AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene073897

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene073897.t1 MTR_1g045040 85.075 134 20 0 1 134 1 134 6.28e-75 219
MS.gene073897.t1 MTR_1g089830 75.573 131 25 2 1 130 1 125 1.48e-67 201
MS.gene073897.t1 MTR_8g089170 38.776 147 64 3 6 127 7 152 1.09e-22 87.4
MS.gene073897.t1 MTR_8g089130 36.424 151 70 2 6 130 7 157 6.74e-22 85.5
MS.gene073897.t1 MTR_8g039350 70.732 41 12 0 4 44 15 55 1.72e-16 69.3
MS.gene073897.t1 MTR_4g028990 40.625 96 47 4 43 130 3 96 1.65e-12 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 20 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACAAAAGCTTCAAAGTCTA+TGG 0.184389 1.3:+26798031 MS.gene073897:CDS
TGTATACCAAGCAATGAAAT+AGG 0.333899 1.3:+26798120 MS.gene073897:CDS
ATTTGATTCTTCACAATCAA+TGG 0.371459 1.3:-26797997 None:intergenic
CCAATGCCTATTTCATTGCT+TGG 0.392772 1.3:-26798126 None:intergenic
CCACAAGCATTACATAGTAT+TGG 0.402584 1.3:-26797420 None:intergenic
TGGAGATTGGTTTGAAAGCT+CGG 0.447768 1.3:-26797547 None:intergenic
GAAACTAAACTTTGGCGTAA+AGG 0.456777 1.3:+26797384 MS.gene073897:CDS
ATCAGACCTTGACGTTGAAA+AGG 0.459163 1.3:+26797509 MS.gene073897:CDS
TGCTTGTGGACTACATTTCA+AGG 0.461822 1.3:+26797434 MS.gene073897:CDS
GGACTACATTTCAAGGCTAA+AGG 0.474721 1.3:+26797441 MS.gene073897:CDS
TCTTCGGAAGATAGTTATCA+AGG 0.478433 1.3:-26797467 None:intergenic
GGAGATTGGTTTGAAAGCTC+GGG 0.493147 1.3:-26797546 None:intergenic
ATTGATTGTGAAGAATCAAA+TGG 0.496633 1.3:+26797999 MS.gene073897:CDS
CCAAGCAATGAAATAGGCAT+TGG 0.500278 1.3:+26798126 MS.gene073897:CDS
CATAGTATTGGATTCTCATA+CGG 0.534177 1.3:-26797408 None:intergenic
ACAAAAGCTTCAAAGTCTAT+GGG 0.556384 1.3:+26798032 MS.gene073897:CDS
GAGCTTTCAAACCAATCTCC+AGG 0.568278 1.3:+26797549 MS.gene073897:CDS
CCAATACTATGTAATGCTTG+TGG 0.568792 1.3:+26797420 MS.gene073897:CDS
CTTCGGAAGATAGTTATCAA+GGG 0.629882 1.3:-26797466 None:intergenic
GATTGTGAAGAATCAAATGG+AGG 0.671995 1.3:+26798002 MS.gene073897:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTATATTTAGTTGAAAAAT+GGG - chr1.3:26797610-26797629 None:intergenic 10.0%
!!! TTTTAATTTTTTTTGTAGAA+AGG + chr1.3:26797971-26797990 MS.gene073897:intron 10.0%
!! CTTTATATTTAGTTGAAAAA+TGG - chr1.3:26797611-26797630 None:intergenic 15.0%
!! TTATATTTAGTTGAAAAATG+GGG - chr1.3:26797609-26797628 None:intergenic 15.0%
!! AACACTACTATTTATATATG+AGG + chr1.3:26797716-26797735 MS.gene073897:intron 20.0%
!! TTATATGTATACATCATACA+CGG - chr1.3:26797949-26797968 None:intergenic 20.0%
!!! ATTGTAAGAATTTTCTTAAG+AGG + chr1.3:26797665-26797684 MS.gene073897:intron 20.0%
!!! TTATTGCATTTTTTATTACC+TGG - chr1.3:26797570-26797589 None:intergenic 20.0%
!!! TTTGAATGAATTGTATTGAT+GGG + chr1.3:26797810-26797829 MS.gene073897:intron 20.0%
!!! TTTTGAATGAATTGTATTGA+TGG + chr1.3:26797809-26797828 MS.gene073897:intron 20.0%
! ATTGACAATGAAAGGAATTA+GGG - chr1.3:26797756-26797775 None:intergenic 25.0%
! ATTGATTGTGAAGAATCAAA+TGG + chr1.3:26797999-26798018 MS.gene073897:CDS 25.0%
! ATTTGATTCTTCACAATCAA+TGG - chr1.3:26798000-26798019 None:intergenic 25.0%
! TATCCATAAATGTATGAATG+TGG - chr1.3:26797859-26797878 None:intergenic 25.0%
! TATTGACAATGAAAGGAATT+AGG - chr1.3:26797757-26797776 None:intergenic 25.0%
!! TTGAATGAATTGTATTGATG+GGG + chr1.3:26797811-26797830 MS.gene073897:intron 25.0%
!! TTTCTTAAGAGGTACAATTT+AGG + chr1.3:26797676-26797695 MS.gene073897:intron 25.0%
!! TTTTGACAGAAACTAAACTT+TGG + chr1.3:26797376-26797395 MS.gene073897:CDS 25.0%
!!! ATTTTTTATTACCTGGAGAT+TGG - chr1.3:26797563-26797582 None:intergenic 25.0%
AACAAAAGCTTCAAAGTCTA+TGG + chr1.3:26798031-26798050 MS.gene073897:CDS 30.0%
ACAAAAGCTTCAAAGTCTAT+GGG + chr1.3:26798032-26798051 MS.gene073897:CDS 30.0%
ACTCCACATTCATACATTTA+TGG + chr1.3:26797853-26797872 MS.gene073897:intron 30.0%
ATGCTCTTATTGACAATGAA+AGG - chr1.3:26797764-26797783 None:intergenic 30.0%
TGTATACCAAGCAATGAAAT+AGG + chr1.3:26798120-26798139 MS.gene073897:CDS 30.0%
! CATAGTATTGGATTCTCATA+CGG - chr1.3:26797411-26797430 None:intergenic 30.0%
!! GTCTGATAATTGATTTTGCT+GGG - chr1.3:26797496-26797515 None:intergenic 30.0%
AGCATTCATTTGAGTAGACA+CGG + chr1.3:26797779-26797798 MS.gene073897:intron 35.0%
ATTTGAGTAGACACGGTATT+AGG + chr1.3:26797786-26797805 MS.gene073897:intron 35.0%
CCAATACTATGTAATGCTTG+TGG + chr1.3:26797420-26797439 MS.gene073897:CDS 35.0%
CCACAAGCATTACATAGTAT+TGG - chr1.3:26797423-26797442 None:intergenic 35.0%
CTTCGGAAGATAGTTATCAA+GGG - chr1.3:26797469-26797488 None:intergenic 35.0%
GAAACTAAACTTTGGCGTAA+AGG + chr1.3:26797384-26797403 MS.gene073897:CDS 35.0%
GATTGTGAAGAATCAAATGG+AGG + chr1.3:26798002-26798021 MS.gene073897:CDS 35.0%
TCATACACGGTACATATCAA+TGG - chr1.3:26797936-26797955 None:intergenic 35.0%
TCTTCGGAAGATAGTTATCA+AGG - chr1.3:26797470-26797489 None:intergenic 35.0%
! GAATTGTATTGATGGGGATT+AGG + chr1.3:26797817-26797836 MS.gene073897:intron 35.0%
!! GGTCTGATAATTGATTTTGC+TGG - chr1.3:26797497-26797516 None:intergenic 35.0%
ATCAGACCTTGACGTTGAAA+AGG + chr1.3:26797509-26797528 MS.gene073897:CDS 40.0%
CCAAGCAATGAAATAGGCAT+TGG + chr1.3:26798126-26798145 MS.gene073897:CDS 40.0%
CCAATGCCTATTTCATTGCT+TGG - chr1.3:26798129-26798148 None:intergenic 40.0%
GGACTACATTTCAAGGCTAA+AGG + chr1.3:26797441-26797460 MS.gene073897:CDS 40.0%
! CAGATTCCTTTTCAACGTCA+AGG - chr1.3:26797518-26797537 None:intergenic 40.0%
! TGATTTTGCTGGGATGTCTT+CGG - chr1.3:26797486-26797505 None:intergenic 40.0%
! TGCTTGTGGACTACATTTCA+AGG + chr1.3:26797434-26797453 MS.gene073897:CDS 40.0%
!! TGGAGATTGGTTTGAAAGCT+CGG - chr1.3:26797550-26797569 None:intergenic 40.0%
GAGCTTTCAAACCAATCTCC+AGG + chr1.3:26797549-26797568 MS.gene073897:CDS 45.0%
!! GGAGATTGGTTTGAAAGCTC+GGG - chr1.3:26797549-26797568 None:intergenic 45.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 26797372 26798194 26797372 ID=MS.gene073897
chr1.3 mRNA 26797372 26798194 26797372 ID=MS.gene073897.t1;Parent=MS.gene073897
chr1.3 exon 26797372 26797570 26797372 ID=MS.gene073897.t1.exon1;Parent=MS.gene073897.t1
chr1.3 CDS 26797372 26797570 26797372 ID=cds.MS.gene073897.t1;Parent=MS.gene073897.t1
chr1.3 exon 26797989 26798194 26797989 ID=MS.gene073897.t1.exon2;Parent=MS.gene073897.t1
chr1.3 CDS 26797989 26798194 26797989 ID=cds.MS.gene073897.t1;Parent=MS.gene073897.t1
Gene Sequence

>MS.gene073897

ATGGTTTTGACAGAAACTAAACTTTGGCGTAAAGGACCGTATGAGAATCCAATACTATGTAATGCTTGTGGACTACATTTCAAGGCTAAAGGAACCCTTGATAACTATCTTCCGAAGACATCCCAGCAAAATCAATTATCAGACCTTGACGTTGAAAAGGAATCTGAAAGTGATCCCGAGCTTTCAAACCAATCTCCAGGTAATAAAAAATGCAATAAGTTAATTAACTATTCACCCCATTTTTCAACTAAATATAAAGCACAATTTATACAAGAAGAGTGAGCGAGAAAGTTATTGTAAGAATTTTCTTAAGAGGTACAATTTAGGAGTATTGTTATGATATAAACACTACTATTTATATATGAGGTGTAACATTGTCAACCCTAATTCCTTTCATTGTCAATAAGAGCATTCATTTGAGTAGACACGGTATTAGGTTTTGAATGAATTGTATTGATGGGGATTAGGTGACATACATACAACTCCACATTCATACATTTATGGATATATTTTTTTCAAATAATAGCATATATTTTTTCAAATATACATATAAATGATTATCCATTGATATGTACCGTGTATGATGTATACATATAAACTTTTAATTTTTTTTGTAGAAAGGACACCATTGATTGTGAAGAATCAAATGGAGGAGTTTCAACAAAAGCTTCAAAGTCTATGGGAATCTGAGAAAGAATCAAATGAATCATCTGAAGACAATATTTTGTTGTTTGATAATATCAACAACTGTATACCAAGCAATGAAATAGGCATTGGATGCACTCTACTAAAGACAGATGTTACTTCTAAAAAATCTGCATGA
Protein sequence

>MS.gene073897.t1

MVLTETKLWRKGPYENPILCNACGLHFKAKGTLDNYLPKTSQQNQLSDLDVEKESESDPELSNQSPERTPLIVKNQMEEFQQKLQSLWESEKESNESSEDNILLFDNINNCIPSNEIGIGCTLLKTDVTSKKSA