AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene47004

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 33 sgRNAs with CRISPR-Local

Find 53 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GACTCATCGTCACCGGAAAT+TGG 0.237543 5.2:-75489223 None:intergenic
AAAGGAACTGCCACTGTTAC+TGG 0.264232 5.2:-75489049 None:intergenic
TTCCTTAGGATGGTTGAAAT+TGG 0.295594 5.2:-75489269 None:intergenic
TCTCCGGCTAGTCCAATTTC+CGG 0.340374 5.2:+75489211 MS.gene47004:CDS
AGCCGGAGACGGAGAATCTT+CGG 0.389032 5.2:-75489197 None:intergenic
TCATCGTCACTGTCTTCCTT+AGG 0.390911 5.2:-75489283 None:intergenic
TTGGATTGTGTCCTTGTCTT+GGG 0.401290 5.2:-75488990 None:intergenic
CTTTAACATCGAAACAGAAC+TGG 0.404508 5.2:-75489341 None:intergenic
ATTGGATTGTGTCCTTGTCT+TGG 0.414041 5.2:-75488991 None:intergenic
TTGGAAGGAATATTTGTGTC+TGG 0.465359 5.2:-75489250 None:intergenic
GTTGCCCCTTCTTTCAGTAA+AGG 0.467797 5.2:-75489067 None:intergenic
GCAGTTCCTTTACTGAAAGA+AGG 0.475413 5.2:+75489061 MS.gene47004:CDS
TGACAAAGATAAAGATAAAG+AGG 0.482717 5.2:+75489315 MS.gene47004:CDS
ACGGATCAACTGATGACCAT+TGG 0.511597 5.2:-75489009 None:intergenic
CGTCACTGTCTTCCTTAGGA+TGG 0.511800 5.2:-75489279 None:intergenic
TTAGGATGGTTGAAATTGGA+AGG 0.515170 5.2:-75489265 None:intergenic
CAGTTCCTTTACTGAAAGAA+GGG 0.524215 5.2:+75489062 MS.gene47004:CDS
TTCAAAATAAATGTGACTCA+TGG 0.525741 5.2:+75489142 MS.gene47004:CDS
TTCCAATTTCAACCATCCTA+AGG 0.526093 5.2:+75489267 MS.gene47004:CDS
ATCCGAAGATTCTCCGTCTC+CGG 0.529783 5.2:+75489195 MS.gene47004:CDS
TATATGTTTGAACAAGAGAG+TGG 0.543824 5.2:-75488931 None:intergenic
ATAATCACATTGTTTGTATG+TGG 0.560805 5.2:-75488960 None:intergenic
TCACCGGAAATTGGACTAGC+CGG 0.571076 5.2:-75489214 None:intergenic
TGGCGCAGACTCATCGTCAC+CGG 0.575216 5.2:-75489230 None:intergenic
TACTGGATGTATATCAGTGT+TGG 0.593017 5.2:-75489032 None:intergenic
AGTTCCTTTACTGAAAGAAG+GGG 0.634152 5.2:+75489063 MS.gene47004:CDS
GAAATTGGACTAGCCGGAGA+CGG 0.643836 5.2:-75489208 None:intergenic
TTATGATGATGCCCAAGACA+AGG 0.650355 5.2:+75488979 MS.gene47004:CDS
ATAAATGTGACTCATGGACA+AGG 0.658209 5.2:+75489148 MS.gene47004:CDS
GGATGTATATCAGTGTTGGA+CGG 0.669469 5.2:-75489028 None:intergenic
GGAGACGGAGAATCTTCGGA+TGG 0.673058 5.2:-75489193 None:intergenic
TGATATACATCCAGTAACAG+TGG 0.677787 5.2:+75489039 MS.gene47004:CDS
AAGACAAGGACACAATCCAA+TGG 0.682396 5.2:+75488993 MS.gene47004:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTATTATAAAATAAATAAA+AGG - chr5.2:75489446-75489465 None:intergenic 0.0%
!! CTTTCAAAAAAAAAAAACAA+CGG - chr5.2:75489628-75489647 None:intergenic 15.0%
!! TTTCAAAAAAAAAAAACAAC+GGG - chr5.2:75489627-75489646 None:intergenic 15.0%
!! AAATTTCACAACATGTTATA+TGG + chr5.2:75489370-75489389 MS.gene47004:intron 20.0%
!! TTATACAACAATAACATAGA+TGG - chr5.2:75489533-75489552 None:intergenic 20.0%
! AAAATGTCCCTAATAAAACA+AGG - chr5.2:75489399-75489418 None:intergenic 25.0%
! ATAATCACATTGTTTGTATG+TGG - chr5.2:75488963-75488982 None:intergenic 25.0%
! GAATTATGAATACGTAGATA+TGG + chr5.2:75489792-75489811 MS.gene47004:intron 25.0%
! GAATTGAACAAATCAAATAC+AGG - chr5.2:75489659-75489678 None:intergenic 25.0%
! TGACAAAGATAAAGATAAAG+AGG + chr5.2:75489315-75489334 MS.gene47004:CDS 25.0%
! TTCAAAATAAATGTGACTCA+TGG + chr5.2:75489142-75489161 MS.gene47004:CDS 25.0%
!! TTTTTCTCTAGTGATTATGA+TGG + chr5.2:75489094-75489113 MS.gene47004:CDS 25.0%
TATATGTTTGAACAAGAGAG+TGG - chr5.2:75488934-75488953 None:intergenic 30.0%
! AATTCCTTTGAGAATCCTAT+TGG + chr5.2:75489674-75489693 MS.gene47004:intron 30.0%
!!! ATGGATGCCTTGTTTTATTA+GGG + chr5.2:75489389-75489408 MS.gene47004:intron 30.0%
!!! TATGGATGCCTTGTTTTATT+AGG + chr5.2:75489388-75489407 MS.gene47004:intron 30.0%
AGAATCCTATTGGATGATCA+AGG + chr5.2:75489684-75489703 MS.gene47004:intron 35.0%
AGTTCCTTTACTGAAAGAAG+GGG + chr5.2:75489063-75489082 MS.gene47004:CDS 35.0%
ATAAATGTGACTCATGGACA+AGG + chr5.2:75489148-75489167 MS.gene47004:CDS 35.0%
CAGTTCCTTTACTGAAAGAA+GGG + chr5.2:75489062-75489081 MS.gene47004:CDS 35.0%
CTTTAACATCGAAACAGAAC+TGG - chr5.2:75489344-75489363 None:intergenic 35.0%
GATGGTGAACAATGCAAAAA+TGG + chr5.2:75489112-75489131 MS.gene47004:CDS 35.0%
TACTGGATGTATATCAGTGT+TGG - chr5.2:75489035-75489054 None:intergenic 35.0%
TCATCCAATAGGATTCTCAA+AGG - chr5.2:75489681-75489700 None:intergenic 35.0%
TGATATACATCCAGTAACAG+TGG + chr5.2:75489039-75489058 MS.gene47004:CDS 35.0%
TGCTTGTGCTACAAGATATA+TGG + chr5.2:75489761-75489780 MS.gene47004:intron 35.0%
TTAGGATGGTTGAAATTGGA+AGG - chr5.2:75489268-75489287 None:intergenic 35.0%
TTCCAATTTCAACCATCCTA+AGG + chr5.2:75489267-75489286 MS.gene47004:CDS 35.0%
TTCCTTAGGATGGTTGAAAT+TGG - chr5.2:75489272-75489291 None:intergenic 35.0%
TTGGAAGGAATATTTGTGTC+TGG - chr5.2:75489253-75489272 None:intergenic 35.0%
AAGACAAGGACACAATCCAA+TGG + chr5.2:75488993-75489012 MS.gene47004:CDS 40.0%
ACGATCCTTGATCATCCAAT+AGG - chr5.2:75489692-75489711 None:intergenic 40.0%
ATTGGATTGTGTCCTTGTCT+TGG - chr5.2:75488994-75489013 None:intergenic 40.0%
GCAGTTCCTTTACTGAAAGA+AGG + chr5.2:75489061-75489080 MS.gene47004:CDS 40.0%
TTGGATTGTGTCCTTGTCTT+GGG - chr5.2:75488993-75489012 None:intergenic 40.0%
! GGATGTATATCAGTGTTGGA+CGG - chr5.2:75489031-75489050 None:intergenic 40.0%
! TTATGATGATGCCCAAGACA+AGG + chr5.2:75488979-75488998 MS.gene47004:CDS 40.0%
!! GATGGCTTTTGAAGACTCTT+CGG - chr5.2:75489178-75489197 None:intergenic 40.0%
AAAGGAACTGCCACTGTTAC+TGG - chr5.2:75489052-75489071 None:intergenic 45.0%
ACGGATCAACTGATGACCAT+TGG - chr5.2:75489012-75489031 None:intergenic 45.0%
GTTGCCCCTTCTTTCAGTAA+AGG - chr5.2:75489070-75489089 None:intergenic 45.0%
TCATCGTCACTGTCTTCCTT+AGG - chr5.2:75489286-75489305 None:intergenic 45.0%
TTGACGTGAGATGTGAGCTA+GGG + chr5.2:75489503-75489522 MS.gene47004:intron 45.0%
ATCCGAAGATTCTCCGTCTC+CGG + chr5.2:75489195-75489214 MS.gene47004:CDS 50.0%
CGTCACTGTCTTCCTTAGGA+TGG - chr5.2:75489282-75489301 None:intergenic 50.0%
GACTCATCGTCACCGGAAAT+TGG - chr5.2:75489226-75489245 None:intergenic 50.0%
GTTGACGTGAGATGTGAGCT+AGG + chr5.2:75489502-75489521 MS.gene47004:intron 50.0%
! TCTCCGGCTAGTCCAATTTC+CGG + chr5.2:75489211-75489230 MS.gene47004:CDS 50.0%
!! GAAATTGGACTAGCCGGAGA+CGG - chr5.2:75489211-75489230 None:intergenic 50.0%
!! TCACCGGAAATTGGACTAGC+CGG - chr5.2:75489217-75489236 None:intergenic 50.0%
AGCCGGAGACGGAGAATCTT+CGG - chr5.2:75489200-75489219 None:intergenic 55.0%
GGAGACGGAGAATCTTCGGA+TGG - chr5.2:75489196-75489215 None:intergenic 55.0%
TGGCGCAGACTCATCGTCAC+CGG - chr5.2:75489233-75489252 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 75488912 75489833 75488912 ID=MS.gene47004
chr5.2 mRNA 75488912 75489833 75488912 ID=MS.gene47004.t1;Parent=MS.gene47004
chr5.2 exon 75488912 75489362 75488912 ID=MS.gene47004.t1.exon1;Parent=MS.gene47004.t1
chr5.2 CDS 75488912 75489362 75488912 ID=cds.MS.gene47004.t1;Parent=MS.gene47004.t1
chr5.2 exon 75489830 75489833 75489830 ID=MS.gene47004.t1.exon2;Parent=MS.gene47004.t1
chr5.2 CDS 75489830 75489833 75489830 ID=cds.MS.gene47004.t1;Parent=MS.gene47004.t1
Gene Sequence

>MS.gene47004

TTTTCAACACAGACAATAACCACTCTCTTGTTCAAACATATAATTTCACCACATACAAACAATGTGATTATGATGATGCCCAAGACAAGGACACAATCCAATGGTCATCAGTTGATCCGTCCAACACTGATATACATCCAGTAACAGTGGCAGTTCCTTTACTGAAAGAAGGGGCAACATACTTTTTCTCTAGTGATTATGATGGTGAACAATGCAAAAATGGACAACATTTCAAAATAAATGTGACTCATGGACAAGGTTTGCCGAAGAGTCTTCAAAAGCCATCCGAAGATTCTCCGTCTCCGGCTAGTCCAATTTCCGGTGACGATGAGTCTGCGCCAGACACAAATATTCCTTCCAATTTCAACCATCCTAAGGAAGACAGTGACGATGAAAAAACTAGTGACAAAGATAAAGATAAAGAGGAATCCAGTTCTGTTTCGATGTTAAAGTATGCAAAATTTCACAACATGTTATATGGATGCCTTGTTTTATTAGGGACATTTTTCTTTTTTTAGTCTGTGTAAGATACCTTTTATTTATTTTATAATAATTTATTATAGATTTTATTATCTTCTCAATTTAATTTTGTTGACGTGAGATGTGAGCTAGGGTATACCATCTATGTTATTGTTGTATAAAACTTCACATTATATTTATTGTGTAAATTTCAATTAATATATTGAGAAAGAACAAGAGTTCAAGAAATAGTCCCGTTGTTTTTTTTTTTTGAAAGACAACAGTCCTGTATTTGATTTGTTCAATTCCTTTGAGAATCCTATTGGATGATCAAGGATCGTGTTTATTTATAGTTGTATCAAAATTTTGTTTTAATATTTGCAACGAAATTGCTTGTGCTACAAGATATATGGTTTTTTTTGAATTATGAATACGTAGATATGGTGATTGATATCTCAGATGA
Protein sequence

>MS.gene47004.t1

FSTQTITTLLFKHIISPHTNNVIMMMPKTRTQSNGHQLIRPTLIYIQUQWQFLYUKKGQHTFSLVIMMVNNAKMDNISKUMULMDKVCRRVFKSHPKILRLRLVQFPVTMSLRQTQIFLPISTILRKTVTMKKLVTKIKIKRNPVLFRCUN