AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1466540


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1466540 MtrunA17_Chr1g0194401 94.595 37 2 0 49 85 1 37 9.17e-18 73.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 7 sgRNAs with CRISPR-Local

Find 42 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAACAATAACATCGTTTCT+AGG 0.240162 tig0047485:-551 Msa1466540:five_prime_UTR
TTGTTGAAACATTCTTAACT+AGG 0.456257 tig0047485:+567 Msa1466540:intergenic
CAACAATAACATCGTTTCTA+GGG 0.472288 tig0047485:-550 Msa1466540:five_prime_UTR
GGGTTCTACCCTTTGACTTG+AGG 0.495824 tig0047485:-530 Msa1466540:intron
AAGGAGGTACCTCAAGTCAA+AGG 0.539248 tig0047485:+521 Msa1466530:intergenic
AGGAGGTACCTCAAGTCAAA+GGG 0.570753 tig0047485:+522 Msa1466530:intergenic
AGGAATGTGTTGATGCACGC+AGG 0.636801 tig0047485:+587 Msa1466530:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTATTAAAAATTGAATCTT+TGG - tig0047485:324-343 Msa1466540:intron 10.0%
!! TAAAAAAAGACAAGAATTTA+AGG + tig0047485:52-71 Msa1466540:intergenic 15.0%
!!! TTGAAATTGATTTAATTAGA+TGG - tig0047485:454-473 Msa1466540:intron 15.0%
!!! TGAAATTGATTTAATTAGAT+GGG - tig0047485:455-474 Msa1466540:intron 15.0%
!! AAAAGAAGATGAAGAAAAAA+GGG + tig0047485:216-235 Msa1466540:intergenic 20.0%
!!! AGGTTTTTCGGTTTTATTAA+TGG + tig0047485:32-51 Msa1466540:intergenic 25.0%
!!! GACAAGAATTTAAGGTTTTT+CGG + tig0047485:44-63 Msa1466540:intergenic 25.0%
! TTGTTGAAACATTCTTAACT+AGG + tig0047485:142-161 Msa1466540:intergenic 25.0%
! AAAGAAGATGAAGAAAAAAG+GGG + tig0047485:215-234 Msa1466540:intergenic 25.0%
! GAAAAGAAGATGAAGAAAAA+AGG + tig0047485:217-236 Msa1466540:intergenic 25.0%
! TCAAAGAGAAAAAGAAAAAG+AGG - tig0047485:487-506 Msa1466540:intron 25.0%
! AATTTAGATGGATCAGAAAA+GGG - tig0047485:620-639 Msa1466540:five_prime_UTR 25.0%
!! TCAAATTCTTGTGATGTTTT+TGG - tig0047485:677-696 Msa1466540:five_prime_UTR 25.0%
CAAAAAGAGAGAAAAACCAT+TGG - tig0047485:6-25 Msa1466540:CDS 30.0%
TCAACAATAACATCGTTTCT+AGG - tig0047485:155-174 Msa1466540:CDS 30.0%
CAACAATAACATCGTTTCTA+GGG - tig0047485:156-175 Msa1466540:CDS 30.0%
AAGAAGATGAAGAAAAAAGG+GGG + tig0047485:214-233 Msa1466540:intergenic 30.0%
!!! GGGTTTTGTTTTTGAGTAAT+TGG - tig0047485:361-380 Msa1466540:intron 30.0%
TCTTTAGCATGATTATGAGA+TGG - tig0047485:412-431 Msa1466540:intron 30.0%
CTTTAGCATGATTATGAGAT+GGG - tig0047485:413-432 Msa1466540:intron 30.0%
GTTGAATTTGACATTGAAAG+TGG - tig0047485:509-528 Msa1466540:intron 30.0%
AGAGATTCAACTTCAAAGAA+TGG - tig0047485:569-588 Msa1466540:five_prime_UTR 30.0%
AATGGGGTTATGAATTTAGA+TGG - tig0047485:608-627 Msa1466540:five_prime_UTR 30.0%
GAATTTAGATGGATCAGAAA+AGG - tig0047485:619-638 Msa1466540:five_prime_UTR 30.0%
!!! TCGGTTTTATTAATGGCCAA+TGG + tig0047485:25-44 Msa1466540:intergenic 35.0%
AGAAGATGAAGAAAAAAGGG+GGG + tig0047485:213-232 Msa1466540:intergenic 35.0%
TCTTTGGCATGATTGTGAAA+TGG - tig0047485:340-359 Msa1466540:intron 35.0%
CTTTGGCATGATTGTGAAAT+GGG - tig0047485:341-360 Msa1466540:intron 35.0%
! CTTCAAAGAATGGTTTTCCT+TGG - tig0047485:579-598 Msa1466540:five_prime_UTR 35.0%
GGATCAGAAAAGGGTAAAAA+TGG - tig0047485:629-648 Msa1466540:five_prime_UTR 35.0%
! AGAATGGTTTTCCTTGGTCA+TGG - tig0047485:585-604 Msa1466540:five_prime_UTR 40.0%
! GTTTTCCTTGGTCATGGAAT+GGG - tig0047485:591-610 Msa1466540:five_prime_UTR 40.0%
! TTTTCCTTGGTCATGGAATG+GGG - tig0047485:592-611 Msa1466540:five_prime_UTR 40.0%
!! AGGAGGTACCTCAAGTCAAA+GGG + tig0047485:187-206 Msa1466540:intergenic 45.0%
!! AAGGAGGTACCTCAAGTCAA+AGG + tig0047485:188-207 Msa1466540:intergenic 45.0%
TGAAGAAAAAAGGGGGGTCA+AGG + tig0047485:207-226 Msa1466540:intergenic 45.0%
! GGTTTTCCTTGGTCATGGAA+TGG - tig0047485:590-609 Msa1466540:five_prime_UTR 45.0%
ATAACCCCATTCCATGACCA+AGG + tig0047485:599-618 Msa1466540:intergenic 45.0%
! AGGAATGTGTTGATGCACGC+AGG + tig0047485:122-141 Msa1466540:intergenic 50.0%
!! GGGTTCTACCCTTTGACTTG+AGG - tig0047485:176-195 Msa1466540:CDS 50.0%
AGAAAAAAGGGGGGTCAAGG+AGG + tig0047485:204-223 Msa1466540:intergenic 50.0%
TGGTGAAAACACGAGCGAAG+AGG - tig0047485:529-548 Msa1466540:intron 50.0%
Chromosome Type Strat End Strand Name
tig0047485 gene 1 727 1 ID=Msa1466540;Name=Msa1466540
tig0047485 mRNA 1 727 1 ID=Msa1466540-mRNA-1;Parent=Msa1466540;Name=Msa1466540-mRNA-1;_AED=0.00;_eAED=0.00;_QI=197|1|1|1|0|0.5|2|0|85
tig0047485 exon 1 255 1 ID=Msa1466540-mRNA-1:exon:25092;Parent=Msa1466540-mRNA-1
tig0047485 exon 531 727 531 ID=Msa1466540-mRNA-1:exon:25091;Parent=Msa1466540-mRNA-1
tig0047485 five_prime_UTR 531 727 531 ID=Msa1466540-mRNA-1:five_prime_utr;Parent=Msa1466540-mRNA-1
tig0047485 CDS 1 255 1 ID=Msa1466540-mRNA-1:cds;Parent=Msa1466540-mRNA-1
Gene Sequence

>Msa1466540

ATGGGTCGTGCTATTCAAAGAGAAAAAGAAAAAGAGGTTGAATTTGACATTGAAAGTGGTGAAAACACGAGCGAAGAGGATACAAGCAATGATGAGAGAGATTCAACTTCAAAGAATGGTTTTCCTTGGTCATGGAATGGGGTTATGAATTTAGATGGATCAGAAAAGGGTAAAAATGGAATTGAAGCATCATGTAGCAGTTCTTCAAATTCTTGTGATGTTTTTGGTGTAGATGAATGTAATCTAGAATTGTTG

Protein sequence

>Msa1466540

MGRAIQREKEKEVEFDIESGENTSEEDTSNDERDSTSKNGFPWSWNGVMNLDGSEKGKNGIEASCSSSSNSCDVFGVDECNLELL