AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0391630

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0391630 MtrunA17_Chr8g0364251 100.000 58 0 0 1 58 537 594 1.42e-32 116
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0391630 AT1G59990.1 68.293 41 13 0 1 41 526 566 4.62e-14 64.7
Msa0391630 AT1G59990.2 65.854 41 14 0 1 41 526 566 1.30e-13 63.2

Find 27 sgRNAs with CRISPR-Local

Find 124 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATATTTGTTCTTCATAATA+TGG 0.143604 3_2:+4068617 None:intergenic
ATCATTCGTCTCTCAGGTTT+TGG 0.235144 3_2:-4068879 Msa0391630:three_prime_UTR
TTTGATTGGTGAACAGATAA+TGG 0.284240 3_2:+4068786 None:intergenic
GTTCACCAATCAAAGTTTAT+AGG 0.286284 3_2:-4068777 Msa0391630:three_prime_UTR
AATATTATATAACTATTATA+AGG 0.328370 3_2:-4068600 Msa0391630:three_prime_UTR
ATATTTGTTCTTCATAATAT+GGG 0.357045 3_2:+4068618 None:intergenic
GCTTTCCTATAAACTTTGAT+TGG 0.368075 3_2:+4068772 None:intergenic
TAATTACAACTCAATTTAGA+AGG 0.388787 3_2:-4068669 Msa0391630:three_prime_UTR
GTAGATGCTGTTCGTCGTGC+AGG 0.390681 3_2:-4069776 Msa0391630:CDS
TGCTGGTAACTAGTCCGATT+TGG 0.414486 3_2:+4069825 None:intergenic
ATAGATATCATTCGTCTCTC+AGG 0.425394 3_2:-4068885 Msa0391630:three_prime_UTR
GTTCGTCGTGCAGGGGAACT+CGG 0.444099 3_2:-4069767 Msa0391630:CDS
TACAAGCTCTCTGTTGGATT+CGG 0.447095 3_2:+4069796 None:intergenic
TGCAGGAGACCGCATTTAGC+AGG 0.463069 3_2:-4069501 Msa0391630:intron
AGCATCTACAAGCTCTCTGT+TGG 0.491017 3_2:+4069790 None:intergenic
TAGATGCTGTTCGTCGTGCA+GGG 0.499759 3_2:-4069775 Msa0391630:CDS
CGCTGTAAGACTCTCTTCAA+TGG 0.506284 3_2:+4068948 None:intergenic
TATTTGTTCTTCATAATATG+GGG 0.537414 3_2:+4068619 None:intergenic
GTTGGATTCGGTATACATGC+TGG 0.545852 3_2:+4069808 None:intergenic
AAGGTGGTTACACATAAGTC+AGG 0.559730 3_2:-4068916 Msa0391630:three_prime_UTR
ATCTTCACATAATTTACATG+TGG 0.601967 3_2:+4068725 None:intergenic
TCTTACAGCGTGAGAACACA+AGG 0.604949 3_2:-4068935 Msa0391630:exon
ATTTGTTCTTCATAATATGG+GGG 0.609996 3_2:+4068620 None:intergenic
GTTACACATAAGTCAGGCGT+AGG 0.629212 3_2:-4068910 Msa0391630:three_prime_UTR
AGATGCTGTTCGTCGTGCAG+GGG 0.648856 3_2:-4069774 Msa0391630:CDS
AGGGGAACTCGGTCTACCTG+TGG 0.664526 3_2:-4069756 Msa0391630:intron
TACAGCGTGAGAACACAAGG+TGG 0.797393 3_2:-4068932 Msa0391630:exon

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTATAAAACTGTATTTAT+TGG - chr3_2:4068699-4068718 Msa0391630:three_prime_UTR 10.0%
!! ATCAAAAAATATTTATACAT+TGG - chr3_2:4068774-4068793 Msa0391630:three_prime_UTR 10.0%
!! TCAAAAAATATTTATACATT+GGG - chr3_2:4068775-4068794 Msa0391630:three_prime_UTR 10.0%
!!! TTATATTTTTTTTTTTACCT+TGG - chr3_2:4069221-4069240 Msa0391630:intron 10.0%
!! AATTATAAAACTGTATTTAT+TGG - chr3_2:4068699-4068718 Msa0391630:three_prime_UTR 10.0%
!! ATCAAAAAATATTTATACAT+TGG - chr3_2:4068774-4068793 Msa0391630:three_prime_UTR 10.0%
!! TCAAAAAATATTTATACATT+GGG - chr3_2:4068775-4068794 Msa0391630:three_prime_UTR 10.0%
!!! TTATATTTTTTTTTTTACCT+TGG - chr3_2:4069221-4069240 Msa0391630:intron 10.0%
!!! TTTTTATTTTTAAAGCTCTA+TGG + chr3_2:4069009-4069028 None:intergenic 15.0%
!! ATATTTGTTCTTCATAATAT+GGG + chr3_2:4069815-4069834 None:intergenic 15.0%
!! AATATTTGTTCTTCATAATA+TGG + chr3_2:4069816-4069835 None:intergenic 15.0%
!!! TTTTTATTTTTAAAGCTCTA+TGG + chr3_2:4069009-4069028 None:intergenic 15.0%
!! ATATTTGTTCTTCATAATAT+GGG + chr3_2:4069815-4069834 None:intergenic 15.0%
!! AATATTTGTTCTTCATAATA+TGG + chr3_2:4069816-4069835 None:intergenic 15.0%
!!! CTTTCTTTTTTATCTTGTTA+CGG + chr3_2:4068966-4068985 None:intergenic 20.0%
!!! TATTGATTTTTAAAGCTCTA+TGG + chr3_2:4069060-4069079 None:intergenic 20.0%
!! TATTATGCATTGAGTTAAAA+AGG - chr3_2:4069097-4069116 Msa0391630:intron 20.0%
!!! TATTTTTTTTTTTACCTTGG+AGG - chr3_2:4069224-4069243 Msa0391630:intron 20.0%
!!! GATTAGTTTTCATATTACTT+CGG - chr3_2:4069255-4069274 Msa0391630:intron 20.0%
!! TAATTACAACTCAATTTAGA+AGG - chr3_2:4069761-4069780 Msa0391630:CDS 20.0%
!! TATTTGTTCTTCATAATATG+GGG + chr3_2:4069814-4069833 None:intergenic 20.0%
!!! CTTTCTTTTTTATCTTGTTA+CGG + chr3_2:4068966-4068985 None:intergenic 20.0%
!!! TATTGATTTTTAAAGCTCTA+TGG + chr3_2:4069060-4069079 None:intergenic 20.0%
!! TATTATGCATTGAGTTAAAA+AGG - chr3_2:4069097-4069116 Msa0391630:intron 20.0%
!!! TATTTTTTTTTTTACCTTGG+AGG - chr3_2:4069224-4069243 Msa0391630:intron 20.0%
!!! GATTAGTTTTCATATTACTT+CGG - chr3_2:4069255-4069274 Msa0391630:intron 20.0%
!! TAATTACAACTCAATTTAGA+AGG - chr3_2:4069761-4069780 Msa0391630:CDS 20.0%
!! TATTTGTTCTTCATAATATG+GGG + chr3_2:4069814-4069833 None:intergenic 20.0%
!!! ACAGTTTTATAATTTACCAC+AGG + chr3_2:4068693-4068712 None:intergenic 25.0%
! TTCAAATATCTCAATGTGTA+TGG + chr3_2:4068746-4068765 None:intergenic 25.0%
!! ATATCAATGACTTGTATAGT+TGG + chr3_2:4068867-4068886 None:intergenic 25.0%
!! TTTGATAGATTCCAACATTT+TGG - chr3_2:4068886-4068905 Msa0391630:three_prime_UTR 25.0%
! CGTAACAAGATAAAAAAGAA+AGG - chr3_2:4068964-4068983 Msa0391630:CDS 25.0%
!! AGTCTTGTATCCTTATAAAT+AGG - chr3_2:4069278-4069297 Msa0391630:intron 25.0%
! GTCTTGTATCCTTATAAATA+GGG - chr3_2:4069279-4069298 Msa0391630:intron 25.0%
! TCTTGTATCCTTATAAATAG+GGG - chr3_2:4069280-4069299 Msa0391630:intron 25.0%
! AATAGTAACCCCTATTTATA+AGG + chr3_2:4069291-4069310 None:intergenic 25.0%
! AAATACAAAATGATGGTTAC+TGG + chr3_2:4069428-4069447 None:intergenic 25.0%
! TTGCTACAAATACAAAATGA+TGG + chr3_2:4069435-4069454 None:intergenic 25.0%
!! ATCATTTTGCAAAAGATGAA+GGG + chr3_2:4069608-4069627 None:intergenic 25.0%
!! TATCATTTTGCAAAAGATGA+AGG + chr3_2:4069609-4069628 None:intergenic 25.0%
! ATCTTCACATAATTTACATG+TGG + chr3_2:4069708-4069727 None:intergenic 25.0%
! ATTTGTTCTTCATAATATGG+GGG + chr3_2:4069813-4069832 None:intergenic 25.0%
!!! ACAGTTTTATAATTTACCAC+AGG + chr3_2:4068693-4068712 None:intergenic 25.0%
! TTCAAATATCTCAATGTGTA+TGG + chr3_2:4068746-4068765 None:intergenic 25.0%
!! ATATCAATGACTTGTATAGT+TGG + chr3_2:4068867-4068886 None:intergenic 25.0%
!! TTTGATAGATTCCAACATTT+TGG - chr3_2:4068886-4068905 Msa0391630:three_prime_UTR 25.0%
! CGTAACAAGATAAAAAAGAA+AGG - chr3_2:4068964-4068983 Msa0391630:CDS 25.0%
!! AGTCTTGTATCCTTATAAAT+AGG - chr3_2:4069278-4069297 Msa0391630:intron 25.0%
! GTCTTGTATCCTTATAAATA+GGG - chr3_2:4069279-4069298 Msa0391630:intron 25.0%
! TCTTGTATCCTTATAAATAG+GGG - chr3_2:4069280-4069299 Msa0391630:intron 25.0%
! AATAGTAACCCCTATTTATA+AGG + chr3_2:4069291-4069310 None:intergenic 25.0%
! AAATACAAAATGATGGTTAC+TGG + chr3_2:4069428-4069447 None:intergenic 25.0%
! TTGCTACAAATACAAAATGA+TGG + chr3_2:4069435-4069454 None:intergenic 25.0%
!! ATCATTTTGCAAAAGATGAA+GGG + chr3_2:4069608-4069627 None:intergenic 25.0%
!! TATCATTTTGCAAAAGATGA+AGG + chr3_2:4069609-4069628 None:intergenic 25.0%
! ATCTTCACATAATTTACATG+TGG + chr3_2:4069708-4069727 None:intergenic 25.0%
! ATTTGTTCTTCATAATATGG+GGG + chr3_2:4069813-4069832 None:intergenic 25.0%
! TTTATTGGCTGTAGTAATCT+TGG - chr3_2:4068714-4068733 Msa0391630:three_prime_UTR 30.0%
!! ATGATGAGAGCATTAACTAT+AGG - chr3_2:4068819-4068838 Msa0391630:three_prime_UTR 30.0%
TAACAATCACTCCAAAATGT+TGG + chr3_2:4068900-4068919 None:intergenic 30.0%
GATTGTTACACTATTAATGC+AGG - chr3_2:4068912-4068931 Msa0391630:three_prime_UTR 30.0%
TGTGTTCGAAATAGAAAATG+CGG - chr3_2:4069141-4069160 Msa0391630:intron 30.0%
! TCATTTTGCAAAAGATGAAG+GGG + chr3_2:4069607-4069626 None:intergenic 30.0%
TTTGATTGGTGAACAGATAA+TGG + chr3_2:4069647-4069666 None:intergenic 30.0%
GTTCACCAATCAAAGTTTAT+AGG - chr3_2:4069653-4069672 Msa0391630:intron 30.0%
GCTTTCCTATAAACTTTGAT+TGG + chr3_2:4069661-4069680 None:intergenic 30.0%
! TTTATTGGCTGTAGTAATCT+TGG - chr3_2:4068714-4068733 Msa0391630:three_prime_UTR 30.0%
!! ATGATGAGAGCATTAACTAT+AGG - chr3_2:4068819-4068838 Msa0391630:three_prime_UTR 30.0%
TAACAATCACTCCAAAATGT+TGG + chr3_2:4068900-4068919 None:intergenic 30.0%
GATTGTTACACTATTAATGC+AGG - chr3_2:4068912-4068931 Msa0391630:three_prime_UTR 30.0%
TGTGTTCGAAATAGAAAATG+CGG - chr3_2:4069141-4069160 Msa0391630:intron 30.0%
! TCATTTTGCAAAAGATGAAG+GGG + chr3_2:4069607-4069626 None:intergenic 30.0%
TTTGATTGGTGAACAGATAA+TGG + chr3_2:4069647-4069666 None:intergenic 30.0%
GTTCACCAATCAAAGTTTAT+AGG - chr3_2:4069653-4069672 Msa0391630:intron 30.0%
GCTTTCCTATAAACTTTGAT+TGG + chr3_2:4069661-4069680 None:intergenic 30.0%
TTATCGTTGTCGAAGTTACA+AGG + chr3_2:4069394-4069413 None:intergenic 35.0%
! CAAAATGATGGTTACTGGTT+AGG + chr3_2:4069423-4069442 None:intergenic 35.0%
ATAGATATCATTCGTCTCTC+AGG - chr3_2:4069545-4069564 Msa0391630:intron 35.0%
TTATCGTTGTCGAAGTTACA+AGG + chr3_2:4069394-4069413 None:intergenic 35.0%
! CAAAATGATGGTTACTGGTT+AGG + chr3_2:4069423-4069442 None:intergenic 35.0%
ATAGATATCATTCGTCTCTC+AGG - chr3_2:4069545-4069564 Msa0391630:intron 35.0%
TACAAGCTCTCTGTTGGATT+CGG + chr3_2:4068637-4068656 None:intergenic 40.0%
! GCTTCTTTTCCTGCTAAATG+CGG + chr3_2:4068941-4068960 None:intergenic 40.0%
CTAATCTTAGAGATCCTCCA+AGG + chr3_2:4069241-4069260 None:intergenic 40.0%
AAGGTGGTTACACATAAGTC+AGG - chr3_2:4069514-4069533 Msa0391630:intron 40.0%
! ATCATTCGTCTCTCAGGTTT+TGG - chr3_2:4069551-4069570 Msa0391630:intron 40.0%
! CATAATATGGGGGTGTAGAT+GGG + chr3_2:4069803-4069822 None:intergenic 40.0%
! TCATAATATGGGGGTGTAGA+TGG + chr3_2:4069804-4069823 None:intergenic 40.0%
TACAAGCTCTCTGTTGGATT+CGG + chr3_2:4068637-4068656 None:intergenic 40.0%
! GCTTCTTTTCCTGCTAAATG+CGG + chr3_2:4068941-4068960 None:intergenic 40.0%
CTAATCTTAGAGATCCTCCA+AGG + chr3_2:4069241-4069260 None:intergenic 40.0%
AAGGTGGTTACACATAAGTC+AGG - chr3_2:4069514-4069533 Msa0391630:intron 40.0%
! ATCATTCGTCTCTCAGGTTT+TGG - chr3_2:4069551-4069570 Msa0391630:intron 40.0%
! CATAATATGGGGGTGTAGAT+GGG + chr3_2:4069803-4069822 None:intergenic 40.0%
! TCATAATATGGGGGTGTAGA+TGG + chr3_2:4069804-4069823 None:intergenic 40.0%
TGCTGGTAACTAGTCCGATT+TGG + chr3_2:4068608-4068627 None:intergenic 45.0%
! GTTGGATTCGGTATACATGC+TGG + chr3_2:4068625-4068644 None:intergenic 45.0%
AGCATCTACAAGCTCTCTGT+TGG + chr3_2:4068643-4068662 None:intergenic 45.0%
CGCTGTAAGACTCTCTTCAA+TGG + chr3_2:4069485-4069504 None:intergenic 45.0%
TCTTACAGCGTGAGAACACA+AGG - chr3_2:4069495-4069514 Msa0391630:CDS 45.0%
GTTACACATAAGTCAGGCGT+AGG - chr3_2:4069520-4069539 Msa0391630:intron 45.0%
TGCTGGTAACTAGTCCGATT+TGG + chr3_2:4068608-4068627 None:intergenic 45.0%
! GTTGGATTCGGTATACATGC+TGG + chr3_2:4068625-4068644 None:intergenic 45.0%
AGCATCTACAAGCTCTCTGT+TGG + chr3_2:4068643-4068662 None:intergenic 45.0%
CGCTGTAAGACTCTCTTCAA+TGG + chr3_2:4069485-4069504 None:intergenic 45.0%
TCTTACAGCGTGAGAACACA+AGG - chr3_2:4069495-4069514 Msa0391630:CDS 45.0%
GTTACACATAAGTCAGGCGT+AGG - chr3_2:4069520-4069539 Msa0391630:intron 45.0%
!! AATATTATATAACTATTATA+AGG - chr3_2:4069830-4069849 Msa0391630:five_prime_UTR 5.0%
!! ATATTATATAACTATTATAA+GGG - chr3_2:4069831-4069850 Msa0391630:five_prime_UTR 5.0%
TAGATGCTGTTCGTCGTGCA+GGG - chr3_2:4068655-4068674 Msa0391630:three_prime_UTR 50.0%
TACAGCGTGAGAACACAAGG+TGG - chr3_2:4069498-4069517 Msa0391630:CDS 50.0%
TAGATGCTGTTCGTCGTGCA+GGG - chr3_2:4068655-4068674 Msa0391630:three_prime_UTR 50.0%
TACAGCGTGAGAACACAAGG+TGG - chr3_2:4069498-4069517 Msa0391630:CDS 50.0%
GTAGATGCTGTTCGTCGTGC+AGG - chr3_2:4068654-4068673 Msa0391630:three_prime_UTR 55.0%
AGATGCTGTTCGTCGTGCAG+GGG - chr3_2:4068656-4068675 Msa0391630:three_prime_UTR 55.0%
TGCAGGAGACCGCATTTAGC+AGG - chr3_2:4068929-4068948 Msa0391630:exon 55.0%
GTAGATGCTGTTCGTCGTGC+AGG - chr3_2:4068654-4068673 Msa0391630:three_prime_UTR 55.0%
AGATGCTGTTCGTCGTGCAG+GGG - chr3_2:4068656-4068675 Msa0391630:three_prime_UTR 55.0%
TGCAGGAGACCGCATTTAGC+AGG - chr3_2:4068929-4068948 Msa0391630:exon 55.0%
GTTCGTCGTGCAGGGGAACT+CGG - chr3_2:4068663-4068682 Msa0391630:three_prime_UTR 60.0%
AGGGGAACTCGGTCTACCTG+TGG - chr3_2:4068674-4068693 Msa0391630:three_prime_UTR 60.0%
GTTCGTCGTGCAGGGGAACT+CGG - chr3_2:4068663-4068682 Msa0391630:three_prime_UTR 60.0%
AGGGGAACTCGGTCTACCTG+TGG - chr3_2:4068674-4068693 Msa0391630:three_prime_UTR 60.0%
Chromosome Type Strat End Strand Name
chr3_2 gene 4068600 4069852 4068600 ID=Msa0391630;Name=Msa0391630
chr3_2 mRNA 4068600 4069852 4068600 ID=Msa0391630-mRNA-1;Parent=Msa0391630;Name=Msa0391630-mRNA-1;_AED=0.00;_eAED=0.00;_QI=27|1|1|1|0.5|0.66|3|345|58
chr3_2 exon 4068600 4069000 4068600 ID=Msa0391630-mRNA-1:exon:1025;Parent=Msa0391630-mRNA-1
chr3_2 exon 4069467 4069518 4069467 ID=Msa0391630-mRNA-1:exon:1024;Parent=Msa0391630-mRNA-1
chr3_2 exon 4069757 4069852 4069757 ID=Msa0391630-mRNA-1:exon:1023;Parent=Msa0391630-mRNA-1
chr3_2 five_prime_UTR 4069826 4069852 4069826 ID=Msa0391630-mRNA-1:five_prime_utr;Parent=Msa0391630-mRNA-1
chr3_2 CDS 4069757 4069825 4069757 ID=Msa0391630-mRNA-1:cds;Parent=Msa0391630-mRNA-1
chr3_2 CDS 4069467 4069518 4069467 ID=Msa0391630-mRNA-1:cds;Parent=Msa0391630-mRNA-1
chr3_2 CDS 4068945 4069000 4068945 ID=Msa0391630-mRNA-1:cds;Parent=Msa0391630-mRNA-1
chr3_2 three_prime_UTR 4068600 4068944 4068600 ID=Msa0391630-mRNA-1:three_prime_utr;Parent=Msa0391630-mRNA-1
Gene Sequence

>Msa0391630

ATGTATACCGAATCCAACAGAGAGCTTGTAGATGCTGTTCGTCGTGCAGGGGAACTCGGTCTACCTGTGGAGACCGCATTTAGCAGGAAAAGAAGCTTCCGTAACAAGATAAAAAAGAAAGCAAGTGCTAACAAAGTCAGAGATTCAGCAACCATTGAAGAGAGTCTTACAGCGTGA
Protein sequence

>Msa0391630

MYTESNRELVDAVRRAGELGLPVETAFSRKRSFRNKIKKKASANKVRDSATIEESLTA*