AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0705100

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0705100 MtrunA17_Chr8g0383161 87.162 148 11 2 1 148 1 140 1.20e-87 251
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0705100 AT5G64820.1 36.029 136 73 4 15 141 13 143 6.48e-17 72.8
Msa0705100 AT1G16850.1 35.659 129 72 2 12 135 13 135 2.63e-15 68.9

Find 35 sgRNAs with CRISPR-Local

Find 129 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTATGAAACAATTTATTTA+TGG 0.128479 4_4:+77638752 Msa0705100:three_prime_UTR
CTACAAACTTACTCCAAATT+TGG 0.167313 4_4:-77638007 None:intergenic
CAAAATTGTGATGCTGTTAT+TGG 0.228818 4_4:+77638707 Msa0705100:three_prime_UTR
TTCCAAGTATTGGCCTAAAT+TGG 0.235754 4_4:-77638811 None:intergenic
AACGGTGTCAGTTAGTAATT+TGG 0.243488 4_4:-77637903 None:intergenic
GAGAATCTTTGGCCACATTT+TGG 0.261276 4_4:-77637862 None:intergenic
AACTAATTGTTCAAGGTTAG+AGG 0.335946 4_4:-77637719 None:intergenic
GAAACGTATGCTAAGGTATA+TGG 0.366174 4_4:-77637691 None:intergenic
CAGGGGTTACATGCTGGAAT+TGG 0.395685 4_4:-77637823 None:intergenic
AAATCAGCAGCTGAATTTGT+TGG 0.419411 4_4:+77638570 Msa0705100:CDS
TACCAATTTAGGCCAATACT+TGG 0.442164 4_4:+77638809 Msa0705100:three_prime_UTR
TGGCCACCTTCATCAGCAGC+AGG 0.453286 4_4:-77637842 None:intergenic
ATTAAAATGACCCCAAAAGA+AGG 0.454890 4_4:-77638684 None:intergenic
CAGCAGCAGGGGTTACATGC+TGG 0.456273 4_4:-77637829 None:intergenic
AAAATCCCATGAAAGCTCTT+GGG 0.505602 4_4:+77637937 Msa0705100:CDS
AAAAGCAAAGAATCAGTTGA+AGG 0.507499 4_4:+77638540 Msa0705100:CDS
GTAACCCCTGCTGCTGATGA+AGG 0.514461 4_4:+77637836 Msa0705100:CDS
CAAACTTACTCCAAATTTGG+TGG 0.516547 4_4:-77638004 None:intergenic
GGCCACCTTCATCAGCAGCA+GGG 0.529923 4_4:-77637841 None:intergenic
AAAACTGCATCTGAAGATCA+TGG 0.536891 4_4:-77637979 None:intergenic
AGACACTACAGATTCTGATA+AGG 0.542472 4_4:+77638626 Msa0705100:CDS
ACTAATTGTTCAAGGTTAGA+GGG 0.547228 4_4:-77637718 None:intergenic
GCCACCTTCATCAGCAGCAG+GGG 0.559916 4_4:-77637840 None:intergenic
TTTCTCCCAAGAGCTTTCAT+GGG 0.569638 4_4:-77637942 None:intergenic
AATTGTGATGCTGTTATTGG+AGG 0.583515 4_4:+77638710 Msa0705100:three_prime_UTR
GGGATGAGAAACGTATGCTA+AGG 0.595808 4_4:-77637698 None:intergenic
AACTAGAAGCGTCATTCACA+TGG 0.599531 4_4:-77638906 None:intergenic
CGTATGCTAAGGTATATGGT+TGG 0.601682 4_4:-77637687 None:intergenic
GATGCTGTTATTGGAGGAGA+TGG 0.605362 4_4:+77638716 Msa0705100:three_prime_UTR
TGTCAGTTAGTAATTTGGAA+AGG 0.607458 4_4:-77637898 None:intergenic
AATCCATAAGACAAAAGAGA+AGG 0.608547 4_4:+77638599 Msa0705100:CDS
GTTAGTAATTTGGAAAGGCG+TGG 0.619952 4_4:-77637893 None:intergenic
AGGGGAAAAGGAGAACATGA+AGG 0.650023 4_4:+77638486 Msa0705100:CDS
ACCCCTGCTGCTGATGAAGG+TGG 0.657057 4_4:+77637839 Msa0705100:CDS
TGATGAAGGTGGCCAAAATG+TGG 0.672717 4_4:+77637850 Msa0705100:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTCATATATATACATTAAAT+TGG - chr4_4:77638422-77638441 None:intergenic 10.0%
!! ATATATATGAATATTAATGT+AGG + chr4_4:77638431-77638450 Msa0705100:intron 10.0%
!! TTCATATATATACATTAAAT+TGG - chr4_4:77638422-77638441 None:intergenic 10.0%
!! ATATATATGAATATTAATGT+AGG + chr4_4:77638431-77638450 Msa0705100:intron 10.0%
!! AATTAAAAACTAATTGTTCA+AGG - chr4_4:77637729-77637748 None:intergenic 15.0%
!! AAAATAGTTTAATGTTGATA+TGG + chr4_4:77638146-77638165 Msa0705100:intron 15.0%
!! TGTAAATTCATAAAAATGAT+TGG - chr4_4:77638221-77638240 None:intergenic 15.0%
!!! ATATATATATGATTTGTTGA+CGG + chr4_4:77638336-77638355 Msa0705100:intron 15.0%
!!! AAATATTTTTTTCCTTCTTT+TGG + chr4_4:77638672-77638691 Msa0705100:three_prime_UTR 15.0%
!!! AATATTTTTTTCCTTCTTTT+GGG + chr4_4:77638673-77638692 Msa0705100:three_prime_UTR 15.0%
!! TGTATGAAACAATTTATTTA+TGG + chr4_4:77638752-77638771 Msa0705100:three_prime_UTR 15.0%
!! AATTAAAAACTAATTGTTCA+AGG - chr4_4:77637729-77637748 None:intergenic 15.0%
!! AAAATAGTTTAATGTTGATA+TGG + chr4_4:77638146-77638165 Msa0705100:intron 15.0%
!! TGTAAATTCATAAAAATGAT+TGG - chr4_4:77638221-77638240 None:intergenic 15.0%
!!! ATATATATATGATTTGTTGA+CGG + chr4_4:77638336-77638355 Msa0705100:intron 15.0%
!!! AAATATTTTTTTCCTTCTTT+TGG + chr4_4:77638672-77638691 Msa0705100:three_prime_UTR 15.0%
!!! AATATTTTTTTCCTTCTTTT+GGG + chr4_4:77638673-77638692 Msa0705100:three_prime_UTR 15.0%
!! TGTATGAAACAATTTATTTA+TGG + chr4_4:77638752-77638771 Msa0705100:three_prime_UTR 15.0%
!! AAAAAGAAGAAAAAGTAGTA+TGG - chr4_4:77637786-77637805 None:intergenic 20.0%
!!! CAAAAGTCTATTTCATTTTT+AGG + chr4_4:77638035-77638054 Msa0705100:intron 20.0%
!! CAATACAATCTTGAAATTAT+AGG + chr4_4:77638068-77638087 Msa0705100:intron 20.0%
!!! TTATGACTGAATATTTTTCA+AGG - chr4_4:77638270-77638289 None:intergenic 20.0%
!! ATATGAATATTAATGTAGGT+AGG + chr4_4:77638435-77638454 Msa0705100:intron 20.0%
!!! ATATTTTTTTCCTTCTTTTG+GGG + chr4_4:77638674-77638693 Msa0705100:three_prime_UTR 20.0%
!!! TTCATACATTTTACCAATTT+AGG + chr4_4:77638798-77638817 Msa0705100:three_prime_UTR 20.0%
!!! GAATTGCTATTATGTATTTT+TGG - chr4_4:77638880-77638899 None:intergenic 20.0%
!! AAAAAGAAGAAAAAGTAGTA+TGG - chr4_4:77637786-77637805 None:intergenic 20.0%
!!! CAAAAGTCTATTTCATTTTT+AGG + chr4_4:77638035-77638054 Msa0705100:intron 20.0%
!! CAATACAATCTTGAAATTAT+AGG + chr4_4:77638068-77638087 Msa0705100:intron 20.0%
!!! TTATGACTGAATATTTTTCA+AGG - chr4_4:77638270-77638289 None:intergenic 20.0%
!! ATATGAATATTAATGTAGGT+AGG + chr4_4:77638435-77638454 Msa0705100:intron 20.0%
!!! ATATTTTTTTCCTTCTTTTG+GGG + chr4_4:77638674-77638693 Msa0705100:three_prime_UTR 20.0%
!!! TTCATACATTTTACCAATTT+AGG + chr4_4:77638798-77638817 Msa0705100:three_prime_UTR 20.0%
!!! GAATTGCTATTATGTATTTT+TGG - chr4_4:77638880-77638899 None:intergenic 20.0%
!!! GTTTTTAATTAGCATTAGCA+TGG + chr4_4:77637739-77637758 Msa0705100:exon 25.0%
!!! TGTATCTATTTTTCAGTTTC+AGG + chr4_4:77638466-77638485 Msa0705100:intron 25.0%
!!! GTATCTATTTTTCAGTTTCA+GGG + chr4_4:77638467-77638486 Msa0705100:intron 25.0%
!!! TATCTATTTTTCAGTTTCAG+GGG + chr4_4:77638468-77638487 Msa0705100:intron 25.0%
!! TTTTCAAATCTTCCAAGTAT+TGG - chr4_4:77638824-77638843 None:intergenic 25.0%
!!! GTTTTTAATTAGCATTAGCA+TGG + chr4_4:77637739-77637758 Msa0705100:exon 25.0%
!!! TGTATCTATTTTTCAGTTTC+AGG + chr4_4:77638466-77638485 Msa0705100:intron 25.0%
!!! GTATCTATTTTTCAGTTTCA+GGG + chr4_4:77638467-77638486 Msa0705100:intron 25.0%
!!! TATCTATTTTTCAGTTTCAG+GGG + chr4_4:77638468-77638487 Msa0705100:intron 25.0%
!! TTTTCAAATCTTCCAAGTAT+TGG - chr4_4:77638824-77638843 None:intergenic 25.0%
ACTAATTGTTCAAGGTTAGA+GGG - chr4_4:77637721-77637740 None:intergenic 30.0%
AACTAATTGTTCAAGGTTAG+AGG - chr4_4:77637722-77637741 None:intergenic 30.0%
TGTCAGTTAGTAATTTGGAA+AGG - chr4_4:77637901-77637920 None:intergenic 30.0%
!!! GGATTTTTTAAGCAGAGAAA+CGG - chr4_4:77637924-77637943 None:intergenic 30.0%
CTACAAACTTACTCCAAATT+TGG - chr4_4:77638010-77638029 None:intergenic 30.0%
TATATGTCTGACTTTAGACA+TGG - chr4_4:77638321-77638340 None:intergenic 30.0%
AAAAGCAAAGAATCAGTTGA+AGG + chr4_4:77638540-77638559 Msa0705100:CDS 30.0%
AATCCATAAGACAAAAGAGA+AGG + chr4_4:77638599-77638618 Msa0705100:CDS 30.0%
ATTAAAATGACCCCAAAAGA+AGG - chr4_4:77638687-77638706 None:intergenic 30.0%
CAAAATTGTGATGCTGTTAT+TGG + chr4_4:77638707-77638726 Msa0705100:three_prime_UTR 30.0%
ACTAATTGTTCAAGGTTAGA+GGG - chr4_4:77637721-77637740 None:intergenic 30.0%
AACTAATTGTTCAAGGTTAG+AGG - chr4_4:77637722-77637741 None:intergenic 30.0%
TGTCAGTTAGTAATTTGGAA+AGG - chr4_4:77637901-77637920 None:intergenic 30.0%
!!! GGATTTTTTAAGCAGAGAAA+CGG - chr4_4:77637924-77637943 None:intergenic 30.0%
CTACAAACTTACTCCAAATT+TGG - chr4_4:77638010-77638029 None:intergenic 30.0%
TATATGTCTGACTTTAGACA+TGG - chr4_4:77638321-77638340 None:intergenic 30.0%
AAAAGCAAAGAATCAGTTGA+AGG + chr4_4:77638540-77638559 Msa0705100:CDS 30.0%
AATCCATAAGACAAAAGAGA+AGG + chr4_4:77638599-77638618 Msa0705100:CDS 30.0%
ATTAAAATGACCCCAAAAGA+AGG - chr4_4:77638687-77638706 None:intergenic 30.0%
CAAAATTGTGATGCTGTTAT+TGG + chr4_4:77638707-77638726 Msa0705100:three_prime_UTR 30.0%
GAAACGTATGCTAAGGTATA+TGG - chr4_4:77637694-77637713 None:intergenic 35.0%
!! TGGTTTTTCTGGAGAATCTT+TGG - chr4_4:77637876-77637895 None:intergenic 35.0%
! AACGGTGTCAGTTAGTAATT+TGG - chr4_4:77637906-77637925 None:intergenic 35.0%
AAAAATCCCATGAAAGCTCT+TGG + chr4_4:77637936-77637955 Msa0705100:CDS 35.0%
AAAATCCCATGAAAGCTCTT+GGG + chr4_4:77637937-77637956 Msa0705100:CDS 35.0%
AAAACTGCATCTGAAGATCA+TGG - chr4_4:77637982-77638001 None:intergenic 35.0%
CAAACTTACTCCAAATTTGG+TGG - chr4_4:77638007-77638026 None:intergenic 35.0%
!! TTTTTCAGTTTCAGGGGAAA+AGG + chr4_4:77638474-77638493 Msa0705100:intron 35.0%
AAATCAGCAGCTGAATTTGT+TGG + chr4_4:77638570-77638589 Msa0705100:CDS 35.0%
! TCACCTTCTCTTTTGTCTTA+TGG - chr4_4:77638605-77638624 None:intergenic 35.0%
AGACACTACAGATTCTGATA+AGG + chr4_4:77638626-77638645 Msa0705100:CDS 35.0%
AATTGTGATGCTGTTATTGG+AGG + chr4_4:77638710-77638729 Msa0705100:three_prime_UTR 35.0%
TACCAATTTAGGCCAATACT+TGG + chr4_4:77638809-77638828 Msa0705100:three_prime_UTR 35.0%
!! TTCCAAGTATTGGCCTAAAT+TGG - chr4_4:77638814-77638833 None:intergenic 35.0%
GAAACGTATGCTAAGGTATA+TGG - chr4_4:77637694-77637713 None:intergenic 35.0%
!! TGGTTTTTCTGGAGAATCTT+TGG - chr4_4:77637876-77637895 None:intergenic 35.0%
! AACGGTGTCAGTTAGTAATT+TGG - chr4_4:77637906-77637925 None:intergenic 35.0%
AAAAATCCCATGAAAGCTCT+TGG + chr4_4:77637936-77637955 Msa0705100:CDS 35.0%
AAAATCCCATGAAAGCTCTT+GGG + chr4_4:77637937-77637956 Msa0705100:CDS 35.0%
AAAACTGCATCTGAAGATCA+TGG - chr4_4:77637982-77638001 None:intergenic 35.0%
CAAACTTACTCCAAATTTGG+TGG - chr4_4:77638007-77638026 None:intergenic 35.0%
!! TTTTTCAGTTTCAGGGGAAA+AGG + chr4_4:77638474-77638493 Msa0705100:intron 35.0%
AAATCAGCAGCTGAATTTGT+TGG + chr4_4:77638570-77638589 Msa0705100:CDS 35.0%
! TCACCTTCTCTTTTGTCTTA+TGG - chr4_4:77638605-77638624 None:intergenic 35.0%
AGACACTACAGATTCTGATA+AGG + chr4_4:77638626-77638645 Msa0705100:CDS 35.0%
AATTGTGATGCTGTTATTGG+AGG + chr4_4:77638710-77638729 Msa0705100:three_prime_UTR 35.0%
TACCAATTTAGGCCAATACT+TGG + chr4_4:77638809-77638828 Msa0705100:three_prime_UTR 35.0%
!! TTCCAAGTATTGGCCTAAAT+TGG - chr4_4:77638814-77638833 None:intergenic 35.0%
! GAGAATCTTTGGCCACATTT+TGG - chr4_4:77637865-77637884 None:intergenic 40.0%
GTTAGTAATTTGGAAAGGCG+TGG - chr4_4:77637896-77637915 None:intergenic 40.0%
TTTCTCCCAAGAGCTTTCAT+GGG - chr4_4:77637945-77637964 None:intergenic 40.0%
! TTTTCTCCCAAGAGCTTTCA+TGG - chr4_4:77637946-77637965 None:intergenic 40.0%
! GCAGTTTTCACCACCAAATT+TGG + chr4_4:77637994-77638013 Msa0705100:CDS 40.0%
!! AACTAGAAGCGTCATTCACA+TGG - chr4_4:77638909-77638928 None:intergenic 40.0%
CGTATGCTAAGGTATATGGT+TGG - chr4_4:77637690-77637709 None:intergenic 40.0%
! GAGAATCTTTGGCCACATTT+TGG - chr4_4:77637865-77637884 None:intergenic 40.0%
GTTAGTAATTTGGAAAGGCG+TGG - chr4_4:77637896-77637915 None:intergenic 40.0%
TTTCTCCCAAGAGCTTTCAT+GGG - chr4_4:77637945-77637964 None:intergenic 40.0%
! TTTTCTCCCAAGAGCTTTCA+TGG - chr4_4:77637946-77637965 None:intergenic 40.0%
! GCAGTTTTCACCACCAAATT+TGG + chr4_4:77637994-77638013 Msa0705100:CDS 40.0%
!! AACTAGAAGCGTCATTCACA+TGG - chr4_4:77638909-77638928 None:intergenic 40.0%
GGGATGAGAAACGTATGCTA+AGG - chr4_4:77637701-77637720 None:intergenic 45.0%
TGATGAAGGTGGCCAAAATG+TGG + chr4_4:77637850-77637869 Msa0705100:CDS 45.0%
!! TTGGAAAGGCGTGGTTTTTC+TGG - chr4_4:77637887-77637906 None:intergenic 45.0%
AGGGGAAAAGGAGAACATGA+AGG + chr4_4:77638486-77638505 Msa0705100:CDS 45.0%
GATGCTGTTATTGGAGGAGA+TGG + chr4_4:77638716-77638735 Msa0705100:three_prime_UTR 45.0%
GGGATGAGAAACGTATGCTA+AGG - chr4_4:77637701-77637720 None:intergenic 45.0%
TGATGAAGGTGGCCAAAATG+TGG + chr4_4:77637850-77637869 Msa0705100:CDS 45.0%
!! TTGGAAAGGCGTGGTTTTTC+TGG - chr4_4:77637887-77637906 None:intergenic 45.0%
AGGGGAAAAGGAGAACATGA+AGG + chr4_4:77638486-77638505 Msa0705100:CDS 45.0%
GATGCTGTTATTGGAGGAGA+TGG + chr4_4:77638716-77638735 Msa0705100:three_prime_UTR 45.0%
CAGGGGTTACATGCTGGAAT+TGG - chr4_4:77637826-77637845 None:intergenic 50.0%
CAGGGGTTACATGCTGGAAT+TGG - chr4_4:77637826-77637845 None:intergenic 50.0%
GTAACCCCTGCTGCTGATGA+AGG + chr4_4:77637836-77637855 Msa0705100:CDS 55.0%
GTAACCCCTGCTGCTGATGA+AGG + chr4_4:77637836-77637855 Msa0705100:CDS 55.0%
CAGCAGCAGGGGTTACATGC+TGG - chr4_4:77637832-77637851 None:intergenic 60.0%
ACCCCTGCTGCTGATGAAGG+TGG + chr4_4:77637839-77637858 Msa0705100:CDS 60.0%
GCCACCTTCATCAGCAGCAG+GGG - chr4_4:77637843-77637862 None:intergenic 60.0%
GGCCACCTTCATCAGCAGCA+GGG - chr4_4:77637844-77637863 None:intergenic 60.0%
TGGCCACCTTCATCAGCAGC+AGG - chr4_4:77637845-77637864 None:intergenic 60.0%
CAGCAGCAGGGGTTACATGC+TGG - chr4_4:77637832-77637851 None:intergenic 60.0%
ACCCCTGCTGCTGATGAAGG+TGG + chr4_4:77637839-77637858 Msa0705100:CDS 60.0%
GCCACCTTCATCAGCAGCAG+GGG - chr4_4:77637843-77637862 None:intergenic 60.0%
GGCCACCTTCATCAGCAGCA+GGG - chr4_4:77637844-77637863 None:intergenic 60.0%
TGGCCACCTTCATCAGCAGC+AGG - chr4_4:77637845-77637864 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr4_4 gene 77637688 77638940 77637688 ID=Msa0705100;Name=Msa0705100
chr4_4 mRNA 77637688 77638940 77637688 ID=Msa0705100-mRNA-1;Parent=Msa0705100;Name=Msa0705100-mRNA-1;_AED=0.00;_eAED=0.00;_QI=70|1|1|1|1|1|2|272|148
chr4_4 exon 77637688 77638017 77637688 ID=Msa0705100-mRNA-1:exon:24669;Parent=Msa0705100-mRNA-1
chr4_4 exon 77638482 77638940 77638482 ID=Msa0705100-mRNA-1:exon:24670;Parent=Msa0705100-mRNA-1
chr4_4 five_prime_UTR 77637688 77637757 77637688 ID=Msa0705100-mRNA-1:five_prime_utr;Parent=Msa0705100-mRNA-1
chr4_4 CDS 77637758 77638017 77637758 ID=Msa0705100-mRNA-1:cds;Parent=Msa0705100-mRNA-1
chr4_4 CDS 77638482 77638668 77638482 ID=Msa0705100-mRNA-1:cds;Parent=Msa0705100-mRNA-1
chr4_4 three_prime_UTR 77638669 77638940 77638669 ID=Msa0705100-mRNA-1:three_prime_utr;Parent=Msa0705100-mRNA-1
Gene Sequence

>Msa0705100

ATGGAAAATAAATTGATTAGCAGAACCATACTACTTTTTCTTCTTTTTAGCATCTTGATCATTCTCCAATTCCAGCATGTAACCCCTGCTGCTGATGAAGGTGGCCAAAATGTGGCCAAAGATTCTCCAGAAAAACCACGCCTTTCCAAATTACTAACTGACACCGTTTCTCTGCTTAAAAAATCCCATGAAAGCTCTTGGGAGAAAATCAAAACTGTCATCCATGATCTTCAGATGCAGTTTTCACCACCAAATTTGGATTTCAGGGGAAAAGGAGAACATGAAGGAGTGAAAGAAGCAGTTGAGAAGAGTTTTGACAAAAGCAAAGAATCAGTTGAAGGAACTGCTAAATCAGCAGCTGAATTTGTTGGAGAAACAATCCATAAGACAAAAGAGAAGGTGAAAGACACTACAGATTCTGATAAGGATTCTAAAGCAGAACTTTGA
Protein sequence

>Msa0705100

MENKLISRTILLFLLFSILIILQFQHVTPAADEGGQNVAKDSPEKPRLSKLLTDTVSLLKKSHESSWEKIKTVIHDLQMQFSPPNLDFRGKGEHEGVKEAVEKSFDKSKESVEGTAKSAAEFVGETIHKTKEKVKDTTDSDKDSKAEL*