AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene06833


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene06833.t1 MTR_3g092600 99.091 110 1 0 1 110 1 110 3.12e-74 215
MS.gene06833.t1 MTR_2g066750 98.182 110 2 0 1 110 1 110 1.07e-73 214
MS.gene06833.t1 MTR_8g024350 64.545 110 37 2 1 110 1 108 1.42e-33 112
MS.gene06833.t1 MTR_7g118060 62.712 59 22 0 1 59 1 59 1.00e-20 80.5
MS.gene06833.t1 MTR_7g005740 66.129 62 2 1 1 62 1 43 1.52e-19 79.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene06833.t1 AT5G24510 57.391 115 40 4 1 110 1 111 4.14e-36 119
MS.gene06833.t1 AT5G47700 57.658 111 45 1 2 110 3 113 7.99e-29 100
MS.gene06833.t1 AT5G47700 57.658 111 45 1 2 110 3 113 7.99e-29 100
MS.gene06833.t1 AT1G01100 60.185 108 42 1 4 110 5 112 4.26e-28 99.0
MS.gene06833.t1 AT1G01100 60.185 108 42 1 4 110 5 112 4.26e-28 99.0
MS.gene06833.t1 AT1G01100 60.185 108 42 1 4 110 5 112 4.26e-28 99.0
MS.gene06833.t1 AT1G01100 50.459 109 39 1 2 110 3 96 2.14e-27 96.7
MS.gene06833.t1 AT4G00810 54.955 111 48 1 2 110 3 113 2.87e-27 97.1
MS.gene06833.t1 AT4G00810 54.955 111 48 1 2 110 3 113 2.87e-27 97.1

Find 32 sgRNAs with CRISPR-Local

Find 82 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATATTAAACTTACGGTGAT+TGG 0.289233 3.1:+74619979 None:intergenic
CAAAATGAGTTCCGGCGAAT+TGG 0.294649 3.1:-74620043 None:intergenic
GTCATCGTCACTTTCTTCCT+TGG 0.329724 3.1:+74618736 None:intergenic
ACGTCACCGTTGAATCTTAC+TGG 0.348075 3.1:-74619842 MS.gene06833:CDS
AAAATGAGTTCCGGCGAATT+GGG 0.368280 3.1:-74620042 MS.gene06833:CDS
TCTGAGCAAGCTTAGCGAAT+AGG 0.392998 3.1:+74619814 None:intergenic
GCCGTATCTGCACCCGCTGC+TGG 0.401410 3.1:-74619735 MS.gene06833:CDS
TCTGCACCCGCTGCTGGTGG+TGG 0.439771 3.1:-74619729 MS.gene06833:CDS
ATATTAAACTTACGGTGATT+GGG 0.443031 3.1:+74619980 None:intergenic
GCGGCTCCACCACCAGCAGC+GGG 0.451994 3.1:+74619723 None:intergenic
GAAGATCGGTACTTTGTTGA+AGG 0.461021 3.1:-74619871 MS.gene06833:CDS
ACCTGCCGCCGTTGAAAAGA+AGG 0.476631 3.1:-74619688 MS.gene06833:intron
TGCGGCTCCACCACCAGCAG+CGG 0.489051 3.1:+74619722 None:intergenic
TTGAACTCCGGCGCTGTTGG+TGG 0.510539 3.1:-74619768 MS.gene06833:CDS
ACAATTCACAAAATGAGTTC+CGG 0.522809 3.1:-74620051 None:intergenic
GGAAGAAAGTGACGATGACA+TGG 0.523361 3.1:-74618732 MS.gene06833:CDS
AGCGGCACCACCAACAGCGC+CGG 0.527844 3.1:+74619761 None:intergenic
ACCAGCAGCGGGTGCAGATA+CGG 0.530473 3.1:+74619734 None:intergenic
TCCATCGTCGTGGAGGATCA+AGG 0.532980 3.1:+74620005 None:intergenic
GCAAGCTTAGCGAATAGGCT+TGG 0.542190 3.1:+74619819 None:intergenic
TTTGTTTAGGCGGAGAAGAT+CGG 0.543289 3.1:-74619885 MS.gene06833:intron
GGCAGGTTCGGCAGCTGCTG+CGG 0.548908 3.1:+74619704 None:intergenic
GTAAATGCAGCCCAATTCGC+CGG 0.571217 3.1:+74620032 None:intergenic
ACCTTGATCCTCCACGACGA+TGG 0.573503 3.1:-74620006 MS.gene06833:CDS
GTATCTGCACCCGCTGCTGG+TGG 0.603091 3.1:-74619732 MS.gene06833:CDS
GCTTGGCCAGTAAGATTCAA+CGG 0.629260 3.1:+74619836 None:intergenic
TTGGGATTCCATCGTCGTGG+AGG 0.650788 3.1:+74619998 None:intergenic
GTGTTTGTAGGAGGAAGCCA+AGG 0.654949 3.1:-74618753 MS.gene06833:intron
TGATTGGGATTCCATCGTCG+TGG 0.662981 3.1:+74619995 None:intergenic
GGGTGCAGATACGGCAACAG+CGG 0.665524 3.1:+74619743 None:intergenic
GAAGAAAGTGACGATGACAT+GGG 0.678372 3.1:-74618731 MS.gene06833:CDS
ATCGTCGTGGAGGATCAAGG+TGG 0.743990 3.1:+74620008 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATTATATGTTTTTATCTTA+AGG + chr3.1:74619263-74619282 None:intergenic 10.0%
!! AATTGTATTGAAATTAGAAA+CGG - chr3.1:74619164-74619183 MS.gene06833:intron 15.0%
!! TATAAAAGATATAATTTCCT+CGG - chr3.1:74619386-74619405 MS.gene06833:intron 15.0%
!!! TTTTCATGCAAAATAATTTT+TGG + chr3.1:74619457-74619476 None:intergenic 15.0%
!! AAAGTAAAAAATGTGGATAT+AGG + chr3.1:74619826-74619845 None:intergenic 20.0%
!! AAGTAAAAAATGTGGATATA+GGG + chr3.1:74619825-74619844 None:intergenic 20.0%
!! ATTGTATTGAAATTAGAAAC+GGG - chr3.1:74619165-74619184 MS.gene06833:intron 20.0%
!!! ATATCCACATTTTTTACTTT+TGG - chr3.1:74619826-74619845 MS.gene06833:CDS 20.0%
!!! ATGAAAACATGTAGTTATTT+TGG - chr3.1:74619494-74619513 MS.gene06833:intron 20.0%
!!! ATTTTTCTTTGTTACTGTTT+GGG - chr3.1:74618841-74618860 MS.gene06833:intron 20.0%
!!! TATCCACATTTTTTACTTTT+GGG - chr3.1:74619827-74619846 MS.gene06833:CDS 20.0%
! AATTGTTGTGTTTCTTCATT+GGG - chr3.1:74619536-74619555 MS.gene06833:intron 25.0%
! ATATTAAACTTACGGTGATT+GGG + chr3.1:74618774-74618793 None:intergenic 25.0%
! GAAGAGAGATATTAAACTTA+CGG + chr3.1:74618782-74618801 None:intergenic 25.0%
! GACAACTCTGAATATAATTA+TGG - chr3.1:74619586-74619605 MS.gene06833:intron 25.0%
! TAATTGTTGTGTTTCTTCAT+TGG - chr3.1:74619535-74619554 MS.gene06833:intron 25.0%
! TTAAATAAGCCAATCATAAC+TGG - chr3.1:74619799-74619818 MS.gene06833:CDS 25.0%
!! AAACAATACCTTCTTTTCAA+CGG + chr3.1:74619074-74619093 None:intergenic 25.0%
!! CATTTTTCTTTGTTACTGTT+TGG - chr3.1:74618840-74618859 MS.gene06833:intron 25.0%
!!! ATAAAGTTAACTTGTTTTCC+TGG - chr3.1:74619716-74619735 MS.gene06833:CDS 25.0%
!!! TAAAGTTAACTTGTTTTCCT+GGG - chr3.1:74619717-74619736 MS.gene06833:CDS 25.0%
AAAAGATATAATTTCCTCGG+AGG - chr3.1:74619389-74619408 MS.gene06833:intron 30.0%
AAAGATATAATTTCCTCGGA+GGG - chr3.1:74619390-74619409 MS.gene06833:intron 30.0%
AATGTAAGCTTATGCATAAG+TGG + chr3.1:74619671-74619690 None:intergenic 30.0%
AGATGCAAGTTCTACAAAAT+AGG + chr3.1:74619363-74619382 None:intergenic 30.0%
ATGTAAGCTTATGCATAAGT+GGG + chr3.1:74619670-74619689 None:intergenic 30.0%
CAGCAAATGACAGTATTTAT+CGG + chr3.1:74619426-74619445 None:intergenic 30.0%
GATATTAAACTTACGGTGAT+TGG + chr3.1:74618775-74618794 None:intergenic 30.0%
TATTCAGAGTTGTCTTGAAA+AGG + chr3.1:74619580-74619599 None:intergenic 30.0%
TCACCCAAAAGTAAAAAATG+TGG + chr3.1:74619833-74619852 None:intergenic 30.0%
TGTAATGATGAGTTACTGAT+TGG - chr3.1:74619135-74619154 MS.gene06833:intron 30.0%
TGTTAAATGAATGCTAGTTC+TGG - chr3.1:74619212-74619231 MS.gene06833:intron 30.0%
TTTGTTTAGTGACACTGTTT+GGG + chr3.1:74619772-74619791 None:intergenic 30.0%
! ATTTTGTAGAACTTGCATCT+AGG - chr3.1:74619363-74619382 MS.gene06833:intron 30.0%
! CGATTTGGAGATTATAGAAA+TGG + chr3.1:74618809-74618828 None:intergenic 30.0%
!! TACTGTTTGGGTTTTTGTTT+AGG - chr3.1:74618853-74618872 MS.gene06833:intron 30.0%
AAGATATAATTTCCTCGGAG+GGG - chr3.1:74619391-74619410 MS.gene06833:intron 35.0%
AATGAGATCTATGAGCGATT+TGG + chr3.1:74618824-74618843 None:intergenic 35.0%
CTTCATTGGGATTTGAGAAT+TGG - chr3.1:74619549-74619568 MS.gene06833:intron 35.0%
GTTTGTTTAGTGACACTGTT+TGG + chr3.1:74619773-74619792 None:intergenic 35.0%
TCATTCCATACTGTGTTTGT+AGG - chr3.1:74619986-74620005 MS.gene06833:intron 35.0%
! ATTTTGTGCTGTGATCAAGT+TGG - chr3.1:74619330-74619349 MS.gene06833:intron 35.0%
! TTTTGTGCTGTGATCAAGTT+GGG - chr3.1:74619331-74619350 MS.gene06833:intron 35.0%
!! TGTTTGGGTTTTTGTTTAGG+CGG - chr3.1:74618856-74618875 MS.gene06833:intron 35.0%
ATCAACAAGACAATCTTCCC+AGG + chr3.1:74619737-74619756 None:intergenic 40.0%
GAAGAAAGTGACGATGACAT+GGG - chr3.1:74620020-74620039 MS.gene06833:CDS 40.0%
GAAGATCGGTACTTTGTTGA+AGG - chr3.1:74618880-74618899 MS.gene06833:intron 40.0%
GATATAGGGCCAGTTATGAT+TGG + chr3.1:74619811-74619830 None:intergenic 40.0%
TTCCATACTGTGTTTGTAGG+AGG - chr3.1:74619989-74620008 MS.gene06833:intron 40.0%
TTCCTCCTACAAACACAGTA+TGG + chr3.1:74619994-74620013 None:intergenic 40.0%
TTTGTTTAGGCGGAGAAGAT+CGG - chr3.1:74618866-74618885 MS.gene06833:intron 40.0%
! CAATACCTTCTTTTCAACGG+CGG + chr3.1:74619071-74619090 None:intergenic 40.0%
! TTTGTGCTGTGATCAAGTTG+GGG - chr3.1:74619332-74619351 MS.gene06833:intron 40.0%
!! GATGATCTCGTTTTGAACTC+CGG - chr3.1:74618971-74618990 MS.gene06833:intron 40.0%
ACGTCACCGTTGAATCTTAC+TGG - chr3.1:74618909-74618928 MS.gene06833:intron 45.0%
GCTTGGCCAGTAAGATTCAA+CGG + chr3.1:74618918-74618937 None:intergenic 45.0%
GGAAGAAAGTGACGATGACA+TGG - chr3.1:74620019-74620038 MS.gene06833:CDS 45.0%
TCTGAGCAAGCTTAGCGAAT+AGG + chr3.1:74618940-74618959 None:intergenic 45.0%
! GTCATCGTCACTTTCTTCCT+TGG + chr3.1:74620018-74620037 None:intergenic 45.0%
GCAAGCTTAGCGAATAGGCT+TGG + chr3.1:74618935-74618954 None:intergenic 50.0%
GTAAATGCAGCCCAATTCGC+CGG + chr3.1:74618722-74618741 None:intergenic 50.0%
GTGTTTGTAGGAGGAAGCCA+AGG - chr3.1:74619998-74620017 MS.gene06833:CDS 50.0%
TGATTGGGATTCCATCGTCG+TGG + chr3.1:74618759-74618778 None:intergenic 50.0%
ACCTGCCGCCGTTGAAAAGA+AGG - chr3.1:74619063-74619082 MS.gene06833:intron 55.0%
ACCTTGATCCTCCACGACGA+TGG - chr3.1:74618745-74618764 MS.gene06833:CDS 55.0%
ATCGTCGTGGAGGATCAAGG+TGG + chr3.1:74618746-74618765 None:intergenic 55.0%
TCCATCGTCGTGGAGGATCA+AGG + chr3.1:74618749-74618768 None:intergenic 55.0%
TTGGGATTCCATCGTCGTGG+AGG + chr3.1:74618756-74618775 None:intergenic 55.0%
! ACCTTCTTTTCAACGGCGGC+AGG + chr3.1:74619067-74619086 None:intergenic 55.0%
! CTTTTCAACGGCGGCAGGTT+CGG + chr3.1:74619062-74619081 None:intergenic 55.0%
!! GTTTTGAACTCCGGCGCTGT+TGG - chr3.1:74618980-74618999 MS.gene06833:intron 55.0%
ACCAGCAGCGGGTGCAGATA+CGG + chr3.1:74619020-74619039 None:intergenic 60.0%
CGGATACAGAATCCCCTCCG+AGG + chr3.1:74619406-74619425 None:intergenic 60.0%
GGGTGCAGATACGGCAACAG+CGG + chr3.1:74619011-74619030 None:intergenic 60.0%
TTGAACTCCGGCGCTGTTGG+TGG - chr3.1:74618983-74619002 MS.gene06833:intron 60.0%
GTATCTGCACCCGCTGCTGG+TGG - chr3.1:74619019-74619038 MS.gene06833:intron 65.0%
AGCGGCACCACCAACAGCGC+CGG + chr3.1:74618993-74619012 None:intergenic 70.0%
GCCGTATCTGCACCCGCTGC+TGG - chr3.1:74619016-74619035 MS.gene06833:intron 70.0%
GGCAGGTTCGGCAGCTGCTG+CGG + chr3.1:74619050-74619069 None:intergenic 70.0%
TCTGCACCCGCTGCTGGTGG+TGG - chr3.1:74619022-74619041 MS.gene06833:intron 70.0%
TGCGGCTCCACCACCAGCAG+CGG + chr3.1:74619032-74619051 None:intergenic 70.0%
GCGGCTCCACCACCAGCAGC+GGG + chr3.1:74619031-74619050 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr3.1 gene 74618712 74620061 74618712 ID=MS.gene06833
chr3.1 mRNA 74618712 74620061 74618712 ID=MS.gene06833.t1;Parent=MS.gene06833
chr3.1 exon 74619993 74620061 74619993 ID=MS.gene06833.t1.exon1;Parent=MS.gene06833.t1
chr3.1 CDS 74619993 74620061 74619993 ID=cds.MS.gene06833.t1;Parent=MS.gene06833.t1
chr3.1 exon 74619689 74619898 74619689 ID=MS.gene06833.t1.exon2;Parent=MS.gene06833.t1
chr3.1 CDS 74619689 74619898 74619689 ID=cds.MS.gene06833.t1;Parent=MS.gene06833.t1
chr3.1 exon 74618712 74618765 74618712 ID=MS.gene06833.t1.exon3;Parent=MS.gene06833.t1
chr3.1 CDS 74618712 74618765 74618712 ID=cds.MS.gene06833.t1;Parent=MS.gene06833.t1
Gene Sequence

>MS.gene06833

ATGAGTTCCGGCGAATTGGGCTGCATTTACGCCACCTTGATCCTCCACGACGATGGAATCCCAATCACCGTAAGTTTAATATCTCTCTTCAATTCCATTTCTATAATCTCCAAATCGCTCATAGATCTCATTTTTCTTTGTTACTGTTTGGGTTTTTGTTTAGGCGGAGAAGATCGGTACTTTGTTGAAGGCTGCTAACGTCACCGTTGAATCTTACTGGCCAAGCCTATTCGCTAAGCTTGCTCAGAGCAAGAACGTTGATGATCTCGTTTTGAACTCCGGCGCTGTTGGTGGTGCCGCTGTTGCCGTATCTGCACCCGCTGCTGGTGGTGGAGCCGCAGCAGCTGCCGAACCTGCCGCCGTTGAAAAGAAGGTATTGTTTTTAATTCTTTTTTTTATGATTATGATTTTTGTATGAAATTGTGTAATGATGAGTTACTGATTGGTGAACTAATTGTATTGAAATTAGAAACGGGTTTTGATAAATCGTTCATCTGTAGTGTTAAATGAATGCTAGTTCTGGAATTGTACAATAGTATTGCAATTTTCCTTAAGATAAAAACATATAATTGATTTTCTTACATTGTTTGTTCTGTTGAATTTGCTTGCAAATTGATGATTTTGTGCTGTGATCAAGTTGGGGTTATACCTATTTTGTAGAACTTGCATCTAGGTATAAAAGATATAATTTCCTCGGAGGGGATTCTGTATCCGATAAATACTGTCATTTGCTGCAATTACTCCAAAAATTATTTTGCATGAAAACATTCACTATAAGTTTTATGAAAACATGTAGTTATTTTGGTTTTTTGAAGAAATAGTATAATTGTTGTGTTTCTTCATTGGGATTTGAGAATTGGACTATCCTTTTCAAGACAACTCTGAATATAATTATGGTACTCTTTTGATTTGCAACTTATGTACAGCTTATTGCTCAAGCGCTTCTCTTGATATGCCCACTTATGCATAAGCTTACATTTTCTATTTTCTATAGAAAAGATAAAATAAAGTTAACTTGTTTTCCTGGGAAGATTGTCTTGTTGATTTCATTAGTTCTCCCAAACAGTGTCACTAAACAAACATAGCTTTAAATAAGCCAATCATAACTGGCCCTATATCCACATTTTTTACTTTTGGGTGAGTTTTTACTCTTTCACAATAATTTAATGTTTAATGTTGTATTATAGCTTTGATGCAGTCAATTATGAGCACTGCACAGACATAGCTTATTACTTCAATTTGTTTTGATTATGTTGTATATAGCAAAACTTAATTCATTCCATACTGTGTTTGTAGGAGGAAGCCAAGGAAGAAAGTGACGATGACATGGGCTTTAGTTTGTTTGATTAA

Protein sequence

>MS.gene06833.t1

MSSGELGCIYATLILHDDGIPITAEKIGTLLKAANVTVESYWPSLFAKLAQSKNVDDLVLNSGAVGGAAVAVSAPAAGGGAAAAAEPAAVEKKEEAKEESDDDMGFSLFD