AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene35422


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene35422.t1 MTR_2g086590 91.603 262 21 1 1 262 1 261 1.25e-168 466
MS.gene35422.t1 MTR_4g052880 38.961 231 114 8 1 220 1 215 1.36e-33 122
MS.gene35422.t1 MTR_7g113950 38.406 138 78 3 112 247 106 238 4.96e-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.gene35422.t1 AT5G22390 33.621 232 93 7 1 221 1 182 1.65e-21 89.7
MS.gene35422.t1 AT1G54740 33.043 115 74 2 106 219 33 145 7.02e-12 64.7

Find 69 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 2.1:-15550979 MS.gene35422:CDS
GGAAGCCTTGGGTTTATTTC+AGG 0.176058 2.1:-15551109 MS.gene35422:CDS
TTCAGGTCTATTAGGAATAA+TGG 0.250900 2.1:-15551092 MS.gene35422:CDS
TCTTCAAGACATCATTCTTA+TGG 0.257835 2.1:-15551194 MS.gene35422:CDS
GGGTTTATTTCAGGTCTATT+AGG 0.260287 2.1:-15551100 MS.gene35422:CDS
TCCTCCTTTACTGAGATATT+TGG 0.276616 2.1:-15551524 MS.gene35422:CDS
AAGAAGCTGAAGATGGAGTT+TGG 0.330013 2.1:+15551414 None:intergenic
GATGAAGGAGAGAATGATAT+AGG 0.348515 2.1:-15550948 MS.gene35422:CDS
GAAATAAACCCAAGGCTTCC+CGG 0.351372 2.1:+15551112 None:intergenic
AGTAAAGGAGGAGGACTCTA+TGG 0.362243 2.1:+15551535 None:intergenic
CATCTTTGCACCGAAGGTCT+TGG 0.374924 2.1:-15551311 MS.gene35422:CDS
GGTCCTCCCTATGCTTGAAA+TGG 0.394454 2.1:+15551133 None:intergenic
TAGGGAGGACCGGGAAGCCT+TGG 0.399372 2.1:-15551121 MS.gene35422:CDS
CTGTTGGTATGCCTTGCTAT+TGG 0.401166 2.1:+15551380 None:intergenic
TATAAGCACGCAGGACCTCC+TGG 0.403062 2.1:+15551036 None:intergenic
AGGGAGGACCGGGAAGCCTT+GGG 0.431578 2.1:-15551120 MS.gene35422:CDS
TTGATGATGATTCCTTGAAA+TGG 0.433133 2.1:+15551495 None:intergenic
TCTTCCAGAAACTCATCATC+AGG 0.449345 2.1:+15550975 None:intergenic
GAAAGGGATTGAAGCAGTGT+TGG 0.454932 2.1:+15551584 None:intergenic
ATTTGGTGAACTCCATTTCA+AGG 0.460735 2.1:-15551507 MS.gene35422:CDS
TTCAGAATTCAGCCATGAAA+AGG 0.472686 2.1:+15551340 None:intergenic
AAGACTCAGACTCTTTGATC+TGG 0.478220 2.1:+15551447 None:intergenic
CAATAGCAAGGCATACCAAC+AGG 0.489567 2.1:-15551379 MS.gene35422:CDS
GTCCTCCCTATGCTTGAAAT+GGG 0.492965 2.1:+15551134 None:intergenic
CTCCTCCCATTTCAAGCATA+GGG 0.493217 2.1:-15551139 MS.gene35422:CDS
GGGTGTCAAAGATGTGTTGT+AGG 0.504528 2.1:+15551621 None:intergenic
TAGGCTGTCACAGGTTGCCA+TGG 0.514804 2.1:+15551640 None:intergenic
CCTCCTCCCATTTCAAGCAT+AGG 0.517066 2.1:-15551140 MS.gene35422:CDS
TCGGTATCCTTACCTCTTCG+AGG 0.517417 2.1:+15551060 None:intergenic
ATGGAGAATGTAGGAGGTCA+AGG 0.523495 2.1:-15551175 MS.gene35422:CDS
ATTTCAAGCATAGGGAGGAC+CGG 0.525710 2.1:-15551131 MS.gene35422:CDS
TTCACCAAATATCTCAGTAA+AGG 0.527789 2.1:+15551520 None:intergenic
AGCATGCATCTTTGCACCGA+AGG 0.535589 2.1:-15551317 MS.gene35422:CDS
GAGGACTCTATGGATTTCAC+TGG 0.537192 2.1:+15551545 None:intergenic
CCTATGCTTGAAATGGGAGG+AGG 0.541240 2.1:+15551140 None:intergenic
CTGCGTGCTTATAGAGAGGA+TGG 0.545087 2.1:-15551026 MS.gene35422:CDS
GATTTGTCCTCGAAGAGGTA+AGG 0.546648 2.1:-15551067 MS.gene35422:CDS
ATAAGCACGCAGGACCTCCT+GGG 0.552052 2.1:+15551037 None:intergenic
ACTCTCAAAACCAAGACCTT+CGG 0.553557 2.1:+15551301 None:intergenic
AGAGGTAAGGATACCGACCC+AGG 0.560235 2.1:-15551054 MS.gene35422:CDS
TTTCAATTACACCAATAGCA+AGG 0.571241 2.1:-15551391 MS.gene35422:CDS
ACCAAATATCTCAGTAAAGG+AGG 0.572346 2.1:+15551523 None:intergenic
AGAAGACATGGCAAAAGAAG+AGG 0.576952 2.1:-15550907 MS.gene35422:CDS
TGATCTGGTTGAAGTTTGTG+TGG 0.577238 2.1:+15551462 None:intergenic
ATCATTCTTATGGAGAATGT+AGG 0.580254 2.1:-15551184 MS.gene35422:CDS
TGAGAGTTCAGACGATGTCG+AGG 0.585948 2.1:-15551285 MS.gene35422:CDS
TTTCAAGCATAGGGAGGACC+GGG 0.586404 2.1:-15551130 MS.gene35422:CDS
AAATATCTCAGTAAAGGAGG+AGG 0.599938 2.1:+15551526 None:intergenic
CTATGCTTGAAATGGGAGGA+GGG 0.601586 2.1:+15551141 None:intergenic
TTTCTGGAAGATGAGGATGA+AGG 0.603701 2.1:-15550963 MS.gene35422:CDS
AGCTGAGGAAGGAGAAGACA+TGG 0.613301 2.1:-15550919 MS.gene35422:CDS
TCCAGAAACTCATCATCAGG+AGG 0.618671 2.1:+15550978 None:intergenic
TGGAGAATGTAGGAGGTCAA+GGG 0.619517 2.1:-15551174 MS.gene35422:CDS
GATGTGTTGTAGGCTGTCAC+AGG 0.621992 2.1:+15551631 None:intergenic
CTCCCTATGCTTGAAATGGG+AGG 0.622171 2.1:+15551137 None:intergenic
GATGTCGAGGACTCAAAGAG+TGG 0.622521 2.1:-15551272 MS.gene35422:CDS
ATAGGATGCATAGCTGAGGA+AGG 0.625542 2.1:-15550930 MS.gene35422:CDS
ATTCTTATGGAGAATGTAGG+AGG 0.629147 2.1:-15551181 MS.gene35422:CDS
GCACGCAGGACCTCCTGGGT+CGG 0.641235 2.1:+15551041 None:intergenic
ATAGACCTGAAATAAACCCA+AGG 0.650033 2.1:+15551104 None:intergenic
TGGAAGATTTGTCCTCGAAG+AGG 0.651915 2.1:-15551072 MS.gene35422:CDS
GTGCTTATAGAGAGGATGGA+AGG 0.652178 2.1:-15551022 MS.gene35422:CDS
CCAGAAACTCATCATCAGGA+GGG 0.654723 2.1:+15550979 None:intergenic
GGTCCTGCGTGCTTATAGAG+AGG 0.655010 2.1:-15551030 MS.gene35422:CDS
TGATGAGTTTCTGGAAGATG+AGG 0.656575 2.1:-15550970 MS.gene35422:CDS
CTCCCATTTCAAGCATAGGG+AGG 0.670101 2.1:-15551136 MS.gene35422:CDS
TGATATAGGATGCATAGCTG+AGG 0.671509 2.1:-15550934 MS.gene35422:CDS
CATCCTCTCTATAAGCACGC+AGG 0.674324 2.1:+15551027 None:intergenic
GGTAAGGATACCGACCCAGG+AGG 0.739295 2.1:-15551051 MS.gene35422:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTAATTTTGTTAAATGAAA+GGG + chr2.1:15550933-15550952 None:intergenic 10.0%
!!! GTTTAATTTTGTTAAATGAA+AGG + chr2.1:15550934-15550953 None:intergenic 15.0%
ATCATTCTTATGGAGAATGT+AGG - chr2.1:15551314-15551333 MS.gene35422:CDS 30.0%
ATTGAAAAAGAAGCTGAAGA+TGG + chr2.1:15551094-15551113 None:intergenic 30.0%
TCTTCAAGACATCATTCTTA+TGG - chr2.1:15551304-15551323 MS.gene35422:CDS 30.0%
TTCACCAAATATCTCAGTAA+AGG + chr2.1:15550981-15551000 None:intergenic 30.0%
TTCAGGTCTATTAGGAATAA+TGG - chr2.1:15551406-15551425 MS.gene35422:CDS 30.0%
TTTCAATTACACCAATAGCA+AGG - chr2.1:15551107-15551126 MS.gene35422:CDS 30.0%
!! TTGATGATGATTCCTTGAAA+TGG + chr2.1:15551006-15551025 None:intergenic 30.0%
AAATATCTCAGTAAAGGAGG+AGG + chr2.1:15550975-15550994 None:intergenic 35.0%
ACCAAATATCTCAGTAAAGG+AGG + chr2.1:15550978-15550997 None:intergenic 35.0%
ATAGACCTGAAATAAACCCA+AGG + chr2.1:15551397-15551416 None:intergenic 35.0%
ATTCTTATGGAGAATGTAGG+AGG - chr2.1:15551317-15551336 MS.gene35422:CDS 35.0%
GATGAAGGAGAGAATGATAT+AGG - chr2.1:15551550-15551569 MS.gene35422:CDS 35.0%
TCCTCCTTTACTGAGATATT+TGG - chr2.1:15550974-15550993 MS.gene35422:CDS 35.0%
TTCAGAATTCAGCCATGAAA+AGG + chr2.1:15551161-15551180 None:intergenic 35.0%
! ATTTGGTGAACTCCATTTCA+AGG - chr2.1:15550991-15551010 MS.gene35422:CDS 35.0%
! GGGTTTATTTCAGGTCTATT+AGG - chr2.1:15551398-15551417 MS.gene35422:CDS 35.0%
!! TGTTGGATTTTCTGGCAATA+GGG + chr2.1:15550900-15550919 None:intergenic 35.0%
AAGAAGCTGAAGATGGAGTT+TGG + chr2.1:15551087-15551106 None:intergenic 40.0%
AAGACTCAGACTCTTTGATC+TGG + chr2.1:15551054-15551073 None:intergenic 40.0%
ACTCTCAAAACCAAGACCTT+CGG + chr2.1:15551200-15551219 None:intergenic 40.0%
AGAAGACATGGCAAAAGAAG+AGG - chr2.1:15551591-15551610 MS.gene35422:CDS 40.0%
TCTTCCAGAAACTCATCATC+AGG + chr2.1:15551526-15551545 None:intergenic 40.0%
TGATATAGGATGCATAGCTG+AGG - chr2.1:15551564-15551583 MS.gene35422:CDS 40.0%
TGATCTGGTTGAAGTTTGTG+TGG + chr2.1:15551039-15551058 None:intergenic 40.0%
! AAAGCAGTGACACCTTTTCA+TGG - chr2.1:15551146-15551165 MS.gene35422:CDS 40.0%
! TGATGAGTTTCTGGAAGATG+AGG - chr2.1:15551528-15551547 MS.gene35422:CDS 40.0%
! TTTCTGGAAGATGAGGATGA+AGG - chr2.1:15551535-15551554 MS.gene35422:CDS 40.0%
!! GTGTTGGATTTTCTGGCAAT+AGG + chr2.1:15550901-15550920 None:intergenic 40.0%
!! TGAAGCAGTGTTGGATTTTC+TGG + chr2.1:15550908-15550927 None:intergenic 40.0%
AGTAAAGGAGGAGGACTCTA+TGG + chr2.1:15550966-15550985 None:intergenic 45.0%
ATAGGATGCATAGCTGAGGA+AGG - chr2.1:15551568-15551587 MS.gene35422:CDS 45.0%
ATGGAGAATGTAGGAGGTCA+AGG - chr2.1:15551323-15551342 MS.gene35422:CDS 45.0%
ATTTCAAGCATAGGGAGGAC+CGG - chr2.1:15551367-15551386 MS.gene35422:CDS 45.0%
CAATAGCAAGGCATACCAAC+AGG - chr2.1:15551119-15551138 MS.gene35422:CDS 45.0%
CCAGAAACTCATCATCAGGA+GGG + chr2.1:15551522-15551541 None:intergenic 45.0%
CTATGCTTGAAATGGGAGGA+GGG + chr2.1:15551360-15551379 None:intergenic 45.0%
CTCCTCCCATTTCAAGCATA+GGG - chr2.1:15551359-15551378 MS.gene35422:CDS 45.0%
GAAAGGGATTGAAGCAGTGT+TGG + chr2.1:15550917-15550936 None:intergenic 45.0%
GAAATAAACCCAAGGCTTCC+CGG + chr2.1:15551389-15551408 None:intergenic 45.0%
GAGGACTCTATGGATTTCAC+TGG + chr2.1:15550956-15550975 None:intergenic 45.0%
GATTTGTCCTCGAAGAGGTA+AGG - chr2.1:15551431-15551450 MS.gene35422:CDS 45.0%
GGAAGCCTTGGGTTTATTTC+AGG - chr2.1:15551389-15551408 MS.gene35422:CDS 45.0%
GGGTGTCAAAGATGTGTTGT+AGG + chr2.1:15550880-15550899 None:intergenic 45.0%
GTCCTCCCTATGCTTGAAAT+GGG + chr2.1:15551367-15551386 None:intergenic 45.0%
GTGCTTATAGAGAGGATGGA+AGG - chr2.1:15551476-15551495 MS.gene35422:CDS 45.0%
TCCAGAAACTCATCATCAGG+AGG + chr2.1:15551523-15551542 None:intergenic 45.0%
TGGAAGATTTGTCCTCGAAG+AGG - chr2.1:15551426-15551445 MS.gene35422:CDS 45.0%
TGGAGAATGTAGGAGGTCAA+GGG - chr2.1:15551324-15551343 MS.gene35422:CDS 45.0%
! CTGTTGGTATGCCTTGCTAT+TGG + chr2.1:15551121-15551140 None:intergenic 45.0%
AGCATGCATCTTTGCACCGA+AGG - chr2.1:15551181-15551200 MS.gene35422:CDS 50.0%
AGCTGAGGAAGGAGAAGACA+TGG - chr2.1:15551579-15551598 MS.gene35422:CDS 50.0%
CATCCTCTCTATAAGCACGC+AGG + chr2.1:15551474-15551493 None:intergenic 50.0%
CATCTTTGCACCGAAGGTCT+TGG - chr2.1:15551187-15551206 MS.gene35422:CDS 50.0%
CCTATGCTTGAAATGGGAGG+AGG + chr2.1:15551361-15551380 None:intergenic 50.0%
CCTCCTCCCATTTCAAGCAT+AGG - chr2.1:15551358-15551377 MS.gene35422:CDS 50.0%
CTCCCATTTCAAGCATAGGG+AGG - chr2.1:15551362-15551381 MS.gene35422:CDS 50.0%
CTCCCTATGCTTGAAATGGG+AGG + chr2.1:15551364-15551383 None:intergenic 50.0%
CTGCGTGCTTATAGAGAGGA+TGG - chr2.1:15551472-15551491 MS.gene35422:CDS 50.0%
GATGTCGAGGACTCAAAGAG+TGG - chr2.1:15551226-15551245 MS.gene35422:CDS 50.0%
GATGTGTTGTAGGCTGTCAC+AGG + chr2.1:15550870-15550889 None:intergenic 50.0%
GGTCCTCCCTATGCTTGAAA+TGG + chr2.1:15551368-15551387 None:intergenic 50.0%
TCGGTATCCTTACCTCTTCG+AGG + chr2.1:15551441-15551460 None:intergenic 50.0%
TGAGAGTTCAGACGATGTCG+AGG - chr2.1:15551213-15551232 MS.gene35422:CDS 50.0%
TTTCAAGCATAGGGAGGACC+GGG - chr2.1:15551368-15551387 MS.gene35422:CDS 50.0%
! CCCTCCTGATGATGAGTTTC+TGG - chr2.1:15551519-15551538 MS.gene35422:CDS 50.0%
!! GTCACTGCTTTTGTGCCTGT+TGG + chr2.1:15551137-15551156 None:intergenic 50.0%
AGAGGTAAGGATACCGACCC+AGG - chr2.1:15551444-15551463 MS.gene35422:CDS 55.0%
ATAAGCACGCAGGACCTCCT+GGG + chr2.1:15551464-15551483 None:intergenic 55.0%
GGTCCTGCGTGCTTATAGAG+AGG - chr2.1:15551468-15551487 MS.gene35422:CDS 55.0%
TATAAGCACGCAGGACCTCC+TGG + chr2.1:15551465-15551484 None:intergenic 55.0%
GGTAAGGATACCGACCCAGG+AGG - chr2.1:15551447-15551466 MS.gene35422:CDS 60.0%
AGGGAGGACCGGGAAGCCTT+GGG - chr2.1:15551378-15551397 MS.gene35422:CDS 65.0%
TAGGGAGGACCGGGAAGCCT+TGG - chr2.1:15551377-15551396 MS.gene35422:CDS 65.0%
GCACGCAGGACCTCCTGGGT+CGG + chr2.1:15551460-15551479 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 15550860 15551660 15550860 ID=MS.gene35422
chr2.1 mRNA 15550860 15551660 15550860 ID=MS.gene35422.t1;Parent=MS.gene35422
chr2.1 exon 15550860 15551660 15550860 ID=MS.gene35422.t1.exon1;Parent=MS.gene35422.t1
chr2.1 CDS 15550860 15551660 15550860 ID=cds.MS.gene35422.t1;Parent=MS.gene35422.t1
Gene Sequence

>MS.gene35422

ATGGCAACCTGTGACAGCCTACAACACATCTTTGACACCCTATTGCCAGAAAATCCAACACTGCTTCAATCCCTTTCATTTAACAAAATTAAACCAGTGAAATCCATAGAGTCCTCCTCCTTTACTGAGATATTTGGTGAACTCCATTTCAAGGAATCATCATCAACAGAGATAAACCACACAAACTTCAACCAGATCAAAGAGTCTGAGTCTTTTGACACTATCCAAACTCCATCTTCAGCTTCTTTTTCAATTACACCAATAGCAAGGCATACCAACAGGCACAAAAGCAGTGACACCTTTTCATGGCTGAATTCTGAAAGCATGCATCTTTGCACCGAAGGTCTTGGTTTTGAGAGTTCAGACGATGTCGAGGACTCAAAGAGTGGAGCGAATGAATCTTTACAAATTGATCAAAATGAGAAACGTGTCGAACATCATTTATCTTCAAGACATCATTCTTATGGAGAATGTAGGAGGTCAAGGGTAAGTGAGTACCCTCCTCCCATTTCAAGCATAGGGAGGACCGGGAAGCCTTGGGTTTATTTCAGGTCTATTAGGAATAATGGAAGATTTGTCCTCGAAGAGGTAAGGATACCGACCCAGGAGGTCCTGCGTGCTTATAGAGAGGATGGAAGGCTCAAGCTGCAGTTTGTTCACCCTCCTGATGATGAGTTTCTGGAAGATGAGGATGAAGGAGAGAATGATATAGGATGCATAGCTGAGGAAGGAGAAGACATGGCAAAAGAAGAGGACGATTGTGTAACACATCATTCAAATGACAAAAAAGAGATTGCTTGA

Protein sequence

>MS.gene35422.t1

MATCDSLQHIFDTLLPENPTLLQSLSFNKIKPVKSIESSSFTEIFGELHFKESSSTEINHTNFNQIKESESFDTIQTPSSASFSITPIARHTNRHKSSDTFSWLNSESMHLCTEGLGFESSDDVEDSKSGANESLQIDQNEKRVEHHLSSRHHSYGECRRSRVSEYPPPISSIGRTGKPWVYFRSIRNNGRFVLEEVRIPTQEVLRAYREDGRLKLQFVHPPDDEFLEDEDEGENDIGCIAEEGEDMAKEEDDCVTHHSNDKKEIA