AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1184640


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1184640 MtrunA17_Chr8g0349971 94.672 244 13 0 1 244 1 244 9.08e-172 473
Msa1184640 MtrunA17_Chr7g0246981 50.000 142 64 3 1 142 1 135 1.90e-40 136
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1184640 AT4G23890.1 54.878 246 96 5 2 240 3 240 3.38e-86 256

Find 60 sgRNAs with CRISPR-Local

Find 68 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTCTGATGAAGAAAGTTTA+AGG 0.154407 8_1:+20564928 None:intergenic
ATACCACAGTACATGTAAAA+AGG 0.226887 8_1:+20564837 None:intergenic
GTTGCCCTTCATAGCCTTCA+TGG 0.229693 8_1:-20565371 Msa1184640:CDS
GAACTTGAGAGAAGAGAAAA+AGG 0.270077 8_1:-20564732 Msa1184640:CDS
CTTCTTAGAACCAAGTTCTT+AGG 0.272715 8_1:-20565344 Msa1184640:CDS
GGGTTTCCTGGTGGTGAAAA+AGG 0.277133 8_1:-20565008 Msa1184640:CDS
TTGTCACCTCTACCAGGTTT+TGG 0.284174 8_1:+20564954 None:intergenic
GATCTGCAGCAAGTCGAATT+TGG 0.288631 8_1:+20565232 None:intergenic
GGGTTAACTGGAGGGTTTCC+TGG 0.308952 8_1:-20565020 Msa1184640:CDS
TATGATTTCTTTACAAGAAA+TGG 0.313320 8_1:+20564672 None:intergenic
AAAGAGTTGATGGGGTTAAC+TGG 0.314813 8_1:-20565032 Msa1184640:CDS
TACTGTTTGAAGGAGGGAAT+TGG 0.328753 8_1:-20564782 Msa1184640:CDS
ACTGTTTGAAGGAGGGAATT+GGG 0.336476 8_1:-20564781 Msa1184640:CDS
GGGATAAGTTGATCACCTTT+AGG 0.350751 8_1:-20564761 Msa1184640:CDS
CATGACTTGGGATTCTTCAT+AGG 0.375962 8_1:+20564705 None:intergenic
TTCACAATAGCAATCATTCC+TGG 0.392991 8_1:+20564873 None:intergenic
AGGGTTTGATAAAGAGTTGA+TGG 0.404058 8_1:-20565042 Msa1184640:CDS
GAACTTCCTATGTTACTTCC+AGG 0.411204 8_1:-20564891 Msa1184640:CDS
ATTCGACTTGCTGCAGATCA+TGG 0.411694 8_1:-20565228 Msa1184640:CDS
GAGAGCCATGAAGGCTATGA+AGG 0.426665 8_1:+20565366 None:intergenic
ATTCTCTTGGCCTAAGAACT+TGG 0.434321 8_1:+20565334 None:intergenic
TTTGTAAGTGTTGCAGAAGA+AGG 0.447129 8_1:-20565062 Msa1184640:CDS
GGAAGTAACATAGGAAGTTC+CGG 0.448635 8_1:+20564894 None:intergenic
AAAGAGCTTAAAAGAGAAGT+TGG 0.459053 8_1:-20565167 Msa1184640:CDS
GGGTTTGATAAAGAGTTGAT+GGG 0.470608 8_1:-20565041 Msa1184640:CDS
TTACTTGCTTCTGATGATGT+TGG 0.471319 8_1:+20565125 None:intergenic
AGAATCACTGATGGTAAAGC+TGG 0.473306 8_1:-20564807 Msa1184640:CDS
GGACTCTGCAAAGGAGAAGA+AGG 0.493957 8_1:-20565197 Msa1184640:CDS
TAAACTTTCTTCATCAGAGA+AGG 0.494465 8_1:-20564925 Msa1184640:CDS
CTCAAGTTCCTCAAGCCTAA+AGG 0.506721 8_1:+20564746 None:intergenic
CTGCAGATCATGGGAGGCAG+AGG 0.507026 8_1:-20565218 Msa1184640:CDS
AGTTGATGGGGTTAACTGGA+GGG 0.519714 8_1:-20565028 Msa1184640:CDS
TTCGACTTGCTGCAGATCAT+GGG 0.525619 8_1:-20565227 Msa1184640:CDS
GTTGATCACCTTTAGGCTTG+AGG 0.527881 8_1:-20564754 Msa1184640:CDS
AAAGCTGGAGTACTGTTTGA+AGG 0.529432 8_1:-20564792 Msa1184640:CDS
AAAGATGAGTGAGATTCTCT+TGG 0.529880 8_1:+20565321 None:intergenic
GAAAACCCTGTTCCAAAACC+TGG 0.534181 8_1:-20564966 Msa1184640:CDS
GAATTTGGCACATGTTTGTA+CGG 0.538297 8_1:+20565247 None:intergenic
TTGTAAGTGTTGCAGAAGAA+GGG 0.538779 8_1:-20565061 Msa1184640:CDS
GGTCGGTTTGCTGTGAAAGA+TGG 0.548431 8_1:+20565277 None:intergenic
TTCTTCTGCAACACTTACAA+AGG 0.552410 8_1:+20565064 None:intergenic
ATCATTCCTGGAAGTAACAT+AGG 0.560101 8_1:+20564885 None:intergenic
TTCTAAGAAGAGAGCCATGA+AGG 0.565277 8_1:+20565357 None:intergenic
TGGTTCAAGAACACATGACT+TGG 0.566757 8_1:+20564692 None:intergenic
GACTTGGGATTCTTCATAGG+AGG 0.576190 8_1:+20564708 None:intergenic
GAGTTGATGGGGTTAACTGG+AGG 0.584401 8_1:-20565029 Msa1184640:CDS
GGTTTGATAAAGAGTTGATG+GGG 0.584525 8_1:-20565040 Msa1184640:CDS
GGTTCAAGAACACATGACTT+GGG 0.587652 8_1:+20564693 None:intergenic
ATCAGAGAAGGCAAAACCAC+CGG 0.591340 8_1:-20564913 Msa1184640:CDS
AAGGCTATGAAGGGCAACAA+AGG 0.600980 8_1:+20565376 None:intergenic
TTAACTGGAGGGTTTCCTGG+TGG 0.603897 8_1:-20565017 Msa1184640:CDS
CCTGTTCCAAAACCTGGTAG+AGG 0.604649 8_1:-20564960 Msa1184640:CDS
CTGGAGTACTGTTTGAAGGA+GGG 0.608018 8_1:-20564788 Msa1184640:CDS
GCTGGAGTACTGTTTGAAGG+AGG 0.608092 8_1:-20564789 Msa1184640:CDS
ATTGTTCAAAGAATCACTGA+TGG 0.621968 8_1:-20564816 Msa1184640:CDS
GGAGGCAGAGGACTCTGCAA+AGG 0.631448 8_1:-20565206 Msa1184640:CDS
GACTTGCTGCAGATCATGGG+AGG 0.640143 8_1:-20565224 Msa1184640:CDS
AGAGCCATGAAGGCTATGAA+GGG 0.649789 8_1:+20565367 None:intergenic
ATGGAAGCTTTATTGCTGTG+AGG 0.676809 8_1:+20565296 None:intergenic
AGTAACATAGGAAGTTCCGG+TGG 0.715020 8_1:+20564897 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATGATTTCTTTACAAGAAA+TGG + chr8_1:20565385-20565404 None:intergenic 20.0%
AAAGAGCTTAAAAGAGAAGT+TGG - chr8_1:20564887-20564906 Msa1184640:CDS 30.0%
TCTCTGATGAAGAAAGTTTA+AGG + chr8_1:20565129-20565148 None:intergenic 30.0%
TAAACTTTCTTCATCAGAGA+AGG - chr8_1:20565129-20565148 Msa1184640:CDS 30.0%
TACCACAGTACATGTAAAAA+GGG + chr8_1:20565219-20565238 None:intergenic 30.0%
ATACCACAGTACATGTAAAA+AGG + chr8_1:20565220-20565239 None:intergenic 30.0%
ATTGTTCAAAGAATCACTGA+TGG - chr8_1:20565238-20565257 Msa1184640:CDS 30.0%
CTTCTTAGAACCAAGTTCTT+AGG - chr8_1:20564710-20564729 Msa1184640:CDS 35.0%
AAAGATGAGTGAGATTCTCT+TGG + chr8_1:20564736-20564755 None:intergenic 35.0%
!! ACATGTTTGTACGGTTTTGT+AGG + chr8_1:20564801-20564820 None:intergenic 35.0%
GAATTTGGCACATGTTTGTA+CGG + chr8_1:20564810-20564829 None:intergenic 35.0%
! TTACTTGCTTCTGATGATGT+TGG + chr8_1:20564932-20564951 None:intergenic 35.0%
TTCTTCTGCAACACTTACAA+AGG + chr8_1:20564993-20565012 None:intergenic 35.0%
! TTTGTAAGTGTTGCAGAAGA+AGG - chr8_1:20564992-20565011 Msa1184640:CDS 35.0%
! TTGTAAGTGTTGCAGAAGAA+GGG - chr8_1:20564993-20565012 Msa1184640:CDS 35.0%
AGGGTTTGATAAAGAGTTGA+TGG - chr8_1:20565012-20565031 Msa1184640:CDS 35.0%
! GGGTTTGATAAAGAGTTGAT+GGG - chr8_1:20565013-20565032 Msa1184640:CDS 35.0%
!! GGTTTGATAAAGAGTTGATG+GGG - chr8_1:20565014-20565033 Msa1184640:CDS 35.0%
ATCATTCCTGGAAGTAACAT+AGG + chr8_1:20565172-20565191 None:intergenic 35.0%
TTCACAATAGCAATCATTCC+TGG + chr8_1:20565184-20565203 None:intergenic 35.0%
! AACCCTTTTTACATGTACTG+TGG - chr8_1:20565214-20565233 Msa1184640:CDS 35.0%
GAACTTGAGAGAAGAGAAAA+AGG - chr8_1:20565322-20565341 Msa1184640:CDS 35.0%
! TTCTAAGAAGAGAGCCATGA+AGG + chr8_1:20564700-20564719 None:intergenic 40.0%
ATTCTCTTGGCCTAAGAACT+TGG + chr8_1:20564723-20564742 None:intergenic 40.0%
!! ATGGAAGCTTTATTGCTGTG+AGG + chr8_1:20564761-20564780 None:intergenic 40.0%
!! GTTTGTACGGTTTTGTAGGT+CGG + chr8_1:20564797-20564816 None:intergenic 40.0%
!! AAAGAGTTGATGGGGTTAAC+TGG - chr8_1:20565022-20565041 Msa1184640:CDS 40.0%
!! TTCAAACCTTTTTCACCACC+AGG + chr8_1:20565055-20565074 None:intergenic 40.0%
GGAAGTAACATAGGAAGTTC+CGG + chr8_1:20565163-20565182 None:intergenic 40.0%
! GAACTTCCTATGTTACTTCC+AGG - chr8_1:20565163-20565182 Msa1184640:CDS 40.0%
AGAATCACTGATGGTAAAGC+TGG - chr8_1:20565247-20565266 Msa1184640:CDS 40.0%
!! AAAGCTGGAGTACTGTTTGA+AGG - chr8_1:20565262-20565281 Msa1184640:CDS 40.0%
TACTGTTTGAAGGAGGGAAT+TGG - chr8_1:20565272-20565291 Msa1184640:CDS 40.0%
ACTGTTTGAAGGAGGGAATT+GGG - chr8_1:20565273-20565292 Msa1184640:CDS 40.0%
!! GGGATAAGTTGATCACCTTT+AGG - chr8_1:20565293-20565312 Msa1184640:CDS 40.0%
! CATGACTTGGGATTCTTCAT+AGG + chr8_1:20565352-20565371 None:intergenic 40.0%
GGTTCAAGAACACATGACTT+GGG + chr8_1:20565364-20565383 None:intergenic 40.0%
TGGTTCAAGAACACATGACT+TGG + chr8_1:20565365-20565384 None:intergenic 40.0%
AAGGCTATGAAGGGCAACAA+AGG + chr8_1:20564681-20564700 None:intergenic 45.0%
AGAGCCATGAAGGCTATGAA+GGG + chr8_1:20564690-20564709 None:intergenic 45.0%
GATCTGCAGCAAGTCGAATT+TGG + chr8_1:20564825-20564844 None:intergenic 45.0%
!! ATTCGACTTGCTGCAGATCA+TGG - chr8_1:20564826-20564845 Msa1184640:CDS 45.0%
!! TTCGACTTGCTGCAGATCAT+GGG - chr8_1:20564827-20564846 Msa1184640:CDS 45.0%
!! AGTTGATGGGGTTAACTGGA+GGG - chr8_1:20565026-20565045 Msa1184640:CDS 45.0%
GAAAACCCTGTTCCAAAACC+TGG - chr8_1:20565088-20565107 Msa1184640:CDS 45.0%
!!! CTCTACCAGGTTTTGGAACA+GGG + chr8_1:20565096-20565115 None:intergenic 45.0%
! TTGTCACCTCTACCAGGTTT+TGG + chr8_1:20565103-20565122 None:intergenic 45.0%
ATCAGAGAAGGCAAAACCAC+CGG - chr8_1:20565141-20565160 Msa1184640:CDS 45.0%
AGTAACATAGGAAGTTCCGG+TGG + chr8_1:20565160-20565179 None:intergenic 45.0%
!! CTGGAGTACTGTTTGAAGGA+GGG - chr8_1:20565266-20565285 Msa1184640:CDS 45.0%
GTTGATCACCTTTAGGCTTG+AGG - chr8_1:20565300-20565319 Msa1184640:CDS 45.0%
CTCAAGTTCCTCAAGCCTAA+AGG + chr8_1:20565311-20565330 None:intergenic 45.0%
GACTTGGGATTCTTCATAGG+AGG + chr8_1:20565349-20565368 None:intergenic 45.0%
GTTGCCCTTCATAGCCTTCA+TGG - chr8_1:20564683-20564702 Msa1184640:CDS 50.0%
GAGAGCCATGAAGGCTATGA+AGG + chr8_1:20564691-20564710 None:intergenic 50.0%
!! GGTCGGTTTGCTGTGAAAGA+TGG + chr8_1:20564780-20564799 None:intergenic 50.0%
GGACTCTGCAAAGGAGAAGA+AGG - chr8_1:20564857-20564876 Msa1184640:CDS 50.0%
!! GAGTTGATGGGGTTAACTGG+AGG - chr8_1:20565025-20565044 Msa1184640:CDS 50.0%
TTAACTGGAGGGTTTCCTGG+TGG - chr8_1:20565037-20565056 Msa1184640:CDS 50.0%
! GGGTTTCCTGGTGGTGAAAA+AGG - chr8_1:20565046-20565065 Msa1184640:CDS 50.0%
!!! CCTCTACCAGGTTTTGGAAC+AGG + chr8_1:20565097-20565116 None:intergenic 50.0%
CCTGTTCCAAAACCTGGTAG+AGG - chr8_1:20565094-20565113 Msa1184640:CDS 50.0%
! AGGCTTTTGTCACCTCTACC+AGG + chr8_1:20565109-20565128 None:intergenic 50.0%
!! GCTGGAGTACTGTTTGAAGG+AGG - chr8_1:20565265-20565284 Msa1184640:CDS 50.0%
!! GACTTGCTGCAGATCATGGG+AGG - chr8_1:20564830-20564849 Msa1184640:CDS 55.0%
GGGTTAACTGGAGGGTTTCC+TGG - chr8_1:20565034-20565053 Msa1184640:CDS 55.0%
CTGCAGATCATGGGAGGCAG+AGG - chr8_1:20564836-20564855 Msa1184640:CDS 60.0%
GGAGGCAGAGGACTCTGCAA+AGG - chr8_1:20564848-20564867 Msa1184640:CDS 60.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 20564671 20565405 20564671 ID=Msa1184640;Name=Msa1184640
chr8_1 mRNA 20564671 20565405 20564671 ID=Msa1184640-mRNA-1;Parent=Msa1184640;Name=Msa1184640-mRNA-1;_AED=0.34;_eAED=0.34;_QI=0|-1|0|1|-1|1|1|0|244
chr8_1 exon 20564671 20565405 20564671 ID=Msa1184640-mRNA-1:exon:7916;Parent=Msa1184640-mRNA-1
chr8_1 CDS 20564671 20565405 20564671 ID=Msa1184640-mRNA-1:cds;Parent=Msa1184640-mRNA-1
Gene Sequence

>Msa1184640

ATGTCTTCCTTTGTTGCCCTTCATAGCCTTCATGGCTCTCTTCTTAGAACCAAGTTCTTAGGCCAAGAGAATCTCACTCATCTTTATCCTCACAGCAATAAAGCTTCCATCTTTCACAGCAAACCGACCTACAAAACCGTACAAACATGTGCCAAATTCGACTTGCTGCAGATCATGGGAGGCAGAGGACTCTGCAAAGGAGAAGAAGGTCTTCAAAAAGAGCTTAAAAGAGAAGTTGGTCTTGATGATCAGAATCAACCAACATCATCAGAAGCAAGTAATGAAGAACAAGAAGACTCGACAAGCAGCTCAACGAAATCCTTTGTAAGTGTTGCAGAAGAAGGGTTTGATAAAGAGTTGATGGGGTTAACTGGAGGGTTTCCTGGTGGTGAAAAAGGTTTGAAAAAATTCATTGAAGAAAACCCTGTTCCAAAACCTGGTAGAGGTGACAAAAGCCTTAAACTTTCTTCATCAGAGAAGGCAAAACCACCGGAACTTCCTATGTTACTTCCAGGAATGATTGCTATTGTGAAGAATCAAAATAACCCTTTTTACATGTACTGTGGTATTGTTCAAAGAATCACTGATGGTAAAGCTGGAGTACTGTTTGAAGGAGGGAATTGGGATAAGTTGATCACCTTTAGGCTTGAGGAACTTGAGAGAAGAGAAAAAGGTCCTCCTATGAAGAATCCCAAGTCATGTGTTCTTGAACCATTTCTTGTAAAGAAATCATAG

Protein sequence

>Msa1184640

MSSFVALHSLHGSLLRTKFLGQENLTHLYPHSNKASIFHSKPTYKTVQTCAKFDLLQIMGGRGLCKGEEGLQKELKREVGLDDQNQPTSSEASNEEQEDSTSSSTKSFVSVAEEGFDKELMGLTGGFPGGEKGLKKFIEENPVPKPGRGDKSLKLSSSEKAKPPELPMLLPGMIAIVKNQNNPFYMYCGIVQRITDGKAGVLFEGGNWDKLITFRLEELERREKGPPMKNPKSCVLEPFLVKKS*