AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene32997

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene32997.t1 MTR_1g016200 56.311 103 34 3 9 100 2 104 2.03e-24 90.1
MS.gene32997.t1 MTR_1g016170 62.500 48 15 1 56 100 187 234 4.86e-13 64.3
MS.gene32997.t1 MTR_7g112330 42.373 59 34 0 56 114 22 80 2.70e-11 57.0
MS.gene32997.t1 MTR_4g121110 48.276 58 25 2 54 111 28 80 5.24e-11 56.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene32997.t1 AT5G56860 49.231 65 29 1 25 89 203 263 6.23e-13 64.3
MS.gene32997.t1 AT4G26150 71.875 32 9 0 56 87 199 230 5.75e-11 58.5

Find 27 sgRNAs with CRISPR-Local

Find 40 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTTCTTTGTGGCTGGAAC+TGG 0.239072 1.1:-5927637 None:intergenic
AGTATTCGCCATTGCCCTTT+TGG 0.253039 1.1:-5927748 None:intergenic
ATGAGTATCAAGACCCTTAT+CGG 0.303482 1.1:-5928031 None:intergenic
ATACAAACACTACTCCTCTT+TGG 0.387924 1.1:+5927800 MS.gene32997:CDS
GGAAGAGGCAAAAGCCGATA+AGG 0.448770 1.1:+5928017 MS.gene32997:CDS
CAATCGAAACAAACCCTAGT+TGG 0.460017 1.1:-5927775 None:intergenic
TCTTGATACTCATAAGGAAA+AGG 0.465163 1.1:+5928041 MS.gene32997:CDS
TTGCCTCTTCCCTTCTTCGT+CGG 0.477939 1.1:-5928005 None:intergenic
CTTGATACTCATAAGGAAAA+GGG 0.489428 1.1:+5928042 MS.gene32997:CDS
TAAGGGTCTTGATACTCATA+AGG 0.492473 1.1:+5928035 MS.gene32997:CDS
ACTGAATACGAATACCCAAA+AGG 0.517161 1.1:+5927733 MS.gene32997:CDS
GAAGAGGCAAAAGCCGATAA+GGG 0.529120 1.1:+5928018 MS.gene32997:CDS
CTGAATACGAATACCCAAAA+GGG 0.529249 1.1:+5927734 MS.gene32997:CDS
ATGTGGACTCCGACGAAGAA+GGG 0.540307 1.1:+5927996 MS.gene32997:CDS
CTTTGGAGGAGTGATCCTAC+AGG 0.546346 1.1:+5927817 MS.gene32997:CDS
GGCGAATACTATATCCAACT+AGG 0.572160 1.1:+5927761 MS.gene32997:CDS
CATGTGGACTCCGACGAAGA+AGG 0.573346 1.1:+5927995 MS.gene32997:CDS
GAGTGATCCTACAGGTTCCA+AGG 0.583772 1.1:+5927825 MS.gene32997:CDS
ACTCCGACGAAGAAGGGAAG+AGG 0.589069 1.1:+5928002 MS.gene32997:CDS
CAAACACTACTCCTCTTTGG+AGG 0.592172 1.1:+5927803 MS.gene32997:CDS
GCGAATACTATATCCAACTA+GGG 0.606852 1.1:+5927762 MS.gene32997:CDS
CAGTCGTTGTGCAATGCATG+TGG 0.610062 1.1:+5927979 MS.gene32997:intron
ACGAATACCCAAAAGGGCAA+TGG 0.610371 1.1:+5927740 MS.gene32997:CDS
ACTCATAAGGAAAAGGGCAA+TGG 0.616678 1.1:+5928048 MS.gene32997:CDS
TGGCGAACGCTCATCATCTG+AGG 0.618644 1.1:+5928068 MS.gene32997:CDS
CTAATTACCTTGGAACCTGT+AGG 0.621221 1.1:-5927832 None:intergenic
GTAGGATCACTCCTCCAAAG+AGG 0.666474 1.1:-5927814 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAGTTAACAAGAAATATGT+TGG + chr1.1:5927954-5927973 MS.gene32997:intron 20.0%
!!! ACCAGTTTTTATTTTCTTTT+TGG - chr1.1:5927713-5927732 None:intergenic 20.0%
! GCCAAAAAGAAAATAAAAAC+TGG + chr1.1:5927709-5927728 MS.gene32997:CDS 25.0%
! TAGAGATTAACTAATTACCT+TGG - chr1.1:5927845-5927864 None:intergenic 25.0%
CTTGATACTCATAAGGAAAA+GGG + chr1.1:5928042-5928061 MS.gene32997:CDS 30.0%
TCTTGATACTCATAAGGAAA+AGG + chr1.1:5928041-5928060 MS.gene32997:CDS 30.0%
ACTGAATACGAATACCCAAA+AGG + chr1.1:5927733-5927752 MS.gene32997:CDS 35.0%
ATACAAACACTACTCCTCTT+TGG + chr1.1:5927800-5927819 MS.gene32997:CDS 35.0%
ATGAGTATCAAGACCCTTAT+CGG - chr1.1:5928034-5928053 None:intergenic 35.0%
CTGAATACGAATACCCAAAA+GGG + chr1.1:5927734-5927753 MS.gene32997:CDS 35.0%
GCGAATACTATATCCAACTA+GGG + chr1.1:5927762-5927781 MS.gene32997:CDS 35.0%
TAAGGGTCTTGATACTCATA+AGG + chr1.1:5928035-5928054 MS.gene32997:CDS 35.0%
!!! AGCAGCTTTTTTCTTCTTTG+TGG - chr1.1:5927650-5927669 None:intergenic 35.0%
ACTCATAAGGAAAAGGGCAA+TGG + chr1.1:5928048-5928067 MS.gene32997:CDS 40.0%
AGAAGAAAAAAGCTGCTGCT+AGG + chr1.1:5927653-5927672 MS.gene32997:CDS 40.0%
ATGAACCAAGAGTGAAAGCT+GGG - chr1.1:5927873-5927892 None:intergenic 40.0%
CAATCGAAACAAACCCTAGT+TGG - chr1.1:5927778-5927797 None:intergenic 40.0%
CTAATTACCTTGGAACCTGT+AGG - chr1.1:5927835-5927854 None:intergenic 40.0%
GAAGAAAAAAGCTGCTGCTA+GGG + chr1.1:5927654-5927673 MS.gene32997:CDS 40.0%
GGCGAATACTATATCCAACT+AGG + chr1.1:5927761-5927780 MS.gene32997:CDS 40.0%
!!! GCTTTTTTCTTCTTTGTGGC+TGG - chr1.1:5927646-5927665 None:intergenic 40.0%
ACGAATACCCAAAAGGGCAA+TGG + chr1.1:5927740-5927759 MS.gene32997:CDS 45.0%
CAAACACTACTCCTCTTTGG+AGG + chr1.1:5927803-5927822 MS.gene32997:CDS 45.0%
CATGAACCAAGAGTGAAAGC+TGG - chr1.1:5927874-5927893 None:intergenic 45.0%
GAAGAGGCAAAAGCCGATAA+GGG + chr1.1:5928018-5928037 MS.gene32997:CDS 45.0%
TGAACCAAGAGTGAAAGCTG+GGG - chr1.1:5927872-5927891 None:intergenic 45.0%
TTCTTCTTTGTGGCTGGAAC+TGG - chr1.1:5927640-5927659 None:intergenic 45.0%
! AGTATTCGCCATTGCCCTTT+TGG - chr1.1:5927751-5927770 None:intergenic 45.0%
! GTATTCGCCATTGCCCTTTT+GGG - chr1.1:5927750-5927769 None:intergenic 45.0%
ATGTGGACTCCGACGAAGAA+GGG + chr1.1:5927996-5928015 MS.gene32997:CDS 50.0%
CAGTCGTTGTGCAATGCATG+TGG + chr1.1:5927979-5927998 MS.gene32997:intron 50.0%
GAGTGATCCTACAGGTTCCA+AGG + chr1.1:5927825-5927844 MS.gene32997:CDS 50.0%
GGAAGAGGCAAAAGCCGATA+AGG + chr1.1:5928017-5928036 MS.gene32997:CDS 50.0%
GTAGGATCACTCCTCCAAAG+AGG - chr1.1:5927817-5927836 None:intergenic 50.0%
TTCTCCCCAGCTTTCACTCT+TGG + chr1.1:5927865-5927884 MS.gene32997:intron 50.0%
TTGCCTCTTCCCTTCTTCGT+CGG - chr1.1:5928008-5928027 None:intergenic 50.0%
! CTTTGGAGGAGTGATCCTAC+AGG + chr1.1:5927817-5927836 MS.gene32997:CDS 50.0%
ACTCCGACGAAGAAGGGAAG+AGG + chr1.1:5928002-5928021 MS.gene32997:CDS 55.0%
CATGTGGACTCCGACGAAGA+AGG + chr1.1:5927995-5928014 MS.gene32997:CDS 55.0%
TGGCGAACGCTCATCATCTG+AGG + chr1.1:5928068-5928087 MS.gene32997:CDS 55.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 5927616 5928122 5927616 ID=MS.gene32997
chr1.1 mRNA 5927616 5928122 5927616 ID=MS.gene32997.t1;Parent=MS.gene32997
chr1.1 exon 5927616 5927846 5927616 ID=MS.gene32997.t1.exon1;Parent=MS.gene32997.t1
chr1.1 CDS 5927616 5927846 5927616 ID=cds.MS.gene32997.t1;Parent=MS.gene32997.t1
chr1.1 exon 5927982 5928122 5927982 ID=MS.gene32997.t1.exon2;Parent=MS.gene32997.t1
chr1.1 CDS 5927982 5928122 5927982 ID=cds.MS.gene32997.t1;Parent=MS.gene32997.t1
Gene Sequence

>MS.gene32997

ATGAGAGTAAGTAACGATGATCCAGTTCCAGCCACAAAGAAGAAAAAAGCTGCTGCTAGGGCTACAAAAAAGAAGAAAACAGCTGCTAGTGCTGCCAAAAAGAAAATAAAAACTGGTACTGAATACGAATACCCAAAAGGGCAATGGCGAATACTATATCCAACTAGGGTTTGTTTCGATTGCAATACAAACACTACTCCTCTTTGGAGGAGTGATCCTACAGGTTCCAAGGTAATTAGTTAATCTCTATTCTCCCCAGCTTTCACTCTTGGTTCATGCAAAAGTGTTATTCTATACTTATACAATGATTAATAATTTGAATATCTAGTTATATATATATAGTTAACAAGAAATATGTTGGTGCAGTCGTTGTGCAATGCATGTGGACTCCGACGAAGAAGGGAAGAGGCAAAAGCCGATAAGGGTCTTGATACTCATAAGGAAAAGGGCAATGGCGAACGCTCATCATCTGAGGATGTGAAGATTAATGTTTTAATGTTCATCTGA
Protein sequence

>MS.gene32997.t1

MRVSNDDPVPATKKKKAAARATKKKKTAASAAKKKIKTGTEYEYPKGQWRILYPTRVCFDCNTNTTPLWRSDPTGSKSLCNACGLRRRREEAKADKGLDTHKEKGNGERSSSEDVKINVLMFI