AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0231790


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0231790 MtrunA17_Chr2g0278531 92.063 63 5 0 30 92 11 73 2.34e-37 120
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0231790 AT1G25275.3 50.000 70 31 1 25 90 2 71 1.19e-17 71.2
Msa0231790 AT1G25275.1 50.000 70 31 1 25 90 2 71 1.21e-17 70.9
Msa0231790 AT1G25275.2 48.571 70 32 1 25 90 2 71 1.10e-16 68.2

Find 27 sgRNAs with CRISPR-Local

Find 109 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATGCTTCTGATTGCCTTGA+TGG 0.154913 2_2:-4073834 Msa0231790:CDS
CTCAACCAAGTTTAATTAGA+AGG 0.298295 2_2:+4073142 None:intergenic
CTCTTTGAACGCAGGCAGTT+TGG 0.316423 2_2:+4073808 None:intergenic
ATGTATTGTGATAGCAGAAT+TGG 0.414963 2_2:+4073018 None:intergenic
GTAGTTTCTCAAGATTATTA+TGG 0.419164 2_2:-4074046 Msa0231790:five_prime_UTR
ACAAGCAGCAAACATTGAAT+AGG 0.443291 2_2:+4073172 None:intergenic
GATGTACTAGTCGTAGTTAA+TGG 0.445314 2_2:-4074146 None:intergenic
CGAGACAGTTGACAAGTTGT+TGG 0.451351 2_2:+4073236 None:intergenic
ATGTAGCAAGTAATTGCTTA+AGG 0.470851 2_2:-4073051 Msa0231790:three_prime_UTR
TGCTCGATTAGATGCGGTCC+AGG 0.477134 2_2:-4073569 Msa0231790:intron
TGCAGATTCTATGGTGGAGA+AGG 0.494670 2_2:-4073305 Msa0231790:intron
TAGTGCCTTCTAATTAAACT+TGG 0.497364 2_2:-4073147 Msa0231790:three_prime_UTR
TAGTTGTGCATTTATGACTT+TGG 0.516007 2_2:-4074076 Msa0231790:five_prime_UTR
TCAAGGCAATCAGAAGCATC+AGG 0.516390 2_2:+4073837 None:intergenic
GTGACATGCAGCAAGGCTTA+CGG 0.519988 2_2:-4073609 Msa0231790:intron
ATAATAATCTTGAGAAACTA+CGG 0.529331 2_2:+4074048 None:intergenic
GCAGATTCTATGGTGGAGAA+GGG 0.551697 2_2:-4073304 Msa0231790:intron
CAACAACTTGTCAACTGTCT+CGG 0.563127 2_2:-4073235 Msa0231790:three_prime_UTR
AGGCAGTTTGGCAACCATCA+AGG 0.564306 2_2:+4073820 None:intergenic
TTCTATGGTGGAGAAGGGCA+TGG 0.592128 2_2:-4073299 Msa0231790:CDS
ATGCAGCAAGGCTTACGGCA+AGG 0.642528 2_2:-4073604 Msa0231790:intron
CGCAAGTGCTCGATTAGATG+CGG 0.643345 2_2:-4073575 Msa0231790:CDS
AGTATGCATGTACTTCCACA+TGG 0.664590 2_2:-4074100 Msa0231790:five_prime_UTR
CTAACAGTCTCTTTGAACGC+AGG 0.676017 2_2:+4073800 None:intergenic
TAAATGCACAACTATCCATG+TGG 0.693119 2_2:+4074085 None:intergenic
GATGATGAAGAAGACGACGG+TGG 0.786514 2_2:-4073910 Msa0231790:CDS
GAAGATGATGAAGAAGACGA+CGG 0.800011 2_2:-4073913 Msa0231790:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTAAGAAAAGTAATTAAA+AGG + chr2_2:4073355-4073374 None:intergenic 10.0%
!!! CATTAAAATAGTATTATTTT+GGG + chr2_2:4073578-4073597 None:intergenic 10.0%
!!! TCATTAAAATAGTATTATTT+TGG + chr2_2:4073579-4073598 None:intergenic 10.0%
!!! AATAATACTATTTTAATGAA+AGG - chr2_2:4073580-4073599 Msa0231790:CDS 10.0%
!! AATTAAGAAAAGTAATTAAA+AGG + chr2_2:4073355-4073374 None:intergenic 10.0%
!!! CATTAAAATAGTATTATTTT+GGG + chr2_2:4073578-4073597 None:intergenic 10.0%
!!! TCATTAAAATAGTATTATTT+TGG + chr2_2:4073579-4073598 None:intergenic 10.0%
!!! AATAATACTATTTTAATGAA+AGG - chr2_2:4073580-4073599 Msa0231790:CDS 10.0%
!! ATCATAAAAAAAAAACATCA+AGG + chr2_2:4073126-4073145 None:intergenic 15.0%
!!! GATTTTCTTCTTTTAATTTA+AGG - chr2_2:4073375-4073394 Msa0231790:intron 15.0%
!! AAATTAATTAAAAAGCTTCA+AGG - chr2_2:4073454-4073473 Msa0231790:intron 15.0%
!!! TTTTTAAGTTAAAAAGCTTA+AGG - chr2_2:4074134-4074153 Msa0231790:five_prime_UTR 15.0%
!! ATCATAAAAAAAAAACATCA+AGG + chr2_2:4073126-4073145 None:intergenic 15.0%
!!! GATTTTCTTCTTTTAATTTA+AGG - chr2_2:4073375-4073394 Msa0231790:intron 15.0%
!! AAATTAATTAAAAAGCTTCA+AGG - chr2_2:4073454-4073473 Msa0231790:intron 15.0%
!!! TTTTTAAGTTAAAAAGCTTA+AGG - chr2_2:4074134-4074153 Msa0231790:five_prime_UTR 15.0%
!! ATAATAATCTTGAGAAACTA+CGG + chr2_2:4073064-4073083 None:intergenic 20.0%
!!! ATTTGTGATATTTTCTCAAA+TGG - chr2_2:4073238-4073257 Msa0231790:three_prime_UTR 20.0%
!! CAAGAAATTTAATTAAACCT+CGG + chr2_2:4073648-4073667 None:intergenic 20.0%
!!! ATTTAATTTTGCAGATTCTA+TGG - chr2_2:4073795-4073814 Msa0231790:intron 20.0%
!! ATAATAATCTTGAGAAACTA+CGG + chr2_2:4073064-4073083 None:intergenic 20.0%
!!! ATTTGTGATATTTTCTCAAA+TGG - chr2_2:4073238-4073257 Msa0231790:three_prime_UTR 20.0%
!! CAAGAAATTTAATTAAACCT+CGG + chr2_2:4073648-4073667 None:intergenic 20.0%
!!! ATTTAATTTTGCAGATTCTA+TGG - chr2_2:4073795-4073814 Msa0231790:intron 20.0%
! GTAGTTTCTCAAGATTATTA+TGG - chr2_2:4073063-4073082 Msa0231790:three_prime_UTR 25.0%
! GTAGTTTCTCAAGATTATTA+TGG - chr2_2:4073063-4073082 Msa0231790:three_prime_UTR 25.0%
TAGTTGTGCATTTATGACTT+TGG - chr2_2:4073033-4073052 Msa0231790:three_prime_UTR 30.0%
TTTGGGTAATGTTAATTACC+TGG + chr2_2:4073561-4073580 None:intergenic 30.0%
CTTGAATAATCGTAAACAAC+AGG - chr2_2:4073664-4073683 Msa0231790:intron 30.0%
! TAATTTTGCAGATTCTATGG+TGG - chr2_2:4073798-4073817 Msa0231790:intron 30.0%
TAGTGCCTTCTAATTAAACT+TGG - chr2_2:4073962-4073981 Msa0231790:CDS 30.0%
CTCAACCAAGTTTAATTAGA+AGG + chr2_2:4073970-4073989 None:intergenic 30.0%
ATGTAGCAAGTAATTGCTTA+AGG - chr2_2:4074058-4074077 Msa0231790:five_prime_UTR 30.0%
ATGTATTGTGATAGCAGAAT+TGG + chr2_2:4074094-4074113 None:intergenic 30.0%
TAGTTGTGCATTTATGACTT+TGG - chr2_2:4073033-4073052 Msa0231790:three_prime_UTR 30.0%
TTTGGGTAATGTTAATTACC+TGG + chr2_2:4073561-4073580 None:intergenic 30.0%
CTTGAATAATCGTAAACAAC+AGG - chr2_2:4073664-4073683 Msa0231790:intron 30.0%
! TAATTTTGCAGATTCTATGG+TGG - chr2_2:4073798-4073817 Msa0231790:intron 30.0%
TAGTGCCTTCTAATTAAACT+TGG - chr2_2:4073962-4073981 Msa0231790:CDS 30.0%
CTCAACCAAGTTTAATTAGA+AGG + chr2_2:4073970-4073989 None:intergenic 30.0%
ATGTAGCAAGTAATTGCTTA+AGG - chr2_2:4074058-4074077 Msa0231790:five_prime_UTR 30.0%
ATGTATTGTGATAGCAGAAT+TGG + chr2_2:4074094-4074113 None:intergenic 30.0%
TAAATGCACAACTATCCATG+TGG + chr2_2:4073027-4073046 None:intergenic 35.0%
! CTCTTTTCTCTTTGATCGTT+TGG + chr2_2:4073162-4073181 None:intergenic 35.0%
ATAATCGTAAACAACAGGTC+TGG - chr2_2:4073669-4073688 Msa0231790:intron 35.0%
TAATCGTAAACAACAGGTCT+GGG - chr2_2:4073670-4073689 Msa0231790:intron 35.0%
ACAAGCAGCAAACATTGAAT+AGG + chr2_2:4073940-4073959 None:intergenic 35.0%
TAAATGCACAACTATCCATG+TGG + chr2_2:4073027-4073046 None:intergenic 35.0%
! CTCTTTTCTCTTTGATCGTT+TGG + chr2_2:4073162-4073181 None:intergenic 35.0%
ATAATCGTAAACAACAGGTC+TGG - chr2_2:4073669-4073688 Msa0231790:intron 35.0%
TAATCGTAAACAACAGGTCT+GGG - chr2_2:4073670-4073689 Msa0231790:intron 35.0%
ACAAGCAGCAAACATTGAAT+AGG + chr2_2:4073940-4073959 None:intergenic 35.0%
AGTATGCATGTACTTCCACA+TGG - chr2_2:4073009-4073028 Msa0231790:three_prime_UTR 40.0%
GAAGATGATGAAGAAGACGA+CGG - chr2_2:4073196-4073215 Msa0231790:three_prime_UTR 40.0%
TATGTATGTGACATGCAGCA+AGG - chr2_2:4073493-4073512 Msa0231790:intron 40.0%
! TTAGTGCTGAAAAGATACCG+AGG - chr2_2:4073628-4073647 Msa0231790:intron 40.0%
GTATAAAATTGTCTGAGCCC+AGG + chr2_2:4073749-4073768 None:intergenic 40.0%
CAACAACTTGTCAACTGTCT+CGG - chr2_2:4073874-4073893 Msa0231790:CDS 40.0%
AGTATGCATGTACTTCCACA+TGG - chr2_2:4073009-4073028 Msa0231790:three_prime_UTR 40.0%
GAAGATGATGAAGAAGACGA+CGG - chr2_2:4073196-4073215 Msa0231790:three_prime_UTR 40.0%
TATGTATGTGACATGCAGCA+AGG - chr2_2:4073493-4073512 Msa0231790:intron 40.0%
! TTAGTGCTGAAAAGATACCG+AGG - chr2_2:4073628-4073647 Msa0231790:intron 40.0%
GTATAAAATTGTCTGAGCCC+AGG + chr2_2:4073749-4073768 None:intergenic 40.0%
CAACAACTTGTCAACTGTCT+CGG - chr2_2:4073874-4073893 Msa0231790:CDS 40.0%
!! TCAAGGCAATCAGAAGCATC+AGG + chr2_2:4073275-4073294 None:intergenic 45.0%
GATGCTTCTGATTGCCTTGA+TGG - chr2_2:4073275-4073294 Msa0231790:exon 45.0%
CTAACAGTCTCTTTGAACGC+AGG + chr2_2:4073312-4073331 None:intergenic 45.0%
! TGCAGATTCTATGGTGGAGA+AGG - chr2_2:4073804-4073823 Msa0231790:intron 45.0%
! GCAGATTCTATGGTGGAGAA+GGG - chr2_2:4073805-4073824 Msa0231790:CDS 45.0%
CGAGACAGTTGACAAGTTGT+TGG + chr2_2:4073876-4073895 None:intergenic 45.0%
!! TCAAGGCAATCAGAAGCATC+AGG + chr2_2:4073275-4073294 None:intergenic 45.0%
GATGCTTCTGATTGCCTTGA+TGG - chr2_2:4073275-4073294 Msa0231790:exon 45.0%
CTAACAGTCTCTTTGAACGC+AGG + chr2_2:4073312-4073331 None:intergenic 45.0%
! TGCAGATTCTATGGTGGAGA+AGG - chr2_2:4073804-4073823 Msa0231790:intron 45.0%
! GCAGATTCTATGGTGGAGAA+GGG - chr2_2:4073805-4073824 Msa0231790:CDS 45.0%
CGAGACAGTTGACAAGTTGT+TGG + chr2_2:4073876-4073895 None:intergenic 45.0%
GATGATGAAGAAGACGACGG+TGG - chr2_2:4073199-4073218 Msa0231790:three_prime_UTR 50.0%
AGGCAGTTTGGCAACCATCA+AGG + chr2_2:4073292-4073311 None:intergenic 50.0%
CTCTTTGAACGCAGGCAGTT+TGG + chr2_2:4073304-4073323 None:intergenic 50.0%
GTGACATGCAGCAAGGCTTA+CGG - chr2_2:4073500-4073519 Msa0231790:intron 50.0%
CGCAAGTGCTCGATTAGATG+CGG - chr2_2:4073534-4073553 Msa0231790:intron 50.0%
TCGTAAACAACAGGTCTGGG+TGG - chr2_2:4073673-4073692 Msa0231790:intron 50.0%
! ACGCTAGTCTCACACACTAG+AGG - chr2_2:4073710-4073729 Msa0231790:intron 50.0%
! TTCTATGGTGGAGAAGGGCA+TGG - chr2_2:4073810-4073829 Msa0231790:CDS 50.0%
TGTGCGCCATTAACTACGAC+AGG + chr2_2:4072972-4072991 None:intergenic 50.0%
GATGATGAAGAAGACGACGG+TGG - chr2_2:4073199-4073218 Msa0231790:three_prime_UTR 50.0%
AGGCAGTTTGGCAACCATCA+AGG + chr2_2:4073292-4073311 None:intergenic 50.0%
CTCTTTGAACGCAGGCAGTT+TGG + chr2_2:4073304-4073323 None:intergenic 50.0%
GTGACATGCAGCAAGGCTTA+CGG - chr2_2:4073500-4073519 Msa0231790:intron 50.0%
CGCAAGTGCTCGATTAGATG+CGG - chr2_2:4073534-4073553 Msa0231790:intron 50.0%
TCGTAAACAACAGGTCTGGG+TGG - chr2_2:4073673-4073692 Msa0231790:intron 50.0%
! ACGCTAGTCTCACACACTAG+AGG - chr2_2:4073710-4073729 Msa0231790:intron 50.0%
! TTCTATGGTGGAGAAGGGCA+TGG - chr2_2:4073810-4073829 Msa0231790:CDS 50.0%
ATGCAGCAAGGCTTACGGCA+AGG - chr2_2:4073505-4073524 Msa0231790:intron 55.0%
TGCTCGATTAGATGCGGTCC+AGG - chr2_2:4073540-4073559 Msa0231790:intron 55.0%
ACAGGTCTGGGTGGTGTAGT+CGG - chr2_2:4073682-4073701 Msa0231790:intron 55.0%
TCTGAGCCCAGGTTCGAACT+GGG + chr2_2:4073738-4073757 None:intergenic 55.0%
ATGCAGCAAGGCTTACGGCA+AGG - chr2_2:4073505-4073524 Msa0231790:intron 55.0%
TGCTCGATTAGATGCGGTCC+AGG - chr2_2:4073540-4073559 Msa0231790:intron 55.0%
ACAGGTCTGGGTGGTGTAGT+CGG - chr2_2:4073682-4073701 Msa0231790:intron 55.0%
TCTGAGCCCAGGTTCGAACT+GGG + chr2_2:4073738-4073757 None:intergenic 55.0%
AGAGGTCCCCAGTTCGAACC+TGG - chr2_2:4073728-4073747 Msa0231790:intron 60.0%
GAGGTCCCCAGTTCGAACCT+GGG - chr2_2:4073729-4073748 Msa0231790:intron 60.0%
CTGAGCCCAGGTTCGAACTG+GGG + chr2_2:4073737-4073756 None:intergenic 60.0%
GTCTGAGCCCAGGTTCGAAC+TGG + chr2_2:4073739-4073758 None:intergenic 60.0%
AGAGGTCCCCAGTTCGAACC+TGG - chr2_2:4073728-4073747 Msa0231790:intron 60.0%
GAGGTCCCCAGTTCGAACCT+GGG - chr2_2:4073729-4073748 Msa0231790:intron 60.0%
CTGAGCCCAGGTTCGAACTG+GGG + chr2_2:4073737-4073756 None:intergenic 60.0%
GTCTGAGCCCAGGTTCGAAC+TGG + chr2_2:4073739-4073758 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 4072972 4074159 4072972 ID=Msa0231790;Name=Msa0231790
chr2_2 mRNA 4072972 4074159 4072972 ID=Msa0231790-mRNA-1;Parent=Msa0231790;Name=Msa0231790-mRNA-1;_AED=0.00;_eAED=0.00;_QI=156|1|1|1|0.5|0.66|3|322|92
chr2_2 exon 4072972 4073322 4072972 ID=Msa0231790-mRNA-1:exon:1654;Parent=Msa0231790-mRNA-1
chr2_2 exon 4073570 4073620 4073570 ID=Msa0231790-mRNA-1:exon:1653;Parent=Msa0231790-mRNA-1
chr2_2 exon 4073805 4074159 4073805 ID=Msa0231790-mRNA-1:exon:1652;Parent=Msa0231790-mRNA-1
chr2_2 five_prime_UTR 4074004 4074159 4074004 ID=Msa0231790-mRNA-1:five_prime_utr;Parent=Msa0231790-mRNA-1
chr2_2 CDS 4073805 4074003 4073805 ID=Msa0231790-mRNA-1:cds;Parent=Msa0231790-mRNA-1
chr2_2 CDS 4073570 4073620 4073570 ID=Msa0231790-mRNA-1:cds;Parent=Msa0231790-mRNA-1
chr2_2 CDS 4073294 4073322 4073294 ID=Msa0231790-mRNA-1:cds;Parent=Msa0231790-mRNA-1
chr2_2 three_prime_UTR 4072972 4073293 4072972 ID=Msa0231790-mRNA-1:three_prime_utr;Parent=Msa0231790-mRNA-1
Gene Sequence

>Msa0231790

ATGTTTTTTTTTTATGATTCAAGAGAATCTACCAAACGATCAAAGAGAAAAGAGAAAGTAAAGTTTGTGAAGATGATGAAGAAGACGACGGTGGTTGCTATGATGCTTTTATTTGTGATATTTTCTCAAATGGATAGCGTTGTTCCTGATGCTTCTGATTGCCTTGATGGTTGCCAAACTGCCTGCGTTCAAAGAGACTCAAGGCTTACGGCAAGGTGTGAGCGCAAGTGCTCGATTAGATGCGGTCCAGATTCTATGGTGGAGAAGGGCATGGATTGA

Protein sequence

>Msa0231790

MFFFYDSRESTKRSKRKEKVKFVKMMKKTTVVAMMLLFVIFSQMDSVVPDASDCLDGCQTACVQRDSRLTARCERKCSIRCGPDSMVEKGMD*