AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene20048

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene20048.t1 MTR_7g100880 94.048 84 5 0 1 84 1 84 1.30e-30 103
MS.gene20048.t1 MTR_7g100905 89.474 76 3 1 9 84 3 73 1.65e-17 70.1
MS.gene20048.t1 MTR_7g100905 94.030 67 4 0 18 84 2 68 5.27e-16 65.9
MS.gene20048.t1 MTR_7g100890 82.716 81 10 2 8 84 417 497 8.48e-15 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.gene20048.t1 AT2G37120 77.778 63 14 0 22 84 14 76 2.45e-15 64.7
MS.gene20048.t1 AT3G53370 78.333 60 13 0 25 84 17 76 6.48e-13 58.5

Find 25 sgRNAs with CRISPR-Local

Find 43 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTAATAGTTCTCCTGGTTAT+TGG 0.281375 7.2:+11324236 MS.gene20048:CDS
TGGGGAAATGTTTAGAAAGC+TGG 0.417081 7.2:+11324191 MS.gene20048:intron
GTCTCTGCACCTGGAGAGTA+GGG 0.431630 7.2:+11324386 MS.gene20048:CDS
GTCCATTGCCCCTACTCTCC+AGG 0.446840 7.2:-11324395 None:intergenic
ATGGCCGATGACTTTGAATT+CGG 0.448197 7.2:+11323838 MS.gene20048:CDS
ACCAGGAGAACTATTAAGCC+TGG 0.450176 7.2:-11324230 None:intergenic
TTGCTGTTGACATTCCTCAT+AGG 0.463310 7.2:+11324263 MS.gene20048:CDS
CCCAGGCTTAATAGTTCTCC+TGG 0.470539 7.2:+11324229 MS.gene20048:CDS
ATAGTTCTCCTGGTTATTGG+TGG 0.478741 7.2:+11324239 MS.gene20048:CDS
GTTTAGAAAGCTGGATCTCA+AGG 0.480415 7.2:+11324200 MS.gene20048:intron
TCCTCCTTCCTTTGATCGCA+TGG 0.481901 7.2:+11323870 MS.gene20048:CDS
TAGTTCTCCTGGTTATTGGT+GGG 0.495632 7.2:+11324240 MS.gene20048:CDS
AAGCAAGGAGTCTCTGCACC+TGG 0.523372 7.2:+11324377 MS.gene20048:CDS
AGTCTCTGCACCTGGAGAGT+AGG 0.526480 7.2:+11324385 MS.gene20048:CDS
GAAGAGTACCATGCGATCAA+AGG 0.548062 7.2:-11323878 None:intergenic
GAATTCAAAGTCATCGGCCA+TGG 0.568004 7.2:-11323836 None:intergenic
AGAGTGCATAATTTCCTATG+AGG 0.578802 7.2:-11324277 None:intergenic
ATCACCGAATTCAAAGTCAT+CGG 0.579370 7.2:-11323842 None:intergenic
CCAGGAGAACTATTAAGCCT+GGG 0.597197 7.2:-11324229 None:intergenic
ACAGCAACCCACCAATAACC+AGG 0.598951 7.2:-11324247 None:intergenic
TTTAGAAAGCTGGATCTCAA+GGG 0.612528 7.2:+11324201 MS.gene20048:intron
AGTACCATGCGATCAAAGGA+AGG 0.619049 7.2:-11323874 None:intergenic
GGATCTCAAGGGTTCAACCC+AGG 0.620507 7.2:+11324212 MS.gene20048:CDS
ACCATGCGATCAAAGGAAGG+AGG 0.683503 7.2:-11323871 None:intergenic
TCTCTGCACCTGGAGAGTAG+GGG 0.689358 7.2:+11324387 MS.gene20048:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAGATAAAAAACTTGATTA+AGG - chr7.2:11324159-11324178 None:intergenic 15.0%
!! ATAGTTAAGTTTAGCTATAT+GGG - chr7.2:11324027-11324046 None:intergenic 20.0%
! ATGAGATGTAAGAAAAGAAA+AGG - chr7.2:11323903-11323922 None:intergenic 25.0%
! CATAGTTAAGTTTAGCTATA+TGG - chr7.2:11324028-11324047 None:intergenic 25.0%
! CTCAAAAAAGAAGATGAAAA+AGG + chr7.2:11324346-11324365 MS.gene20048:CDS 25.0%
! TTCAAATTATTATGCTAGCT+CGG + chr7.2:11324055-11324074 MS.gene20048:intron 25.0%
TCTTTAGATTAGACATGTCT+TGG + chr7.2:11323971-11323990 MS.gene20048:intron 30.0%
TTAAGTTTAGCTATATGGGT+TGG - chr7.2:11324023-11324042 None:intergenic 30.0%
TTAATAGTTCTCCTGGTTAT+TGG + chr7.2:11324236-11324255 MS.gene20048:CDS 30.0%
!!! TATCTTTTGTTGTTGCTCTT+GGG + chr7.2:11324172-11324191 MS.gene20048:intron 30.0%
!!! TTATCTTTTGTTGTTGCTCT+TGG + chr7.2:11324171-11324190 MS.gene20048:intron 30.0%
!!! TTCATCTTCTTTTTTGAGAG+TGG - chr7.2:11324344-11324363 None:intergenic 30.0%
AGAGTGCATAATTTCCTATG+AGG - chr7.2:11324280-11324299 None:intergenic 35.0%
ATCACCGAATTCAAAGTCAT+CGG - chr7.2:11323845-11323864 None:intergenic 35.0%
TTTAGAAAGCTGGATCTCAA+GGG + chr7.2:11324201-11324220 MS.gene20048:intron 35.0%
!!! ATCTTTTGTTGTTGCTCTTG+GGG + chr7.2:11324173-11324192 MS.gene20048:intron 35.0%
AAAAAGGAGAGACTGAAGCA+AGG + chr7.2:11324362-11324381 MS.gene20048:CDS 40.0%
ATAGTTCTCCTGGTTATTGG+TGG + chr7.2:11324239-11324258 MS.gene20048:CDS 40.0%
ATGGCCGATGACTTTGAATT+CGG + chr7.2:11323838-11323857 MS.gene20048:CDS 40.0%
GTTTAGAAAGCTGGATCTCA+AGG + chr7.2:11324200-11324219 MS.gene20048:intron 40.0%
TAGTTCTCCTGGTTATTGGT+GGG + chr7.2:11324240-11324259 MS.gene20048:CDS 40.0%
TGGGGAAATGTTTAGAAAGC+TGG + chr7.2:11324191-11324210 MS.gene20048:intron 40.0%
! ATTATTATGCTAGCTCGGTG+TGG + chr7.2:11324060-11324079 MS.gene20048:intron 40.0%
! GATTAGACATGTCTTGGTGT+AGG + chr7.2:11323977-11323996 MS.gene20048:intron 40.0%
! TTGCTGTTGACATTCCTCAT+AGG + chr7.2:11324263-11324282 MS.gene20048:CDS 40.0%
!! TTAGCTATATGGGTTGGTGT+CGG - chr7.2:11324017-11324036 None:intergenic 40.0%
!!! AGTGGCTTCTTTTTTCTAGG+AGG - chr7.2:11324326-11324345 None:intergenic 40.0%
!!! CTTCTTTTTTCTAGGAGGGA+GGG - chr7.2:11324321-11324340 None:intergenic 40.0%
!!! GAGAGTGGCTTCTTTTTTCT+AGG - chr7.2:11324329-11324348 None:intergenic 40.0%
!!! GTGGCTTCTTTTTTCTAGGA+GGG - chr7.2:11324325-11324344 None:intergenic 40.0%
ACCAGGAGAACTATTAAGCC+TGG - chr7.2:11324233-11324252 None:intergenic 45.0%
AGTACCATGCGATCAAAGGA+AGG - chr7.2:11323877-11323896 None:intergenic 45.0%
CCAGGAGAACTATTAAGCCT+GGG - chr7.2:11324232-11324251 None:intergenic 45.0%
!! GAAGAGTACCATGCGATCAA+AGG - chr7.2:11323881-11323900 None:intergenic 45.0%
!!! GCTTCTTTTTTCTAGGAGGG+AGG - chr7.2:11324322-11324341 None:intergenic 45.0%
ACAGCAACCCACCAATAACC+AGG - chr7.2:11324250-11324269 None:intergenic 50.0%
ACCATGCGATCAAAGGAAGG+AGG - chr7.2:11323874-11323893 None:intergenic 50.0%
CCCAGGCTTAATAGTTCTCC+TGG + chr7.2:11324229-11324248 MS.gene20048:CDS 50.0%
TCCTCCTTCCTTTGATCGCA+TGG + chr7.2:11323870-11323889 MS.gene20048:CDS 50.0%
!! AAGAGTGTCTGCGTGTGAGA+TGG - chr7.2:11323955-11323974 None:intergenic 50.0%
!! CTATATGGGTTGGTGTCGGA+CGG - chr7.2:11324013-11324032 None:intergenic 50.0%
AAGCAAGGAGTCTCTGCACC+TGG + chr7.2:11324377-11324396 MS.gene20048:CDS 55.0%
GGATCTCAAGGGTTCAACCC+AGG + chr7.2:11324212-11324231 MS.gene20048:CDS 55.0%


Chromosome Type Strat End Strand Name
chr7.2 gene 11323838 11324406 11323838 ID=MS.gene20048
chr7.2 mRNA 11323838 11324406 11323838 ID=MS.gene20048.t1;Parent=MS.gene20048
chr7.2 exon 11323838 11323891 11323838 ID=MS.gene20048.t1.exon1;Parent=MS.gene20048.t1
chr7.2 CDS 11323838 11323891 11323838 ID=cds.MS.gene20048.t1;Parent=MS.gene20048.t1
chr7.2 exon 11324206 11324406 11324206 ID=MS.gene20048.t1.exon2;Parent=MS.gene20048.t1
chr7.2 CDS 11324206 11324406 11324206 ID=cds.MS.gene20048.t1;Parent=MS.gene20048.t1
Gene Sequence

>MS.gene20048

ATGGCCGATGACTTTGAATTCGGTGATAAAGTTCCTCCTTCCTTTGATCGCATGGTACTCTTCCTTTTCTTTTCTTACATCTCATTATTTGTATCATTTCATTCTTTATAGCATCCATCTCACACGCAGACACTCTTTAGATTAGACATGTCTTGGTGTAGGACACGTGACACCGTCCGACACCAACCCATATAGCTAAACTTAACTATGTGATCTTTTCAAATTATTATGCTAGCTCGGTGTGGTATCTGATGTATGTGTATGTATTCGTGTTTTGCTAACATGTCTGATTTAATTGCTCTGTGTTATCTGATATGACCTTAATCAAGTTTTTTATCTTTTGTTGTTGCTCTTGGGGAAATGTTTAGAAAGCTGGATCTCAAGGGTTCAACCCAGGCTTAATAGTTCTCCTGGTTATTGGTGGGTTGCTGTTGACATTCCTCATAGGAAATTATGCACTCTACGTTTATGCACAGAAGACCCTCCCTCCTAGAAAAAAGAAGCCACTCTCAAAAAAGAAGATGAAAAAGGAGAGACTGAAGCAAGGAGTCTCTGCACCTGGAGAGTAG
Protein sequence

>MS.gene20048.t1

MADDFEFGDKVPPSFDRMKAGSQGFNPGLIVLLVIGGLLLTFLIGNYALYVYAQKTLPPRKKKPLSKKKMKKERLKQGVSAPGE