AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene72313

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene72313.t1 MTR_1g060610 100.000 149 0 0 1 149 1 149 4.81e-109 306
MS.gene72313.t1 MTR_3g080800 44.286 140 75 2 5 144 66 202 1.26e-28 105
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene72313.t1 AT4G35490 85.315 143 21 0 7 149 13 155 1.15e-91 263
MS.gene72313.t1 AT4G35490 85.315 143 21 0 7 149 13 155 1.15e-91 263
MS.gene72313.t1 AT1G32990 44.286 140 75 2 5 144 72 208 7.44e-28 103

Find 54 sgRNAs with CRISPR-Local

Find 54 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCATTTCTAAATCCATTAT+TGG 0.175466 1.4:+49690768 MS.gene72313:CDS
GTAACAGCCATTGGTGTATC+AGG 0.275383 1.4:-49690543 None:intergenic
CGATACCCGCAGCTTTCTTC+AGG 0.313010 1.4:-49690629 None:intergenic
GCTCCTGGCTGTACCAATAA+TGG 0.324875 1.4:-49690781 None:intergenic
ACAGTCTGATCCTTACTTGC+AGG 0.357839 1.4:+49690731 MS.gene72313:CDS
ACCAATAATGGATTTAGAAA+TGG 0.398795 1.4:-49690769 None:intergenic
GAAAGCTGCGGGTATCGAAT+TGG 0.398936 1.4:+49690635 MS.gene72313:CDS
GGAGGTGGCGGTCACATGAC+CGG 0.412632 1.4:-49690670 None:intergenic
ATTGTCGCTGCTACCACTTT+CGG 0.429301 1.4:-49690396 None:intergenic
AGTGGCATACCCTGCAAGTA+AGG 0.435747 1.4:-49690741 None:intergenic
AACGATGAGCGTTCCGAAAG+TGG 0.442624 1.4:+49690383 None:intergenic
CCTCCTGTGGGACCTGCGCT+AGG 0.444053 1.4:+49690456 MS.gene72313:CDS
CTCCAGCTGGAACTCTCAAC+CGG 0.454096 1.4:-49690419 None:intergenic
TCCAGCTGGAGGAGCACGTC+CGG 0.454983 1.4:+49690431 MS.gene72313:CDS
AGCACGTCCGGCGCCTCCTG+TGG 0.466575 1.4:+49690443 MS.gene72313:CDS
AAAGCTGCGGGTATCGAATT+GGG 0.473529 1.4:+49690636 MS.gene72313:CDS
AGTCTTTGCAGAAAGCCATA+AGG 0.492679 1.4:-49690494 None:intergenic
GCTGTTATTGTAACAGCCAT+TGG 0.492932 1.4:-49690552 None:intergenic
GGCGGTCACATGACCGGGAC+GGG 0.494244 1.4:-49690664 None:intergenic
TCAGTACCGACTGAACCTTA+TGG 0.497875 1.4:+49690479 MS.gene72313:CDS
AAGTGGTAGCAGCGACAATC+CGG 0.509428 1.4:+49690400 MS.gene72313:CDS
GCCGGACGTGCTCCTCCAGC+TGG 0.512277 1.4:-49690432 None:intergenic
GCACGTCCGGCGCCTCCTGT+GGG 0.517535 1.4:+49690444 MS.gene72313:CDS
CATACACGTGCCGAAGTGAC+AGG 0.517596 1.4:-49690692 None:intergenic
GAGGTGGCGGTCACATGACC+GGG 0.519759 1.4:-49690669 None:intergenic
CCGAAGTGACAGGGAGGTGG+CGG 0.522973 1.4:-49690682 None:intergenic
TGTTACAATAACAGCTTACA+AGG 0.549953 1.4:+49690560 MS.gene72313:CDS
TGACCTAGCGCAGGTCCCAC+AGG 0.552959 1.4:-49690459 None:intergenic
ATTGGTACAGCCAGGAGCAT+GGG 0.557515 1.4:+49690786 MS.gene72313:CDS
GCAGGTCCCACAGGAGGCGC+CGG 0.567732 1.4:-49690450 None:intergenic
TATTGGTACAGCCAGGAGCA+TGG 0.577587 1.4:+49690785 MS.gene72313:CDS
AATCCATTATTGGTACAGCC+AGG 0.580050 1.4:+49690778 MS.gene72313:CDS
CCGCCACCTCCCTGTCACTT+CGG 0.584871 1.4:+49690682 MS.gene72313:CDS
TGGTACCTGAAGAAAGCTGC+GGG 0.584881 1.4:+49690624 MS.gene72313:CDS
ATCCGGTTGAGAGTTCCAGC+TGG 0.592293 1.4:+49690417 MS.gene72313:CDS
CAGTCTGATCCTTACTTGCA+GGG 0.597928 1.4:+49690732 MS.gene72313:CDS
GTGCCGAAGTGACAGGGAGG+TGG 0.602083 1.4:-49690685 None:intergenic
TTAAATCTCCTTCCGTCTCG+TGG 0.602388 1.4:+49690604 MS.gene72313:CDS
TTCAGGTACCACGAGACGGA+AGG 0.605506 1.4:-49690612 None:intergenic
TGGCGGTCACATGACCGGGA+CGG 0.607191 1.4:-49690665 None:intergenic
TTTCTTCAGGTACCACGAGA+CGG 0.610355 1.4:-49690616 None:intergenic
AGTCGGTACTGACCTAGCGC+AGG 0.626095 1.4:-49690468 None:intergenic
GAATTGGGAAGTACCCGTCC+CGG 0.626450 1.4:+49690651 MS.gene72313:CDS
CCTAGCGCAGGTCCCACAGG+AGG 0.638505 1.4:-49690456 None:intergenic
ATACACGTGCCGAAGTGACA+GGG 0.645886 1.4:-49690691 None:intergenic
AGAAAGCCATAAGGTTCAGT+CGG 0.648161 1.4:-49690485 None:intergenic
TCTGCAAAGACTTCAACGCA+CGG 0.650245 1.4:+49690505 MS.gene72313:CDS
AGATTTAACAGTGAACTCAA+AGG 0.651355 1.4:-49690589 None:intergenic
GATTTAGAAATGGACTCAAG+TGG 0.655714 1.4:-49690759 None:intergenic
ATTCAAGCCTGATACACCAA+TGG 0.658568 1.4:+49690536 MS.gene72313:CDS
GTGGTACCTGAAGAAAGCTG+CGG 0.662466 1.4:+49690623 MS.gene72313:CDS
CGGTTGAGAGTTCCAGCTGG+AGG 0.663118 1.4:+49690420 MS.gene72313:CDS
GCACGTGTATGAGATCGCTA+AGG 0.664058 1.4:+49690704 MS.gene72313:CDS
CACGTGCCGAAGTGACAGGG+AGG 0.790794 1.4:-49690688 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TCCATTTCTAAATCCATTAT+TGG + chr1.4:49690768-49690787 MS.gene72313:CDS 25.0%
!!! ACCAATAATGGATTTAGAAA+TGG - chr1.4:49690772-49690791 None:intergenic 25.0%
AGATTTAACAGTGAACTCAA+AGG - chr1.4:49690592-49690611 None:intergenic 30.0%
TGTTACAATAACAGCTTACA+AGG + chr1.4:49690560-49690579 MS.gene72313:CDS 30.0%
! GATTTAGAAATGGACTCAAG+TGG - chr1.4:49690762-49690781 None:intergenic 35.0%
AATCCATTATTGGTACAGCC+AGG + chr1.4:49690778-49690797 MS.gene72313:CDS 40.0%
AGAAAGCCATAAGGTTCAGT+CGG - chr1.4:49690488-49690507 None:intergenic 40.0%
AGTCTTTGCAGAAAGCCATA+AGG - chr1.4:49690497-49690516 None:intergenic 40.0%
ATTCAAGCCTGATACACCAA+TGG + chr1.4:49690536-49690555 MS.gene72313:CDS 40.0%
GCTGTTATTGTAACAGCCAT+TGG - chr1.4:49690555-49690574 None:intergenic 40.0%
!!! AATTTTGATTCCCATGCTCC+TGG - chr1.4:49690799-49690818 None:intergenic 40.0%
ACAGTCTGATCCTTACTTGC+AGG + chr1.4:49690731-49690750 MS.gene72313:CDS 45.0%
ATTGTCGCTGCTACCACTTT+CGG - chr1.4:49690399-49690418 None:intergenic 45.0%
CAGTCTGATCCTTACTTGCA+GGG + chr1.4:49690732-49690751 MS.gene72313:CDS 45.0%
GTAACAGCCATTGGTGTATC+AGG - chr1.4:49690546-49690565 None:intergenic 45.0%
TCTGCAAAGACTTCAACGCA+CGG + chr1.4:49690505-49690524 MS.gene72313:CDS 45.0%
TTAAATCTCCTTCCGTCTCG+TGG + chr1.4:49690604-49690623 MS.gene72313:CDS 45.0%
TTTCTTCAGGTACCACGAGA+CGG - chr1.4:49690619-49690638 None:intergenic 45.0%
!! AAAGCTGCGGGTATCGAATT+GGG + chr1.4:49690636-49690655 MS.gene72313:CDS 45.0%
!! TCAGTACCGACTGAACCTTA+TGG + chr1.4:49690479-49690498 MS.gene72313:CDS 45.0%
AAGTGGTAGCAGCGACAATC+CGG + chr1.4:49690400-49690419 MS.gene72313:CDS 50.0%
AGTGGCATACCCTGCAAGTA+AGG - chr1.4:49690744-49690763 None:intergenic 50.0%
ATACACGTGCCGAAGTGACA+GGG - chr1.4:49690694-49690713 None:intergenic 50.0%
GCACGTGTATGAGATCGCTA+AGG + chr1.4:49690704-49690723 MS.gene72313:CDS 50.0%
GCTCCTGGCTGTACCAATAA+TGG - chr1.4:49690784-49690803 None:intergenic 50.0%
GTGGTACCTGAAGAAAGCTG+CGG + chr1.4:49690623-49690642 MS.gene72313:CDS 50.0%
TATTGGTACAGCCAGGAGCA+TGG + chr1.4:49690785-49690804 MS.gene72313:CDS 50.0%
TGGTACCTGAAGAAAGCTGC+GGG + chr1.4:49690624-49690643 MS.gene72313:CDS 50.0%
! ATTGGTACAGCCAGGAGCAT+GGG + chr1.4:49690786-49690805 MS.gene72313:CDS 50.0%
!! GAAAGCTGCGGGTATCGAAT+TGG + chr1.4:49690635-49690654 MS.gene72313:CDS 50.0%
ATCCGGTTGAGAGTTCCAGC+TGG + chr1.4:49690417-49690436 MS.gene72313:CDS 55.0%
CATACACGTGCCGAAGTGAC+AGG - chr1.4:49690695-49690714 None:intergenic 55.0%
CGATACCCGCAGCTTTCTTC+AGG - chr1.4:49690632-49690651 None:intergenic 55.0%
CTCCAGCTGGAACTCTCAAC+CGG - chr1.4:49690422-49690441 None:intergenic 55.0%
TTCAGGTACCACGAGACGGA+AGG - chr1.4:49690615-49690634 None:intergenic 55.0%
!! GAATTGGGAAGTACCCGTCC+CGG + chr1.4:49690651-49690670 MS.gene72313:CDS 55.0%
CGGTTGAGAGTTCCAGCTGG+AGG + chr1.4:49690420-49690439 MS.gene72313:CDS 60.0%
!! AGTCGGTACTGACCTAGCGC+AGG - chr1.4:49690471-49690490 None:intergenic 60.0%
CACGTGCCGAAGTGACAGGG+AGG - chr1.4:49690691-49690710 None:intergenic 65.0%
CCGAAGTGACAGGGAGGTGG+CGG - chr1.4:49690685-49690704 None:intergenic 65.0%
GTGCCGAAGTGACAGGGAGG+TGG - chr1.4:49690688-49690707 None:intergenic 65.0%
TGACCTAGCGCAGGTCCCAC+AGG - chr1.4:49690462-49690481 None:intergenic 65.0%
TGGCGGTCACATGACCGGGA+CGG - chr1.4:49690668-49690687 None:intergenic 65.0%
! CCGCCACCTCCCTGTCACTT+CGG + chr1.4:49690682-49690701 MS.gene72313:CDS 65.0%
! GAGGTGGCGGTCACATGACC+GGG - chr1.4:49690672-49690691 None:intergenic 65.0%
! GGAGGTGGCGGTCACATGAC+CGG - chr1.4:49690673-49690692 None:intergenic 65.0%
! TCCAGCTGGAGGAGCACGTC+CGG + chr1.4:49690431-49690450 MS.gene72313:CDS 65.0%
CCTAGCGCAGGTCCCACAGG+AGG - chr1.4:49690459-49690478 None:intergenic 70.0%
CCTCCTGTGGGACCTGCGCT+AGG + chr1.4:49690456-49690475 MS.gene72313:CDS 70.0%
GGCGGTCACATGACCGGGAC+GGG - chr1.4:49690667-49690686 None:intergenic 70.0%
AGCACGTCCGGCGCCTCCTG+TGG + chr1.4:49690443-49690462 MS.gene72313:CDS 75.0%
GCACGTCCGGCGCCTCCTGT+GGG + chr1.4:49690444-49690463 MS.gene72313:CDS 75.0%
GCCGGACGTGCTCCTCCAGC+TGG - chr1.4:49690435-49690454 None:intergenic 75.0%
! GCAGGTCCCACAGGAGGCGC+CGG - chr1.4:49690453-49690472 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 49690387 49690836 49690387 ID=MS.gene72313
chr1.4 mRNA 49690387 49690836 49690387 ID=MS.gene72313.t1;Parent=MS.gene72313
chr1.4 exon 49690387 49690836 49690387 ID=MS.gene72313.t1.exon1;Parent=MS.gene72313.t1
chr1.4 CDS 49690387 49690836 49690387 ID=cds.MS.gene72313.t1;Parent=MS.gene72313.t1
Gene Sequence

>MS.gene72313

ATGAGCGTTCCGAAAGTGGTAGCAGCGACAATCCGGTTGAGAGTTCCAGCTGGAGGAGCACGTCCGGCGCCTCCTGTGGGACCTGCGCTAGGTCAGTACCGACTGAACCTTATGGCTTTCTGCAAAGACTTCAACGCACGGACTCAGAAATTCAAGCCTGATACACCAATGGCTGTTACAATAACAGCTTACAAGGACAACACCTTTGAGTTCACTGTTAAATCTCCTTCCGTCTCGTGGTACCTGAAGAAAGCTGCGGGTATCGAATTGGGAAGTACCCGTCCCGGTCATGTGACCGCCACCTCCCTGTCACTTCGGCACGTGTATGAGATCGCTAAGGTGAAACAGTCTGATCCTTACTTGCAGGGTATGCCACTTGAGTCCATTTCTAAATCCATTATTGGTACAGCCAGGAGCATGGGAATCAAAATTGTCAAAGATCTTGAATGA
Protein sequence

>MS.gene72313.t1

MSVPKVVAATIRLRVPAGGARPAPPVGPALGQYRLNLMAFCKDFNARTQKFKPDTPMAVTITAYKDNTFEFTVKSPSVSWYLKKAAGIELGSTRPGHVTATSLSLRHVYEIAKVKQSDPYLQGMPLESISKSIIGTARSMGIKIVKDLE