATCTGTGAATG+GGG 0.616607 4.4:+15792058 MS.gene023404:CDS
ATGATCCTCACATATGCTGG+TGG 0.628209 4.4:+15791936 MS.gene023404:CDS
AAACTCCACCAGCATATGTG+AGG 0.666193 4.4:-15791941 None:intergenic
CCAACCACTTAAGAGGATGG+TGG 0.689439 4.4:-15792007 None:intergenic
ATTGGGAATAGTGACTAATG+TGG 0.776405 4.4:-15791970 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
ATTGGGAATAGTGACTAATG+TGG - chr4.4:15791973-15791992 None:intergenic 35.0%
CATATGTGAGGATCATTGTT+TGG - chr4.4:15791932-15791951 None:intergenic 35.0%
CATTAGTCACTATTCCCAAT+TGG + chr4.4:15791973-15791992 MS.gene023404:CDS 35.0%
ACAATGATCCTCACATATGC+TGG + chr4.4:15791933-15791952 MS.gene023404:CDS 40.0%
! ATTTGGAGCTGGATATCTCA+CGG + chr4.4:15791899-15791918 MS.gene023404:CDS 40.0%
!! GCATTTGCTGTGATTGCATT+TGG + chr4.4:15791882-15791901 MS.gene023404:CDS 40.0%
!!! TTCTGGCTTTGGATGCTTTT+CGG - chr4.4:15792045-15792064 None:intergenic 40.0%
AAACTCCACCAGCATATGTG+AGG - chr4.4:15791944-15791963 None:intergenic 45.0%
AAGCCAGAACCATCTGTGAA+TGG + chr4.4:15792056-15792075 MS.gene023404:CDS 45.0%
AGCCAGAACCATCTGTGAAT+GGG + chr4.4:15792057-15792076 MS.gene023404:CDS 45.0%
ATGATCCTCACATATGCTGG+TGG + chr4.4:15791936-15791955 MS.gene023404:CDS 45.0%
TCAACCACCATCCTCTTAAG+TGG + chr4.4:15792003-15792022 MS.gene023404:CDS 45.0%
TGGTTGAAGAAGGGCCAATT+GGG - chr4.4:15791990-15792009 None:intergenic 45.0%
TTTGTAGCCCCATTCACAGA+TGG - chr4.4:15792068-15792087 None:intergenic 45.0%
! AAGAGGATGGTGGTTGAAGA+AGG - chr4.4:15792000-15792019 None:intergenic 45.0%
! AGAGGATGGTGGTTGAAGAA+GGG - chr4.4:15791999-15792018 None:intergenic 45.0%
!! TTCACAGATGGTTCTGGCTT+TGG - chr4.4:15792056-15792075 None:intergenic 45.0%
CCAACCACTTAAGAGGATGG+TGG - chr4.4:15792010-15792029 None:intergenic 50.0%
CCACCATCCTCTTAAGTGGT+TGG + chr4.4:15792007-15792026 MS.gene023404:CDS 50.0%
GCCAGAACCATCTGTGAATG+GGG + chr4.4:15792058-15792077 MS.gene023404:CDS 50.0%
GGTCCAACCACTTAAGAGGA+TGG - chr4.4:15792013-15792032 None:intergenic 50.0%
GTGGTTGAAGAAGGGCCAAT+TGG - chr4.4:15791991-15792010 None:intergenic 50.0%
! GCTGTGATTGCATTTGGAGC+TGG + chr4.4:15791888-15791907 MS.gene023404:CDS 50.0%
CTCGGGTCCAACCACTTAAG+AGG - chr4.4:15792017-15792036 None:intergenic 55.0%
GCCCCATTCACAGATGGTTC+TGG - chr4.4:15792062-15792081 None:intergenic 55.0%
! GATGCTTTTCGGCTTCGCTC+GGG - chr4.4:15792034-15792053 None:intergenic 55.0%
! GGATGCTTTTCGGCTTCGCT+CGG - chr4.4:15792035-15792054 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr4.4 gene 15791828 15792109 15791828 ID=MS.gene023404
chr4.4 mRNA 15791828 15792109 15791828 ID=MS.gene023404.t1;Parent=MS.gene023404
chr4.4 exon 15791828 15792109 15791828 ID=MS.gene023404.t1.exon1;Parent=MS.gene023404.t1
chr4.4 CDS 15791828 15792109 15791828 ID=cds.MS.gene023404.t1;Parent=MS.gene023404.t1
Gene Sequence

>MS.gene023404

ATGGATTGGGAAGGACAAAAGCTAGCAGAGCAACTGATGCAGATACTGCTGCTTGCATTTGCTGTGATTGCATTTGGAGCTGGATATCTCACGGCTTCTTTCCAAACAATGATCCTCACATATGCTGGTGGAGTTTTTCTCACCACATTAGTCACTATTCCCAATTGGCCCTTCTTCAACCACCATCCTCTTAAGTGGTTGGACCCGAGCGAAGCCGAAAAGCATCCAAAGCCAGAACCATCTGTGAATGGGGCTACAAAGAAGAAATCCATTAAAAAGTAG
Protein sequence

>MS.gene023404.t1

MDWEGQKLAEQLMQILLLAFAVIAFGAGYLTASFQTMILTYAGGVFLTTLVTIPNWPFFNHHPLKWLDPSEAEKHPKPEPSVNGATKKKSIKK