AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene53529

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene53529.t1 MTR_1g045040 87.313 134 17 0 1 134 1 134 8.24e-78 226
MS.gene53529.t1 MTR_1g089830 76.336 131 24 2 1 130 1 125 1.24e-68 203
MS.gene53529.t1 MTR_8g089170 39.456 147 63 3 6 127 7 152 2.69e-23 89.0
MS.gene53529.t1 MTR_8g089130 36.424 151 70 3 6 130 7 157 5.67e-22 85.9
MS.gene53529.t1 MTR_8g039350 73.171 41 11 0 4 44 15 55 3.68e-17 70.9
MS.gene53529.t1 MTR_4g028990 40.625 96 47 4 43 130 3 96 1.84e-12 59.7
MS.gene53529.t1 MTR_5g013370 51.852 54 25 1 3 56 12 64 3.22e-11 59.7
MS.gene53529.t1 MTR_5g013370 51.852 54 25 1 3 56 12 64 4.83e-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 20 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:+27882250 MS.gene53529:CDS
CGCTTGTGGACTACATTTCA+AGG 0.405648 1.2:+27881655 MS.gene53529:CDS
TGGAGATTGGTTTGAAAGCT+CGG 0.447768 1.2:-27881768 None:intergenic
CCACAAGCGTTACATAGTAT+TGG 0.448818 1.2:-27881641 None:intergenic
GAAACTAAACTTTGGCGTAA+AGG 0.456777 1.2:+27881605 MS.gene53529:CDS
ATCAGACCTTGACGTTGAAA+AGG 0.465983 1.2:+27881730 MS.gene53529:CDS
GGACTACATTTCAAGGCTAA+AGG 0.474721 1.2:+27881662 MS.gene53529:CDS
TCTTCGGAAGATAGTTATCA+AGG 0.478433 1.2:-27881688 None:intergenic
TGTATACCAAGCAATGAGAT+AGG 0.478624 1.2:+27882339 MS.gene53529:CDS
CATAGTATTGGCTTCTCATA+CGG 0.490978 1.2:-27881629 None:intergenic
ATCGATTGTGAAGAATCAAA+TGG 0.491491 1.2:+27882218 MS.gene53529:CDS
GGAGATTGGTTTGAAAGCTC+GGG 0.493147 1.2:-27881767 None:intergenic
CCAAGCAATGAGATAGGCAT+TGG 0.496933 1.2:+27882345 MS.gene53529:CDS
ATTTGATTCTTCACAATCGA+TGG 0.523804 1.2:-27882216 None:intergenic
ACAAAAGCTTCAAAGTCTAT+GGG 0.556384 1.2:+27882251 MS.gene53529:CDS
CCAATGCCTATCTCATTGCT+TGG 0.566560 1.2:-27882345 None:intergenic
GAGCTTTCAAACCAATCTCC+AGG 0.568278 1.2:+27881770 MS.gene53529:CDS
CCAATACTATGTAACGCTTG+TGG 0.608782 1.2:+27881641 MS.gene53529:CDS
CTTCGGAAGATAGTTATCAA+GGG 0.629882 1.2:-27881687 None:intergenic
GATTGTGAAGAATCAAATGG+AGG 0.680011 1.2:+27882221 MS.gene53529:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ACTTTTAATTTTTTGTAGAA+AGG + chr1.2:27882190-27882209 MS.gene53529:intron 15.0%
!!! CTTTATATTTGTTGAAAAAT+GGG - chr1.2:27881831-27881850 None:intergenic 15.0%
!!! TTTATATTTGTTGAAAAATG+GGG - chr1.2:27881830-27881849 None:intergenic 15.0%
!! AACACTACTATTTATATATG+AGG + chr1.2:27881936-27881955 MS.gene53529:intron 20.0%
!! TTATATGTATACATCATACA+CGG - chr1.2:27882170-27882189 None:intergenic 20.0%
!!! ATTGTAAGAATTTTCTTAAG+AGG + chr1.2:27881885-27881904 MS.gene53529:intron 20.0%
!!! GCTTTATATTTGTTGAAAAA+TGG - chr1.2:27881832-27881851 None:intergenic 20.0%
!!! TTATTGCATTTTTTATTACC+TGG - chr1.2:27881791-27881810 None:intergenic 20.0%
!!! TTTGAATGAATTGTATTGAT+GGG + chr1.2:27882030-27882049 MS.gene53529:intron 20.0%
!!! TTTTGAATGAATTGTATTGA+TGG + chr1.2:27882029-27882048 MS.gene53529:intron 20.0%
! ATTCATTCAAAACCTAATAC+CGG - chr1.2:27882021-27882040 None:intergenic 25.0%
! ATTGACAATGAAAGGAATTA+GGG - chr1.2:27881976-27881995 None:intergenic 25.0%
! TATCCATAAATGTATGAATG+TGG - chr1.2:27882079-27882098 None:intergenic 25.0%
! TATTGACAATGAAAGGAATT+AGG - chr1.2:27881977-27881996 None:intergenic 25.0%
!! TTGAATGAATTGTATTGATG+GGG + chr1.2:27882031-27882050 MS.gene53529:intron 25.0%
!! TTTCTTAAGAGGTACAATTT+AGG + chr1.2:27881896-27881915 MS.gene53529:intron 25.0%
!! TTTTGACAGAAACTAAACTT+TGG + chr1.2:27881597-27881616 MS.gene53529:CDS 25.0%
!!! ATTTTTTATTACCTGGAGAT+TGG - chr1.2:27881784-27881803 None:intergenic 25.0%
AACAAAAGCTTCAAAGTCTA+TGG + chr1.2:27882250-27882269 MS.gene53529:CDS 30.0%
ACAAAAGCTTCAAAGTCTAT+GGG + chr1.2:27882251-27882270 MS.gene53529:CDS 30.0%
ACTCCACATTCATACATTTA+TGG + chr1.2:27882073-27882092 MS.gene53529:intron 30.0%
ATCGATTGTGAAGAATCAAA+TGG + chr1.2:27882218-27882237 MS.gene53529:CDS 30.0%
ATGCTCTTATTGACAATGAA+AGG - chr1.2:27881984-27882003 None:intergenic 30.0%
ATTTGATTCTTCACAATCGA+TGG - chr1.2:27882219-27882238 None:intergenic 30.0%
TTCATTCAAAACCTAATACC+GGG - chr1.2:27882020-27882039 None:intergenic 30.0%
!! GTCTGATAACTGATTTTGTT+GGG - chr1.2:27881717-27881736 None:intergenic 30.0%
CTTCGGAAGATAGTTATCAA+GGG - chr1.2:27881690-27881709 None:intergenic 35.0%
GAAACTAAACTTTGGCGTAA+AGG + chr1.2:27881605-27881624 MS.gene53529:CDS 35.0%
GATTGTGAAGAATCAAATGG+AGG + chr1.2:27882221-27882240 MS.gene53529:CDS 35.0%
TCATACACGGTACATATCAA+TGG - chr1.2:27882157-27882176 None:intergenic 35.0%
TCTTCGGAAGATAGTTATCA+AGG - chr1.2:27881691-27881710 None:intergenic 35.0%
TGTATACCAAGCAATGAGAT+AGG + chr1.2:27882339-27882358 MS.gene53529:CDS 35.0%
! GAATTGTATTGATGGGGATT+AGG + chr1.2:27882037-27882056 MS.gene53529:intron 35.0%
! TGATTTTGTTGGGATGTCTT+CGG - chr1.2:27881707-27881726 None:intergenic 35.0%
!! CATAGTATTGGCTTCTCATA+CGG - chr1.2:27881632-27881651 None:intergenic 35.0%
!! GGTCTGATAACTGATTTTGT+TGG - chr1.2:27881718-27881737 None:intergenic 35.0%
AGCATTCATTTGAGTAGACC+CGG + chr1.2:27881999-27882018 MS.gene53529:intron 40.0%
ATCAGACCTTGACGTTGAAA+AGG + chr1.2:27881730-27881749 MS.gene53529:CDS 40.0%
ATTTGAGTAGACCCGGTATT+AGG + chr1.2:27882006-27882025 MS.gene53529:intron 40.0%
CCAATACTATGTAACGCTTG+TGG + chr1.2:27881641-27881660 MS.gene53529:CDS 40.0%
CCACAAGCGTTACATAGTAT+TGG - chr1.2:27881644-27881663 None:intergenic 40.0%
GGACTACATTTCAAGGCTAA+AGG + chr1.2:27881662-27881681 MS.gene53529:CDS 40.0%
! CAGATTCCTTTTCAACGTCA+AGG - chr1.2:27881739-27881758 None:intergenic 40.0%
!! TGGAGATTGGTTTGAAAGCT+CGG - chr1.2:27881771-27881790 None:intergenic 40.0%
CCAAGCAATGAGATAGGCAT+TGG + chr1.2:27882345-27882364 MS.gene53529:CDS 45.0%
CCAATGCCTATCTCATTGCT+TGG - chr1.2:27882348-27882367 None:intergenic 45.0%
GAGCTTTCAAACCAATCTCC+AGG + chr1.2:27881770-27881789 MS.gene53529:CDS 45.0%
! CGCTTGTGGACTACATTTCA+AGG + chr1.2:27881655-27881674 MS.gene53529:CDS 45.0%
!! GGAGATTGGTTTGAAAGCTC+GGG - chr1.2:27881770-27881789 None:intergenic 45.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 27881593 27882413 27881593 ID=MS.gene53529
chr1.2 mRNA 27881593 27882413 27881593 ID=MS.gene53529.t1;Parent=MS.gene53529
chr1.2 exon 27881593 27881791 27881593 ID=MS.gene53529.t1.exon1;Parent=MS.gene53529.t1
chr1.2 CDS 27881593 27881791 27881593 ID=cds.MS.gene53529.t1;Parent=MS.gene53529.t1
chr1.2 exon 27882208 27882413 27882208 ID=MS.gene53529.t1.exon2;Parent=MS.gene53529.t1
chr1.2 CDS 27882208 27882413 27882208 ID=cds.MS.gene53529.t1;Parent=MS.gene53529.t1
Gene Sequence

>MS.gene53529

ATGGTTTTGACAGAAACTAAACTTTGGCGTAAAGGACCGTATGAGAAGCCAATACTATGTAACGCTTGTGGACTACATTTCAAGGCTAAAGGAACCCTTGATAACTATCTTCCGAAGACATCCCAACAAAATCAGTTATCAGACCTTGACGTTGAAAAGGAATCTGAAAGTGATCCCGAGCTTTCAAACCAATCTCCAGGTAATAAAAAATGCAATAAGTTAATTAACTATTCACCCCATTTTTCAACAAATATAAAGCACAATTTATACAAGAAGAGTGAGCGAGAAAGTTATTGTAAGAATTTTCTTAAGAGGTACAATTTAGGAGTATTGTTATGATATAAACACTACTATTTATATATGAGGTGTAACATTGTCAACCCTAATTCCTTTCATTGTCAATAAGAGCATTCATTTGAGTAGACCCGGTATTAGGTTTTGAATGAATTGTATTGATGGGGATTAGGTGACATACATACAACTCCACATTCATACATTTATGGATATATTTTTTTCAAATAATAGCATATATTTTTTCAAATAATACATATAAATGATTATCCATTGATATGTACCGTGTATGATGTATACATATAAACTTTTAATTTTTTGTAGAAAGGACACCATCGATTGTGAAGAATCAAATGGAGGAGTTTCAACAAAAGCTTCAAAGTCTATGGGAATCTGAGAAAGAATCAAATGAATCATCTGCAGACAATATTTTGTTGTTTGATAATATGAACAACTGTATACCAAGCAATGAGATAGGCATTGGATGCACTCTACTGAAGACAGATGTTACTTCTAAAAAATCTGCATGA
Protein sequence

>MS.gene53529.t1

MVLTETKLWRKGPYEKPILCNACGLHFKAKGTLDNYLPKTSQQNQLSDLDVEKESESDPELSNQSPERTPSIVKNQMEEFQQKLQSLWESEKESNESSADNILLFDNMNNCIPSNEIGIGCTLLKTDVTSKKSA