AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0042550


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0042550 MtrunA17_Chr1g0150771 100.000 93 0 0 1 93 378 470 3.95e-63 199
Msa0042550 MtrunA17_Chr4g0070891 70.000 90 26 1 3 92 331 419 4.20e-41 140
Msa0042550 MtrunA17_Chr2g0299761 81.356 59 11 0 36 94 1 59 1.14e-33 112
Msa0042550 MtrunA17_Chr1g0212591 36.275 102 49 2 3 88 232 333 3.83e-13 63.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0042550 AT5G12010.1 79.570 93 19 0 1 93 345 437 2.42e-51 168
Msa0042550 AT4G29780.1 68.478 92 29 0 1 92 383 474 7.38e-41 140

Find 18 sgRNAs with CRISPR-Local

Find 22 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTTGGATTGTTGGTAGTTC+AGG 0.230857 1_1:+73438843 Msa0042550:CDS
TAGTTCAGGGTATCCTTTAA+TGG 0.269828 1_1:+73438857 Msa0042550:CDS
CTCAAAGGTGTTTGGATTGT+TGG 0.301353 1_1:+73438834 Msa0042550:CDS
AGGGTATCCTTTAATGGATT+GGG 0.331257 1_1:+73438863 Msa0042550:CDS
ACTAAAACCCAATCCATTAA+AGG 0.331503 1_1:-73438870 None:intergenic
GAGGACTTCTCAAAGGTGTT+TGG 0.343408 1_1:+73438826 Msa0042550:CDS
CAGGGTATCCTTTAATGGAT+TGG 0.376667 1_1:+73438862 Msa0042550:CDS
GGTGGTCTTGTTTGCAGAAA+AGG 0.390719 1_1:+73438997 Msa0042550:CDS
TTTGGATTGTTGGTAGTTCA+GGG 0.411269 1_1:+73438844 Msa0042550:CDS
ATACTCAACAAAATCTTACT+TGG 0.425165 1_1:+73438898 Msa0042550:CDS
CATGGTTTCAATGAGAAGAT+TGG 0.432259 1_1:+73438927 Msa0042550:CDS
GATGCATTTGCTAGATTGAA+AGG 0.474433 1_1:+73438972 Msa0042550:CDS
TCTCACAAATGTTAAGCTAC+TGG 0.493745 1_1:-73439044 None:intergenic
CATTTGCTAGATTGAAAGGT+AGG 0.539789 1_1:+73438976 Msa0042550:CDS
TTTCAAAGGGCTAATAATGG+AGG 0.561620 1_1:+73438807 Msa0042550:CDS
AATCTTACTTGGACACAACA+TGG 0.563523 1_1:+73438909 Msa0042550:CDS
AATAATGGAGGACTTCTCAA+AGG 0.617005 1_1:+73438819 Msa0042550:CDS
TTGCTAGATTGAAAGGTAGG+TGG 0.638704 1_1:+73438979 Msa0042550:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTAAGATTTTGTTGAGTATA+AGG - chr1_1:73438897-73438916 None:intergenic 25.0%
! ATACTCAACAAAATCTTACT+TGG + chr1_1:73438898-73438917 Msa0042550:CDS 25.0%
! TTTTCTAACACTTGATCATC+AGG - chr1_1:73438777-73438796 None:intergenic 30.0%
!!! AAAAATCAGCGCTTTTTCAA+AGG + chr1_1:73438793-73438812 Msa0042550:CDS 30.0%
!!! AAAATCAGCGCTTTTTCAAA+GGG + chr1_1:73438794-73438813 Msa0042550:CDS 30.0%
!!! CTTTTTCAAAGGGCTAATAA+TGG + chr1_1:73438804-73438823 Msa0042550:CDS 30.0%
ACTAAAACCCAATCCATTAA+AGG - chr1_1:73438873-73438892 None:intergenic 30.0%
TTTCAAAGGGCTAATAATGG+AGG + chr1_1:73438807-73438826 Msa0042550:CDS 35.0%
! AATAATGGAGGACTTCTCAA+AGG + chr1_1:73438819-73438838 Msa0042550:CDS 35.0%
!! TTTGGATTGTTGGTAGTTCA+GGG + chr1_1:73438844-73438863 Msa0042550:CDS 35.0%
! TAGTTCAGGGTATCCTTTAA+TGG + chr1_1:73438857-73438876 Msa0042550:CDS 35.0%
!! AGGGTATCCTTTAATGGATT+GGG + chr1_1:73438863-73438882 Msa0042550:CDS 35.0%
AATCTTACTTGGACACAACA+TGG + chr1_1:73438909-73438928 Msa0042550:CDS 35.0%
CATGGTTTCAATGAGAAGAT+TGG + chr1_1:73438927-73438946 Msa0042550:CDS 35.0%
! GATGCATTTGCTAGATTGAA+AGG + chr1_1:73438972-73438991 Msa0042550:CDS 35.0%
! CATTTGCTAGATTGAAAGGT+AGG + chr1_1:73438976-73438995 Msa0042550:CDS 35.0%
!! CTCAAAGGTGTTTGGATTGT+TGG + chr1_1:73438834-73438853 Msa0042550:CDS 40.0%
!! GTTTGGATTGTTGGTAGTTC+AGG + chr1_1:73438843-73438862 Msa0042550:CDS 40.0%
! CAGGGTATCCTTTAATGGAT+TGG + chr1_1:73438862-73438881 Msa0042550:CDS 40.0%
TTGCTAGATTGAAAGGTAGG+TGG + chr1_1:73438979-73438998 Msa0042550:CDS 40.0%
!! GAGGACTTCTCAAAGGTGTT+TGG + chr1_1:73438826-73438845 Msa0042550:CDS 45.0%
!! GGTGGTCTTGTTTGCAGAAA+AGG + chr1_1:73438997-73439016 Msa0042550:CDS 45.0%
Chromosome Type Strat End Strand Name
chr1_1 gene 73438771 73439055 73438771 ID=Msa0042550;Name=Msa0042550
chr1_1 mRNA 73438771 73439055 73438771 ID=Msa0042550-mRNA-1;Parent=Msa0042550;Name=Msa0042550-mRNA-1;_AED=0.14;_eAED=0.14;_QI=0|-1|0|1|-1|1|1|0|94
chr1_1 exon 73438771 73439055 73438771 ID=Msa0042550-mRNA-1:exon:24584;Parent=Msa0042550-mRNA-1
chr1_1 CDS 73438771 73439055 73438771 ID=Msa0042550-mRNA-1:cds;Parent=Msa0042550-mRNA-1
Gene Sequence

>Msa0042550

ATGCCTGATGATCAAGTGTTAGAAAAATCAGCGCTTTTTCAAAGGGCTAATAATGGAGGACTTCTCAAAGGTGTTTGGATTGTTGGTAGTTCAGGGTATCCTTTAATGGATTGGGTTTTAGTACCTTATACTCAACAAAATCTTACTTGGACACAACATGGTTTCAATGAGAAGATTGGTGAGATACAAAAAGTTGCTAAAGATGCATTTGCTAGATTGAAAGGTAGGTGGTCTTGTTTGCAGAAAAGGACTGAAGTTAAGCTACAAGATTTGCCAGTAGCTTAA

Protein sequence

>Msa0042550

MPDDQVLEKSALFQRANNGGLLKGVWIVGSSGYPLMDWVLVPYTQQNLTWTQHGFNEKIGEIQKVAKDAFARLKGRWSCLQKRTEVKLQDLPVA*