AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene53522

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene53522.t1 MTR_2g012700 38.462 104 58 2 27 130 22 119 3.54e-18 75.1
MS.gene53522.t1 MTR_2g062330 39.423 104 56 3 27 130 42 138 9.95e-17 72.0
MS.gene53522.t1 MTR_5g071410 37.255 102 60 1 27 128 169 266 3.97e-16 72.8
MS.gene53522.t1 MTR_7g117585 34.314 102 63 1 27 128 46 143 5.73e-15 67.4
MS.gene53522.t1 MTR_6g477950 35.644 101 61 1 33 133 51 147 2.09e-12 62.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 20 sgRNAs with CRISPR-Local

Find 31 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTCTTCACGTTTGCTATC+AGG 0.245648 1.2:+27821248 None:intergenic
CACCTCATTTCCTGTTTGTT+CGG 0.249853 1.2:-27821142 MS.gene53522:CDS
CGAGAAGAAACGTCAAGTTT+TGG 0.381037 1.2:-27821472 MS.gene53522:intron
GAAGGATGGTACAAGTTTCT+TGG 0.386296 1.2:-27821215 MS.gene53522:CDS
AAACGTGAAGAGAATTATAT+TGG 0.388153 1.2:-27821239 MS.gene53522:CDS
ACCTCATTTCCTGTTTGTTC+GGG 0.389186 1.2:-27821141 MS.gene53522:CDS
AGAAAACAACCCGAACAAAC+AGG 0.431572 1.2:+27821132 None:intergenic
GTGGAAAAGATTCTTCTTCA+AGG 0.435979 1.2:-27821347 MS.gene53522:CDS
TTTGGTGAAGATTGGGTGGC+AGG 0.440881 1.2:-27821540 MS.gene53522:CDS
TTGTAATGGATGAGGACATT+TGG 0.446953 1.2:-27821593 None:intergenic
CTTCTCGTCGACAACTGACT+TGG 0.485430 1.2:+27821488 None:intergenic
TGGCAGGTGAAGAATATCAT+TGG 0.497212 1.2:-27821524 MS.gene53522:CDS
GGTGATAGTACTTTGAAAGT+TGG 0.503942 1.2:-27821194 MS.gene53522:CDS
GAAGAGAATTATATTGGCGA+AGG 0.578432 1.2:-27821233 MS.gene53522:CDS
AGAATTATATTGGCGAAGGA+TGG 0.592958 1.2:-27821229 MS.gene53522:CDS
ACCCGAACAAACAGGAAATG+AGG 0.598128 1.2:+27821140 None:intergenic
ATAAGTCTTAAGAGTGTCCA+AGG 0.599637 1.2:+27821301 None:intergenic
TCGTGGCGTTGTAATGGATG+AGG 0.648388 1.2:-27821601 None:intergenic
GTGTATTCCTAGCAAGACCG+TGG 0.669961 1.2:-27821366 MS.gene53522:CDS
CGAACAAACAGGAAATGAGG+TGG 0.689376 1.2:+27821143 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGGTCAGAAAAAAATTATTT+TGG - chr1.2:27821376-27821395 MS.gene53522:intron 20.0%
!!! CATTTTTTAAAAATTGAGCT+TGG - chr1.2:27821287-27821306 MS.gene53522:CDS 20.0%
!!! TTTTTCGTTCATTTTGTTTA+CGG - chr1.2:27821262-27821281 MS.gene53522:CDS 20.0%
! AAACGTGAAGAGAATTATAT+TGG - chr1.2:27821464-27821483 MS.gene53522:intron 25.0%
!!! AAAAATTATTTTGGAGTCCT+TGG - chr1.2:27821385-27821404 MS.gene53522:intron 25.0%
!!! TAGAATTTTTGGTGAAGATT+GGG - chr1.2:27821156-27821175 MS.gene53522:CDS 25.0%
! TTGAAGAAGAATCTTTTCCA+CGG + chr1.2:27821357-27821376 None:intergenic 30.0%
!!! GTAGAATTTTTGGTGAAGAT+TGG - chr1.2:27821155-27821174 MS.gene53522:CDS 30.0%
AGAATTATATTGGCGAAGGA+TGG - chr1.2:27821474-27821493 MS.gene53522:CDS 35.0%
GAAGAGAATTATATTGGCGA+AGG - chr1.2:27821470-27821489 MS.gene53522:intron 35.0%
GTGGAAAAGATTCTTCTTCA+AGG - chr1.2:27821356-27821375 MS.gene53522:CDS 35.0%
TCTTCACCAAAAATTCTACG+AGG + chr1.2:27821154-27821173 None:intergenic 35.0%
! GGTGATAGTACTTTGAAAGT+TGG - chr1.2:27821509-27821528 MS.gene53522:CDS 35.0%
! TCTCTTCCTCGTAGAATTTT+TGG - chr1.2:27821145-27821164 MS.gene53522:CDS 35.0%
!! ATAAGTCTTAAGAGTGTCCA+AGG + chr1.2:27821405-27821424 None:intergenic 35.0%
!!! AATTTTTGGTGAAGATTGGG+TGG - chr1.2:27821159-27821178 MS.gene53522:CDS 35.0%
!!! AGAAACGTCAAGTTTTGGTT+AGG - chr1.2:27821236-27821255 MS.gene53522:CDS 35.0%
ACCTCATTTCCTGTTTGTTC+GGG - chr1.2:27821562-27821581 MS.gene53522:CDS 40.0%
AGAAAACAACCCGAACAAAC+AGG + chr1.2:27821574-27821593 None:intergenic 40.0%
CACCTCATTTCCTGTTTGTT+CGG - chr1.2:27821561-27821580 MS.gene53522:CDS 40.0%
GAAGGATGGTACAAGTTTCT+TGG - chr1.2:27821488-27821507 MS.gene53522:CDS 40.0%
TGGCAGGTGAAGAATATCAT+TGG - chr1.2:27821179-27821198 MS.gene53522:CDS 40.0%
! CGAGAAGAAACGTCAAGTTT+TGG - chr1.2:27821231-27821250 MS.gene53522:CDS 40.0%
!! TTCTCTTCACGTTTGCTATC+AGG + chr1.2:27821458-27821477 None:intergenic 40.0%
!!! TTGTTCGGGTTGTTTTCTCT+AGG - chr1.2:27821576-27821595 MS.gene53522:CDS 40.0%
ACCCGAACAAACAGGAAATG+AGG + chr1.2:27821566-27821585 None:intergenic 45.0%
CGAACAAACAGGAAATGAGG+TGG + chr1.2:27821563-27821582 None:intergenic 45.0%
! ATCTTTTCCACGGTCTTGCT+AGG + chr1.2:27821347-27821366 None:intergenic 45.0%
CTTCTCGTCGACAACTGACT+TGG + chr1.2:27821218-27821237 None:intergenic 50.0%
GTGTATTCCTAGCAAGACCG+TGG - chr1.2:27821337-27821356 MS.gene53522:CDS 50.0%
TTTGGTGAAGATTGGGTGGC+AGG - chr1.2:27821163-27821182 MS.gene53522:CDS 50.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 27821115 27821610 27821115 ID=MS.gene53522
chr1.2 mRNA 27821115 27821610 27821115 ID=MS.gene53522.t1;Parent=MS.gene53522
chr1.2 exon 27821473 27821610 27821473 ID=MS.gene53522.t1.exon1;Parent=MS.gene53522.t1
chr1.2 CDS 27821473 27821610 27821473 ID=cds.MS.gene53522.t1;Parent=MS.gene53522.t1
chr1.2 exon 27821115 27821387 27821115 ID=MS.gene53522.t1.exon2;Parent=MS.gene53522.t1
chr1.2 CDS 27821115 27821387 27821115 ID=cds.MS.gene53522.t1;Parent=MS.gene53522.t1
Gene Sequence

>MS.gene53522

ATGGATGAGGACATTTGGCTTCATTTTGATTCTCTTCCTCGTAGAATTTTTGGTGAAGATTGGGTGGCAGGTGAAGAATATCATTGGAAGCTAGATTTAACCAAGTCAGTTGTCGACGAGAAGAAACGTCAAGTTTTGGTTAGGTTCTTTTTCGTTCATTTTGTTTACGGATCATTTTTTAAAAATTGAGCTTGGCTAATTGTCTCTTCGTACGTTTTTGCAGTGTATTCCTAGCAAGACCGTGGAAAAGATTCTTCTTCAAGGTCAGAAAAAAATTATTTTGGAGTCCTTGGACACTCTTAAGACTTATGAGTGTGATATCATCACTTTTGTAAGAAATCCTGATAGCAAACGTGAAGAGAATTATATTGGCGAAGGATGGTACAAGTTTCTTGGTGATAGTACTTTGAAAGTTGGTGACGTTTTATTGTTTGATGTATCTCAGCCACCTCATTTCCTGTTTGTTCGGGTTGTTTTCTCTAGGCTATTTCATTGA
Protein sequence

>MS.gene53522.t1

MDEDIWLHFDSLPRRIFGEDWVAGEEYHWKLDLTKSVVDEKKRQVLCIPSKTVEKILLQGQKKIILESLDTLKTYECDIITFVRNPDSKREENYIGEGWYKFLGDSTLKVGDVLLFDVSQPPHFLFVRVVFSRLFH