AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene53526

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene53526.t1 MTR_1g045040 87.313 134 17 0 1 134 1 134 1.31e-77 226
MS.gene53526.t1 MTR_1g089830 76.336 131 24 2 1 130 1 125 2.34e-68 202
MS.gene53526.t1 MTR_8g089170 39.456 147 63 3 6 127 7 152 4.51e-23 88.6
MS.gene53526.t1 MTR_8g089130 36.424 151 70 3 6 130 7 157 9.01e-22 85.1
MS.gene53526.t1 MTR_8g039350 73.171 41 11 0 4 44 15 55 3.76e-17 70.9
MS.gene53526.t1 MTR_4g028990 40.625 96 47 4 43 130 3 96 2.54e-12 59.3
MS.gene53526.t1 MTR_5g013370 51.852 54 25 1 3 56 12 64 2.98e-11 60.1
MS.gene53526.t1 MTR_5g013370 51.852 54 25 1 3 56 12 64 4.52e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 22 sgRNAs with CRISPR-Local

Find 49 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACAAAAGCTTCAAAGTCTA+TGG 0.184389 1.2:+27850793 MS.gene53526:CDS
CGCTTGTGGGCTACATTTCA+AGG 0.378248 1.2:+27850198 MS.gene53526:CDS
CAATACTATGTAACGCTTGT+GGG 0.416623 1.2:+27850185 MS.gene53526:CDS
CCACAAGCGTTACATAGTAT+TGG 0.447482 1.2:-27850184 None:intergenic
TGGAGATTGGTTTGAAAGCT+CGG 0.447768 1.2:-27850311 None:intergenic
GAAACTAAACTTTGGCGTAA+AGG 0.456777 1.2:+27850148 MS.gene53526:CDS
ATCAGACCTTGACGTGGAAA+AGG 0.466063 1.2:+27850273 MS.gene53526:CDS
TCTTCGGAAGATAGTTATCA+AGG 0.478433 1.2:-27850231 None:intergenic
TGTATACCAAGCAATGAGAT+AGG 0.478624 1.2:+27850882 MS.gene53526:CDS
CATAGTATTGGCTTCTCATA+CGG 0.490978 1.2:-27850172 None:intergenic
ATCGATTGTGAAGAATCAAA+TGG 0.491491 1.2:+27850761 MS.gene53526:CDS
GGGCTACATTTCAAGGCTAA+AGG 0.492067 1.2:+27850205 MS.gene53526:CDS
GGAGATTGGTTTGAAAGCTC+GGG 0.493147 1.2:-27850310 None:intergenic
CCAAGCAATGAGATAGGCAT+TGG 0.496933 1.2:+27850888 MS.gene53526:CDS
ATTTGATTCTTCACAATCGA+TGG 0.523804 1.2:-27850759 None:intergenic
CCAATACTATGTAACGCTTG+TGG 0.549603 1.2:+27850184 MS.gene53526:CDS
ACAAAAGCTTCAAAGTCTAT+GGG 0.556384 1.2:+27850794 MS.gene53526:CDS
CCAATGCCTATCTCATTGCT+TGG 0.566560 1.2:-27850888 None:intergenic
GAGCTTTCAAACCAATCTCC+AGG 0.568278 1.2:+27850313 MS.gene53526:CDS
CTTCGGAAGATAGTTATCAA+GGG 0.629882 1.2:-27850230 None:intergenic
GATTGTGAAGAATCAAATGG+AGG 0.680011 1.2:+27850764 MS.gene53526:CDS
TCAGTTATCAGACCTTGACG+TGG 0.685195 1.2:+27850267 MS.gene53526:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ACTTTATATTTGTTGAAAAA+TGG - chr1.2:27850375-27850394 None:intergenic 15.0%
!!! ACTTTTAATTTTTTGTAGAA+AGG + chr1.2:27850733-27850752 MS.gene53526:intron 15.0%
!!! CTTTATATTTGTTGAAAAAT+GGG - chr1.2:27850374-27850393 None:intergenic 15.0%
!!! TTTATATTTGTTGAAAAATG+GGG - chr1.2:27850373-27850392 None:intergenic 15.0%
!! AACACTACTATTTATATATG+AGG + chr1.2:27850479-27850498 MS.gene53526:intron 20.0%
!! TTATATGTATACATCATACA+CGG - chr1.2:27850713-27850732 None:intergenic 20.0%
!!! ATTGTAAGAATTTTCTTAAG+AGG + chr1.2:27850428-27850447 MS.gene53526:intron 20.0%
!!! TTATTGCATTTTTTATTACC+TGG - chr1.2:27850334-27850353 None:intergenic 20.0%
!!! TTTGAATGAATTGTATTGAT+GGG + chr1.2:27850573-27850592 MS.gene53526:intron 20.0%
!!! TTTTGAATGAATTGTATTGA+TGG + chr1.2:27850572-27850591 MS.gene53526:intron 20.0%
! ATTGACAATGAAAGGAATTA+GGG - chr1.2:27850519-27850538 None:intergenic 25.0%
! TATCCATAAATGTATGAATG+TGG - chr1.2:27850622-27850641 None:intergenic 25.0%
! TATTGACAATGAAAGGAATT+AGG - chr1.2:27850520-27850539 None:intergenic 25.0%
!! TTGAATGAATTGTATTGATG+GGG + chr1.2:27850574-27850593 MS.gene53526:intron 25.0%
!! TTTCTTAAGAGGTACAATTT+AGG + chr1.2:27850439-27850458 MS.gene53526:intron 25.0%
!! TTTTGACAGAAACTAAACTT+TGG + chr1.2:27850140-27850159 MS.gene53526:CDS 25.0%
!!! ATTTTTTATTACCTGGAGAT+TGG - chr1.2:27850327-27850346 None:intergenic 25.0%
AACAAAAGCTTCAAAGTCTA+TGG + chr1.2:27850793-27850812 MS.gene53526:CDS 30.0%
ACAAAAGCTTCAAAGTCTAT+GGG + chr1.2:27850794-27850813 MS.gene53526:CDS 30.0%
ACTCCACATTCATACATTTA+TGG + chr1.2:27850616-27850635 MS.gene53526:intron 30.0%
ATCGATTGTGAAGAATCAAA+TGG + chr1.2:27850761-27850780 MS.gene53526:CDS 30.0%
ATGCTCTTATTGACAATGAA+AGG - chr1.2:27850527-27850546 None:intergenic 30.0%
ATTTGATTCTTCACAATCGA+TGG - chr1.2:27850762-27850781 None:intergenic 30.0%
AGCATTCATTTGAGTAGACA+CGG + chr1.2:27850542-27850561 MS.gene53526:intron 35.0%
ATTTGAGTAGACACGGTATT+AGG + chr1.2:27850549-27850568 MS.gene53526:intron 35.0%
CAATACTATGTAACGCTTGT+GGG + chr1.2:27850185-27850204 MS.gene53526:CDS 35.0%
CTTCGGAAGATAGTTATCAA+GGG - chr1.2:27850233-27850252 None:intergenic 35.0%
GAAACTAAACTTTGGCGTAA+AGG + chr1.2:27850148-27850167 MS.gene53526:CDS 35.0%
GATTGTGAAGAATCAAATGG+AGG + chr1.2:27850764-27850783 MS.gene53526:CDS 35.0%
TCATACACGGTACATATCAA+TGG - chr1.2:27850700-27850719 None:intergenic 35.0%
TCTTCGGAAGATAGTTATCA+AGG - chr1.2:27850234-27850253 None:intergenic 35.0%
TGTATACCAAGCAATGAGAT+AGG + chr1.2:27850882-27850901 MS.gene53526:CDS 35.0%
! GAATTGTATTGATGGGGATT+AGG + chr1.2:27850580-27850599 MS.gene53526:intron 35.0%
!! CATAGTATTGGCTTCTCATA+CGG - chr1.2:27850175-27850194 None:intergenic 35.0%
!! GTCTGATAACTGATTTTGCT+GGG - chr1.2:27850260-27850279 None:intergenic 35.0%
CCAATACTATGTAACGCTTG+TGG + chr1.2:27850184-27850203 MS.gene53526:CDS 40.0%
CCACAAGCGTTACATAGTAT+TGG - chr1.2:27850187-27850206 None:intergenic 40.0%
! TGATTTTGCTGGGATGTCTT+CGG - chr1.2:27850250-27850269 None:intergenic 40.0%
!! GGTCTGATAACTGATTTTGC+TGG - chr1.2:27850261-27850280 None:intergenic 40.0%
!! TGGAGATTGGTTTGAAAGCT+CGG - chr1.2:27850314-27850333 None:intergenic 40.0%
ATCAGACCTTGACGTGGAAA+AGG + chr1.2:27850273-27850292 MS.gene53526:CDS 45.0%
CCAAGCAATGAGATAGGCAT+TGG + chr1.2:27850888-27850907 MS.gene53526:CDS 45.0%
CCAATGCCTATCTCATTGCT+TGG - chr1.2:27850891-27850910 None:intergenic 45.0%
GAGCTTTCAAACCAATCTCC+AGG + chr1.2:27850313-27850332 MS.gene53526:CDS 45.0%
GGGCTACATTTCAAGGCTAA+AGG + chr1.2:27850205-27850224 MS.gene53526:CDS 45.0%
TCAGTTATCAGACCTTGACG+TGG + chr1.2:27850267-27850286 MS.gene53526:CDS 45.0%
! CAGATTCCTTTTCCACGTCA+AGG - chr1.2:27850282-27850301 None:intergenic 45.0%
!! GGAGATTGGTTTGAAAGCTC+GGG - chr1.2:27850313-27850332 None:intergenic 45.0%
! CGCTTGTGGGCTACATTTCA+AGG + chr1.2:27850198-27850217 MS.gene53526:CDS 50.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 27850136 27850956 27850136 ID=MS.gene53526
chr1.2 mRNA 27850136 27850956 27850136 ID=MS.gene53526.t1;Parent=MS.gene53526
chr1.2 exon 27850136 27850334 27850136 ID=MS.gene53526.t1.exon1;Parent=MS.gene53526.t1
chr1.2 CDS 27850136 27850334 27850136 ID=cds.MS.gene53526.t1;Parent=MS.gene53526.t1
chr1.2 exon 27850751 27850956 27850751 ID=MS.gene53526.t1.exon2;Parent=MS.gene53526.t1
chr1.2 CDS 27850751 27850956 27850751 ID=cds.MS.gene53526.t1;Parent=MS.gene53526.t1
Gene Sequence

>MS.gene53526

ATGGTTTTGACAGAAACTAAACTTTGGCGTAAAGGACCGTATGAGAAGCCAATACTATGTAACGCTTGTGGGCTACATTTCAAGGCTAAAGGAACCCTTGATAACTATCTTCCGAAGACATCCCAGCAAAATCAGTTATCAGACCTTGACGTGGAAAAGGAATCTGAAAGTGATCCCGAGCTTTCAAACCAATCTCCAGGTAATAAAAAATGCAATAAGTTAATTAACTATTCACCCCATTTTTCAACAAATATAAAGTACAATTTATACAAGAAGAGTGAGCGAGAAAGTTATTGTAAGAATTTTCTTAAGAGGTACAATTTAGGAGTATTGTTATGATATAAACACTACTATTTATATATGAGGTGTAACATTGTCAACCCTAATTCCTTTCATTGTCAATAAGAGCATTCATTTGAGTAGACACGGTATTAGGTTTTGAATGAATTGTATTGATGGGGATTAGGTGACATACATACAACTCCACATTCATACATTTATGGATATATTTTTTTCAAATAATAGCATATATTTTTTCAAATAATACATATAAATGATTATCCATTGATATGTACCGTGTATGATGTATACATATAAACTTTTAATTTTTTGTAGAAAGGACACCATCGATTGTGAAGAATCAAATGGAGGAGTTTCAACAAAAGCTTCAAAGTCTATGGGAATCTGAGAAAGAATCAAATGAATCATCTGAAGACAATATTTTGTTGTTTGATAATATGAACAACTGTATACCAAGCAATGAGATAGGCATTGGATGCACTCTACTAAAGACTGATGTTACTTCTAAAAAATCTGCATGA
Protein sequence

>MS.gene53526.t1

MVLTETKLWRKGPYEKPILCNACGLHFKAKGTLDNYLPKTSQQNQLSDLDVEKESESDPELSNQSPERTPSIVKNQMEEFQQKLQSLWESEKESNESSEDNILLFDNMNNCIPSNEIGIGCTLLKTDVTSKKSA