AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1348880


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1348880 MtrunA17_Chr4g0005821 89.394 66 7 0 4 69 534 599 5.03e-36 127
Msa1348880 MtrunA17_Chr7g0241611 74.603 63 16 0 4 66 540 602 1.26e-27 103
Msa1348880 MtrunA17_Chr7g0259681 70.312 64 18 1 4 66 481 544 4.79e-26 98.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1348880 AT5G01290.1 63.077 65 22 1 4 66 508 572 5.05e-23 90.5
Msa1348880 AT3G09100.2 64.062 64 22 1 4 66 524 587 9.72e-23 89.7

Find 20 sgRNAs with CRISPR-Local

Find 32 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAGTCAACTGAATTTAAAT+TGG 0.286326 tig0010575:-763 Msa1348880:intergenic
GAAACTCTTGGATGGGAATA+AGG 0.299659 tig0010575:+948 Msa1348880:CDS
TTCAGTTGACTTTCTGTTTG+AGG 0.348533 tig0010575:+773 Msa1348880:CDS
ATTATATTACTTACCAGGGT+TGG 0.417822 tig0010575:+688 Msa1348880:CDS
TTATATTACTTACCAGGGTT+GGG 0.435094 tig0010575:+689 Msa1348880:CDS
CCCTGGTAAGTAATATAATC+AGG 0.439481 tig0010575:-684 Msa1348880:intergenic
TGCTTCCATCGGCAGGTTGA+AGG 0.440873 tig0010575:+886 Msa1348880:intron
TCCTGATTATATTACTTACC+AGG 0.458394 tig0010575:+683 Msa1348880:CDS
TCATGAGTACGTGGTACATA+AGG 0.478867 tig0010575:-717 Msa1348880:intergenic
GGGAATAAGGTTGCTTTCAA+AGG 0.488951 tig0010575:+961 Msa1348880:CDS
ATCGGCAGGTTGAAGGTGAT+CGG 0.499299 tig0010575:+893 Msa1348880:intron
TCGGCAGGTTGAAGGTGATC+GGG 0.508639 tig0010575:+894 Msa1348880:intron
CTCATGAAGGACTCTTAAAG+TGG 0.522723 tig0010575:+733 Msa1348880:CDS
GTGGGGAAAGAAGAAACTCT+TGG 0.533193 tig0010575:+936 Msa1348880:CDS
CCTGATTATATTACTTACCA+GGG 0.561320 tig0010575:+684 Msa1348880:CDS
GGAAAGAAGAAACTCTTGGA+TGG 0.566495 tig0010575:+940 Msa1348880:CDS
TATGTACCACGTACTCATGA+AGG 0.583824 tig0010575:+720 Msa1348880:CDS
GAAAGAAGAAACTCTTGGAT+GGG 0.601410 tig0010575:+941 Msa1348880:CDS
CATAAGGATCGTCCCAACCC+TGG 0.604861 tig0010575:-701 Msa1348870:intergenic
AAGAGTCCTTCATGAGTACG+TGG 0.699809 tig0010575:-726 Msa1348870:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAGTCAACTGAATTTAAAT+TGG - tig0010575:766-785 Msa1348880:intergenic 20.0%
!!! TTGGAATTTTTGATATTACT+TGG + tig0010575:824-843 Msa1348880:intron 20.0%
TCCTGATTATATTACTTACC+AGG + tig0010575:683-702 Msa1348880:CDS 30.0%
CCTGATTATATTACTTACCA+GGG + tig0010575:684-703 Msa1348880:CDS 30.0%
ATTATATTACTTACCAGGGT+TGG + tig0010575:688-707 Msa1348880:CDS 30.0%
TTATATTACTTACCAGGGTT+GGG + tig0010575:689-708 Msa1348880:CDS 30.0%
! TATCATCACCTTCTTTTGTA+TGG + tig0010575:797-816 Msa1348880:intron 30.0%
!!! TAATTTTTAGCTGCTTCCAT+CGG + tig0010575:875-894 Msa1348880:intron 30.0%
CCCTGGTAAGTAATATAATC+AGG - tig0010575:687-706 Msa1348880:intergenic 35.0%
! TTCAGTTGACTTTCTGTTTG+AGG + tig0010575:773-792 Msa1348880:CDS 35.0%
CCAAAACACCATACAAAAGA+AGG - tig0010575:808-827 Msa1348880:intergenic 35.0%
! CCTTCTTTTGTATGGTGTTT+TGG + tig0010575:805-824 Msa1348880:intron 35.0%
AGCAGCTAAAAATTAGATGG+CGG - tig0010575:870-889 Msa1348880:intergenic 35.0%
GGAAGCAGCTAAAAATTAGA+TGG - tig0010575:873-892 Msa1348880:intergenic 35.0%
!!! AGCTACTTTTTGTGTATGAG+TGG + tig0010575:917-936 Msa1348880:CDS 35.0%
!!! GCTACTTTTTGTGTATGAGT+GGG + tig0010575:918-937 Msa1348880:CDS 35.0%
!!! CTACTTTTTGTGTATGAGTG+GGG + tig0010575:919-938 Msa1348880:CDS 35.0%
GAAAGAAGAAACTCTTGGAT+GGG + tig0010575:941-960 Msa1348880:CDS 35.0%
TCATGAGTACGTGGTACATA+AGG - tig0010575:720-739 Msa1348880:intergenic 40.0%
TATGTACCACGTACTCATGA+AGG + tig0010575:720-739 Msa1348880:CDS 40.0%
CTCATGAAGGACTCTTAAAG+TGG + tig0010575:733-752 Msa1348880:CDS 40.0%
GGAAAGAAGAAACTCTTGGA+TGG + tig0010575:940-959 Msa1348880:CDS 40.0%
GAAACTCTTGGATGGGAATA+AGG + tig0010575:948-967 Msa1348880:CDS 40.0%
! GGGAATAAGGTTGCTTTCAA+AGG + tig0010575:961-980 Msa1348880:CDS 40.0%
AAGAGTCCTTCATGAGTACG+TGG - tig0010575:729-748 Msa1348880:intergenic 45.0%
GTGGGGAAAGAAGAAACTCT+TGG + tig0010575:936-955 Msa1348880:CDS 45.0%
!! TTTTAGCTGCTTCCATCGGC+AGG + tig0010575:879-898 Msa1348880:intron 50.0%
! ATCGGCAGGTTGAAGGTGAT+CGG + tig0010575:893-912 Msa1348880:intron 50.0%
CATAAGGATCGTCCCAACCC+TGG - tig0010575:704-723 Msa1348880:intergenic 55.0%
! TGCTTCCATCGGCAGGTTGA+AGG + tig0010575:886-905 Msa1348880:intron 55.0%
GATCACCTTCAACCTGCCGA+TGG - tig0010575:894-913 Msa1348880:intergenic 55.0%
! TCGGCAGGTTGAAGGTGATC+GGG + tig0010575:894-913 Msa1348880:intron 55.0%
Chromosome Type Strat End Strand Name
tig0010575 gene 678 990 678 ID=Msa1348880;Name=Msa1348880
tig0010575 mRNA 678 990 678 ID=Msa1348880-mRNA-1;Parent=Msa1348880;Name=Msa1348880-mRNA-1;_AED=0.07;_eAED=0.07;_QI=0|0|0|1|1|1|2|0|69
tig0010575 exon 678 794 678 ID=Msa1348880-mRNA-1:exon:6644;Parent=Msa1348880-mRNA-1
tig0010575 exon 901 990 901 ID=Msa1348880-mRNA-1:exon:6645;Parent=Msa1348880-mRNA-1
tig0010575 CDS 678 794 678 ID=Msa1348880-mRNA-1:cds;Parent=Msa1348880-mRNA-1
tig0010575 CDS 901 990 901 ID=Msa1348880-mRNA-1:cds;Parent=Msa1348880-mRNA-1
Gene Sequence

>Msa1348880

TTTGTTCCTGATTATATTACTTACCAGGGTTGGGACGATCCTTATGTACCACGTACTCATGAAGGACTCTTAAAGTGGAAATACGCCAATTTAAATTCAGTTGACTTTCTGTTTGAGGTTGAAGGTGATCGGGAGCTACTTTTTGTGTATGAGTGGGGAAAGAAGAAACTCTTGGATGGGAATAAGGTTGCTTTCAAAGGTCAGACA

Protein sequence

>Msa1348880

FVPDYITYQGWDDPYVPRTHEGLLKWKYANLNSVDFLFEVEGDRELLFVYEWGKKKLLDGNKVAFKGQT