AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene79872

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene79872.t1 MTR_3g083880 93.689 206 7 1 1 206 1 200 8.85e-139 386
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene79872.t1 AT1G55300 61.244 209 72 3 1 206 1 203 1.42e-84 249
MS.gene79872.t1 AT1G55300 71.154 156 44 1 1 156 1 155 9.21e-79 236

Find 50 sgRNAs with CRISPR-Local

Find 70 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GACTTATGATGATAACTCTT+TGG 0.299738 3.1:-65663669 MS.gene79872:CDS
GTTATCATCATAAGTCTTGT+AGG 0.342174 3.1:+65663676 None:intergenic
GATCTTCTCAAAATCATTGC+TGG 0.365224 3.1:-65663259 MS.gene79872:CDS
GAAGCGGTACGTTTGTGATT+GGG 0.368830 3.1:-65663748 MS.gene79872:CDS
ATGATTATGGTGAGGGAATC+TGG 0.375382 3.1:-65663518 MS.gene79872:CDS
GATTTGCAATTTACCGATGA+TGG 0.382947 3.1:-65663773 MS.gene79872:CDS
TCAATCCGCTCCGCAACATT+AGG 0.383040 3.1:+65663845 None:intergenic
ATCCAATTAACAGATGATTA+TGG 0.395551 3.1:-65663531 MS.gene79872:intron
TCTGCGGAATCTACGCTTAC+GGG 0.407200 3.1:+65663436 None:intergenic
GGAAGGTCCAGCAGAGAAGC+TGG 0.408243 3.1:+65663713 None:intergenic
AGAAGCGGTACGTTTGTGAT+TGG 0.414235 3.1:-65663749 MS.gene79872:CDS
CCAGCATTTGTATGAGTCTC+TGG 0.415981 3.1:+65662840 None:intergenic
TTGGTTAAGACTGCTGATAT+TGG 0.419842 3.1:-65663650 MS.gene79872:CDS
CGCTTACGGGCATCTCTCAT+GGG 0.466049 3.1:+65663449 None:intergenic
CTCTGCGGAATCTACGCTTA+CGG 0.471366 3.1:+65663435 None:intergenic
ACGCTTACGGGCATCTCTCA+TGG 0.476622 3.1:+65663448 None:intergenic
TGTCGACACTCAATTACATC+TGG 0.485186 3.1:+65663485 None:intergenic
CATCTCTCATGGGAGGGGTG+AGG 0.487949 3.1:+65663459 None:intergenic
GCATTACCCAGCTTCTCTGC+TGG 0.493380 3.1:-65663720 MS.gene79872:CDS
TGGAACATCATTCTTTGATG+TGG 0.505743 3.1:+65662860 None:intergenic
AAGCGGTACGTTTGTGATTG+GGG 0.509827 3.1:-65663747 MS.gene79872:CDS
TAAGACTGCTGATATTGGTC+AGG 0.517098 3.1:-65663645 MS.gene79872:intron
CCAGAGACTCATACAAATGC+TGG 0.519889 3.1:-65662840 MS.gene79872:CDS
TACGGGCATCTCTCATGGGA+GGG 0.526533 3.1:+65663453 None:intergenic
TTTGATGTGGATGTAGCTGC+AGG 0.533860 3.1:+65662873 None:intergenic
TTGTAGGATTCAACGACAGC+AGG 0.536746 3.1:+65663692 None:intergenic
GAATGTATTACATTAAGGTC+AGG 0.543174 3.1:+65663410 None:intergenic
TCAACACGGGAGACAAGCTC+AGG 0.549986 3.1:+65663286 None:intergenic
TTACGGGCATCTCTCATGGG+AGG 0.551219 3.1:+65663452 None:intergenic
ACGGGCATCTCTCATGGGAG+GGG 0.554455 3.1:+65663454 None:intergenic
CAAAATCATTGCTGGAGGAA+CGG 0.557535 3.1:-65663251 MS.gene79872:CDS
ATCCGCTCCGCAACATTAGG+TGG 0.567255 3.1:+65663848 None:intergenic
GAGAAGATCTTTCTCAACAC+GGG 0.572853 3.1:+65663273 None:intergenic
TTAACAGATGATTATGGTGA+GGG 0.581913 3.1:-65663525 MS.gene79872:intron
CTTGAAACAAACAAGATGAA+AGG 0.591470 3.1:+65663212 None:intergenic
GAAGGTCCAGCAGAGAAGCT+GGG 0.594836 3.1:+65663714 None:intergenic
TAGAGTTCCACCTAATGTTG+CGG 0.600957 3.1:-65663855 MS.gene79872:CDS
ATTAACAGATGATTATGGTG+AGG 0.615154 3.1:-65663526 MS.gene79872:intron
CTTCTCAAAATCATTGCTGG+AGG 0.618086 3.1:-65663256 MS.gene79872:CDS
GATGTAATTGAGTGTCGACA+TGG 0.622447 3.1:-65663482 MS.gene79872:CDS
GTGGAAGTAGCTGAGCAAGA+AGG 0.629194 3.1:-65662927 MS.gene79872:CDS
TGAGAAGATCTTTCTCAACA+CGG 0.645887 3.1:+65663272 None:intergenic
CGTACCGCTTCTTCCATCAT+CGG 0.650430 3.1:+65663760 None:intergenic
TTTACCGATGATGGAAGAAG+CGG 0.653044 3.1:-65663764 MS.gene79872:CDS
AGGATTCAACGACAGCAGGA+AGG 0.676349 3.1:+65663696 None:intergenic
GAAGTAGCTGAGCAAGAAGG+CGG 0.683444 3.1:-65662924 MS.gene79872:CDS
GAAGGCGGTGAGAATGCTCG+AGG 0.701876 3.1:-65662909 MS.gene79872:CDS
TTCCACCTAATGTTGCGGAG+CGG 0.701947 3.1:-65663850 MS.gene79872:CDS
CATTAAGGTCAGGCTCTCTG+CGG 0.708159 3.1:+65663420 None:intergenic
TCTTGACTGAGATTCACATG+TGG 0.720236 3.1:-65662946 MS.gene79872:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTAAAAAAAATCTTTGAAA+TGG - chr3.1:65663530-65663549 MS.gene79872:intron 10.0%
!! AAATAGAGAAATGAGTTATA+AGG + chr3.1:65663595-65663614 None:intergenic 20.0%
!! AATAGAGAAATGAGTTATAA+GGG + chr3.1:65663594-65663613 None:intergenic 20.0%
!! TTACTAAACATTCTAAATCT+TGG - chr3.1:65663487-65663506 MS.gene79872:CDS 20.0%
!!! AAAAAAAATCTTTGAAATGG+AGG - chr3.1:65663533-65663552 MS.gene79872:intron 20.0%
! AAACGAAGAATGAAAACATA+CGG + chr3.1:65663358-65663377 None:intergenic 25.0%
! ATCCAATTAACAGATGATTA+TGG - chr3.1:65663138-65663157 MS.gene79872:intron 25.0%
! CGAATGAATGTATTACATTA+AGG + chr3.1:65663267-65663286 None:intergenic 25.0%
! GTTAATTGGATTCATTAAGA+AGG + chr3.1:65663129-65663148 None:intergenic 25.0%
! TTATTTAATCATCCGAATCT+AGG + chr3.1:65663099-65663118 None:intergenic 25.0%
ACTCATTTCTCTATTTGAAC+TGG - chr3.1:65663599-65663618 MS.gene79872:intron 30.0%
ATTAACAGATGATTATGGTG+AGG - chr3.1:65663143-65663162 MS.gene79872:intron 30.0%
CACCATAATCATCTGTTAAT+TGG + chr3.1:65663143-65663162 None:intergenic 30.0%
CTCATTTCTCTATTTGAACT+GGG - chr3.1:65663600-65663619 MS.gene79872:intron 30.0%
CTTAATCATACACCTAGATT+CGG - chr3.1:65663084-65663103 MS.gene79872:intron 30.0%
CTTGAAACAAACAAGATGAA+AGG + chr3.1:65663460-65663479 None:intergenic 30.0%
GAATGTATTACATTAAGGTC+AGG + chr3.1:65663262-65663281 None:intergenic 30.0%
GACTTATGATGATAACTCTT+TGG - chr3.1:65663000-65663019 MS.gene79872:intron 30.0%
TCATTTCTCTATTTGAACTG+GGG - chr3.1:65663601-65663620 MS.gene79872:intron 30.0%
TTAACAGATGATTATGGTGA+GGG - chr3.1:65663144-65663163 MS.gene79872:intron 30.0%
! GTTATCATCATAAGTCTTGT+AGG + chr3.1:65662996-65663015 None:intergenic 30.0%
ACAGATAATAGAGCAGTATC+AGG + chr3.1:65663312-65663331 None:intergenic 35.0%
GATCTTCTCAAAATCATTGC+TGG - chr3.1:65663410-65663429 MS.gene79872:intron 35.0%
GATTTGCAATTTACCGATGA+TGG - chr3.1:65662896-65662915 MS.gene79872:CDS 35.0%
TCAGTCAAGAAAATAGCCAA+AGG + chr3.1:65663713-65663732 None:intergenic 35.0%
TGAGAAGATCTTTCTCAACA+CGG + chr3.1:65663400-65663419 None:intergenic 35.0%
TGGAACATCATTCTTTGATG+TGG + chr3.1:65663812-65663831 None:intergenic 35.0%
TGTTAAGTGTGAACAACCTT+TGG - chr3.1:65663694-65663713 MS.gene79872:CDS 35.0%
TTGGTTAAGACTGCTGATAT+TGG - chr3.1:65663019-65663038 MS.gene79872:intron 35.0%
ATGATTATGGTGAGGGAATC+TGG - chr3.1:65663151-65663170 MS.gene79872:intron 40.0%
CAAAATCATTGCTGGAGGAA+CGG - chr3.1:65663418-65663437 MS.gene79872:intron 40.0%
CTTCTCAAAATCATTGCTGG+AGG - chr3.1:65663413-65663432 MS.gene79872:intron 40.0%
GAGAAGATCTTTCTCAACAC+GGG + chr3.1:65663399-65663418 None:intergenic 40.0%
TAAGACTGCTGATATTGGTC+AGG - chr3.1:65663024-65663043 MS.gene79872:intron 40.0%
TAGAGTTCCACCTAATGTTG+CGG - chr3.1:65662814-65662833 MS.gene79872:CDS 40.0%
TCTATTTGAACTGGGGTTCA+TGG - chr3.1:65663608-65663627 MS.gene79872:intron 40.0%
TCTTGACTGAGATTCACATG+TGG - chr3.1:65663723-65663742 MS.gene79872:CDS 40.0%
TGTCGACACTCAATTACATC+TGG + chr3.1:65663187-65663206 None:intergenic 40.0%
!! GATGTAATTGAGTGTCGACA+TGG - chr3.1:65663187-65663206 MS.gene79872:intron 40.0%
!! TTTACCGATGATGGAAGAAG+CGG - chr3.1:65662905-65662924 MS.gene79872:CDS 40.0%
AAGCGGTACGTTTGTGATTG+GGG - chr3.1:65662922-65662941 MS.gene79872:CDS 45.0%
AGAAGCGGTACGTTTGTGAT+TGG - chr3.1:65662920-65662939 MS.gene79872:CDS 45.0%
CCAGAGACTCATACAAATGC+TGG - chr3.1:65663829-65663848 MS.gene79872:CDS 45.0%
CCAGCATTTGTATGAGTCTC+TGG + chr3.1:65663832-65663851 None:intergenic 45.0%
GAAGCGGTACGTTTGTGATT+GGG - chr3.1:65662921-65662940 MS.gene79872:CDS 45.0%
TTGTAGGATTCAACGACAGC+AGG + chr3.1:65662980-65662999 None:intergenic 45.0%
TTTGATGTGGATGTAGCTGC+AGG + chr3.1:65663799-65663818 None:intergenic 45.0%
AGGATTCAACGACAGCAGGA+AGG + chr3.1:65662976-65662995 None:intergenic 50.0%
CATTAAGGTCAGGCTCTCTG+CGG + chr3.1:65663252-65663271 None:intergenic 50.0%
CGTACCGCTTCTTCCATCAT+CGG + chr3.1:65662912-65662931 None:intergenic 50.0%
CTCTGCGGAATCTACGCTTA+CGG + chr3.1:65663237-65663256 None:intergenic 50.0%
CTGCTGATATTGGTCAGGTC+AGG - chr3.1:65663029-65663048 MS.gene79872:intron 50.0%
GAAGTAGCTGAGCAAGAAGG+CGG - chr3.1:65663745-65663764 MS.gene79872:CDS 50.0%
GTGGAAGTAGCTGAGCAAGA+AGG - chr3.1:65663742-65663761 MS.gene79872:CDS 50.0%
TCAATCCGCTCCGCAACATT+AGG + chr3.1:65662827-65662846 None:intergenic 50.0%
TCTGCGGAATCTACGCTTAC+GGG + chr3.1:65663236-65663255 None:intergenic 50.0%
TTCCACCTAATGTTGCGGAG+CGG - chr3.1:65662819-65662838 MS.gene79872:CDS 50.0%
ACGCTTACGGGCATCTCTCA+TGG + chr3.1:65663224-65663243 None:intergenic 55.0%
ATCCGCTCCGCAACATTAGG+TGG + chr3.1:65662824-65662843 None:intergenic 55.0%
CGCTTACGGGCATCTCTCAT+GGG + chr3.1:65663223-65663242 None:intergenic 55.0%
GAAGGTCCAGCAGAGAAGCT+GGG + chr3.1:65662958-65662977 None:intergenic 55.0%
GCATTACCCAGCTTCTCTGC+TGG - chr3.1:65662949-65662968 MS.gene79872:intron 55.0%
TACGGGCATCTCTCATGGGA+GGG + chr3.1:65663219-65663238 None:intergenic 55.0%
TCAACACGGGAGACAAGCTC+AGG + chr3.1:65663386-65663405 None:intergenic 55.0%
TTACGGGCATCTCTCATGGG+AGG + chr3.1:65663220-65663239 None:intergenic 55.0%
ACGGGCATCTCTCATGGGAG+GGG + chr3.1:65663218-65663237 None:intergenic 60.0%
CATCTCTCATGGGAGGGGTG+AGG + chr3.1:65663213-65663232 None:intergenic 60.0%
GAAGGCGGTGAGAATGCTCG+AGG - chr3.1:65663760-65663779 MS.gene79872:CDS 60.0%
GGAAGGTCCAGCAGAGAAGC+TGG + chr3.1:65662959-65662978 None:intergenic 60.0%
CACGGGAGACAAGCTCAGGC+TGG + chr3.1:65663382-65663401 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr3.1 gene 65662794 65663897 65662794 ID=MS.gene79872
chr3.1 mRNA 65662794 65663897 65662794 ID=MS.gene79872.t1;Parent=MS.gene79872
chr3.1 exon 65663646 65663897 65663646 ID=MS.gene79872.t1.exon1;Parent=MS.gene79872.t1
chr3.1 CDS 65663646 65663897 65663646 ID=cds.MS.gene79872.t1;Parent=MS.gene79872.t1
chr3.1 exon 65663421 65663540 65663421 ID=MS.gene79872.t1.exon2;Parent=MS.gene79872.t1
chr3.1 CDS 65663421 65663540 65663421 ID=cds.MS.gene79872.t1;Parent=MS.gene79872.t1
chr3.1 exon 65663224 65663308 65663224 ID=MS.gene79872.t1.exon3;Parent=MS.gene79872.t1
chr3.1 CDS 65663224 65663308 65663224 ID=cds.MS.gene79872.t1;Parent=MS.gene79872.t1
chr3.1 exon 65662794 65662957 65662794 ID=MS.gene79872.t1.exon4;Parent=MS.gene79872.t1
chr3.1 CDS 65662794 65662957 65662794 ID=cds.MS.gene79872.t1;Parent=MS.gene79872.t1
Gene Sequence

>MS.gene79872

ATGGAGGAGCAATTCATACTTAGAGTTCCACCTAATGTTGCGGAGCGGATTGAGCGTCTTTTGAATGAAAACAATGCTTCTTCATCTGAAGACAAGTCGCTAGATTTGCAATTTACCGATGATGGAAGAAGCGGTACGTTTGTGATTGGGGATGAGCATTACCCAGCTTCTCTGCTGGACCTTCCTGCTGTCGTTGAATCCTACAAGACTTATGATGATAACTCTTTGGTTAAGACTGCTGATATTGGTCAGGTCAGGTATCTATCGTTAATTCATATTATTTGTTTATTCTTAATCATACACCTAGATTCGGATGATTAAATAACTGATTGCCTTCTTAATGAATCCAATTAACAGATGATTATGGTGAGGGAATCTGGTGATGCTGCTCCAGATGTAATTGAGTGTCGACATGGCCTCACCCCTCCCATGAGAGATGCCCGTAAGCGTAGATTCCGCAGAGAGCCTGACCTTAATGTAATACATTCATTCGTGCATTATATTATCTAAGCATACCTGATACTGCTCTATTATCTGTGCGTTTGTGTGCTCTCTTACTTACCGTATGTTTTCATTCTTCGTTTTCCAGCCTGAGCTTGTCTCCCGTGTTGAGAAAGATCTTCTCAAAATCATTGCTGGAGGAACGGCTGAAAATATTGATATCCTTTCATCTTGTTTGTTTCAAGCAGTAGTTTACTAAACATTCTAAATCTTGGATACAAATTTATGATTTCACTTTAAAAAAAATCTTTGAAATGGAGGTCTGTTGAGATCTTTTTTGTTGATTACTTTCTTTGCCCTTATAACTCATTTCTCTATTTGAACTGGGGTTCATGGAATAAGTAGCATCTATTTGCATTTGCATCAATGACAAAAGCAAGTTTTTCGCTTTCATTATATTGTTAAGTGTGAACAACCTTTGGCTATTTTCTTGACTGAGATTCACATGTGGAAGTAGCTGAGCAAGAAGGCGGTGAGAATGCTCGAGGTTCTAATAAAAAACCTGCAGCTACATCCACATCAAAGAATGATGTTCCAGAGACTCATACAAATGCTGGTGATGCTGACAGAAGTGACTCTGATGAATCTGATGACTCAGTTTGA
Protein sequence

>MS.gene79872.t1

MEEQFILRVPPNVAERIERLLNENNASSSEDKSLDLQFTDDGRSGTFVIGDEHYPASLLDLPAVVESYKTYDDNSLVKTADIGQMIMVRESGDAAPDVIECRHGLTPPMRDARKRRFRREPDLNPELVSRVEKDLLKIIAGGTAENIDILSSYSHVEVAEQEGGENARGSNKKPAATSTSKNDVPETHTNAGDADRSDSDESDDSV