AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1412640


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1412640 MtrunA17_Chr4g0005821 100.000 91 0 0 1 91 598 688 1.09e-58 190
Msa1412640 MtrunA17_Chr7g0241611 71.429 84 24 0 1 84 604 687 9.63e-37 130
Msa1412640 MtrunA17_Chr7g0259681 70.115 87 24 1 5 91 550 634 1.70e-34 123
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1412640 AT3G09100.2 72.152 79 22 0 2 80 590 668 7.48e-34 122
Msa1412640 AT5G01290.1 65.823 79 27 0 2 80 575 653 3.51e-30 112
Msa1412640 AT5G28210.1 56.164 73 32 0 7 79 541 613 7.24e-22 88.6

Find 47 sgRNAs with CRISPR-Local

Find 117 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTGGATTTGGCTATATATT+TGG 0.139270 tig0023923:-84468 Msa1412640:three_prime_UTR
CCCACCAGTGAAATAATTTA+AGG 0.144290 tig0023923:+84570 None:intergenic
TGTCTGCTTCTGGTATTTAT+TGG 0.225810 tig0023923:-84486 Msa1412640:three_prime_UTR
CTTCTGGTATTTATTGGATT+TGG 0.247314 tig0023923:-84480 Msa1412640:three_prime_UTR
CTTTAGTTGTCTAGATCAAT+AGG 0.277033 tig0023923:-84357 Msa1412640:three_prime_UTR
TAACCATTGGTGTCTGCTTC+TGG 0.303633 tig0023923:-84496 Msa1412640:three_prime_UTR
CTGTAAGTATTAAACTCATT+TGG 0.310885 tig0023923:+84854 None:intergenic
GTGATTCGTTGTGGTTAGAT+AGG 0.323605 tig0023923:-84604 Msa1412640:exon
AGAACACTCGATGATCTTTC+CGG 0.326134 tig0023923:+84934 None:intergenic
AGATCAATAGGGTTAGGTTT+AGG 0.374635 tig0023923:-84345 Msa1412640:three_prime_UTR
TGTTTGTAGGGTAGAAGATC+AGG 0.375622 tig0023923:-84538 Msa1412640:three_prime_UTR
GAAAGATCATCGAGTGTTCT+TGG 0.397309 tig0023923:-84931 Msa1412640:CDS
GTGATTATAAGTTATTGAAA+TGG 0.407052 tig0023923:-84286 Msa1412640:three_prime_UTR
TTCGCAGGAATATCCATTCC+AGG 0.421148 tig0023923:+84897 None:intergenic
TTGTCTAGATCAATAGGGTT+AGG 0.424051 tig0023923:-84351 Msa1412640:three_prime_UTR
AATGCCTTAAATTATTTCAC+TGG 0.432603 tig0023923:-84574 Msa1412640:three_prime_UTR
TTTAGTTGTCTAGATCAATA+GGG 0.449208 tig0023923:-84356 Msa1412640:three_prime_UTR
AAAGATCATCGAGTGTTCTT+GGG 0.450552 tig0023923:-84930 Msa1412640:CDS
GAAAATTCTAACCAATGTAA+TGG 0.474535 tig0023923:+84237 None:intergenic
AGGTTGCTTATGTAATTAGT+TGG 0.477860 tig0023923:-84434 Msa1412640:three_prime_UTR
CTAATTACATAAGCAACCTT+AGG 0.479770 tig0023923:+84438 None:intergenic
GCCTTAAATTATTTCACTGG+TGG 0.481047 tig0023923:-84571 Msa1412640:three_prime_UTR
TGGGAGAATGAGATGTTTGT+AGG 0.486998 tig0023923:-84551 Msa1412640:three_prime_UTR
GAATCACCTTCGCTGCTTTG+CGG 0.489232 tig0023923:+84620 None:intergenic
ATTTATCTGTTCTAATTCGC+AGG 0.489727 tig0023923:+84882 None:intergenic
GATCTTTCCGGAATAAAATG+AGG 0.503180 tig0023923:+84946 None:intergenic
ATGAAATTTGTGACGCAACT+CGG 0.504231 tig0023923:+84394 None:intergenic
CCTTAAATTATTTCACTGGT+GGG 0.508594 tig0023923:-84570 Msa1412640:three_prime_UTR
TATGTATGTGATATATACAT+TGG 0.517188 tig0023923:-84214 Msa1412640:three_prime_UTR
CATAAGCAACCTTAGGATGA+TGG 0.518880 tig0023923:+84445 None:intergenic
CTCATGCCGCAAAGCAGCGA+AGG 0.526270 tig0023923:-84626 Msa1412640:CDS
CTATTGATCTAGACAACTAA+AGG 0.526569 tig0023923:+84358 None:intergenic
TGAGTTTAATACTTACAGAA+AGG 0.527213 tig0023923:-84849 Msa1412640:intron
GCCTTCCCATGTATGCGGAC+AGG 0.528594 tig0023923:-84680 Msa1412640:CDS
TATATTTGGCCATCATCCTA+AGG 0.530710 tig0023923:-84454 Msa1412640:three_prime_UTR
TGATTCGTTGTGGTTAGATA+GGG 0.530949 tig0023923:-84603 Msa1412640:three_prime_UTR
AGACTCAAGTTCCATTACAT+TGG 0.532366 tig0023923:-84248 Msa1412640:three_prime_UTR
AACTCGGCAGCACTGCTGCA+AGG 0.544386 tig0023923:+84410 None:intergenic
ACATAAACATATGTAACCAT+TGG 0.547919 tig0023923:-84509 Msa1412640:three_prime_UTR
TCCTGTCCGCATACATGGGA+AGG 0.564771 tig0023923:+84679 None:intergenic
ATCTTTCCGGAATAAAATGA+GGG 0.606895 tig0023923:+84947 None:intergenic
GGGAGAATGAGATGTTTGTA+GGG 0.614069 tig0023923:-84550 Msa1412640:three_prime_UTR
TTTATCCTGTCCGCATACAT+GGG 0.615995 tig0023923:+84675 None:intergenic
GCAGCGAAGGTGATTCGTTG+TGG 0.625865 tig0023923:-84613 Msa1412640:exon
ATACCAGAAGCAGACACCAA+TGG 0.662343 tig0023923:+84493 None:intergenic
AATTCGCCTTCCCATGTATG+CGG 0.681083 tig0023923:-84685 Msa1412640:CDS
CATAAAAGACAACATCACAG+AGG 0.751598 tig0023923:-84736 Msa1412640:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GATAAAAGAAACTAAAAATT+GGG + tig0023923:84291-84310 None:intergenic 15.0%
!! AGATAAAAGAAACTAAAAAT+TGG + tig0023923:84292-84311 None:intergenic 15.0%
!! GATAAAAGAAACTAAAAATT+GGG + tig0023923:84291-84310 None:intergenic 15.0%
!! AGATAAAAGAAACTAAAAAT+TGG + tig0023923:84292-84311 None:intergenic 15.0%
!!! AGCCATTTACTTAATTTTAT+AGG - tig0023923:84332-84351 Msa1412640:three_prime_UTR 20.0%
!! CACCTATAAAATTAAGTAAA+TGG + tig0023923:84337-84356 None:intergenic 20.0%
!! GTGATTATAAGTTATTGAAA+TGG - tig0023923:84815-84834 Msa1412640:intron 20.0%
!! TATGTATGTGATATATACAT+TGG - tig0023923:84887-84906 Msa1412640:CDS 20.0%
!!! AGCCATTTACTTAATTTTAT+AGG - tig0023923:84332-84351 Msa1412640:three_prime_UTR 20.0%
!! CACCTATAAAATTAAGTAAA+TGG + tig0023923:84337-84356 None:intergenic 20.0%
!! GTGATTATAAGTTATTGAAA+TGG - tig0023923:84815-84834 Msa1412640:intron 20.0%
!! TATGTATGTGATATATACAT+TGG - tig0023923:84887-84906 Msa1412640:CDS 20.0%
! CTGTAAGTATTAAACTCATT+TGG + tig0023923:84250-84269 None:intergenic 25.0%
! TGAGTTTAATACTTACAGAA+AGG - tig0023923:84252-84271 Msa1412640:three_prime_UTR 25.0%
! TAAAAATTGGGAGTTAGTAT+TGG + tig0023923:84279-84298 None:intergenic 25.0%
! TTTATCTCTAAATCTGTACT+TGG - tig0023923:84305-84324 Msa1412640:three_prime_UTR 25.0%
! AATGCCTTAAATTATTTCAC+TGG - tig0023923:84527-84546 Msa1412640:three_prime_UTR 25.0%
! ACATAAACATATGTAACCAT+TGG - tig0023923:84592-84611 Msa1412640:three_prime_UTR 25.0%
! ATTGGATTTGGCTATATATT+TGG - tig0023923:84633-84652 Msa1412640:CDS 25.0%
! TTTAGTTGTCTAGATCAATA+GGG - tig0023923:84745-84764 Msa1412640:CDS 25.0%
! GAAAATTCTAACCAATGTAA+TGG + tig0023923:84867-84886 None:intergenic 25.0%
! CTGTAAGTATTAAACTCATT+TGG + tig0023923:84250-84269 None:intergenic 25.0%
! TGAGTTTAATACTTACAGAA+AGG - tig0023923:84252-84271 Msa1412640:three_prime_UTR 25.0%
! TAAAAATTGGGAGTTAGTAT+TGG + tig0023923:84279-84298 None:intergenic 25.0%
! TTTATCTCTAAATCTGTACT+TGG - tig0023923:84305-84324 Msa1412640:three_prime_UTR 25.0%
! AATGCCTTAAATTATTTCAC+TGG - tig0023923:84527-84546 Msa1412640:three_prime_UTR 25.0%
! ACATAAACATATGTAACCAT+TGG - tig0023923:84592-84611 Msa1412640:three_prime_UTR 25.0%
! ATTGGATTTGGCTATATATT+TGG - tig0023923:84633-84652 Msa1412640:CDS 25.0%
! TTTAGTTGTCTAGATCAATA+GGG - tig0023923:84745-84764 Msa1412640:CDS 25.0%
! GAAAATTCTAACCAATGTAA+TGG + tig0023923:84867-84886 None:intergenic 25.0%
ATCTTTCCGGAATAAAATGA+GGG + tig0023923:84157-84176 None:intergenic 30.0%
ATTTATCTGTTCTAATTCGC+AGG + tig0023923:84222-84241 None:intergenic 30.0%
CCTTAAATTATTTCACTGGT+GGG - tig0023923:84531-84550 Msa1412640:three_prime_UTR 30.0%
CTTCTGGTATTTATTGGATT+TGG - tig0023923:84621-84640 Msa1412640:exon 30.0%
CTAATTACATAAGCAACCTT+AGG + tig0023923:84666-84685 None:intergenic 30.0%
AGGTTGCTTATGTAATTAGT+TGG - tig0023923:84667-84686 Msa1412640:CDS 30.0%
CTATTGATCTAGACAACTAA+AGG + tig0023923:84746-84765 None:intergenic 30.0%
CTTTAGTTGTCTAGATCAAT+AGG - tig0023923:84744-84763 Msa1412640:CDS 30.0%
ATCTTTCCGGAATAAAATGA+GGG + tig0023923:84157-84176 None:intergenic 30.0%
ATTTATCTGTTCTAATTCGC+AGG + tig0023923:84222-84241 None:intergenic 30.0%
CCTTAAATTATTTCACTGGT+GGG - tig0023923:84531-84550 Msa1412640:three_prime_UTR 30.0%
CTTCTGGTATTTATTGGATT+TGG - tig0023923:84621-84640 Msa1412640:exon 30.0%
CTAATTACATAAGCAACCTT+AGG + tig0023923:84666-84685 None:intergenic 30.0%
AGGTTGCTTATGTAATTAGT+TGG - tig0023923:84667-84686 Msa1412640:CDS 30.0%
CTATTGATCTAGACAACTAA+AGG + tig0023923:84746-84765 None:intergenic 30.0%
CTTTAGTTGTCTAGATCAAT+AGG - tig0023923:84744-84763 Msa1412640:CDS 30.0%
! ACAGAACCCTCATTTTATTC+CGG - tig0023923:84148-84167 Msa1412640:three_prime_UTR 35.0%
GATCTTTCCGGAATAAAATG+AGG + tig0023923:84158-84177 None:intergenic 35.0%
AAAGATCATCGAGTGTTCTT+GGG - tig0023923:84171-84190 Msa1412640:three_prime_UTR 35.0%
!! TTCTTGGGATTTTGATAACC+TGG - tig0023923:84186-84205 Msa1412640:three_prime_UTR 35.0%
CATAAAAGACAACATCACAG+AGG - tig0023923:84365-84384 Msa1412640:three_prime_UTR 35.0%
TGATTCGTTGTGGTTAGATA+GGG - tig0023923:84498-84517 Msa1412640:three_prime_UTR 35.0%
GCCTTAAATTATTTCACTGG+TGG - tig0023923:84530-84549 Msa1412640:three_prime_UTR 35.0%
CCCACCAGTGAAATAATTTA+AGG + tig0023923:84534-84553 None:intergenic 35.0%
TGTCTGCTTCTGGTATTTAT+TGG - tig0023923:84615-84634 Msa1412640:exon 35.0%
TATATTTGGCCATCATCCTA+AGG - tig0023923:84647-84666 Msa1412640:CDS 35.0%
ATGAAATTTGTGACGCAACT+CGG + tig0023923:84710-84729 None:intergenic 35.0%
TTGTCTAGATCAATAGGGTT+AGG - tig0023923:84750-84769 Msa1412640:CDS 35.0%
AGATCAATAGGGTTAGGTTT+AGG - tig0023923:84756-84775 Msa1412640:intron 35.0%
AGACTCAAGTTCCATTACAT+TGG - tig0023923:84853-84872 Msa1412640:CDS 35.0%
! ACAGAACCCTCATTTTATTC+CGG - tig0023923:84148-84167 Msa1412640:three_prime_UTR 35.0%
GATCTTTCCGGAATAAAATG+AGG + tig0023923:84158-84177 None:intergenic 35.0%
AAAGATCATCGAGTGTTCTT+GGG - tig0023923:84171-84190 Msa1412640:three_prime_UTR 35.0%
!! TTCTTGGGATTTTGATAACC+TGG - tig0023923:84186-84205 Msa1412640:three_prime_UTR 35.0%
CATAAAAGACAACATCACAG+AGG - tig0023923:84365-84384 Msa1412640:three_prime_UTR 35.0%
TGATTCGTTGTGGTTAGATA+GGG - tig0023923:84498-84517 Msa1412640:three_prime_UTR 35.0%
GCCTTAAATTATTTCACTGG+TGG - tig0023923:84530-84549 Msa1412640:three_prime_UTR 35.0%
CCCACCAGTGAAATAATTTA+AGG + tig0023923:84534-84553 None:intergenic 35.0%
TGTCTGCTTCTGGTATTTAT+TGG - tig0023923:84615-84634 Msa1412640:exon 35.0%
TATATTTGGCCATCATCCTA+AGG - tig0023923:84647-84666 Msa1412640:CDS 35.0%
ATGAAATTTGTGACGCAACT+CGG + tig0023923:84710-84729 None:intergenic 35.0%
TTGTCTAGATCAATAGGGTT+AGG - tig0023923:84750-84769 Msa1412640:CDS 35.0%
AGATCAATAGGGTTAGGTTT+AGG - tig0023923:84756-84775 Msa1412640:intron 35.0%
AGACTCAAGTTCCATTACAT+TGG - tig0023923:84853-84872 Msa1412640:CDS 35.0%
AGAACACTCGATGATCTTTC+CGG + tig0023923:84170-84189 None:intergenic 40.0%
GAAAGATCATCGAGTGTTCT+TGG - tig0023923:84170-84189 Msa1412640:three_prime_UTR 40.0%
!! GGGATTTTGATAACCTGGAA+TGG - tig0023923:84191-84210 Msa1412640:three_prime_UTR 40.0%
TTTATCCTGTCCGCATACAT+GGG + tig0023923:84429-84448 None:intergenic 40.0%
! TTTTATCCTGTCCGCATACA+TGG + tig0023923:84430-84449 None:intergenic 40.0%
GTGATTCGTTGTGGTTAGAT+AGG - tig0023923:84497-84516 Msa1412640:three_prime_UTR 40.0%
TGGGAGAATGAGATGTTTGT+AGG - tig0023923:84550-84569 Msa1412640:three_prime_UTR 40.0%
GGGAGAATGAGATGTTTGTA+GGG - tig0023923:84551-84570 Msa1412640:three_prime_UTR 40.0%
TGTTTGTAGGGTAGAAGATC+AGG - tig0023923:84563-84582 Msa1412640:three_prime_UTR 40.0%
CATAAGCAACCTTAGGATGA+TGG + tig0023923:84659-84678 None:intergenic 40.0%
! GCAAGCCTTCCATTCTTTTT+AGG - tig0023923:84953-84972 Msa1412640:CDS 40.0%
AGAACACTCGATGATCTTTC+CGG + tig0023923:84170-84189 None:intergenic 40.0%
GAAAGATCATCGAGTGTTCT+TGG - tig0023923:84170-84189 Msa1412640:three_prime_UTR 40.0%
!! GGGATTTTGATAACCTGGAA+TGG - tig0023923:84191-84210 Msa1412640:three_prime_UTR 40.0%
TTTATCCTGTCCGCATACAT+GGG + tig0023923:84429-84448 None:intergenic 40.0%
! TTTTATCCTGTCCGCATACA+TGG + tig0023923:84430-84449 None:intergenic 40.0%
GTGATTCGTTGTGGTTAGAT+AGG - tig0023923:84497-84516 Msa1412640:three_prime_UTR 40.0%
TGGGAGAATGAGATGTTTGT+AGG - tig0023923:84550-84569 Msa1412640:three_prime_UTR 40.0%
GGGAGAATGAGATGTTTGTA+GGG - tig0023923:84551-84570 Msa1412640:three_prime_UTR 40.0%
TGTTTGTAGGGTAGAAGATC+AGG - tig0023923:84563-84582 Msa1412640:three_prime_UTR 40.0%
CATAAGCAACCTTAGGATGA+TGG + tig0023923:84659-84678 None:intergenic 40.0%
! GCAAGCCTTCCATTCTTTTT+AGG - tig0023923:84953-84972 Msa1412640:CDS 40.0%
TTCGCAGGAATATCCATTCC+AGG + tig0023923:84207-84226 None:intergenic 45.0%
AATTCGCCTTCCCATGTATG+CGG - tig0023923:84416-84435 Msa1412640:three_prime_UTR 45.0%
! TAACCATTGGTGTCTGCTTC+TGG - tig0023923:84605-84624 Msa1412640:exon 45.0%
ATACCAGAAGCAGACACCAA+TGG + tig0023923:84611-84630 None:intergenic 45.0%
!! CCTTCCATTCTTTTTAGGCG+CGG - tig0023923:84958-84977 Msa1412640:CDS 45.0%
TTCGCAGGAATATCCATTCC+AGG + tig0023923:84207-84226 None:intergenic 45.0%
AATTCGCCTTCCCATGTATG+CGG - tig0023923:84416-84435 Msa1412640:three_prime_UTR 45.0%
! TAACCATTGGTGTCTGCTTC+TGG - tig0023923:84605-84624 Msa1412640:exon 45.0%
ATACCAGAAGCAGACACCAA+TGG + tig0023923:84611-84630 None:intergenic 45.0%
! GAATCACCTTCGCTGCTTTG+CGG + tig0023923:84484-84503 None:intergenic 50.0%
! GAATCACCTTCGCTGCTTTG+CGG + tig0023923:84484-84503 None:intergenic 50.0%
TCCTGTCCGCATACATGGGA+AGG + tig0023923:84425-84444 None:intergenic 55.0%
GCAGCGAAGGTGATTCGTTG+TGG - tig0023923:84488-84507 Msa1412640:three_prime_UTR 55.0%
TCCTGTCCGCATACATGGGA+AGG + tig0023923:84425-84444 None:intergenic 55.0%
GCAGCGAAGGTGATTCGTTG+TGG - tig0023923:84488-84507 Msa1412640:three_prime_UTR 55.0%
GCCTTCCCATGTATGCGGAC+AGG - tig0023923:84421-84440 Msa1412640:three_prime_UTR 60.0%
CTCATGCCGCAAAGCAGCGA+AGG - tig0023923:84475-84494 Msa1412640:three_prime_UTR 60.0%
AACTCGGCAGCACTGCTGCA+AGG + tig0023923:84694-84713 None:intergenic 60.0%
GCCTTCCCATGTATGCGGAC+AGG - tig0023923:84421-84440 Msa1412640:three_prime_UTR 60.0%
CTCATGCCGCAAAGCAGCGA+AGG - tig0023923:84475-84494 Msa1412640:three_prime_UTR 60.0%
AACTCGGCAGCACTGCTGCA+AGG + tig0023923:84694-84713 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
tig0023923 gene 84145 84978 84145 ID=Msa1412640;Name=Msa1412640
tig0023923 mRNA 84145 84978 84145 ID=Msa1412640-mRNA-1;Parent=Msa1412640;Name=Msa1412640-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|1|0.5|1|1|0.5|2|478|91
tig0023923 exon 84145 84769 84145 ID=Msa1412640-mRNA-1:exon:20681;Parent=Msa1412640-mRNA-1
tig0023923 exon 84850 84978 84850 ID=Msa1412640-mRNA-1:exon:20680;Parent=Msa1412640-mRNA-1
tig0023923 CDS 84850 84978 84850 ID=Msa1412640-mRNA-1:cds;Parent=Msa1412640-mRNA-1
tig0023923 CDS 84623 84769 84623 ID=Msa1412640-mRNA-1:cds;Parent=Msa1412640-mRNA-1
tig0023923 three_prime_UTR 84145 84622 84145 ID=Msa1412640-mRNA-1:three_prime_utr;Parent=Msa1412640-mRNA-1
Gene Sequence

>Msa1412640

GGCACAGAACCCTCATTTTATTCCGGAAAGATCATCGAGTGTTCTTGGGATTTTGATAACCTGGAATGGATATTCCTGCGAATTAGAACAGATAAATCAACTCCAAATGAGTTTAATACTTACAGAAAGGTGATGCGAAGCATAAAAGACAACATCACAGAGGAAGACTTGTTGAATGAAATAAATGAGATAATTCGCCTTCCCATGTATGCGGACAGGATAAAAAGTGATAGTAAAGCAAATCAGATTGCTCATGCCGCAAAGCAGCGAAGGTGA

Protein sequence

>Msa1412640

GTEPSFYSGKIIECSWDFDNLEWIFLRIRTDKSTPNEFNTYRKVMRSIKDNITEEDLLNEINEIIRLPMYADRIKSDSKANQIAHAAKQRR*