AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene24058

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24058.t1 MTR_2g084220 86.420 81 11 0 5 85 3 83 1.75e-45 143
MS.gene24058.t1 MTR_4g080090 76.471 85 20 0 1 85 1 85 5.96e-37 121
MS.gene24058.t1 MTR_6g018330 54.762 84 22 1 2 85 19 86 1.71e-20 79.7
MS.gene24058.t1 MTR_4g103930 78.947 38 8 0 32 69 45 82 3.20e-12 58.9
MS.gene24058.t1 MTR_6g086280 42.424 66 38 0 4 69 9 74 8.64e-12 57.4
MS.gene24058.t1 MTR_6g086280 42.424 66 38 0 4 69 9 74 9.66e-12 57.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24058.t1 AT3G58680 64.706 85 30 0 1 85 1 85 1.52e-37 123
MS.gene24058.t1 AT2G42680 65.882 85 29 0 1 85 1 85 4.23e-36 119
MS.gene24058.t1 AT3G24500 40.244 82 47 1 5 84 7 88 9.46e-11 55.1

Find 24 sgRNAs with CRISPR-Local

Find 27 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTCTTCATGGTTTCAATAT+CGG 0.263054 1.4:-55050974 None:intergenic
CAAAGAATTTAGCTCATGTT+TGG 0.307412 1.4:+55051067 MS.gene24058:CDS
CCCAACTGAACTCAAGAAAA+AGG 0.324733 1.4:+55051092 MS.gene24058:CDS
CGCAGCATAATGTTTCTTCA+TGG 0.338481 1.4:-55050986 None:intergenic
TCGGGCCTGTTTCACAAGAT+TGG 0.356885 1.4:+55050866 MS.gene24058:CDS
GGTTCCCAATCTTGTGAAAC+AGG 0.382368 1.4:-55050871 None:intergenic
AAAGAATTTAGCTCATGTTT+GGG 0.398502 1.4:+55051068 MS.gene24058:CDS
CGGGCCTGTTTCACAAGATT+GGG 0.408200 1.4:+55050867 MS.gene24058:CDS
CATTCAACCATGTCAGGAAT+CGG 0.423504 1.4:+55050847 None:intergenic
GAGCTAAATTCTTTGTATCC+TGG 0.425930 1.4:-55051059 None:intergenic
GTCAATGCCACTCGCCGTGC+CGG 0.443823 1.4:+55050949 MS.gene24058:CDS
GCACTTCATTAAACACTAAG+AGG 0.463082 1.4:+55051031 MS.gene24058:CDS
TCAAACCATTCAACCATGTC+AGG 0.470982 1.4:+55050841 None:intergenic
ACTTTCTTGCGGAGAACGAC+GGG 0.502022 1.4:-55050892 None:intergenic
GTTTAATGAAGTGCTGCTAC+AGG 0.504584 1.4:-55051022 None:intergenic
ATTCAACCATGTCAGGAATC+GGG 0.523627 1.4:+55050848 None:intergenic
CATGGTTTCAATATCGGCAC+CGG 0.541173 1.4:-55050968 None:intergenic
ATCGGCACCGGCACGGCGAG+TGG 0.549171 1.4:-55050956 None:intergenic
AACAGGCCCGATTCCTGACA+TGG 0.561106 1.4:-55050854 None:intergenic
AACTTTCTTGCGGAGAACGA+CGG 0.584018 1.4:-55050893 None:intergenic
AAACACTAAGAGGCTAAACC+AGG 0.598430 1.4:+55051041 MS.gene24058:CDS
TTTCAATATCGGCACCGGCA+CGG 0.609948 1.4:-55050963 None:intergenic
AGGCGGTGGGAACTTTCTTG+CGG 0.612045 1.4:-55050903 None:intergenic
TAATGAAGTGCTGCTACAGG+CGG 0.634944 1.4:-55051019 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TTTCTTCATGGTTTCAATAT+CGG - chr1.4:55050977-55050996 None:intergenic 25.0%
!! AAAGAATTTAGCTCATGTTT+GGG + chr1.4:55051068-55051087 MS.gene24058:CDS 25.0%
! CAAAGAATTTAGCTCATGTT+TGG + chr1.4:55051067-55051086 MS.gene24058:CDS 30.0%
GAGCTAAATTCTTTGTATCC+TGG - chr1.4:55051062-55051081 None:intergenic 35.0%
GCACTTCATTAAACACTAAG+AGG + chr1.4:55051031-55051050 MS.gene24058:CDS 35.0%
! CCTTTTTCTTGAGTTCAGTT+GGG - chr1.4:55051095-55051114 None:intergenic 35.0%
! TCCTTTTTCTTGAGTTCAGT+TGG - chr1.4:55051096-55051115 None:intergenic 35.0%
AAACACTAAGAGGCTAAACC+AGG + chr1.4:55051041-55051060 MS.gene24058:CDS 40.0%
CCCAACTGAACTCAAGAAAA+AGG + chr1.4:55051092-55051111 MS.gene24058:CDS 40.0%
CGCAGCATAATGTTTCTTCA+TGG - chr1.4:55050989-55051008 None:intergenic 40.0%
!! GACAGCTTTGTCATCTTTTC+TGG - chr1.4:55050932-55050951 None:intergenic 40.0%
!! GTTTAATGAAGTGCTGCTAC+AGG - chr1.4:55051025-55051044 None:intergenic 40.0%
!! TTTGTCATCTTTTCTGGCAC+AGG - chr1.4:55050926-55050945 None:intergenic 40.0%
AACTTTCTTGCGGAGAACGA+CGG - chr1.4:55050896-55050915 None:intergenic 45.0%
CATGGTTTCAATATCGGCAC+CGG - chr1.4:55050971-55050990 None:intergenic 45.0%
GGTTCCCAATCTTGTGAAAC+AGG - chr1.4:55050874-55050893 None:intergenic 45.0%
!! TAATGAAGTGCTGCTACAGG+CGG - chr1.4:55051022-55051041 None:intergenic 45.0%
ACTTTCTTGCGGAGAACGAC+GGG - chr1.4:55050895-55050914 None:intergenic 50.0%
CGGGCCTGTTTCACAAGATT+GGG + chr1.4:55050867-55050886 MS.gene24058:CDS 50.0%
TCGGGCCTGTTTCACAAGAT+TGG + chr1.4:55050866-55050885 MS.gene24058:CDS 50.0%
!! GTCATCTTTTCTGGCACAGG+CGG - chr1.4:55050923-55050942 None:intergenic 50.0%
!! TTTCAATATCGGCACCGGCA+CGG - chr1.4:55050966-55050985 None:intergenic 50.0%
AGGCGGTGGGAACTTTCTTG+CGG - chr1.4:55050906-55050925 None:intergenic 55.0%
!! ATCTTTTCTGGCACAGGCGG+TGG - chr1.4:55050920-55050939 None:intergenic 55.0%
!! TCTTTTCTGGCACAGGCGGT+GGG - chr1.4:55050919-55050938 None:intergenic 55.0%
GTCAATGCCACTCGCCGTGC+CGG + chr1.4:55050949-55050968 MS.gene24058:CDS 65.0%
!! ATCGGCACCGGCACGGCGAG+TGG - chr1.4:55050959-55050978 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 55050856 55051131 55050856 ID=MS.gene24058
chr1.4 mRNA 55050856 55051131 55050856 ID=MS.gene24058.t1;Parent=MS.gene24058
chr1.4 exon 55050856 55051131 55050856 ID=MS.gene24058.t1.exon1;Parent=MS.gene24058.t1
chr1.4 CDS 55050856 55051131 55050856 ID=cds.MS.gene24058.t1;Parent=MS.gene24058.t1
Gene Sequence

>MS.gene24058

ATGTCAGGAATCGGGCCTGTTTCACAAGATTGGGAACCCGTCGTTCTCCGCAAGAAAGTTCCCACCGCCTGTGCCAGAAAAGATGACAAAGCTGTCAATGCCACTCGCCGTGCCGGTGCCGATATTGAAACCATGAAGAAACATTATGCTGCGACAAACAATGCCGCCTGTAGCAGCACTTCATTAAACACTAAGAGGCTAAACCAGGATACAAAGAATTTAGCTCATGTTTGGGTCCCAACTGAACTCAAGAAAAAGGAAAATCGAAAAATATGA
Protein sequence

>MS.gene24058.t1

MSGIGPVSQDWEPVVLRKKVPTACARKDDKAVNATRRAGADIETMKKHYAATNNAACSSTSLNTKRLNQDTKNLAHVWVPTELKKKENRKI