AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene35618

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene35618.t1 MTR_3g073960 64.744 156 2 1 1 103 1 156 1.90e-49 154
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 24 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCAGGAGAAGTTGGTGGATA+TGG 0.255956 3.3:+63838085 None:intergenic
AGAAGTAAGAAGATGATGTT+AGG 0.329332 3.3:-63838250 None:intergenic
TGATCTGAACCGTTGATTCC+AGG 0.372333 3.3:+63838067 None:intergenic
AAACAAGTTGTGGTTGCAGC+TGG 0.401801 3.3:-63837440 MS.gene35618:CDS
GAAGAAAGATAAGTGTTCTA+TGG 0.419584 3.3:-63837471 MS.gene35618:CDS
TTTCATATGCTACAAATTTG+TGG 0.444162 3.3:+63837403 None:intergenic
CCATATCCACCAACTTCTCC+TGG 0.454006 3.3:-63838085 MS.gene35618:CDS
GAAGTAAGAAGATGATGTTA+GGG 0.462099 3.3:-63838249 None:intergenic
CAGGTCCATGACGGTTGAAA+AGG 0.471195 3.3:+63838125 None:intergenic
AACCGTCATGGACCTGGTGT+TGG 0.498303 3.3:-63838118 MS.gene35618:CDS
GGACCTGGTGTTGGTCCGTA+CGG 0.509388 3.3:-63838109 MS.gene35618:CDS
TCAACGGTTCAGATCAGAGC+AGG 0.509698 3.3:-63838060 MS.gene35618:CDS
CCGTTGATTCCAGGAGAAGT+TGG 0.513302 3.3:+63838076 None:intergenic
TGTTACTGTGTTCAGATCGA+AGG 0.548881 3.3:+63838177 None:intergenic
TTGATTCCAGGAGAAGTTGG+TGG 0.560507 3.3:+63838079 None:intergenic
AACAAGTTGTGGTTGCAGCT+GGG 0.564935 3.3:-63837439 MS.gene35618:CDS
TCAGAGCAGGGTTATGTCCA+TGG 0.575433 3.3:-63838047 MS.gene35618:intron
GGTTGCAGCTGGGTCTAAAG+TGG 0.592297 3.3:-63837429 MS.gene35618:CDS
GTTGGTGGATATGGACCGTA+CGG 0.599015 3.3:+63838094 None:intergenic
GGACCGTACGGACCAACACC+AGG 0.604586 3.3:+63838106 None:intergenic
CCAACTTCTCCTGGAATCAA+CGG 0.605664 3.3:-63838076 MS.gene35618:CDS
GGTATCAAAGAAACAAGTTG+TGG 0.623158 3.3:-63837450 MS.gene35618:CDS
GACCAACACCAGGTCCATGA+CGG 0.641553 3.3:+63838116 None:intergenic
CAACGGTTCAGATCAGAGCA+GGG 0.716813 3.3:-63838059 MS.gene35618:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTATTATTATTAATTTTGTG+TGG - chr3.3:63838044-63838063 MS.gene35618:intron 10.0%
! GTGAAAAATTAAATTTGCAG+AGG - chr3.3:63838102-63838121 MS.gene35618:CDS 25.0%
!! AATTTTGTGTGGATATAGAA+GGG - chr3.3:63838055-63838074 MS.gene35618:CDS 25.0%
!! TAATTTTGTGTGGATATAGA+AGG - chr3.3:63838054-63838073 MS.gene35618:CDS 25.0%
!!! TTTTTTGCATCTAAAAGTCT+TGG - chr3.3:63837871-63837890 MS.gene35618:intron 25.0%
GAAGAAAGATAAGTGTTCTA+TGG - chr3.3:63838179-63838198 MS.gene35618:CDS 30.0%
TATCAGCTGAATTTCTTCTA+AGG + chr3.3:63837642-63837661 None:intergenic 30.0%
! AAAAGGTTGTTGTTGTTGTT+AGG + chr3.3:63837511-63837530 None:intergenic 30.0%
!! GAATTTCTTCTAAGGTTTCT+AGG + chr3.3:63837634-63837653 None:intergenic 30.0%
!!! ATGCTTGTTGTTCTTTTCAT+TGG + chr3.3:63837442-63837461 None:intergenic 30.0%
CAGAGACATTTGATACGTTA+GGG + chr3.3:63837958-63837977 None:intergenic 35.0%
GGTATCAAAGAAACAAGTTG+TGG - chr3.3:63838200-63838219 MS.gene35618:CDS 35.0%
! ATAGAAGGGTGTGTGATAAT+TGG - chr3.3:63838069-63838088 MS.gene35618:CDS 35.0%
!!! CTTGTTGTTCTTTTCATTGG+AGG + chr3.3:63837439-63837458 None:intergenic 35.0%
ACTAAGTTTGATACCAGACG+CGG - chr3.3:63837909-63837928 MS.gene35618:intron 40.0%
CTTTCTCTGTAAACGTCGTT+TGG - chr3.3:63837693-63837712 MS.gene35618:intron 40.0%
GCAGAGACATTTGATACGTT+AGG + chr3.3:63837959-63837978 None:intergenic 40.0%
TGTTACTGTGTTCAGATCGA+AGG + chr3.3:63837476-63837495 None:intergenic 40.0%
! AACAACCTTTTCAACCGTCA+TGG - chr3.3:63837520-63837539 MS.gene35618:intron 40.0%
! AAGCAAGAGCGTAAGAAATC+AGG + chr3.3:63837676-63837695 None:intergenic 40.0%
! AAGGTTTCTAGGTGATACCA+TGG + chr3.3:63837623-63837642 None:intergenic 40.0%
! AGCAAGAGCGTAAGAAATCA+GGG + chr3.3:63837675-63837694 None:intergenic 40.0%
AAACAAGTTGTGGTTGCAGC+TGG - chr3.3:63838210-63838229 MS.gene35618:CDS 45.0%
AACAAGTTGTGGTTGCAGCT+GGG - chr3.3:63838211-63838230 MS.gene35618:CDS 45.0%
CCAACTTCTCCTGGAATCAA+CGG - chr3.3:63837574-63837593 MS.gene35618:intron 45.0%
TACATGTAGATGTCACGACC+AGG + chr3.3:63837721-63837740 None:intergenic 45.0%
TGTAAACGTCGTTTGGTACC+TGG - chr3.3:63837700-63837719 MS.gene35618:intron 45.0%
TTGATTCCAGGAGAAGTTGG+TGG + chr3.3:63837574-63837593 None:intergenic 45.0%
! GTTCTTTTCATTGGAGGACG+AGG + chr3.3:63837433-63837452 None:intergenic 45.0%
!! TGATCTGAACCGTTGATTCC+AGG + chr3.3:63837586-63837605 None:intergenic 45.0%
CAACGGTTCAGATCAGAGCA+GGG - chr3.3:63837591-63837610 MS.gene35618:intron 50.0%
CAGGTCCATGACGGTTGAAA+AGG + chr3.3:63837528-63837547 None:intergenic 50.0%
CCATATCCACCAACTTCTCC+TGG - chr3.3:63837565-63837584 MS.gene35618:intron 50.0%
TCAACGGTTCAGATCAGAGC+AGG - chr3.3:63837590-63837609 MS.gene35618:intron 50.0%
TCAGAGCAGGGTTATGTCCA+TGG - chr3.3:63837603-63837622 MS.gene35618:intron 50.0%
! CTTTTCAACCGTCATGGACC+TGG - chr3.3:63837526-63837545 MS.gene35618:intron 50.0%
! GTTGGTGGATATGGACCGTA+CGG + chr3.3:63837559-63837578 None:intergenic 50.0%
!! CCAGGAGAAGTTGGTGGATA+TGG + chr3.3:63837568-63837587 None:intergenic 50.0%
!! CCGTTGATTCCAGGAGAAGT+TGG + chr3.3:63837577-63837596 None:intergenic 50.0%
AACCGTCATGGACCTGGTGT+TGG - chr3.3:63837532-63837551 MS.gene35618:intron 55.0%
AACCTGCAATTCTCCGCGTC+TGG + chr3.3:63837925-63837944 None:intergenic 55.0%
GACCAACACCAGGTCCATGA+CGG + chr3.3:63837537-63837556 None:intergenic 55.0%
GGTTGCAGCTGGGTCTAAAG+TGG - chr3.3:63838221-63838240 MS.gene35618:CDS 55.0%
TACCAGACGCGGAGAATTGC+AGG - chr3.3:63837920-63837939 MS.gene35618:intron 55.0%
!! GGACCTGGTGTTGGTCCGTA+CGG - chr3.3:63837541-63837560 MS.gene35618:intron 60.0%
GGACCGTACGGACCAACACC+AGG + chr3.3:63837547-63837566 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 63837412 63838260 63837412 ID=MS.gene35618
chr3.3 mRNA 63837412 63838260 63837412 ID=MS.gene35618.t1;Parent=MS.gene35618
chr3.3 exon 63838048 63838260 63838048 ID=MS.gene35618.t1.exon1;Parent=MS.gene35618.t1
chr3.3 CDS 63838048 63838260 63838048 ID=cds.MS.gene35618.t1;Parent=MS.gene35618.t1
chr3.3 exon 63837412 63837510 63837412 ID=MS.gene35618.t1.exon2;Parent=MS.gene35618.t1
chr3.3 CDS 63837412 63837510 63837412 ID=cds.MS.gene35618.t1;Parent=MS.gene35618.t1
Gene Sequence

>MS.gene35618

ATGATGTTAGGGAAGAGACCTCGTCCTCCAATGAAAAGAACAACAAGCATGTCAGAGATAACCTTCGATCTGAACACAGTAACAACAGAAGAAGATCCTAACAACAACAACAACCTTTTCAACCGTCATGGACCTGGTGTTGGTCCGTACGGTCCATATCCACCAACTTCTCCTGGAATCAACGGTTCAGATCAGAGCAGGGTTATGTCCATGGTATCACCTAGAAACCTTAGAAGAAATTCAGCTGATATGACTCACAACCCTGATTTCTTACGCTCTTGCTTTCTCTGTAAACGTCGTTTGGTACCTGGTCGTGACATCTACATGTACAAGTATAATCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATATATATATATATATATGTATATATCTCTACTTTTTTTTGCATCTAAAAGTCTTGGTCGAAACTTATACATACTAAGTTTGATACCAGACGCGGAGAATTGCAGGTTCAAACTTGTGCCCTAACGTATCAAATGTCTCTGCAACATTTTCTGATATGAGATGTGTTCACAAGATTATTTTTTATTAATTATACATACTAAGTTTTTTTATTATTATTAATTTTGTGTGGATATAGAAGGGTGTGTGATAATTGGAAATTAATTTGTGAAAAATTAAATTTGCAGAGGAGATAGTGCTTTCTGCAGTCTAGAGTGTCGTCAACAGCAGATGAATCAAGATGAGAAGAAAGATAAGTGTTCTATGGTATCAAAGAAACAAGTTGTGGTTGCAGCTGGGTCTAAAGTGGCTGCCACAAATTTGTAG
Protein sequence

>MS.gene35618.t1

MMLGKRPRPPMKRTTSMSEITFDLNTVTTEEDPNNNNNLFNRHGPGVGPYGPYPPTSPGINGSDQSRVMSMQMNQDEKKDKCSMVSKKQVVVAAGSKVAATNL