AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1394300

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1394300 MtrunA17_Chr5g0438181 100.000 69 0 0 1 69 1 69 1.09e-44 139
Msa1394300 MtrunA17_Chr4g0071611 100.000 69 0 0 1 69 1 69 1.72e-44 139
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1394300 AT4G24920.1 92.647 68 5 0 1 68 1 68 4.96e-41 128
Msa1394300 AT5G50460.1 92.647 68 5 0 1 68 1 68 4.96e-41 128
Msa1394300 AT3G48570.1 86.957 69 9 0 1 69 1 69 2.17e-39 124

Find 43 sgRNAs with CRISPR-Local

Find 128 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTAGATATGGAACTATAATT+TGG 0.198586 tig0021786:+16002 Msa1394300:three_prime_UTR
CCAACGATGATGTTGTTAAT+TGG 0.213895 tig0021786:-14081 None:intergenic
ATTCTTAGATCGAAAGAAAA+TGG 0.228279 tig0021786:+13787 Msa1394300:intron
TGATTGGTATCTATGTAAAT+TGG 0.291365 tig0021786:+16061 Msa1394300:three_prime_UTR
TGGTTATTTCCACAGGATAA+TGG 0.303863 tig0021786:+15766 Msa1394300:intron
CGCTTTGCTCCTTGAACAAT+GGG 0.363239 tig0021786:-15978 None:intergenic
TCGTATTGTAGAATTCTCTA+AGG 0.363993 tig0021786:+13987 Msa1394300:intron
AGACCTTTGTTCTGTGTGTT+GGG 0.368248 tig0021786:-13562 None:intergenic
AGGAGCAAAGCGTTTAGATA+TGG 0.380566 tig0021786:+15989 Msa1394300:three_prime_UTR
TGCCATCGGTTTCGTTGTGA+TGG 0.408671 tig0021786:+14023 Msa1394300:CDS
TACCTTTGCGATCGGGTTTG+TGG 0.417825 tig0021786:-13880 None:intergenic
AACAACATCATCGTTGGATC+TGG 0.426526 tig0021786:+14087 Msa1394300:CDS
CCACCAAGACTTCGATCGTT+AGG 0.433712 tig0021786:+13592 Msa1394300:five_prime_UTR
CATCATCGTTGGATCTGGTT+AGG 0.451612 tig0021786:+14092 Msa1394300:CDS
AGTATGAAGGTGACGAAGGA+TGG 0.463697 tig0021786:+16131 Msa1394300:three_prime_UTR
GAGACCTTTGTTCTGTGTGT+TGG 0.472045 tig0021786:-13563 None:intergenic
ACGCTTTGCTCCTTGAACAA+TGG 0.473873 tig0021786:-15979 None:intergenic
TTCGTTGTGATGGGATTCGT+TGG 0.482699 tig0021786:+14033 Msa1394300:CDS
AAACCTAACGATCGAAGTCT+TGG 0.490690 tig0021786:-13595 None:intergenic
GCCATCGGTTTCGTTGTGAT+GGG 0.492846 tig0021786:+14024 Msa1394300:CDS
CCTAACGATCGAAGTCTTGG+TGG 0.495860 tig0021786:-13592 None:intergenic
CCAATTAACAACATCATCGT+TGG 0.497266 tig0021786:+14081 Msa1394300:CDS
GTTGCTGTGCGCACTGCCAT+CGG 0.516428 tig0021786:+14009 Msa1394300:CDS
GACCTTTGTTCTGTGTGTTG+GGG 0.517962 tig0021786:-13561 None:intergenic
TGGATCGAAAACAGAATCAA+TGG 0.519751 tig0021786:-13813 None:intergenic
ATGGAAACTACAATCGCCTC+AGG 0.536961 tig0021786:+15785 Msa1394300:three_prime_UTR
TGAAGCGTATGGAGGCAGTA+GGG 0.546648 tig0021786:+15819 Msa1394300:three_prime_UTR
GTGAAGCGTATGGAGGCAGT+AGG 0.563634 tig0021786:+15818 Msa1394300:three_prime_UTR
ACTAACTACATAAAGTATGA+AGG 0.574058 tig0021786:+16118 Msa1394300:intron
CACTGAATGTTCTATTAAAG+CGG 0.574715 tig0021786:-15846 None:intergenic
AATTCAAGTTGTGAAGCGTA+TGG 0.586553 tig0021786:+15808 Msa1394300:three_prime_UTR
ACTGAATGTTCTATTAAAGC+GGG 0.590322 tig0021786:-15845 None:intergenic
TCTGTCTGCAACAAAACGAA+AGG 0.600043 tig0021786:-13533 None:intergenic
AATTCGCTAAGGACAGCGTA+AGG 0.605053 tig0021786:+13843 Msa1394300:CDS
CTTCACAACTTGAATTCCTG+AGG 0.631270 tig0021786:-15801 None:intergenic
GAAGCGTATGGAGGCAGTAG+GGG 0.637258 tig0021786:+15820 Msa1394300:three_prime_UTR
TGCCACAAACCCGATCGCAA+AGG 0.641795 tig0021786:+13878 Msa1394300:CDS
TCCCATCACAACGAAACCGA+TGG 0.648968 tig0021786:-14025 None:intergenic
TCCACTCAGAGAATTCGCTA+AGG 0.652105 tig0021786:+13832 Msa1394300:CDS
ATCCCCAACACACAGAACAA+AGG 0.654430 tig0021786:+13559 Msa1394300:five_prime_UTR
ATAAAGTATGAAGGTGACGA+AGG 0.659214 tig0021786:+16127 Msa1394300:intron
TCAAGTTGTGAAGCGTATGG+AGG 0.660190 tig0021786:+15811 Msa1394300:three_prime_UTR
TCCTTAGCGAATTCTCTGAG+TGG 0.675399 tig0021786:-13833 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTAGAAAAAAAAGAAATA+TGG - tig0021786:15907-15926 None:intergenic 10.0%
!!! TGTAAAATTTTATTTTTACA+TGG + tig0021786:15942-15961 Msa1394300:three_prime_UTR 10.0%
!!! GTAAAATTTTATTTTTACAT+GGG + tig0021786:15943-15962 Msa1394300:three_prime_UTR 10.0%
!!! ACATTTTTTTTTTTTTTTGA+GGG - tig0021786:16091-16110 None:intergenic 10.0%
!!! TACATTTTTTTTTTTTTTTG+AGG - tig0021786:16092-16111 None:intergenic 10.0%
!!! AATGAAGTATTAAATGATTA+AGG + tig0021786:15055-15074 Msa1394300:intron 15.0%
!! TAAATGATTAAGGTTATTAT+AGG + tig0021786:15065-15084 Msa1394300:intron 15.0%
!! ACTATATAAAAAACTTTCAA+AGG - tig0021786:15526-15545 None:intergenic 15.0%
!! ATTCAAAGTAAACAAAGAAA+GGG - tig0021786:13641-13660 None:intergenic 20.0%
!! TATTCAAAGTAAACAAAGAA+AGG - tig0021786:13642-13661 None:intergenic 20.0%
!! ATCTAAGAATTGAAACAAAT+TGG - tig0021786:13777-13796 None:intergenic 20.0%
!! AAATATGTCCTTCAAATTAA+AGG - tig0021786:14173-14192 None:intergenic 20.0%
!! AATAATTGTTTATCCAAACA+GGG - tig0021786:14254-14273 None:intergenic 20.0%
!! AAATAATTGTTTATCCAAAC+AGG - tig0021786:14255-14274 None:intergenic 20.0%
!! AAACAATTATTTGCAGTTTA+TGG + tig0021786:14263-14282 Msa1394300:intron 20.0%
!! GACTATTTGATAAAACTATA+TGG - tig0021786:14455-14474 None:intergenic 20.0%
!!! AGCTGTTTTAATATAAATCA+AGG + tig0021786:14507-14526 Msa1394300:intron 20.0%
!!! GCTGTTTTAATATAAATCAA+GGG + tig0021786:14508-14527 Msa1394300:intron 20.0%
!!! AAGTATGTTTGTTGTATTTA+TGG + tig0021786:14538-14557 Msa1394300:intron 20.0%
!! ATGATTAATTGATTACATCT+TGG + tig0021786:14781-14800 Msa1394300:intron 20.0%
!!! GTTCAAAGTATTATTAAATG+TGG + tig0021786:14982-15001 Msa1394300:intron 20.0%
!! TAAATATATAGGGGTAATAT+AGG - tig0021786:15013-15032 None:intergenic 20.0%
!! TCAAAATGTGACAATTAAAA+AGG + tig0021786:15151-15170 Msa1394300:intron 20.0%
!! GAAAATAATTATACAATCTC+TGG - tig0021786:15372-15391 None:intergenic 20.0%
!!! ATAATTATTTTCTTAGTGAC+CGG + tig0021786:15380-15399 Msa1394300:intron 20.0%
!! TTAGATATGGAACTATAATT+TGG + tig0021786:16002-16021 Msa1394300:three_prime_UTR 20.0%
! ATTCTTAGATCGAAAGAAAA+TGG + tig0021786:13787-13806 Msa1394300:intron 25.0%
!!! TTATCCTTCCTTTAATTTGA+AGG + tig0021786:14162-14181 Msa1394300:intron 25.0%
! AATTTGAAGGACATATTTGA+TGG + tig0021786:14175-14194 Msa1394300:intron 25.0%
! AAGTGACAATTATAAAGGAA+CGG - tig0021786:14921-14940 None:intergenic 25.0%
! TGCAAAAGTGACAATTATAA+AGG - tig0021786:14926-14945 None:intergenic 25.0%
! TCTCTGCAATAAATATATAG+GGG - tig0021786:15022-15041 None:intergenic 25.0%
! CTCTCTGCAATAAATATATA+GGG - tig0021786:15023-15042 None:intergenic 25.0%
! TCTCTCTGCAATAAATATAT+AGG - tig0021786:15024-15043 None:intergenic 25.0%
!!! AGTAAAAGTATTTGTTGTCT+TGG + tig0021786:15115-15134 Msa1394300:intron 25.0%
! AACAGAAGTAAACTTAAAAC+AGG - tig0021786:15207-15226 None:intergenic 25.0%
!!! CATTGAGTTGATATTTTGAT+TGG + tig0021786:15646-15665 Msa1394300:intron 25.0%
! ACATATGATACGATTTCTAT+TGG - tig0021786:15684-15703 None:intergenic 25.0%
! AATCGTATCATATGTTACTA+AGG + tig0021786:15689-15708 Msa1394300:intron 25.0%
! TGATTGGTATCTATGTAAAT+TGG + tig0021786:16061-16080 Msa1394300:three_prime_UTR 25.0%
! ACTAACTACATAAAGTATGA+AGG + tig0021786:16118-16137 Msa1394300:intron 25.0%
! GAAAGACAATGACTTTTGAT+TGG + tig0021786:13467-13486 Msa1394300:five_prime_UTR 30.0%
ATCTAGTAGATCGAAATCAA+AGG - tig0021786:13683-13702 None:intergenic 30.0%
!!! AGTTTTTTTACCTTTGCGAT+CGG - tig0021786:13891-13910 None:intergenic 30.0%
AAGATCAAAGAGGAATGAAA+GGG - tig0021786:13920-13939 None:intergenic 30.0%
TCATAAAACCAAGATCAAAG+AGG - tig0021786:13930-13949 None:intergenic 30.0%
! TTTTATGAATCTCTGTGCTA+TGG + tig0021786:13942-13961 Msa1394300:intron 30.0%
TCGTATTGTAGAATTCTCTA+AGG + tig0021786:13987-14006 Msa1394300:intron 30.0%
AAAATTAGAGTTCAGTGTGA+GGG - tig0021786:14130-14149 None:intergenic 30.0%
AAAAATTAGAGTTCAGTGTG+AGG - tig0021786:14131-14150 None:intergenic 30.0%
ATGTCCTTCAAATTAAAGGA+AGG - tig0021786:14169-14188 None:intergenic 30.0%
GACATATTTGATGGAATGAT+TGG + tig0021786:14184-14203 Msa1394300:intron 30.0%
! TTGAAACGATTTGAGATCTT+AGG + tig0021786:14228-14247 Msa1394300:intron 30.0%
TAGCTTATGAAAACAGCTTA+TGG - tig0021786:14373-14392 None:intergenic 30.0%
ACAAGTAAATCCATTATGCA+GGG - tig0021786:14568-14587 None:intergenic 30.0%
!! TTGCTTTTGCTTGTTCTAAA+TGG + tig0021786:14713-14732 Msa1394300:intron 30.0%
TGTTGAATGATAACACCTTA+TGG + tig0021786:14815-14834 Msa1394300:intron 30.0%
! AGCAACTTTTTGTAACCATA+AGG - tig0021786:14833-14852 None:intergenic 30.0%
TGACAATTAAAAAGGAACAG+AGG + tig0021786:15159-15178 Msa1394300:intron 30.0%
GACAATTAAAAAGGAACAGA+GGG + tig0021786:15160-15179 Msa1394300:intron 30.0%
TGAACATATTTGCGACAATA+TGG + tig0021786:15245-15264 Msa1394300:intron 30.0%
CATTACATTACAGAAATAGC+TGG - tig0021786:15437-15456 None:intergenic 30.0%
TGTAATGTAATGAGAGAGTT+TGG + tig0021786:15445-15464 Msa1394300:intron 30.0%
! ACTAATGTCAAGGATGTTTT+TGG + tig0021786:15489-15508 Msa1394300:intron 30.0%
ACTGAATGTTCTATTAAAGC+GGG - tig0021786:15848-15867 None:intergenic 30.0%
CACTGAATGTTCTATTAAAG+CGG - tig0021786:15849-15868 None:intergenic 30.0%
! AAACTCACAAAAAGCATGAT+TGG + tig0021786:16045-16064 Msa1394300:three_prime_UTR 30.0%
TGGATCGAAAACAGAATCAA+TGG - tig0021786:13816-13835 None:intergenic 35.0%
!!! GTTTTTTTACCTTTGCGATC+GGG - tig0021786:13890-13909 None:intergenic 35.0%
CAAGATCAAAGAGGAATGAA+AGG - tig0021786:13921-13940 None:intergenic 35.0%
CTTTCATTCCTCTTTGATCT+TGG + tig0021786:13919-13938 Msa1394300:intron 35.0%
CCAACGATGATGTTGTTAAT+TGG - tig0021786:14084-14103 None:intergenic 35.0%
CCAATTAACAACATCATCGT+TGG + tig0021786:14081-14100 Msa1394300:CDS 35.0%
! TTATGGTTTTCCCTGCATAA+TGG + tig0021786:14555-14574 Msa1394300:intron 35.0%
CACAAGTAAATCCATTATGC+AGG - tig0021786:14569-14588 None:intergenic 35.0%
AGCTTTCTCTTTGTCATGAT+TGG + tig0021786:14653-14672 Msa1394300:intron 35.0%
GTTAGTGACTTTCTCTTTGT+TGG + tig0021786:14675-14694 Msa1394300:intron 35.0%
!!! GACTTTCTCTTTGTTGGTTT+TGG + tig0021786:14681-14700 Msa1394300:intron 35.0%
TGACAATTATAAAGGAACGG+AGG - tig0021786:14918-14937 None:intergenic 35.0%
ATGACGATGTAATTAACGCT+TGG + tig0021786:15746-15765 Msa1394300:intron 35.0%
! TGGTTATTTCCACAGGATAA+TGG + tig0021786:15766-15785 Msa1394300:intron 35.0%
TTGTAGTTTCCATTATCCTG+TGG - tig0021786:15778-15797 None:intergenic 35.0%
!! AATTCAAGTTGTGAAGCGTA+TGG + tig0021786:15808-15827 Msa1394300:three_prime_UTR 35.0%
ATAAAGTATGAAGGTGACGA+AGG + tig0021786:16127-16146 Msa1394300:intron 35.0%
TCTGTCTGCAACAAAACGAA+AGG - tig0021786:13536-13555 None:intergenic 40.0%
AGACCTTTGTTCTGTGTGTT+GGG - tig0021786:13565-13584 None:intergenic 40.0%
AAACCTAACGATCGAAGTCT+TGG - tig0021786:13598-13617 None:intergenic 40.0%
AACAACATCATCGTTGGATC+TGG + tig0021786:14087-14106 Msa1394300:CDS 40.0%
GTCATTACACAAGCTCCTTA+GGG - tig0021786:15415-15434 None:intergenic 40.0%
GAGAGTTTGGTATTAGTCGT+AGG + tig0021786:15458-15477 Msa1394300:intron 40.0%
! TAACGCTTGGTTATTTCCAC+AGG + tig0021786:15759-15778 Msa1394300:intron 40.0%
CTTCACAACTTGAATTCCTG+AGG - tig0021786:15804-15823 None:intergenic 40.0%
! GACTTTTGACCCATTGTTCA+AGG + tig0021786:15969-15988 Msa1394300:three_prime_UTR 40.0%
! AGGAGCAAAGCGTTTAGATA+TGG + tig0021786:15989-16008 Msa1394300:three_prime_UTR 40.0%
ATCCCCAACACACAGAACAA+AGG + tig0021786:13559-13578 Msa1394300:five_prime_UTR 45.0%
GACCTTTGTTCTGTGTGTTG+GGG - tig0021786:13564-13583 None:intergenic 45.0%
GAGACCTTTGTTCTGTGTGT+TGG - tig0021786:13566-13585 None:intergenic 45.0%
TCCACTCAGAGAATTCGCTA+AGG + tig0021786:13832-13851 Msa1394300:CDS 45.0%
TCCTTAGCGAATTCTCTGAG+TGG - tig0021786:13836-13855 None:intergenic 45.0%
AATTCGCTAAGGACAGCGTA+AGG + tig0021786:13843-13862 Msa1394300:CDS 45.0%
! TTCGTTGTGATGGGATTCGT+TGG + tig0021786:14033-14052 Msa1394300:CDS 45.0%
CATCATCGTTGGATCTGGTT+AGG + tig0021786:14092-14111 Msa1394300:CDS 45.0%
TTGAGATCTTAGGCCCTGTT+TGG + tig0021786:14238-14257 Msa1394300:intron 45.0%
CGACTTGCATAAGCACTTGT+GGG - tig0021786:14477-14496 None:intergenic 45.0%
! TCGACTTGCATAAGCACTTG+TGG - tig0021786:14478-14497 None:intergenic 45.0%
GGTCATTACACAAGCTCCTT+AGG - tig0021786:15416-15435 None:intergenic 45.0%
ATGGAAACTACAATCGCCTC+AGG + tig0021786:15785-15804 Msa1394300:three_prime_UTR 45.0%
! TCAAGTTGTGAAGCGTATGG+AGG + tig0021786:15811-15830 Msa1394300:three_prime_UTR 45.0%
CGCTTTGCTCCTTGAACAAT+GGG - tig0021786:15981-16000 None:intergenic 45.0%
ACGCTTTGCTCCTTGAACAA+TGG - tig0021786:15982-16001 None:intergenic 45.0%
!! AAAAAAAAAAAAATGTAAAT+TGG + tig0021786:16095-16114 Msa1394300:intron 5.0%
CCTAACGATCGAAGTCTTGG+TGG - tig0021786:13595-13614 None:intergenic 50.0%
CCACCAAGACTTCGATCGTT+AGG + tig0021786:13592-13611 Msa1394300:five_prime_UTR 50.0%
TACCTTTGCGATCGGGTTTG+TGG - tig0021786:13883-13902 None:intergenic 50.0%
!! TGCCATCGGTTTCGTTGTGA+TGG + tig0021786:14023-14042 Msa1394300:CDS 50.0%
!! GCCATCGGTTTCGTTGTGAT+GGG + tig0021786:14024-14043 Msa1394300:CDS 50.0%
TCCCATCACAACGAAACCGA+TGG - tig0021786:14028-14047 None:intergenic 50.0%
ACACAAGCTCCTTAGGGCAT+AGG - tig0021786:15409-15428 None:intergenic 50.0%
GGCTGCAGCAACTAATGTCA+AGG + tig0021786:15479-15498 Msa1394300:intron 50.0%
GAAAATCCGTGTCTCGAGCA+AGG + tig0021786:15716-15735 Msa1394300:intron 50.0%
TACACACCTTGCTCGAGACA+CGG - tig0021786:15725-15744 None:intergenic 50.0%
TGAAGCGTATGGAGGCAGTA+GGG + tig0021786:15819-15838 Msa1394300:three_prime_UTR 50.0%
TGCCACAAACCCGATCGCAA+AGG + tig0021786:13878-13897 Msa1394300:CDS 55.0%
CTCCTTAGGGCATAGGTAGC+CGG - tig0021786:15402-15421 None:intergenic 55.0%
GTGAAGCGTATGGAGGCAGT+AGG + tig0021786:15818-15837 Msa1394300:three_prime_UTR 55.0%
GAAGCGTATGGAGGCAGTAG+GGG + tig0021786:15820-15839 Msa1394300:three_prime_UTR 55.0%
GTTGCTGTGCGCACTGCCAT+CGG + tig0021786:14009-14028 Msa1394300:CDS 60.0%
GACCGGCTACCTATGCCCTA+AGG + tig0021786:15397-15416 Msa1394300:intron 60.0%
Chromosome Type Strat End Strand Name
tig0021786 gene 13458 16153 13458 ID=Msa1394300;Name=Msa1394300
tig0021786 mRNA 13458 16153 13458 ID=Msa1394300-mRNA-1;Parent=Msa1394300;Name=Msa1394300-mRNA-1;_AED=0.24;_eAED=0.24;_QI=167|1|1|1|0.5|0.6|5|341|69
tig0021786 exon 13458 13613 13458 ID=Msa1394300-mRNA-1:exon:14279;Parent=Msa1394300-mRNA-1
tig0021786 exon 13795 13899 13795 ID=Msa1394300-mRNA-1:exon:14280;Parent=Msa1394300-mRNA-1
tig0021786 exon 13998 14113 13998 ID=Msa1394300-mRNA-1:exon:14281;Parent=Msa1394300-mRNA-1
tig0021786 exon 15781 16096 15781 ID=Msa1394300-mRNA-1:exon:14282;Parent=Msa1394300-mRNA-1
tig0021786 exon 16129 16153 16129 ID=Msa1394300-mRNA-1:exon:14283;Parent=Msa1394300-mRNA-1
tig0021786 five_prime_UTR 13458 13613 13458 ID=Msa1394300-mRNA-1:five_prime_utr;Parent=Msa1394300-mRNA-1
tig0021786 five_prime_UTR 13795 13805 13795 ID=Msa1394300-mRNA-1:five_prime_utr;Parent=Msa1394300-mRNA-1
tig0021786 CDS 13806 13899 13806 ID=Msa1394300-mRNA-1:cds;Parent=Msa1394300-mRNA-1
tig0021786 CDS 13998 14113 13998 ID=Msa1394300-mRNA-1:cds;Parent=Msa1394300-mRNA-1
tig0021786 three_prime_UTR 15781 16096 15781 ID=Msa1394300-mRNA-1:three_prime_utr;Parent=Msa1394300-mRNA-1
tig0021786 three_prime_UTR 16129 16153 16129 ID=Msa1394300-mRNA-1:three_prime_utr;Parent=Msa1394300-mRNA-1
Gene Sequence

>Msa1394300

ATGGACGCCATTGATTCTGTTTTCGATCCACTCAGAGAATTCGCTAAGGACAGCGTAAGGCTCGTCAAGCGATGCCACAAACCCGATCGCAAAGAATTCTCTAAGGTTGCTGTGCGCACTGCCATCGGTTTCGTTGTGATGGGATTCGTTGGCTTTTTCGTTAAGCTCATTTTCATTCCAATTAACAACATCATCGTTGGATCTGGTTAG
Protein sequence

>Msa1394300

MDAIDSVFDPLREFAKDSVRLVKRCHKPDRKEFSKVAVRTAIGFVVMGFVGFFVKLIFIPINNIIVGSG*