AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene72735


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene72735.t1 MTR_5g025520 97.744 133 3 0 1 133 1 133 3.30e-93 265
MS.gene72735.t1 MTR_5g025500 37.662 77 48 0 26 102 54 130 1.42e-11 58.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 46 sgRNAs with CRISPR-Local

Find 81 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCATCAAACTCTACAGTTTC+CGG 0.200149 5.4:-16596396 MS.gene72735:CDS
ATGAATCCGGCGGGTTTAAC+AGG 0.280966 5.4:-16596568 MS.gene72735:CDS
GGAAATGATGGAAGCAATTT+CGG 0.295914 5.4:+16596423 None:intergenic
CATGATTTCGGCGACGGCTT+TGG 0.360532 5.4:+16596522 None:intergenic
CAGTGAACTCTGCACTTTCA+TGG 0.368977 5.4:-16596467 MS.gene72735:CDS
CATCAAACTCTACAGTTTCC+GGG 0.376717 5.4:-16596395 MS.gene72735:intron
ATCGCACCCTGGCTGAATTC+CGG 0.377231 5.4:+16595322 None:intergenic
TTTGCCGACACCCATGATTT+CGG 0.381159 5.4:+16596510 None:intergenic
TTTGATGAACTTGGAAATGA+TGG 0.402949 5.4:+16596411 None:intergenic
ACTGGTAGCTTTGCGTGTCT+TGG 0.404946 5.4:+16596486 None:intergenic
CAAAGCCGTCGCCGAAATCA+TGG 0.409452 5.4:-16596521 MS.gene72735:CDS
GTATCAAGAAAGACAAGCTT+TGG 0.428352 5.4:-16595417 MS.gene72735:CDS
ACTGTAGAGTTTGATGAACT+TGG 0.446589 5.4:+16596402 None:intergenic
GGGAAAGGCCAACAGAAGAA+AGG 0.464992 5.4:-16595253 MS.gene72735:CDS
GACAGAATCTTAGCAATCTC+AGG 0.466374 5.4:+16595346 None:intergenic
TAATATCAAGGATACTAATA+CGG 0.503603 5.4:-16595299 MS.gene72735:CDS
TCTGTCTCCGGAATTCAGCC+AGG 0.504471 5.4:-16595329 MS.gene72735:CDS
GACACCCATGATTTCGGCGA+CGG 0.507275 5.4:+16596516 None:intergenic
GGAAAGGCCAACAGAAGAAA+GGG 0.508550 5.4:-16595252 MS.gene72735:CDS
GATTGCTAAGATTCTGTCTC+CGG 0.511219 5.4:-16595341 MS.gene72735:CDS
AGTGAACTCTGCACTTTCAT+GGG 0.512210 5.4:-16596466 MS.gene72735:CDS
AGCTTGTCTTTCTTGATACC+AGG 0.515565 5.4:+16595421 None:intergenic
TATGGTGTTGTGCAGAGTCC+TGG 0.516143 5.4:-16595439 MS.gene72735:intron
CCAGGGTGCGATTAATATCA+AGG 0.519238 5.4:-16595311 MS.gene72735:CDS
CATGAAAGTGCAGAGTTCAC+TGG 0.524418 5.4:+16596468 None:intergenic
ATCCAGCAGAAGGATGAATC+CGG 0.526821 5.4:-16596581 None:intergenic
CTTCGCCCTGTTAAACCCGC+CGG 0.548257 5.4:+16596562 None:intergenic
TATCAAGAAAGACAAGCTTT+GGG 0.550356 5.4:-16595416 MS.gene72735:CDS
TCTTCCGCGGATAACACAAA+GGG 0.561908 5.4:-16595274 MS.gene72735:CDS
AAAGCCGTCGCCGAAATCAT+GGG 0.576114 5.4:-16596520 MS.gene72735:CDS
GCGGATAACACAAAGGGGAA+AGG 0.582569 5.4:-16595268 MS.gene72735:CDS
TTCTTCCGCGGATAACACAA+AGG 0.602214 5.4:-16595275 MS.gene72735:CDS
CGGCGGGTTTAACAGGGCGA+AGG 0.602549 5.4:-16596561 MS.gene72735:CDS
TGAATCCGGCGGGTTTAACA+GGG 0.604481 5.4:-16596567 MS.gene72735:CDS
GTCGCCGAAATCATGGGTGT+CGG 0.610089 5.4:-16596514 MS.gene72735:CDS
AGCAGAAGGATGAATCCGGC+GGG 0.612519 5.4:-16596577 None:intergenic
AATTTGCAAACACTGTTGCG+TGG 0.632781 5.4:-16595388 MS.gene72735:CDS
TTGCGTGGCAGAAACAGCGT+TGG 0.639499 5.4:-16595373 MS.gene72735:CDS
ATTTCGGAACGAGATTGATG+AGG 0.642540 5.4:+16596439 None:intergenic
CTGTCTCCGGAATTCAGCCA+GGG 0.642587 5.4:-16595328 MS.gene72735:CDS
AGGGCGAAGGAGCATGTCGA+CGG 0.655015 5.4:-16596548 MS.gene72735:CDS
CAGCAGAAGGATGAATCCGG+CGG 0.656372 5.4:-16596578 None:intergenic
TACTAATACGGATTCTTCCG+CGG 0.657291 5.4:-16595287 MS.gene72735:CDS
CCTTGATATTAATCGCACCC+TGG 0.662781 5.4:+16595311 None:intergenic
TTTCCCCTTTGTGTTATCCG+CGG 0.666626 5.4:+16595270 None:intergenic
CTTCCGCGGATAACACAAAG+GGG 0.722706 5.4:-16595273 MS.gene72735:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CTATAATAAAAGATAAAATA+AGG + chr5.4:16596189-16596208 None:intergenic 10.0%
!! AATGAAACAAAAAGAAAAAT+GGG + chr5.4:16595450-16595469 None:intergenic 15.0%
!! TAATGAAACAAAAAGAAAAA+TGG + chr5.4:16595451-16595470 None:intergenic 15.0%
!!! TTTATTTACTTTTGCTTATT+TGG - chr5.4:16596338-16596357 MS.gene72735:intron 15.0%
!! ATTAAGCTGTTTATAAAAAC+AGG - chr5.4:16596132-16596151 MS.gene72735:intron 20.0%
!! CTTTCCATAAAATAAGATAT+AGG + chr5.4:16596159-16596178 None:intergenic 20.0%
!! TAATATCAAGGATACTAATA+CGG - chr5.4:16596509-16596528 MS.gene72735:CDS 20.0%
!! TCAAATAAACCAATTCAAAT+AGG + chr5.4:16595818-16595837 None:intergenic 20.0%
!! TTAAGCTGTTTATAAAAACA+GGG - chr5.4:16596133-16596152 MS.gene72735:intron 20.0%
!!! TAAGTTTGTTTCTATAACAA+AGG + chr5.4:16596098-16596117 None:intergenic 20.0%
! AAGATTAAAGACTAATCAGT+AGG + chr5.4:16595691-16595710 None:intergenic 25.0%
! AGATTAAAGACTAATCAGTA+GGG + chr5.4:16595690-16595709 None:intergenic 25.0%
! TTGAAAATAATCACTAGTCA+GGG + chr5.4:16595777-16595796 None:intergenic 25.0%
! TTTGAAAATAATCACTAGTC+AGG + chr5.4:16595778-16595797 None:intergenic 25.0%
!! TAAACTATCTCTGAAAAACA+TGG + chr5.4:16595527-16595546 None:intergenic 25.0%
!! TACTTTTGCTTATTTGGAAA+TGG - chr5.4:16596344-16596363 MS.gene72735:intron 25.0%
!! TTTTCATAAGTTCTCTCAAA+CGG + chr5.4:16595962-16595981 None:intergenic 25.0%
ATTAAAGACTAATCAGTAGG+GGG + chr5.4:16595688-16595707 None:intergenic 30.0%
GATTAAAGACTAATCAGTAG+GGG + chr5.4:16595689-16595708 None:intergenic 30.0%
GCTTATTTGGAAATGGTATA+TGG - chr5.4:16596351-16596370 MS.gene72735:intron 30.0%
TATCAAGAAAGACAAGCTTT+GGG - chr5.4:16596392-16596411 MS.gene72735:intron 30.0%
TCTGAAAAACATGGAAATGA+TGG + chr5.4:16595518-16595537 None:intergenic 30.0%
TTGAGAGAACTTATGAAAAC+AGG - chr5.4:16595963-16595982 MS.gene72735:intron 30.0%
TTTGATGAACTTGGAAATGA+TGG + chr5.4:16595400-16595419 None:intergenic 30.0%
!!! AGGGCCTATATCTTATTTTA+TGG - chr5.4:16596152-16596171 MS.gene72735:intron 30.0%
AAATGGGAAGAATTGAAACC+CGG + chr5.4:16595434-16595453 None:intergenic 35.0%
AACCAATTCAAATAGGCTCA+TGG + chr5.4:16595811-16595830 None:intergenic 35.0%
AACCATGAGCCTATTTGAAT+TGG - chr5.4:16595806-16595825 MS.gene72735:intron 35.0%
ACTGTAGAGTTTGATGAACT+TGG + chr5.4:16595409-16595428 None:intergenic 35.0%
CAAGTGCTTGTTTCAATACA+TGG + chr5.4:16595847-16595866 None:intergenic 35.0%
GAGAACATTGATCAAACAGT+TGG + chr5.4:16595481-16595500 None:intergenic 35.0%
GGATAAACAACTTCATTGAG+TGG + chr5.4:16596263-16596282 None:intergenic 35.0%
GTATCAAGAAAGACAAGCTT+TGG - chr5.4:16596391-16596410 MS.gene72735:intron 35.0%
TCATCAAACTCTACAGTTTC+CGG - chr5.4:16595412-16595431 MS.gene72735:CDS 35.0%
! AGCGATAAGCTCTTTTCATA+AGG + chr5.4:16596046-16596065 None:intergenic 35.0%
! GGAAATGATGGAAGCAATTT+CGG + chr5.4:16595388-16595407 None:intergenic 35.0%
! TCTTTTTCCCTTTCTTCTGT+TGG + chr5.4:16596566-16596585 None:intergenic 35.0%
AATTTGCAAACACTGTTGCG+TGG - chr5.4:16596420-16596439 MS.gene72735:CDS 40.0%
AGCTTGTCTTTCTTGATACC+AGG + chr5.4:16596390-16596409 None:intergenic 40.0%
AGTCCCTATCAGTGATTAAG+TGG + chr5.4:16595733-16595752 None:intergenic 40.0%
AGTGAACTCTGCACTTTCAT+GGG - chr5.4:16595342-16595361 MS.gene72735:CDS 40.0%
ATTTCGGAACGAGATTGATG+AGG + chr5.4:16595372-16595391 None:intergenic 40.0%
CAATGGCAACACTCTTACTT+AGG + chr5.4:16596293-16596312 None:intergenic 40.0%
CACCCACTTAATCACTGATA+GGG - chr5.4:16595727-16595746 MS.gene72735:intron 40.0%
CACTCTTACTTAGGCTCATT+TGG + chr5.4:16596284-16596303 None:intergenic 40.0%
CATCAAACTCTACAGTTTCC+GGG - chr5.4:16595413-16595432 MS.gene72735:CDS 40.0%
CTTTCACTTTAGTCGCTCAA+TGG + chr5.4:16596310-16596329 None:intergenic 40.0%
GACAGAATCTTAGCAATCTC+AGG + chr5.4:16596465-16596484 None:intergenic 40.0%
GATTGCTAAGATTCTGTCTC+CGG - chr5.4:16596467-16596486 MS.gene72735:CDS 40.0%
GTCCCTATCAGTGATTAAGT+GGG + chr5.4:16595732-16595751 None:intergenic 40.0%
TACTAATACGGATTCTTCCG+CGG - chr5.4:16596521-16596540 MS.gene72735:CDS 40.0%
TCACCCACTTAATCACTGAT+AGG - chr5.4:16595726-16595745 MS.gene72735:intron 40.0%
TTGAGTGGTTATAGCACAAG+CGG + chr5.4:16596248-16596267 None:intergenic 40.0%
CAGTGAACTCTGCACTTTCA+TGG - chr5.4:16595341-16595360 MS.gene72735:CDS 45.0%
CCAGGGTGCGATTAATATCA+AGG - chr5.4:16596497-16596516 MS.gene72735:CDS 45.0%
CCTTGATATTAATCGCACCC+TGG + chr5.4:16596500-16596519 None:intergenic 45.0%
GGAAAGGCCAACAGAAGAAA+GGG - chr5.4:16596556-16596575 MS.gene72735:CDS 45.0%
TCTTCCGCGGATAACACAAA+GGG - chr5.4:16596534-16596553 MS.gene72735:CDS 45.0%
TTCTTCCGCGGATAACACAA+AGG - chr5.4:16596533-16596552 MS.gene72735:CDS 45.0%
TTTCCCCTTTGTGTTATCCG+CGG + chr5.4:16596541-16596560 None:intergenic 45.0%
TTTGCCGACACCCATGATTT+CGG + chr5.4:16595301-16595320 None:intergenic 45.0%
! CATGAAAGTGCAGAGTTCAC+TGG + chr5.4:16595343-16595362 None:intergenic 45.0%
AAAGCCGTCGCCGAAATCAT+GGG - chr5.4:16595288-16595307 MS.gene72735:CDS 50.0%
CTTCCGCGGATAACACAAAG+GGG - chr5.4:16596535-16596554 MS.gene72735:CDS 50.0%
GCGGATAACACAAAGGGGAA+AGG - chr5.4:16596540-16596559 MS.gene72735:CDS 50.0%
GGGAAAGGCCAACAGAAGAA+AGG - chr5.4:16596555-16596574 MS.gene72735:CDS 50.0%
! ACTGGTAGCTTTGCGTGTCT+TGG + chr5.4:16595325-16595344 None:intergenic 50.0%
! ATGAATCCGGCGGGTTTAAC+AGG - chr5.4:16595240-16595259 MS.gene72735:CDS 50.0%
! TGAATCCGGCGGGTTTAACA+GGG - chr5.4:16595241-16595260 MS.gene72735:CDS 50.0%
!! TATGGTGTTGTGCAGAGTCC+TGG - chr5.4:16596369-16596388 MS.gene72735:intron 50.0%
ATCGCACCCTGGCTGAATTC+CGG + chr5.4:16596489-16596508 None:intergenic 55.0%
CAAAGCCGTCGCCGAAATCA+TGG - chr5.4:16595287-16595306 MS.gene72735:CDS 55.0%
CATGATTTCGGCGACGGCTT+TGG + chr5.4:16595289-16595308 None:intergenic 55.0%
CTGTCTCCGGAATTCAGCCA+GGG - chr5.4:16596480-16596499 MS.gene72735:CDS 55.0%
GACACCCATGATTTCGGCGA+CGG + chr5.4:16595295-16595314 None:intergenic 55.0%
GTCGCCGAAATCATGGGTGT+CGG - chr5.4:16595294-16595313 MS.gene72735:CDS 55.0%
TCTGTCTCCGGAATTCAGCC+AGG - chr5.4:16596479-16596498 MS.gene72735:CDS 55.0%
TTGCGTGGCAGAAACAGCGT+TGG - chr5.4:16596435-16596454 MS.gene72735:CDS 55.0%
CTTCGCCCTGTTAAACCCGC+CGG + chr5.4:16595249-16595268 None:intergenic 60.0%
! AGGGCGAAGGAGCATGTCGA+CGG - chr5.4:16595260-16595279 MS.gene72735:CDS 60.0%
! CGGCGGGTTTAACAGGGCGA+AGG - chr5.4:16595247-16595266 MS.gene72735:CDS 65.0%


Chromosome Type Strat End Strand Name
chr5.4 gene 16595240 16596590 16595240 ID=MS.gene72735
chr5.4 mRNA 16595240 16596590 16595240 ID=MS.gene72735.t1;Parent=MS.gene72735
chr5.4 exon 16596396 16596590 16596396 ID=MS.gene72735.t1.exon1;Parent=MS.gene72735.t1
chr5.4 CDS 16596396 16596590 16596396 ID=cds.MS.gene72735.t1;Parent=MS.gene72735.t1
chr5.4 exon 16595240 16595446 16595240 ID=MS.gene72735.t1.exon2;Parent=MS.gene72735.t1
chr5.4 CDS 16595240 16595446 16595240 ID=cds.MS.gene72735.t1;Parent=MS.gene72735.t1
Gene Sequence

>MS.gene72735

ATGAATCCGGCGGGTTTAACAGGGCGAAGGAGCATGTCGACGGTATCCAAAGCCGTCGCCGAAATCATGGGTGTCGGCAAAACCAAGACACGCAAAGCTACCAGTGAACTCTGCACTTTCATGGGCATTCCTCATCAATCTCGTTCCGAAATTGCTTCCATCATTTCCAAGTTCATCAAACTCTACAGTTTCCGGGTTTCAATTCTTCCCATTTTTCTTTTTGTTTCATTATTGCATACCAACTGTTTGATCAATGTTCTCACTCACAAAACATGCCATCATTTCCATGTTTTTCAGAGATAGTTTATGAAAATAGCTTAGACTTAACACGAAAACAATTTAACTTTATTTTATTTTTGTTATAGAAATAGCTTAGCAGTTAGCAGCTATAAGCTGCAAATTATTATTATACTATGACACTCAATTTATTTGTTCAAGTTTAACTCCCCCTACTGATTAGTCTTTAATCTTTACATATATGATAACTCACCCACTTAATCACTGATAGGGACTAACGAGATGAATTTTCATATACCCTGACTAGTGATTATTTTCAAATATTTTAGAACCATGAGCCTATTTGAATTGGTTTATTTGAGCTTATCCATGTATTGAAACAAGCACTTGTGAGACTGTTTGAGAGAACATATAGAAGCAACACATGACATAAGAAATTATGACTTATTTGAGCTTATCTCTTGACATAAGAACTTGTGAGACCGTTTGAGAGAACTTATGAAAACAGGTTATAGCACATTATTCATATGTTGTTTTCAGCTTGTTTGCGTAAGCTCTTAAAAAAACCTTATGAAAAGAGCTTATCGCTTATACTAAAACAATTCAACTTTATTTTATCCTTTGTTATAGAAACAAACTTATACATAAGCTGCAAATTAAGCTGTTTATAAAAACAGGGCCTATATCTTATTTTATGGAAAGAATTTGACCTTATTTTATCTTTTATTATAGAAATAGCTTATATATACATAAATACTTATGTGAGAACCGCTTGTGCTATAACCACTCAATGAAGTTGTTTATCCAAATGAGCCTAAGTAAGAGTGTTGCCATTGAGCGACTAAAGTGAAAGTTTACTGTTTTATTTACTTTTGCTTATTTGGAAATGGTATATGGTGTTGTGCAGAGTCCTGGTATCAAGAAAGACAAGCTTTGGGAGCAGAATTTGCAAACACTGTTGCGTGGCAGAAACAGCGTTGGTTTTCCTGAGATTGCTAAGATTCTGTCTCCGGAATTCAGCCAGGGTGCGATTAATATCAAGGATACTAATACGGATTCTTCCGCGGATAACACAAAGGGGAAAGGCCAACAGAAGAAAGGGAAAAAGAAATAG

Protein sequence

>MS.gene72735.t1

MNPAGLTGRRSMSTVSKAVAEIMGVGKTKTRKATSELCTFMGIPHQSRSEIASIISKFIKLYSFRSPGIKKDKLWEQNLQTLLRGRNSVGFPEIAKILSPEFSQGAINIKDTNTDSSADNTKGKGQQKKGKKK