AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene067086

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene067086.t1 MTR_3g086600 95.161 124 6 0 8 131 40 163 1.44e-80 234
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene067086.t1 AT4G17010 53.922 102 47 0 6 107 38 139 2.32e-31 109

Find 22 sgRNAs with CRISPR-Local

Find 45 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGCTCGGGTACTTTATTTA+TGG 0.207230 3.4:-80668809 None:intergenic
CCACAGACGCAGATTCCTTC+TGG 0.295433 3.4:-80669809 None:intergenic
TTGGTTTCAATGTTGTCTGT+TGG 0.452215 3.4:-80669786 None:intergenic
TTCAGTTAAAATAATCTGCT+CGG 0.461306 3.4:-80668824 None:intergenic
AGGCTTGAAGTATTCTTCAA+TGG 0.467844 3.4:-80669628 None:intergenic
TCAGTTAAAATAATCTGCTC+GGG 0.516412 3.4:-80668823 None:intergenic
TATGATATTCTCTGATGAAA+AGG 0.517745 3.4:+80668768 None:intergenic
TTGATGACAATGCAACTACA+AGG 0.518334 3.4:+80669672 MS.gene067086:CDS
TTTAACTGAAGTCCGTCGTA+TGG 0.526702 3.4:+80668837 MS.gene067086:CDS
AGACGCAGATTCCTTCTGGT+TGG 0.540890 3.4:-80669805 None:intergenic
TCTGTGGCGAAAACGTGTAT+AGG 0.543265 3.4:+80669825 MS.gene067086:CDS
CCAGAAGGAATCTGCGTCTG+TGG 0.551476 3.4:+80669809 MS.gene067086:CDS
ATCTCTGCCTCCTTGTCAAG+AGG 0.555790 3.4:-80669648 None:intergenic
GATGATGATGAAAGCACTAC+AGG 0.566553 3.4:+80669713 MS.gene067086:CDS
GATGACAATGCAACTACAAG+GGG 0.572764 3.4:+80669674 MS.gene067086:CDS
TGATGACAATGCAACTACAA+GGG 0.595742 3.4:+80669673 MS.gene067086:CDS
ATACTTCAAGCCTCTTGACA+AGG 0.618848 3.4:+80669638 MS.gene067086:CDS
CAACATTGAAACCAACCAGA+AGG 0.626019 3.4:+80669794 MS.gene067086:CDS
CTGATGAAAAGGCACAAGCA+AGG 0.626848 3.4:+80668779 MS.gene067086:CDS
ACAAGGGGAAGAGAAAACTT+CGG 0.659791 3.4:+80669689 MS.gene067086:CDS
GCATCTCTTCAACCATACGA+CGG 0.691032 3.4:-80668849 None:intergenic
CTTCAAGCCTCTTGACAAGG+AGG 0.695783 3.4:+80669641 MS.gene067086:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGATTCTATAAAATTAATTT+TGG - chr3.4:80669134-80669153 None:intergenic 10.0%
!! AATATGAACCTTTATCAATT+TGG + chr3.4:80669227-80669246 MS.gene067086:intron 20.0%
!!! ATAATTGATTTTGACATGTT+TGG + chr3.4:80668946-80668965 MS.gene067086:intron 20.0%
!!! TCTTTCATTTTGTTTTTTGT+GGG + chr3.4:80669439-80669458 MS.gene067086:intron 20.0%
!!! TTCTTTCATTTTGTTTTTTG+TGG + chr3.4:80669438-80669457 MS.gene067086:intron 20.0%
!!! TTGATAAAGTGGATTATATT+TGG - chr3.4:80669100-80669119 None:intergenic 20.0%
! AATCCTAACCAAATTGATAA+AGG - chr3.4:80669238-80669257 None:intergenic 25.0%
! AGAAGAAGAAAAAACTTTGA+AGG + chr3.4:80669848-80669867 MS.gene067086:CDS 25.0%
! TAAAGTTGTTGTGTGATATA+TGG + chr3.4:80669514-80669533 MS.gene067086:intron 25.0%
! TTCAGTTAAAATAATCTGCT+CGG - chr3.4:80668827-80668846 None:intergenic 25.0%
!! AAACAGTAAGTGTATGTTTT+TGG + chr3.4:80668896-80668915 MS.gene067086:intron 25.0%
!! GAAGTCAAAATTGATTCTAA+AGG + chr3.4:80668920-80668939 MS.gene067086:intron 25.0%
AAGACAAACATGACACAATA+TGG - chr3.4:80669474-80669493 None:intergenic 30.0%
CATTGAATCTAACTTGAAGT+TGG + chr3.4:80668999-80669018 MS.gene067086:intron 30.0%
GAACCTTTATCAATTTGGTT+AGG + chr3.4:80669232-80669251 MS.gene067086:intron 30.0%
TCAGTTAAAATAATCTGCTC+GGG - chr3.4:80668826-80668845 None:intergenic 30.0%
!! CTAAAAGTGAGTTGATAAAG+TGG - chr3.4:80669111-80669130 None:intergenic 30.0%
ATATTCACGAGTGAAGGAAA+AGG - chr3.4:80669281-80669300 None:intergenic 35.0%
TGATGACAATGCAACTACAA+GGG + chr3.4:80669673-80669692 MS.gene067086:CDS 35.0%
TGCTCTTGATAGAATTCACT+TGG + chr3.4:80668970-80668989 MS.gene067086:intron 35.0%
TTCTCCATGAGAATACAACT+TGG - chr3.4:80669207-80669226 None:intergenic 35.0%
TTGGTTTCAATGTTGTCTGT+TGG - chr3.4:80669789-80669808 None:intergenic 35.0%
! AGGCTTGAAGTATTCTTCAA+TGG - chr3.4:80669631-80669650 None:intergenic 35.0%
! TTGATGACAATGCAACTACA+AGG + chr3.4:80669672-80669691 MS.gene067086:CDS 35.0%
ACAAGATGCGATTTACATGC+AGG + chr3.4:80669599-80669618 MS.gene067086:intron 40.0%
ACAAGGGGAAGAGAAAACTT+CGG + chr3.4:80669689-80669708 MS.gene067086:CDS 40.0%
ATACTTCAAGCCTCTTGACA+AGG + chr3.4:80669638-80669657 MS.gene067086:CDS 40.0%
ATTAATGCATGCTCTGCAGT+TGG + chr3.4:80669546-80669565 MS.gene067086:intron 40.0%
CAACATTGAAACCAACCAGA+AGG + chr3.4:80669794-80669813 MS.gene067086:CDS 40.0%
CACACCAAGTTGTATTCTCA+TGG + chr3.4:80669200-80669219 MS.gene067086:intron 40.0%
GATGACAATGCAACTACAAG+GGG + chr3.4:80669674-80669693 MS.gene067086:CDS 40.0%
TCCTTCACTCGTGAATATGA+AGG + chr3.4:80669283-80669302 MS.gene067086:intron 40.0%
TTTAACTGAAGTCCGTCGTA+TGG + chr3.4:80668837-80668856 MS.gene067086:CDS 40.0%
! CTGCTCGGGTACTTTATTTA+TGG - chr3.4:80668812-80668831 None:intergenic 40.0%
!! GATGATGATGAAAGCACTAC+AGG + chr3.4:80669713-80669732 MS.gene067086:CDS 40.0%
AGATGCGATTTACATGCAGG+AGG + chr3.4:80669602-80669621 MS.gene067086:intron 45.0%
GCATCTCTTCAACCATACGA+CGG - chr3.4:80668852-80668871 None:intergenic 45.0%
GCCTTCATATTCACGAGTGA+AGG - chr3.4:80669287-80669306 None:intergenic 45.0%
TCTGTGGCGAAAACGTGTAT+AGG + chr3.4:80669825-80669844 MS.gene067086:CDS 45.0%
! CTGATGAAAAGGCACAAGCA+AGG + chr3.4:80668779-80668798 MS.gene067086:CDS 45.0%
AGACGCAGATTCCTTCTGGT+TGG - chr3.4:80669808-80669827 None:intergenic 50.0%
ATCTCTGCCTCCTTGTCAAG+AGG - chr3.4:80669651-80669670 None:intergenic 50.0%
CTTCAAGCCTCTTGACAAGG+AGG + chr3.4:80669641-80669660 MS.gene067086:CDS 50.0%
CCACAGACGCAGATTCCTTC+TGG - chr3.4:80669812-80669831 None:intergenic 55.0%
CCAGAAGGAATCTGCGTCTG+TGG + chr3.4:80669809-80669828 MS.gene067086:CDS 55.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 80668769 80669884 80668769 ID=MS.gene067086
chr3.4 mRNA 80668769 80669884 80668769 ID=MS.gene067086.t1;Parent=MS.gene067086
chr3.4 exon 80668769 80668900 80668769 ID=MS.gene067086.t1.exon1;Parent=MS.gene067086.t1
chr3.4 CDS 80668769 80668900 80668769 ID=cds.MS.gene067086.t1;Parent=MS.gene067086.t1
chr3.4 exon 80669621 80669884 80669621 ID=MS.gene067086.t1.exon2;Parent=MS.gene067086.t1
chr3.4 CDS 80669621 80669884 80669621 ID=cds.MS.gene067086.t1;Parent=MS.gene067086.t1
Gene Sequence

>MS.gene067086

ATGATATTCTCTGATGAAAAGGCACAAGCAAGGAAAGCAGCCATAAATAAAGTACCCGAGCAGATTATTTTAACTGAAGTCCGTCGTATGGTTGAAGAGATGCAAGCTTTGAACAAGAAGCTCGAAGAAACAGTAAGTGTATGTTTTTGGAGAAGTCAAAATTGATTCTAAAGGTGTATAATTGATTTTGACATGTTTGGTTGCTCTTGATAGAATTCACTTGGCTTCAGCATTGAATCTAACTTGAAGTTGGAAATCAGAGCTTTTAATTCTAAAATTGATTTTGACACTCATATTTACTGTTCAACTCAATTTTAGATGAATGAATCCAAATATAATCCACTTTATCAACTCACTTTTAGCCAAAATTAATTTTATAGAATCTGTTCACTAAAAATTAATTTGTCACTGCATAAACAGACACAGTGACACACACCAAGTTGTATTCTCATGGAGAAAATATGAACCTTTATCAATTTGGTTAGGATTTTTCTTTTTAAAATTTCAATCCTTTTCCTTCACTCGTGAATATGAAGGCACAATGACTTTTAAATAAAAAGTTTTATTTATTTTATTATTGATAAGATCTGCTACGACATATTTTGCACATTTCTGTGTGAAATGTAATTTTTCACTATTTTTGTTGATATTGAATTTAGACAATTCACATTCTTTCATTTTGTTTTTTGTGGGATAAAACATCCATATTGTGTCATGTTTGTCTTGAGATCTTTATCTGTTATATTAAAGTTGTTGTGTGATATATGGCTTCTTTTCATTAATGCATGCTCTGCAGTTGGTTCATTTGTAGCACTCAAATTTGTTGCATAACAAGATGCGATTTACATGCAGGAGGTAGCCATTGAAGAATACTTCAAGCCTCTTGACAAGGAGGCAGAGATTTTGATGACAATGCAACTACAAGGGGAAGAGAAAACTTCGGAGATGATGATGAAAGCACTACAGGAACAAGCTATGCGTCAACAAGTTGAAGCAGAAAAAAGTGCAAGTTTGCATCCAACAGACAACATTGAAACCAACCAGAAGGAATCTGCGTCTGTGGCGAAAACGTGTATAGGAGAAGAAGAAAAAACTTTGAAGGACAGTGTGCATTAA
Protein sequence

>MS.gene067086.t1

MIFSDEKAQARKAAINKVPEQIILTEVRRMVEEMQALNKKLEETEVAIEEYFKPLDKEAEILMTMQLQGEEKTSEMMMKALQEQAMRQQVEAEKSASLHPTDNIETNQKESASVAKTCIGEEEKTLKDSVH