AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1467010


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1467010 MtrunA17_Chr2g0315561 99.213 127 1 0 1 127 101 227 7.85e-90 259
Msa1467010 MtrunA17_Chr2g0315601 89.764 127 13 0 1 127 101 227 7.69e-83 242
Msa1467010 MtrunA17_Chr8g0359751 73.282 131 30 2 1 126 106 236 5.44e-67 202
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1467010 AT1G78780.1 64.748 139 37 2 1 127 38 176 3.28e-62 188
Msa1467010 AT1G78780.4 64.748 139 37 2 1 127 97 235 1.21e-61 189
Msa1467010 AT1G78780.2 64.748 139 37 2 1 127 100 238 1.34e-61 189
Msa1467010 AT1G78780.3 64.748 139 37 2 1 127 114 252 2.21e-61 189
Msa1467010 AT1G78780.5 64.748 139 37 2 1 127 114 252 2.21e-61 189

Find 21 sgRNAs with CRISPR-Local

Find 124 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGAAATTGCTTTCAAGTTT+AGG 0.246221 tig0049574:-836 Msa1467010:CDS
CTAAACTTGAAAGCAATTTC+AGG 0.282078 tig0049574:+820 Msa1467010:intergenic
TGCTTTCAAGTTTAGGCATT+GGG 0.293525 tig0049574:-829 Msa1467010:CDS
GGGAAGATGGTCCAATTCTT+TGG 0.327141 tig0049574:-768 Msa1467010:CDS
GATGGTCCAATTCTTTGGTC+TGG 0.350753 tig0049574:-763 Msa1467010:CDS
TTCAAGGGACATTCCCCTAC+TGG 0.422890 tig0049574:-789 Msa1467010:CDS
GAGTTCCCAGACCAAAGAAT+TGG 0.426282 tig0049574:+740 Msa1467010:intergenic
ACTTCCCATGCAAACCCTCT+TGG 0.426714 tig0049574:+865 Msa1467010:intergenic
ATGGTCCAATTCTTTGGTCT+GGG 0.454410 tig0049574:-762 Msa1467010:CDS
GTCTCTTCATTTGACTTGTA+CGG 0.456033 tig0049574:+925 Msa1467010:intergenic
GAAGTGATTAAAGTTTATAC+AGG 0.461844 tig0049574:-864 Msa1467010:CDS
TTGCTTTCAAGTTTAGGCAT+TGG 0.497447 tig0049574:-830 Msa1467010:CDS
ACATTCCCCTACTGGGAAGA+TGG 0.513266 tig0049574:-781 Msa1467010:CDS
CTTTGGTCTGGGAACTCTCA+AGG 0.519446 tig0049574:-751 Msa1467010:CDS
TCAAGGGACATTCCCCTACT+GGG 0.534157 tig0049574:-788 Msa1467010:CDS
ATTGGACCATCTTCCCAGTA+GGG 0.563870 tig0049574:+758 Msa1467010:intergenic
AATTGGACCATCTTCCCAGT+AGG 0.580984 tig0049574:+757 Msa1467010:intergenic
GTAGGGGAATGTCCCTTGAA+AGG 0.591507 tig0049574:+775 Msa1467010:intergenic
GCTTTCAAGTTTAGGCATTG+GGG 0.594203 tig0049574:-828 Msa1467010:CDS
AACTTGAAAGCAATTTCAGG+TGG 0.634134 tig0049574:+823 Msa1467000:intergenic
TTGGACCATCTTCCCAGTAG+GGG 0.659212 tig0049574:+759 Msa1467000:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAATTATCACTAATTAAAA+TGG - tig0049574:467-486 Msa1467010:intron 10.0%
!! TATATAAAATCTATTATTGA+GGG + tig0049574:680-699 Msa1467010:intergenic 10.0%
!! ATATATAAAATCTATTATTG+AGG + tig0049574:681-700 Msa1467010:intergenic 10.0%
!! AAAATTATCACTAATTAAAA+TGG - tig0049574:467-486 Msa1467010:intron 10.0%
!! TATATAAAATCTATTATTGA+GGG + tig0049574:680-699 Msa1467010:intergenic 10.0%
!! ATATATAAAATCTATTATTG+AGG + tig0049574:681-700 Msa1467010:intergenic 10.0%
!!! ATGAAAAATTTGTTTTTATC+AGG + tig0049574:347-366 Msa1467010:intergenic 15.0%
!!! ATTTTACACTTTTTTTTTGA+AGG - tig0049574:501-520 Msa1467010:intron 15.0%
!! AAATAAAAACTCATAAAGTA+GGG + tig0049574:757-776 Msa1467010:intergenic 15.0%
!!! TGATCAATATTTTTTAACAT+AGG - tig0049574:857-876 Msa1467010:CDS 15.0%
!!! ATGAAAAATTTGTTTTTATC+AGG + tig0049574:347-366 Msa1467010:intergenic 15.0%
!!! ATTTTACACTTTTTTTTTGA+AGG - tig0049574:501-520 Msa1467010:intron 15.0%
!! AAATAAAAACTCATAAAGTA+GGG + tig0049574:757-776 Msa1467010:intergenic 15.0%
!!! TGATCAATATTTTTTAACAT+AGG - tig0049574:857-876 Msa1467010:CDS 15.0%
!! TGCTCTTAAAAAAATGTATA+TGG + tig0049574:389-408 Msa1467010:intergenic 20.0%
!!! ATGTCTAATGATATTTTTAG+AGG - tig0049574:614-633 Msa1467010:intron 20.0%
!! GAAATAAAAACTCATAAAGT+AGG + tig0049574:758-777 Msa1467010:intergenic 20.0%
!!! TCAATATTTTTTAACATAGG+TGG - tig0049574:860-879 Msa1467010:CDS 20.0%
!! TGCTCTTAAAAAAATGTATA+TGG + tig0049574:389-408 Msa1467010:intergenic 20.0%
!!! ATGTCTAATGATATTTTTAG+AGG - tig0049574:614-633 Msa1467010:intron 20.0%
!! GAAATAAAAACTCATAAAGT+AGG + tig0049574:758-777 Msa1467010:intergenic 20.0%
!!! TCAATATTTTTTAACATAGG+TGG - tig0049574:860-879 Msa1467010:CDS 20.0%
! GAAGTGATTAAAGTTTATAC+AGG - tig0049574:131-150 Msa1467010:intron 25.0%
!! ATCAGGAATTCTTAAACTTT+TGG + tig0049574:330-349 Msa1467010:intergenic 25.0%
!!! TCTAATGATATTTTTAGAGG+AGG - tig0049574:617-636 Msa1467010:intron 25.0%
!! TTTTATCACCCTTTACATTT+TGG - tig0049574:799-818 Msa1467010:CDS 25.0%
!! TTTATCACCCTTTACATTTT+GGG - tig0049574:800-819 Msa1467010:CDS 25.0%
! ATCAAATCCCAAAATGTAAA+GGG + tig0049574:810-829 Msa1467010:intergenic 25.0%
! TATCAAATCCCAAAATGTAA+AGG + tig0049574:811-830 Msa1467010:intergenic 25.0%
! GAAGTGATTAAAGTTTATAC+AGG - tig0049574:131-150 Msa1467010:intron 25.0%
!! ATCAGGAATTCTTAAACTTT+TGG + tig0049574:330-349 Msa1467010:intergenic 25.0%
!!! TCTAATGATATTTTTAGAGG+AGG - tig0049574:617-636 Msa1467010:intron 25.0%
!! TTTTATCACCCTTTACATTT+TGG - tig0049574:799-818 Msa1467010:CDS 25.0%
!! TTTATCACCCTTTACATTTT+GGG - tig0049574:800-819 Msa1467010:CDS 25.0%
! ATCAAATCCCAAAATGTAAA+GGG + tig0049574:810-829 Msa1467010:intergenic 25.0%
! TATCAAATCCCAAAATGTAA+AGG + tig0049574:811-830 Msa1467010:intergenic 25.0%
CTAAACTTGAAAGCAATTTC+AGG + tig0049574:161-180 Msa1467010:intergenic 30.0%
!! CTGAAATTGCTTTCAAGTTT+AGG - tig0049574:159-178 Msa1467010:intron 30.0%
! TTGAGGGATTTAGATTTTGA+TGG + tig0049574:664-683 Msa1467010:intergenic 30.0%
ACTCATAAAGTAGGGTAAAA+TGG + tig0049574:749-768 Msa1467010:intergenic 30.0%
AAAAGGACAAGCTGAAATTT+GGG + tig0049574:970-989 Msa1467010:intergenic 30.0%
AAAAAGGACAAGCTGAAATT+TGG + tig0049574:971-990 Msa1467010:intergenic 30.0%
CTAAACTTGAAAGCAATTTC+AGG + tig0049574:161-180 Msa1467010:intergenic 30.0%
!! CTGAAATTGCTTTCAAGTTT+AGG - tig0049574:159-178 Msa1467010:intron 30.0%
! TTGAGGGATTTAGATTTTGA+TGG + tig0049574:664-683 Msa1467010:intergenic 30.0%
ACTCATAAAGTAGGGTAAAA+TGG + tig0049574:749-768 Msa1467010:intergenic 30.0%
AAAAGGACAAGCTGAAATTT+GGG + tig0049574:970-989 Msa1467010:intergenic 30.0%
AAAAAGGACAAGCTGAAATT+TGG + tig0049574:971-990 Msa1467010:intergenic 30.0%
! TTGTACGGCTTGAAATTTTC+TGG + tig0049574:41-60 Msa0565270:intergenic 35.0%
!! GTCTCTTCATTTGACTTGTA+CGG + tig0049574:56-75 Msa0565270:intergenic 35.0%
! TTCAAATCAGCTTTTCCAAG+AGG - tig0049574:98-117 Msa1467010:CDS 35.0%
! TCAAATCAGCTTTTCCAAGA+GGG - tig0049574:99-118 Msa1467010:CDS 35.0%
AACTTGAAAGCAATTTCAGG+TGG + tig0049574:158-177 Msa1467010:intergenic 35.0%
!! TTGCTTTCAAGTTTAGGCAT+TGG - tig0049574:165-184 Msa1467010:intron 35.0%
!! TGCTTTCAAGTTTAGGCATT+GGG - tig0049574:166-185 Msa1467010:intron 35.0%
!! ATTTTTCGAAGGTCCTTTCA+AGG - tig0049574:190-209 Msa1467010:intron 35.0%
!! TTTTTCGAAGGTCCTTTCAA+GGG - tig0049574:191-210 Msa1467010:intron 35.0%
!! ATTTGAGTTTTGTCACCTTG+AGG - tig0049574:553-572 Msa1467010:intron 35.0%
ATGAAGTGTGAACTACTTAG+AGG + tig0049574:585-604 Msa1467010:intergenic 35.0%
TCTAAGTAGTTCACACTTCA+TGG - tig0049574:584-603 Msa1467010:intron 35.0%
! TTGTACGGCTTGAAATTTTC+TGG + tig0049574:41-60 Msa1467010:intergenic 35.0%
!! GTCTCTTCATTTGACTTGTA+CGG + tig0049574:56-75 Msa1467010:intergenic 35.0%
! TTCAAATCAGCTTTTCCAAG+AGG - tig0049574:98-117 Msa1467010:CDS 35.0%
! TCAAATCAGCTTTTCCAAGA+GGG - tig0049574:99-118 Msa1467010:CDS 35.0%
AACTTGAAAGCAATTTCAGG+TGG + tig0049574:158-177 Msa1467010:intergenic 35.0%
!! TTGCTTTCAAGTTTAGGCAT+TGG - tig0049574:165-184 Msa1467010:intron 35.0%
!! TGCTTTCAAGTTTAGGCATT+GGG - tig0049574:166-185 Msa1467010:intron 35.0%
!! ATTTTTCGAAGGTCCTTTCA+AGG - tig0049574:190-209 Msa1467010:intron 35.0%
!! TTTTTCGAAGGTCCTTTCAA+GGG - tig0049574:191-210 Msa1467010:intron 35.0%
!! ATTTGAGTTTTGTCACCTTG+AGG - tig0049574:553-572 Msa1467010:intron 35.0%
ATGAAGTGTGAACTACTTAG+AGG + tig0049574:585-604 Msa1467010:intergenic 35.0%
TCTAAGTAGTTCACACTTCA+TGG - tig0049574:584-603 Msa1467010:intron 35.0%
! TTTTCCAAGAGGGTTTGCAT+GGG - tig0049574:109-128 Msa1467010:intron 40.0%
!! GCTTTCAAGTTTAGGCATTG+GGG - tig0049574:167-186 Msa1467010:intron 40.0%
ATGGTCCAATTCTTTGGTCT+GGG - tig0049574:233-252 Msa1467010:intron 40.0%
ATAGGTGGATGATGCTTTGA+AGG - tig0049574:875-894 Msa1467010:CDS 40.0%
!! TGATGCTTTGAAGGTTGAAG+AGG - tig0049574:884-903 Msa1467010:CDS 40.0%
! TGCTATCTCCACTTGTTAGA+AGG + tig0049574:947-966 Msa1467010:intergenic 40.0%
! TTTTCCAAGAGGGTTTGCAT+GGG - tig0049574:109-128 Msa1467010:intron 40.0%
!! GCTTTCAAGTTTAGGCATTG+GGG - tig0049574:167-186 Msa1467010:intron 40.0%
ATGGTCCAATTCTTTGGTCT+GGG - tig0049574:233-252 Msa1467010:intron 40.0%
ATAGGTGGATGATGCTTTGA+AGG - tig0049574:875-894 Msa1467010:CDS 40.0%
!! TGATGCTTTGAAGGTTGAAG+AGG - tig0049574:884-903 Msa1467010:CDS 40.0%
! TGCTATCTCCACTTGTTAGA+AGG + tig0049574:947-966 Msa1467010:intergenic 40.0%
! CTTTTCCAAGAGGGTTTGCA+TGG - tig0049574:108-127 Msa1467010:intron 45.0%
!!! AGGCATTGGGGATTTTTCGA+AGG - tig0049574:179-198 Msa1467010:intron 45.0%
ATTGGACCATCTTCCCAGTA+GGG + tig0049574:223-242 Msa1467010:intergenic 45.0%
AATTGGACCATCTTCCCAGT+AGG + tig0049574:224-243 Msa1467010:intergenic 45.0%
GGGAAGATGGTCCAATTCTT+TGG - tig0049574:227-246 Msa1467010:intron 45.0%
GATGGTCCAATTCTTTGGTC+TGG - tig0049574:232-251 Msa1467010:intron 45.0%
GAGTTCCCAGACCAAAGAAT+TGG + tig0049574:241-260 Msa1467010:intergenic 45.0%
!! ACTTAGAGGTGTTGACCTCA+AGG + tig0049574:571-590 Msa1467010:intergenic 45.0%
! CTTTTCCAAGAGGGTTTGCA+TGG - tig0049574:108-127 Msa1467010:intron 45.0%
!!! AGGCATTGGGGATTTTTCGA+AGG - tig0049574:179-198 Msa1467010:intron 45.0%
ATTGGACCATCTTCCCAGTA+GGG + tig0049574:223-242 Msa1467010:intergenic 45.0%
AATTGGACCATCTTCCCAGT+AGG + tig0049574:224-243 Msa1467010:intergenic 45.0%
GGGAAGATGGTCCAATTCTT+TGG - tig0049574:227-246 Msa1467010:intron 45.0%
GATGGTCCAATTCTTTGGTC+TGG - tig0049574:232-251 Msa1467010:intron 45.0%
GAGTTCCCAGACCAAAGAAT+TGG + tig0049574:241-260 Msa1467010:intergenic 45.0%
!! ACTTAGAGGTGTTGACCTCA+AGG + tig0049574:571-590 Msa1467010:intergenic 45.0%
ACTTCCCATGCAAACCCTCT+TGG + tig0049574:116-135 Msa1467010:intergenic 50.0%
GTAGGGGAATGTCCCTTGAA+AGG + tig0049574:206-225 Msa1467010:intergenic 50.0%
TTCAAGGGACATTCCCCTAC+TGG - tig0049574:206-225 Msa1467010:intron 50.0%
TCAAGGGACATTCCCCTACT+GGG - tig0049574:207-226 Msa1467010:intron 50.0%
ACATTCCCCTACTGGGAAGA+TGG - tig0049574:214-233 Msa1467010:intron 50.0%
TTGGACCATCTTCCCAGTAG+GGG + tig0049574:222-241 Msa1467010:intergenic 50.0%
CTTTGGTCTGGGAACTCTCA+AGG - tig0049574:244-263 Msa1467010:intron 50.0%
TATGACCCAGCAGAGTTGCT+TGG - tig0049574:918-937 Msa1467010:CDS 50.0%
CTTGGAGGCCTTCTAACAAG+TGG - tig0049574:936-955 Msa1467010:CDS 50.0%
ACTTCCCATGCAAACCCTCT+TGG + tig0049574:116-135 Msa1467010:intergenic 50.0%
GTAGGGGAATGTCCCTTGAA+AGG + tig0049574:206-225 Msa1467010:intergenic 50.0%
TTCAAGGGACATTCCCCTAC+TGG - tig0049574:206-225 Msa1467010:intron 50.0%
TCAAGGGACATTCCCCTACT+GGG - tig0049574:207-226 Msa1467010:intron 50.0%
ACATTCCCCTACTGGGAAGA+TGG - tig0049574:214-233 Msa1467010:intron 50.0%
TTGGACCATCTTCCCAGTAG+GGG + tig0049574:222-241 Msa1467010:intergenic 50.0%
CTTTGGTCTGGGAACTCTCA+AGG - tig0049574:244-263 Msa1467010:intron 50.0%
TATGACCCAGCAGAGTTGCT+TGG - tig0049574:918-937 Msa1467010:CDS 50.0%
CTTGGAGGCCTTCTAACAAG+TGG - tig0049574:936-955 Msa1467010:CDS 50.0%
GACCCAGCAGAGTTGCTTGG+AGG - tig0049574:921-940 Msa1467010:CDS 60.0%
GGCCTCCAAGCAACTCTGCT+GGG + tig0049574:926-945 Msa1467010:intergenic 60.0%
AGGCCTCCAAGCAACTCTGC+TGG + tig0049574:927-946 Msa1467010:intergenic 60.0%
GACCCAGCAGAGTTGCTTGG+AGG - tig0049574:921-940 Msa1467010:CDS 60.0%
GGCCTCCAAGCAACTCTGCT+GGG + tig0049574:926-945 Msa1467010:intergenic 60.0%
AGGCCTCCAAGCAACTCTGC+TGG + tig0049574:927-946 Msa1467010:intergenic 60.0%
Chromosome Type Strat End Strand Name
tig0049574 gene 2 998 2 ID=Msa1467010;Name=Msa1467010
tig0049574 mRNA 2 998 2 ID=Msa1467010-mRNA-1;Parent=Msa1467010;Name=Msa1467010-mRNA-1;_AED=0.04;_eAED=0.04;_QI=0|0|0|1|1|1|2|0|127
tig0049574 exon 735 998 735 ID=Msa1467010-mRNA-1:exon:25183;Parent=Msa1467010-mRNA-1
tig0049574 exon 2 121 2 ID=Msa1467010-mRNA-1:exon:25182;Parent=Msa1467010-mRNA-1
tig0049574 CDS 735 998 735 ID=Msa1467010-mRNA-1:cds;Parent=Msa1467010-mRNA-1
tig0049574 CDS 2 121 2 ID=Msa1467010-mRNA-1:cds;Parent=Msa1467010-mRNA-1
Gene Sequence

>Msa1467010

TTAGGAAGTTATAATGCATTGTTGAAAAGTTCTCTACCAGAAAATTTCAAGCCGTACAAGTCAAATGAAGAGACTTTTGAATCATCTCATGAAGTCTTCAAATCAGCTTTTCCAAGAGGGTTTGCATGGGAAGTGATTAAAGTTTATACAGGACCACCTGAAATTGCTTTCAAGTTTAGGCATTGGGGATTTTTCGAAGGTCCTTTCAAGGGACATTCCCCTACTGGGAAGATGGTCCAATTCTTTGGTCTGGGAACTCTCAAGGTGGATGATGCTTTGAAGGTTGAAGAGGTAGAGATTTACTATGACCCAGCAGAGTTGCTTGGAGGCCTTCTAACAAGTGGAGATAGCACCCAAATTTCAGCTTGTCCTTTTTCTAATTAA

Protein sequence

>Msa1467010

LGSYNALLKSSLPENFKPYKSNEETFESSHEVFKSAFPRGFAWEVIKVYTGPPEIAFKFRHWGFFEGPFKGHSPTGKMVQFFGLGTLKVDDALKVEEVEIYYDPAELLGGLLTSGDSTQISACPFSN*