AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene039072

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene039072.t1 MTR_1g058250 96.552 116 4 0 1 116 1 116 2.47e-78 228
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene039072.t1 AT5G04800 80.292 137 25 2 1 136 1 136 3.96e-74 218
MS.gene039072.t1 AT5G04800 80.292 137 25 2 1 136 1 136 3.96e-74 218
MS.gene039072.t1 AT5G04800 80.292 137 25 2 1 136 1 136 3.96e-74 218
MS.gene039072.t1 AT5G04800 80.292 137 25 2 1 136 1 136 3.96e-74 218
MS.gene039072.t1 AT2G05220 79.412 136 27 1 1 136 1 135 1.27e-73 216
MS.gene039072.t1 AT2G05220 79.412 136 27 1 1 136 1 135 1.27e-73 216
MS.gene039072.t1 AT2G04390 80.292 137 25 2 1 136 1 136 8.45e-73 214
MS.gene039072.t1 AT3G10610 79.699 133 26 1 1 133 1 132 1.38e-71 211

Find 41 sgRNAs with CRISPR-Local

Find 41 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAACAACAACACCGGGAATC+TGG 0.255977 2.4:+26674473 None:intergenic
AGAGGATTTCTTCACGGTTT+TGG 0.259892 2.4:+26674792 None:intergenic
CTTCTTGTTCGTGTGGAAAT+CGG 0.265901 2.4:+26674732 None:intergenic
GATTCCCGGTGTTGTTGTTC+AGG 0.304413 2.4:-26674470 MS.gene039072:CDS
CTTCCAACACCACCAGTAAC+AGG 0.324593 2.4:+26674424 None:intergenic
CAGCAGCAGATCCCTGTTAC+TGG 0.358701 2.4:-26674436 MS.gene039072:CDS
TTGTTACGAAGACGCTTTGA+TGG 0.364180 2.4:+26674685 None:intergenic
ACAGGGATCTGCTGCTGAAC+AGG 0.364890 2.4:+26674442 None:intergenic
CTTGGTATGTCCCAGATTCC+CGG 0.382777 2.4:-26674484 MS.gene039072:CDS
CTTGACATGCTTGCTGCTCT+TGG 0.389228 2.4:-26674502 MS.gene039072:CDS
CTCAATATAGTCGGTCCTAA+TGG 0.392260 2.4:+26674540 None:intergenic
TTCTTGTTCGTGTGGAAATC+GGG 0.406221 2.4:+26674733 None:intergenic
TTCCTGATGTTTCTGCCATT+AGG 0.411319 2.4:-26674555 MS.gene039072:CDS
TCTCATGAAGCGTATTCAAA+AGG 0.441131 2.4:-26674641 MS.gene039072:CDS
TTCAATGAAATTCCACGAAC+AGG 0.443778 2.4:+26674616 None:intergenic
CGACTATATTGAGGTTGATA+AGG 0.451902 2.4:-26674530 MS.gene039072:CDS
AACAACAACACCGGGAATCT+GGG 0.464609 2.4:+26674474 None:intergenic
GTCCTAATGGCAGAAACATC+AGG 0.475552 2.4:+26674553 None:intergenic
ATCCCTGTTACTGGTGGTGT+TGG 0.478633 2.4:-26674427 MS.gene039072:CDS
GTGGAAATCGGGTGTCATCT+TGG 0.489567 2.4:+26674744 None:intergenic
CGACGATCTTCTTGTTCGTG+TGG 0.496948 2.4:+26674725 None:intergenic
GGAGGAGCGTGAGCGTCGTA+TGG 0.521163 2.4:-26674584 MS.gene039072:CDS
ATTCAAAAGGGACCTGTTCG+TGG 0.521534 2.4:-26674628 MS.gene039072:CDS
TTTGGTTCGGACTCGTCCCA+TGG 0.523667 2.4:+26674810 None:intergenic
TTGACGAGAGGATTTCTTCA+CGG 0.526494 2.4:+26674786 None:intergenic
CTCATGAAGCGTATTCAAAA+GGG 0.527634 2.4:-26674640 MS.gene039072:CDS
CGTCTTCGTAACAAGATCGC+TGG 0.539364 2.4:-26674676 MS.gene039072:CDS
CATTAGGACCGACTATATTG+AGG 0.545899 2.4:-26674539 MS.gene039072:CDS
CTGTTACTGGTGGTGTTGGA+AGG 0.556457 2.4:-26674423 MS.gene039072:CDS
CAAGAGCAGCAAGCATGTCA+AGG 0.564418 2.4:+26674503 None:intergenic
CTTATCAACCTCAATATAGT+CGG 0.565136 2.4:+26674531 None:intergenic
TTCATTGAAGCTGCAAGAGG+AGG 0.567846 2.4:-26674602 MS.gene039072:CDS
TTACTGGTGGTGTTGGAAGG+AGG 0.588210 2.4:-26674420 MS.gene039072:CDS
AATACGCTTCATGAGATGAG+TGG 0.589822 2.4:+26674648 None:intergenic
ATCAACCTGAACAACAACAC+CGG 0.603304 2.4:+26674465 None:intergenic
CAGCAGATCCCTGTTACTGG+TGG 0.604301 2.4:-26674433 MS.gene039072:CDS
AAGAGCAGCAAGCATGTCAA+GGG 0.613477 2.4:+26674504 None:intergenic
TCAACCTGAACAACAACACC+GGG 0.615929 2.4:+26674466 None:intergenic
TTCCAACACCACCAGTAACA+GGG 0.631505 2.4:+26674425 None:intergenic
AATTTCATTGAAGCTGCAAG+AGG 0.634258 2.4:-26674605 MS.gene039072:CDS
ACGCTCAATGACTTGACGAG+AGG 0.686494 2.4:+26674774 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
CTTATCAACCTCAATATAGT+CGG + chr2.4:26674694-26674713 None:intergenic 30.0%
AATTTCATTGAAGCTGCAAG+AGG - chr2.4:26674617-26674636 MS.gene039072:CDS 35.0%
CTCATGAAGCGTATTCAAAA+GGG - chr2.4:26674582-26674601 MS.gene039072:CDS 35.0%
TCTCATGAAGCGTATTCAAA+AGG - chr2.4:26674581-26674600 MS.gene039072:CDS 35.0%
TTCAATGAAATTCCACGAAC+AGG + chr2.4:26674609-26674628 None:intergenic 35.0%
!! CGACTATATTGAGGTTGATA+AGG - chr2.4:26674692-26674711 MS.gene039072:CDS 35.0%
!!! ATTTCTTCACGGTTTTGGTT+CGG + chr2.4:26674428-26674447 None:intergenic 35.0%
AATACGCTTCATGAGATGAG+TGG + chr2.4:26674577-26674596 None:intergenic 40.0%
ATCAACCTGAACAACAACAC+CGG + chr2.4:26674760-26674779 None:intergenic 40.0%
CATTAGGACCGACTATATTG+AGG - chr2.4:26674683-26674702 MS.gene039072:CDS 40.0%
CTCAATATAGTCGGTCCTAA+TGG + chr2.4:26674685-26674704 None:intergenic 40.0%
CTTCTTGTTCGTGTGGAAAT+CGG + chr2.4:26674493-26674512 None:intergenic 40.0%
TTCTTGTTCGTGTGGAAATC+GGG + chr2.4:26674492-26674511 None:intergenic 40.0%
TTGACGAGAGGATTTCTTCA+CGG + chr2.4:26674439-26674458 None:intergenic 40.0%
TTGTTACGAAGACGCTTTGA+TGG + chr2.4:26674540-26674559 None:intergenic 40.0%
! AGAGGATTTCTTCACGGTTT+TGG + chr2.4:26674433-26674452 None:intergenic 40.0%
! TTCCTGATGTTTCTGCCATT+AGG - chr2.4:26674667-26674686 MS.gene039072:CDS 40.0%
AACAACAACACCGGGAATCT+GGG + chr2.4:26674751-26674770 None:intergenic 45.0%
AAGAGCAGCAAGCATGTCAA+GGG + chr2.4:26674721-26674740 None:intergenic 45.0%
ATTCAAAAGGGACCTGTTCG+TGG - chr2.4:26674594-26674613 MS.gene039072:CDS 45.0%
GTCCTAATGGCAGAAACATC+AGG + chr2.4:26674672-26674691 None:intergenic 45.0%
TCAACCTGAACAACAACACC+GGG + chr2.4:26674759-26674778 None:intergenic 45.0%
TTCATTGAAGCTGCAAGAGG+AGG - chr2.4:26674620-26674639 MS.gene039072:CDS 45.0%
TTCCAACACCACCAGTAACA+GGG + chr2.4:26674800-26674819 None:intergenic 45.0%
ACGCTCAATGACTTGACGAG+AGG + chr2.4:26674451-26674470 None:intergenic 50.0%
CAAGAGCAGCAAGCATGTCA+AGG + chr2.4:26674722-26674741 None:intergenic 50.0%
CGACGATCTTCTTGTTCGTG+TGG + chr2.4:26674500-26674519 None:intergenic 50.0%
CGTCTTCGTAACAAGATCGC+TGG - chr2.4:26674546-26674565 MS.gene039072:CDS 50.0%
CTTCCAACACCACCAGTAAC+AGG + chr2.4:26674801-26674820 None:intergenic 50.0%
CTTGGTATGTCCCAGATTCC+CGG - chr2.4:26674738-26674757 MS.gene039072:CDS 50.0%
GAACAACAACACCGGGAATC+TGG + chr2.4:26674752-26674771 None:intergenic 50.0%
! ATCCCTGTTACTGGTGGTGT+TGG - chr2.4:26674795-26674814 MS.gene039072:CDS 50.0%
! CTGTTACTGGTGGTGTTGGA+AGG - chr2.4:26674799-26674818 MS.gene039072:CDS 50.0%
! CTTGACATGCTTGCTGCTCT+TGG - chr2.4:26674720-26674739 MS.gene039072:CDS 50.0%
! GTGGAAATCGGGTGTCATCT+TGG + chr2.4:26674481-26674500 None:intergenic 50.0%
! TTACTGGTGGTGTTGGAAGG+AGG - chr2.4:26674802-26674821 MS.gene039072:CDS 50.0%
!! GATTCCCGGTGTTGTTGTTC+AGG - chr2.4:26674752-26674771 MS.gene039072:CDS 50.0%
ACAGGGATCTGCTGCTGAAC+AGG + chr2.4:26674783-26674802 None:intergenic 55.0%
CAGCAGATCCCTGTTACTGG+TGG - chr2.4:26674789-26674808 MS.gene039072:CDS 55.0%
CAGCAGCAGATCCCTGTTAC+TGG - chr2.4:26674786-26674805 MS.gene039072:CDS 55.0%
! GGAGGAGCGTGAGCGTCGTA+TGG - chr2.4:26674638-26674657 MS.gene039072:CDS 65.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 26674414 26674830 26674414 ID=MS.gene039072
chr2.4 mRNA 26674414 26674830 26674414 ID=MS.gene039072.t1;Parent=MS.gene039072
chr2.4 exon 26674414 26674830 26674414 ID=MS.gene039072.t1.exon1;Parent=MS.gene039072.t1
chr2.4 CDS 26674414 26674830 26674414 ID=cds.MS.gene039072.t1;Parent=MS.gene039072.t1
Gene Sequence

>MS.gene039072

ATGGGACGAGTCCGAACCAAAACCGTGAAGAAATCCTCTCGTCAAGTCATTGAGCGTTATTACTCCAAGATGACACCCGATTTCCACACGAACAAGAAGATCGTCGAAGAAGTTGCTTTGATACCATCAAAGCGTCTTCGTAACAAGATCGCTGGTTTCTCCACTCATCTCATGAAGCGTATTCAAAAGGGACCTGTTCGTGGAATTTCATTGAAGCTGCAAGAGGAGGAGCGTGAGCGTCGTATGGATTTCGTTCCTGATGTTTCTGCCATTAGGACCGACTATATTGAGGTTGATAAGGAAACCCTTGACATGCTTGCTGCTCTTGGTATGTCCCAGATTCCCGGTGTTGTTGTTCAGGTTGATCCTGTTCAGCAGCAGATCCCTGTTACTGGTGGTGTTGGAAGGAGGTTTTAA
Protein sequence

>MS.gene039072.t1

MGRVRTKTVKKSSRQVIERYYSKMTPDFHTNKKIVEEVALIPSKRLRNKIAGFSTHLMKRIQKGPVRGISLKLQEEERERRMDFVPDVSAIRTDYIEVDKETLDMLAALGMSQIPGVVVQVDPVQQQIPVTGGVGRRF