AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0998750

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0998750 MtrunA17_Chr5g0393501 30.120 166 101 3 2 152 76 241 1.19e-19 82.0
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
TAATACACTGTCTAACTTCT+AGG 0.168588 6_4:+80043673 Msa0998750:five_prime_UTR
ATGAAAATTAAATCCTCTTT+TGG 0.264170 6_4:+80043592 Msa0998750:five_prime_UTR
TTGAAGTTCCTATCTGGATA+TGG 0.289906 6_4:+80044002 Msa0998750:CDS
GTACCTTTGAAGTTCCTATC+TGG 0.333773 6_4:+80043996 Msa0998750:CDS
CGATTATTCTACGAGTTTAG+TGG 0.386306 6_4:+80043848 Msa0998750:CDS
TCCGAACATCACATTTGGTA+TGG 0.417548 6_4:-80044254 None:intergenic
ATCTACTTCCACCAAGGTAC+TGG 0.428620 6_4:-80043889 None:intergenic
GAGCAATGGCACTTGCTAGA+TGG 0.450654 6_4:+80043749 Msa0998750:five_prime_UTR
CCGAACATCACATTTGGTAT+GGG 0.451435 6_4:-80044253 None:intergenic
TGCCGCACTCATGGAATGAT+AGG 0.462626 6_4:-80043960 None:intergenic
TTGTGCTGCCAATGGTATTG+AGG 0.463000 6_4:+80044294 Msa0998750:CDS
AAATATTTAGCAACGAAGAA+TGG 0.465634 6_4:-80043713 None:intergenic
TGATAGGGTGGATAATCAAC+TGG 0.472004 6_4:-80043944 None:intergenic
CCAAATGTGATGTTCGGAAA+AGG 0.475440 6_4:+80044259 Msa0998750:CDS
CCCATACCAAATGTGATGTT+CGG 0.477035 6_4:+80044253 Msa0998750:CDS
TCGTCGATCCATATCCAGAT+AGG 0.486078 6_4:-80044010 None:intergenic
GGCCGTTGTTGACAGATGGT+TGG 0.487397 6_4:+80043816 Msa0998750:CDS
ACACGATGCTGCCGCACTCA+TGG 0.487735 6_4:-80043969 None:intergenic
GTCATGCGTTTATCAACGCT+TGG 0.494559 6_4:-80044377 None:intergenic
TGTGCTGCCAATGGTATTGA+GGG 0.501205 6_4:+80044295 Msa0998750:CDS
ATTATTGCTTTCCAGTACCT+TGG 0.503165 6_4:+80043878 Msa0998750:CDS
TAAATATTTCTATGAGCTGC+CGG 0.503453 6_4:+80043727 Msa0998750:five_prime_UTR
TCTAGCAAGTGCCATTGCTC+CGG 0.526455 6_4:-80043746 None:intergenic
ACAGGAATGATATTGTCATA+AGG 0.528831 6_4:-80044208 None:intergenic
AGTCGGCCGTTGTTGACAGA+TGG 0.531450 6_4:+80043812 Msa0998750:CDS
ATATTAAATCCAACCAAAAG+AGG 0.531474 6_4:-80043605 None:intergenic
ATTGCTTTCCAGTACCTTGG+TGG 0.549152 6_4:+80043881 Msa0998750:CDS
CGAACATCACATTTGGTATG+GGG 0.552019 6_4:-80044252 None:intergenic
TCTGTATATTTGAGTCTCAC+AGG 0.555272 6_4:-80044226 None:intergenic
TCTATGAGCTGCCGGAGCAA+TGG 0.563067 6_4:+80043735 Msa0998750:five_prime_UTR
TTTCAAGTGCAAGTGCGTCA+TGG 0.567746 6_4:+80044333 Msa0998750:CDS
TGGATCGACGAAATCATTGA+AGG 0.568346 6_4:+80044022 Msa0998750:CDS
CTGTCTAACTTCTAGGATGT+CGG 0.570416 6_4:+80043680 Msa0998750:five_prime_UTR
GTCTCCGCCCTCAATACCAT+TGG 0.581950 6_4:-80044302 None:intergenic
GGCACTTGCTAGATGGTGAT+GGG 0.587848 6_4:+80043756 Msa0998750:five_prime_UTR
CACGATTACGTCATGTTGTG+CGG 0.590860 6_4:+80044184 Msa0998750:CDS
TGGCACTTGCTAGATGGTGA+TGG 0.594754 6_4:+80043755 Msa0998750:five_prime_UTR
TATCCAGATAGGAACTTCAA+AGG 0.596572 6_4:-80043999 None:intergenic
ATGTGATGTTCGGAAAAGGT+TGG 0.606400 6_4:+80044263 Msa0998750:CDS
TGTTCAACAAATCAGTTAGT+CGG 0.609582 6_4:+80043795 Msa0998750:CDS
GCCGCACTCATGGAATGATA+GGG 0.629158 6_4:-80043959 None:intergenic
ACCCTATCATTCCATGAGTG+CGG 0.640367 6_4:+80043958 Msa0998750:CDS
GCACTCATGGAATGATAGGG+TGG 0.649652 6_4:-80043956 None:intergenic
CTCCAACCATCTGTCAACAA+CGG 0.679074 6_4:-80043818 None:intergenic
TTTGAAATCTACTTCCACCA+AGG 0.681040 6_4:-80043895 None:intergenic
GCTGCCAATGGTATTGAGGG+CGG 0.739556 6_4:+80044298 Msa0998750:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTTATATATGCTATAATAA+AGG + chr6_4:80044079-80044098 Msa0998750:intron 10.0%
!! ATTTATATATGCTATAATAA+AGG + chr6_4:80044079-80044098 Msa0998750:intron 10.0%
!!! CAATTTTTTTTTCTTCTTTT+AGG + chr6_4:80044120-80044139 Msa0998750:intron 15.0%
!!! CAATTTTTTTTTCTTCTTTT+AGG + chr6_4:80044120-80044139 Msa0998750:intron 15.0%
!!! ATGAAAATTAAATCCTCTTT+TGG + chr6_4:80043592-80043611 Msa0998750:five_prime_UTR 20.0%
!! TTAGACAGTGTATTAAAAAA+GGG - chr6_4:80043668-80043687 None:intergenic 20.0%
!!! ATGAAAATTAAATCCTCTTT+TGG + chr6_4:80043592-80043611 Msa0998750:five_prime_UTR 20.0%
!! TTAGACAGTGTATTAAAAAA+GGG - chr6_4:80043668-80043687 None:intergenic 20.0%
!! AAATTAAATCCTCTTTTGGT+TGG + chr6_4:80043596-80043615 Msa0998750:five_prime_UTR 25.0%
! ATATTAAATCCAACCAAAAG+AGG - chr6_4:80043608-80043627 None:intergenic 25.0%
! GTTAGACAGTGTATTAAAAA+AGG - chr6_4:80043669-80043688 None:intergenic 25.0%
! AAATATTTAGCAACGAAGAA+TGG - chr6_4:80043716-80043735 None:intergenic 25.0%
!! AAATTAAATCCTCTTTTGGT+TGG + chr6_4:80043596-80043615 Msa0998750:five_prime_UTR 25.0%
! ATATTAAATCCAACCAAAAG+AGG - chr6_4:80043608-80043627 None:intergenic 25.0%
! GTTAGACAGTGTATTAAAAA+AGG - chr6_4:80043669-80043688 None:intergenic 25.0%
! AAATATTTAGCAACGAAGAA+TGG - chr6_4:80043716-80043735 None:intergenic 25.0%
TAATACACTGTCTAACTTCT+AGG + chr6_4:80043673-80043692 Msa0998750:five_prime_UTR 30.0%
! TAAATATTTCTATGAGCTGC+CGG + chr6_4:80043727-80043746 Msa0998750:five_prime_UTR 30.0%
TGTTCAACAAATCAGTTAGT+CGG + chr6_4:80043795-80043814 Msa0998750:CDS 30.0%
AATCGTGATGTTTCACTATA+AGG - chr6_4:80044171-80044190 None:intergenic 30.0%
ACAGGAATGATATTGTCATA+AGG - chr6_4:80044211-80044230 None:intergenic 30.0%
TAATACACTGTCTAACTTCT+AGG + chr6_4:80043673-80043692 Msa0998750:five_prime_UTR 30.0%
! TAAATATTTCTATGAGCTGC+CGG + chr6_4:80043727-80043746 Msa0998750:five_prime_UTR 30.0%
TGTTCAACAAATCAGTTAGT+CGG + chr6_4:80043795-80043814 Msa0998750:CDS 30.0%
AATCGTGATGTTTCACTATA+AGG - chr6_4:80044171-80044190 None:intergenic 30.0%
ACAGGAATGATATTGTCATA+AGG - chr6_4:80044211-80044230 None:intergenic 30.0%
CGATTATTCTACGAGTTTAG+TGG + chr6_4:80043848-80043867 Msa0998750:CDS 35.0%
ATTATTGCTTTCCAGTACCT+TGG + chr6_4:80043878-80043897 Msa0998750:CDS 35.0%
! TTTGAAATCTACTTCCACCA+AGG - chr6_4:80043898-80043917 None:intergenic 35.0%
TATCCAGATAGGAACTTCAA+AGG - chr6_4:80044002-80044021 None:intergenic 35.0%
TTGAAGTTCCTATCTGGATA+TGG + chr6_4:80044002-80044021 Msa0998750:CDS 35.0%
TAGGAACTACCTGATACTTT+CGG + chr6_4:80044139-80044158 Msa0998750:intron 35.0%
TCTGTATATTTGAGTCTCAC+AGG - chr6_4:80044229-80044248 None:intergenic 35.0%
CGATTATTCTACGAGTTTAG+TGG + chr6_4:80043848-80043867 Msa0998750:CDS 35.0%
ATTATTGCTTTCCAGTACCT+TGG + chr6_4:80043878-80043897 Msa0998750:CDS 35.0%
! TTTGAAATCTACTTCCACCA+AGG - chr6_4:80043898-80043917 None:intergenic 35.0%
TATCCAGATAGGAACTTCAA+AGG - chr6_4:80044002-80044021 None:intergenic 35.0%
TTGAAGTTCCTATCTGGATA+TGG + chr6_4:80044002-80044021 Msa0998750:CDS 35.0%
TAGGAACTACCTGATACTTT+CGG + chr6_4:80044139-80044158 Msa0998750:intron 35.0%
TCTGTATATTTGAGTCTCAC+AGG - chr6_4:80044229-80044248 None:intergenic 35.0%
!! CTGTCTAACTTCTAGGATGT+CGG + chr6_4:80043680-80043699 Msa0998750:five_prime_UTR 40.0%
TGATAGGGTGGATAATCAAC+TGG - chr6_4:80043947-80043966 None:intergenic 40.0%
!! GTACCTTTGAAGTTCCTATC+TGG + chr6_4:80043996-80044015 Msa0998750:CDS 40.0%
TGGATCGACGAAATCATTGA+AGG + chr6_4:80044022-80044041 Msa0998750:CDS 40.0%
!! AGGAATTTGCCGAAAGTATC+AGG - chr6_4:80044151-80044170 None:intergenic 40.0%
CGAACATCACATTTGGTATG+GGG - chr6_4:80044255-80044274 None:intergenic 40.0%
CCGAACATCACATTTGGTAT+GGG - chr6_4:80044256-80044275 None:intergenic 40.0%
CCCATACCAAATGTGATGTT+CGG + chr6_4:80044253-80044272 Msa0998750:CDS 40.0%
TCCGAACATCACATTTGGTA+TGG - chr6_4:80044257-80044276 None:intergenic 40.0%
! CCTTTTCCGAACATCACATT+TGG - chr6_4:80044262-80044281 None:intergenic 40.0%
CCAAATGTGATGTTCGGAAA+AGG + chr6_4:80044259-80044278 Msa0998750:CDS 40.0%
ATGTGATGTTCGGAAAAGGT+TGG + chr6_4:80044263-80044282 Msa0998750:CDS 40.0%
!! CTGTCTAACTTCTAGGATGT+CGG + chr6_4:80043680-80043699 Msa0998750:five_prime_UTR 40.0%
TGATAGGGTGGATAATCAAC+TGG - chr6_4:80043947-80043966 None:intergenic 40.0%
!! GTACCTTTGAAGTTCCTATC+TGG + chr6_4:80043996-80044015 Msa0998750:CDS 40.0%
TGGATCGACGAAATCATTGA+AGG + chr6_4:80044022-80044041 Msa0998750:CDS 40.0%
!! AGGAATTTGCCGAAAGTATC+AGG - chr6_4:80044151-80044170 None:intergenic 40.0%
CGAACATCACATTTGGTATG+GGG - chr6_4:80044255-80044274 None:intergenic 40.0%
CCGAACATCACATTTGGTAT+GGG - chr6_4:80044256-80044275 None:intergenic 40.0%
CCCATACCAAATGTGATGTT+CGG + chr6_4:80044253-80044272 Msa0998750:CDS 40.0%
TCCGAACATCACATTTGGTA+TGG - chr6_4:80044257-80044276 None:intergenic 40.0%
! CCTTTTCCGAACATCACATT+TGG - chr6_4:80044262-80044281 None:intergenic 40.0%
CCAAATGTGATGTTCGGAAA+AGG + chr6_4:80044259-80044278 Msa0998750:CDS 40.0%
ATGTGATGTTCGGAAAAGGT+TGG + chr6_4:80044263-80044282 Msa0998750:CDS 40.0%
CTCCAACCATCTGTCAACAA+CGG - chr6_4:80043821-80043840 None:intergenic 45.0%
ATTGCTTTCCAGTACCTTGG+TGG + chr6_4:80043881-80043900 Msa0998750:CDS 45.0%
ATCTACTTCCACCAAGGTAC+TGG - chr6_4:80043892-80043911 None:intergenic 45.0%
ACCCTATCATTCCATGAGTG+CGG + chr6_4:80043958-80043977 Msa0998750:CDS 45.0%
TCGTCGATCCATATCCAGAT+AGG - chr6_4:80044013-80044032 None:intergenic 45.0%
CACGATTACGTCATGTTGTG+CGG + chr6_4:80044184-80044203 Msa0998750:CDS 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG + chr6_4:80044286-80044305 Msa0998750:CDS 45.0%
TTGTGCTGCCAATGGTATTG+AGG + chr6_4:80044294-80044313 Msa0998750:CDS 45.0%
! TGTGCTGCCAATGGTATTGA+GGG + chr6_4:80044295-80044314 Msa0998750:CDS 45.0%
! TTTCAAGTGCAAGTGCGTCA+TGG + chr6_4:80044333-80044352 Msa0998750:CDS 45.0%
CTCCAACCATCTGTCAACAA+CGG - chr6_4:80043821-80043840 None:intergenic 45.0%
ATTGCTTTCCAGTACCTTGG+TGG + chr6_4:80043881-80043900 Msa0998750:CDS 45.0%
ATCTACTTCCACCAAGGTAC+TGG - chr6_4:80043892-80043911 None:intergenic 45.0%
ACCCTATCATTCCATGAGTG+CGG + chr6_4:80043958-80043977 Msa0998750:CDS 45.0%
TCGTCGATCCATATCCAGAT+AGG - chr6_4:80044013-80044032 None:intergenic 45.0%
CACGATTACGTCATGTTGTG+CGG + chr6_4:80044184-80044203 Msa0998750:CDS 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG + chr6_4:80044286-80044305 Msa0998750:CDS 45.0%
TTGTGCTGCCAATGGTATTG+AGG + chr6_4:80044294-80044313 Msa0998750:CDS 45.0%
! TGTGCTGCCAATGGTATTGA+GGG + chr6_4:80044295-80044314 Msa0998750:CDS 45.0%
! TTTCAAGTGCAAGTGCGTCA+TGG + chr6_4:80044333-80044352 Msa0998750:CDS 45.0%
! TCTAGCAAGTGCCATTGCTC+CGG - chr6_4:80043749-80043768 None:intergenic 50.0%
! GAGCAATGGCACTTGCTAGA+TGG + chr6_4:80043749-80043768 Msa0998750:five_prime_UTR 50.0%
! TGGCACTTGCTAGATGGTGA+TGG + chr6_4:80043755-80043774 Msa0998750:five_prime_UTR 50.0%
! GGCACTTGCTAGATGGTGAT+GGG + chr6_4:80043756-80043775 Msa0998750:five_prime_UTR 50.0%
GCACTCATGGAATGATAGGG+TGG - chr6_4:80043959-80043978 None:intergenic 50.0%
GCCGCACTCATGGAATGATA+GGG - chr6_4:80043962-80043981 None:intergenic 50.0%
TGCCGCACTCATGGAATGAT+AGG - chr6_4:80043963-80043982 None:intergenic 50.0%
! TCTAGCAAGTGCCATTGCTC+CGG - chr6_4:80043749-80043768 None:intergenic 50.0%
! GAGCAATGGCACTTGCTAGA+TGG + chr6_4:80043749-80043768 Msa0998750:five_prime_UTR 50.0%
! TGGCACTTGCTAGATGGTGA+TGG + chr6_4:80043755-80043774 Msa0998750:five_prime_UTR 50.0%
! GGCACTTGCTAGATGGTGAT+GGG + chr6_4:80043756-80043775 Msa0998750:five_prime_UTR 50.0%
GCACTCATGGAATGATAGGG+TGG - chr6_4:80043959-80043978 None:intergenic 50.0%
GCCGCACTCATGGAATGATA+GGG - chr6_4:80043962-80043981 None:intergenic 50.0%
TGCCGCACTCATGGAATGAT+AGG - chr6_4:80043963-80043982 None:intergenic 50.0%
TCTATGAGCTGCCGGAGCAA+TGG + chr6_4:80043735-80043754 Msa0998750:five_prime_UTR 55.0%
AGTCGGCCGTTGTTGACAGA+TGG + chr6_4:80043812-80043831 Msa0998750:CDS 55.0%
GGCCGTTGTTGACAGATGGT+TGG + chr6_4:80043816-80043835 Msa0998750:CDS 55.0%
! GCTGCCAATGGTATTGAGGG+CGG + chr6_4:80044298-80044317 Msa0998750:CDS 55.0%
GTCTCCGCCCTCAATACCAT+TGG - chr6_4:80044305-80044324 None:intergenic 55.0%
TCTATGAGCTGCCGGAGCAA+TGG + chr6_4:80043735-80043754 Msa0998750:five_prime_UTR 55.0%
AGTCGGCCGTTGTTGACAGA+TGG + chr6_4:80043812-80043831 Msa0998750:CDS 55.0%
GGCCGTTGTTGACAGATGGT+TGG + chr6_4:80043816-80043835 Msa0998750:CDS 55.0%
! GCTGCCAATGGTATTGAGGG+CGG + chr6_4:80044298-80044317 Msa0998750:CDS 55.0%
GTCTCCGCCCTCAATACCAT+TGG - chr6_4:80044305-80044324 None:intergenic 55.0%
ACACGATGCTGCCGCACTCA+TGG - chr6_4:80043972-80043991 None:intergenic 60.0%
ACACGATGCTGCCGCACTCA+TGG - chr6_4:80043972-80043991 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr6_4 gene 80043580 80044387 80043580 ID=Msa0998750;Name=Msa0998750
chr6_4 mRNA 80043580 80044387 80043580 ID=Msa0998750-mRNA-1;Parent=Msa0998750;Name=Msa0998750-mRNA-1;_AED=0.12;_eAED=0.12;_QI=214|0|0.5|1|1|1|2|0|153
chr6_4 exon 80043580 80044043 80043580 ID=Msa0998750-mRNA-1:exon:15176;Parent=Msa0998750-mRNA-1
chr6_4 exon 80044176 80044387 80044176 ID=Msa0998750-mRNA-1:exon:15177;Parent=Msa0998750-mRNA-1
chr6_4 five_prime_UTR 80043580 80043793 80043580 ID=Msa0998750-mRNA-1:five_prime_utr;Parent=Msa0998750-mRNA-1
chr6_4 CDS 80043794 80044043 80043794 ID=Msa0998750-mRNA-1:cds;Parent=Msa0998750-mRNA-1
chr6_4 CDS 80044176 80044387 80044176 ID=Msa0998750-mRNA-1:cds;Parent=Msa0998750-mRNA-1
Gene Sequence

>Msa0998750

ATGTTCAACAAATCAGTTAGTCGGCCGTTGTTGACAGATGGTTGGAGTGCATTGCGATTATTCTACGAGTTTAGTGGAAGTAAGATTATTGCTTTCCAGTACCTTGGTGGAAGTAGATTTCAAATCTTTGTTTTTGCTTATAACATTACTCCAGTTGATTATCCACCCTATCATTCCATGAGTGCGGCAGCATCGTGTTATTGTACCTTTGAAGTTCCTATCTGGATATGGATCGACGAAATCATTGAAGTGAAACATCACGATTACGTCATGTTGTGCGGACCTTATGACAATATCATTCCTGTGAGACTCAAATATACAGACGACCCCATACCAAATGTGATGTTCGGAAAAGGTTGGACGAGTTTTTGTGCTGCCAATGGTATTGAGGGCGGAGACGTGTTGATTTTCAAGTGCAAGTGCGTCATGGACAAAAAATATGTTATCGTATCCAAGCGTTGA
Protein sequence

>Msa0998750

MFNKSVSRPLLTDGWSALRLFYEFSGSKIIAFQYLGGSRFQIFVFAYNITPVDYPPYHSMSAAASCYCTFEVPIWIWIDEIIEVKHHDYVMLCGPYDNIIPVRLKYTDDPIPNVMFGKGWTSFCAANGIEGGDVLIFKCKCVMDKKYVIVSKR*