AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene20426

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 28 sgRNAs with CRISPR-Local

Find 92 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCCTGGTGCGGCTGCATTT+TGG 0.233223 6.3:+7007584 MS.gene20426:CDS
AACTCTCGCTTTACAGCCCT+TGG 0.412131 6.3:+7007171 MS.gene20426:CDS
GCTTTAACGATAGGCCATTC+CGG 0.421820 6.3:+7007495 MS.gene20426:intron
GGTGGTCTTGTGATAGGAGG+TGG 0.468959 6.3:+7005654 MS.gene20426:CDS
TACCAAAATGCAGCCGCACC+AGG 0.472463 6.3:-7007586 None:intergenic
AAATGCAGCCGCACCAGGGA+GGG 0.482111 6.3:-7007581 None:intergenic
ACCGGCGGTGGTCTTGTGAT+AGG 0.499272 6.3:+7005648 MS.gene20426:CDS
GCACTTCATCAGTTCAGAAA+AGG 0.512979 6.3:+7006727 MS.gene20426:CDS
AAAAGAACCTACAGCAGCTA+AGG 0.518289 6.3:-7006694 None:intergenic
GTGGTCTTGTGATAGGAGGT+GGG 0.523769 6.3:+7005655 MS.gene20426:CDS
ACCTACAGCAGCTAAGGAAA+GGG 0.525680 6.3:-7006688 None:intergenic
TCCCTTTCCTTAGCTGCTGT+AGG 0.527333 6.3:+7006687 MS.gene20426:CDS
TTCGTCTATCTCTTCATCAC+AGG 0.536559 6.3:+7007215 MS.gene20426:CDS
AACCTACAGCAGCTAAGGAA+AGG 0.547182 6.3:-7006689 None:intergenic
TTATTGAAAGGTACCGGCGG+TGG 0.550462 6.3:+7005636 MS.gene20426:CDS
TCCTATCACAAGACCACCGC+CGG 0.569038 6.3:-7005649 None:intergenic
ACCAAAATGCAGCCGCACCA+GGG 0.576567 6.3:-7007585 None:intergenic
TGAAGAGATAGACGAAGGAC+AGG 0.583603 6.3:-7007208 None:intergenic
GTCTAAACGCAAAACCAAAG+AGG 0.606877 6.3:-7007621 None:intergenic
CAAGAAAAGAAACACCGGAA+TGG 0.609378 6.3:-7007509 None:intergenic
GGCGGTGGTCTTGTGATAGG+AGG 0.613484 6.3:+7005651 MS.gene20426:CDS
TCTAAACGCAAAACCAAAGA+GGG 0.613976 6.3:-7007620 None:intergenic
GACAGCAAGAAAAGAAACAC+CGG 0.621651 6.3:-7007514 None:intergenic
AAAATGCAGCCGCACCAGGG+AGG 0.648091 6.3:-7007582 None:intergenic
GGACAACAGTTGAAGACCAA+GGG 0.650365 6.3:-7007187 None:intergenic
AGGACAACAGTTGAAGACCA+AGG 0.669909 6.3:-7007188 None:intergenic
TGGTCTTGTGATAGGAGGTG+GGG 0.682551 6.3:+7005656 MS.gene20426:CDS
TGTGATGAAGAGATAGACGA+AGG 0.699654 6.3:-7007213 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATTTGTTTGTTTTTTTTTT+TGG + chr6.3:7005794-7005813 MS.gene20426:intron 10.0%
!!! ATATTTTGCATATATTTTAT+CGG + chr6.3:7007288-7007307 MS.gene20426:intron 10.0%
!!! TAATTTGTTTGTTTTTTTTT+TGG + chr6.3:7005793-7005812 MS.gene20426:intron 10.0%
!!! TTTATTGTATTTTCATATTT+GGG + chr6.3:7006037-7006056 MS.gene20426:intron 10.0%
!!! TTTTATTGTATTTTCATATT+TGG + chr6.3:7006036-7006055 MS.gene20426:intron 10.0%
!!! TTTTTTTTTTTGGTGAATTT+TGG + chr6.3:7006209-7006228 MS.gene20426:intron 15.0%
!! CAATGGACATTTAATAATAT+TGG + chr6.3:7006611-7006630 MS.gene20426:intron 20.0%
!! GATAAAACTAACATTTAATC+AGG - chr6.3:7006576-7006595 None:intergenic 20.0%
!! GTATTAGAAATCATTATGTT+GGG + chr6.3:7006883-7006902 MS.gene20426:intron 20.0%
!! TAATCAGTCAAATTTATGAA+TGG - chr6.3:7006813-7006832 None:intergenic 20.0%
!! TATGAAAAAAAATCACACAT+TGG - chr6.3:7006520-7006539 None:intergenic 20.0%
!! TTCTTTAGTATGTTCATATT+TGG + chr6.3:7006008-7006027 MS.gene20426:intron 20.0%
!!! AATCTGAATTATGAAGTTTT+TGG + chr6.3:7007045-7007064 MS.gene20426:intron 20.0%
!!! AATTTAGAATAGAATCTTCT+TGG + chr6.3:7005711-7005730 MS.gene20426:intron 20.0%
!!! AGTTATTTACTGATTTTGAA+TGG + chr6.3:7007090-7007109 MS.gene20426:intron 20.0%
!!! GTTATTTACTGATTTTGAAT+GGG + chr6.3:7007091-7007110 MS.gene20426:intron 20.0%
!!! GTTTTTTTTTTGGTGAATTT+TGG + chr6.3:7005803-7005822 MS.gene20426:intron 20.0%
!!! TTATTTACTGATTTTGAATG+GGG + chr6.3:7007092-7007111 MS.gene20426:intron 20.0%
! ATGCAAAATATATGCTTCAA+CGG - chr6.3:7007279-7007298 None:intergenic 25.0%
! GGTATTAGAAATCATTATGT+TGG + chr6.3:7006882-7006901 MS.gene20426:intron 25.0%
! TCATGAAAAACTATAAGCAA+TGG + chr6.3:7006594-7006613 MS.gene20426:intron 25.0%
!!! ATGATTTTATTGAAAGGTAC+CGG + chr6.3:7005630-7005649 MS.gene20426:CDS 25.0%
!!! CGGTGATAGTTTAAATTTTT+TGG + chr6.3:7006761-7006780 MS.gene20426:intron 25.0%
AACAACTTCAGATTAAGACA+AGG + chr6.3:7006949-7006968 MS.gene20426:intron 30.0%
AACACTCATTCACTTCATTA+TGG + chr6.3:7006856-7006875 MS.gene20426:intron 30.0%
AATACATGTAGTTGTTACTG+TGG + chr6.3:7007327-7007346 MS.gene20426:intron 30.0%
CACTATTTAGTAGCACTATT+TGG + chr6.3:7007399-7007418 MS.gene20426:intron 30.0%
GTAAGATGCAAAACATTGTA+GGG + chr6.3:7005855-7005874 MS.gene20426:intron 30.0%
TCATTCACTTCATTATGGTT+GGG + chr6.3:7006861-7006880 MS.gene20426:intron 30.0%
TGTAAGATGCAAAACATTGT+AGG + chr6.3:7005854-7005873 MS.gene20426:intron 30.0%
! CAAATAGTGCTACTAAATAG+TGG - chr6.3:7007401-7007420 None:intergenic 30.0%
! TTGTCTTAATCTGAAGTTGT+TGG - chr6.3:7006950-7006969 None:intergenic 30.0%
!! AGAGTATTGAAGCTAAATTG+GGG - chr6.3:7006649-7006668 None:intergenic 30.0%
!! CAGAGTATTGAAGCTAAATT+GGG - chr6.3:7006650-7006669 None:intergenic 30.0%
!! TCAGAGTATTGAAGCTAAAT+TGG - chr6.3:7006651-7006670 None:intergenic 30.0%
ACTCTGACATTGTTGAACTT+AGG + chr6.3:7006664-7006683 MS.gene20426:intron 35.0%
CAAAACATTGTAGGGATTGT+TGG + chr6.3:7005863-7005882 MS.gene20426:intron 35.0%
CTCATTCACTTCATTATGGT+TGG + chr6.3:7006860-7006879 MS.gene20426:intron 35.0%
GAATGAAAGATGACTCTTCT+TGG + chr6.3:7006116-7006135 MS.gene20426:intron 35.0%
TCTAAACGCAAAACCAAAGA+GGG - chr6.3:7007623-7007642 None:intergenic 35.0%
TTGGAATGTGAAGTTGTGTT+TGG + chr6.3:7007064-7007083 MS.gene20426:intron 35.0%
! ATCAGTTCAGAAAAGGTGTA+AGG + chr6.3:7006734-7006753 MS.gene20426:intron 35.0%
!! ATATGCTTCAACGGATTATG+AGG - chr6.3:7007270-7007289 None:intergenic 35.0%
!! ATTTTGGTAGTCATGCATAG+TGG + chr6.3:7005819-7005838 MS.gene20426:intron 35.0%
!! TGAAGTGAATGAGTGTTGAA+AGG - chr6.3:7006853-7006872 None:intergenic 35.0%
!!! ATTTTATTGAAAGGTACCGG+CGG + chr6.3:7005633-7005652 MS.gene20426:CDS 35.0%
AAAAGAACCTACAGCAGCTA+AGG - chr6.3:7006697-7006716 None:intergenic 40.0%
AGCTAAATTGGGGATAACAC+AGG - chr6.3:7006639-7006658 None:intergenic 40.0%
ATATGACTATCAGAGCAAGC+AGG - chr6.3:7006998-7007017 None:intergenic 40.0%
ATTTGGTTGCAGTAGCAGTA+GGG + chr6.3:7007416-7007435 MS.gene20426:intron 40.0%
CAAGAAAAGAAACACCGGAA+TGG - chr6.3:7007512-7007531 None:intergenic 40.0%
GACAGCAAGAAAAGAAACAC+CGG - chr6.3:7007517-7007536 None:intergenic 40.0%
GCACTTCATCAGTTCAGAAA+AGG + chr6.3:7006727-7006746 MS.gene20426:CDS 40.0%
GTCTAAACGCAAAACCAAAG+AGG - chr6.3:7007624-7007643 None:intergenic 40.0%
TATTTGGTTGCAGTAGCAGT+AGG + chr6.3:7007415-7007434 MS.gene20426:intron 40.0%
TGTGATGAAGAGATAGACGA+AGG - chr6.3:7007216-7007235 None:intergenic 40.0%
TTCGTCTATCTCTTCATCAC+AGG + chr6.3:7007215-7007234 MS.gene20426:CDS 40.0%
! CAGAAAAGGTGTAAGGAAGT+CGG + chr6.3:7006741-7006760 MS.gene20426:intron 40.0%
!! ACTGCGAATTGAGTTTGCTA+TGG + chr6.3:7006921-7006940 MS.gene20426:intron 40.0%
!!! TATTTTGGTGTGTCCCTCTT+TGG + chr6.3:7007607-7007626 MS.gene20426:CDS 40.0%
AACCTACAGCAGCTAAGGAA+AGG - chr6.3:7006692-7006711 None:intergenic 45.0%
ACCTACAGCAGCTAAGGAAA+GGG - chr6.3:7006691-7006710 None:intergenic 45.0%
AGGACAACAGTTGAAGACCA+AGG - chr6.3:7007191-7007210 None:intergenic 45.0%
GCGTGCTTTGCTTTAACGAT+AGG + chr6.3:7007486-7007505 MS.gene20426:intron 45.0%
GCTTTAACGATAGGCCATTC+CGG + chr6.3:7007495-7007514 MS.gene20426:intron 45.0%
GGACAACAGTTGAAGACCAA+GGG - chr6.3:7007190-7007209 None:intergenic 45.0%
TGAAGAGATAGACGAAGGAC+AGG - chr6.3:7007211-7007230 None:intergenic 45.0%
TTTGGTTGCAGTAGCAGTAG+GGG + chr6.3:7007417-7007436 MS.gene20426:intron 45.0%
! GGATTATGAGGAACTTGCTC+AGG - chr6.3:7007258-7007277 None:intergenic 45.0%
!! GCGGCTGCATTTTGGTATTT+TGG + chr6.3:7007592-7007611 MS.gene20426:CDS 45.0%
!!! GGATCGGTTTGGTTTTGTGT+TGG + chr6.3:7007453-7007472 MS.gene20426:intron 45.0%
AACTCTCGCTTTACAGCCCT+TGG + chr6.3:7007171-7007190 MS.gene20426:CDS 50.0%
TCCCTTTCCTTAGCTGCTGT+AGG + chr6.3:7006687-7006706 MS.gene20426:CDS 50.0%
TTGTGGTCAGTGGATCGGTT+TGG + chr6.3:7007442-7007461 MS.gene20426:intron 50.0%
! TGATTTTTCCCTCCCTGGTG+CGG + chr6.3:7007573-7007592 MS.gene20426:CDS 50.0%
! TGCTGTGATTTTTCCCTCCC+TGG + chr6.3:7007568-7007587 MS.gene20426:CDS 50.0%
!! GTGGTCTTGTGATAGGAGGT+GGG + chr6.3:7005655-7005674 MS.gene20426:CDS 50.0%
!! TGGTCTTGTGATAGGAGGTG+GGG + chr6.3:7005656-7005675 MS.gene20426:CDS 50.0%
!! TTATTGAAAGGTACCGGCGG+TGG + chr6.3:7005636-7005655 MS.gene20426:CDS 50.0%
ACCAAAATGCAGCCGCACCA+GGG - chr6.3:7007588-7007607 None:intergenic 55.0%
CAGTAGCAGTAGGGGTCTTG+TGG + chr6.3:7007425-7007444 MS.gene20426:intron 55.0%
CGAGCGAGAGCTGAAACAAG+AGG - chr6.3:7007150-7007169 None:intergenic 55.0%
TACCAAAATGCAGCCGCACC+AGG - chr6.3:7007589-7007608 None:intergenic 55.0%
TCCTATCACAAGACCACCGC+CGG - chr6.3:7005652-7005671 None:intergenic 55.0%
! AGTAGGGGTCTTGTGGTCAG+TGG + chr6.3:7007432-7007451 MS.gene20426:intron 55.0%
! GGGTCTTGTGGTCAGTGGAT+CGG + chr6.3:7007437-7007456 MS.gene20426:intron 55.0%
!! GGTGGTCTTGTGATAGGAGG+TGG + chr6.3:7005654-7005673 MS.gene20426:CDS 55.0%
AAAATGCAGCCGCACCAGGG+AGG - chr6.3:7007585-7007604 None:intergenic 60.0%
AAATGCAGCCGCACCAGGGA+GGG - chr6.3:7007584-7007603 None:intergenic 60.0%
! TCCCTGGTGCGGCTGCATTT+TGG + chr6.3:7007584-7007603 MS.gene20426:CDS 60.0%
!! ACCGGCGGTGGTCTTGTGAT+AGG + chr6.3:7005648-7005667 MS.gene20426:CDS 60.0%
!! GGCGGTGGTCTTGTGATAGG+AGG + chr6.3:7005651-7005670 MS.gene20426:CDS 60.0%


Chromosome Type Strat End Strand Name
chr6.3 gene 7005630 7007648 7005630 ID=MS.gene20426
chr6.3 mRNA 7005630 7007648 7005630 ID=MS.gene20426.t1;Parent=MS.gene20426
chr6.3 exon 7005630 7005694 7005630 ID=MS.gene20426.t1.exon1;Parent=MS.gene20426.t1
chr6.3 CDS 7005630 7005694 7005630 ID=cds.MS.gene20426.t1;Parent=MS.gene20426.t1
chr6.3 exon 7006686 7006750 7006686 ID=MS.gene20426.t1.exon2;Parent=MS.gene20426.t1
chr6.3 CDS 7006686 7006750 7006686 ID=cds.MS.gene20426.t1;Parent=MS.gene20426.t1
chr6.3 exon 7007160 7007236 7007160 ID=MS.gene20426.t1.exon3;Parent=MS.gene20426.t1
chr6.3 CDS 7007160 7007236 7007160 ID=cds.MS.gene20426.t1;Parent=MS.gene20426.t1
chr6.3 exon 7007508 7007648 7007508 ID=MS.gene20426.t1.exon4;Parent=MS.gene20426.t1
chr6.3 CDS 7007508 7007648 7007508 ID=cds.MS.gene20426.t1;Parent=MS.gene20426.t1
Gene Sequence

>MS.gene20426

ATGATTTTATTGAAAGGTACCGGCGGTGGTCTTGTGATAGGAGGTGGGGTTGTTTCACTTTCACTGTATTTTTTGTTTTAGAATTTAGAATAGAATCTTCTTGGCTCTTCAACGTGTAGAGAGAGTGTGAAGTTTGAGAAGTGTGTGATGATGAGTGAGTTTATAATTTGTTTGTTTTTTTTTTGGTGAATTTTGGTAGTCATGCATAGTGGATTAATGTGTTGTGTAAGATGCAAAACATTGTAGGGATTGTTGGATTAAAAGAAAAATATTATAGATAACTCAAAGTTTTCAATCTTTTTTCTTCTATTATTTTCTGCTCAATATGCAAATTATATTTTTATATAATTTATTTTTTTTGTAGCAGTTTAAGAGACTTTCTTTAGTATGTTCATATTTGGAAAAGTTTTATTGTATTTTCATATTTGGGTAAGTTTGATTGAATTGTTAATAGCAAGTTACTATGATGATGTGAATGAAAGATATGAATGAAAGATGACTCTTCTTGGCTCTTCAACGTGTAGAGAGAGTGTGAAGTTTGAGAAGTGTGTGATGATGAGTGAGTTTATAATTTGTTTGTTTTTTTTTTTGGTGAATTTTGGTAGTCATGCATAGTGGATTAATGTGTTGTGTAAGATGCAAAACATTGTAGGGATTGTTGGATTAAAAGAAAAATATTATAGATAACTCAAAGTTTTCAATCTTTTTTCTTCTATTATTTTCTGCTCAATATGCAAATTATATTTTTATATAATTTATTTTTTTTGTAGCAGTTTAAGAGACTTTCTTTAGTATGTTCATATTTGGAAAAGTTTTATTGTATTTTCATATTTGGGTAAGTTTGATTGAATTGTTAAACATTTAAAATTATATTTTCATTCTAGCATCCAATGTGTGATTTTTTTTCATAAGATTATATTATGCATTAGTTTGTGTATGACTGCCTGATTAAATGTTAGTTTTATCATGAAAAACTATAAGCAATGGACATTTAATAATATTGGTTCCTGTGTTATCCCCAATTTAGCTTCAATACTCTGACATTGTTGAACTTAGGTCCCTTTCCTTAGCTGCTGTAGGTTCTTTTCTGTGTTTACGCACTTCATCAGTTCAGAAAAGGTGTAAGGAAGTCGGTGATAGTTTAAATTTTTTGGTGCATTTTTAGTAAAAACAGTATCAACCATTCATAAATTTGACTGATTAATCTTTTCGAATTTGTTCCTTTCAACACTCATTCACTTCATTATGGTTGGGTATTAGAAATCATTATGTTGGGTATTAGAAATCATTGACTGCGAATTGAGTTTGCTATGGTTTCCAACAACTTCAGATTAAGACAAGGCATTTTGTGATTATTAATACTTTCCTGCTTGCTCTGATAGTCATATCTTGTCTAGATGTTCATGTAAATTATAAATCTGAATTATGAAGTTTTTGGAATGTGAAGTTGTGTTTGGTTTAGTTATTTACTGATTTTGAATGGGGAAAATAACTCAAATTTGAATAATCTCTTTTTACCTCTTGTTTCAGCTCTCGCTCGCAACTCTCGCTTTACAGCCCTTGGTCTTCAACTGTTGTCCTGTCCTTCGTCTATCTCTTCATCACAGGTAATCTTCATTCAATTTCCTGAGCAAGTTCCTCATAATCCGTTGAAGCATATATTTTGCATATATTTTATCGGATTAATCTATGTATGCAATACATGTAGTTGTTACTGTGGTAGTATCAATTGAGCTTTATACATATTTTGTTTGACATTTTTGACAAACCACTATTTAGTAGCACTATTTGGTTGCAGTAGCAGTAGGGGTCTTGTGGTCAGTGGATCGGTTTGGTTTTGTGTTGGTGCTGTCTGTGCGTGCTTTGCTTTAACGATAGGCCATTCCGGTGTTTCTTTTCTTGCTGTCTGCTGCTGTTTTAGCAGATCACAGCAGCTGCTGCTGTGATTTTTCCCTCCCTGGTGCGGCTGCATTTTGGTATTTTGGTGTGTCCCTCTTTGGTTTTGCGTTTAGACTATAG
Protein sequence

>MS.gene20426.t1

MILLKGTGGGLVIGGGVVSLSLSLSLAAVGSFLCLRTSSVQKRSLARNSRFTALGLQLLSCPSSISSSQAIPVFLFLLSAAVLADHSSCCCDFSLPGAAAFWYFGVSLFGFAFRL