AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene054405


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene054405.t1 MTR_7g112110 96.682 211 7 0 1 211 5 215 1.26e-151 419
MS.gene054405.t1 MTR_7g112120 78.641 206 40 2 1 202 1 206 2.33e-115 328
MS.gene054405.t1 MTR_1g084040 74.020 204 53 0 1 204 3 206 1.46e-105 305
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene054405.t1 AT1G56423 66.010 203 69 0 1 203 1 203 9.21e-98 285
MS.gene054405.t1 AT1G56423 66.010 203 69 0 1 203 1 203 1.05e-97 285

Find 53 sgRNAs with CRISPR-Local

Find 100 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTATTAAATTGCTTTGATA+TGG 0.171309 7.4:-4402134 MS.gene054405:CDS
TAATGTAAACTTCCCACTTT+TGG 0.220946 7.4:+4402153 None:intergenic
TGTGATGCGGTTGGCCTTAC+GGG 0.286048 7.4:+4401916 None:intergenic
AGAGGAACTGGTACGTTGTT+TGG 0.307326 7.4:-4401818 MS.gene054405:CDS
GAGCAAAGGCTTGGAAGATT+TGG 0.325168 7.4:-4401770 MS.gene054405:CDS
CTGTGATGCGGTTGGCCTTA+CGG 0.349279 7.4:+4401915 None:intergenic
AACTTACGGTGTAGGTTTCA+TGG 0.367784 7.4:-4401795 MS.gene054405:CDS
TTATTAAATTGCTTTGATAT+GGG 0.378126 7.4:-4402133 MS.gene054405:CDS
GGAAGATTTGGTTATCTTGT+TGG 0.387002 7.4:-4401758 MS.gene054405:CDS
TTATCTTGTTGGAAGTCAAT+TGG 0.396840 7.4:-4401747 MS.gene054405:CDS
TTGGAAGTCAATTGGGAAGT+TGG 0.398362 7.4:-4401739 MS.gene054405:CDS
AGTTGGATTGGAAGTAGAAT+AGG 0.408974 7.4:-4401722 MS.gene054405:CDS
TCTTGTTGATGCTGCTTCAC+AGG 0.412869 7.4:-4402005 MS.gene054405:CDS
AATTGCTTTGATATGGGCTC+AGG 0.437174 7.4:-4402127 MS.gene054405:CDS
GTGCATTTCGTGTTGCAGTA+TGG 0.438736 7.4:-4401671 MS.gene054405:CDS
TATCTTGTTGGAAGTCAATT+GGG 0.442064 7.4:-4401746 MS.gene054405:CDS
GAGGGATTCCTCAGAGGAAC+TGG 0.444285 7.4:-4401830 MS.gene054405:CDS
GGTACGTTGTTTGGAACTTA+CGG 0.445217 7.4:-4401809 MS.gene054405:CDS
AGTCAATTGGGAAGTTGGAT+TGG 0.450366 7.4:-4401734 MS.gene054405:CDS
GTCCCATCCGGAAGAGATGA+TGG 0.461346 7.4:+4401889 None:intergenic
ATGGTATATGATGTGGCTAA+TGG 0.468429 7.4:-4401695 MS.gene054405:CDS
TTTGAAGCTGTTTACTATGG+TGG 0.481190 7.4:-4401863 MS.gene054405:CDS
CAATGATGGCAGATACAGAT+AGG 0.486572 7.4:+4402929 None:intergenic
GAGAACGCGTCATCCAAAAG+TGG 0.497930 7.4:-4402166 MS.gene054405:CDS
GTTGGATTGGAAGTAGAATA+GGG 0.502946 7.4:-4401721 MS.gene054405:CDS
ACAGGTCCCATCATCTCTTC+CGG 0.504313 7.4:-4401896 MS.gene054405:CDS
ATCATTGTTCTTAGCATCAC+AGG 0.509850 7.4:-4402913 MS.gene054405:intron
CTTGTTGATGCTGCTTCACA+GGG 0.511056 7.4:-4402004 MS.gene054405:CDS
CAGCATCAACAAGAGCAGAT+TGG 0.514551 7.4:+4402014 None:intergenic
TTGTTTGGAACTTACGGTGT+AGG 0.526991 7.4:-4401803 MS.gene054405:CDS
CGTAAGGCCAACCGCATCAC+AGG 0.530423 7.4:-4401914 MS.gene054405:CDS
ACTTACGGTGTAGGTTTCAT+GGG 0.535716 7.4:-4401794 MS.gene054405:CDS
TCCCATCATCTCTTCCGGAT+GGG 0.537093 7.4:-4401891 MS.gene054405:CDS
GGCGAAATTGGCTACCCGTA+AGG 0.540905 7.4:-4401930 MS.gene054405:CDS
GGCTCAGGAACGCTAGCATG+TGG 0.544815 7.4:-4402112 MS.gene054405:CDS
GTCCCATCATCTCTTCCGGA+TGG 0.557344 7.4:-4401892 MS.gene054405:CDS
TCTGAGGAATCCCTCTGTAA+AGG 0.559119 7.4:+4401838 None:intergenic
CTCAGGAACGCTAGCATGTG+GGG 0.570098 7.4:-4402110 MS.gene054405:CDS
TGGAAGTAGAATAGGGCTCA+TGG 0.576358 7.4:-4401714 MS.gene054405:CDS
TCTCCTCTTCTGAAAATCCA+TGG 0.583117 7.4:+4402963 None:intergenic
TATGGTGGTACCTTTACAGA+GGG 0.585211 7.4:-4401848 MS.gene054405:CDS
GCTCAGGAACGCTAGCATGT+GGG 0.607284 7.4:-4402111 MS.gene054405:CDS
TCCCATCCGGAAGAGATGAT+GGG 0.613844 7.4:+4401890 None:intergenic
TGTGATGCTAAGAACAATGA+TGG 0.627342 7.4:+4402915 None:intergenic
GATGGGACCTGTGATGCGGT+TGG 0.637538 7.4:+4401907 None:intergenic
AGAACGCGTCATCCAAAAGT+GGG 0.637848 7.4:-4402165 MS.gene054405:CDS
AGGGCTCATGGTATATGATG+TGG 0.638967 7.4:-4401702 MS.gene054405:CDS
CTATGGTGGTACCTTTACAG+AGG 0.649919 7.4:-4401849 MS.gene054405:CDS
CTTACGGTGTAGGTTTCATG+GGG 0.659609 7.4:-4401793 MS.gene054405:CDS
TTTACAGAGGGATTCCTCAG+AGG 0.683356 7.4:-4401836 MS.gene054405:CDS
ACAACGTACCAGTTCCTCTG+AGG 0.700531 7.4:+4401822 None:intergenic
AGATGATGGGACCTGTGATG+CGG 0.719348 7.4:+4401903 None:intergenic
TTACGGTGTAGGTTTCATGG+GGG 0.787530 7.4:-4401792 MS.gene054405:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GAAATTATAATTAATGAAAA+TGG + chr7.4:4402378-4402397 None:intergenic 10.0%
!! ATTATTAAATTGCTTTGATA+TGG - chr7.4:4402476-4402495 MS.gene054405:intron 15.0%
!! ATTTGAATTTATCTATCTAA+TGG + chr7.4:4402217-4402236 None:intergenic 15.0%
!! TTATTAAATTGCTTTGATAT+GGG - chr7.4:4402477-4402496 MS.gene054405:intron 15.0%
!! AGGTTCAAAAATAGTATTAA+TGG + chr7.4:4401738-4401757 None:intergenic 20.0%
!! GGTTCAAAAATAGTATTAAT+GGG + chr7.4:4401737-4401756 None:intergenic 20.0%
!!! AATTGTCTTTATAACGTTTT+GGG - chr7.4:4401786-4401805 MS.gene054405:CDS 20.0%
!!! TAATTGTCTTTATAACGTTT+TGG - chr7.4:4401785-4401804 MS.gene054405:CDS 20.0%
!!! TTTTTTGAAAAAGTGATGTA+AGG + chr7.4:4402296-4402315 None:intergenic 20.0%
! AAATTATTGACCCCAAAAAT+TGG - chr7.4:4401876-4401895 MS.gene054405:CDS 25.0%
! CTATAACAACTTTAGTGTAT+AGG - chr7.4:4402017-4402036 MS.gene054405:CDS 25.0%
!!! AATTTTTGGGGTCAATAATT+TGG + chr7.4:4401877-4401896 None:intergenic 25.0%
!!! TTTTTTGAAGCTGTTTACTA+TGG - chr7.4:4402744-4402763 MS.gene054405:intron 25.0%
AATTAACGGCAGTAATTTAG+GGG - chr7.4:4401812-4401831 MS.gene054405:CDS 30.0%
AATTGTTCCTTACATCAAAG+TGG - chr7.4:4402314-4402333 MS.gene054405:intron 30.0%
CAATTAACGGCAGTAATTTA+GGG - chr7.4:4401811-4401830 MS.gene054405:CDS 30.0%
TATCTTGTTGGAAGTCAATT+GGG - chr7.4:4402864-4402883 MS.gene054405:intron 30.0%
TCAATTAACGGCAGTAATTT+AGG - chr7.4:4401810-4401829 MS.gene054405:CDS 30.0%
TGAATAAGATAAACCTGATC+AGG + chr7.4:4401844-4401863 None:intergenic 30.0%
TGGGTTCTCATATTTAACTA+TGG - chr7.4:4402349-4402368 MS.gene054405:intron 30.0%
TTATCTTGTTGGAAGTCAAT+TGG - chr7.4:4402863-4402882 MS.gene054405:intron 30.0%
! CTATTCTAGCATGGATTTTA+TGG - chr7.4:4401922-4401941 MS.gene054405:CDS 30.0%
! CTTTCTTTTCTATTCTAGCA+TGG - chr7.4:4401913-4401932 MS.gene054405:CDS 30.0%
! TAATGTAAACTTCCCACTTT+TGG + chr7.4:4402460-4402479 None:intergenic 30.0%
!!! AACGTTTTGGGTTCAATTAA+CGG - chr7.4:4401798-4401817 MS.gene054405:CDS 30.0%
AAGCTATCTTGAAGAGTTTG+TGG - chr7.4:4402108-4402127 MS.gene054405:CDS 35.0%
ATCATTGTTCTTAGCATCAC+AGG - chr7.4:4401697-4401716 MS.gene054405:CDS 35.0%
ATGGTATATGATGTGGCTAA+TGG - chr7.4:4402915-4402934 MS.gene054405:CDS 35.0%
CCTGAAACAAGGTAAAAAAG+CGG - chr7.4:4402659-4402678 MS.gene054405:intron 35.0%
TGTGATGCTAAGAACAATGA+TGG + chr7.4:4401698-4401717 None:intergenic 35.0%
TTGAATTGAGTCTGATGTGA+AGG + chr7.4:4401758-4401777 None:intergenic 35.0%
! AGTTGGATTGGAAGTAGAAT+AGG - chr7.4:4402888-4402907 MS.gene054405:intron 35.0%
! ATTTTCAGAAGAGGAGAGTT+CGG - chr7.4:4401653-4401672 MS.gene054405:CDS 35.0%
! GGAAGATTTGGTTATCTTGT+TGG - chr7.4:4402852-4402871 MS.gene054405:intron 35.0%
! GTTGGATTGGAAGTAGAATA+GGG - chr7.4:4402889-4402908 MS.gene054405:intron 35.0%
! TTTGAAGCTGTTTACTATGG+TGG - chr7.4:4402747-4402766 MS.gene054405:intron 35.0%
!!! CGCTTTTTTACCTTGTTTCA+GGG + chr7.4:4402661-4402680 None:intergenic 35.0%
!!! GCATGTTTTTCTGAAGCAAT+TGG + chr7.4:4402639-4402658 None:intergenic 35.0%
AAATATGAGAACCCAGAGCT+AGG + chr7.4:4402344-4402363 None:intergenic 40.0%
AACTTACGGTGTAGGTTTCA+TGG - chr7.4:4402815-4402834 MS.gene054405:intron 40.0%
AATATGAGAACCCAGAGCTA+GGG + chr7.4:4402343-4402362 None:intergenic 40.0%
AATTGCTTTGATATGGGCTC+AGG - chr7.4:4402483-4402502 MS.gene054405:intron 40.0%
ACTTACGGTGTAGGTTTCAT+GGG - chr7.4:4402816-4402835 MS.gene054405:intron 40.0%
AGCTTCAAAAAAGTCCCATC+CGG + chr7.4:4402736-4402755 None:intergenic 40.0%
AGGGAAACCACTTTGATGTA+AGG + chr7.4:4402324-4402343 None:intergenic 40.0%
AGGTAAAAAAGCGGCGAAAT+TGG - chr7.4:4402668-4402687 MS.gene054405:intron 40.0%
AGTCAATTGGGAAGTTGGAT+TGG - chr7.4:4402876-4402895 MS.gene054405:intron 40.0%
CAATGATGGCAGATACAGAT+AGG + chr7.4:4401684-4401703 None:intergenic 40.0%
GAAAAACATGCCCTGAAACA+AGG - chr7.4:4402648-4402667 MS.gene054405:intron 40.0%
TATGGTGGTACCTTTACAGA+GGG - chr7.4:4402762-4402781 MS.gene054405:intron 40.0%
TTGACCCCAAAAATTGGCAT+AGG - chr7.4:4401882-4401901 MS.gene054405:CDS 40.0%
TTGGAAGTCAATTGGGAAGT+TGG - chr7.4:4402871-4402890 MS.gene054405:intron 40.0%
! CGTCTCCTATGCCAATTTTT+GGG + chr7.4:4401890-4401909 None:intergenic 40.0%
! GGTACGTTGTTTGGAACTTA+CGG - chr7.4:4402801-4402820 MS.gene054405:intron 40.0%
! GTCTCCTATGCCAATTTTTG+GGG + chr7.4:4401889-4401908 None:intergenic 40.0%
! TCGTCTCCTATGCCAATTTT+TGG + chr7.4:4401891-4401910 None:intergenic 40.0%
! TTGTTTGGAACTTACGGTGT+AGG - chr7.4:4402807-4402826 MS.gene054405:intron 40.0%
!!! CCGCTTTTTTACCTTGTTTC+AGG + chr7.4:4402662-4402681 None:intergenic 40.0%
AACAGACATGTGTCGTGATG+TGG - chr7.4:4402248-4402267 MS.gene054405:intron 45.0%
AGAACGCGTCATCCAAAAGT+GGG - chr7.4:4402445-4402464 MS.gene054405:intron 45.0%
AGAGGAACTGGTACGTTGTT+TGG - chr7.4:4402792-4402811 MS.gene054405:intron 45.0%
AGGGCTCATGGTATATGATG+TGG - chr7.4:4402908-4402927 MS.gene054405:intron 45.0%
CAGCATCAACAAGAGCAGAT+TGG + chr7.4:4402599-4402618 None:intergenic 45.0%
CATCACGACACATGTCTGTT+TGG + chr7.4:4402248-4402267 None:intergenic 45.0%
CCGTTCAGCTGAAAAATGCA+GGG - chr7.4:4402410-4402429 MS.gene054405:intron 45.0%
CTATGGTGGTACCTTTACAG+AGG - chr7.4:4402761-4402780 MS.gene054405:intron 45.0%
CTTACGGTGTAGGTTTCATG+GGG - chr7.4:4402817-4402836 MS.gene054405:intron 45.0%
GAAAAATGCAGGGAGCTTGT+TGG - chr7.4:4402420-4402439 MS.gene054405:intron 45.0%
GAGCAAAGGCTTGGAAGATT+TGG - chr7.4:4402840-4402859 MS.gene054405:intron 45.0%
GTGCATTTCGTGTTGCAGTA+TGG - chr7.4:4402939-4402958 MS.gene054405:CDS 45.0%
TCCGTTCAGCTGAAAAATGC+AGG - chr7.4:4402409-4402428 MS.gene054405:intron 45.0%
TCTGAGGAATCCCTCTGTAA+AGG + chr7.4:4402775-4402794 None:intergenic 45.0%
TGGAAGTAGAATAGGGCTCA+TGG - chr7.4:4402896-4402915 MS.gene054405:intron 45.0%
TTACGGTGTAGGTTTCATGG+GGG - chr7.4:4402818-4402837 MS.gene054405:intron 45.0%
TTTACAGAGGGATTCCTCAG+AGG - chr7.4:4402774-4402793 MS.gene054405:intron 45.0%
! AAAGTGGTTTCCCTAGCTCT+GGG - chr7.4:4402330-4402349 MS.gene054405:intron 45.0%
! CTTGTTGATGCTGCTTCACA+GGG - chr7.4:4402606-4402625 MS.gene054405:intron 45.0%
! TCTTGTTGATGCTGCTTCAC+AGG - chr7.4:4402605-4402624 MS.gene054405:intron 45.0%
! TTAGGGGAGTTTTCCTGATC+AGG - chr7.4:4401828-4401847 MS.gene054405:CDS 45.0%
!! CCCTGCATTTTTCAGCTGAA+CGG + chr7.4:4402413-4402432 None:intergenic 45.0%
ACAACGTACCAGTTCCTCTG+AGG + chr7.4:4402791-4402810 None:intergenic 50.0%
ACAGGTCCCATCATCTCTTC+CGG - chr7.4:4402714-4402733 MS.gene054405:intron 50.0%
CAAAGTGGTTTCCCTAGCTC+TGG - chr7.4:4402329-4402348 MS.gene054405:intron 50.0%
GAGAACGCGTCATCCAAAAG+TGG - chr7.4:4402444-4402463 MS.gene054405:intron 50.0%
TAGGTTTCATGGGGGAGCAA+AGG - chr7.4:4402826-4402845 MS.gene054405:intron 50.0%
TCCCATCATCTCTTCCGGAT+GGG - chr7.4:4402719-4402738 MS.gene054405:intron 50.0%
TCCCATCCGGAAGAGATGAT+GGG + chr7.4:4402723-4402742 None:intergenic 50.0%
!! AGATGATGGGACCTGTGATG+CGG + chr7.4:4402710-4402729 None:intergenic 50.0%
CTCAGGAACGCTAGCATGTG+GGG - chr7.4:4402500-4402519 MS.gene054405:intron 55.0%
GAGGGATTCCTCAGAGGAAC+TGG - chr7.4:4402780-4402799 MS.gene054405:intron 55.0%
GCTCAGGAACGCTAGCATGT+GGG - chr7.4:4402499-4402518 MS.gene054405:intron 55.0%
GGCGAAATTGGCTACCCGTA+AGG - chr7.4:4402680-4402699 MS.gene054405:intron 55.0%
GTCCCATCATCTCTTCCGGA+TGG - chr7.4:4402718-4402737 MS.gene054405:intron 55.0%
GTCCCATCCGGAAGAGATGA+TGG + chr7.4:4402724-4402743 None:intergenic 55.0%
TTCATGGGGGAGCAAAGGCT+TGG - chr7.4:4402831-4402850 MS.gene054405:intron 55.0%
!! CTGTGATGCGGTTGGCCTTA+CGG + chr7.4:4402698-4402717 None:intergenic 55.0%
!! TGTGATGCGGTTGGCCTTAC+GGG + chr7.4:4402697-4402716 None:intergenic 55.0%
CGTAAGGCCAACCGCATCAC+AGG - chr7.4:4402696-4402715 MS.gene054405:intron 60.0%
GATGGGACCTGTGATGCGGT+TGG + chr7.4:4402706-4402725 None:intergenic 60.0%
GGCTCAGGAACGCTAGCATG+TGG - chr7.4:4402498-4402517 MS.gene054405:intron 60.0%


Chromosome Type Strat End Strand Name
chr7.4 gene 4401649 4402983 4401649 ID=MS.gene054405
chr7.4 mRNA 4401649 4402983 4401649 ID=MS.gene054405.t1;Parent=MS.gene054405
chr7.4 exon 4402914 4402983 4402914 ID=MS.gene054405.t1.exon1;Parent=MS.gene054405.t1
chr7.4 CDS 4402914 4402983 4402914 ID=cds.MS.gene054405.t1;Parent=MS.gene054405.t1
chr7.4 exon 4401649 4402214 4401649 ID=MS.gene054405.t1.exon2;Parent=MS.gene054405.t1
chr7.4 CDS 4401649 4402214 4401649 ID=cds.MS.gene054405.t1;Parent=MS.gene054405.t1
Gene Sequence

>MS.gene054405

ATGGATTTTCAGAAGAGGAGAGTTCGGTTTCTCCTATCTGTATCTGCCATCATTGTTCTTAGCATCACAGGTATCTATAGCACTTCCCATTAATACTATTTTTGAACCTTCACATCAGACTCAATTCAACACTCAATAATTGTCTTTATAACGTTTTGGGTTCAATTAACGGCAGTAATTTAGGGGAGTTTTCCTGATCAGGTTTATCTTATTCAATGCAAATCTCCAAATTATTGACCCCAAAAATTGGCATAGGAGACGAATCTTTCTTTTCTATTCTAGCATGGATTTTATGGATTGCTTTGAGTTTGTTGTGTGTAAATGTTTTAGACTATATTTTGATAAACAACTTTAGTGTTTATCATATGCTATAACAACTTTAGTGTATAGGCTATTTCTATAACAAATGATGAAAACAAATCAAATTGTTTTCTTATATACTATAAGTTGTTTTCATATAAGCTATCTTGAAGAGTTTGTGGAAATAAGCTGAAACAACGTATGAAAATGTCATAACATGTTTTCATAAGCTCTCTTAAATAGTCTCACAAATGTATAGTTTATACCATTAGATAGATAAATTCAAATAAGTCAATCCAAACAGACATGTGTCGTGATGTGGTAATAAATTCTTAACTATTGTTCCTTACATCACTTTTTCAAAAAATTGTTCCTTACATCAAAGTGGTTTCCCTAGCTCTGGGTTCTCATATTTAACTATGGAAGCCATTTTCATTAATTATAATTTCTGCTTGTTTGCTCCGTTCAGCTGAAAAATGCAGGGAGCTTGTTGGCGAGAACGCGTCATCCAAAAGTGGGAAGTTTACATTATTAAATTGCTTTGATATGGGCTCAGGAACGCTAGCATGTGGGGTTAAAGAAAGTGTGAAGCTCTATGTTAATAATATTAGATCTGCTCATGTTGAAAAAGCAAGACATGATGCAATCCAATCTGCTCTTGTTGATGCTGCTTCACAGGGTATGTCGCCAATTGCTTCAGAAAAACATGCCCTGAAACAAGGTAAAAAAGCGGCGAAATTGGCTACCCGTAAGGCCAACCGCATCACAGGTCCCATCATCTCTTCCGGATGGGACTTTTTTGAAGCTGTTTACTATGGTGGTACCTTTACAGAGGGATTCCTCAGAGGAACTGGTACGTTGTTTGGAACTTACGGTGTAGGTTTCATGGGGGAGCAAAGGCTTGGAAGATTTGGTTATCTTGTTGGAAGTCAATTGGGAAGTTGGATTGGAAGTAGAATAGGGCTCATGGTATATGATGTGGCTAATGGAGTGCATTTCGTGTTGCAGTATGGAAGTAAAATTCAAGAAACATAA

Protein sequence

>MS.gene054405.t1

MDFQKRRVRFLLSVSAIIVLSITAEKCRELVGENASSKSGKFTLLNCFDMGSGTLACGVKESVKLYVNNIRSAHVEKARHDAIQSALVDAASQGMSPIASEKHALKQGKKAAKLATRKANRITGPIISSGWDFFEAVYYGGTFTEGFLRGTGTLFGTYGVGFMGEQRLGRFGYLVGSQLGSWIGSRIGLMVYDVANGVHFVLQYGSKIQET