AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1272970

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1272970 MtrunA17_Chr5g0393501 31.928 166 110 1 2 164 76 241 5.78e-25 96.7
Msa1272970 MtrunA17_Chr4g0044671 27.517 149 108 0 2 150 59 207 1.28e-12 63.2
Msa1272970 MtrunA17_Chr4g0034781 26.846 149 109 0 2 150 53 201 9.44e-12 60.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 48 sgRNAs with CRISPR-Local

Find 106 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAATACATTGTCTAACTTCT+AGG 0.159906 8_3:+6629193 Msa1272970:five_prime_UTR
CTGTAAATTAAATCCTCTTT+TGG 0.220274 8_3:+6629112 None:intergenic
GAAGTTCCTATCGCTGGATA+TGG 0.291188 8_3:+6629524 Msa1272970:CDS
TAGGAACTACCTTATACTTT+TGG 0.309505 8_3:+6629664 Msa1272970:intron
AGGAATTTGCCAAAAGTATA+AGG 0.322050 8_3:-6629673 None:intergenic
AATCGTGATGTTTCACTCTA+AGG 0.341127 8_3:-6629693 None:intergenic
CGATTATTCTACGAGTTTAG+TGG 0.386306 8_3:+6629368 Msa1272970:CDS
ATCTAATTCCACCAAGGTAC+TGG 0.401470 8_3:-6629409 None:intergenic
ACCTTTGAAGTTCCTATCGC+TGG 0.405792 8_3:+6629518 Msa1272970:CDS
TCCGAACATCACATTTGGTA+TGG 0.417548 8_3:-6629779 None:intergenic
ATTATTGCTTTCCAGTACCT+TGG 0.445011 8_3:+6629398 Msa1272970:CDS
CCGAACATCACATTTGGTAT+GGG 0.451435 8_3:-6629778 None:intergenic
TAGCAATGGCACTTGCTAGA+TGG 0.455163 8_3:+6629269 Msa1272970:five_prime_UTR
TGCCGCACTCATGGAATGAT+AGG 0.462626 8_3:-6629480 None:intergenic
TTGTGCTGCCAATGGTATTG+AGG 0.463000 8_3:+6629819 Msa1272970:CDS
GTCAAGCATTTATCAACGCT+TGG 0.466111 8_3:-6629902 None:intergenic
TGATAGGGTGGATAATCAAC+TGG 0.472004 8_3:-6629464 None:intergenic
CCAAATGTGATGTTCGGAAA+AGG 0.475440 8_3:+6629784 Msa1272970:CDS
CCCATACCAAATGTGATGTT+CGG 0.477035 8_3:+6629778 Msa1272970:CDS
GGCCGTTGTTGACAGATGGT+TGG 0.487397 8_3:+6629336 Msa1272970:CDS
GCACGATGCTGCCGCACTCA+TGG 0.495354 8_3:-6629489 None:intergenic
TGTGCTGCCAATGGTATTGA+GGG 0.501205 8_3:+6629820 Msa1272970:CDS
ATTGCTTTCCAGTACCTTGG+TGG 0.518466 8_3:+6629401 Msa1272970:CDS
AAATATTCACAAACAAAGAA+TGG 0.520659 8_3:-6629233 None:intergenic
ACAGGAATGATATTGTCATA+AGG 0.528831 8_3:-6629733 None:intergenic
AGTCGGCCGTTGTTGACAGA+TGG 0.531450 8_3:+6629332 Msa1272970:CDS
ATATTAAATCCAACCAAAAG+AGG 0.531474 8_3:-6629125 None:intergenic
CGAACATCACATTTGGTATG+GGG 0.552019 8_3:-6629777 None:intergenic
TCTGTATATTTGAGTCTCAC+AGG 0.555272 8_3:-6629751 None:intergenic
TTTCAAGTGCAAGTGCGTCA+TGG 0.567746 8_3:+6629858 Msa1272970:CDS
TTGTCTAACTTCTAGGATGT+CGG 0.574486 8_3:+6629200 Msa1272970:five_prime_UTR
TGTTCAACAAATCAGTTAGT+CGG 0.579019 8_3:+6629315 Msa1272970:CDS
GTCTCCGCCCTCAATACCAT+TGG 0.581950 8_3:-6629827 None:intergenic
TGGCACTTGCTAGATGGTGA+TGG 0.587936 8_3:+6629275 Msa1272970:five_prime_UTR
TCTAGCAAGTGCCATTGCTA+CGG 0.595706 8_3:-6629266 None:intergenic
CACGATTACGTCGTGTTGTG+CGG 0.599800 8_3:+6629709 Msa1272970:CDS
ATGTGATGTTCGGAAAAGGT+TGG 0.606400 8_3:+6629788 Msa1272970:CDS
GGCACTTGCTAGATGGTGAT+GGG 0.608333 8_3:+6629276 Msa1272970:five_prime_UTR
GCCGCACTCATGGAATGATA+GGG 0.629158 8_3:-6629479 None:intergenic
GACGATCCATATCCAGCGAT+AGG 0.639854 8_3:-6629530 None:intergenic
ACCCTATCATTCCATGAGTG+CGG 0.640367 8_3:+6629478 Msa1272970:CDS
TCCAGCGATAGGAACTTCAA+AGG 0.641566 8_3:-6629519 None:intergenic
TCTACGAGCTACCGTAGCAA+TGG 0.643591 8_3:+6629255 Msa1272970:five_prime_UTR
GCACTCATGGAATGATAGGG+TGG 0.649652 8_3:-6629476 None:intergenic
TTTGAAATCTAATTCCACCA+AGG 0.668103 8_3:-6629415 None:intergenic
CTCCAACCATCTGTCAACAA+CGG 0.679074 8_3:-6629338 None:intergenic
TGGATCGTCGAAATCACCGA+AGG 0.694031 8_3:+6629544 Msa1272970:CDS
GCTGCCAATGGTATTGAGGG+CGG 0.739556 8_3:+6629823 Msa1272970:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GTTTTTTTTTCTTTTTTTTT+AGG + chr8_3:6629645-6629664 Msa1272970:intron 10.0%
!!! GTTTTTTTTTCTTTTTTTTT+AGG + chr8_3:6629645-6629664 Msa1272970:intron 10.0%
!! GTTTATATATGCTATAATAA+AGG + chr8_3:6629602-6629621 Msa1272970:intron 15.0%
!! GTTTATATATGCTATAATAA+AGG + chr8_3:6629602-6629621 Msa1272970:intron 15.0%
!! AAATATTCACAAACAAAGAA+TGG - chr8_3:6629236-6629255 None:intergenic 20.0%
!! AAAAAACAATAAACAACCTT+CGG - chr8_3:6629563-6629582 None:intergenic 20.0%
!! AAATATTCACAAACAAAGAA+TGG - chr8_3:6629236-6629255 None:intergenic 20.0%
!! AAAAAACAATAAACAACCTT+CGG - chr8_3:6629563-6629582 None:intergenic 20.0%
!! AAATTAAATCCTCTTTTGGT+TGG + chr8_3:6629116-6629135 Msa1272970:five_prime_UTR 25.0%
! ATATTAAATCCAACCAAAAG+AGG - chr8_3:6629128-6629147 None:intergenic 25.0%
! TAATACATTGTCTAACTTCT+AGG + chr8_3:6629193-6629212 Msa1272970:five_prime_UTR 25.0%
!! TTTTGATGCTATTCATTTAG+AGG + chr8_3:6629580-6629599 Msa1272970:intron 25.0%
!! AAATTAAATCCTCTTTTGGT+TGG + chr8_3:6629116-6629135 Msa1272970:five_prime_UTR 25.0%
! ATATTAAATCCAACCAAAAG+AGG - chr8_3:6629128-6629147 None:intergenic 25.0%
! TAATACATTGTCTAACTTCT+AGG + chr8_3:6629193-6629212 Msa1272970:five_prime_UTR 25.0%
!! TTTTGATGCTATTCATTTAG+AGG + chr8_3:6629580-6629599 Msa1272970:intron 25.0%
TGTTCAACAAATCAGTTAGT+CGG + chr8_3:6629315-6629334 Msa1272970:CDS 30.0%
! TTTGAAATCTAATTCCACCA+AGG - chr8_3:6629418-6629437 None:intergenic 30.0%
! TAGGAACTACCTTATACTTT+TGG + chr8_3:6629664-6629683 Msa1272970:intron 30.0%
! AGGAATTTGCCAAAAGTATA+AGG - chr8_3:6629676-6629695 None:intergenic 30.0%
ACAGGAATGATATTGTCATA+AGG - chr8_3:6629736-6629755 None:intergenic 30.0%
TGTTCAACAAATCAGTTAGT+CGG + chr8_3:6629315-6629334 Msa1272970:CDS 30.0%
! TTTGAAATCTAATTCCACCA+AGG - chr8_3:6629418-6629437 None:intergenic 30.0%
! TAGGAACTACCTTATACTTT+TGG + chr8_3:6629664-6629683 Msa1272970:intron 30.0%
! AGGAATTTGCCAAAAGTATA+AGG - chr8_3:6629676-6629695 None:intergenic 30.0%
ACAGGAATGATATTGTCATA+AGG - chr8_3:6629736-6629755 None:intergenic 30.0%
!! TTGTCTAACTTCTAGGATGT+CGG + chr8_3:6629200-6629219 Msa1272970:five_prime_UTR 35.0%
CGATTATTCTACGAGTTTAG+TGG + chr8_3:6629368-6629387 Msa1272970:CDS 35.0%
ATTATTGCTTTCCAGTACCT+TGG + chr8_3:6629398-6629417 Msa1272970:CDS 35.0%
AATCGTGATGTTTCACTCTA+AGG - chr8_3:6629696-6629715 None:intergenic 35.0%
TCTGTATATTTGAGTCTCAC+AGG - chr8_3:6629754-6629773 None:intergenic 35.0%
!! TTGTCTAACTTCTAGGATGT+CGG + chr8_3:6629200-6629219 Msa1272970:five_prime_UTR 35.0%
CGATTATTCTACGAGTTTAG+TGG + chr8_3:6629368-6629387 Msa1272970:CDS 35.0%
ATTATTGCTTTCCAGTACCT+TGG + chr8_3:6629398-6629417 Msa1272970:CDS 35.0%
AATCGTGATGTTTCACTCTA+AGG - chr8_3:6629696-6629715 None:intergenic 35.0%
TCTGTATATTTGAGTCTCAC+AGG - chr8_3:6629754-6629773 None:intergenic 35.0%
ATCTAATTCCACCAAGGTAC+TGG - chr8_3:6629412-6629431 None:intergenic 40.0%
TGATAGGGTGGATAATCAAC+TGG - chr8_3:6629467-6629486 None:intergenic 40.0%
CGAACATCACATTTGGTATG+GGG - chr8_3:6629780-6629799 None:intergenic 40.0%
CCGAACATCACATTTGGTAT+GGG - chr8_3:6629781-6629800 None:intergenic 40.0%
CCCATACCAAATGTGATGTT+CGG + chr8_3:6629778-6629797 Msa1272970:CDS 40.0%
TCCGAACATCACATTTGGTA+TGG - chr8_3:6629782-6629801 None:intergenic 40.0%
! CCTTTTCCGAACATCACATT+TGG - chr8_3:6629787-6629806 None:intergenic 40.0%
CCAAATGTGATGTTCGGAAA+AGG + chr8_3:6629784-6629803 Msa1272970:CDS 40.0%
ATGTGATGTTCGGAAAAGGT+TGG + chr8_3:6629788-6629807 Msa1272970:CDS 40.0%
ATCTAATTCCACCAAGGTAC+TGG - chr8_3:6629412-6629431 None:intergenic 40.0%
TGATAGGGTGGATAATCAAC+TGG - chr8_3:6629467-6629486 None:intergenic 40.0%
CGAACATCACATTTGGTATG+GGG - chr8_3:6629780-6629799 None:intergenic 40.0%
CCGAACATCACATTTGGTAT+GGG - chr8_3:6629781-6629800 None:intergenic 40.0%
CCCATACCAAATGTGATGTT+CGG + chr8_3:6629778-6629797 Msa1272970:CDS 40.0%
TCCGAACATCACATTTGGTA+TGG - chr8_3:6629782-6629801 None:intergenic 40.0%
! CCTTTTCCGAACATCACATT+TGG - chr8_3:6629787-6629806 None:intergenic 40.0%
CCAAATGTGATGTTCGGAAA+AGG + chr8_3:6629784-6629803 Msa1272970:CDS 40.0%
ATGTGATGTTCGGAAAAGGT+TGG + chr8_3:6629788-6629807 Msa1272970:CDS 40.0%
! TCTAGCAAGTGCCATTGCTA+CGG - chr8_3:6629269-6629288 None:intergenic 45.0%
! TAGCAATGGCACTTGCTAGA+TGG + chr8_3:6629269-6629288 Msa1272970:five_prime_UTR 45.0%
CTCCAACCATCTGTCAACAA+CGG - chr8_3:6629341-6629360 None:intergenic 45.0%
ATTGCTTTCCAGTACCTTGG+TGG + chr8_3:6629401-6629420 Msa1272970:CDS 45.0%
ACCCTATCATTCCATGAGTG+CGG + chr8_3:6629478-6629497 Msa1272970:CDS 45.0%
!! ACCTTTGAAGTTCCTATCGC+TGG + chr8_3:6629518-6629537 Msa1272970:CDS 45.0%
TCCAGCGATAGGAACTTCAA+AGG - chr8_3:6629522-6629541 None:intergenic 45.0%
GAAGTTCCTATCGCTGGATA+TGG + chr8_3:6629524-6629543 Msa1272970:CDS 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG + chr8_3:6629811-6629830 Msa1272970:CDS 45.0%
TTGTGCTGCCAATGGTATTG+AGG + chr8_3:6629819-6629838 Msa1272970:CDS 45.0%
! TGTGCTGCCAATGGTATTGA+GGG + chr8_3:6629820-6629839 Msa1272970:CDS 45.0%
! TTTCAAGTGCAAGTGCGTCA+TGG + chr8_3:6629858-6629877 Msa1272970:CDS 45.0%
! TCTAGCAAGTGCCATTGCTA+CGG - chr8_3:6629269-6629288 None:intergenic 45.0%
! TAGCAATGGCACTTGCTAGA+TGG + chr8_3:6629269-6629288 Msa1272970:five_prime_UTR 45.0%
CTCCAACCATCTGTCAACAA+CGG - chr8_3:6629341-6629360 None:intergenic 45.0%
ATTGCTTTCCAGTACCTTGG+TGG + chr8_3:6629401-6629420 Msa1272970:CDS 45.0%
ACCCTATCATTCCATGAGTG+CGG + chr8_3:6629478-6629497 Msa1272970:CDS 45.0%
!! ACCTTTGAAGTTCCTATCGC+TGG + chr8_3:6629518-6629537 Msa1272970:CDS 45.0%
TCCAGCGATAGGAACTTCAA+AGG - chr8_3:6629522-6629541 None:intergenic 45.0%
GAAGTTCCTATCGCTGGATA+TGG + chr8_3:6629524-6629543 Msa1272970:CDS 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG + chr8_3:6629811-6629830 Msa1272970:CDS 45.0%
TTGTGCTGCCAATGGTATTG+AGG + chr8_3:6629819-6629838 Msa1272970:CDS 45.0%
! TGTGCTGCCAATGGTATTGA+GGG + chr8_3:6629820-6629839 Msa1272970:CDS 45.0%
! TTTCAAGTGCAAGTGCGTCA+TGG + chr8_3:6629858-6629877 Msa1272970:CDS 45.0%
TCTACGAGCTACCGTAGCAA+TGG + chr8_3:6629255-6629274 Msa1272970:five_prime_UTR 50.0%
! TGGCACTTGCTAGATGGTGA+TGG + chr8_3:6629275-6629294 Msa1272970:five_prime_UTR 50.0%
! GGCACTTGCTAGATGGTGAT+GGG + chr8_3:6629276-6629295 Msa1272970:five_prime_UTR 50.0%
GCACTCATGGAATGATAGGG+TGG - chr8_3:6629479-6629498 None:intergenic 50.0%
GCCGCACTCATGGAATGATA+GGG - chr8_3:6629482-6629501 None:intergenic 50.0%
TGCCGCACTCATGGAATGAT+AGG - chr8_3:6629483-6629502 None:intergenic 50.0%
GACGATCCATATCCAGCGAT+AGG - chr8_3:6629533-6629552 None:intergenic 50.0%
TGGATCGTCGAAATCACCGA+AGG + chr8_3:6629544-6629563 Msa1272970:CDS 50.0%
CACGATTACGTCGTGTTGTG+CGG + chr8_3:6629709-6629728 Msa1272970:CDS 50.0%
TCTACGAGCTACCGTAGCAA+TGG + chr8_3:6629255-6629274 Msa1272970:five_prime_UTR 50.0%
! TGGCACTTGCTAGATGGTGA+TGG + chr8_3:6629275-6629294 Msa1272970:five_prime_UTR 50.0%
! GGCACTTGCTAGATGGTGAT+GGG + chr8_3:6629276-6629295 Msa1272970:five_prime_UTR 50.0%
GCACTCATGGAATGATAGGG+TGG - chr8_3:6629479-6629498 None:intergenic 50.0%
GCCGCACTCATGGAATGATA+GGG - chr8_3:6629482-6629501 None:intergenic 50.0%
TGCCGCACTCATGGAATGAT+AGG - chr8_3:6629483-6629502 None:intergenic 50.0%
GACGATCCATATCCAGCGAT+AGG - chr8_3:6629533-6629552 None:intergenic 50.0%
TGGATCGTCGAAATCACCGA+AGG + chr8_3:6629544-6629563 Msa1272970:CDS 50.0%
CACGATTACGTCGTGTTGTG+CGG + chr8_3:6629709-6629728 Msa1272970:CDS 50.0%
AGTCGGCCGTTGTTGACAGA+TGG + chr8_3:6629332-6629351 Msa1272970:CDS 55.0%
GGCCGTTGTTGACAGATGGT+TGG + chr8_3:6629336-6629355 Msa1272970:CDS 55.0%
! GCTGCCAATGGTATTGAGGG+CGG + chr8_3:6629823-6629842 Msa1272970:CDS 55.0%
GTCTCCGCCCTCAATACCAT+TGG - chr8_3:6629830-6629849 None:intergenic 55.0%
AGTCGGCCGTTGTTGACAGA+TGG + chr8_3:6629332-6629351 Msa1272970:CDS 55.0%
GGCCGTTGTTGACAGATGGT+TGG + chr8_3:6629336-6629355 Msa1272970:CDS 55.0%
! GCTGCCAATGGTATTGAGGG+CGG + chr8_3:6629823-6629842 Msa1272970:CDS 55.0%
GTCTCCGCCCTCAATACCAT+TGG - chr8_3:6629830-6629849 None:intergenic 55.0%
GCACGATGCTGCCGCACTCA+TGG - chr8_3:6629492-6629511 None:intergenic 65.0%
GCACGATGCTGCCGCACTCA+TGG - chr8_3:6629492-6629511 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr8_3 gene 6629113 6629912 6629113 ID=Msa1272970;Name=Msa1272970
chr8_3 mRNA 6629113 6629912 6629113 ID=Msa1272970-mRNA-1;Parent=Msa1272970;Name=Msa1272970-mRNA-1;_AED=0.05;_eAED=0.05;_QI=201|1|0.5|1|1|1|2|0|165
chr8_3 exon 6629113 6629565 6629113 ID=Msa1272970-mRNA-1:exon:2508;Parent=Msa1272970-mRNA-1
chr8_3 exon 6629667 6629912 6629667 ID=Msa1272970-mRNA-1:exon:2509;Parent=Msa1272970-mRNA-1
chr8_3 five_prime_UTR 6629113 6629313 6629113 ID=Msa1272970-mRNA-1:five_prime_utr;Parent=Msa1272970-mRNA-1
chr8_3 CDS 6629314 6629565 6629314 ID=Msa1272970-mRNA-1:cds;Parent=Msa1272970-mRNA-1
chr8_3 CDS 6629667 6629912 6629667 ID=Msa1272970-mRNA-1:cds;Parent=Msa1272970-mRNA-1
Gene Sequence

>Msa1272970

ATGTTCAACAAATCAGTTAGTCGGCCGTTGTTGACAGATGGTTGGAGTGCATTGCGATTATTCTACGAGTTTAGTGGAAGTTTGATTATTGCTTTCCAGTACCTTGGTGGAATTAGATTTCAAATCTTTGTTTTTGCTCATAACATTACTCCAGTTGATTATCCACCCTATCATTCCATGAGTGCGGCAGCATCGTGCTATTGTACCTTTGAAGTTCCTATCGCTGGATATGGATCGTCGAAATCACCGAAGGAACTACCTTATACTTTTGGCAAATTCCTTAGAGTGAAACATCACGATTACGTCGTGTTGTGCGGACCTTATGACAATATCATTCCTGTGAGACTCAAATATACAGACGACCCCATACCAAATGTGATGTTCGGAAAAGGTTGGACGAGTTTTTGTGCTGCCAATGGTATTGAGGGCGGAGACGTGTTGATTTTCAAGTGCAAGTGCGTCATGGACAAAAAATATGTTATCGTATCCAAGCGTTGA
Protein sequence

>Msa1272970

MFNKSVSRPLLTDGWSALRLFYEFSGSLIIAFQYLGGIRFQIFVFAHNITPVDYPPYHSMSAAASCYCTFEVPIAGYGSSKSPKELPYTFGKFLRVKHHDYVVLCGPYDNIIPVRLKYTDDPIPNVMFGKGWTSFCAANGIEGGDVLIFKCKCVMDKKYVIVSKR*