AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene030990

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene030990.t1 MTR_6g011470 58.673 196 31 5 1 146 15 210 1.39e-68 206
MS.gene030990.t1 MTR_6g011450 68.944 161 22 2 14 146 515 675 2.58e-64 208
MS.gene030990.t1 MTR_6g011450 68.944 161 22 2 14 146 653 813 1.02e-63 208
MS.gene030990.t1 MTR_4g073340 64.596 161 29 2 14 146 334 494 4.13e-57 186
MS.gene030990.t1 MTR_1g061130 34.211 114 71 3 15 126 847 958 9.98e-17 76.3
MS.gene030990.t1 MTR_1g061130 34.211 114 71 3 15 126 847 958 1.04e-16 76.3
MS.gene030990.t1 MTR_7g103840 28.916 166 78 6 15 146 854 1013 2.32e-14 69.3
MS.gene030990.t1 MTR_7g103840 28.916 166 78 6 15 146 856 1015 2.71e-14 69.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene030990.t1 AT4G04885 59.064 171 39 3 6 145 619 789 2.02e-60 199
MS.gene030990.t1 AT1G66500 47.500 120 55 3 14 125 233 352 7.90e-31 114
MS.gene030990.t1 AT5G43620 45.455 121 57 3 14 125 226 346 5.95e-29 109

Find 43 sgRNAs with CRISPR-Local

Find 49 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGACGAACCTTGAGAATATT+TGG 0.171658 6.2:-5628614 None:intergenic
GTGACTGCTGTGCTCATCTT+TGG 0.248435 6.2:-5628708 None:intergenic
AGAATATTTGGATCAGGATT+TGG 0.287072 6.2:-5628602 None:intergenic
TGCGAGAGGGCTTCTGCTTA+AGG 0.331127 6.2:-5628769 None:intergenic
TCTAGGAAAATCACCATATA+AGG 0.334486 6.2:-5628654 None:intergenic
CTGCATTTAGCATGAATAAT+GGG 0.336904 6.2:-5628983 None:intergenic
TCTGCATTTAGCATGAATAA+TGG 0.356112 6.2:-5628984 None:intergenic
GCTTAAAGGTGCCGAGGCAT+TGG 0.418088 6.2:+5628817 MS.gene030990:CDS
TCTGTAATCCGTGCCTTATA+TGG 0.421993 6.2:+5628641 MS.gene030990:CDS
ACCTTGAGAATATTTGGATC+AGG 0.433909 6.2:-5628608 None:intergenic
AGTGAGACGATGTGGCTTAA+AGG 0.439793 6.2:+5628803 MS.gene030990:CDS
GGAATGGACAGGTCGGAGTT+AGG 0.452200 6.2:+5628959 MS.gene030990:CDS
CTTAAAGGTGCCGAGGCATT+GGG 0.453885 6.2:+5628818 MS.gene030990:CDS
CGTGGGCCAGCTGGAGGTAA+AGG 0.456461 6.2:-5628578 None:intergenic
GGATTTGGACGTGGGCCAGC+TGG 0.467981 6.2:-5628587 None:intergenic
GCTCATCTTTGGATTTGAAT+CGG 0.471012 6.2:-5628697 None:intergenic
CATGGATTGGCATGTGACTA+AGG 0.476811 6.2:+5628730 MS.gene030990:CDS
TTGGGAGTCAAGTCAGCTCC+AGG 0.502567 6.2:+5628836 MS.gene030990:CDS
CCACAAGTTGTGCACTGTCT+AGG 0.510068 6.2:-5628671 None:intergenic
AGCACAGCAGTCACATGGAT+TGG 0.529243 6.2:+5628717 MS.gene030990:CDS
ATGCGACCTTTACCTCCAGC+TGG 0.541534 6.2:+5628572 MS.gene030990:CDS
CCTAGACAGTGCACAACTTG+TGG 0.549023 6.2:+5628671 MS.gene030990:CDS
AGCAGAAGCCCTCTCGCAAG+TGG 0.549289 6.2:+5628774 MS.gene030990:CDS
TTTGGATCAGGATTTGGACG+TGG 0.554965 6.2:-5628596 None:intergenic
CATCTTTGGATTTGAATCGG+TGG 0.563255 6.2:-5628694 None:intergenic
TTGGATCAGGATTTGGACGT+GGG 0.571398 6.2:-5628595 None:intergenic
ATTTGCAGTTCCTGCTGACG+AGG 0.577430 6.2:+5628901 MS.gene030990:CDS
TCCTGATCCAAATATTCTCA+AGG 0.580092 6.2:+5628607 MS.gene030990:CDS
GCATTGTGTGGAATAACAAC+AGG 0.585216 6.2:+5628938 MS.gene030990:CDS
GTGTGGAATAACAACAGGAA+TGG 0.585521 6.2:+5628943 MS.gene030990:CDS
AGATGAGCACAGCAGTCACA+TGG 0.587427 6.2:+5628712 MS.gene030990:CDS
GAATAACAACAGGAATGGAC+AGG 0.595748 6.2:+5628948 MS.gene030990:CDS
TTTGGACGTGGGCCAGCTGG+AGG 0.611386 6.2:-5628584 None:intergenic
CTCACAAACCACTTGCGAGA+GGG 0.612344 6.2:-5628782 None:intergenic
CAAAATACATGTGCATTGTG+TGG 0.618714 6.2:+5628926 MS.gene030990:CDS
GAAAATCACCATATAAGGCA+CGG 0.619885 6.2:-5628649 None:intergenic
GCTGGAGGTAAAGGTCGCAT+AGG 0.626586 6.2:-5628569 None:intergenic
ACTCACAAACCACTTGCGAG+AGG 0.632815 6.2:-5628783 None:intergenic
TGCATTTAGCATGAATAATG+GGG 0.635399 6.2:-5628982 None:intergenic
AACAACAGGAATGGACAGGT+CGG 0.643585 6.2:+5628952 MS.gene030990:CDS
TGACTTGACTCCCAATGCCT+CGG 0.643816 6.2:-5628828 None:intergenic
GATGTGGCTTAAAGGTGCCG+AGG 0.696373 6.2:+5628811 MS.gene030990:CDS
GGTTTGTGAGTGAGACGATG+TGG 0.711325 6.2:+5628795 MS.gene030990:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTCTTCATCTTTCTTTTCTT+CGG - chr6.2:5628882-5628901 None:intergenic 25.0%
AGAATATTTGGATCAGGATT+TGG - chr6.2:5628605-5628624 None:intergenic 30.0%
CTGCATTTAGCATGAATAAT+GGG - chr6.2:5628986-5629005 None:intergenic 30.0%
TCTAGGAAAATCACCATATA+AGG - chr6.2:5628657-5628676 None:intergenic 30.0%
TCTGCATTTAGCATGAATAA+TGG - chr6.2:5628987-5629006 None:intergenic 30.0%
TGCATTTAGCATGAATAATG+GGG - chr6.2:5628985-5629004 None:intergenic 30.0%
!! GCTTAAGGTTTTTAGACATA+TGG - chr6.2:5628757-5628776 None:intergenic 30.0%
ACCTTGAGAATATTTGGATC+AGG - chr6.2:5628611-5628630 None:intergenic 35.0%
CAAAATACATGTGCATTGTG+TGG + chr6.2:5628926-5628945 MS.gene030990:CDS 35.0%
GAAAATCACCATATAAGGCA+CGG - chr6.2:5628652-5628671 None:intergenic 35.0%
GCTCATCTTTGGATTTGAAT+CGG - chr6.2:5628700-5628719 None:intergenic 35.0%
TCCTGATCCAAATATTCTCA+AGG + chr6.2:5628607-5628626 MS.gene030990:CDS 35.0%
TGACGAACCTTGAGAATATT+TGG - chr6.2:5628617-5628636 None:intergenic 35.0%
! TTCATCTTTCTTTTCTTCGG+TGG - chr6.2:5628879-5628898 None:intergenic 35.0%
CATCTTTGGATTTGAATCGG+TGG - chr6.2:5628697-5628716 None:intergenic 40.0%
GAATAACAACAGGAATGGAC+AGG + chr6.2:5628948-5628967 MS.gene030990:CDS 40.0%
GCATTGTGTGGAATAACAAC+AGG + chr6.2:5628938-5628957 MS.gene030990:CDS 40.0%
GTGTGGAATAACAACAGGAA+TGG + chr6.2:5628943-5628962 MS.gene030990:CDS 40.0%
TCTGTAATCCGTGCCTTATA+TGG + chr6.2:5628641-5628660 MS.gene030990:CDS 40.0%
! TTTCTTTTCTTCGGTGGTCT+CGG - chr6.2:5628873-5628892 None:intergenic 40.0%
AACAACAGGAATGGACAGGT+CGG + chr6.2:5628952-5628971 MS.gene030990:CDS 45.0%
AGTGAGACGATGTGGCTTAA+AGG + chr6.2:5628803-5628822 MS.gene030990:CDS 45.0%
TTGGATCAGGATTTGGACGT+GGG - chr6.2:5628598-5628617 None:intergenic 45.0%
TTTGGATCAGGATTTGGACG+TGG - chr6.2:5628599-5628618 None:intergenic 45.0%
!! CATGGATTGGCATGTGACTA+AGG + chr6.2:5628730-5628749 MS.gene030990:CDS 45.0%
!!! GTATTTTGATCCTCGTCAGC+AGG - chr6.2:5628914-5628933 None:intergenic 45.0%
ACTCACAAACCACTTGCGAG+AGG - chr6.2:5628786-5628805 None:intergenic 50.0%
AGATGAGCACAGCAGTCACA+TGG + chr6.2:5628712-5628731 MS.gene030990:CDS 50.0%
AGCACAGCAGTCACATGGAT+TGG + chr6.2:5628717-5628736 MS.gene030990:CDS 50.0%
ATTTGCAGTTCCTGCTGACG+AGG + chr6.2:5628901-5628920 MS.gene030990:CDS 50.0%
CCACAAGTTGTGCACTGTCT+AGG - chr6.2:5628674-5628693 None:intergenic 50.0%
CCTAGACAGTGCACAACTTG+TGG + chr6.2:5628671-5628690 MS.gene030990:CDS 50.0%
CTCACAAACCACTTGCGAGA+GGG - chr6.2:5628785-5628804 None:intergenic 50.0%
GGTTTGTGAGTGAGACGATG+TGG + chr6.2:5628795-5628814 MS.gene030990:CDS 50.0%
GTCTCGGTTGGCAAAAAACC+TGG - chr6.2:5628857-5628876 None:intergenic 50.0%
GTGACTGCTGTGCTCATCTT+TGG - chr6.2:5628711-5628730 None:intergenic 50.0%
TGACTTGACTCCCAATGCCT+CGG - chr6.2:5628831-5628850 None:intergenic 50.0%
! TTTTCTTCGGTGGTCTCGGT+TGG - chr6.2:5628869-5628888 None:intergenic 50.0%
!! CTTAAAGGTGCCGAGGCATT+GGG + chr6.2:5628818-5628837 MS.gene030990:CDS 50.0%
ATGCGACCTTTACCTCCAGC+TGG + chr6.2:5628572-5628591 MS.gene030990:CDS 55.0%
GGAATGGACAGGTCGGAGTT+AGG + chr6.2:5628959-5628978 MS.gene030990:CDS 55.0%
TGCGAGAGGGCTTCTGCTTA+AGG - chr6.2:5628772-5628791 None:intergenic 55.0%
TTGGGAGTCAAGTCAGCTCC+AGG + chr6.2:5628836-5628855 MS.gene030990:CDS 55.0%
!! GATGTGGCTTAAAGGTGCCG+AGG + chr6.2:5628811-5628830 MS.gene030990:CDS 55.0%
!! GCTTAAAGGTGCCGAGGCAT+TGG + chr6.2:5628817-5628836 MS.gene030990:CDS 55.0%
AGCAGAAGCCCTCTCGCAAG+TGG + chr6.2:5628774-5628793 MS.gene030990:CDS 60.0%
CGTGGGCCAGCTGGAGGTAA+AGG - chr6.2:5628581-5628600 None:intergenic 65.0%
GGATTTGGACGTGGGCCAGC+TGG - chr6.2:5628590-5628609 None:intergenic 65.0%
TTTGGACGTGGGCCAGCTGG+AGG - chr6.2:5628587-5628606 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 5628572 5629012 5628572 ID=MS.gene030990
chr6.2 mRNA 5628572 5629012 5628572 ID=MS.gene030990.t1;Parent=MS.gene030990
chr6.2 exon 5628572 5629012 5628572 ID=MS.gene030990.t1.exon1;Parent=MS.gene030990.t1
chr6.2 CDS 5628572 5629012 5628572 ID=cds.MS.gene030990.t1;Parent=MS.gene030990.t1
Gene Sequence

>MS.gene030990

ATGCGACCTTTACCTCCAGCTGGCCCACGTCCAAATCCTGATCCAAATATTCTCAAGGTTCGTCATGAATCTGTAATCCGTGCCTTATATGGTGATTTTCCTAGACAGTGCACAACTTGTGGCCACCGATTCAAATCCAAAGATGAGCACAGCAGTCACATGGATTGGCATGTGACTAAGGACCATATGTCTAAAAACCTTAAGCAGAAGCCCTCTCGCAAGTGGTTTGTGAGTGAGACGATGTGGCTTAAAGGTGCCGAGGCATTGGGAGTCAAGTCAGCTCCAGGTTTTTTGCCAACCGAGACCACCGAAGAAAAGAAAGATGAAGAATTTGCAGTTCCTGCTGACGAGGATCAAAATACATGTGCATTGTGTGGAATAACAACAGGAATGGACAGGTCGGAGTTAGGCCCCATTATTCATGCTAAATGCAGATCTTAA
Protein sequence

>MS.gene030990.t1

MRPLPPAGPRPNPDPNILKVRHESVIRALYGDFPRQCTTCGHRFKSKDEHSSHMDWHVTKDHMSKNLKQKPSRKWFVSETMWLKGAEALGVKSAPGFLPTETTEEKKDEEFAVPADEDQNTCALCGITTGMDRSELGPIIHAKCRS