AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene054376


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene054376.t1 MTR_7g111880 96.000 250 9 1 1 249 1 250 3.30e-172 474
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene054376.t1 AT4G15510 64.659 249 76 5 10 247 40 287 4.09e-105 306
MS.gene054376.t1 AT4G15510 73.039 204 52 2 46 247 3 205 2.02e-103 298
MS.gene054376.t1 AT4G15510 73.039 204 52 2 46 247 3 205 2.02e-103 298
MS.gene054376.t1 AT4G15510 73.039 204 52 2 46 247 3 205 2.02e-103 298
MS.gene054376.t1 AT4G15510 69.595 148 40 3 35 178 72 218 1.67e-62 196

Find 55 sgRNAs with CRISPR-Local

Find 70 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATTCAACTATCCATCAAAT+TGG 0.259378 7.4:+4688923 MS.gene054376:CDS
GGCTTCGTTTCGAGCAAATA+AGG 0.293344 7.4:+4689582 MS.gene054376:CDS
CTTACTTGAATCCAATTTGA+TGG 0.303876 7.4:-4688934 None:intergenic
AGGAGGTACCTGTCTGTTCT+AGG 0.353510 7.4:+4689472 MS.gene054376:CDS
GAATATGTTGATACATTTGA+TGG 0.354613 7.4:+4688895 MS.gene054376:CDS
ATGGATGGAATTTACCGAAT+TGG 0.356971 7.4:-4688679 None:intergenic
ACAAGATAGGGTGGTGCGTT+TGG 0.360551 7.4:+4689441 MS.gene054376:CDS
TTGCTGTTATGCCACAAGAT+AGG 0.370954 7.4:+4689428 MS.gene054376:CDS
TGGATGGAATTTACCGAATT+GGG 0.381934 7.4:-4688678 None:intergenic
CGAATTGGGTGTGGGAGAAA+TGG 0.397956 7.4:-4688664 None:intergenic
CATTTCTCCCACACCCAATT+CGG 0.411234 7.4:+4688665 MS.gene054376:CDS
GCCAATACAATCACAACAAC+GGG 0.413254 7.4:+4688591 MS.gene054376:CDS
TATTCTTGATGAAAATATAT+CGG 0.441156 7.4:+4688993 MS.gene054376:CDS
TAGGGTGGTGCGTTTGGAAT+GGG 0.452062 7.4:+4689447 MS.gene054376:CDS
ATTCAAGACTGTTCAAGACT+TGG 0.455381 7.4:+4689044 MS.gene054376:CDS
GGAATTTACCGAATTGGGTG+TGG 0.465108 7.4:-4688673 None:intergenic
TTGGGTTCGCCTCAACAAGC+TGG 0.465683 7.4:+4689063 MS.gene054376:CDS
TCAAATTGGATTCAAGTAAG+AGG 0.471228 7.4:+4688937 MS.gene054376:CDS
CGAGGGGAATGGAAGTGAAA+TGG 0.477757 7.4:-4688636 None:intergenic
ACTTACATTCTCTCCGACAT+TGG 0.478283 7.4:+4688838 MS.gene054376:CDS
TTCAAGACTGTTCAAGACTT+GGG 0.478605 7.4:+4689045 MS.gene054376:CDS
TGGGAGAAATGGAGCAGCGA+GGG 0.485253 7.4:-4688653 None:intergenic
ACCCGTTGTTGTGATTGTAT+TGG 0.491544 7.4:-4688592 None:intergenic
AAATGGAGCAGCGAGGGGAA+TGG 0.491691 7.4:-4688647 None:intergenic
TGCTGTTATGCCACAAGATA+GGG 0.492092 7.4:+4689429 MS.gene054376:CDS
GTGAAATGGTGACATGGGTC+GGG 0.494548 7.4:-4688622 None:intergenic
GAGTTTATGTCCACTAGGCT+TGG 0.508538 7.4:+4689114 MS.gene054376:CDS
TGGATTCAAGTAAGAGGTGC+TGG 0.510176 7.4:+4688943 MS.gene054376:CDS
AGAAAATGTGTTTCAAGAAG+AGG 0.524955 7.4:+4689537 MS.gene054376:CDS
TCTGAGAGAGTTGCTGATGA+TGG 0.533806 7.4:+4689168 MS.gene054376:CDS
ATAGGGTGGTGCGTTTGGAA+TGG 0.545277 7.4:+4689446 MS.gene054376:CDS
TGGGTTCGCCTCAACAAGCT+GGG 0.554823 7.4:+4689064 MS.gene054376:CDS
TGGTGCGTTTGGAATGGGAT+AGG 0.554855 7.4:+4689452 MS.gene054376:CDS
TTACTGAGTTTATGTCCACT+AGG 0.557448 7.4:+4689109 MS.gene054376:CDS
GTCTTGAATTTCGAAGAAGA+AGG 0.559580 7.4:-4689030 None:intergenic
GTAATCTCAACTCATACAGT+TGG 0.560478 7.4:-4689507 None:intergenic
ACTTTCTTCCCAGCTTGTTG+AGG 0.564235 7.4:-4689072 None:intergenic
AGTGAAATGGTGACATGGGT+CGG 0.571672 7.4:-4688623 None:intergenic
ATCAGCAACTCTCTCAGAGG+TGG 0.572411 7.4:-4689163 None:intergenic
GAATTTACCGAATTGGGTGT+GGG 0.577884 7.4:-4688672 None:intergenic
TTTCAACTCCTAGAACAGAC+AGG 0.577991 7.4:-4689480 None:intergenic
ATGGAAGTGAAATGGTGACA+TGG 0.594314 7.4:-4688628 None:intergenic
GAGTGAACTTCGTCAAGTCA+TGG 0.596736 7.4:+4689561 MS.gene054376:CDS
ACGTTTAACACCAAGCCTAG+TGG 0.600812 7.4:-4689124 None:intergenic
CAAATTGTACTATCAAGTTG+AGG 0.601868 7.4:+4689191 MS.gene054376:CDS
TGCTAATGCTGTACCAATGT+CGG 0.609859 7.4:-4688851 None:intergenic
GGCCAATACAATCACAACAA+CGG 0.609937 7.4:+4688590 MS.gene054376:CDS
GTGGGAGAAATGGAGCAGCG+AGG 0.622596 7.4:-4688654 None:intergenic
TGCGTTTGGAATGGGATAGG+AGG 0.627210 7.4:+4689455 MS.gene054376:CDS
AAACGCACCACCCTATCTTG+TGG 0.644066 7.4:-4689439 None:intergenic
TGGAAGTGAAATGGTGACAT+GGG 0.658481 7.4:-4688627 None:intergenic
GGGAGAAATGGAGCAGCGAG+GGG 0.672235 7.4:-4688652 None:intergenic
ATCATCAGCAACTCTCTCAG+AGG 0.672975 7.4:-4689166 None:intergenic
TGTTATGCCACAAGATAGGG+TGG 0.714139 7.4:+4689432 MS.gene054376:CDS
ACATATTCACGAAACACACG+AGG 0.719885 7.4:-4688880 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATTCTTGATGAAAATATAT+CGG + chr7.4:4688993-4689012 MS.gene054376:CDS 15.0%
!!! ATATTTTCATCAAGAATATA+AGG - chr7.4:4688991-4689010 None:intergenic 15.0%
!! AAATAAAATAATTGTGACAG+AGG - chr7.4:4688719-4688738 None:intergenic 20.0%
!! TACATTTATCAGAAAAATTG+TGG + chr7.4:4689220-4689239 MS.gene054376:intron 20.0%
! GAATATGTTGATACATTTGA+TGG + chr7.4:4688895-4688914 MS.gene054376:CDS 25.0%
AAAACTTACGGTAATTTGAG+GGG + chr7.4:4689268-4689287 MS.gene054376:intron 30.0%
AGAAAATGTGTTTCAAGAAG+AGG + chr7.4:4689537-4689556 MS.gene054376:CDS 30.0%
CAAAACTTACGGTAATTTGA+GGG + chr7.4:4689267-4689286 MS.gene054376:intron 30.0%
CATTCAACTATCCATCAAAT+TGG + chr7.4:4688923-4688942 MS.gene054376:CDS 30.0%
CTTACTTGAATCCAATTTGA+TGG - chr7.4:4688937-4688956 None:intergenic 30.0%
TCAAATTGGATTCAAGTAAG+AGG + chr7.4:4688937-4688956 MS.gene054376:CDS 30.0%
! CAAATTGTACTATCAAGTTG+AGG + chr7.4:4689191-4689210 MS.gene054376:CDS 30.0%
! TCTTCTTGAAACACATTTTC+TGG - chr7.4:4689538-4689557 None:intergenic 30.0%
!! AATGACATTGCTTTTCTTCT+AGG - chr7.4:4688808-4688827 None:intergenic 30.0%
ATGGATGGAATTTACCGAAT+TGG - chr7.4:4688682-4688701 None:intergenic 35.0%
ATTCAAGACTGTTCAAGACT+TGG + chr7.4:4689044-4689063 MS.gene054376:CDS 35.0%
CTCTGTTCTTGCAAAACTTA+CGG + chr7.4:4689256-4689275 MS.gene054376:intron 35.0%
GCAAAACTTACGGTAATTTG+AGG + chr7.4:4689266-4689285 MS.gene054376:intron 35.0%
GTAATCTCAACTCATACAGT+TGG - chr7.4:4689510-4689529 None:intergenic 35.0%
GTCTTGAATTTCGAAGAAGA+AGG - chr7.4:4689033-4689052 None:intergenic 35.0%
TGGATGGAATTTACCGAATT+GGG - chr7.4:4688681-4688700 None:intergenic 35.0%
TTACTGAGTTTATGTCCACT+AGG + chr7.4:4689109-4689128 MS.gene054376:CDS 35.0%
TTCAAGACTGTTCAAGACTT+GGG + chr7.4:4689045-4689064 MS.gene054376:CDS 35.0%
!!! TGGTGCTGATATTTTCTTCA+GGG + chr7.4:4688963-4688982 MS.gene054376:CDS 35.0%
!!! TTTGAGGGGTGTCTTTTATA+TGG + chr7.4:4689282-4689301 MS.gene054376:intron 35.0%
ACATATTCACGAAACACACG+AGG - chr7.4:4688883-4688902 None:intergenic 40.0%
ACCCGTTGTTGTGATTGTAT+TGG - chr7.4:4688595-4688614 None:intergenic 40.0%
ACTTACATTCTCTCCGACAT+TGG + chr7.4:4688838-4688857 MS.gene054376:CDS 40.0%
AGAGGAGAAAGCTCATGAAA+TGG - chr7.4:4688701-4688720 None:intergenic 40.0%
ATGGAAGTGAAATGGTGACA+TGG - chr7.4:4688631-4688650 None:intergenic 40.0%
GAATTTACCGAATTGGGTGT+GGG - chr7.4:4688675-4688694 None:intergenic 40.0%
GAGAAAGCTCATGAAATGGA+TGG - chr7.4:4688697-4688716 None:intergenic 40.0%
GCCAATACAATCACAACAAC+GGG + chr7.4:4688591-4688610 MS.gene054376:CDS 40.0%
GGCCAATACAATCACAACAA+CGG + chr7.4:4688590-4688609 MS.gene054376:CDS 40.0%
TGCTAATGCTGTACCAATGT+CGG - chr7.4:4688854-4688873 None:intergenic 40.0%
TGCTGTTATGCCACAAGATA+GGG + chr7.4:4689429-4689448 MS.gene054376:CDS 40.0%
TGGAAGTGAAATGGTGACAT+GGG - chr7.4:4688630-4688649 None:intergenic 40.0%
TTTCAACTCCTAGAACAGAC+AGG - chr7.4:4689483-4689502 None:intergenic 40.0%
! TTGCTGTTATGCCACAAGAT+AGG + chr7.4:4689428-4689447 MS.gene054376:CDS 40.0%
!! TGTGTGTTGTTTGTGTTGCT+AGG + chr7.4:4689372-4689391 MS.gene054376:intron 40.0%
!!! CTGGTGCTGATATTTTCTTC+AGG + chr7.4:4688962-4688981 MS.gene054376:CDS 40.0%
ACGTTTAACACCAAGCCTAG+TGG - chr7.4:4689127-4689146 None:intergenic 45.0%
AGTGAAATGGTGACATGGGT+CGG - chr7.4:4688626-4688645 None:intergenic 45.0%
ATCATCAGCAACTCTCTCAG+AGG - chr7.4:4689169-4689188 None:intergenic 45.0%
CATTTCTCCCACACCCAATT+CGG + chr7.4:4688665-4688684 MS.gene054376:CDS 45.0%
GAGTGAACTTCGTCAAGTCA+TGG + chr7.4:4689561-4689580 MS.gene054376:CDS 45.0%
GAGTTTATGTCCACTAGGCT+TGG + chr7.4:4689114-4689133 MS.gene054376:CDS 45.0%
GGAATTTACCGAATTGGGTG+TGG - chr7.4:4688676-4688695 None:intergenic 45.0%
GGCTTCGTTTCGAGCAAATA+AGG + chr7.4:4689582-4689601 MS.gene054376:CDS 45.0%
TCTGAGAGAGTTGCTGATGA+TGG + chr7.4:4689168-4689187 MS.gene054376:CDS 45.0%
TGTTATGCCACAAGATAGGG+TGG + chr7.4:4689432-4689451 MS.gene054376:CDS 45.0%
! TGGATTCAAGTAAGAGGTGC+TGG + chr7.4:4688943-4688962 MS.gene054376:CDS 45.0%
!! ACTTTCTTCCCAGCTTGTTG+AGG - chr7.4:4689075-4689094 None:intergenic 45.0%
AAACGCACCACCCTATCTTG+TGG - chr7.4:4689442-4689461 None:intergenic 50.0%
ACAAGATAGGGTGGTGCGTT+TGG + chr7.4:4689441-4689460 MS.gene054376:CDS 50.0%
ATAGGGTGGTGCGTTTGGAA+TGG + chr7.4:4689446-4689465 MS.gene054376:CDS 50.0%
ATCAGCAACTCTCTCAGAGG+TGG - chr7.4:4689166-4689185 None:intergenic 50.0%
CGAATTGGGTGTGGGAGAAA+TGG - chr7.4:4688667-4688686 None:intergenic 50.0%
CGAGGGGAATGGAAGTGAAA+TGG - chr7.4:4688639-4688658 None:intergenic 50.0%
GTGAAATGGTGACATGGGTC+GGG - chr7.4:4688625-4688644 None:intergenic 50.0%
! TAGGGTGGTGCGTTTGGAAT+GGG + chr7.4:4689447-4689466 MS.gene054376:CDS 50.0%
! TGCGTTTGGAATGGGATAGG+AGG + chr7.4:4689455-4689474 MS.gene054376:CDS 50.0%
! TGGTGCGTTTGGAATGGGAT+AGG + chr7.4:4689452-4689471 MS.gene054376:CDS 50.0%
!! AGGAGGTACCTGTCTGTTCT+AGG + chr7.4:4689472-4689491 MS.gene054376:CDS 50.0%
AAATGGAGCAGCGAGGGGAA+TGG - chr7.4:4688650-4688669 None:intergenic 55.0%
TGGGAGAAATGGAGCAGCGA+GGG - chr7.4:4688656-4688675 None:intergenic 55.0%
TGGGTTCGCCTCAACAAGCT+GGG + chr7.4:4689064-4689083 MS.gene054376:CDS 55.0%
TTGGGTTCGCCTCAACAAGC+TGG + chr7.4:4689063-4689082 MS.gene054376:CDS 55.0%
GGGAGAAATGGAGCAGCGAG+GGG - chr7.4:4688655-4688674 None:intergenic 60.0%
GTGGGAGAAATGGAGCAGCG+AGG - chr7.4:4688657-4688676 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr7.4 gene 4688588 4689615 4688588 ID=MS.gene054376
chr7.4 mRNA 4688588 4689615 4688588 ID=MS.gene054376.t1;Parent=MS.gene054376
chr7.4 exon 4688588 4688686 4688588 ID=MS.gene054376.t1.exon1;Parent=MS.gene054376.t1
chr7.4 CDS 4688588 4688686 4688588 ID=cds.MS.gene054376.t1;Parent=MS.gene054376.t1
chr7.4 exon 4688784 4689212 4688784 ID=MS.gene054376.t1.exon2;Parent=MS.gene054376.t1
chr7.4 CDS 4688784 4689212 4688784 ID=cds.MS.gene054376.t1;Parent=MS.gene054376.t1
chr7.4 exon 4689394 4689615 4689394 ID=MS.gene054376.t1.exon3;Parent=MS.gene054376.t1
chr7.4 CDS 4689394 4689615 4689394 ID=cds.MS.gene054376.t1;Parent=MS.gene054376.t1
Gene Sequence

>MS.gene054376

ATGGCCAATACAATCACAACAACGGGTTTTCTAGCCCGACCCATGTCACCATTTCACTTCCATTCCCCTCGCTGCTCCATTTCTCCCACACCCAATTCGGTAAATTCCATCCATTTCATGAGCTTTCTCCTCTGTCACAATTATTTTATTTTATTTACTAAATCTTTGATTTTTGTCTCTGCTAATATATAATCAGATTAAAGCAGCTTTTGCAGTTCCTAGAAGAAAAGCAATGTCATTAATCTTATCAACTTACATTCTCTCCGACATTGGTACAGCATTAGCACAACAACCTCGTGTGTTTCGTGAATATGTTGATACATTTGATGGTTATTCATTCAACTATCCATCAAATTGGATTCAAGTAAGAGGTGCTGGTGCTGATATTTTCTTCAGGGATCCTTATATTCTTGATGAAAATATATCGGTCGAAGTTTCTTCGCCTTCTTCTTCGAAATTCAAGACTGTTCAAGACTTGGGTTCGCCTCAACAAGCTGGGAAGAAAGTTCTTGATCAGTATCTTACTGAGTTTATGTCCACTAGGCTTGGTGTTAAACGTGAATCTAATATTCTTTCCACCTCTGAGAGAGTTGCTGATGATGGCAAATTGTACTATCAAGTTGAGGTTCGTTTACATTTATCAGAAAAATTGTGGTTAATCACGTTAACTCTGTTCTTGCAAAACTTACGGTAATTTGAGGGGTGTCTTTTATATGGTAATGAAATCATACATTGTAGTCTAGCGCTACTTGTTGCAAAATGACATTAAATGATTGATTGATTGTGTGTGTTGTTTGTGTTGCTAGGCGAACATTAAGTCATATGCTAGTAACAACGAGCTTGCTGTTATGCCACAAGATAGGGTGGTGCGTTTGGAATGGGATAGGAGGTACCTGTCTGTTCTAGGAGTTGAAAACAACCAACTGTATGAGTTGAGATTACAAGTGCCAGAAAATGTGTTTCAAGAAGAGGAGAGTGAACTTCGTCAAGTCATGGCTTCGTTTCGAGCAAATAAGGTTGTTCGTTAG

Protein sequence

>MS.gene054376.t1

MANTITTTGFLARPMSPFHFHSPRCSISPTPNSIKAAFAVPRRKAMSLILSTYILSDIGTALAQQPRVFREYVDTFDGYSFNYPSNWIQVRGAGADIFFRDPYILDENISVEVSSPSSSKFKTVQDLGSPQQAGKKVLDQYLTEFMSTRLGVKRESNILSTSERVADDGKLYYQVEANIKSYASNNELAVMPQDRVVRLEWDRRYLSVLGVENNQLYELRLQVPENVFQEEESELRQVMASFRANKVVR