AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene052211


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene052211.t1 MTR_3g087270 93.970 199 12 0 1 199 1 199 9.20e-141 390
MS.gene052211.t1 MTR_3g087280 88.945 199 22 0 1 199 1 199 9.71e-133 370
MS.gene052211.t1 MTR_3g087278 89.447 199 21 0 1 199 1 199 1.12e-131 368
MS.gene052211.t1 MTR_3g087330 84.925 199 30 0 1 199 1 199 1.26e-127 357
MS.gene052211.t1 MTR_3g087325 86.935 199 26 0 1 199 1 199 5.58e-127 356
MS.gene052211.t1 MTR_3g087275 85.930 199 27 1 1 199 1 198 2.62e-123 347
MS.gene052211.t1 MTR_3g087300 66.497 197 22 3 1 197 1 153 1.77e-86 254
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene052211.t1 AT5G65030 30.964 197 124 3 11 199 10 202 1.94e-26 100
MS.gene052211.t1 AT5G10210 32.124 193 109 7 15 196 13 194 1.97e-24 95.5

Find 37 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTTGCCCCAAAGAATTCT+TGG 0.233772 3.2:-74501960 MS.gene052211:CDS
CTACCAAATCAGTACCCTTT+TGG 0.251571 3.2:-74502006 MS.gene052211:CDS
ATAAGAGTAGGTTGAATAAT+TGG 0.258714 3.2:-74501691 MS.gene052211:CDS
TGCGCTTGGCGCAGCTTTGG+AGG 0.349292 3.2:-74501600 MS.gene052211:CDS
TTAATCTCCACTTCTACTTC+CGG 0.353807 3.2:+74501752 None:intergenic
AGCTAAGGCAAAGGAAGATA+TGG 0.356544 3.2:-74501907 MS.gene052211:CDS
ATTTGCGCTTGGCGCAGCTT+TGG 0.402289 3.2:-74501603 MS.gene052211:CDS
GCTCCAACACTAGGCTTTGT+TGG 0.406615 3.2:+74501927 None:intergenic
AGTGGCTTCGGTTCATGAAA+TGG 0.417821 3.2:-74501723 MS.gene052211:CDS
GTCCCAAAAGGGTACTGATT+TGG 0.428896 3.2:+74502003 None:intergenic
GATTCAAGAATCACTTTCCA+TGG 0.437928 3.2:+74501854 None:intergenic
GCAAGGCTGTATCTTCCAAC+AGG 0.447411 3.2:-74502067 MS.gene052211:CDS
GATTAAAATAAGAGTGGCTT+CGG 0.448073 3.2:-74501735 MS.gene052211:CDS
TGCACCAAGCGCGATGATCA+TGG 0.461361 3.2:+74501645 None:intergenic
GCTAAGGCAAAGGAAGATAT+GGG 0.463318 3.2:-74501906 MS.gene052211:CDS
ATTAAATGACTCGTCCCAAA+AGG 0.469911 3.2:+74501991 None:intergenic
TTGGAAAAGGTGAGATTCCA+TGG 0.470388 3.2:-74501871 MS.gene052211:CDS
AAAGCCTAGTGTTGGAGCTA+AGG 0.499139 3.2:-74501922 MS.gene052211:CDS
TTTGCCTTAGCTCCAACACT+AGG 0.507447 3.2:+74501918 None:intergenic
CAACTGAAGTTTGCATATGC+AGG 0.509989 3.2:+74502151 None:intergenic
GGGTCACAACTTATTGGAAA+AGG 0.523568 3.2:-74501884 MS.gene052211:CDS
TTAAATGACTCGTCCCAAAA+GGG 0.547621 3.2:+74501992 None:intergenic
AGTGGAGATTAAAATAAGAG+TGG 0.548596 3.2:-74501741 MS.gene052211:CDS
AATGAGTGTGGATGCAAGAA+TGG 0.549203 3.2:-74501668 MS.gene052211:CDS
ATGGCCATGATCATCGCGCT+TGG 0.550412 3.2:-74501649 MS.gene052211:CDS
GATTGTGATATATTTGCGCT+TGG 0.560902 3.2:-74501614 MS.gene052211:CDS
TAACCAACAAAGCCTAGTGT+TGG 0.564525 3.2:-74501930 MS.gene052211:CDS
TTGAATAATTGGAATGAGTG+TGG 0.579695 3.2:-74501680 MS.gene052211:CDS
GATTCTTGAATCACAAAACA+TGG 0.583125 3.2:-74501843 MS.gene052211:CDS
TAGTGTTGGAGCTAAGGCAA+AGG 0.590191 3.2:-74501916 MS.gene052211:CDS
CTCAACACCGGAAGTAGAAG+TGG 0.592858 3.2:-74501759 MS.gene052211:CDS
AGAGGAAATGTTCTCAACAC+CGG 0.624098 3.2:-74501771 MS.gene052211:CDS
TTGAAGATGTATTTAGTGAG+TGG 0.629374 3.2:-74501806 MS.gene052211:CDS
GAGTGGAAGTGATTGCAAAG+AGG 0.644927 3.2:-74501789 MS.gene052211:CDS
AAACGTTGAATTCATCAAGT+CGG 0.660973 3.2:-74502104 MS.gene052211:CDS
CTAAGGCAAAGGAAGATATG+GGG 0.679009 3.2:-74501905 MS.gene052211:CDS
TAAGGCAAAGGAAGATATGG+GGG 0.682962 3.2:-74501904 MS.gene052211:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAACATGGAGTTGAAAAAA+TGG - chr3.2:74501932-74501951 MS.gene052211:CDS 25.0%
! TGGAAAAGAAAAATAAGAGT+AGG - chr3.2:74502058-74502077 MS.gene052211:CDS 25.0%
!! AAGATTTTCCAAGAATTCTT+TGG + chr3.2:74501812-74501831 None:intergenic 25.0%
!! AGATTTTCCAAGAATTCTTT+GGG + chr3.2:74501811-74501830 None:intergenic 25.0%
!! ATAAGAGTAGGTTGAATAAT+TGG - chr3.2:74502070-74502089 MS.gene052211:CDS 25.0%
AAACGTTGAATTCATCAAGT+CGG - chr3.2:74501657-74501676 MS.gene052211:CDS 30.0%
AGTGGAGATTAAAATAAGAG+TGG - chr3.2:74502020-74502039 MS.gene052211:CDS 30.0%
GATTAAAATAAGAGTGGCTT+CGG - chr3.2:74502026-74502045 MS.gene052211:CDS 30.0%
GATTCTTGAATCACAAAACA+TGG - chr3.2:74501918-74501937 MS.gene052211:CDS 30.0%
TTGAAGATGTATTTAGTGAG+TGG - chr3.2:74501955-74501974 MS.gene052211:CDS 30.0%
TTGAATAATTGGAATGAGTG+TGG - chr3.2:74502081-74502100 MS.gene052211:CDS 30.0%
! GATTTTCCAAGAATTCTTTG+GGG + chr3.2:74501810-74501829 None:intergenic 30.0%
!!! ATACTTTTGTTGTTTCCTGT+TGG + chr3.2:74501712-74501731 None:intergenic 30.0%
ATTAAATGACTCGTCCCAAA+AGG + chr3.2:74501773-74501792 None:intergenic 35.0%
GATTCAAGAATCACTTTCCA+TGG + chr3.2:74501910-74501929 None:intergenic 35.0%
GATTGTGATATATTTGCGCT+TGG - chr3.2:74502147-74502166 MS.gene052211:CDS 35.0%
TTAAATGACTCGTCCCAAAA+GGG + chr3.2:74501772-74501791 None:intergenic 35.0%
TTAATCTCCACTTCTACTTC+CGG + chr3.2:74502012-74502031 None:intergenic 35.0%
! TACCAAATCAGTACCCTTTT+GGG - chr3.2:74501756-74501775 MS.gene052211:CDS 35.0%
AATGAGTGTGGATGCAAGAA+TGG - chr3.2:74502093-74502112 MS.gene052211:CDS 40.0%
AGAGGAAATGTTCTCAACAC+CGG - chr3.2:74501990-74502009 MS.gene052211:CDS 40.0%
AGCTAAGGCAAAGGAAGATA+TGG - chr3.2:74501854-74501873 MS.gene052211:CDS 40.0%
ATATGGGGGTCACAACTTAT+TGG - chr3.2:74501871-74501890 MS.gene052211:CDS 40.0%
CAACTGAAGTTTGCATATGC+AGG + chr3.2:74501613-74501632 None:intergenic 40.0%
CGGCAAAAAACATGTTTGCA+AGG - chr3.2:74501677-74501696 MS.gene052211:CDS 40.0%
CTAAGGCAAAGGAAGATATG+GGG - chr3.2:74501856-74501875 MS.gene052211:CDS 40.0%
GCTAAGGCAAAGGAAGATAT+GGG - chr3.2:74501855-74501874 MS.gene052211:CDS 40.0%
GGGTCACAACTTATTGGAAA+AGG - chr3.2:74501877-74501896 MS.gene052211:CDS 40.0%
TAACCAACAAAGCCTAGTGT+TGG - chr3.2:74501831-74501850 MS.gene052211:CDS 40.0%
TAAGGCAAAGGAAGATATGG+GGG - chr3.2:74501857-74501876 MS.gene052211:CDS 40.0%
TTCTTGCCCCAAAGAATTCT+TGG - chr3.2:74501801-74501820 MS.gene052211:CDS 40.0%
TTGGAAAAGGTGAGATTCCA+TGG - chr3.2:74501890-74501909 MS.gene052211:CDS 40.0%
! CTACCAAATCAGTACCCTTT+TGG - chr3.2:74501755-74501774 MS.gene052211:CDS 40.0%
AGTGGCTTCGGTTCATGAAA+TGG - chr3.2:74502038-74502057 MS.gene052211:CDS 45.0%
GAGTGGAAGTGATTGCAAAG+AGG - chr3.2:74501972-74501991 MS.gene052211:CDS 45.0%
TTTGCCTTAGCTCCAACACT+AGG + chr3.2:74501846-74501865 None:intergenic 45.0%
! AAAGCCTAGTGTTGGAGCTA+AGG - chr3.2:74501839-74501858 MS.gene052211:CDS 45.0%
! GCATATGCAGGTGTTTTCGA+TGG + chr3.2:74501601-74501620 None:intergenic 45.0%
! TAGTGTTGGAGCTAAGGCAA+AGG - chr3.2:74501845-74501864 MS.gene052211:CDS 45.0%
!! GTCCCAAAAGGGTACTGATT+TGG + chr3.2:74501761-74501780 None:intergenic 45.0%
CTCAACACCGGAAGTAGAAG+TGG - chr3.2:74502002-74502021 MS.gene052211:CDS 50.0%
GCAAGGCTGTATCTTCCAAC+AGG - chr3.2:74501694-74501713 MS.gene052211:CDS 50.0%
! GCTCCAACACTAGGCTTTGT+TGG + chr3.2:74501837-74501856 None:intergenic 50.0%
ATGGCCATGATCATCGCGCT+TGG - chr3.2:74502112-74502131 MS.gene052211:CDS 55.0%
ATTTGCGCTTGGCGCAGCTT+TGG - chr3.2:74502158-74502177 MS.gene052211:CDS 55.0%
TGCACCAAGCGCGATGATCA+TGG + chr3.2:74502119-74502138 None:intergenic 55.0%
! TGCGCTTGGCGCAGCTTTGG+AGG - chr3.2:74502161-74502180 MS.gene052211:CDS 65.0%


Chromosome Type Strat End Strand Name
chr3.2 gene 74501592 74502191 74501592 ID=MS.gene052211
chr3.2 mRNA 74501592 74502191 74501592 ID=MS.gene052211.t1;Parent=MS.gene052211
chr3.2 exon 74501592 74502191 74501592 ID=MS.gene052211.t1.exon1;Parent=MS.gene052211.t1
chr3.2 CDS 74501592 74502191 74501592 ID=cds.MS.gene052211.t1;Parent=MS.gene052211.t1
Gene Sequence

>MS.gene052211

ATGGATCCATCGAAAACACCTGCATATGCAAACTTCAGTTGTGAACTGAGAATAATACAAGCACGAAACGTTGAATTCATCAAGTCGGCAAAAAACATGTTTGCAAGGCTGTATCTTCCAACAGGAAACAACAAAAGTATTCAACTCAACAGCAAAAAAGTTTCTACCAAATCAGTACCCTTTTGGGACGAGTCATTTAATCTAGATTGTTCTTGCCCCAAAGAATTCTTGGAAAATCTTAACCAACAAAGCCTAGTGTTGGAGCTAAGGCAAAGGAAGATATGGGGGTCACAACTTATTGGAAAAGGTGAGATTCCATGGAAAGTGATTCTTGAATCACAAAACATGGAGTTGAAAAAATGGTTGAAGATGTATTTAGTGAGTGGAAGTGATTGCAAAGAGGAAATGTTCTCAACACCGGAAGTAGAAGTGGAGATTAAAATAAGAGTGGCTTCGGTTCATGAAATGGAAAAGAAAAATAAGAGTAGGTTGAATAATTGGAATGAGTGTGGATGCAAGAATGGCCATGATCATCGCGCTTGGTGCAGCGCTGAAGATTGTGATATATTTGCGCTTGGCGCAGCTTTGGAGGCTTTTTGA

Protein sequence

>MS.gene052211.t1

MDPSKTPAYANFSCELRIIQARNVEFIKSAKNMFARLYLPTGNNKSIQLNSKKVSTKSVPFWDESFNLDCSCPKEFLENLNQQSLVLELRQRKIWGSQLIGKGEIPWKVILESQNMELKKWLKMYLVSGSDCKEEMFSTPEVEVEIKIRVASVHEMEKKNKSRLNNWNECGCKNGHDHRAWCSAEDCDIFALGAALEAF