AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1421400

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1421400 MtrunA17_Chr5g0393501 32.530 166 109 1 2 164 76 241 1.21e-26 100
Msa1421400 MtrunA17_Chr4g0044671 28.188 149 107 0 2 150 59 207 5.81e-14 67.0
Msa1421400 MtrunA17_Chr4g0034781 27.517 149 108 0 2 150 53 201 3.77e-13 64.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 46 sgRNAs with CRISPR-Local

Find 110 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAATACATTGTCTAACTTAT+AGG 0.141145 tig0025010:-20881 Msa1421400:five_prime_UTR
CAACAAATTAAATCCTCTTT+TGG 0.252930 tig0025010:-20962 Msa1421400:five_prime_UTR
GAAGTTCATATCGCTGGATA+TGG 0.269440 tig0025010:-20550 Msa1421400:CDS
TAGGAACTACCTTATACTTT+TGG 0.309505 tig0025010:-20410 Msa1421400:CDS
AGGAATTTGCCAAAAGTATA+AGG 0.322050 tig0025010:+20401 None:intergenic
GATCGTGATGTTTCACTCTA+AGG 0.371626 tig0025010:+20381 None:intergenic
CGATTATTCTACGAGTTTAG+TGG 0.386306 tig0025010:-20706 Msa1421400:CDS
ACCTTTGAAGTTCATATCGC+TGG 0.402501 tig0025010:-20556 Msa1421400:CDS
TCCGAACATCACATTTGGTA+TGG 0.417548 tig0025010:+20295 None:intergenic
AGTTAGTCGGCCGTTGTTGA+CGG 0.438454 tig0025010:-20746 Msa1421400:CDS
CCGAACATCACATTTGGTAT+GGG 0.451435 tig0025010:+20296 None:intergenic
GAGCAATGGCACTTCCTAGA+TGG 0.461198 tig0025010:-20805 Msa1421400:five_prime_UTR
TGCCGCACTCATGGAATGAT+AGG 0.462626 tig0025010:+20594 None:intergenic
TTGTGCTGCCAATGGTATTG+AGG 0.463000 tig0025010:-20255 Msa1421400:CDS
AAATATTTAGCAACAAAGAA+TGG 0.465634 tig0025010:+20841 None:intergenic
TGATAGGGTGGATAATTAGC+TGG 0.472671 tig0025010:+20610 None:intergenic
GAGTATTCCCATCACCATCT+AGG 0.474224 tig0025010:+20791 None:intergenic
CCAAATGTGATGTTCGGAAA+AGG 0.475440 tig0025010:-20290 Msa1421400:CDS
CCCATACCAAATGTGATGTT+CGG 0.477035 tig0025010:-20296 Msa1421400:CDS
GTCAAGCGTTTATCAACGCT+TGG 0.478441 tig0025010:+20172 None:intergenic
GGCCGTTGTTGACGGATGGT+TGG 0.485275 tig0025010:-20738 Msa1421400:CDS
GCACGATGCTGCCGCACTCA+TGG 0.495354 tig0025010:+20585 None:intergenic
TGTGCTGCCAATGGTATTGA+GGG 0.501205 tig0025010:-20254 Msa1421400:CDS
TAAATATTTCTACGAGCTAC+CGG 0.507354 tig0025010:-20827 Msa1421400:five_prime_UTR
ATATTAAATCCAACCAAAAG+AGG 0.531474 tig0025010:+20949 None:intergenic
TCTAGGAAGTGCCATTGCTC+CGG 0.534587 tig0025010:+20808 None:intergenic
ACAGGAGTGATATTGTCATA+AGG 0.544509 tig0025010:+20341 None:intergenic
AGTCGGCCGTTGTTGACGGA+TGG 0.547692 tig0025010:-20742 Msa1421400:CDS
TGGCACTTCCTAGATGGTGA+TGG 0.549344 tig0025010:-20799 Msa1421400:five_prime_UTR
CGAACATCACATTTGGTATG+GGG 0.552019 tig0025010:+20297 None:intergenic
TCTGTATATTTGAGTCTCAC+AGG 0.553253 tig0025010:+20323 None:intergenic
TTTCAAGTGCAAATGCGTCA+TGG 0.564910 tig0025010:-20216 Msa1421400:CDS
GGCACTTCCTAGATGGTGAT+GGG 0.565961 tig0025010:-20798 Msa1421400:five_prime_UTR
GTCTCCGCCCTCAATACCAT+TGG 0.581950 tig0025010:+20247 None:intergenic
CACGATCACGTCGTGTTGTG+CGG 0.595062 tig0025010:-20365 Msa1421400:CDS
ATGTGATGTTCGGAAAAGGT+TGG 0.606400 tig0025010:-20286 Msa1421400:CDS
TCCAGCGATATGAACTTCAA+AGG 0.607035 tig0025010:+20555 None:intergenic
TGTTCAACAAATCAGTTAGT+CGG 0.609582 tig0025010:-20759 Msa1421400:CDS
TCTACGAGCTACCGGAGCAA+TGG 0.612965 tig0025010:-20819 Msa1421400:five_prime_UTR
GCCGCACTCATGGAATGATA+GGG 0.629158 tig0025010:+20595 None:intergenic
ACCCTATCATTCCATGAGTG+CGG 0.640367 tig0025010:-20596 Msa1421400:CDS
CTCCAACCATCCGTCAACAA+CGG 0.643466 tig0025010:+20736 None:intergenic
GCACTCATGGAATGATAGGG+TGG 0.649652 tig0025010:+20598 None:intergenic
TTTGAAATCTACTTCCACCA+AGG 0.681040 tig0025010:+20659 None:intergenic
TGGATCGACGAAATCACCGA+AGG 0.700849 tig0025010:-20530 Msa1421400:intron
GCTGCCAATGGTATTGAGGG+CGG 0.739556 tig0025010:-20251 Msa1421400:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAGACAATGTATTAAAAAA+AGG + tig0025010:20271-20290 None:intergenic 15.0%
!! GTTTATATATGCTATAATAA+AGG - tig0025010:20684-20703 Msa1421400:CDS 15.0%
!! TTAGACAATGTATTAAAAAA+AGG + tig0025010:20271-20290 None:intergenic 15.0%
!! GTTTATATATGCTATAATAA+AGG - tig0025010:20684-20703 Msa1421400:CDS 15.0%
!! TAATACATTGTCTAACTTAT+AGG - tig0025010:20276-20295 Msa1421400:CDS 20.0%
!! AAATATTTAGCAACAAAGAA+TGG + tig0025010:20319-20338 None:intergenic 20.0%
!!! TTTTTATGCTATTCATTTAG+AGG - tig0025010:20662-20681 Msa1421400:CDS 20.0%
!! TAATACATTGTCTAACTTAT+AGG - tig0025010:20276-20295 Msa1421400:CDS 20.0%
!! AAATATTTAGCAACAAAGAA+TGG + tig0025010:20319-20338 None:intergenic 20.0%
!!! TTTTTATGCTATTCATTTAG+AGG - tig0025010:20662-20681 Msa1421400:CDS 20.0%
!! CAACAAATTAAATCCTCTTT+TGG - tig0025010:20195-20214 Msa1421400:CDS 25.0%
!! AAATTAAATCCTCTTTTGGT+TGG - tig0025010:20199-20218 Msa1421400:CDS 25.0%
! ATATTAAATCCAACCAAAAG+AGG + tig0025010:20211-20230 None:intergenic 25.0%
! AAAAAACAATACACAACCTT+CGG + tig0025010:20646-20665 None:intergenic 25.0%
!! CAACAAATTAAATCCTCTTT+TGG - tig0025010:20195-20214 Msa1421400:CDS 25.0%
!! AAATTAAATCCTCTTTTGGT+TGG - tig0025010:20199-20218 Msa1421400:CDS 25.0%
! ATATTAAATCCAACCAAAAG+AGG + tig0025010:20211-20230 None:intergenic 25.0%
! AAAAAACAATACACAACCTT+CGG + tig0025010:20646-20665 None:intergenic 25.0%
! TAAATATTTCTACGAGCTAC+CGG - tig0025010:20330-20349 Msa1421400:CDS 30.0%
TGTTCAACAAATCAGTTAGT+CGG - tig0025010:20398-20417 Msa1421400:CDS 30.0%
!! ATTATTGCTTTTCAGTACCT+TGG - tig0025010:20481-20500 Msa1421400:intron 30.0%
! TAGGAACTACCTTATACTTT+TGG - tig0025010:20747-20766 Msa1421400:CDS 30.0%
! AGGAATTTGCCAAAAGTATA+AGG + tig0025010:20759-20778 None:intergenic 30.0%
! TAAATATTTCTACGAGCTAC+CGG - tig0025010:20330-20349 Msa1421400:CDS 30.0%
TGTTCAACAAATCAGTTAGT+CGG - tig0025010:20398-20417 Msa1421400:CDS 30.0%
!! ATTATTGCTTTTCAGTACCT+TGG - tig0025010:20481-20500 Msa1421400:intron 30.0%
! TAGGAACTACCTTATACTTT+TGG - tig0025010:20747-20766 Msa1421400:CDS 30.0%
! AGGAATTTGCCAAAAGTATA+AGG + tig0025010:20759-20778 None:intergenic 30.0%
CGATTATTCTACGAGTTTAG+TGG - tig0025010:20451-20470 Msa1421400:intron 35.0%
! TTTGAAATCTACTTCCACCA+AGG + tig0025010:20501-20520 None:intergenic 35.0%
ACAGGAGTGATATTGTCATA+AGG + tig0025010:20819-20838 None:intergenic 35.0%
TCTGTATATTTGAGTCTCAC+AGG + tig0025010:20837-20856 None:intergenic 35.0%
CGATTATTCTACGAGTTTAG+TGG - tig0025010:20451-20470 Msa1421400:intron 35.0%
! TTTGAAATCTACTTCCACCA+AGG + tig0025010:20501-20520 None:intergenic 35.0%
ACAGGAGTGATATTGTCATA+AGG + tig0025010:20819-20838 None:intergenic 35.0%
TCTGTATATTTGAGTCTCAC+AGG + tig0025010:20837-20856 None:intergenic 35.0%
!! ATTGCTTTTCAGTACCTTGG+TGG - tig0025010:20484-20503 Msa1421400:intron 40.0%
TGATAGGGTGGATAATTAGC+TGG + tig0025010:20550-20569 None:intergenic 40.0%
!! ACCTTTGAAGTTCATATCGC+TGG - tig0025010:20601-20620 Msa1421400:CDS 40.0%
TCCAGCGATATGAACTTCAA+AGG + tig0025010:20605-20624 None:intergenic 40.0%
GAAGTTCATATCGCTGGATA+TGG - tig0025010:20607-20626 Msa1421400:CDS 40.0%
GATCGTGATGTTTCACTCTA+AGG + tig0025010:20779-20798 None:intergenic 40.0%
CGAACATCACATTTGGTATG+GGG + tig0025010:20863-20882 None:intergenic 40.0%
CCGAACATCACATTTGGTAT+GGG + tig0025010:20864-20883 None:intergenic 40.0%
CCCATACCAAATGTGATGTT+CGG - tig0025010:20861-20880 Msa1421400:five_prime_UTR 40.0%
TCCGAACATCACATTTGGTA+TGG + tig0025010:20865-20884 None:intergenic 40.0%
! CCTTTTCCGAACATCACATT+TGG + tig0025010:20870-20889 None:intergenic 40.0%
CCAAATGTGATGTTCGGAAA+AGG - tig0025010:20867-20886 Msa1421400:five_prime_UTR 40.0%
ATGTGATGTTCGGAAAAGGT+TGG - tig0025010:20871-20890 Msa1421400:five_prime_UTR 40.0%
! TTTCAAGTGCAAATGCGTCA+TGG - tig0025010:20941-20960 Msa1421400:five_prime_UTR 40.0%
!! ATTGCTTTTCAGTACCTTGG+TGG - tig0025010:20484-20503 Msa1421400:intron 40.0%
TGATAGGGTGGATAATTAGC+TGG + tig0025010:20550-20569 None:intergenic 40.0%
!! ACCTTTGAAGTTCATATCGC+TGG - tig0025010:20601-20620 Msa1421400:CDS 40.0%
TCCAGCGATATGAACTTCAA+AGG + tig0025010:20605-20624 None:intergenic 40.0%
GAAGTTCATATCGCTGGATA+TGG - tig0025010:20607-20626 Msa1421400:CDS 40.0%
GATCGTGATGTTTCACTCTA+AGG + tig0025010:20779-20798 None:intergenic 40.0%
CGAACATCACATTTGGTATG+GGG + tig0025010:20863-20882 None:intergenic 40.0%
CCGAACATCACATTTGGTAT+GGG + tig0025010:20864-20883 None:intergenic 40.0%
CCCATACCAAATGTGATGTT+CGG - tig0025010:20861-20880 Msa1421400:five_prime_UTR 40.0%
TCCGAACATCACATTTGGTA+TGG + tig0025010:20865-20884 None:intergenic 40.0%
! CCTTTTCCGAACATCACATT+TGG + tig0025010:20870-20889 None:intergenic 40.0%
CCAAATGTGATGTTCGGAAA+AGG - tig0025010:20867-20886 Msa1421400:five_prime_UTR 40.0%
ATGTGATGTTCGGAAAAGGT+TGG - tig0025010:20871-20890 Msa1421400:five_prime_UTR 40.0%
! TTTCAAGTGCAAATGCGTCA+TGG - tig0025010:20941-20960 Msa1421400:five_prime_UTR 40.0%
GAGTATTCCCATCACCATCT+AGG + tig0025010:20369-20388 None:intergenic 45.0%
ACCCTATCATTCCATGAGTG+CGG - tig0025010:20561-20580 Msa1421400:CDS 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG - tig0025010:20894-20913 Msa1421400:five_prime_UTR 45.0%
TTGTGCTGCCAATGGTATTG+AGG - tig0025010:20902-20921 Msa1421400:five_prime_UTR 45.0%
! TGTGCTGCCAATGGTATTGA+GGG - tig0025010:20903-20922 Msa1421400:five_prime_UTR 45.0%
GAGTATTCCCATCACCATCT+AGG + tig0025010:20369-20388 None:intergenic 45.0%
ACCCTATCATTCCATGAGTG+CGG - tig0025010:20561-20580 Msa1421400:CDS 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG - tig0025010:20894-20913 Msa1421400:five_prime_UTR 45.0%
TTGTGCTGCCAATGGTATTG+AGG - tig0025010:20902-20921 Msa1421400:five_prime_UTR 45.0%
! TGTGCTGCCAATGGTATTGA+GGG - tig0025010:20903-20922 Msa1421400:five_prime_UTR 45.0%
!!! TTTTTTTTTCTTTTTTTTTT+AGG - tig0025010:20728-20747 Msa1421400:CDS 5.0%
!!! TTTTTTTTTCTTTTTTTTTT+AGG - tig0025010:20728-20747 Msa1421400:CDS 5.0%
!! TCTAGGAAGTGCCATTGCTC+CGG + tig0025010:20352-20371 None:intergenic 50.0%
GAGCAATGGCACTTCCTAGA+TGG - tig0025010:20352-20371 Msa1421400:CDS 50.0%
TGGCACTTCCTAGATGGTGA+TGG - tig0025010:20358-20377 Msa1421400:CDS 50.0%
GGCACTTCCTAGATGGTGAT+GGG - tig0025010:20359-20378 Msa1421400:CDS 50.0%
AGTTAGTCGGCCGTTGTTGA+CGG - tig0025010:20411-20430 Msa1421400:intron 50.0%
CTCCAACCATCCGTCAACAA+CGG + tig0025010:20424-20443 None:intergenic 50.0%
GCACTCATGGAATGATAGGG+TGG + tig0025010:20562-20581 None:intergenic 50.0%
GCCGCACTCATGGAATGATA+GGG + tig0025010:20565-20584 None:intergenic 50.0%
TGCCGCACTCATGGAATGAT+AGG + tig0025010:20566-20585 None:intergenic 50.0%
TGGATCGACGAAATCACCGA+AGG - tig0025010:20627-20646 Msa1421400:CDS 50.0%
!! TCTAGGAAGTGCCATTGCTC+CGG + tig0025010:20352-20371 None:intergenic 50.0%
GAGCAATGGCACTTCCTAGA+TGG - tig0025010:20352-20371 Msa1421400:CDS 50.0%
TGGCACTTCCTAGATGGTGA+TGG - tig0025010:20358-20377 Msa1421400:CDS 50.0%
GGCACTTCCTAGATGGTGAT+GGG - tig0025010:20359-20378 Msa1421400:CDS 50.0%
AGTTAGTCGGCCGTTGTTGA+CGG - tig0025010:20411-20430 Msa1421400:intron 50.0%
CTCCAACCATCCGTCAACAA+CGG + tig0025010:20424-20443 None:intergenic 50.0%
GCACTCATGGAATGATAGGG+TGG + tig0025010:20562-20581 None:intergenic 50.0%
GCCGCACTCATGGAATGATA+GGG + tig0025010:20565-20584 None:intergenic 50.0%
TGCCGCACTCATGGAATGAT+AGG + tig0025010:20566-20585 None:intergenic 50.0%
TGGATCGACGAAATCACCGA+AGG - tig0025010:20627-20646 Msa1421400:CDS 50.0%
TCTACGAGCTACCGGAGCAA+TGG - tig0025010:20338-20357 Msa1421400:CDS 55.0%
CACGATCACGTCGTGTTGTG+CGG - tig0025010:20792-20811 Msa1421400:five_prime_UTR 55.0%
! GCTGCCAATGGTATTGAGGG+CGG - tig0025010:20906-20925 Msa1421400:five_prime_UTR 55.0%
GTCTCCGCCCTCAATACCAT+TGG + tig0025010:20913-20932 None:intergenic 55.0%
TCTACGAGCTACCGGAGCAA+TGG - tig0025010:20338-20357 Msa1421400:CDS 55.0%
CACGATCACGTCGTGTTGTG+CGG - tig0025010:20792-20811 Msa1421400:five_prime_UTR 55.0%
! GCTGCCAATGGTATTGAGGG+CGG - tig0025010:20906-20925 Msa1421400:five_prime_UTR 55.0%
GTCTCCGCCCTCAATACCAT+TGG + tig0025010:20913-20932 None:intergenic 55.0%
AGTCGGCCGTTGTTGACGGA+TGG - tig0025010:20415-20434 Msa1421400:intron 60.0%
! GGCCGTTGTTGACGGATGGT+TGG - tig0025010:20419-20438 Msa1421400:intron 60.0%
AGTCGGCCGTTGTTGACGGA+TGG - tig0025010:20415-20434 Msa1421400:intron 60.0%
! GGCCGTTGTTGACGGATGGT+TGG - tig0025010:20419-20438 Msa1421400:intron 60.0%
GCACGATGCTGCCGCACTCA+TGG + tig0025010:20575-20594 None:intergenic 65.0%
GCACGATGCTGCCGCACTCA+TGG + tig0025010:20575-20594 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
tig0025010 gene 20184 20995 20184 ID=Msa1421400;Name=Msa1421400
tig0025010 mRNA 20184 20995 20184 ID=Msa1421400-mRNA-1;Parent=Msa1421400;Name=Msa1421400-mRNA-1;_AED=0.05;_eAED=0.05;_QI=213|1|0.5|1|1|1|2|0|165
tig0025010 exon 20184 20429 20184 ID=Msa1421400-mRNA-1:exon:2093;Parent=Msa1421400-mRNA-1
tig0025010 exon 20531 20995 20531 ID=Msa1421400-mRNA-1:exon:2092;Parent=Msa1421400-mRNA-1
tig0025010 five_prime_UTR 20783 20995 20783 ID=Msa1421400-mRNA-1:five_prime_utr;Parent=Msa1421400-mRNA-1
tig0025010 CDS 20531 20782 20531 ID=Msa1421400-mRNA-1:cds;Parent=Msa1421400-mRNA-1
tig0025010 CDS 20184 20429 20184 ID=Msa1421400-mRNA-1:cds;Parent=Msa1421400-mRNA-1
Gene Sequence

>Msa1421400

ATGTTCAACAAATCAGTTAGTCGGCCGTTGTTGACGGATGGTTGGAGTGCATTGCGATTATTCTACGAGTTTAGTGGAAGTAAGATTATTGCTTTTCAGTACCTTGGTGGAAGTAGATTTCAAATCTTTGTTTTTGCTCATAACATTACTCCAGCTAATTATCCACCCTATCATTCCATGAGTGCGGCAGCATCGTGCTATTGTACCTTTGAAGTTCATATCGCTGGATATGGATCGACGAAATCACCGAAGGAACTACCTTATACTTTTGGCAAATTCCTTAGAGTGAAACATCACGATCACGTCGTGTTGTGCGGACCTTATGACAATATCACTCCTGTGAGACTCAAATATACAGACGACCCCATACCAAATGTGATGTTCGGAAAAGGTTGGACGAGTTTTTGTGCTGCCAATGGTATTGAGGGCGGAGACGTGTTGATTTTCAAGTGCAAATGCGTCATGGACAAAAAATATGTTATCGTATCCAAGCGTTGA
Protein sequence

>Msa1421400

MFNKSVSRPLLTDGWSALRLFYEFSGSKIIAFQYLGGSRFQIFVFAHNITPANYPPYHSMSAAASCYCTFEVHIAGYGSTKSPKELPYTFGKFLRVKHHDHVVLCGPYDNITPVRLKYTDDPIPNVMFGKGWTSFCAANGIEGGDVLIFKCKCVMDKKYVIVSKR*