AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene35701


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene35701.t1 MTR_2g086590 91.603 262 21 1 1 262 1 261 5.41e-169 468
MS.gene35701.t1 MTR_4g052880 38.961 231 114 8 1 220 1 215 1.58e-33 122
MS.gene35701.t1 MTR_7g113950 38.406 138 78 3 112 247 106 238 5.90e-13 67.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene35701.t1 AT5G22390 33.190 232 94 7 1 221 1 182 6.05e-21 88.2
MS.gene35701.t1 AT1G54740 33.043 115 74 2 106 219 33 145 6.82e-12 64.7

Find 68 sgRNAs with CRISPR-Local

Find 76 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCCTCCTGATGATGAGTTTC+TGG 0.094474 2.4:-13697718 MS.gene35701:CDS
GGAAGCCTTGGGTTTATTTC+AGG 0.143738 2.4:-13697848 MS.gene35701:CDS
TTCAGGTCTATTAGGAATAA+TGG 0.250900 2.4:-13697831 MS.gene35701:CDS
TCTTCAAGACATCATTCTTA+TGG 0.257835 2.4:-13697933 MS.gene35701:CDS
GGGTTTATTTCAGGTCTATT+AGG 0.260287 2.4:-13697839 MS.gene35701:CDS
TCCTCCTTTACTGAGATATT+TGG 0.276616 2.4:-13698263 MS.gene35701:CDS
AAGAAGCTGAAGATGGAGTT+TGG 0.330013 2.4:+13698153 None:intergenic
GATGAAGGAGAGAATGATAT+AGG 0.348515 2.4:-13697687 MS.gene35701:CDS
AGTAAAGGAGGAGGACTCTA+TGG 0.362243 2.4:+13698274 None:intergenic
CATCTTTGCACCGAAGGTCT+TGG 0.374924 2.4:-13698050 MS.gene35701:CDS
AGTCCTCCCTATGCTTGAAA+TGG 0.379725 2.4:+13697872 None:intergenic
CTGTTGGTATGCCTTGCTAT+TGG 0.401166 2.4:+13698119 None:intergenic
TATAAGCACGCAGGACCTCC+TGG 0.403062 2.4:+13697775 None:intergenic
TAGGGAGGACTGGGAAGCCT+TGG 0.408356 2.4:-13697860 MS.gene35701:CDS
AGGGAGGACTGGGAAGCCTT+GGG 0.428523 2.4:-13697859 MS.gene35701:CDS
TTGATGATGATTCCTTGAAA+TGG 0.433133 2.4:+13698234 None:intergenic
TCTTCCAGAAACTCATCATC+AGG 0.449345 2.4:+13697714 None:intergenic
GAAAGGGATTGAAGCAGTGT+TGG 0.454932 2.4:+13698323 None:intergenic
ATTTGGTGAACTCCATTTCA+AGG 0.460735 2.4:-13698246 MS.gene35701:CDS
TTCAGAATTCAGCCATGAAA+AGG 0.472686 2.4:+13698079 None:intergenic
AAGACTCAGACTCTTTGATC+TGG 0.478220 2.4:+13698186 None:intergenic
CAATAGCAAGGCATACCAAC+AGG 0.489567 2.4:-13698118 MS.gene35701:CDS
CTCCTCCCATTTCAAGCATA+GGG 0.493217 2.4:-13697878 MS.gene35701:CDS
GGGTGTCAAAGATGTGTTGT+AGG 0.504528 2.4:+13698360 None:intergenic
ATTTCAAGCATAGGGAGGAC+TGG 0.507716 2.4:-13697870 MS.gene35701:CDS
GTCCTCCCTATGCTTGAAAT+GGG 0.513543 2.4:+13697873 None:intergenic
TAGGCTGTCACAGGTTGCCA+TGG 0.514804 2.4:+13698379 None:intergenic
CCTCCTCCCATTTCAAGCAT+AGG 0.517066 2.4:-13697879 MS.gene35701:CDS
TCGGTATCCTTACCTCTTCG+AGG 0.517417 2.4:+13697799 None:intergenic
ATGGAGAATGTAGGAGGTCA+AGG 0.523495 2.4:-13697914 MS.gene35701:CDS
TTCACCAAATATCTCAGTAA+AGG 0.527789 2.4:+13698259 None:intergenic
TTTCAAGCATAGGGAGGACT+GGG 0.533628 2.4:-13697869 MS.gene35701:CDS
AGCATGCATCTTTGCACCGA+AGG 0.535589 2.4:-13698056 MS.gene35701:CDS
GAGGACTCTATGGATTTCAC+TGG 0.537192 2.4:+13698284 None:intergenic
CCTATGCTTGAAATGGGAGG+AGG 0.541240 2.4:+13697879 None:intergenic
CTGCGTGCTTATAGAGAGGA+TGG 0.545087 2.4:-13697765 MS.gene35701:CDS
GATTTGTCCTCGAAGAGGTA+AGG 0.546648 2.4:-13697806 MS.gene35701:CDS
ATAAGCACGCAGGACCTCCT+GGG 0.552052 2.4:+13697776 None:intergenic
ACTCTCAAAACCAAGACCTT+CGG 0.553557 2.4:+13698040 None:intergenic
AGAGGTAAGGATACCGACCC+AGG 0.560235 2.4:-13697793 MS.gene35701:CDS
TTTCAATTACACCAATAGCA+AGG 0.571241 2.4:-13698130 MS.gene35701:CDS
ACCAAATATCTCAGTAAAGG+AGG 0.572346 2.4:+13698262 None:intergenic
AGAAGACATGGCAAAAGAAG+AGG 0.576952 2.4:-13697646 MS.gene35701:CDS
TGATCTGGTTGAAGTTTGTG+TGG 0.577238 2.4:+13698201 None:intergenic
ATCATTCTTATGGAGAATGT+AGG 0.580254 2.4:-13697923 MS.gene35701:CDS
TGAGAGTTCAGACGATGTCA+AGG 0.583846 2.4:-13698024 MS.gene35701:CDS
AAATATCTCAGTAAAGGAGG+AGG 0.599938 2.4:+13698265 None:intergenic
CTATGCTTGAAATGGGAGGA+GGG 0.601586 2.4:+13697880 None:intergenic
TTTCTGGAAGATGAGGATGA+AGG 0.603701 2.4:-13697702 MS.gene35701:CDS
AGCTGAGGAAGGAGAAGACA+TGG 0.613301 2.4:-13697658 MS.gene35701:CDS
GATGTCAAGGACTCAAAGAG+TGG 0.617159 2.4:-13698011 MS.gene35701:CDS
TCCAGAAACTCATCATCAGG+AGG 0.618671 2.4:+13697717 None:intergenic
TGGAGAATGTAGGAGGTCAA+GGG 0.619517 2.4:-13697913 MS.gene35701:CDS
GATGTGTTGTAGGCTGTCAC+AGG 0.621992 2.4:+13698370 None:intergenic
ATAGGATGCATAGCTGAGGA+AGG 0.625542 2.4:-13697669 MS.gene35701:CDS
ATTCTTATGGAGAATGTAGG+AGG 0.629147 2.4:-13697920 MS.gene35701:CDS
CTCCCTATGCTTGAAATGGG+AGG 0.629607 2.4:+13697876 None:intergenic
GCACGCAGGACCTCCTGGGT+CGG 0.641235 2.4:+13697780 None:intergenic
CTCCCATTTCAAGCATAGGG+AGG 0.649676 2.4:-13697875 MS.gene35701:CDS
ATAGACCTGAAATAAACCCA+AGG 0.650033 2.4:+13697843 None:intergenic
TGGAAGATTTGTCCTCGAAG+AGG 0.651915 2.4:-13697811 MS.gene35701:CDS
GTGCTTATAGAGAGGATGGA+AGG 0.652178 2.4:-13697761 MS.gene35701:CDS
CCAGAAACTCATCATCAGGA+GGG 0.654723 2.4:+13697718 None:intergenic
GGTCCTGCGTGCTTATAGAG+AGG 0.655010 2.4:-13697769 MS.gene35701:CDS
TGATGAGTTTCTGGAAGATG+AGG 0.656575 2.4:-13697709 MS.gene35701:CDS
TGATATAGGATGCATAGCTG+AGG 0.671509 2.4:-13697673 MS.gene35701:CDS
CATCCTCTCTATAAGCACGC+AGG 0.674324 2.4:+13697766 None:intergenic
GGTAAGGATACCGACCCAGG+AGG 0.739295 2.4:-13697790 MS.gene35701:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTAATTTTGTTAAATGAAA+GGG + chr2.4:13697672-13697691 None:intergenic 10.0%
!!! GTTTAATTTTGTTAAATGAA+AGG + chr2.4:13697673-13697692 None:intergenic 15.0%
ATCATTCTTATGGAGAATGT+AGG - chr2.4:13698053-13698072 MS.gene35701:CDS 30.0%
ATTGAAAAAGAAGCTGAAGA+TGG + chr2.4:13697833-13697852 None:intergenic 30.0%
TCTTCAAGACATCATTCTTA+TGG - chr2.4:13698043-13698062 MS.gene35701:CDS 30.0%
TTCACCAAATATCTCAGTAA+AGG + chr2.4:13697720-13697739 None:intergenic 30.0%
TTCAGGTCTATTAGGAATAA+TGG - chr2.4:13698145-13698164 MS.gene35701:CDS 30.0%
TTTCAATTACACCAATAGCA+AGG - chr2.4:13697846-13697865 MS.gene35701:CDS 30.0%
!! TTGATGATGATTCCTTGAAA+TGG + chr2.4:13697745-13697764 None:intergenic 30.0%
!!! GCAATCTCTTTTTTGTCATT+TGG + chr2.4:13698376-13698395 None:intergenic 30.0%
AAATATCTCAGTAAAGGAGG+AGG + chr2.4:13697714-13697733 None:intergenic 35.0%
ACCAAATATCTCAGTAAAGG+AGG + chr2.4:13697717-13697736 None:intergenic 35.0%
ATAGACCTGAAATAAACCCA+AGG + chr2.4:13698136-13698155 None:intergenic 35.0%
ATTCTTATGGAGAATGTAGG+AGG - chr2.4:13698056-13698075 MS.gene35701:CDS 35.0%
GATGAAGGAGAGAATGATAT+AGG - chr2.4:13698289-13698308 MS.gene35701:CDS 35.0%
TCCTCCTTTACTGAGATATT+TGG - chr2.4:13697713-13697732 MS.gene35701:CDS 35.0%
TTCAGAATTCAGCCATGAAA+AGG + chr2.4:13697900-13697919 None:intergenic 35.0%
! ATTTGGTGAACTCCATTTCA+AGG - chr2.4:13697730-13697749 MS.gene35701:CDS 35.0%
! GGGTTTATTTCAGGTCTATT+AGG - chr2.4:13698137-13698156 MS.gene35701:CDS 35.0%
!! TGTTGGATTTTCTGGCAATA+GGG + chr2.4:13697639-13697658 None:intergenic 35.0%
AAGAAGCTGAAGATGGAGTT+TGG + chr2.4:13697826-13697845 None:intergenic 40.0%
AAGACTCAGACTCTTTGATC+TGG + chr2.4:13697793-13697812 None:intergenic 40.0%
ACTCTCAAAACCAAGACCTT+CGG + chr2.4:13697939-13697958 None:intergenic 40.0%
AGAAGACATGGCAAAAGAAG+AGG - chr2.4:13698330-13698349 MS.gene35701:CDS 40.0%
TCTTCCAGAAACTCATCATC+AGG + chr2.4:13698265-13698284 None:intergenic 40.0%
TGATATAGGATGCATAGCTG+AGG - chr2.4:13698303-13698322 MS.gene35701:CDS 40.0%
TGATCTGGTTGAAGTTTGTG+TGG + chr2.4:13697778-13697797 None:intergenic 40.0%
! AAAGCAGTGACACCTTTTCA+TGG - chr2.4:13697885-13697904 MS.gene35701:CDS 40.0%
! TGATGAGTTTCTGGAAGATG+AGG - chr2.4:13698267-13698286 MS.gene35701:CDS 40.0%
! TTTCTGGAAGATGAGGATGA+AGG - chr2.4:13698274-13698293 MS.gene35701:CDS 40.0%
!! GTGTTGGATTTTCTGGCAAT+AGG + chr2.4:13697640-13697659 None:intergenic 40.0%
!! TGAAGCAGTGTTGGATTTTC+TGG + chr2.4:13697647-13697666 None:intergenic 40.0%
AGTAAAGGAGGAGGACTCTA+TGG + chr2.4:13697705-13697724 None:intergenic 45.0%
AGTCCTCCCTATGCTTGAAA+TGG + chr2.4:13698107-13698126 None:intergenic 45.0%
ATAGGATGCATAGCTGAGGA+AGG - chr2.4:13698307-13698326 MS.gene35701:CDS 45.0%
ATGGAGAATGTAGGAGGTCA+AGG - chr2.4:13698062-13698081 MS.gene35701:CDS 45.0%
ATTTCAAGCATAGGGAGGAC+TGG - chr2.4:13698106-13698125 MS.gene35701:CDS 45.0%
CAATAGCAAGGCATACCAAC+AGG - chr2.4:13697858-13697877 MS.gene35701:CDS 45.0%
CCAGAAACTCATCATCAGGA+GGG + chr2.4:13698261-13698280 None:intergenic 45.0%
CTATGCTTGAAATGGGAGGA+GGG + chr2.4:13698099-13698118 None:intergenic 45.0%
CTCCTCCCATTTCAAGCATA+GGG - chr2.4:13698098-13698117 MS.gene35701:CDS 45.0%
GAAAGGGATTGAAGCAGTGT+TGG + chr2.4:13697656-13697675 None:intergenic 45.0%
GAGGACTCTATGGATTTCAC+TGG + chr2.4:13697695-13697714 None:intergenic 45.0%
GATGTCAAGGACTCAAAGAG+TGG - chr2.4:13697965-13697984 MS.gene35701:CDS 45.0%
GATTTGTCCTCGAAGAGGTA+AGG - chr2.4:13698170-13698189 MS.gene35701:CDS 45.0%
GGAAGCCTTGGGTTTATTTC+AGG - chr2.4:13698128-13698147 MS.gene35701:CDS 45.0%
GGGTGTCAAAGATGTGTTGT+AGG + chr2.4:13697619-13697638 None:intergenic 45.0%
GTCCTCCCTATGCTTGAAAT+GGG + chr2.4:13698106-13698125 None:intergenic 45.0%
GTGCTTATAGAGAGGATGGA+AGG - chr2.4:13698215-13698234 MS.gene35701:CDS 45.0%
TCCAGAAACTCATCATCAGG+AGG + chr2.4:13698262-13698281 None:intergenic 45.0%
TGAGAGTTCAGACGATGTCA+AGG - chr2.4:13697952-13697971 MS.gene35701:CDS 45.0%
TGGAAGATTTGTCCTCGAAG+AGG - chr2.4:13698165-13698184 MS.gene35701:CDS 45.0%
TGGAGAATGTAGGAGGTCAA+GGG - chr2.4:13698063-13698082 MS.gene35701:CDS 45.0%
TTTCAAGCATAGGGAGGACT+GGG - chr2.4:13698107-13698126 MS.gene35701:CDS 45.0%
! CTGTTGGTATGCCTTGCTAT+TGG + chr2.4:13697860-13697879 None:intergenic 45.0%
AGCATGCATCTTTGCACCGA+AGG - chr2.4:13697920-13697939 MS.gene35701:CDS 50.0%
AGCTGAGGAAGGAGAAGACA+TGG - chr2.4:13698318-13698337 MS.gene35701:CDS 50.0%
CATCCTCTCTATAAGCACGC+AGG + chr2.4:13698213-13698232 None:intergenic 50.0%
CATCTTTGCACCGAAGGTCT+TGG - chr2.4:13697926-13697945 MS.gene35701:CDS 50.0%
CCTATGCTTGAAATGGGAGG+AGG + chr2.4:13698100-13698119 None:intergenic 50.0%
CCTCCTCCCATTTCAAGCAT+AGG - chr2.4:13698097-13698116 MS.gene35701:CDS 50.0%
CTCCCATTTCAAGCATAGGG+AGG - chr2.4:13698101-13698120 MS.gene35701:CDS 50.0%
CTCCCTATGCTTGAAATGGG+AGG + chr2.4:13698103-13698122 None:intergenic 50.0%
CTGCGTGCTTATAGAGAGGA+TGG - chr2.4:13698211-13698230 MS.gene35701:CDS 50.0%
GATGTGTTGTAGGCTGTCAC+AGG + chr2.4:13697609-13697628 None:intergenic 50.0%
TCGGTATCCTTACCTCTTCG+AGG + chr2.4:13698180-13698199 None:intergenic 50.0%
! CCCTCCTGATGATGAGTTTC+TGG - chr2.4:13698258-13698277 MS.gene35701:CDS 50.0%
!! GTCACTGCTTTTGTGCCTGT+TGG + chr2.4:13697876-13697895 None:intergenic 50.0%
AGAGGTAAGGATACCGACCC+AGG - chr2.4:13698183-13698202 MS.gene35701:CDS 55.0%
ATAAGCACGCAGGACCTCCT+GGG + chr2.4:13698203-13698222 None:intergenic 55.0%
GGTCCTGCGTGCTTATAGAG+AGG - chr2.4:13698207-13698226 MS.gene35701:CDS 55.0%
TATAAGCACGCAGGACCTCC+TGG + chr2.4:13698204-13698223 None:intergenic 55.0%
AGGGAGGACTGGGAAGCCTT+GGG - chr2.4:13698117-13698136 MS.gene35701:CDS 60.0%
GGTAAGGATACCGACCCAGG+AGG - chr2.4:13698186-13698205 MS.gene35701:CDS 60.0%
TAGGGAGGACTGGGAAGCCT+TGG - chr2.4:13698116-13698135 MS.gene35701:CDS 60.0%
GCACGCAGGACCTCCTGGGT+CGG + chr2.4:13698199-13698218 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 13697599 13698399 13697599 ID=MS.gene35701
chr2.4 mRNA 13697599 13698399 13697599 ID=MS.gene35701.t1;Parent=MS.gene35701
chr2.4 exon 13697599 13698399 13697599 ID=MS.gene35701.t1.exon1;Parent=MS.gene35701.t1
chr2.4 CDS 13697599 13698399 13697599 ID=cds.MS.gene35701.t1;Parent=MS.gene35701.t1
Gene Sequence

>MS.gene35701

ATGGCAACCTGTGACAGCCTACAACACATCTTTGACACCCTATTGCCAGAAAATCCAACACTGCTTCAATCCCTTTCATTTAACAAAATTAAACCAGTGAAATCCATAGAGTCCTCCTCCTTTACTGAGATATTTGGTGAACTCCATTTCAAGGAATCATCATCAACAGAGATAAACCACACAAACTTCAACCAGATCAAAGAGTCTGAGTCTTTTGACACTATCCAAACTCCATCTTCAGCTTCTTTTTCAATTACACCAATAGCAAGGCATACCAACAGGCACAAAAGCAGTGACACCTTTTCATGGCTGAATTCTGAAAGCATGCATCTTTGCACCGAAGGTCTTGGTTTTGAGAGTTCAGACGATGTCAAGGACTCAAAGAGTGGAGCGAATGAATCTTTACAAATTGATCAAAATGAGAAACGTGTCGAACATCATTTATCTTCAAGACATCATTCTTATGGAGAATGTAGGAGGTCAAGGGTAAGTGAGTACCCTCCTCCCATTTCAAGCATAGGGAGGACTGGGAAGCCTTGGGTTTATTTCAGGTCTATTAGGAATAATGGAAGATTTGTCCTCGAAGAGGTAAGGATACCGACCCAGGAGGTCCTGCGTGCTTATAGAGAGGATGGAAGGCTCAAGCTGCAGTTTGTTCACCCTCCTGATGATGAGTTTCTGGAAGATGAGGATGAAGGAGAGAATGATATAGGATGCATAGCTGAGGAAGGAGAAGACATGGCAAAAGAAGAGGACGATTGTGTAACACATCATCCAAATGACAAAAAAGAGATTGCTTGA

Protein sequence

>MS.gene35701.t1

MATCDSLQHIFDTLLPENPTLLQSLSFNKIKPVKSIESSSFTEIFGELHFKESSSTEINHTNFNQIKESESFDTIQTPSSASFSITPIARHTNRHKSSDTFSWLNSESMHLCTEGLGFESSDDVKDSKSGANESLQIDQNEKRVEHHLSSRHHSYGECRRSRVSEYPPPISSIGRTGKPWVYFRSIRNNGRFVLEEVRIPTQEVLRAYREDGRLKLQFVHPPDDEFLEDEDEGENDIGCIAEEGEDMAKEEDDCVTHHPNDKKEIA