AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0592440


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 25 sgRNAs with CRISPR-Local

Find 86 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAACACTTGTGTACTTTCT+TGG 0.204133 4_2:+17803938 None:intergenic
TATCTCAACAGGAAGGTTAT+AGG 0.294052 4_2:+17804559 None:intergenic
CATTTAGTGAACAAGGTTAA+TGG 0.303914 4_2:-17803735 Msa0592440:three_prime_UTR
TTATTTATTGGTTATATGTA+AGG 0.348319 4_2:-17803908 Msa0592440:exon
TGAAACACATTTATCTCAAC+AGG 0.371957 4_2:+17804548 None:intergenic
TTTAGAAATAATGATAGTTA+TGG 0.385787 4_2:-17804501 Msa0592440:CDS
CACTTGTGTACTTTCTTGGT+TGG 0.423151 4_2:+17803942 None:intergenic
AAGGAGTAATACAATTTACT+TGG 0.436068 4_2:-17804414 Msa0592440:CDS
ACTTGTGTACTTTCTTGGTT+GGG 0.439578 4_2:+17803943 None:intergenic
TGCAAACGTCTCTAATGTAC+TGG 0.480257 4_2:-17804463 Msa0592440:CDS
AGGAGTAATACAATTTACTT+GGG 0.495944 4_2:-17804413 Msa0592440:CDS
CTAGTTACATTTAGTGAACA+AGG 0.512646 4_2:-17803742 Msa0592440:three_prime_UTR
CAAGCTTCATTGTAGTGCTA+TGG 0.530793 4_2:+17804041 None:intergenic
AAATACCGCAGGCCGTACTA+AGG 0.533904 4_2:-17804433 Msa0592440:CDS
AATTGTATTACTCCTTAGTA+CGG 0.552663 4_2:+17804421 None:intergenic
TAAATGTGTTTCAATCTGAA+AGG 0.571002 4_2:-17804538 Msa0592440:CDS
CTGGCTTGGTGAAATACCGC+AGG 0.602239 4_2:-17804444 Msa0592440:CDS
ACGTCTCTAATGTACTGGCT+TGG 0.607846 4_2:-17804458 Msa0592440:CDS
AGTAATACAATTTACTTGGG+GGG 0.611558 4_2:-17804410 Msa0592440:intron
ACATGAGTAACGAGTAGAGC+TGG 0.614984 4_2:+17804069 None:intergenic
GCACTACAATGAAGCTTGCG+AGG 0.627527 4_2:-17804036 Msa0592440:CDS
GGAGTAATACAATTTACTTG+GGG 0.628992 4_2:-17804412 Msa0592440:CDS
GAGTAATACAATTTACTTGG+GGG 0.646252 4_2:-17804411 Msa0592440:CDS
ACACATTTATCTCAACAGGA+AGG 0.654860 4_2:+17804552 None:intergenic
TTACTCCTTAGTACGGCCTG+CGG 0.713651 4_2:+17804428 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTAGAAATAATGATAGTTA+TGG - chr4_2:17803793-17803812 Msa0592440:three_prime_UTR 15.0%
!!! TTATTTATTGGTTATATGTA+AGG - chr4_2:17804386-17804405 Msa0592440:intron 15.0%
!!! AGTTCTGTTTTATATATTTT+TGG - chr4_2:17804516-17804535 Msa0592440:CDS 15.0%
!!! GTTCTGTTTTATATATTTTT+GGG - chr4_2:17804517-17804536 Msa0592440:CDS 15.0%
!! TTTAGAAATAATGATAGTTA+TGG - chr4_2:17803793-17803812 Msa0592440:three_prime_UTR 15.0%
!!! TTATTTATTGGTTATATGTA+AGG - chr4_2:17804386-17804405 Msa0592440:intron 15.0%
!!! AGTTCTGTTTTATATATTTT+TGG - chr4_2:17804516-17804535 Msa0592440:CDS 15.0%
!!! GTTCTGTTTTATATATTTTT+GGG - chr4_2:17804517-17804536 Msa0592440:CDS 15.0%
!!! TGCTAACTAGTATATTTTTT+TGG - chr4_2:17803927-17803946 Msa0592440:CDS 20.0%
!!! GCTAACTAGTATATTTTTTT+GGG - chr4_2:17803928-17803947 Msa0592440:CDS 20.0%
!!! TTTTCCTGATTTATCTTTAT+AGG - chr4_2:17804182-17804201 Msa0592440:intron 20.0%
!!! GTTTTGATGTCATTATTTAT+TGG - chr4_2:17804374-17804393 Msa0592440:intron 20.0%
!!! ACTTTTGTTTTGTAGAAATA+CGG - chr4_2:17804456-17804475 Msa0592440:CDS 20.0%
!!! TGCTAACTAGTATATTTTTT+TGG - chr4_2:17803927-17803946 Msa0592440:CDS 20.0%
!!! GCTAACTAGTATATTTTTTT+GGG - chr4_2:17803928-17803947 Msa0592440:CDS 20.0%
!!! TTTTCCTGATTTATCTTTAT+AGG - chr4_2:17804182-17804201 Msa0592440:intron 20.0%
!!! GTTTTGATGTCATTATTTAT+TGG - chr4_2:17804374-17804393 Msa0592440:intron 20.0%
!!! ACTTTTGTTTTGTAGAAATA+CGG - chr4_2:17804456-17804475 Msa0592440:CDS 20.0%
! TAAATGTGTTTCAATCTGAA+AGG - chr4_2:17803756-17803775 Msa0592440:three_prime_UTR 25.0%
! AATTGTATTACTCCTTAGTA+CGG + chr4_2:17803876-17803895 None:intergenic 25.0%
! AAGGAGTAATACAATTTACT+TGG - chr4_2:17803880-17803899 Msa0592440:three_prime_UTR 25.0%
! AGGAGTAATACAATTTACTT+GGG - chr4_2:17803881-17803900 Msa0592440:three_prime_UTR 25.0%
! CTTCAATTGTAGTAGAATTA+GGG + chr4_2:17804061-17804080 None:intergenic 25.0%
! TCTTCAATTGTAGTAGAATT+AGG + chr4_2:17804062-17804081 None:intergenic 25.0%
! CTTACCTATAAAGATAAATC+AGG + chr4_2:17804189-17804208 None:intergenic 25.0%
! TAAATGTGTTTCAATCTGAA+AGG - chr4_2:17803756-17803775 Msa0592440:three_prime_UTR 25.0%
! AATTGTATTACTCCTTAGTA+CGG + chr4_2:17803876-17803895 None:intergenic 25.0%
! AAGGAGTAATACAATTTACT+TGG - chr4_2:17803880-17803899 Msa0592440:three_prime_UTR 25.0%
! AGGAGTAATACAATTTACTT+GGG - chr4_2:17803881-17803900 Msa0592440:three_prime_UTR 25.0%
! CTTCAATTGTAGTAGAATTA+GGG + chr4_2:17804061-17804080 None:intergenic 25.0%
! TCTTCAATTGTAGTAGAATT+AGG + chr4_2:17804062-17804081 None:intergenic 25.0%
! CTTACCTATAAAGATAAATC+AGG + chr4_2:17804189-17804208 None:intergenic 25.0%
TGAAACACATTTATCTCAAC+AGG + chr4_2:17803749-17803768 None:intergenic 30.0%
GGAGTAATACAATTTACTTG+GGG - chr4_2:17803882-17803901 Msa0592440:three_prime_UTR 30.0%
GAGTAATACAATTTACTTGG+GGG - chr4_2:17803883-17803902 Msa0592440:three_prime_UTR 30.0%
AGTAATACAATTTACTTGGG+GGG - chr4_2:17803884-17803903 Msa0592440:three_prime_UTR 30.0%
CAATTGAAGTTGACTAAGAT+TGG - chr4_2:17804010-17804029 Msa0592440:CDS 30.0%
! CATTTTCACACTCATTTACA+AGG + chr4_2:17804125-17804144 None:intergenic 30.0%
AAAACACTTGTGTACTTTCT+TGG + chr4_2:17804359-17804378 None:intergenic 30.0%
CTAGTTACATTTAGTGAACA+AGG - chr4_2:17804552-17804571 Msa0592440:CDS 30.0%
CATTTAGTGAACAAGGTTAA+TGG - chr4_2:17804559-17804578 Msa0592440:CDS 30.0%
TGAAACACATTTATCTCAAC+AGG + chr4_2:17803749-17803768 None:intergenic 30.0%
GGAGTAATACAATTTACTTG+GGG - chr4_2:17803882-17803901 Msa0592440:three_prime_UTR 30.0%
GAGTAATACAATTTACTTGG+GGG - chr4_2:17803883-17803902 Msa0592440:three_prime_UTR 30.0%
AGTAATACAATTTACTTGGG+GGG - chr4_2:17803884-17803903 Msa0592440:three_prime_UTR 30.0%
CAATTGAAGTTGACTAAGAT+TGG - chr4_2:17804010-17804029 Msa0592440:CDS 30.0%
! CATTTTCACACTCATTTACA+AGG + chr4_2:17804125-17804144 None:intergenic 30.0%
AAAACACTTGTGTACTTTCT+TGG + chr4_2:17804359-17804378 None:intergenic 30.0%
CTAGTTACATTTAGTGAACA+AGG - chr4_2:17804552-17804571 Msa0592440:CDS 30.0%
CATTTAGTGAACAAGGTTAA+TGG - chr4_2:17804559-17804578 Msa0592440:CDS 30.0%
TATCTCAACAGGAAGGTTAT+AGG + chr4_2:17803738-17803757 None:intergenic 35.0%
ACACATTTATCTCAACAGGA+AGG + chr4_2:17803745-17803764 None:intergenic 35.0%
TTTATGCATGTAAACTGACC+TGG - chr4_2:17803970-17803989 Msa0592440:CDS 35.0%
TTACAAGGAAAGTTCAAGAC+AGG + chr4_2:17804110-17804129 None:intergenic 35.0%
ACTTGTGTACTTTCTTGGTT+GGG + chr4_2:17804354-17804373 None:intergenic 35.0%
TCACAGAGACAACTAAACAT+GGG + chr4_2:17803713-17803732 None:intergenic 35.0%
TTCACAGAGACAACTAAACA+TGG + chr4_2:17803714-17803733 None:intergenic 35.0%
TATCTCAACAGGAAGGTTAT+AGG + chr4_2:17803738-17803757 None:intergenic 35.0%
ACACATTTATCTCAACAGGA+AGG + chr4_2:17803745-17803764 None:intergenic 35.0%
TTTATGCATGTAAACTGACC+TGG - chr4_2:17803970-17803989 Msa0592440:CDS 35.0%
TTACAAGGAAAGTTCAAGAC+AGG + chr4_2:17804110-17804129 None:intergenic 35.0%
ACTTGTGTACTTTCTTGGTT+GGG + chr4_2:17804354-17804373 None:intergenic 35.0%
TGCAAACGTCTCTAATGTAC+TGG - chr4_2:17803831-17803850 Msa0592440:three_prime_UTR 40.0%
ATTTACTTGGGGGGTAAATC+AGG - chr4_2:17803893-17803912 Msa0592440:exon 40.0%
TTTACTTGGGGGGTAAATCA+GGG - chr4_2:17803894-17803913 Msa0592440:exon 40.0%
CAAGCTTCATTGTAGTGCTA+TGG + chr4_2:17804256-17804275 None:intergenic 40.0%
CACTTGTGTACTTTCTTGGT+TGG + chr4_2:17804355-17804374 None:intergenic 40.0%
TGCAAACGTCTCTAATGTAC+TGG - chr4_2:17803831-17803850 Msa0592440:three_prime_UTR 40.0%
ATTTACTTGGGGGGTAAATC+AGG - chr4_2:17803893-17803912 Msa0592440:exon 40.0%
TTTACTTGGGGGGTAAATCA+GGG - chr4_2:17803894-17803913 Msa0592440:exon 40.0%
CAAGCTTCATTGTAGTGCTA+TGG + chr4_2:17804256-17804275 None:intergenic 40.0%
CACTTGTGTACTTTCTTGGT+TGG + chr4_2:17804355-17804374 None:intergenic 40.0%
!! ACGTCTCTAATGTACTGGCT+TGG - chr4_2:17803836-17803855 Msa0592440:three_prime_UTR 45.0%
ACATGAGTAACGAGTAGAGC+TGG + chr4_2:17804228-17804247 None:intergenic 45.0%
!! ACGTCTCTAATGTACTGGCT+TGG - chr4_2:17803836-17803855 Msa0592440:three_prime_UTR 45.0%
ACATGAGTAACGAGTAGAGC+TGG + chr4_2:17804228-17804247 None:intergenic 45.0%
AAATACCGCAGGCCGTACTA+AGG - chr4_2:17803861-17803880 Msa0592440:three_prime_UTR 50.0%
TTACTCCTTAGTACGGCCTG+CGG + chr4_2:17803869-17803888 None:intergenic 50.0%
GCACTACAATGAAGCTTGCG+AGG - chr4_2:17804258-17804277 Msa0592440:intron 50.0%
AAATACCGCAGGCCGTACTA+AGG - chr4_2:17803861-17803880 Msa0592440:three_prime_UTR 50.0%
TTACTCCTTAGTACGGCCTG+CGG + chr4_2:17803869-17803888 None:intergenic 50.0%
GCACTACAATGAAGCTTGCG+AGG - chr4_2:17804258-17804277 Msa0592440:intron 50.0%
!! CTGGCTTGGTGAAATACCGC+AGG - chr4_2:17803850-17803869 Msa0592440:three_prime_UTR 55.0%
GTGTGCACTGAGCACTTACC+AGG + chr4_2:17803991-17804010 None:intergenic 55.0%
!! CTGGCTTGGTGAAATACCGC+AGG - chr4_2:17803850-17803869 Msa0592440:three_prime_UTR 55.0%
GTGTGCACTGAGCACTTACC+AGG + chr4_2:17803991-17804010 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 17803713 17804603 17803713 ID=Msa0592440;Name=Msa0592440
chr4_2 mRNA 17803713 17804603 17803713 ID=Msa0592440-mRNA-1;Parent=Msa0592440;Name=Msa0592440-mRNA-1;_AED=0.58;_eAED=0.58;_QI=0|0|0.5|0.5|1|1|2|197|131
chr4_2 exon 17803713 17804112 17803713 ID=Msa0592440-mRNA-1:exon:5152;Parent=Msa0592440-mRNA-1
chr4_2 exon 17804411 17804603 17804411 ID=Msa0592440-mRNA-1:exon:5151;Parent=Msa0592440-mRNA-1
chr4_2 CDS 17804411 17804603 17804411 ID=Msa0592440-mRNA-1:cds;Parent=Msa0592440-mRNA-1
chr4_2 CDS 17803910 17804112 17803910 ID=Msa0592440-mRNA-1:cds;Parent=Msa0592440-mRNA-1
chr4_2 three_prime_UTR 17803713 17803909 17803713 ID=Msa0592440-mRNA-1:three_prime_utr;Parent=Msa0592440-mRNA-1
Gene Sequence

>Msa0592440

ATGTTTAGTTGTCTCTGTGAATCCTATAACCTTCCTGTTGAGATAAATGTGTTTCAATCTGAAAGGAAACTTAAATTGAGTTTAGAAATAATGATAGTTATGGCTTACAAATTACTATTGCAAACGTCTCTAATGTACTGGCTTGGTGAAATACCGCAGGCCGTACTAAGGAGTAATACAATTTACTTGGGGGGTAAGTTTACAGTCACAAGTACCAGCTCTACTCGTTACTCATGTGTCTGCCATAGCACTACAATGAAGCTTGCGAGGTTTTATGATGTTTTCATACATCAGTACGAAGTTTTTTCACATAAGACACATGACTTTTGTGTGTCTTTTGCCCAACCAAGAAAGTACACAAGTGTTTTGATGTCATTATTTATTGGTTATATGTAA

Protein sequence

>Msa0592440

MFSCLCESYNLPVEINVFQSERKLKLSLEIMIVMAYKLLLQTSLMYWLGEIPQAVLRSNTIYLGGKFTVTSTSSTRYSCVCHSTTMKLARFYDVFIHQYEVFSHKTHDFCVSFAQPRKYTSVLMSLFIGYM*