AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene24696

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24696.t1 MTR_7g104870 98.113 106 2 0 1 106 51 156 6.83e-74 216
MS.gene24696.t1 MTR_1g112020 54.206 107 48 1 1 106 1 107 2.60e-38 124
MS.gene24696.t1 MTR_1g112040 55.140 107 47 1 1 106 1 107 9.06e-38 123
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24696.t1 AT4G18590 58.491 106 44 0 1 106 1 106 2.64e-46 144
MS.gene24696.t1 AT3G52630 55.140 107 47 1 1 106 1 107 7.44e-42 133
MS.gene24696.t1 AT3G52630 55.140 107 47 1 1 106 1 107 7.44e-42 133

Find 22 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACCCTTCTTCCGACATAAA+AGG 0.241109 7.3:+9644826 None:intergenic
ACAAGGACTGCAGGGCTTAA+TGG 0.275580 7.3:+9644866 None:intergenic
GAGAAGCAGTTGATTGTAAA+AGG 0.288767 7.3:-9644743 MS.gene24696:CDS
ACCAACTTTGGTGATGAAAT+TGG 0.344480 7.3:-9644638 MS.gene24696:intron
TTGCAAGCTGACATAGCTTA+TGG 0.355631 7.3:+9644432 None:intergenic
GGTCCATAACTCAGCTTTGA+TGG 0.369681 7.3:+9644658 None:intergenic
ACAATCAACTGCTTCTCATC+TGG 0.376539 7.3:+9644749 None:intergenic
TCTGACGCTCTAGCCGTCAT+TGG 0.414293 7.3:-9644779 MS.gene24696:CDS
ACCAATTTCATCACCAAAGT+TGG 0.430140 7.3:+9644637 None:intergenic
ACAAAACTTGTAAGAGGAGC+AGG 0.439485 7.3:+9644713 None:intergenic
ACTTCTACAAAACTTGTAAG+AGG 0.459678 7.3:+9644707 None:intergenic
GCTGAGTTATGGACCAACTT+TGG 0.463853 7.3:-9644650 MS.gene24696:CDS
TCTGCATTGACAAGGACTGC+AGG 0.468536 7.3:+9644857 None:intergenic
ACCCTTCTTCCGACATAAAA+GGG 0.468915 7.3:+9644827 None:intergenic
AAGCTATGTCAGCTTGCAAA+TGG 0.472567 7.3:-9644428 MS.gene24696:CDS
AGTCCATCAAAGCTGAGTTA+TGG 0.498331 7.3:-9644661 MS.gene24696:CDS
AAGGGTTCGTACAGTGATGC+AGG 0.527340 7.3:-9644810 MS.gene24696:CDS
CTGCATTGACAAGGACTGCA+GGG 0.550141 7.3:+9644858 None:intergenic
CAAAACTTGTAAGAGGAGCA+GGG 0.615820 7.3:+9644714 None:intergenic
AAAACTTGTAAGAGGAGCAG+GGG 0.643901 7.3:+9644715 None:intergenic
GCAACAGTTCTGCATTGACA+AGG 0.657999 7.3:+9644849 None:intergenic
AAACTTGTAAGAGGAGCAGG+GGG 0.714728 7.3:+9644716 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTAATGATATTTATTCTCTA+TGG - chr7.3:9644730-9644749 MS.gene24696:CDS 20.0%
!! TTGAAATTTCACTTATAACA+AGG + chr7.3:9644757-9644776 None:intergenic 20.0%
!!! ACAAGTTTTGTAGAAGTTAT+TGG - chr7.3:9644574-9644593 MS.gene24696:intron 25.0%
ACTTCTACAAAACTTGTAAG+AGG + chr7.3:9644571-9644590 None:intergenic 30.0%
TTCTAAGCATATTAAGCTGT+GGG - chr7.3:9644779-9644798 MS.gene24696:CDS 30.0%
TTTCTAAGCATATTAAGCTG+TGG - chr7.3:9644778-9644797 MS.gene24696:CDS 30.0%
! TTTATTCCCTTTTCTCAAAC+TGG - chr7.3:9644668-9644687 MS.gene24696:CDS 30.0%
ACCAATTTCATCACCAAAGT+TGG + chr7.3:9644641-9644660 None:intergenic 35.0%
ATGACAACCAGTTTGAGAAA+AGG + chr7.3:9644678-9644697 None:intergenic 35.0%
GAGAAGCAGTTGATTGTAAA+AGG - chr7.3:9644532-9644551 MS.gene24696:intron 35.0%
TGACAACCAGTTTGAGAAAA+GGG + chr7.3:9644677-9644696 None:intergenic 35.0%
! ATCTGGTGATTTTCCAATGA+CGG + chr7.3:9644512-9644531 None:intergenic 35.0%
!! ACCAACTTTGGTGATGAAAT+TGG - chr7.3:9644637-9644656 MS.gene24696:intron 35.0%
AAAACTTGTAAGAGGAGCAG+GGG + chr7.3:9644563-9644582 None:intergenic 40.0%
AACCCTTCTTCCGACATAAA+AGG + chr7.3:9644452-9644471 None:intergenic 40.0%
AAGCTATGTCAGCTTGCAAA+TGG - chr7.3:9644847-9644866 MS.gene24696:CDS 40.0%
ACAAAACTTGTAAGAGGAGC+AGG + chr7.3:9644565-9644584 None:intergenic 40.0%
ACAATCAACTGCTTCTCATC+TGG + chr7.3:9644529-9644548 None:intergenic 40.0%
ACCCTTCTTCCGACATAAAA+GGG + chr7.3:9644451-9644470 None:intergenic 40.0%
AGTCCATCAAAGCTGAGTTA+TGG - chr7.3:9644614-9644633 MS.gene24696:intron 40.0%
CAAAACTTGTAAGAGGAGCA+GGG + chr7.3:9644564-9644583 None:intergenic 40.0%
TTGCAAGCTGACATAGCTTA+TGG + chr7.3:9644846-9644865 None:intergenic 40.0%
! GAACTGTTGCCCTTTTATGT+CGG - chr7.3:9644439-9644458 MS.gene24696:CDS 40.0%
AAACTTGTAAGAGGAGCAGG+GGG + chr7.3:9644562-9644581 None:intergenic 45.0%
GCTGAGTTATGGACCAACTT+TGG - chr7.3:9644625-9644644 MS.gene24696:intron 45.0%
! GCAACAGTTCTGCATTGACA+AGG + chr7.3:9644429-9644448 None:intergenic 45.0%
! GCCCTTTTATGTCGGAAGAA+GGG - chr7.3:9644447-9644466 MS.gene24696:CDS 45.0%
! GGTCCATAACTCAGCTTTGA+TGG + chr7.3:9644620-9644639 None:intergenic 45.0%
! TGCCCTTTTATGTCGGAAGA+AGG - chr7.3:9644446-9644465 MS.gene24696:CDS 45.0%
AAGGGTTCGTACAGTGATGC+AGG - chr7.3:9644465-9644484 MS.gene24696:intron 50.0%
ACAAGGACTGCAGGGCTTAA+TGG + chr7.3:9644412-9644431 None:intergenic 50.0%
! CTGCATTGACAAGGACTGCA+GGG + chr7.3:9644420-9644439 None:intergenic 50.0%
! TCTGCATTGACAAGGACTGC+AGG + chr7.3:9644421-9644440 None:intergenic 50.0%
TCTGACGCTCTAGCCGTCAT+TGG - chr7.3:9644496-9644515 MS.gene24696:intron 55.0%


Chromosome Type Strat End Strand Name
chr7.3 gene 9644403 9644894 9644403 ID=MS.gene24696
chr7.3 mRNA 9644403 9644894 9644403 ID=MS.gene24696.t1;Parent=MS.gene24696
chr7.3 exon 9644639 9644894 9644639 ID=MS.gene24696.t1.exon1;Parent=MS.gene24696.t1
chr7.3 CDS 9644639 9644894 9644639 ID=cds.MS.gene24696.t1;Parent=MS.gene24696.t1
chr7.3 exon 9644403 9644467 9644403 ID=MS.gene24696.t1.exon2;Parent=MS.gene24696.t1
chr7.3 CDS 9644403 9644467 9644403 ID=cds.MS.gene24696.t1;Parent=MS.gene24696.t1
Gene Sequence

>MS.gene24696

ATGGATCCATTAAGCCCTGCAGTCCTTGTCAATGCAGAACTGTTGCCCTTTTATGTCGGAAGAAGGGTTCGTACAGTGATGCAGGTTGTGCGATCTGACGCTCTAGCCGTCATTGGAAAATCACCAGATGAGAAGCAGTTGATTGTAAAAGGATCACCCCCTGCTCCTCTTACAAGTTTTGTAGAAGTTATTGGTATTGTTAACAGTGACAAGTCCATCAAAGCTGAGTTATGGACCAACTTTGGTGATGAAATTGGTATTGTTTTTTATTCCCTTTTCTCAAACTGGTTGTCATATTGATTTTGAGACATGACTCTTAAACTTAATGTAATGATATTTATTCTCTATGGTCCTTGTTATAAGTGAAATTTCAAATTTCTAAGCATATTAAGCTGTGGGTTTTGATATTGTTTCAATGCTTTTGCAGATATGCTCAGCTACCATAAGCTATGTCAGCTTGCAAATGGAGAATTTAAACACTTGTTCCTGTGA
Protein sequence

>MS.gene24696.t1

MDPLSPAVLVNAELLPFYVGRRVRTVMQVVRSDALAVIGKSPDEKQLIVKGSPPAPLTSFVEVIGIVNSDKSIKAELWTNFGDEIDMLSYHKLCQLANGEFKHLFL