AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene21655

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene21655.t1 MTR_5g009460 90.361 83 5 1 5 84 9 91 1.42e-48 149
MS.gene21655.t1 MTR_4g046737 51.515 66 32 0 12 77 8 73 1.11e-19 75.5
MS.gene21655.t1 MTR_2g088730 67.391 46 15 0 30 75 32 77 3.24e-18 72.0
MS.gene21655.t1 MTR_2g023100 41.096 73 43 0 5 77 2 74 5.73e-16 66.2
MS.gene21655.t1 MTR_8g060940 56.410 39 17 0 32 70 65 103 2.94e-11 57.4
MS.gene21655.t1 MTR_4g100720 56.410 39 17 0 32 70 71 109 3.46e-11 56.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene21655.t1 AT2G30420 67.089 79 23 1 6 84 17 92 9.14e-31 104
MS.gene21655.t1 AT5G53200 71.212 66 19 0 19 84 20 85 1.19e-30 104
MS.gene21655.t1 AT2G46410 63.750 80 24 1 4 83 15 89 5.22e-30 102
MS.gene21655.t1 AT2G30432 66.667 66 22 0 16 81 19 84 8.64e-28 96.3
MS.gene21655.t1 AT2G30424 58.904 73 30 0 12 84 16 88 3.65e-26 92.8
MS.gene21655.t1 AT4G01060 58.108 74 31 0 1 74 1 74 6.42e-26 91.3
MS.gene21655.t1 AT4G01060 62.319 69 26 0 6 74 9 77 8.29e-26 91.3
MS.gene21655.t1 AT1G01380 75.556 45 11 0 30 74 32 76 1.41e-20 78.2
MS.gene21655.t1 AT4G01060 69.565 46 14 0 29 74 30 75 1.50e-19 75.1
MS.gene21655.t1 AT5G52600 58.974 39 16 0 32 70 70 108 1.01e-11 58.2

Find 21 sgRNAs with CRISPR-Local

Find 55 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTATCTTCACTTCTTTCTTT+TGG 0.236926 5.2:+3095278 None:intergenic
CGGAGGTTTGACTTGTGTTT+CGG 0.239671 5.2:+3096227 None:intergenic
CAGAAGAAATAGAGAGATTC+TGG 0.240435 5.2:-3095329 MS.gene21655:CDS
GGAGGTTTGACTTGTGTTTC+GGG 0.242590 5.2:+3096228 None:intergenic
GGGAGATATTTGCCTTAGTT+TGG 0.291933 5.2:+3096248 None:intergenic
TTGATAGCAGGTCGCATTCC+GGG 0.323951 5.2:-3095360 MS.gene21655:CDS
GGAGATATTTGCCTTAGTTT+GGG 0.373654 5.2:+3096249 None:intergenic
TTTGATAGCAGGTCGCATTC+CGG 0.383477 5.2:-3095361 MS.gene21655:CDS
GGAAGAACGTTCCCAAACTA+AGG 0.483455 5.2:-3096260 MS.gene21655:CDS
TGTACGACCTAGTTGGAGAT+AGG 0.497484 5.2:-3095928 MS.gene21655:intron
CAGAAGTGAGCAGCAATGAG+TGG 0.497509 5.2:-3095997 MS.gene21655:CDS
CGCAGGATGTACGACCTAGT+TGG 0.536525 5.2:-3095935 MS.gene21655:CDS
AACAGGTGGAATTTGATAGC+AGG 0.543963 5.2:-3095372 MS.gene21655:intron
ATTTCTTCTGCTTTACGACC+CGG 0.559635 5.2:+3095342 None:intergenic
CATAGAGATGAGCGAGCAAG+AGG 0.568119 5.2:-3095969 MS.gene21655:CDS
AAGAGGAGGATCTCATTCGC+AGG 0.581290 5.2:-3095952 MS.gene21655:CDS
AGAAGTGAGCAGCAATGAGT+GGG 0.602111 5.2:-3095996 MS.gene21655:CDS
AGAGATGAGCGAGCAAGAGG+AGG 0.612798 5.2:-3095966 MS.gene21655:CDS
AGATTAGAAACCACCTTCGG+AGG 0.612968 5.2:+3096210 None:intergenic
AATATTACCTATCTCCAACT+AGG 0.621481 5.2:+3095921 None:intergenic
AACACAAGTCAAACCTCCGA+AGG 0.653483 5.2:-3096223 MS.gene21655:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAGCAATAGAGAAAATAA+TGG + chr5.2:3095397-3095416 None:intergenic 20.0%
!! AAACATTAAATACTAGTATG+AGG + chr5.2:3095504-3095523 None:intergenic 20.0%
!! ATTAGAACTAATTAGAAACA+CGG - chr5.2:3095913-3095932 MS.gene21655:intron 20.0%
!!! TATCTTTTGCAAAATCATAA+TGG + chr5.2:3095791-3095810 None:intergenic 20.0%
!!! TCTAATTAGTTCTAATAACT+TGG + chr5.2:3095909-3095928 None:intergenic 20.0%
! TTACTAAAGATGTGTTTGAT+AGG - chr5.2:3095970-3095989 MS.gene21655:CDS 25.0%
!! AAAGTTGGTCAATACTTTAA+AGG + chr5.2:3096038-3096057 None:intergenic 25.0%
!!! TTTTAAGCTTTGACGTTTTA+AGG - chr5.2:3095685-3095704 MS.gene21655:intron 25.0%
AAAAAACCTCAAAACGTCAA+AGG + chr5.2:3095665-3095684 None:intergenic 30.0%
AATATTACCTATCTCCAACT+AGG + chr5.2:3095628-3095647 None:intergenic 30.0%
AGAGAAAATAATGGCATGTT+GGG + chr5.2:3095388-3095407 None:intergenic 30.0%
CATCATACAGCATAAAAAGT+TGG + chr5.2:3096053-3096072 None:intergenic 30.0%
TAATTAGAAACACGGTGAAA+AGG - chr5.2:3095921-3095940 MS.gene21655:intron 30.0%
TACAATTACAAAGAAGCTGA+GGG - chr5.2:3095741-3095760 MS.gene21655:intron 30.0%
TACGATACTAATTGCATGTT+TGG + chr5.2:3095876-3095895 None:intergenic 30.0%
TAGAGAAAATAATGGCATGT+TGG + chr5.2:3095389-3095408 None:intergenic 30.0%
TTATACGTGTACCAATTAAG+AGG - chr5.2:3095446-3095465 MS.gene21655:intron 30.0%
TTATGCTGTATGATGTTTGA+TGG - chr5.2:3096058-3096077 MS.gene21655:intron 30.0%
! GTCATAAGCTTTTACATGAA+AGG - chr5.2:3096122-3096141 MS.gene21655:intron 30.0%
! GTTCTAATAACTTGGTCTTT+CGG + chr5.2:3095901-3095920 None:intergenic 30.0%
! TAATTGCATGTTTGGTAACA+TGG + chr5.2:3095868-3095887 None:intergenic 30.0%
! TATATTCCTTTGACGTTTTG+AGG - chr5.2:3095656-3095675 MS.gene21655:intron 30.0%
AAGAAACTACACAATGCAAC+AGG - chr5.2:3096157-3096176 MS.gene21655:intron 35.0%
AGAAAATAATGGCATGTTGG+GGG + chr5.2:3095386-3095405 None:intergenic 35.0%
ATGCATCATGTCCTCTTAAT+TGG + chr5.2:3095460-3095479 None:intergenic 35.0%
CAGAAGAAATAGAGAGATTC+TGG - chr5.2:3096217-3096236 MS.gene21655:intron 35.0%
CTACAATTACAAAGAAGCTG+AGG - chr5.2:3095740-3095759 MS.gene21655:intron 35.0%
GAGAAAATAATGGCATGTTG+GGG + chr5.2:3095387-3095406 None:intergenic 35.0%
GGAGATATTTGCCTTAGTTT+GGG + chr5.2:3095300-3095319 None:intergenic 35.0%
AAACTACACAATGCAACAGG+TGG - chr5.2:3096160-3096179 MS.gene21655:intron 40.0%
ATTTCTTCTGCTTTACGACC+CGG + chr5.2:3096207-3096226 None:intergenic 40.0%
GGGAGATATTTGCCTTAGTT+TGG + chr5.2:3095301-3095320 None:intergenic 40.0%
GGTAGATTAGAAACCACCTT+CGG + chr5.2:3095342-3095361 None:intergenic 40.0%
! AACAGGTGGAATTTGATAGC+AGG - chr5.2:3096174-3096193 MS.gene21655:intron 40.0%
AAATAATGGCATGTTGGGGG+TGG + chr5.2:3095383-3095402 None:intergenic 45.0%
AACACAAGTCAAACCTCCGA+AGG - chr5.2:3095323-3095342 MS.gene21655:CDS 45.0%
AATAATGGCATGTTGGGGGT+GGG + chr5.2:3095382-3095401 None:intergenic 45.0%
AGAAGTGAGCAGCAATGAGT+GGG - chr5.2:3095550-3095569 MS.gene21655:intron 45.0%
AGATTAGAAACCACCTTCGG+AGG + chr5.2:3095339-3095358 None:intergenic 45.0%
GGAAGAACGTTCCCAAACTA+AGG - chr5.2:3095286-3095305 MS.gene21655:CDS 45.0%
TGTACGACCTAGTTGGAGAT+AGG - chr5.2:3095618-3095637 MS.gene21655:intron 45.0%
! TTTGATAGCAGGTCGCATTC+CGG - chr5.2:3096185-3096204 MS.gene21655:intron 45.0%
!! CGGAGGTTTGACTTGTGTTT+CGG + chr5.2:3095322-3095341 None:intergenic 45.0%
!! GGAGGTTTGACTTGTGTTTC+GGG + chr5.2:3095321-3095340 None:intergenic 45.0%
AAGAGGAGGATCTCATTCGC+AGG - chr5.2:3095594-3095613 MS.gene21655:intron 50.0%
ACAAGTCAAACCTCCGAAGG+TGG - chr5.2:3095326-3095345 MS.gene21655:CDS 50.0%
CAGAAGTGAGCAGCAATGAG+TGG - chr5.2:3095549-3095568 MS.gene21655:intron 50.0%
CATAGAGATGAGCGAGCAAG+AGG - chr5.2:3095577-3095596 MS.gene21655:intron 50.0%
! TTGATAGCAGGTCGCATTCC+GGG - chr5.2:3096186-3096205 MS.gene21655:intron 50.0%
AGAGATGAGCGAGCAAGAGG+AGG - chr5.2:3095580-3095599 MS.gene21655:intron 55.0%
CGCAGGATGTACGACCTAGT+TGG - chr5.2:3095611-3095630 MS.gene21655:intron 55.0%
GGTGGGTGTGTGTGTGTGTT+GGG + chr5.2:3095365-3095384 None:intergenic 55.0%
GTGGGTGTGTGTGTGTGTTG+GGG + chr5.2:3095364-3095383 None:intergenic 55.0%
TGGGTGTGTGTGTGTGTTGG+GGG + chr5.2:3095363-3095382 None:intergenic 55.0%
GGGTGGGTGTGTGTGTGTGT+TGG + chr5.2:3095366-3095385 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 3095284 3096284 3095284 ID=MS.gene21655
chr5.2 mRNA 3095284 3096284 3095284 ID=MS.gene21655.t1;Parent=MS.gene21655
chr5.2 exon 3096224 3096284 3096224 ID=MS.gene21655.t1.exon1;Parent=MS.gene21655.t1
chr5.2 CDS 3096224 3096284 3096224 ID=cds.MS.gene21655.t1;Parent=MS.gene21655.t1
chr5.2 exon 3095929 3096016 3095929 ID=MS.gene21655.t1.exon2;Parent=MS.gene21655.t1
chr5.2 CDS 3095929 3096016 3095929 ID=cds.MS.gene21655.t1;Parent=MS.gene21655.t1
chr5.2 exon 3095284 3095389 3095284 ID=MS.gene21655.t1.exon3;Parent=MS.gene21655.t1
chr5.2 CDS 3095284 3095389 3095284 ID=cds.MS.gene21655.t1;Parent=MS.gene21655.t1
Gene Sequence

>MS.gene21655

ATGGAAGAACGTTCCCAAACTAAGGCAAATATCTCCCGAAACACAAGTCAAACCTCCGAAGGTGGTTTCTAATCTACCCCCAACACACACACACACCCACCCCCAACATGCCATTATTTTCTCTATTGCTTTTTCTAATTTCAATTTTTTCTCTTTTATTACTTATACGTGTACCAATTAAGAGGACATGATGCATCTATGAGTATAACTAACTGAGCCTCATACTAGTATTTAATGTTTGTTGTTTGTTAAATGTTAGCTGATGCAGAAGTGAGCAGCAATGAGTGGGAGTTCATAGAGATGAGCGAGCAAGAGGAGGATCTCATTCGCAGGATGTACGACCTAGTTGGAGATAGGTAATATTACTTTGTCTATATTCCTTTGACGTTTTGAGGTTTTTTTTTTAAGCTTTGACGTTTTAAGGTTAATAGATAAGAACAAATAATTCTGCAAGAGCTACAATTACAAAGAAGCTGAGGGTTTCTCAAAATCACAGTCAGTGAACCATTATGATTTTGCAAAAGATATACAGTGTAGCTTTTATTAAATCATGATGACTCAACATGATTTCGACAAATTCACCATGTTACCAAACATGCAATTAGTATCGTATACCGAAAGACCAAGTTATTAGAACTAATTAGAAACACGGTGAAAAGGATAAAATGTGATTGTGAAGAGAAATTTTACTAAAGATGTGTTTGATAGGTTAAAAAGTAAATACTAGACACAACAAACAACATATGACAAACCTTTAAAGTATTGACCAACTTTTTATGCTGTATGATGTTTGATGGACAAAATGTTATTTTGACATTTTAGAGACATATGTTATTTTGTCATAAGCTTTTACATGAAAGGATTGATTTATAGAAGAAACTACACAATGCAACAGGTGGAATTTGATAGCAGGTCGCATTCCGGGTCGTAAAGCAGAAGAAATAGAGAGATTCTGGATTATGAAACACGCTGATGCTTTTTCCGCCAAAAGAAAGAAGTGA
Protein sequence

>MS.gene21655.t1

MEERSQTKANISRNTSQTSEEVSSNEWEFIEMSEQEEDLIRRMYDLVGDRWNLIAGRIPGRKAEEIERFWIMKHADAFSAKRKK