AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0087670


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 45 sgRNAs with CRISPR-Local

Find 105 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAGATTAACCAACAAGAATT+TGG 0.215065 1_2:-68615804 Msa0087670:five_prime_UTR
AGTTCACTTTCTCAACGTTT+TGG 0.264629 1_2:+68615061 None:intergenic
TGAAGGTGATTCTTGTGTTT+TGG 0.303850 1_2:-68615886 Msa0087670:five_prime_UTR
TTGCACCTACAGTTTCATTA+TGG 0.321692 1_2:-68614554 Msa0087670:three_prime_UTR
ACTGTTGGTGTCGGTGTTGC+TGG 0.340769 1_2:-68615653 Msa0087670:CDS
TTAGTGTTCTGGTGCAAATC+AGG 0.390681 1_2:-68614721 Msa0087670:intron
TGTGTTGAGATTTAGTGTTC+TGG 0.393710 1_2:-68614732 Msa0087670:three_prime_UTR
CGATGTCGGCGAAGTTAGTT+CGG 0.393719 1_2:-68615699 Msa0087670:CDS
TTCATCACATTGGCAATCAT+TGG 0.396788 1_2:+68613771 None:intergenic
TCCATTTGCACCTACACTCC+TGG 0.409884 1_2:-68614579 Msa0087670:three_prime_UTR
GAAATGAAACATTGTTCTAA+AGG 0.420124 1_2:-68614515 Msa0087670:intron
AGAAAGTGAACTGGGAAACT+TGG 0.423349 1_2:-68615050 Msa0087670:CDS
TATTGCTCTGGTTGTACTCT+CGG 0.424030 1_2:-68615630 Msa0087670:CDS
CTTAAGAAGTGTAATTATGA+AGG 0.426449 1_2:-68615748 Msa0087670:five_prime_UTR
ACCAGGAGTGTAGGTGCAAA+TGG 0.432206 1_2:+68614578 None:intergenic
CGGTGTTGCTGGTATTGCTC+TGG 0.450550 1_2:-68615642 Msa0087670:CDS
TGGTTAATCTCATATACTTA+CGG 0.460145 1_2:+68615816 None:intergenic
TGAGGTGGTTTCCTATGATA+TGG 0.460675 1_2:-68614755 Msa0087670:three_prime_UTR
TTATGGCAAGTGACAAGATC+AGG 0.462078 1_2:-68614537 Msa0087670:three_prime_UTR
ATCTCAACACACCATATCAT+AGG 0.464654 1_2:+68614744 None:intergenic
CATTTCCCTCATCAACATAT+CGG 0.470848 1_2:-68615199 Msa0087670:CDS
AAAACGTTGAGAAAGTGAAC+TGG 0.473660 1_2:-68615059 Msa0087670:CDS
AACGCTAATGTTATCACTGT+TGG 0.479387 1_2:-68615668 Msa0087670:CDS
CTCATCAACATATCGGCATC+AGG 0.481451 1_2:-68615192 Msa0087670:intron
GCAGTTATCAACATCTTCGT+TGG 0.491361 1_2:-68615236 Msa0087670:intron
ACTTCTTAAGCATCTTTACA+AGG 0.508307 1_2:+68615761 None:intergenic
GTTGGATGCCAAATTCTTGT+TGG 0.510438 1_2:+68615796 None:intergenic
CAGGCATAAGCAAGTGATGT+AGG 0.512448 1_2:-68613797 Msa0087670:three_prime_UTR
ACAAGGATCTTAAGCCATGT+TGG 0.517216 1_2:+68615778 None:intergenic
ATTGCTCTGGTTGTACTCTC+GGG 0.525362 1_2:-68615629 Msa0087670:CDS
CAAGAATTTGGCATCCAACA+TGG 0.531190 1_2:-68615792 Msa0087670:five_prime_UTR
TTCTTGAGGCTTCATCACAT+TGG 0.566647 1_2:+68613761 None:intergenic
CTCTGGTTGTACTCTCGGGA+AGG 0.577901 1_2:-68615625 Msa0087670:intron
GATTAGAGTTACTCATGAGG+TGG 0.581584 1_2:-68614770 Msa0087670:exon
AGGTGCAAAACCAGGAGTGT+AGG 0.604566 1_2:+68614569 None:intergenic
AATGTTATCACTGTTGGTGT+CGG 0.605324 1_2:-68615662 Msa0087670:CDS
AAACGTTGAGAAAGTGAACT+GGG 0.630136 1_2:-68615058 Msa0087670:CDS
GAAACTGTAGGTGCAAAACC+AGG 0.636631 1_2:+68614561 None:intergenic
ATTGTGACGATTATCGATGT+CGG 0.639449 1_2:-68615713 Msa0087670:exon
CTGATGCCGATATGTTGATG+AGG 0.659856 1_2:+68615193 None:intergenic
GTGAACTGGGAAACTTGGAT+AGG 0.670748 1_2:-68615045 Msa0087670:intron
GTATTCAGGAGATATTCTTG+AGG 0.672009 1_2:+68613747 None:intergenic
TGATGCCGATATGTTGATGA+GGG 0.679239 1_2:+68615194 None:intergenic
ACTTGCCATAATGAAACTGT+AGG 0.704994 1_2:+68614549 None:intergenic
TCTGATTAGAGTTACTCATG+AGG 0.713055 1_2:-68614773 Msa0087670:exon

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATAGATTGATTTTATATTT+GGG - chr1_2:68614190-68614209 Msa0087670:intron 10.0%
!!! ATATTTTTTTTTTTTGCATA+TGG - chr1_2:68614789-68614808 Msa0087670:CDS 10.0%
!!! AAGTTTTGATTTGATTTATT+TGG - chr1_2:68613918-68613937 Msa0087670:intron 15.0%
!!! CTATAGATTGATTTTATATT+TGG - chr1_2:68614189-68614208 Msa0087670:intron 15.0%
!! AAATATGCATAAAAAATTGT+AGG + chr1_2:68614775-68614794 None:intergenic 15.0%
!! AATGAAACAAACAAGAAAAT+AGG + chr1_2:68614078-68614097 None:intergenic 20.0%
!! TTACATATAAACAAAACACA+CGG + chr1_2:68614102-68614121 None:intergenic 20.0%
!! AAGTGAGAATAATAAAGAAA+AGG + chr1_2:68614339-68614358 None:intergenic 20.0%
!!! TTCTTTATTATTCTCACTTT+TGG - chr1_2:68614340-68614359 Msa0087670:intron 20.0%
!!! TAGTTCCTTTATCTTTTAAT+AGG - chr1_2:68615017-68615036 Msa0087670:intron 20.0%
!! AGTTTGCATTAAAAATAACT+AGG + chr1_2:68615043-68615062 None:intergenic 20.0%
!!! AGTTTTTTTTACTATTCTAC+AGG - chr1_2:68615647-68615666 Msa0087670:CDS 20.0%
!!! GAATCAATGTTTTTTTTAAG+AGG - chr1_2:68615788-68615807 Msa0087670:five_prime_UTR 20.0%
! TGGTTAATCTCATATACTTA+CGG + chr1_2:68613650-68613669 None:intergenic 25.0%
!! CTTAAGAAGTGTAATTATGA+AGG - chr1_2:68613715-68613734 Msa0087670:three_prime_UTR 25.0%
! TTGTAATTTAGTCAAACCAT+TGG - chr1_2:68613863-68613882 Msa0087670:intron 25.0%
!! GATTTTCAATTCTGTTTTAC+AGG - chr1_2:68614507-68614526 Msa0087670:intron 25.0%
!! TTACTTGTTTGCTTCATTTT+AGG - chr1_2:68614642-68614661 Msa0087670:intron 25.0%
!! TACTTGTTTGCTTCATTTTA+GGG - chr1_2:68614643-68614662 Msa0087670:intron 25.0%
! TATGGTATACTTATTTGAGT+AGG - chr1_2:68614807-68614826 Msa0087670:intron 25.0%
! GAAATGAAACATTGTTCTAA+AGG - chr1_2:68614948-68614967 Msa0087670:intron 25.0%
!! TTATCTGAAATAGAATCCAT+AGG - chr1_2:68615192-68615211 Msa0087670:intron 25.0%
! ATAGACATTCTTAATTCCTA+TGG + chr1_2:68615211-68615230 None:intergenic 25.0%
! AGGAATTAAGAATGTCTATT+TGG - chr1_2:68615212-68615231 Msa0087670:CDS 25.0%
!!! TTGATGATTTTGACATTGAA+TGG - chr1_2:68615603-68615622 Msa0087670:intron 25.0%
!! CAATGACTTTTATTGTATTC+AGG + chr1_2:68615733-68615752 None:intergenic 25.0%
GAGATTAACCAACAAGAATT+TGG - chr1_2:68613659-68613678 Msa0087670:three_prime_UTR 30.0%
ACTTCTTAAGCATCTTTACA+AGG + chr1_2:68613705-68613724 None:intergenic 30.0%
!! GAGTTTGTTACTGTAAATAG+CGG - chr1_2:68614559-68614578 Msa0087670:three_prime_UTR 30.0%
CTAGGCCTATTAAAAGATAA+AGG + chr1_2:68615025-68615044 None:intergenic 30.0%
!! TATTTGGAAGAAAGTGTTGA+AGG - chr1_2:68615228-68615247 Msa0087670:CDS 30.0%
AGAGAGATAATAAACATCCA+TGG - chr1_2:68615320-68615339 Msa0087670:intron 30.0%
! TTAGCTTAAGCTTTTAACCA+TGG + chr1_2:68615340-68615359 None:intergenic 30.0%
TTTGTCAAATGTGATGTAGA+AGG - chr1_2:68615527-68615546 Msa0087670:intron 30.0%
ATTGTGACGATTATCGATGT+CGG - chr1_2:68613750-68613769 Msa0087670:three_prime_UTR 35.0%
AACGCTAATGTTATCACTGT+TGG - chr1_2:68613795-68613814 Msa0087670:three_prime_UTR 35.0%
AATGTTATCACTGTTGGTGT+CGG - chr1_2:68613801-68613820 Msa0087670:intron 35.0%
ACAAGCAGCAAATTCAATCA+AGG + chr1_2:68614031-68614050 None:intergenic 35.0%
CATTTCCCTCATCAACATAT+CGG - chr1_2:68614264-68614283 Msa0087670:intron 35.0%
AGGAATGTGAAAGACAAAAG+TGG + chr1_2:68614319-68614338 None:intergenic 35.0%
!! TCTCACTTTTGGTTAAATGC+AGG - chr1_2:68614351-68614370 Msa0087670:intron 35.0%
! GTTCACTTTCTCAACGTTTT+GGG + chr1_2:68614404-68614423 None:intergenic 35.0%
! AGTTCACTTTCTCAACGTTT+TGG + chr1_2:68614405-68614424 None:intergenic 35.0%
AAAACGTTGAGAAAGTGAAC+TGG - chr1_2:68614404-68614423 Msa0087670:intron 35.0%
AAACGTTGAGAAAGTGAACT+GGG - chr1_2:68614405-68614424 Msa0087670:intron 35.0%
TCTGATTAGAGTTACTCATG+AGG - chr1_2:68614690-68614709 Msa0087670:intron 35.0%
ATCTCAACACACCATATCAT+AGG + chr1_2:68614722-68614741 None:intergenic 35.0%
TGTGTTGAGATTTAGTGTTC+TGG - chr1_2:68614731-68614750 Msa0087670:three_prime_UTR 35.0%
TTGCACCTACAGTTTCATTA+TGG - chr1_2:68614909-68614928 Msa0087670:intron 35.0%
ACTTGCCATAATGAAACTGT+AGG + chr1_2:68614917-68614936 None:intergenic 35.0%
! GACTGACTTAATGGTACTAA+TGG + chr1_2:68615149-68615168 None:intergenic 35.0%
TAGTACCATTAAGTCAGTCT+TGG - chr1_2:68615150-68615169 Msa0087670:intron 35.0%
!! AAGAAAGTGTTGAAGGAAAG+TGG - chr1_2:68615235-68615254 Msa0087670:CDS 35.0%
TTCATCACATTGGCAATCAT+TGG + chr1_2:68615695-68615714 None:intergenic 35.0%
GTATTCAGGAGATATTCTTG+AGG + chr1_2:68615719-68615738 None:intergenic 35.0%
!!! GTGATTCTTGTGTTTTGGGA+GGG - chr1_2:68613582-68613601 Msa0087670:three_prime_UTR 40.0%
GTTGGATGCCAAATTCTTGT+TGG + chr1_2:68613670-68613689 None:intergenic 40.0%
CAAGAATTTGGCATCCAACA+TGG - chr1_2:68613671-68613690 Msa0087670:three_prime_UTR 40.0%
ACAAGGATCTTAAGCCATGT+TGG + chr1_2:68613688-68613707 None:intergenic 40.0%
TATTGCTCTGGTTGTACTCT+CGG - chr1_2:68613833-68613852 Msa0087670:intron 40.0%
AGAGATGAACTTGGATCCAA+TGG + chr1_2:68613882-68613901 None:intergenic 40.0%
CATGCAACAAGAGATGAACT+TGG + chr1_2:68613891-68613910 None:intergenic 40.0%
GCAGTTATCAACATCTTCGT+TGG - chr1_2:68614227-68614246 Msa0087670:intron 40.0%
! TGATGCCGATATGTTGATGA+GGG + chr1_2:68614272-68614291 None:intergenic 40.0%
AGAAAGTGAACTGGGAAACT+TGG - chr1_2:68614413-68614432 Msa0087670:intron 40.0%
GAGTTAGACAGAACGATTCA+TGG - chr1_2:68614442-68614461 Msa0087670:intron 40.0%
!!! GCTTCATTTTAGGGTTCTCT+TGG - chr1_2:68614652-68614671 Msa0087670:intron 40.0%
GATTAGAGTTACTCATGAGG+TGG - chr1_2:68614693-68614712 Msa0087670:intron 40.0%
TGAGGTGGTTTCCTATGATA+TGG - chr1_2:68614708-68614727 Msa0087670:intron 40.0%
TTAGTGTTCTGGTGCAAATC+AGG - chr1_2:68614742-68614761 Msa0087670:three_prime_UTR 40.0%
TGAGTAGGAATGTTGTGTGT+AGG - chr1_2:68614822-68614841 Msa0087670:intron 40.0%
GAGTAGGAATGTTGTGTGTA+GGG - chr1_2:68614823-68614842 Msa0087670:intron 40.0%
TTATGGCAAGTGACAAGATC+AGG - chr1_2:68614926-68614945 Msa0087670:intron 40.0%
! TGTGACCAAGACTGACTTAA+TGG + chr1_2:68615158-68615177 None:intergenic 40.0%
CAGTATGGTTAGGCTATGTT+TGG + chr1_2:68615451-68615470 None:intergenic 40.0%
! AATTTTCCCCATCAGCAGTA+TGG + chr1_2:68615466-68615485 None:intergenic 40.0%
GAAAAGAGACAAACACTAGC+TGG + chr1_2:68615505-68615524 None:intergenic 40.0%
TTCTTGAGGCTTCATCACAT+TGG + chr1_2:68615705-68615724 None:intergenic 40.0%
!! GGTGATTCTTGTGTTTTGGG+AGG - chr1_2:68613581-68613600 Msa0087670:three_prime_UTR 45.0%
!!! TTCTTGTGTTTTGGGAGGGT+AGG - chr1_2:68613586-68613605 Msa0087670:three_prime_UTR 45.0%
TGGGAGGGTAGGAGTAAAAA+TGG - chr1_2:68613597-68613616 Msa0087670:three_prime_UTR 45.0%
GGGAGGGTAGGAGTAAAAAT+GGG - chr1_2:68613598-68613617 Msa0087670:three_prime_UTR 45.0%
ATTGCTCTGGTTGTACTCTC+GGG - chr1_2:68613834-68613853 Msa0087670:intron 45.0%
CTGATGCCGATATGTTGATG+AGG + chr1_2:68614273-68614292 None:intergenic 45.0%
CTCATCAACATATCGGCATC+AGG - chr1_2:68614271-68614290 Msa0087670:intron 45.0%
ATATCGGCATCAGGTCAACA+TGG - chr1_2:68614280-68614299 Msa0087670:intron 45.0%
GTGAACTGGGAAACTTGGAT+AGG - chr1_2:68614418-68614437 Msa0087670:intron 45.0%
GAAACTGTAGGTGCAAAACC+AGG + chr1_2:68614905-68614924 None:intergenic 45.0%
TAGCCTAACCATACTGCTGA+TGG - chr1_2:68615455-68615474 Msa0087670:intron 45.0%
AGCCTAACCATACTGCTGAT+GGG - chr1_2:68615456-68615475 Msa0087670:intron 45.0%
CAGGCATAAGCAAGTGATGT+AGG - chr1_2:68615666-68615685 Msa0087670:CDS 45.0%
CGATGTCGGCGAAGTTAGTT+CGG - chr1_2:68613764-68613783 Msa0087670:three_prime_UTR 50.0%
TCCATTTGCACCTACACTCC+TGG - chr1_2:68614884-68614903 Msa0087670:intron 50.0%
! ACCAGGAGTGTAGGTGCAAA+TGG + chr1_2:68614888-68614907 None:intergenic 50.0%
! AGGTGCAAAACCAGGAGTGT+AGG + chr1_2:68614897-68614916 None:intergenic 50.0%
TATCCCTCAGAAGACGTAGC+AGG - chr1_2:68615388-68615407 Msa0087670:intron 50.0%
ACGTAGCAGGCTCTTGTGTA+GGG - chr1_2:68615401-68615420 Msa0087670:intron 50.0%
GCCTAACCATACTGCTGATG+GGG - chr1_2:68615457-68615476 Msa0087670:intron 50.0%
TCCCCATCAGCAGTATGGTT+AGG + chr1_2:68615461-68615480 None:intergenic 50.0%
!! ACTGTTGGTGTCGGTGTTGC+TGG - chr1_2:68613810-68613829 Msa0087670:intron 55.0%
!! CGGTGTTGCTGGTATTGCTC+TGG - chr1_2:68613821-68613840 Msa0087670:intron 55.0%
CTCTGGTTGTACTCTCGGGA+AGG - chr1_2:68613838-68613857 Msa0087670:intron 55.0%
GAGCCTGCTACGTCTTCTGA+GGG + chr1_2:68615394-68615413 None:intergenic 55.0%
AGAGCCTGCTACGTCTTCTG+AGG + chr1_2:68615395-68615414 None:intergenic 55.0%
GACGTAGCAGGCTCTTGTGT+AGG - chr1_2:68615400-68615419 Msa0087670:intron 55.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 68613580 68615905 68613580 ID=Msa0087670;Name=Msa0087670
chr1_2 mRNA 68613580 68615905 68613580 ID=Msa0087670-mRNA-1;Parent=Msa0087670;Name=Msa0087670-mRNA-1;_AED=0.23;_eAED=0.23;_QI=186|0.8|0.83|1|0.6|0.5|6|428|85
chr1_2 exon 68613580 68613816 68613580 ID=Msa0087670-mRNA-1:exon:23523;Parent=Msa0087670-mRNA-1
chr1_2 exon 68614516 68614641 68614516 ID=Msa0087670-mRNA-1:exon:23522;Parent=Msa0087670-mRNA-1
chr1_2 exon 68614722 68614821 68614722 ID=Msa0087670-mRNA-1:exon:23521;Parent=Msa0087670-mRNA-1
chr1_2 exon 68615046 68615112 68615046 ID=Msa0087670-mRNA-1:exon:23520;Parent=Msa0087670-mRNA-1
chr1_2 exon 68615193 68615254 68615193 ID=Msa0087670-mRNA-1:exon:23519;Parent=Msa0087670-mRNA-1
chr1_2 exon 68615626 68615905 68615626 ID=Msa0087670-mRNA-1:exon:23518;Parent=Msa0087670-mRNA-1
chr1_2 five_prime_UTR 68615720 68615905 68615720 ID=Msa0087670-mRNA-1:five_prime_utr;Parent=Msa0087670-mRNA-1
chr1_2 CDS 68615626 68615719 68615626 ID=Msa0087670-mRNA-1:cds;Parent=Msa0087670-mRNA-1
chr1_2 CDS 68615193 68615254 68615193 ID=Msa0087670-mRNA-1:cds;Parent=Msa0087670-mRNA-1
chr1_2 CDS 68615046 68615112 68615046 ID=Msa0087670-mRNA-1:cds;Parent=Msa0087670-mRNA-1
chr1_2 CDS 68614787 68614821 68614787 ID=Msa0087670-mRNA-1:cds;Parent=Msa0087670-mRNA-1
chr1_2 three_prime_UTR 68614722 68614786 68614722 ID=Msa0087670-mRNA-1:three_prime_utr;Parent=Msa0087670-mRNA-1
chr1_2 three_prime_UTR 68614516 68614641 68614516 ID=Msa0087670-mRNA-1:three_prime_utr;Parent=Msa0087670-mRNA-1
chr1_2 three_prime_UTR 68613580 68613816 68613580 ID=Msa0087670-mRNA-1:three_prime_utr;Parent=Msa0087670-mRNA-1
Gene Sequence

>Msa0087670

ATGTCGGCGAAGTTAGTTCGGAAATATTCAACGCTAATGTTATCACTGTTGGTGTCGGTGTTGCTGGTATTGCTCTGGTTGTACTCTCGGGAAGTTATCAACATCTTCGTTGGCATTTGTGTATCTGCATTTCCCTCATCAACATATCGGCATCAGGTGAACAAGCTTAAAAGAGAACTTGAAACCCAAAACGTTGAGAAAGTGAACTGGGAAACTTGGATAGGGTTCTCTTGGTTGCAGTTTCTGCAGTCTGATTAG

Protein sequence

>Msa0087670

MSAKLVRKYSTLMLSLLVSVLLVLLWLYSREVINIFVGICVSAFPSSTYRHQVNKLKRELETQNVEKVNWETWIGFSWLQFLQSD*