AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene007500

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene007500.t1 MTR_7g100905 100.000 73 0 0 1 73 1 73 9.50e-47 143
MS.gene007500.t1 MTR_7g100905 100.000 66 0 0 8 73 3 68 3.29e-41 129
MS.gene007500.t1 MTR_7g100880 85.897 78 6 1 1 73 7 84 2.78e-18 71.6
MS.gene007500.t1 MTR_7g100890 90.411 73 6 1 1 73 426 497 2.80e-16 71.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene007500.t1 AT2G37120 76.190 63 15 0 11 73 14 76 5.32e-15 63.2
MS.gene007500.t1 AT3G53370 80.000 60 12 0 14 73 17 76 1.71e-12 57.0

Find 16 sgRNAs with CRISPR-Local

Find 81 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGATTGTTCTCCTGGTTAT+TGG 0.231388 7.4:+9465976 MS.gene007500:CDS
CCCAGGCTTGATTGTTCTCC+TGG 0.358351 7.4:+9465969 MS.gene007500:CDS
TGGGGAAATGTTTAGAATGC+TGG 0.422488 7.4:+9465931 MS.gene007500:intron
GTTTAGAATGCTGGATCTCA+AGG 0.468079 7.4:+9465940 MS.gene007500:intron
ACCAGGAGAACAATCAAGCC+TGG 0.470447 7.4:-9465970 None:intergenic
AAGCAAGGAGTCTCTGCGCC+TGG 0.476753 7.4:+9466117 MS.gene007500:CDS
ATTGTTCTCCTGGTTATTGG+TGG 0.489076 7.4:+9465979 MS.gene007500:CDS
TTGCTGTTGACATTTCTCAT+TGG 0.497549 7.4:+9466003 MS.gene007500:CDS
TTGTTCTCCTGGTTATTGGT+GGG 0.546594 7.4:+9465980 MS.gene007500:CDS
GTACAGTGCCTCTACTCTCC+AGG 0.557609 7.4:-9466135 None:intergenic
GCTTTACGTTTATGCACAGA+AGG 0.577488 7.4:+9466035 MS.gene007500:CDS
ACAGCAACCCACCAATAACC+AGG 0.598951 7.4:-9465987 None:intergenic
CCAGGAGAACAATCAAGCCT+GGG 0.608678 7.4:-9465969 None:intergenic
GGATCTCAAGGGTTCAACCC+AGG 0.613072 7.4:+9465952 MS.gene007500:CDS
TTTAGAATGCTGGATCTCAA+GGG 0.619147 7.4:+9465941 MS.gene007500:intron
TCTCTGCGCCTGGAGAGTAG+AGG 0.652078 7.4:+9466127 MS.gene007500:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTTTTTTATTCACATTT+AGG + chr7.4:9465085-9465104 MS.gene007500:intron 10.0%
!! AAAATAAATAATGAAGAATG+TGG - chr7.4:9464891-9464910 None:intergenic 15.0%
!! AAATAAATAATGAAGAATGT+GGG - chr7.4:9464890-9464909 None:intergenic 15.0%
!! CAATAAAAAAATATTTCCAA+AGG - chr7.4:9465861-9465880 None:intergenic 15.0%
!! GATCTATTCATAATTAAATT+AGG + chr7.4:9465061-9465080 MS.gene007500:intron 15.0%
!! TTATTTGAGAATAACAATAA+GGG - chr7.4:9465452-9465471 None:intergenic 15.0%
!! AGATTCTACTTTGAATATAA+TGG + chr7.4:9465675-9465694 MS.gene007500:intron 20.0%
!! CTTATTTGAGAATAACAATA+AGG - chr7.4:9465453-9465472 None:intergenic 20.0%
!! GATTCTACTTTGAATATAAT+GGG + chr7.4:9465676-9465695 MS.gene007500:intron 20.0%
!! TTTCAGATCTTAAAAATTCA+TGG + chr7.4:9464910-9464929 MS.gene007500:intron 20.0%
!!! CAAAAAAAAGCACTTAAATA+AGG - chr7.4:9465904-9465923 None:intergenic 20.0%
!!! TTTTATTCACATTTAGGTTA+AGG + chr7.4:9465091-9465110 MS.gene007500:intron 20.0%
! AAAATGCATATGATAAAACC+TGG - chr7.4:9465408-9465427 None:intergenic 25.0%
! CATATTACTATTTGCATACA+TGG + chr7.4:9465793-9465812 MS.gene007500:intron 25.0%
! CTCAAAAAAGAAGATGAAAA+AGG + chr7.4:9466086-9466105 MS.gene007500:CDS 25.0%
! GGTTACAAATAACATCAATA+TGG - chr7.4:9465431-9465450 None:intergenic 25.0%
!! TTTACATGTCAATTTTCCTT+TGG + chr7.4:9465842-9465861 MS.gene007500:intron 25.0%
!!! GGAATTGATTTGAAGAAAAT+CGG - chr7.4:9464869-9464888 None:intergenic 25.0%
!!! TGCTTTATTAGACACTTTTA+AGG + chr7.4:9465164-9465183 MS.gene007500:intron 25.0%
!!! TTAATTTGAGAGTGATTTTG+TGG - chr7.4:9465614-9465633 None:intergenic 25.0%
AAAAGAAGATGAAAAAGGAG+AGG + chr7.4:9466091-9466110 MS.gene007500:CDS 30.0%
AACCATTCAACACAAATTGA+TGG - chr7.4:9465383-9465402 None:intergenic 30.0%
ATTCTCAAATAAGTCTGTGT+AGG + chr7.4:9465460-9465479 MS.gene007500:intron 30.0%
ATTGCAGAGCAAATAAAGAA+TGG - chr7.4:9465772-9465791 None:intergenic 30.0%
TATGAATAGATCCACAAGTA+AGG - chr7.4:9465053-9465072 None:intergenic 30.0%
! ATTTTGTGGAGACATACAAA+AGG - chr7.4:9465600-9465619 None:intergenic 30.0%
! TTAGATCATGATGATGATGA+TGG + chr7.4:9465274-9465293 MS.gene007500:intron 30.0%
! TTTTGTGGAGACATACAAAA+GGG - chr7.4:9465599-9465618 None:intergenic 30.0%
!!! AATTTTTTACCTCCATCACT+GGG + chr7.4:9465010-9465029 MS.gene007500:intron 30.0%
!!! TAATTTTTTACCTCCATCAC+TGG + chr7.4:9465009-9465028 MS.gene007500:intron 30.0%
!!! TGCTTTTTTTTGTTGCTCTT+GGG + chr7.4:9465912-9465931 MS.gene007500:intron 30.0%
!!! TTCATCTTCTTTTTTGAGAC+TGG - chr7.4:9466084-9466103 None:intergenic 30.0%
AGAAAATCGGATCTAAGAAG+AGG - chr7.4:9464856-9464875 None:intergenic 35.0%
AGGGCATAGAATATGAGAAA+GGG - chr7.4:9464952-9464971 None:intergenic 35.0%
AGTTATATACGCCTTACTTG+TGG + chr7.4:9465039-9465058 MS.gene007500:intron 35.0%
ATAACTGAAAAACCCAGTGA+TGG - chr7.4:9465025-9465044 None:intergenic 35.0%
ATTGTATTGTACACGCGTTA+AGG + chr7.4:9465500-9465519 MS.gene007500:intron 35.0%
TGCCATCAATTTGTGTTGAA+TGG + chr7.4:9465378-9465397 MS.gene007500:intron 35.0%
TTGATTGTTCTCCTGGTTAT+TGG + chr7.4:9465976-9465995 MS.gene007500:CDS 35.0%
! AAGGGCATAGAATATGAGAA+AGG - chr7.4:9464953-9464972 None:intergenic 35.0%
! AAGTAGAATCTCTGATTTGC+AGG - chr7.4:9465666-9465685 None:intergenic 35.0%
! CCTTTGTTTCAAAGAATCTC+TGG + chr7.4:9465714-9465733 MS.gene007500:intron 35.0%
! TCAACACAAATTGATGGCAT+TGG - chr7.4:9465377-9465396 None:intergenic 35.0%
! TGAAAGTATGAACGAGCAAA+GGG - chr7.4:9464971-9464990 None:intergenic 35.0%
! TTGAAAGTATGAACGAGCAA+AGG - chr7.4:9464972-9464991 None:intergenic 35.0%
! TTGCTGTTGACATTTCTCAT+TGG + chr7.4:9466003-9466022 MS.gene007500:CDS 35.0%
! TTTAGAATGCTGGATCTCAA+GGG + chr7.4:9465941-9465960 MS.gene007500:intron 35.0%
! TTTGAAACAAAGGAGAGAAG+TGG - chr7.4:9465707-9465726 None:intergenic 35.0%
! TTTGTGTTGAATGGTTTTCC+AGG + chr7.4:9465387-9465406 MS.gene007500:intron 35.0%
!! CCAGAGATTCTTTGAAACAA+AGG - chr7.4:9465717-9465736 None:intergenic 35.0%
!!! GCTTTTTTTTGTTGCTCTTG+GGG + chr7.4:9465913-9465932 MS.gene007500:intron 35.0%
!!! GTGCTTTTTTTTGTTGCTCT+TGG + chr7.4:9465911-9465930 MS.gene007500:intron 35.0%
AGAAGAGGAGAGAAGAATAC+CGG - chr7.4:9464841-9464860 None:intergenic 40.0%
ATTGTTCTCCTGGTTATTGG+TGG + chr7.4:9465979-9465998 MS.gene007500:CDS 40.0%
CATACATGGATGATTGTGAG+TGG + chr7.4:9465807-9465826 MS.gene007500:intron 40.0%
GCTTTACGTTTATGCACAGA+AGG + chr7.4:9466035-9466054 MS.gene007500:CDS 40.0%
GGGACTGTGAATCATAAATC+AGG - chr7.4:9465579-9465598 None:intergenic 40.0%
GGGCATAGAATATGAGAAAG+GGG - chr7.4:9464951-9464970 None:intergenic 40.0%
TTGTTCTCCTGGTTATTGGT+GGG + chr7.4:9465980-9465999 MS.gene007500:CDS 40.0%
! ATGATGGTGATACTGCAGAA+TGG + chr7.4:9465290-9465309 MS.gene007500:intron 40.0%
! GTTTAGAATGCTGGATCTCA+AGG + chr7.4:9465940-9465959 MS.gene007500:intron 40.0%
! TGGGGAAATGTTTAGAATGC+TGG + chr7.4:9465931-9465950 MS.gene007500:intron 40.0%
!!! ACTGGCTTCTTTTTTCTAGG+AGG - chr7.4:9466066-9466085 None:intergenic 40.0%
!!! CTGGCTTCTTTTTTCTAGGA+GGG - chr7.4:9466065-9466084 None:intergenic 40.0%
!!! GAGACTGGCTTCTTTTTTCT+AGG - chr7.4:9466069-9466088 None:intergenic 40.0%
AAAAAGGAGAGGCTGAAGCA+AGG + chr7.4:9466102-9466121 MS.gene007500:CDS 45.0%
AAGAGGAGAGAAGAATACCG+GGG - chr7.4:9464839-9464858 None:intergenic 45.0%
ACATGGATGATTGTGAGTGG+TGG + chr7.4:9465810-9465829 MS.gene007500:intron 45.0%
ACTGAAAAACCCAGTGATGG+AGG - chr7.4:9465022-9465041 None:intergenic 45.0%
GAAGAGGAGAGAAGAATACC+GGG - chr7.4:9464840-9464859 None:intergenic 45.0%
! ATATGAGAAAGGGGCATGCA+AGG - chr7.4:9464942-9464961 None:intergenic 45.0%
! TATGAGAAAGGGGCATGCAA+GGG - chr7.4:9464941-9464960 None:intergenic 45.0%
ACAGCAACCCACCAATAACC+AGG - chr7.4:9465990-9466009 None:intergenic 50.0%
ACCAGGAGAACAATCAAGCC+TGG - chr7.4:9465973-9465992 None:intergenic 50.0%
AGAGGAGAGAAGAATACCGG+GGG - chr7.4:9464838-9464857 None:intergenic 50.0%
CCAGGAGAACAATCAAGCCT+GGG - chr7.4:9465972-9465991 None:intergenic 50.0%
GAATACCGGGGGGACTTTAT+CGG - chr7.4:9464827-9464846 None:intergenic 50.0%
CCCAGGCTTGATTGTTCTCC+TGG + chr7.4:9465969-9465988 MS.gene007500:CDS 55.0%
GAGGAGAGAAGAATACCGGG+GGG - chr7.4:9464837-9464856 None:intergenic 55.0%
GGATCTCAAGGGTTCAACCC+AGG + chr7.4:9465952-9465971 MS.gene007500:CDS 55.0%
AAGCAAGGAGTCTCTGCGCC+TGG + chr7.4:9466117-9466136 MS.gene007500:CDS 60.0%


Chromosome Type Strat End Strand Name
chr7.4 gene 9464820 9466146 9464820 ID=MS.gene007500
chr7.4 mRNA 9464820 9466146 9464820 ID=MS.gene007500.t1;Parent=MS.gene007500
chr7.4 exon 9464820 9464840 9464820 ID=MS.gene007500.t1.exon1;Parent=MS.gene007500.t1
chr7.4 CDS 9464820 9464840 9464820 ID=cds.MS.gene007500.t1;Parent=MS.gene007500.t1
chr7.4 exon 9465946 9466146 9465946 ID=MS.gene007500.t1.exon2;Parent=MS.gene007500.t1
chr7.4 CDS 9465946 9466146 9465946 ID=cds.MS.gene007500.t1;Parent=MS.gene007500.t1
Gene Sequence

>MS.gene007500

ATGGCCGATAAAGTCCCCCCGGTATTCTTCTCTCCTCTTCTTAGATCCGATTTTCTTCAAATCAATTCCCACATTCTTCATTATTTATTTTTTCAGATCTTAAAAATTCATGGATCAACCCTTGCATGCCCCTTTCTCATATTCTATGCCCTTTGCTCGTTCATACTTTCAATCATCATCAAATTTGCTTAATTTTTTACCTCCATCACTGGGTTTTTCAGTTATATACGCCTTACTTGTGGATCTATTCATAATTAAATTAGGATTTTTTTTTTATTCACATTTAGGTTAAGGTTAATTTCACATTTAGATTTAACAATTTAATGATACTTATCTATTTGTTTTGCTTTATTAGACACTTTTAAGGTTTTTTGTTACATTGCTGTCTCTGTAAAAATATAACTTTTATTTAATGCATTGCTGTTTAGTGTTGATCTAATCTATGATTTAGATTTTAGATCATGATGATGATGATGGTGATACTGCAGAATGGAATATTAATACTGAAAGTTTGTATTTTTTGATTCATAAAATTCATTTTTGAGCTAAGTTTACCAATGCCATCAATTTGTGTTGAATGGTTTTCCAGGTTTTATCATATGCATTTTCCATATTGATGTTATTTGTAACCCTTATTGTTATTCTCAAATAAGTCTGTGTAGGAAAAAATTGTACACAAGATTGTATTGTACACGCGTTAAGGATCAAAGATATGAATACACAGAAGATGCTCTAGAAAGTAAATAGTGAAAGAATCCTGATTTATGATTCACAGTCCCTTTTGTATGTCTCCACAAAATCACTCTCAAATTAAGAAAACAAGTTTTGTGAATTGTCGATCATCCTGCAAATCAGAGATTCTACTTTGAATATAATGGGAAAAACCACTTCTCTCCTTTGTTTCAAAGAATCTCTGGTTGATTAAGAAGATTGCACTTGCACATTGTAGCCATTCTTTATTTGCTCTGCAATTCATATTACTATTTGCATACATGGATGATTGTGAGTGGTGGTTAATTACATTTACATGTCAATTTTCCTTTGGAAATATTTTTTTATTGCTTTTTGCTCTGTTATATGACCTTATTTAAGTGCTTTTTTTTGTTGCTCTTGGGGAAATGTTTAGAATGCTGGATCTCAAGGGTTCAACCCAGGCTTGATTGTTCTCCTGGTTATTGGTGGGTTGCTGTTGACATTTCTCATTGGAAATTATGCGCTTTACGTTTATGCACAGAAGGCTCTCCCTCCTAGAAAAAAGAAGCCAGTCTCAAAAAAGAAGATGAAAAAGGAGAGGCTGAAGCAAGGAGTCTCTGCGCCTGGAGAGTAG
Protein sequence

>MS.gene007500.t1

MADKVPPNAGSQGFNPGLIVLLVIGGLLLTFLIGNYALYVYAQKALPPRKKKPVSKKKMKKERLKQGVSAPGE