AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene76694

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene76694.t1 MTR_4g027440 91.200 125 10 1 1 124 1 125 5.39e-63 197
MS.gene76694.t1 MTR_0160s0030 57.895 133 28 7 2 114 1 125 6.21e-29 108
MS.gene76694.t1 MTR_4g100860 44.737 114 61 2 2 113 1 114 1.24e-21 88.6
MS.gene76694.t1 MTR_5g012630 41.727 139 54 7 2 122 1 130 3.26e-20 84.0
MS.gene76694.t1 MTR_4g109340 45.070 71 39 0 4 74 10 80 8.42e-14 67.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene76694.t1 AT4G16610 40.179 112 55 3 1 112 1 100 3.07e-16 72.4
MS.gene76694.t1 AT1G02030 40.367 109 26 4 1 109 1 70 6.38e-13 64.3
MS.gene76694.t1 AT3G60580 38.793 116 48 6 2 117 1 93 3.33e-11 59.7
MS.gene76694.t1 AT2G45120 66.667 33 11 0 2 34 1 33 5.72e-11 59.3

Find 26 sgRNAs with CRISPR-Local

Find 69 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTCATTGCTCAGCAAATT+GGG 0.202212 4.1:+71534759 MS.gene76694:CDS
TTGCTCATTGCTCAGCAAAT+TGG 0.257224 4.1:+71534758 MS.gene76694:CDS
TCAGCAAATTGGGGTTATAA+TGG 0.370820 4.1:+71534769 MS.gene76694:CDS
GGTGATGACTCAGTTTGTTT+TGG 0.382829 4.1:-71533604 None:intergenic
ATCAACTTTCTTGACCCGTT+TGG 0.394557 4.1:-71533833 None:intergenic
GTGAATCGAAAGCTTCGCTT+TGG 0.412150 4.1:-71533715 None:intergenic
GCTTCATCTCTTTCATCCTA+TGG 0.420837 4.1:+71533679 MS.gene76694:CDS
TGGGCCAGTTGGATTCTTTG+AGG 0.421097 4.1:-71533806 None:intergenic
ACCAGCGTCGATGAATTGAT+TGG 0.461470 4.1:-71533743 None:intergenic
GTTGGTGCTGCTCGCGGCGG+TGG 0.464935 4.1:-71533628 None:intergenic
TGGATTCTCTCTTAGACCAT+AGG 0.471463 4.1:-71533695 None:intergenic
AACTGGCCCACGATCCAAAC+GGG 0.477505 4.1:+71533819 MS.gene76694:CDS
CGTTTGGATCGTGGGCCAGT+TGG 0.485267 4.1:-71533817 None:intergenic
GAGTCCTCAAAGAATCCAAC+TGG 0.487670 4.1:+71533802 MS.gene76694:CDS
TCTTGACCCGTTTGGATCGT+GGG 0.488842 4.1:-71533825 None:intergenic
TTCTTGACCCGTTTGGATCG+TGG 0.496085 4.1:-71533826 None:intergenic
GGTGCTGCTCGCGGCGGTGG+TGG 0.503220 4.1:-71533625 None:intergenic
CCAGCGTCGATGAATTGATT+GGG 0.505485 4.1:-71533742 None:intergenic
TCCACCTAAAGCTCTACCAT+TGG 0.552290 4.1:-71533554 None:intergenic
CAACTGGCCCACGATCCAAA+CGG 0.561624 4.1:+71533818 MS.gene76694:CDS
TCGAAACTGAGCTGAACAGT+TGG 0.568717 4.1:-71533646 None:intergenic
CCCAATCAATTCATCGACGC+TGG 0.575794 4.1:+71533742 MS.gene76694:CDS
GCTCATTGCTCAGCAAATTG+GGG 0.586512 4.1:+71534760 MS.gene76694:CDS
TCCAATGGTAGAGCTTTAGG+TGG 0.603163 4.1:+71533553 MS.gene76694:CDS
TGAACAGTTGGTGCTGCTCG+CGG 0.604272 4.1:-71533634 None:intergenic
ACAGTTGGTGCTGCTCGCGG+CGG 0.667210 4.1:-71533631 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TCATTTTTTATTTAGTTTGA+TGG + chr4.1:71534680-71534699 MS.gene76694:intron 15.0%
!!! GAAAATTCTCTAAAACAAAT+TGG - chr4.1:71534366-71534385 None:intergenic 20.0%
! AGAACACATAATATTGGATT+CGG + chr4.1:71534414-71534433 MS.gene76694:intron 25.0%
!!! TGTTTTAGAGAATTTTCTTC+AGG + chr4.1:71534369-71534388 MS.gene76694:intron 25.0%
!!! TGTTTTTGCAGAACAATTTT+AGG + chr4.1:71534734-71534753 MS.gene76694:intron 25.0%
!!! TTTCTTTTTCAACCTTAATG+AGG - chr4.1:71534651-71534670 None:intergenic 25.0%
AATAAACAAGTTGCAGAAAG+TGG + chr4.1:71534249-71534268 MS.gene76694:intron 30.0%
CATAGGAGAACACATAATAT+TGG + chr4.1:71534408-71534427 MS.gene76694:intron 30.0%
GAATTTGTCAAACCTCATTA+AGG + chr4.1:71534636-71534655 MS.gene76694:intron 30.0%
! GAACCAAAATTTTGTACCTT+TGG - chr4.1:71534708-71534727 None:intergenic 30.0%
!! ATTTAGTTTGATGGATCCAA+AGG + chr4.1:71534689-71534708 MS.gene76694:intron 30.0%
!! GATCCAAAGGTACAAAATTT+TGG + chr4.1:71534702-71534721 MS.gene76694:intron 30.0%
AGGTTTGACAAATTCAGCAT+CGG - chr4.1:71534631-71534650 None:intergenic 35.0%
TCAGCAAATTGGGGTTATAA+TGG + chr4.1:71534769-71534788 MS.gene76694:CDS 35.0%
TGAACAGTATGAACAACAAC+AGG + chr4.1:71534038-71534057 MS.gene76694:intron 35.0%
TTCTGTACTGAGTTCTTCAT+CGG + chr4.1:71533888-71533907 MS.gene76694:intron 35.0%
TTTCGTTCATATCAAGCACT+AGG + chr4.1:71534201-71534220 MS.gene76694:intron 35.0%
! GTCTGTACTGAGTTTTTCAT+AGG - chr4.1:71533859-71533878 None:intergenic 35.0%
! TGCTTGAGAAGTTTTTCCAA+TGG + chr4.1:71533538-71533557 MS.gene76694:CDS 35.0%
! TTTTCCAATGGTAGAGCTTT+AGG + chr4.1:71533550-71533569 MS.gene76694:CDS 35.0%
AAACAAGTTGCAGAAAGTGG+TGG + chr4.1:71534252-71534271 MS.gene76694:intron 40.0%
AGAACTGAAACCGTTGAAGA+AGG + chr4.1:71534140-71534159 MS.gene76694:intron 40.0%
ATCAACTTTCTTGACCCGTT+TGG - chr4.1:71533836-71533855 None:intergenic 40.0%
CAAACTATCTCCAACATTCG+CGG - chr4.1:71534511-71534530 None:intergenic 40.0%
CTCGCGAAGATAACAACATA+TGG + chr4.1:71533956-71533975 MS.gene76694:intron 40.0%
GAAGATGAAGACGAAGATGA+TGG + chr4.1:71534567-71534586 MS.gene76694:intron 40.0%
GATGGTTAGAACAAACGTTG+AGG + chr4.1:71534473-71534492 MS.gene76694:intron 40.0%
GCTTCATCTCTTTCATCCTA+TGG + chr4.1:71533679-71533698 MS.gene76694:CDS 40.0%
TCATCTTCATCTTCGTCCAT+CGG - chr4.1:71534555-71534574 None:intergenic 40.0%
TGCTCATTGCTCAGCAAATT+GGG + chr4.1:71534759-71534778 MS.gene76694:CDS 40.0%
TGGATTCTCTCTTAGACCAT+AGG - chr4.1:71533698-71533717 None:intergenic 40.0%
TTGCTCATTGCTCAGCAAAT+TGG + chr4.1:71534758-71534777 MS.gene76694:CDS 40.0%
! TCTAAATTTTCCTGCTCCGA+TGG + chr4.1:71534536-71534555 MS.gene76694:intron 40.0%
! TTTTCTTCAGGTCAAGCACT+AGG + chr4.1:71534381-71534400 MS.gene76694:intron 40.0%
!! GACGATGTTAGTCAAGTTGA+AGG + chr4.1:71534594-71534613 MS.gene76694:intron 40.0%
!! GGTGATGACTCAGTTTGTTT+TGG - chr4.1:71533607-71533626 None:intergenic 40.0%
!!! ATGACTCAGTTTGTTTTGGC+AGG - chr4.1:71533603-71533622 None:intergenic 40.0%
AGCAGCAACAACAACAACGA+TGG + chr4.1:71534455-71534474 MS.gene76694:intron 45.0%
CGACATCTTCATCTTCTTCC+TGG - chr4.1:71534080-71534099 None:intergenic 45.0%
CGTTCATATCAAGCACTAGG+TGG + chr4.1:71534204-71534223 MS.gene76694:intron 45.0%
CTTCCTCGTACCTTCTTCAA+CGG - chr4.1:71534153-71534172 None:intergenic 45.0%
GAGTCCTCAAAGAATCCAAC+TGG + chr4.1:71533802-71533821 MS.gene76694:CDS 45.0%
GCTCATTGCTCAGCAAATTG+GGG + chr4.1:71534760-71534779 MS.gene76694:CDS 45.0%
GGAAGAAGATGAAGATGTCG+AGG + chr4.1:71534080-71534099 MS.gene76694:intron 45.0%
GGTTGAAGAAGATGAAGTCC+AGG + chr4.1:71534059-71534078 MS.gene76694:intron 45.0%
GTGAATCGAAAGCTTCGCTT+TGG - chr4.1:71533718-71533737 None:intergenic 45.0%
TCCACCTAAAGCTCTACCAT+TGG - chr4.1:71533557-71533576 None:intergenic 45.0%
TCGAAACTGAGCTGAACAGT+TGG - chr4.1:71533649-71533668 None:intergenic 45.0%
! AAACCGTTGAAGAAGGTACG+AGG + chr4.1:71534147-71534166 MS.gene76694:intron 45.0%
! GATGAAGACGAAGATGATGG+TGG + chr4.1:71534570-71534589 MS.gene76694:intron 45.0%
!! ACCAGCGTCGATGAATTGAT+TGG - chr4.1:71533746-71533765 None:intergenic 45.0%
!! CCAGCGTCGATGAATTGATT+GGG - chr4.1:71533745-71533764 None:intergenic 45.0%
!! TCCAATGGTAGAGCTTTAGG+TGG + chr4.1:71533553-71533572 MS.gene76694:CDS 45.0%
ACAAACGTTGAGGTTGCTCG+AGG + chr4.1:71534483-71534502 MS.gene76694:intron 50.0%
CCCAATCAATTCATCGACGC+TGG + chr4.1:71533742-71533761 MS.gene76694:CDS 50.0%
GTCAAGCACTAGGTGGACAT+AGG + chr4.1:71534391-71534410 MS.gene76694:intron 50.0%
TCTTCAGGTCAAGCACTAGG+TGG + chr4.1:71534384-71534403 MS.gene76694:intron 50.0%
TCTTGACCCGTTTGGATCGT+GGG - chr4.1:71533828-71533847 None:intergenic 50.0%
TGGGCCAGTTGGATTCTTTG+AGG - chr4.1:71533809-71533828 None:intergenic 50.0%
TTCTTGACCCGTTTGGATCG+TGG - chr4.1:71533829-71533848 None:intergenic 50.0%
AACTGGCCCACGATCCAAAC+GGG + chr4.1:71533819-71533838 MS.gene76694:CDS 55.0%
CAACTGGCCCACGATCCAAA+CGG + chr4.1:71533818-71533837 MS.gene76694:CDS 55.0%
TCATCTTCGTCCATCGGAGC+AGG - chr4.1:71534549-71534568 None:intergenic 55.0%
!! TGAACAGTTGGTGCTGCTCG+CGG - chr4.1:71533637-71533656 None:intergenic 55.0%
CGTTTGGATCGTGGGCCAGT+TGG - chr4.1:71533820-71533839 None:intergenic 60.0%
GCTCGAGGTTCCGCGAATGT+TGG + chr4.1:71534498-71534517 MS.gene76694:intron 60.0%
!! ACAGTTGGTGCTGCTCGCGG+CGG - chr4.1:71533634-71533653 None:intergenic 65.0%
!! GTTGGTGCTGCTCGCGGCGG+TGG - chr4.1:71533631-71533650 None:intergenic 75.0%
!!! GGTGCTGCTCGCGGCGGTGG+TGG - chr4.1:71533628-71533647 None:intergenic 80.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 71533511 71534802 71533511 ID=MS.gene76694
chr4.1 mRNA 71533511 71534802 71533511 ID=MS.gene76694.t1;Parent=MS.gene76694
chr4.1 exon 71533511 71533881 71533511 ID=MS.gene76694.t1.exon1;Parent=MS.gene76694.t1
chr4.1 CDS 71533511 71533881 71533511 ID=cds.MS.gene76694.t1;Parent=MS.gene76694.t1
chr4.1 exon 71534745 71534802 71534745 ID=MS.gene76694.t1.exon2;Parent=MS.gene76694.t1
chr4.1 CDS 71534745 71534802 71534745 ID=cds.MS.gene76694.t1;Parent=MS.gene76694.t1
Gene Sequence

>MS.gene76694

ATGATGGAGAAACACAAGTGCAAATTTTGCTTGAGAAGTTTTTCCAATGGTAGAGCTTTAGGTGGACACATGAGATCACACATGATGAACCTGCCAAAACAAACTGAGTCATCACCACCACCGCCGCGAGCAGCACCAACTGTTCAGCTCAGTTTCGAAGCTGAATCAGCTTCATCTCTTTCATCCTATGGTCTAAGAGAGAATCCAAAGCGAAGCTTTCGATTCACAGATCCCAATCAATTCATCGACGCTGGTTCGATAATTCATCAAGAAGATAGAGAAAGTGAAACTGAGTCCTCAAAGAATCCAACTGGCCCACGATCCAAACGGGTCAAGAAAGTTGATCCTATGAAAAACTCAGTACAGACTGAGTCTGTTTCTGTACTGAGTTCTTCATCGGATATAACAACTGAAGAAGACGTCGCTTTTTTTCTCATATCACTGTCTCGCGAAGATAACAACATATGGAAAACTCATACACAACATCATGATCAACAACATAATCAGCATCATGAAGAACAAGAAGATGAACAGTATGAACAACAACAGGTTGAAGAAGATGAAGTCCAGGAAGAAGATGAAGATGTCGAGGAAGAAGAAGAAAGTGAAGCTGAATCTGAAGAAGAAGAAGAACTGAAACCGTTGAAGAAGGTACGAGGAAGATACAAATGCGACACGTGTAACAAAGTGTTTCGTTCATATCAAGCACTAGGTGGACACAGAGCGAGTCACAAGAAAAATAAACAAGTTGCAGAAAGTGGTGGTGATTATTCAATTTCACAAGAGAAAATTAACATTGAAAAAAATATCAATGTTAATAATAATAAGAGTGAAAAGAAAATTCATGAATGTCCAATTTGTTTTAGAGAATTTTCTTCAGGTCAAGCACTAGGTGGACATAGGAGAACACATAATATTGGATTCGGATCAGCATCAACATCAGCAGCAGCAACAACAACAACGATGGTTAGAACAAACGTTGAGGTTGCTCGAGGTTCCGCGAATGTTGGAGATAGTTTGTTAGATCTAAATTTTCCTGCTCCGATGGACGAAGATGAAGATGAAGACGAAGATGATGGTGGTGACGATGTTAGTCAAGTTGAAGGTTCTGCTGTTTCCGATGCTGAATTTGTCAAACCTCATTAAGGTTGAAAAAGAAAATGATGAATTCATTTTTTATTTAGTTTGATGGATCCAAAGGTACAAAATTTTGGTTCTGTTTTTGTTTTTGCAGAACAATTTTAGGTTTGCTCATTGCTCAGCAAATTGGGGTTATAATGGTTATTTCATAG
Protein sequence

>MS.gene76694.t1

MMEKHKCKFCLRSFSNGRALGGHMRSHMMNLPKQTESSPPPPRAAPTVQLSFEAESASSLSSYGLRENPKRSFRFTDPNQFIDAGSIIHQEDRESETESSKNPTGPRSKRVKKVDPMKNSVQTETILGLLIAQQIGVIMVIS