AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1319520


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1319520 MtrunA17_Chr8g0349971 95.492 244 11 0 1 244 1 244 6.52e-173 475
Msa1319520 MtrunA17_Chr7g0246981 50.704 142 63 3 1 142 1 135 7.57e-41 137
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1319520 AT4G23890.1 55.285 246 95 5 2 240 3 240 8.74e-87 258

Find 58 sgRNAs with CRISPR-Local

Find 67 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTCCGACGAAGAAAGTTTA+AGG 0.169983 8_4:+22748091 None:intergenic
ATACCACAGTACATGTAAAA+AGG 0.226887 8_4:+22748000 None:intergenic
GTTGCCCTTCATAGCCTTCA+TGG 0.229693 8_4:-22748534 Msa1319520:CDS
CTTCTTAGATCAAAGTTCTT+AGG 0.254892 8_4:-22748507 Msa1319520:CDS
GAACTTGAGAGAAGAGAAAA+AGG 0.270077 8_4:-22747895 Msa1319520:CDS
GGGTTTCCTGGTGGTGAAAA+AGG 0.277133 8_4:-22748171 Msa1319520:CDS
TTGTCACCTCTACCAGGTTT+TGG 0.284174 8_4:+22748117 None:intergenic
GATCTGCAGCAAGTCGAATT+TGG 0.288631 8_4:+22748395 None:intergenic
GGGTTAACTGGAGGGTTTCC+TGG 0.308952 8_4:-22748183 Msa1319520:CDS
TTCACAATGGCAATCATTCC+TGG 0.313115 8_4:+22748036 None:intergenic
TATGATTTCTTTACAAGAAA+TGG 0.313320 8_4:+22747835 None:intergenic
AAAGAGTTGATGGGGTTAAC+TGG 0.314813 8_4:-22748195 Msa1319520:CDS
TACTGTTTGAAGGAGGGAAT+TGG 0.328753 8_4:-22747945 Msa1319520:CDS
ACTGTTTGAAGGAGGGAATT+GGG 0.336476 8_4:-22747944 Msa1319520:CDS
GGGATAAGTTGATCACCTTT+AGG 0.350751 8_4:-22747924 Msa1319520:CDS
GGAAGTAACATAGGAAGTTC+TGG 0.393252 8_4:+22748057 None:intergenic
AGGGTTTGATAAAGAGTTGA+TGG 0.404058 8_4:-22748205 Msa1319520:CDS
ATTCGACTTGCTGCAGATCA+TGG 0.411694 8_4:-22748391 Msa1319520:CDS
GAACTTCCTATGTTACTTCC+AGG 0.414155 8_4:-22748054 Msa1319520:CDS
GAGAGCCATGAAGGCTATGA+AGG 0.426665 8_4:+22748529 None:intergenic
CAAGACTTAGGATTCTTCAT+AGG 0.437208 8_4:+22747868 None:intergenic
TTTGTAAGTGTTGCAGAAGA+AGG 0.447129 8_4:-22748225 Msa1319520:CDS
AAAGAGCTTAAAAGAGAAGT+TGG 0.459053 8_4:-22748330 Msa1319520:CDS
GGGTTTGATAAAGAGTTGAT+GGG 0.470608 8_4:-22748204 Msa1319520:CDS
GGTTCAAGAACACAAGACTT+AGG 0.485751 8_4:+22747856 None:intergenic
TTACTTGCTTCTGATGATGT+TGG 0.495487 8_4:+22748288 None:intergenic
TAAACTTTCTTCGTCGGAGA+AGG 0.497501 8_4:-22748088 Msa1319520:CDS
CTCAAGTTCCTCAAGCCTAA+AGG 0.506721 8_4:+22747909 None:intergenic
CTGCAGATCATGGGAGGCAG+AGG 0.507026 8_4:-22748381 Msa1319520:CDS
AGAATCACTGATGGTAAAGC+AGG 0.515714 8_4:-22747970 Msa1319520:CDS
GGACTTTGCAAAGGAGAAGA+AGG 0.517875 8_4:-22748360 Msa1319520:CDS
AGTTGATGGGGTTAACTGGA+GGG 0.519714 8_4:-22748191 Msa1319520:CDS
TTCGACTTGCTGCAGATCAT+GGG 0.525619 8_4:-22748390 Msa1319520:CDS
GTTGATCACCTTTAGGCTTG+AGG 0.527881 8_4:-22747917 Msa1319520:CDS
AAAGATGAGTGAGATTCTCT+TGG 0.529880 8_4:+22748484 None:intergenic
GACTTAGGATTCTTCATAGG+AGG 0.531635 8_4:+22747871 None:intergenic
GAAAACCCTGTTCCAAAACC+TGG 0.534181 8_4:-22748129 Msa1319520:CDS
AAGCCTTAAACTTTCTTCGT+CGG 0.537850 8_4:-22748094 Msa1319520:CDS
GAATTTGGCACATGTTTGTA+CGG 0.538297 8_4:+22748410 None:intergenic
TTGTAAGTGTTGCAGAAGAA+GGG 0.538779 8_4:-22748224 Msa1319520:CDS
GGTCGGTTTGCTGTGAAAGA+TGG 0.548431 8_4:+22748440 None:intergenic
TTCTTCTGCAACACTTACAA+AGG 0.552410 8_4:+22748227 None:intergenic
ATCTAAGAAGAGAGCCATGA+AGG 0.554919 8_4:+22748520 None:intergenic
AAAGCAGGAGTACTGTTTGA+AGG 0.555664 8_4:-22747955 Msa1319520:CDS
ATCATTCCTGGAAGTAACAT+AGG 0.572472 8_4:+22748048 None:intergenic
GAGTTGATGGGGTTAACTGG+AGG 0.584401 8_4:-22748192 Msa1319520:CDS
GGTTTGATAAAGAGTTGATG+GGG 0.584525 8_4:-22748203 Msa1319520:CDS
AAGGCTATGAAGGGCAACAA+AGG 0.600980 8_4:+22748539 None:intergenic
GCAGGAGTACTGTTTGAAGG+AGG 0.603818 8_4:-22747952 Msa1319520:CDS
TTAACTGGAGGGTTTCCTGG+TGG 0.603897 8_4:-22748180 Msa1319520:CDS
CCTGTTCCAAAACCTGGTAG+AGG 0.604649 8_4:-22748123 Msa1319520:CDS
CAGGAGTACTGTTTGAAGGA+GGG 0.618790 8_4:-22747951 Msa1319520:CDS
ATTGTTCAAAGAATCACTGA+TGG 0.621968 8_4:-22747979 Msa1319520:CDS
GACTTGCTGCAGATCATGGG+AGG 0.640143 8_4:-22748387 Msa1319520:CDS
GGAGGCAGAGGACTTTGCAA+AGG 0.645470 8_4:-22748369 Msa1319520:CDS
AGAGCCATGAAGGCTATGAA+GGG 0.649789 8_4:+22748530 None:intergenic
ATGGAAGCTTTATTGCTGTG+AGG 0.676809 8_4:+22748459 None:intergenic
AGTAACATAGGAAGTTCTGG+TGG 0.678770 8_4:+22748060 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATGATTTCTTTACAAGAAA+TGG + chr8_4:22748548-22748567 None:intergenic 20.0%
!!! GTTATTTTGATTCTTCACAA+TGG + chr8_4:22748360-22748379 None:intergenic 25.0%
CTTCTTAGATCAAAGTTCTT+AGG - chr8_4:22747873-22747892 Msa1319520:CDS 30.0%
AAAGAGCTTAAAAGAGAAGT+TGG - chr8_4:22748050-22748069 Msa1319520:CDS 30.0%
TACCACAGTACATGTAAAAA+GGG + chr8_4:22748382-22748401 None:intergenic 30.0%
ATACCACAGTACATGTAAAA+AGG + chr8_4:22748383-22748402 None:intergenic 30.0%
ATTGTTCAAAGAATCACTGA+TGG - chr8_4:22748401-22748420 Msa1319520:CDS 30.0%
AAAGATGAGTGAGATTCTCT+TGG + chr8_4:22747899-22747918 None:intergenic 35.0%
!! ACATGTTTGTACGGTTTTGT+AGG + chr8_4:22747964-22747983 None:intergenic 35.0%
GAATTTGGCACATGTTTGTA+CGG + chr8_4:22747973-22747992 None:intergenic 35.0%
! TTACTTGCTTCTGATGATGT+TGG + chr8_4:22748095-22748114 None:intergenic 35.0%
TTCTTCTGCAACACTTACAA+AGG + chr8_4:22748156-22748175 None:intergenic 35.0%
! TTTGTAAGTGTTGCAGAAGA+AGG - chr8_4:22748155-22748174 Msa1319520:CDS 35.0%
! TTGTAAGTGTTGCAGAAGAA+GGG - chr8_4:22748156-22748175 Msa1319520:CDS 35.0%
AGGGTTTGATAAAGAGTTGA+TGG - chr8_4:22748175-22748194 Msa1319520:CDS 35.0%
! GGGTTTGATAAAGAGTTGAT+GGG - chr8_4:22748176-22748195 Msa1319520:CDS 35.0%
!! GGTTTGATAAAGAGTTGATG+GGG - chr8_4:22748177-22748196 Msa1319520:CDS 35.0%
AAGCCTTAAACTTTCTTCGT+CGG - chr8_4:22748286-22748305 Msa1319520:CDS 35.0%
ATCATTCCTGGAAGTAACAT+AGG + chr8_4:22748335-22748354 None:intergenic 35.0%
! AACCCTTTTTACATGTACTG+TGG - chr8_4:22748377-22748396 Msa1319520:CDS 35.0%
GAACTTGAGAGAAGAGAAAA+AGG - chr8_4:22748485-22748504 Msa1319520:CDS 35.0%
CAAGACTTAGGATTCTTCAT+AGG + chr8_4:22748515-22748534 None:intergenic 35.0%
ATCTAAGAAGAGAGCCATGA+AGG + chr8_4:22747863-22747882 None:intergenic 40.0%
!! ATGGAAGCTTTATTGCTGTG+AGG + chr8_4:22747924-22747943 None:intergenic 40.0%
!! GTTTGTACGGTTTTGTAGGT+CGG + chr8_4:22747960-22747979 None:intergenic 40.0%
!! AAAGAGTTGATGGGGTTAAC+TGG - chr8_4:22748185-22748204 Msa1319520:CDS 40.0%
!! TTCAAACCTTTTTCACCACC+AGG + chr8_4:22748218-22748237 None:intergenic 40.0%
TCTCCGACGAAGAAAGTTTA+AGG + chr8_4:22748292-22748311 None:intergenic 40.0%
TAAACTTTCTTCGTCGGAGA+AGG - chr8_4:22748292-22748311 Msa1319520:CDS 40.0%
! AGTAACATAGGAAGTTCTGG+TGG + chr8_4:22748323-22748342 None:intergenic 40.0%
GGAAGTAACATAGGAAGTTC+TGG + chr8_4:22748326-22748345 None:intergenic 40.0%
! GAACTTCCTATGTTACTTCC+AGG - chr8_4:22748326-22748345 Msa1319520:CDS 40.0%
TTCACAATGGCAATCATTCC+TGG + chr8_4:22748347-22748366 None:intergenic 40.0%
AGAATCACTGATGGTAAAGC+AGG - chr8_4:22748410-22748429 Msa1319520:CDS 40.0%
!! AAAGCAGGAGTACTGTTTGA+AGG - chr8_4:22748425-22748444 Msa1319520:CDS 40.0%
TACTGTTTGAAGGAGGGAAT+TGG - chr8_4:22748435-22748454 Msa1319520:CDS 40.0%
ACTGTTTGAAGGAGGGAATT+GGG - chr8_4:22748436-22748455 Msa1319520:CDS 40.0%
!! GGGATAAGTTGATCACCTTT+AGG - chr8_4:22748456-22748475 Msa1319520:CDS 40.0%
GACTTAGGATTCTTCATAGG+AGG + chr8_4:22748512-22748531 None:intergenic 40.0%
GGTTCAAGAACACAAGACTT+AGG + chr8_4:22748527-22748546 None:intergenic 40.0%
AAGGCTATGAAGGGCAACAA+AGG + chr8_4:22747844-22747863 None:intergenic 45.0%
AGAGCCATGAAGGCTATGAA+GGG + chr8_4:22747853-22747872 None:intergenic 45.0%
GATCTGCAGCAAGTCGAATT+TGG + chr8_4:22747988-22748007 None:intergenic 45.0%
!! ATTCGACTTGCTGCAGATCA+TGG - chr8_4:22747989-22748008 Msa1319520:CDS 45.0%
!! TTCGACTTGCTGCAGATCAT+GGG - chr8_4:22747990-22748009 Msa1319520:CDS 45.0%
GGACTTTGCAAAGGAGAAGA+AGG - chr8_4:22748020-22748039 Msa1319520:CDS 45.0%
!! AGTTGATGGGGTTAACTGGA+GGG - chr8_4:22748189-22748208 Msa1319520:CDS 45.0%
GAAAACCCTGTTCCAAAACC+TGG - chr8_4:22748251-22748270 Msa1319520:CDS 45.0%
!!! CTCTACCAGGTTTTGGAACA+GGG + chr8_4:22748259-22748278 None:intergenic 45.0%
! TTGTCACCTCTACCAGGTTT+TGG + chr8_4:22748266-22748285 None:intergenic 45.0%
!! CAGGAGTACTGTTTGAAGGA+GGG - chr8_4:22748429-22748448 Msa1319520:CDS 45.0%
GTTGATCACCTTTAGGCTTG+AGG - chr8_4:22748463-22748482 Msa1319520:CDS 45.0%
CTCAAGTTCCTCAAGCCTAA+AGG + chr8_4:22748474-22748493 None:intergenic 45.0%
GTTGCCCTTCATAGCCTTCA+TGG - chr8_4:22747846-22747865 Msa1319520:CDS 50.0%
GAGAGCCATGAAGGCTATGA+AGG + chr8_4:22747854-22747873 None:intergenic 50.0%
!! GGTCGGTTTGCTGTGAAAGA+TGG + chr8_4:22747943-22747962 None:intergenic 50.0%
!! GAGTTGATGGGGTTAACTGG+AGG - chr8_4:22748188-22748207 Msa1319520:CDS 50.0%
TTAACTGGAGGGTTTCCTGG+TGG - chr8_4:22748200-22748219 Msa1319520:CDS 50.0%
! GGGTTTCCTGGTGGTGAAAA+AGG - chr8_4:22748209-22748228 Msa1319520:CDS 50.0%
!!! CCTCTACCAGGTTTTGGAAC+AGG + chr8_4:22748260-22748279 None:intergenic 50.0%
CCTGTTCCAAAACCTGGTAG+AGG - chr8_4:22748257-22748276 Msa1319520:CDS 50.0%
! AGGCTTTTGTCACCTCTACC+AGG + chr8_4:22748272-22748291 None:intergenic 50.0%
!! GCAGGAGTACTGTTTGAAGG+AGG - chr8_4:22748428-22748447 Msa1319520:CDS 50.0%
!! GACTTGCTGCAGATCATGGG+AGG - chr8_4:22747993-22748012 Msa1319520:CDS 55.0%
GGAGGCAGAGGACTTTGCAA+AGG - chr8_4:22748011-22748030 Msa1319520:CDS 55.0%
GGGTTAACTGGAGGGTTTCC+TGG - chr8_4:22748197-22748216 Msa1319520:CDS 55.0%
CTGCAGATCATGGGAGGCAG+AGG - chr8_4:22747999-22748018 Msa1319520:CDS 60.0%
Chromosome Type Strat End Strand Name
chr8_4 gene 22747834 22748568 22747834 ID=Msa1319520;Name=Msa1319520
chr8_4 mRNA 22747834 22748568 22747834 ID=Msa1319520-mRNA-1;Parent=Msa1319520;Name=Msa1319520-mRNA-1;_AED=0.34;_eAED=0.34;_QI=0|-1|0|1|-1|1|1|0|244
chr8_4 exon 22747834 22748568 22747834 ID=Msa1319520-mRNA-1:exon:8081;Parent=Msa1319520-mRNA-1
chr8_4 CDS 22747834 22748568 22747834 ID=Msa1319520-mRNA-1:cds;Parent=Msa1319520-mRNA-1
Gene Sequence

>Msa1319520

ATGTCTTCCTTTGTTGCCCTTCATAGCCTTCATGGCTCTCTTCTTAGATCAAAGTTCTTAGGCCAAGAGAATCTCACTCATCTTTATCCTCACAGCAATAAAGCTTCCATCTTTCACAGCAAACCGACCTACAAAACCGTACAAACATGTGCCAAATTCGACTTGCTGCAGATCATGGGAGGCAGAGGACTTTGCAAAGGAGAAGAAGGTCTTCAAAAAGAGCTTAAAAGAGAAGTTGGTCTTGATGATCAGAATCAACCAACATCATCAGAAGCAAGTAACGAAGAACAAGAAGACTCGACAAGTAACTCAACAAAATCCTTTGTAAGTGTTGCAGAAGAAGGGTTTGATAAAGAGTTGATGGGGTTAACTGGAGGGTTTCCTGGTGGTGAAAAAGGTTTGAAAAAATTCATTGAAGAAAACCCTGTTCCAAAACCTGGTAGAGGTGACAAAAGCCTTAAACTTTCTTCGTCGGAGAAGGCAAAACCACCAGAACTTCCTATGTTACTTCCAGGAATGATTGCCATTGTGAAGAATCAAAATAACCCTTTTTACATGTACTGTGGTATTGTTCAAAGAATCACTGATGGTAAAGCAGGAGTACTGTTTGAAGGAGGGAATTGGGATAAGTTGATCACCTTTAGGCTTGAGGAACTTGAGAGAAGAGAAAAAGGTCCTCCTATGAAGAATCCTAAGTCTTGTGTTCTTGAACCATTTCTTGTAAAGAAATCATAG

Protein sequence

>Msa1319520

MSSFVALHSLHGSLLRSKFLGQENLTHLYPHSNKASIFHSKPTYKTVQTCAKFDLLQIMGGRGLCKGEEGLQKELKREVGLDDQNQPTSSEASNEEQEDSTSNSTKSFVSVAEEGFDKELMGLTGGFPGGEKGLKKFIEENPVPKPGRGDKSLKLSSSEKAKPPELPMLLPGMIAIVKNQNNPFYMYCGIVQRITDGKAGVLFEGGNWDKLITFRLEELERREKGPPMKNPKSCVLEPFLVKKS*