AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene53531

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene53531.t1 MTR_1g045040 85.821 134 19 0 1 134 1 134 1.31e-75 221
MS.gene53531.t1 MTR_1g089830 74.809 131 26 2 1 130 1 125 1.80e-66 198
MS.gene53531.t1 MTR_8g089170 38.776 147 64 3 6 127 7 152 1.16e-21 84.7
MS.gene53531.t1 MTR_8g089130 35.762 151 71 3 6 130 7 157 2.56e-20 81.6
MS.gene53531.t1 MTR_8g039350 70.732 41 12 0 4 44 15 55 6.47e-17 70.1
MS.gene53531.t1 MTR_4g028990 40.625 96 47 4 43 130 3 96 1.50e-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 49 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACAAAAGCTTCAAAGTCTA+TGG 0.184389 1.2:+27921240 MS.gene53531:CDS
CCACAAGCGTTACTTAGTAT+TGG 0.413611 1.2:-27920631 None:intergenic
GGACTATATTTCAAGGCTAA+AGG 0.442562 1.2:+27920652 MS.gene53531:CDS
TGGAGATTGGTTTGAAAGCT+CGG 0.447768 1.2:-27920758 None:intergenic
CGCTTGTGGACTATATTTCA+AGG 0.451874 1.2:+27920645 MS.gene53531:CDS
CTTAGTATTGGCTTCTCATA+CGG 0.455064 1.2:-27920619 None:intergenic
GAAACTAAACTTTGGCGTAA+AGG 0.456777 1.2:+27920595 MS.gene53531:CDS
ATCAGACCTTGACGTTGAAA+AGG 0.465983 1.2:+27920720 MS.gene53531:CDS
TCTTCGGAAGATAGTTATCA+AGG 0.478433 1.2:-27920678 None:intergenic
TGTATACCAAGCAATGAGAT+AGG 0.478624 1.2:+27921329 MS.gene53531:CDS
ATCGATTGTGAAGAATCAAA+TGG 0.491491 1.2:+27921208 MS.gene53531:CDS
GGAGATTGGTTTGAAAGCTC+GGG 0.493147 1.2:-27920757 None:intergenic
CCAAGCAATGAGATAGGCAT+TGG 0.496933 1.2:+27921335 MS.gene53531:CDS
ATTTGATTCTTCACAATCGA+TGG 0.523804 1.2:-27921206 None:intergenic
ACAAAAGCTTCAAAGTCTAT+GGG 0.556384 1.2:+27921241 MS.gene53531:CDS
CCAATGCCTATCTCATTGCT+TGG 0.566560 1.2:-27921335 None:intergenic
GAGCTTTCAAACCAATCTCC+AGG 0.568278 1.2:+27920760 MS.gene53531:CDS
CTTCGGAAGATAGTTATCAA+GGG 0.629882 1.2:-27920677 None:intergenic
GATTGTGAAGAATCAAATGG+AGG 0.680011 1.2:+27921211 MS.gene53531:CDS
CCAATACTAAGTAACGCTTG+TGG 0.691772 1.2:+27920631 MS.gene53531:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ACTTTTAATTTTTTGTAGAA+AGG + chr1.2:27921180-27921199 MS.gene53531:intron 15.0%
!!! CTTTATATTTGTTGAAAAAT+GGG - chr1.2:27920821-27920840 None:intergenic 15.0%
!!! TTTATATTTGTTGAAAAATG+GGG - chr1.2:27920820-27920839 None:intergenic 15.0%
!! AACACTACTATTTATATATG+AGG + chr1.2:27920926-27920945 MS.gene53531:intron 20.0%
!! TTATATGTATACATCATACA+CGG - chr1.2:27921160-27921179 None:intergenic 20.0%
!!! ATTGTAAGAATTTTCTTAAG+AGG + chr1.2:27920875-27920894 MS.gene53531:intron 20.0%
!!! GCTTTATATTTGTTGAAAAA+TGG - chr1.2:27920822-27920841 None:intergenic 20.0%
!!! TTATTGCATTTTTTATTACC+TGG - chr1.2:27920781-27920800 None:intergenic 20.0%
!!! TTTGAATGAATTGTATTGAT+GGG + chr1.2:27921020-27921039 MS.gene53531:intron 20.0%
!!! TTTTGAATGAATTGTATTGA+TGG + chr1.2:27921019-27921038 MS.gene53531:intron 20.0%
! ATTCATTCAAAACCTAATAC+CGG - chr1.2:27921011-27921030 None:intergenic 25.0%
! ATTGACAATGAAAGGAATTA+GGG - chr1.2:27920966-27920985 None:intergenic 25.0%
! TATCCATAAATGTATGAATG+TGG - chr1.2:27921069-27921088 None:intergenic 25.0%
! TATTGACAATGAAAGGAATT+AGG - chr1.2:27920967-27920986 None:intergenic 25.0%
!! TTGAATGAATTGTATTGATG+GGG + chr1.2:27921021-27921040 MS.gene53531:intron 25.0%
!! TTTCTTAAGAGGTACAATTT+AGG + chr1.2:27920886-27920905 MS.gene53531:intron 25.0%
!! TTTTGACAGAAACTAAACTT+TGG + chr1.2:27920587-27920606 MS.gene53531:CDS 25.0%
!!! ATTTTTTATTACCTGGAGAT+TGG - chr1.2:27920774-27920793 None:intergenic 25.0%
AACAAAAGCTTCAAAGTCTA+TGG + chr1.2:27921240-27921259 MS.gene53531:CDS 30.0%
ACAAAAGCTTCAAAGTCTAT+GGG + chr1.2:27921241-27921260 MS.gene53531:CDS 30.0%
ACTCCACATTCATACATTTA+TGG + chr1.2:27921063-27921082 MS.gene53531:intron 30.0%
ATCGATTGTGAAGAATCAAA+TGG + chr1.2:27921208-27921227 MS.gene53531:CDS 30.0%
ATGCTCTTATTGACAATGAA+AGG - chr1.2:27920974-27920993 None:intergenic 30.0%
ATTTGATTCTTCACAATCGA+TGG - chr1.2:27921209-27921228 None:intergenic 30.0%
TTCATTCAAAACCTAATACC+GGG - chr1.2:27921010-27921029 None:intergenic 30.0%
!! GTCTGATAACTGATTTTGTT+GGG - chr1.2:27920707-27920726 None:intergenic 30.0%
CTTCGGAAGATAGTTATCAA+GGG - chr1.2:27920680-27920699 None:intergenic 35.0%
GAAACTAAACTTTGGCGTAA+AGG + chr1.2:27920595-27920614 MS.gene53531:CDS 35.0%
GATTGTGAAGAATCAAATGG+AGG + chr1.2:27921211-27921230 MS.gene53531:CDS 35.0%
GGACTATATTTCAAGGCTAA+AGG + chr1.2:27920652-27920671 MS.gene53531:CDS 35.0%
TCATACACGGTACATATCAA+TGG - chr1.2:27921147-27921166 None:intergenic 35.0%
TCTTCGGAAGATAGTTATCA+AGG - chr1.2:27920681-27920700 None:intergenic 35.0%
TGTATACCAAGCAATGAGAT+AGG + chr1.2:27921329-27921348 MS.gene53531:CDS 35.0%
! GAATTGTATTGATGGGGATT+AGG + chr1.2:27921027-27921046 MS.gene53531:intron 35.0%
! TGATTTTGTTGGGATGTCTT+CGG - chr1.2:27920697-27920716 None:intergenic 35.0%
!! CTTAGTATTGGCTTCTCATA+CGG - chr1.2:27920622-27920641 None:intergenic 35.0%
!! GGTCTGATAACTGATTTTGT+TGG - chr1.2:27920708-27920727 None:intergenic 35.0%
AGCATTCATTTGAGTAGACC+CGG + chr1.2:27920989-27921008 MS.gene53531:intron 40.0%
ATCAGACCTTGACGTTGAAA+AGG + chr1.2:27920720-27920739 MS.gene53531:CDS 40.0%
ATTTGAGTAGACCCGGTATT+AGG + chr1.2:27920996-27921015 MS.gene53531:intron 40.0%
CCAATACTAAGTAACGCTTG+TGG + chr1.2:27920631-27920650 MS.gene53531:CDS 40.0%
CCACAAGCGTTACTTAGTAT+TGG - chr1.2:27920634-27920653 None:intergenic 40.0%
! CAGATTCCTTTTCAACGTCA+AGG - chr1.2:27920729-27920748 None:intergenic 40.0%
! CGCTTGTGGACTATATTTCA+AGG + chr1.2:27920645-27920664 MS.gene53531:CDS 40.0%
!! TGGAGATTGGTTTGAAAGCT+CGG - chr1.2:27920761-27920780 None:intergenic 40.0%
CCAAGCAATGAGATAGGCAT+TGG + chr1.2:27921335-27921354 MS.gene53531:CDS 45.0%
CCAATGCCTATCTCATTGCT+TGG - chr1.2:27921338-27921357 None:intergenic 45.0%
GAGCTTTCAAACCAATCTCC+AGG + chr1.2:27920760-27920779 MS.gene53531:CDS 45.0%
!! GGAGATTGGTTTGAAAGCTC+GGG - chr1.2:27920760-27920779 None:intergenic 45.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 27920583 27921403 27920583 ID=MS.gene53531
chr1.2 mRNA 27920583 27921403 27920583 ID=MS.gene53531.t1;Parent=MS.gene53531
chr1.2 exon 27920583 27920781 27920583 ID=MS.gene53531.t1.exon1;Parent=MS.gene53531.t1
chr1.2 CDS 27920583 27920781 27920583 ID=cds.MS.gene53531.t1;Parent=MS.gene53531.t1
chr1.2 exon 27921198 27921403 27921198 ID=MS.gene53531.t1.exon2;Parent=MS.gene53531.t1
chr1.2 CDS 27921198 27921403 27921198 ID=cds.MS.gene53531.t1;Parent=MS.gene53531.t1
Gene Sequence

>MS.gene53531

ATGGTTTTGACAGAAACTAAACTTTGGCGTAAAGGACCGTATGAGAAGCCAATACTAAGTAACGCTTGTGGACTATATTTCAAGGCTAAAGGAACCCTTGATAACTATCTTCCGAAGACATCCCAACAAAATCAGTTATCAGACCTTGACGTTGAAAAGGAATCTGAAAGTGATCCCGAGCTTTCAAACCAATCTCCAGGTAATAAAAAATGCAATAAGTTAATTAACTATTCACCCCATTTTTCAACAAATATAAAGCACAATTTATACAAGAAGAGTGAGCGAGAAAGTTATTGTAAGAATTTTCTTAAGAGGTACAATTTAGGAGTATTGTTATGATATAAACACTACTATTTATATATGAGGTGTAACATTGTCAACCCTAATTCCTTTCATTGTCAATAAGAGCATTCATTTGAGTAGACCCGGTATTAGGTTTTGAATGAATTGTATTGATGGGGATTAGGTGACATACATACAACTCCACATTCATACATTTATGGATATATTTTTTTCAAATAATAGCATATATTTTTTCAAATAATACATATAAATGATTATCCATTGATATGTACCGTGTATGATGTATACATATAAACTTTTAATTTTTTGTAGAAAGGACACCATCGATTGTGAAGAATCAAATGGAGGAGTTTCAACAAAAGCTTCAAAGTCTATGGGAATCTGAGAAAGAATCAAATGAATCATCTGCAGACAATATTTTGTTGTTTGATAATATGAACAACTGTATACCAAGCAATGAGATAGGCATTGGATGCACTCTACTGAAGACAGATGTTACTTCTAAAAAATCTGCATGA
Protein sequence

>MS.gene53531.t1

MVLTETKLWRKGPYEKPILSNACGLYFKAKGTLDNYLPKTSQQNQLSDLDVEKESESDPELSNQSPERTPSIVKNQMEEFQQKLQSLWESEKESNESSADNILLFDNMNNCIPSNEIGIGCTLLKTDVTSKKSA