AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0901790


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0901790 MtrunA17_Chr3g0131571 82.812 64 2 2 26 80 96 159 9.22e-19 75.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0901790 AT5G51010.1 58.730 63 17 2 26 79 91 153 2.20e-16 69.3

Find 15 sgRNAs with CRISPR-Local

Find 134 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATACGTAAGATGTCTGATT+TGG 0.295596 6_1:+98644723 None:intergenic
AGCATACATTTCAAACTTAT+CGG 0.341806 6_1:-98644790 None:intergenic
GTGGGAGTTGTAGTTCTTGC+AGG 0.375454 6_1:+98645851 Msa0901790:CDS
ACTCCCACGGCAACTGCAAT+AGG 0.395621 6_1:-98645836 None:intergenic
ATCAATAGTTTCTTGATCCT+TGG 0.407175 6_1:-98644764 None:intergenic
TTTGTTGACATCTGTTGCAT+AGG 0.431914 6_1:-98645627 None:intergenic
TAGGGCTCAAACCTTCGTTT+AGG 0.438783 6_1:-98645608 None:intergenic
TTGTTGACATCTGTTGCATA+GGG 0.445845 6_1:-98645626 None:intergenic
TAACTTTATCATATTTGCCA+AGG 0.528266 6_1:+98644747 Msa0901790:CDS
ACTTCCTATTGCAGTTGCCG+TGG 0.541016 6_1:+98645832 Msa0901790:CDS
CTTCCTATTGCAGTTGCCGT+GGG 0.547663 6_1:+98645833 Msa0901790:CDS
ATGTTAGAAAGGCGTTAGAA+AGG 0.548907 6_1:+98645666 Msa0901790:CDS
AAATGAAACAGATGTTAGAA+AGG 0.550334 6_1:+98645655 Msa0901790:CDS
TGCAAGAACTACAACTCCCA+CGG 0.635141 6_1:-98645849 None:intergenic
TTTGTGGTGCTCCTAAACGA+AGG 0.648339 6_1:+98645597 Msa0901790:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAATATTATACTGATAAGAA+AGG + chr6_1:98645491-98645510 Msa0901790:intron 15.0%
!! TAATATTATACTGATAAGAA+AGG + chr6_1:98645491-98645510 Msa0901790:intron 15.0%
!! TGGTAAGATATATATTTAGT+TGG + chr6_1:98645152-98645171 Msa0901790:intron 20.0%
!!! TATATATTTAGTTGGTTTTG+TGG + chr6_1:98645160-98645179 Msa0901790:intron 20.0%
!! ATATTAGACCTTAATAAACT+TGG - chr6_1:98645477-98645496 None:intergenic 20.0%
!! ATGTCAAAAACAGAAATAAT+TGG - chr6_1:98645782-98645801 None:intergenic 20.0%
!! TGGTAAGATATATATTTAGT+TGG + chr6_1:98645152-98645171 Msa0901790:intron 20.0%
!!! TATATATTTAGTTGGTTTTG+TGG + chr6_1:98645160-98645179 Msa0901790:intron 20.0%
!! ATATTAGACCTTAATAAACT+TGG - chr6_1:98645477-98645496 None:intergenic 20.0%
!! ATGTCAAAAACAGAAATAAT+TGG - chr6_1:98645782-98645801 None:intergenic 20.0%
! TAACTTTATCATATTTGCCA+AGG + chr6_1:98644747-98644766 Msa0901790:CDS 25.0%
! AGCATACATTTCAAACTTAT+CGG - chr6_1:98644793-98644812 None:intergenic 25.0%
! TTAATGTGTTACAATAATGC+TGG + chr6_1:98644868-98644887 Msa0901790:intron 25.0%
! AAAATGTATTGCCTAAATTG+TGG - chr6_1:98645364-98645383 None:intergenic 25.0%
! TTAGAGTTTCGATAAAATCA+TGG + chr6_1:98645382-98645401 Msa0901790:intron 25.0%
! GAAATGAGAATCTTTATGAT+TGG - chr6_1:98645446-98645465 None:intergenic 25.0%
! TTTCTCTACCAAGTTTATTA+AGG + chr6_1:98645466-98645485 Msa0901790:intron 25.0%
! TACTGATAAGAAAGGAAAAA+TGG + chr6_1:98645499-98645518 Msa0901790:intron 25.0%
! ACTGATAAGAAAGGAAAAAT+GGG + chr6_1:98645500-98645519 Msa0901790:intron 25.0%
! TTGTAAGAAGCAAAAGAAAT+AGG + chr6_1:98645528-98645547 Msa0901790:intron 25.0%
! TGTAAGAAGCAAAAGAAATA+GGG + chr6_1:98645529-98645548 Msa0901790:intron 25.0%
! AAATGAAACAGATGTTAGAA+AGG + chr6_1:98645655-98645674 Msa0901790:CDS 25.0%
! ATGCAAAAAGAAAATGACTA+TGG - chr6_1:98645738-98645757 None:intergenic 25.0%
!!! TTTATTATGCTGATTTCAAC+AGG + chr6_1:98645804-98645823 Msa0901790:intron 25.0%
! TAACTTTATCATATTTGCCA+AGG + chr6_1:98644747-98644766 Msa0901790:CDS 25.0%
! AGCATACATTTCAAACTTAT+CGG - chr6_1:98644793-98644812 None:intergenic 25.0%
! TTAATGTGTTACAATAATGC+TGG + chr6_1:98644868-98644887 Msa0901790:intron 25.0%
! AAAATGTATTGCCTAAATTG+TGG - chr6_1:98645364-98645383 None:intergenic 25.0%
! TTAGAGTTTCGATAAAATCA+TGG + chr6_1:98645382-98645401 Msa0901790:intron 25.0%
! GAAATGAGAATCTTTATGAT+TGG - chr6_1:98645446-98645465 None:intergenic 25.0%
! TTTCTCTACCAAGTTTATTA+AGG + chr6_1:98645466-98645485 Msa0901790:intron 25.0%
! TACTGATAAGAAAGGAAAAA+TGG + chr6_1:98645499-98645518 Msa0901790:intron 25.0%
! ACTGATAAGAAAGGAAAAAT+GGG + chr6_1:98645500-98645519 Msa0901790:intron 25.0%
! TTGTAAGAAGCAAAAGAAAT+AGG + chr6_1:98645528-98645547 Msa0901790:intron 25.0%
! TGTAAGAAGCAAAAGAAATA+GGG + chr6_1:98645529-98645548 Msa0901790:intron 25.0%
! AAATGAAACAGATGTTAGAA+AGG + chr6_1:98645655-98645674 Msa0901790:CDS 25.0%
! ATGCAAAAAGAAAATGACTA+TGG - chr6_1:98645738-98645757 None:intergenic 25.0%
!!! TTTATTATGCTGATTTCAAC+AGG + chr6_1:98645804-98645823 Msa0901790:intron 25.0%
ATCAATAGTTTCTTGATCCT+TGG - chr6_1:98644767-98644786 None:intergenic 30.0%
CTCAATTTCATCAAGTCATT+AGG - chr6_1:98644916-98644935 None:intergenic 30.0%
!!! TCTGTTTCTATTCCGTTTTA+TGG + chr6_1:98644993-98645012 Msa0901790:intron 30.0%
! ATTAACTGTCATGGATTACT+TGG + chr6_1:98645251-98645270 Msa0901790:intron 30.0%
! TTAACTGTCATGGATTACTT+GGG + chr6_1:98645252-98645271 Msa0901790:intron 30.0%
TCAAATTCTAAGTGCATGTT+AGG + chr6_1:98645295-98645314 Msa0901790:intron 30.0%
CACAATTGTTACCACAATTT+AGG + chr6_1:98645350-98645369 Msa0901790:intron 30.0%
CTCTTAATTTCTGAATTTGG+TGG - chr6_1:98645410-98645429 None:intergenic 30.0%
CTGCTCTTAATTTCTGAATT+TGG - chr6_1:98645413-98645432 None:intergenic 30.0%
GTAAGAAGCAAAAGAAATAG+GGG + chr6_1:98645530-98645549 Msa0901790:intron 30.0%
GCATTATGATTGTCTGAAAA+TGG + chr6_1:98645564-98645583 Msa0901790:intron 30.0%
ATCAATAGTTTCTTGATCCT+TGG - chr6_1:98644767-98644786 None:intergenic 30.0%
CTCAATTTCATCAAGTCATT+AGG - chr6_1:98644916-98644935 None:intergenic 30.0%
!!! TCTGTTTCTATTCCGTTTTA+TGG + chr6_1:98644993-98645012 Msa0901790:intron 30.0%
! ATTAACTGTCATGGATTACT+TGG + chr6_1:98645251-98645270 Msa0901790:intron 30.0%
! TTAACTGTCATGGATTACTT+GGG + chr6_1:98645252-98645271 Msa0901790:intron 30.0%
TCAAATTCTAAGTGCATGTT+AGG + chr6_1:98645295-98645314 Msa0901790:intron 30.0%
CACAATTGTTACCACAATTT+AGG + chr6_1:98645350-98645369 Msa0901790:intron 30.0%
CTCTTAATTTCTGAATTTGG+TGG - chr6_1:98645410-98645429 None:intergenic 30.0%
CTGCTCTTAATTTCTGAATT+TGG - chr6_1:98645413-98645432 None:intergenic 30.0%
GTAAGAAGCAAAAGAAATAG+GGG + chr6_1:98645530-98645549 Msa0901790:intron 30.0%
GCATTATGATTGTCTGAAAA+TGG + chr6_1:98645564-98645583 Msa0901790:intron 30.0%
ATGTGTTACAATAATGCTGG+TGG + chr6_1:98644871-98644890 Msa0901790:intron 35.0%
TGTGTTACAATAATGCTGGT+GGG + chr6_1:98644872-98644891 Msa0901790:intron 35.0%
GAAATTGAGAACATTTCACG+TGG + chr6_1:98644927-98644946 Msa0901790:intron 35.0%
ATTGTGTGGTGAAACTTTGT+GGG - chr6_1:98645091-98645110 None:intergenic 35.0%
AATTGTGTGGTGAAACTTTG+TGG - chr6_1:98645092-98645111 None:intergenic 35.0%
GTTTCACCACACAATTGTTA+AGG + chr6_1:98645096-98645115 Msa0901790:intron 35.0%
TCAACTCCTTAACAATTGTG+TGG - chr6_1:98645105-98645124 None:intergenic 35.0%
!!! TGATGTGGTTTTTGGCAATT+TGG + chr6_1:98645132-98645151 Msa0901790:intron 35.0%
ATGTCTTTCAGAAGATGTCT+TGG + chr6_1:98645186-98645205 Msa0901790:intron 35.0%
TTTCAGAAGATGTCTTGGTT+TGG + chr6_1:98645191-98645210 Msa0901790:intron 35.0%
CGAAACAGAATTAACTGTCA+TGG + chr6_1:98645242-98645261 Msa0901790:intron 35.0%
GTTAGGTTCAGTGAATTTGA+TGG + chr6_1:98645312-98645331 Msa0901790:intron 35.0%
! AAATGGTGTTTTGCAGTTTG+TGG + chr6_1:98645581-98645600 Msa0901790:intron 35.0%
TTGTTGACATCTGTTGCATA+GGG - chr6_1:98645629-98645648 None:intergenic 35.0%
TTTGTTGACATCTGTTGCAT+AGG - chr6_1:98645630-98645649 None:intergenic 35.0%
!! ATGTTAGAAAGGCGTTAGAA+AGG + chr6_1:98645666-98645685 Msa0901790:CDS 35.0%
TCCAAAGAGATGAAGCAATT+GGG + chr6_1:98645704-98645723 Msa0901790:intron 35.0%
ATGTGTTACAATAATGCTGG+TGG + chr6_1:98644871-98644890 Msa0901790:intron 35.0%
TGTGTTACAATAATGCTGGT+GGG + chr6_1:98644872-98644891 Msa0901790:intron 35.0%
GAAATTGAGAACATTTCACG+TGG + chr6_1:98644927-98644946 Msa0901790:intron 35.0%
ATTGTGTGGTGAAACTTTGT+GGG - chr6_1:98645091-98645110 None:intergenic 35.0%
AATTGTGTGGTGAAACTTTG+TGG - chr6_1:98645092-98645111 None:intergenic 35.0%
GTTTCACCACACAATTGTTA+AGG + chr6_1:98645096-98645115 Msa0901790:intron 35.0%
TCAACTCCTTAACAATTGTG+TGG - chr6_1:98645105-98645124 None:intergenic 35.0%
!!! TGATGTGGTTTTTGGCAATT+TGG + chr6_1:98645132-98645151 Msa0901790:intron 35.0%
ATGTCTTTCAGAAGATGTCT+TGG + chr6_1:98645186-98645205 Msa0901790:intron 35.0%
TTTCAGAAGATGTCTTGGTT+TGG + chr6_1:98645191-98645210 Msa0901790:intron 35.0%
CGAAACAGAATTAACTGTCA+TGG + chr6_1:98645242-98645261 Msa0901790:intron 35.0%
GTTAGGTTCAGTGAATTTGA+TGG + chr6_1:98645312-98645331 Msa0901790:intron 35.0%
! AAATGGTGTTTTGCAGTTTG+TGG + chr6_1:98645581-98645600 Msa0901790:intron 35.0%
TTGTTGACATCTGTTGCATA+GGG - chr6_1:98645629-98645648 None:intergenic 35.0%
TTTGTTGACATCTGTTGCAT+AGG - chr6_1:98645630-98645649 None:intergenic 35.0%
!! ATGTTAGAAAGGCGTTAGAA+AGG + chr6_1:98645666-98645685 Msa0901790:CDS 35.0%
TCCAAAGAGATGAAGCAATT+GGG + chr6_1:98645704-98645723 Msa0901790:intron 35.0%
GTGTTACAATAATGCTGGTG+GGG + chr6_1:98644873-98644892 Msa0901790:intron 40.0%
GTGCTGCAAAAGCCATAAAA+CGG - chr6_1:98645008-98645027 None:intergenic 40.0%
!! AAGAGAGTAGAAGCACCATT+TGG - chr6_1:98645064-98645083 None:intergenic 40.0%
! ACAACCTCTGATGTGGTTTT+TGG + chr6_1:98645124-98645143 Msa0901790:intron 40.0%
ATTGCCAAAAACCACATCAG+AGG - chr6_1:98645131-98645150 None:intergenic 40.0%
GTTAATTCTGTTTCGTCAGC+AGG - chr6_1:98645237-98645256 None:intergenic 40.0%
CTCCAAAGAGATGAAGCAAT+TGG + chr6_1:98645703-98645722 Msa0901790:intron 40.0%
ACCCAATTGCTTCATCTCTT+TGG - chr6_1:98645708-98645727 None:intergenic 40.0%
GTGTTACAATAATGCTGGTG+GGG + chr6_1:98644873-98644892 Msa0901790:intron 40.0%
GTGCTGCAAAAGCCATAAAA+CGG - chr6_1:98645008-98645027 None:intergenic 40.0%
!! AAGAGAGTAGAAGCACCATT+TGG - chr6_1:98645064-98645083 None:intergenic 40.0%
! ACAACCTCTGATGTGGTTTT+TGG + chr6_1:98645124-98645143 Msa0901790:intron 40.0%
ATTGCCAAAAACCACATCAG+AGG - chr6_1:98645131-98645150 None:intergenic 40.0%
GTTAATTCTGTTTCGTCAGC+AGG - chr6_1:98645237-98645256 None:intergenic 40.0%
CTCCAAAGAGATGAAGCAAT+TGG + chr6_1:98645703-98645722 Msa0901790:intron 40.0%
ACCCAATTGCTTCATCTCTT+TGG - chr6_1:98645708-98645727 None:intergenic 40.0%
TTTGTGGTGCTCCTAAACGA+AGG + chr6_1:98645597-98645616 Msa0901790:CDS 45.0%
TAGGGCTCAAACCTTCGTTT+AGG - chr6_1:98645611-98645630 None:intergenic 45.0%
TGCAAGAACTACAACTCCCA+CGG - chr6_1:98645852-98645871 None:intergenic 45.0%
TTTGTGGTGCTCCTAAACGA+AGG + chr6_1:98645597-98645616 Msa0901790:CDS 45.0%
TAGGGCTCAAACCTTCGTTT+AGG - chr6_1:98645611-98645630 None:intergenic 45.0%
TGCAAGAACTACAACTCCCA+CGG - chr6_1:98645852-98645871 None:intergenic 45.0%
ATTTGGACTGCTGGAGCAGT+CGG - chr6_1:98645047-98645066 None:intergenic 50.0%
!! AGAAGCACCATTTGGACTGC+TGG - chr6_1:98645056-98645075 None:intergenic 50.0%
GGAGTTGACAACCTCTGATG+TGG + chr6_1:98645117-98645136 Msa0901790:intron 50.0%
ACTTCCTATTGCAGTTGCCG+TGG + chr6_1:98645832-98645851 Msa0901790:CDS 50.0%
CTTCCTATTGCAGTTGCCGT+GGG + chr6_1:98645833-98645852 Msa0901790:CDS 50.0%
GTGGGAGTTGTAGTTCTTGC+AGG + chr6_1:98645851-98645870 Msa0901790:CDS 50.0%
ATTTGGACTGCTGGAGCAGT+CGG - chr6_1:98645047-98645066 None:intergenic 50.0%
!! AGAAGCACCATTTGGACTGC+TGG - chr6_1:98645056-98645075 None:intergenic 50.0%
GGAGTTGACAACCTCTGATG+TGG + chr6_1:98645117-98645136 Msa0901790:intron 50.0%
ACTTCCTATTGCAGTTGCCG+TGG + chr6_1:98645832-98645851 Msa0901790:CDS 50.0%
CTTCCTATTGCAGTTGCCGT+GGG + chr6_1:98645833-98645852 Msa0901790:CDS 50.0%
GTGGGAGTTGTAGTTCTTGC+AGG + chr6_1:98645851-98645870 Msa0901790:CDS 50.0%
TGCTGGTGGGGTTGTAAGCA+AGG + chr6_1:98644885-98644904 Msa0901790:intron 55.0%
GACTGCTCCAGCAGTCCAAA+TGG + chr6_1:98645046-98645065 Msa0901790:intron 55.0%
ACTCCCACGGCAACTGCAAT+AGG - chr6_1:98645839-98645858 None:intergenic 55.0%
TGCTGGTGGGGTTGTAAGCA+AGG + chr6_1:98644885-98644904 Msa0901790:intron 55.0%
GACTGCTCCAGCAGTCCAAA+TGG + chr6_1:98645046-98645065 Msa0901790:intron 55.0%
ACTCCCACGGCAACTGCAAT+AGG - chr6_1:98645839-98645858 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr6_1 gene 98644733 98645904 98644733 ID=Msa0901790;Name=Msa0901790
chr6_1 mRNA 98644733 98645904 98644733 ID=Msa0901790-mRNA-1;Parent=Msa0901790;Name=Msa0901790-mRNA-1;_AED=0.54;_eAED=0.85;_QI=0|0|0|0.66|0.5|0.66|3|0|80
chr6_1 exon 98644733 98644805 98644733 ID=Msa0901790-mRNA-1:exon:17435;Parent=Msa0901790-mRNA-1
chr6_1 exon 98645597 98645687 98645597 ID=Msa0901790-mRNA-1:exon:17436;Parent=Msa0901790-mRNA-1
chr6_1 exon 98645826 98645904 98645826 ID=Msa0901790-mRNA-1:exon:17437;Parent=Msa0901790-mRNA-1
chr6_1 CDS 98644733 98644805 98644733 ID=Msa0901790-mRNA-1:cds;Parent=Msa0901790-mRNA-1
chr6_1 CDS 98645597 98645687 98645597 ID=Msa0901790-mRNA-1:cds;Parent=Msa0901790-mRNA-1
chr6_1 CDS 98645826 98645904 98645826 ID=Msa0901790-mRNA-1:cds;Parent=Msa0901790-mRNA-1
Gene Sequence

>Msa0901790

ATGTCTGATTTGGATAACTTTATCATATTTGCCAAGGATCAAGAAACTATTGATGCACCGATAAGTTTGAAATTTTGTGGTGCTCCTAAACGAAGGTTTGAGCCCTATGCAACAGATGTCAACAAAAAAGCAAATGAAACAGATGTTAGAAAGGCGTTAGAAAGGAAAGCACTTCCTATTGCAGTTGCCGTGGGAGTTGTAGTTCTTGCAGGATTATACTTCTATCTCAATAGCACATTTTAG

Protein sequence

>Msa0901790

MSDLDNFIIFAKDQETIDAPISLKFCGAPKRRFEPYATDVNKKANETDVRKALERKALPIAVAVGVVVLAGLYFYLNSTF*