AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene051609

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene051609.t1 MTR_1g016200 56.311 103 34 3 9 100 2 104 6.46e-25 91.3
MS.gene051609.t1 MTR_1g016170 62.500 48 15 1 56 100 187 234 4.10e-13 64.3
MS.gene051609.t1 MTR_7g112330 42.373 59 34 0 56 114 22 80 2.31e-11 57.0
MS.gene051609.t1 MTR_4g121110 48.276 58 25 2 54 111 28 80 3.95e-11 57.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene051609.t1 AT5G56860 47.692 65 30 1 25 89 203 263 1.24e-12 63.5
MS.gene051609.t1 AT5G49300 44.928 69 32 2 56 120 36 102 8.24e-12 58.5
MS.gene051609.t1 AT4G26150 71.875 32 9 0 56 87 199 230 4.20e-11 58.9
MS.gene051609.t1 AT5G26930 47.826 46 24 0 55 100 25 70 8.74e-11 55.5

Find 27 sgRNAs with CRISPR-Local

Find 39 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTTCTTTGTGGCTGGAAC+TGG 0.239072 1.3:-5984502 None:intergenic
AGTATTCGCCATTGCCCTTT+TGG 0.253039 1.3:-5984613 None:intergenic
ATGAGTATCAAGACCCTTAT+CGG 0.303482 1.3:-5984909 None:intergenic
ATACAAACACTACTCCTCTT+TGG 0.387924 1.3:+5984665 MS.gene051609:CDS
GGAAGAGGCAAAAGCCGATA+AGG 0.448770 1.3:+5984895 MS.gene051609:CDS
CAATCGAAACAAACCCTAGT+TGG 0.460017 1.3:-5984640 None:intergenic
TCTTGATACTCATAAGGAAA+AGG 0.465163 1.3:+5984919 MS.gene051609:CDS
TTGCCTCTTCCCTTCTTCGT+CGG 0.477939 1.3:-5984883 None:intergenic
CTTGATACTCATAAGGAAAA+GGG 0.489428 1.3:+5984920 MS.gene051609:CDS
TAAGGGTCTTGATACTCATA+AGG 0.492473 1.3:+5984913 MS.gene051609:CDS
ACCGAATACGAATACCCAAA+AGG 0.493067 1.3:+5984598 MS.gene051609:CDS
CCGAATACGAATACCCAAAA+GGG 0.528839 1.3:+5984599 MS.gene051609:CDS
GAAGAGGCAAAAGCCGATAA+GGG 0.529120 1.3:+5984896 MS.gene051609:CDS
ATGTGGACTCCGACGAAGAA+GGG 0.540307 1.3:+5984874 MS.gene051609:CDS
CTTTGGAGGAGTGATCCTAC+AGG 0.546346 1.3:+5984682 MS.gene051609:CDS
GGCGAATACTATATCCAACT+AGG 0.572160 1.3:+5984626 MS.gene051609:CDS
CATGTGGACTCCGACGAAGA+AGG 0.573346 1.3:+5984873 MS.gene051609:CDS
GAGTGATCCTACAGGTTCCA+AGG 0.583772 1.3:+5984690 MS.gene051609:CDS
ACTCCGACGAAGAAGGGAAG+AGG 0.589069 1.3:+5984880 MS.gene051609:CDS
CAAACACTACTCCTCTTTGG+AGG 0.592172 1.3:+5984668 MS.gene051609:CDS
GCGAATACTATATCCAACTA+GGG 0.606852 1.3:+5984627 MS.gene051609:CDS
CAGTCGTTGTGCAATGCATG+TGG 0.610062 1.3:+5984857 MS.gene051609:intron
ACGAATACCCAAAAGGGCAA+TGG 0.610371 1.3:+5984605 MS.gene051609:CDS
ACTCATAAGGAAAAGGGCAA+TGG 0.616678 1.3:+5984926 MS.gene051609:CDS
TGGCGAACGCTCATCATCTG+AGG 0.618644 1.3:+5984946 MS.gene051609:CDS
CTAATTACCTTGGAACCTGT+AGG 0.621221 1.3:-5984697 None:intergenic
GTAGGATCACTCCTCCAAAG+AGG 0.666474 1.3:-5984679 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAGTTAACAAGAAATATGT+TGG + chr1.3:5984832-5984851 MS.gene051609:intron 20.0%
!!! AGCAGTTTTTATTTTCTTTT+TGG - chr1.3:5984578-5984597 None:intergenic 20.0%
! TAGAGATTAACTAATTACCT+TGG - chr1.3:5984710-5984729 None:intergenic 25.0%
ATGAACCAAAATGAAAGTTG+GGG - chr1.3:5984737-5984756 None:intergenic 30.0%
CATGAACCAAAATGAAAGTT+GGG - chr1.3:5984738-5984757 None:intergenic 30.0%
CTTGATACTCATAAGGAAAA+GGG + chr1.3:5984920-5984939 MS.gene051609:CDS 30.0%
TCTTGATACTCATAAGGAAA+AGG + chr1.3:5984919-5984938 MS.gene051609:CDS 30.0%
!!! AGCAGTTTTTTTCTTCTTTG+TGG - chr1.3:5984515-5984534 None:intergenic 30.0%
ATACAAACACTACTCCTCTT+TGG + chr1.3:5984665-5984684 MS.gene051609:CDS 35.0%
ATGAGTATCAAGACCCTTAT+CGG - chr1.3:5984912-5984931 None:intergenic 35.0%
GCATGAACCAAAATGAAAGT+TGG - chr1.3:5984739-5984758 None:intergenic 35.0%
GCGAATACTATATCCAACTA+GGG + chr1.3:5984627-5984646 MS.gene051609:CDS 35.0%
TAAGGGTCTTGATACTCATA+AGG + chr1.3:5984913-5984932 MS.gene051609:CDS 35.0%
! ATTCTCCCCAACTTTCATTT+TGG + chr1.3:5984729-5984748 MS.gene051609:intron 35.0%
!! AGCAGCTGATTTCTTCTTTT+TGG - chr1.3:5984548-5984567 None:intergenic 35.0%
!!! GTTTTTTTCTTCTTTGTGGC+TGG - chr1.3:5984511-5984530 None:intergenic 35.0%
ACCGAATACGAATACCCAAA+AGG + chr1.3:5984598-5984617 MS.gene051609:CDS 40.0%
ACTCATAAGGAAAAGGGCAA+TGG + chr1.3:5984926-5984945 MS.gene051609:CDS 40.0%
CAATCGAAACAAACCCTAGT+TGG - chr1.3:5984643-5984662 None:intergenic 40.0%
CCGAATACGAATACCCAAAA+GGG + chr1.3:5984599-5984618 MS.gene051609:CDS 40.0%
CTAATTACCTTGGAACCTGT+AGG - chr1.3:5984700-5984719 None:intergenic 40.0%
GGCGAATACTATATCCAACT+AGG + chr1.3:5984626-5984645 MS.gene051609:CDS 40.0%
!! CCCTTTTGGGTATTCGTATT+CGG - chr1.3:5984602-5984621 None:intergenic 40.0%
ACGAATACCCAAAAGGGCAA+TGG + chr1.3:5984605-5984624 MS.gene051609:CDS 45.0%
CAAACACTACTCCTCTTTGG+AGG + chr1.3:5984668-5984687 MS.gene051609:CDS 45.0%
GAAGAGGCAAAAGCCGATAA+GGG + chr1.3:5984896-5984915 MS.gene051609:CDS 45.0%
TTCTTCTTTGTGGCTGGAAC+TGG - chr1.3:5984505-5984524 None:intergenic 45.0%
! AGTATTCGCCATTGCCCTTT+TGG - chr1.3:5984616-5984635 None:intergenic 45.0%
! GTATTCGCCATTGCCCTTTT+GGG - chr1.3:5984615-5984634 None:intergenic 45.0%
ATGTGGACTCCGACGAAGAA+GGG + chr1.3:5984874-5984893 MS.gene051609:CDS 50.0%
CAGTCGTTGTGCAATGCATG+TGG + chr1.3:5984857-5984876 MS.gene051609:intron 50.0%
GAGTGATCCTACAGGTTCCA+AGG + chr1.3:5984690-5984709 MS.gene051609:CDS 50.0%
GGAAGAGGCAAAAGCCGATA+AGG + chr1.3:5984895-5984914 MS.gene051609:CDS 50.0%
GTAGGATCACTCCTCCAAAG+AGG - chr1.3:5984682-5984701 None:intergenic 50.0%
TTGCCTCTTCCCTTCTTCGT+CGG - chr1.3:5984886-5984905 None:intergenic 50.0%
! CTTTGGAGGAGTGATCCTAC+AGG + chr1.3:5984682-5984701 MS.gene051609:CDS 50.0%
ACTCCGACGAAGAAGGGAAG+AGG + chr1.3:5984880-5984899 MS.gene051609:CDS 55.0%
CATGTGGACTCCGACGAAGA+AGG + chr1.3:5984873-5984892 MS.gene051609:CDS 55.0%
TGGCGAACGCTCATCATCTG+AGG + chr1.3:5984946-5984965 MS.gene051609:CDS 55.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 5984481 5984997 5984481 ID=MS.gene051609
chr1.3 mRNA 5984481 5984997 5984481 ID=MS.gene051609.t1;Parent=MS.gene051609
chr1.3 exon 5984481 5984711 5984481 ID=MS.gene051609.t1.exon1;Parent=MS.gene051609.t1
chr1.3 CDS 5984481 5984711 5984481 ID=cds.MS.gene051609.t1;Parent=MS.gene051609.t1
chr1.3 exon 5984860 5984997 5984860 ID=MS.gene051609.t1.exon2;Parent=MS.gene051609.t1
chr1.3 CDS 5984860 5984997 5984860 ID=cds.MS.gene051609.t1;Parent=MS.gene051609.t1
Gene Sequence

>MS.gene051609

ATGAGAGTAAGTAACGATGATCCAGTTCCAGCCACAAAGAAGAAAAAAACTGCTGCTAGTGCTGCCAAAAAGAAGAAATCAGCTGCTAGTGCTGCCAAAAAGAAAATAAAAACTGCTACCGAATACGAATACCCAAAAGGGCAATGGCGAATACTATATCCAACTAGGGTTTGTTTCGATTGCAATACAAACACTACTCCTCTTTGGAGGAGTGATCCTACAGGTTCCAAGGTAATTAGTTAATCTCTATTCTCCCCAACTTTCATTTTGGTTCATGCAAAAGTGTTATTCTATACTAATACAATGATTAATAATTTGAATATCTATATATATATATATATATATATATATATAGTTAACAAGAAATATGTTGGTGCAGTCGTTGTGCAATGCATGTGGACTCCGACGAAGAAGGGAAGAGGCAAAAGCCGATAAGGGTCTTGATACTCATAAGGAAAAGGGCAATGGCGAACGCTCATCATCTGAGGATGTGAAGAATGTTTTAATGTTCATCTGA
Protein sequence

>MS.gene051609.t1

MRVSNDDPVPATKKKKTAASAAKKKKSAASAAKKKIKTATEYEYPKGQWRILYPTRVCFDCNTNTTPLWRSDPTGSKSLCNACGLRRRREEAKADKGLDTHKEKGNGERSSSEDVKNVLMFI