AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene53528

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene53528.t1 MTR_1g045040 87.313 134 17 0 1 134 1 134 8.24e-78 226
MS.gene53528.t1 MTR_1g089830 76.336 131 24 2 1 130 1 125 1.24e-68 203
MS.gene53528.t1 MTR_8g089170 39.456 147 63 3 6 127 7 152 2.69e-23 89.0
MS.gene53528.t1 MTR_8g089130 36.424 151 70 3 6 130 7 157 5.67e-22 85.9
MS.gene53528.t1 MTR_8g039350 73.171 41 11 0 4 44 15 55 3.68e-17 70.9
MS.gene53528.t1 MTR_4g028990 40.625 96 47 4 43 130 3 96 1.84e-12 59.7
MS.gene53528.t1 MTR_5g013370 51.852 54 25 1 3 56 12 64 3.22e-11 59.7
MS.gene53528.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:+27874635 MS.gene53528:CDS
CGCTTGTGGACTACATTTCA+AGG 0.405648 1.2:+27874040 MS.gene53528:CDS
TGGAGATTGGTTTGAAAGCT+CGG 0.447768 1.2:-27874153 None:intergenic
CCACAAGCGTTACATAGTAT+TGG 0.448818 1.2:-27874026 None:intergenic
GAAACTAAACTTTGGCGTAA+AGG 0.456777 1.2:+27873990 MS.gene53528:CDS
ATCAGACCTTGACGTTGAAA+AGG 0.465983 1.2:+27874115 MS.gene53528:CDS
GGACTACATTTCAAGGCTAA+AGG 0.474721 1.2:+27874047 MS.gene53528:CDS
TCTTCGGAAGATAGTTATCA+AGG 0.478433 1.2:-27874073 None:intergenic
TGTATACCAAGCAATGAGAT+AGG 0.478624 1.2:+27874724 MS.gene53528:CDS
CATAGTATTGGCTTCTCATA+CGG 0.490978 1.2:-27874014 None:intergenic
ATCGATTGTGAAGAATCAAA+TGG 0.491491 1.2:+27874603 MS.gene53528:CDS
GGAGATTGGTTTGAAAGCTC+GGG 0.493147 1.2:-27874152 None:intergenic
CCAAGCAATGAGATAGGCAT+TGG 0.496933 1.2:+27874730 MS.gene53528:CDS
ATTTGATTCTTCACAATCGA+TGG 0.523804 1.2:-27874601 None:intergenic
ACAAAAGCTTCAAAGTCTAT+GGG 0.556384 1.2:+27874636 MS.gene53528:CDS
CCAATGCCTATCTCATTGCT+TGG 0.566560 1.2:-27874730 None:intergenic
GAGCTTTCAAACCAATCTCC+AGG 0.568278 1.2:+27874155 MS.gene53528:CDS
CCAATACTATGTAACGCTTG+TGG 0.608782 1.2:+27874026 MS.gene53528:CDS
CTTCGGAAGATAGTTATCAA+GGG 0.629882 1.2:-27874072 None:intergenic
GATTGTGAAGAATCAAATGG+AGG 0.680011 1.2:+27874606 MS.gene53528:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ACTTTTAATTTTTTGTAGAA+AGG + chr1.2:27874575-27874594 MS.gene53528:intron 15.0%
!!! CTTTATATTTGTTGAAAAAT+GGG - chr1.2:27874216-27874235 None:intergenic 15.0%
!!! TTTATATTTGTTGAAAAATG+GGG - chr1.2:27874215-27874234 None:intergenic 15.0%
!! AACACTACTATTTATATATG+AGG + chr1.2:27874321-27874340 MS.gene53528:intron 20.0%
!! TTATATGTATACATCATACA+CGG - chr1.2:27874555-27874574 None:intergenic 20.0%
!!! ATTGTAAGAATTTTCTTAAG+AGG + chr1.2:27874270-27874289 MS.gene53528:intron 20.0%
!!! GCTTTATATTTGTTGAAAAA+TGG - chr1.2:27874217-27874236 None:intergenic 20.0%
!!! TTATTGCATTTTTTATTACC+TGG - chr1.2:27874176-27874195 None:intergenic 20.0%
!!! TTTGAATGAATTGTATTGAT+GGG + chr1.2:27874415-27874434 MS.gene53528:intron 20.0%
!!! TTTTGAATGAATTGTATTGA+TGG + chr1.2:27874414-27874433 MS.gene53528:intron 20.0%
! ATTCATTCAAAACCTAATAC+CGG - chr1.2:27874406-27874425 None:intergenic 25.0%
! ATTGACAATGAAAGGAATTA+GGG - chr1.2:27874361-27874380 None:intergenic 25.0%
! TATCCATAAATGTATGAATG+TGG - chr1.2:27874464-27874483 None:intergenic 25.0%
! TATTGACAATGAAAGGAATT+AGG - chr1.2:27874362-27874381 None:intergenic 25.0%
!! TTGAATGAATTGTATTGATG+GGG + chr1.2:27874416-27874435 MS.gene53528:intron 25.0%
!! TTTCTTAAGAGGTACAATTT+AGG + chr1.2:27874281-27874300 MS.gene53528:intron 25.0%
!! TTTTGACAGAAACTAAACTT+TGG + chr1.2:27873982-27874001 MS.gene53528:CDS 25.0%
!!! ATTTTTTATTACCTGGAGAT+TGG - chr1.2:27874169-27874188 None:intergenic 25.0%
AACAAAAGCTTCAAAGTCTA+TGG + chr1.2:27874635-27874654 MS.gene53528:CDS 30.0%
ACAAAAGCTTCAAAGTCTAT+GGG + chr1.2:27874636-27874655 MS.gene53528:CDS 30.0%
ACTCCACATTCATACATTTA+TGG + chr1.2:27874458-27874477 MS.gene53528:intron 30.0%
ATCGATTGTGAAGAATCAAA+TGG + chr1.2:27874603-27874622 MS.gene53528:CDS 30.0%
ATGCTCTTATTGACAATGAA+AGG - chr1.2:27874369-27874388 None:intergenic 30.0%
ATTTGATTCTTCACAATCGA+TGG - chr1.2:27874604-27874623 None:intergenic 30.0%
TTCATTCAAAACCTAATACC+GGG - chr1.2:27874405-27874424 None:intergenic 30.0%
!! GTCTGATAACTGATTTTGTT+GGG - chr1.2:27874102-27874121 None:intergenic 30.0%
CTTCGGAAGATAGTTATCAA+GGG - chr1.2:27874075-27874094 None:intergenic 35.0%
GAAACTAAACTTTGGCGTAA+AGG + chr1.2:27873990-27874009 MS.gene53528:CDS 35.0%
GATTGTGAAGAATCAAATGG+AGG + chr1.2:27874606-27874625 MS.gene53528:CDS 35.0%
TCATACACGGTACATATCAA+TGG - chr1.2:27874542-27874561 None:intergenic 35.0%
TCTTCGGAAGATAGTTATCA+AGG - chr1.2:27874076-27874095 None:intergenic 35.0%
TGTATACCAAGCAATGAGAT+AGG + chr1.2:27874724-27874743 MS.gene53528:CDS 35.0%
! GAATTGTATTGATGGGGATT+AGG + chr1.2:27874422-27874441 MS.gene53528:intron 35.0%
! TGATTTTGTTGGGATGTCTT+CGG - chr1.2:27874092-27874111 None:intergenic 35.0%
!! CATAGTATTGGCTTCTCATA+CGG - chr1.2:27874017-27874036 None:intergenic 35.0%
!! GGTCTGATAACTGATTTTGT+TGG - chr1.2:27874103-27874122 None:intergenic 35.0%
AGCATTCATTTGAGTAGACC+CGG + chr1.2:27874384-27874403 MS.gene53528:intron 40.0%
ATCAGACCTTGACGTTGAAA+AGG + chr1.2:27874115-27874134 MS.gene53528:CDS 40.0%
ATTTGAGTAGACCCGGTATT+AGG + chr1.2:27874391-27874410 MS.gene53528:intron 40.0%
CCAATACTATGTAACGCTTG+TGG + chr1.2:27874026-27874045 MS.gene53528:CDS 40.0%
CCACAAGCGTTACATAGTAT+TGG - chr1.2:27874029-27874048 None:intergenic 40.0%
GGACTACATTTCAAGGCTAA+AGG + chr1.2:27874047-27874066 MS.gene53528:CDS 40.0%
! CAGATTCCTTTTCAACGTCA+AGG - chr1.2:27874124-27874143 None:intergenic 40.0%
!! TGGAGATTGGTTTGAAAGCT+CGG - chr1.2:27874156-27874175 None:intergenic 40.0%
CCAAGCAATGAGATAGGCAT+TGG + chr1.2:27874730-27874749 MS.gene53528:CDS 45.0%
CCAATGCCTATCTCATTGCT+TGG - chr1.2:27874733-27874752 None:intergenic 45.0%
GAGCTTTCAAACCAATCTCC+AGG + chr1.2:27874155-27874174 MS.gene53528:CDS 45.0%
! CGCTTGTGGACTACATTTCA+AGG + chr1.2:27874040-27874059 MS.gene53528:CDS 45.0%
!! GGAGATTGGTTTGAAAGCTC+GGG - chr1.2:27874155-27874174 None:intergenic 45.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 27873978 27874798 27873978 ID=MS.gene53528
chr1.2 mRNA 27873978 27874798 27873978 ID=MS.gene53528.t1;Parent=MS.gene53528
chr1.2 exon 27873978 27874176 27873978 ID=MS.gene53528.t1.exon1;Parent=MS.gene53528.t1
chr1.2 CDS 27873978 27874176 27873978 ID=cds.MS.gene53528.t1;Parent=MS.gene53528.t1
chr1.2 exon 27874593 27874798 27874593 ID=MS.gene53528.t1.exon2;Parent=MS.gene53528.t1
chr1.2 CDS 27874593 27874798 27874593 ID=cds.MS.gene53528.t1;Parent=MS.gene53528.t1
Gene Sequence

>MS.gene53528

ATGGTTTTGACAGAAACTAAACTTTGGCGTAAAGGACCGTATGAGAAGCCAATACTATGTAACGCTTGTGGACTACATTTCAAGGCTAAAGGAACCCTTGATAACTATCTTCCGAAGACATCCCAACAAAATCAGTTATCAGACCTTGACGTTGAAAAGGAATCTGAAAGTGATCCCGAGCTTTCAAACCAATCTCCAGGTAATAAAAAATGCAATAAGTTAATTAACTATTCACCCCATTTTTCAACAAATATAAAGCACAATTTATACAAGAAGAGTGAGCGAGAAAGTTATTGTAAGAATTTTCTTAAGAGGTACAATTTAGGAGTATTGTTATGATATAAACACTACTATTTATATATGAGGTGTAACATTGTCAACCCTAATTCCTTTCATTGTCAATAAGAGCATTCATTTGAGTAGACCCGGTATTAGGTTTTGAATGAATTGTATTGATGGGGATTAGGTGACATACATACAACTCCACATTCATACATTTATGGATATATTTTTTTCAAATAATAGCATATATTTTTTCAAATAATACATATGAGTGATTATCCATTGATATGTACCGTGTATGATGTATACATATAAACTTTTAATTTTTTGTAGAAAGGACACCATCGATTGTGAAGAATCAAATGGAGGAGTTTCAACAAAAGCTTCAAAGTCTATGGGAATCTGAGAAAGAATCAAATGAATCATCTGCAGACAATATTTTGTTGTTTGATAATATGAACAACTGTATACCAAGCAATGAGATAGGCATTGGATGCACTCTACTGAAGACAGATGTTACTTCTAAAAAATCTGCATGA
Protein sequence

>MS.gene53528.t1

MVLTETKLWRKGPYEKPILCNACGLHFKAKGTLDNYLPKTSQQNQLSDLDVEKESESDPELSNQSPERTPSIVKNQMEEFQQKLQSLWESEKESNESSADNILLFDNMNNCIPSNEIGIGCTLLKTDVTSKKSA