AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene53533

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene53533.t1 MTR_1g045040 83.908 87 14 0 1 87 1 87 1.85e-51 157
MS.gene53533.t1 MTR_1g089830 72.727 88 17 2 1 87 1 82 6.22e-40 129
MS.gene53533.t1 MTR_8g039350 73.171 41 11 0 4 44 15 55 1.53e-17 70.1
MS.gene53533.t1 MTR_5g013370 52.830 53 24 1 3 55 12 63 5.08e-12 60.1
MS.gene53533.t1 MTR_5g013370 52.830 53 24 1 3 55 12 63 8.45e-12 59.3
MS.gene53533.t1 MTR_4g099410 63.158 38 14 0 1 38 15 52 8.42e-11 56.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene53533.t1 AT4G17570 63.889 36 13 0 3 38 12 47 3.37e-11 57.8
MS.gene53533.t1 AT4G17570 63.889 36 13 0 3 38 12 47 3.37e-11 57.8

Find 15 sgRNAs with CRISPR-Local

Find 42 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCACAAGCATTACATAGTAT+TGG 0.433061 1.2:-27938767 None:intergenic
TGGAGATTGGTTTGAAAGCT+CGG 0.447768 1.2:-27938894 None:intergenic
GAAACTAAACTTTGGCGTAA+AGG 0.456777 1.2:+27938731 MS.gene53533:CDS
TGCTTGTGGACTACATTTCA+AGG 0.461822 1.2:+27938781 MS.gene53533:CDS
GGACTACATTTCAAGGCTAA+AGG 0.474721 1.2:+27938788 MS.gene53533:CDS
TCTTCGGAAGATAGTTATCA+AGG 0.478433 1.2:-27938814 None:intergenic
ATCAGACCTTGACATTGAAA+AGG 0.486095 1.2:+27938856 MS.gene53533:CDS
ATCGATTGTGAAGAATCAAA+TGG 0.491491 1.2:+27939344 MS.gene53533:CDS
CATAGTATTGGCTTCTCATA+CGG 0.492997 1.2:-27938755 None:intergenic
GGAGATTGGTTTGAAAGCTC+GGG 0.493147 1.2:-27938893 None:intergenic
ATTTGATTCTTCACAATCGA+TGG 0.523804 1.2:-27939342 None:intergenic
GAGCTTTCAAACCAATCTCC+AGG 0.568278 1.2:+27938896 MS.gene53533:CDS
CCAATACTATGTAATGCTTG+TGG 0.579274 1.2:+27938767 MS.gene53533:CDS
CTTCGGAAGATAGTTATCAA+GGG 0.629882 1.2:-27938813 None:intergenic
GATTGTGAAGAATCAAATGG+AGG 0.680011 1.2:+27939347 MS.gene53533:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CTTTATATTTGTTGAAAAAT+GGG - chr1.2:27938957-27938976 None:intergenic 15.0%
!!! CTTTTAATTTTTTTGTAGAA+AGG + chr1.2:27939316-27939335 MS.gene53533:intron 15.0%
!!! TTTATATTTGTTGAAAAATG+GGG - chr1.2:27938956-27938975 None:intergenic 15.0%
!! AACACTACTATTTATATATG+AGG + chr1.2:27939062-27939081 MS.gene53533:intron 20.0%
!! TTATATGTATACATCATACA+CGG - chr1.2:27939295-27939314 None:intergenic 20.0%
!!! ATTGTAAGAATTTTCTTAAG+AGG + chr1.2:27939011-27939030 MS.gene53533:intron 20.0%
!!! GCTTTATATTTGTTGAAAAA+TGG - chr1.2:27938958-27938977 None:intergenic 20.0%
!!! TTATTGCATTTTTTATTACC+TGG - chr1.2:27938917-27938936 None:intergenic 20.0%
!!! TTTGAATGAATTGTATTGAT+GGG + chr1.2:27939155-27939174 MS.gene53533:intron 20.0%
!!! TTTTGAATGAATTGTATTGA+TGG + chr1.2:27939154-27939173 MS.gene53533:intron 20.0%
! ATTGACAATGAAAGGAATTA+GGG - chr1.2:27939101-27939120 None:intergenic 25.0%
! TATCCATAAATGTATGAATG+TGG - chr1.2:27939204-27939223 None:intergenic 25.0%
! TATTGACAATGAAAGGAATT+AGG - chr1.2:27939102-27939121 None:intergenic 25.0%
!! TTGAATGAATTGTATTGATG+GGG + chr1.2:27939156-27939175 MS.gene53533:intron 25.0%
!! TTTCTTAAGAGGTACAATTT+AGG + chr1.2:27939022-27939041 MS.gene53533:intron 25.0%
!! TTTTGACAGAAACTAAACTT+TGG + chr1.2:27938723-27938742 MS.gene53533:CDS 25.0%
!!! ATTTTTTATTACCTGGAGAT+TGG - chr1.2:27938910-27938929 None:intergenic 25.0%
ACTCCACATTCATACATTTA+TGG + chr1.2:27939198-27939217 MS.gene53533:intron 30.0%
ATCGATTGTGAAGAATCAAA+TGG + chr1.2:27939344-27939363 MS.gene53533:CDS 30.0%
ATGCTCTTATTGACAATGAA+AGG - chr1.2:27939109-27939128 None:intergenic 30.0%
ATTTGATTCTTCACAATCGA+TGG - chr1.2:27939345-27939364 None:intergenic 30.0%
AGCATTCATTTGAGTAGACA+CGG + chr1.2:27939124-27939143 MS.gene53533:intron 35.0%
ATCAGACCTTGACATTGAAA+AGG + chr1.2:27938856-27938875 MS.gene53533:CDS 35.0%
ATTTGAGTAGACACGGTATT+AGG + chr1.2:27939131-27939150 MS.gene53533:intron 35.0%
CCAATACTATGTAATGCTTG+TGG + chr1.2:27938767-27938786 MS.gene53533:CDS 35.0%
CCACAAGCATTACATAGTAT+TGG - chr1.2:27938770-27938789 None:intergenic 35.0%
CTTCGGAAGATAGTTATCAA+GGG - chr1.2:27938816-27938835 None:intergenic 35.0%
GAAACTAAACTTTGGCGTAA+AGG + chr1.2:27938731-27938750 MS.gene53533:CDS 35.0%
GATTGTGAAGAATCAAATGG+AGG + chr1.2:27939347-27939366 MS.gene53533:CDS 35.0%
TCATACACGGTACATATCAA+TGG - chr1.2:27939282-27939301 None:intergenic 35.0%
TCTTCGGAAGATAGTTATCA+AGG - chr1.2:27938817-27938836 None:intergenic 35.0%
! CAGATTCCTTTTCAATGTCA+AGG - chr1.2:27938865-27938884 None:intergenic 35.0%
! GAATTGTATTGATGGGGATT+AGG + chr1.2:27939162-27939181 MS.gene53533:intron 35.0%
!! CATAGTATTGGCTTCTCATA+CGG - chr1.2:27938758-27938777 None:intergenic 35.0%
!! GTCTGATAACTGATTTTGCT+GGG - chr1.2:27938843-27938862 None:intergenic 35.0%
GGACTACATTTCAAGGCTAA+AGG + chr1.2:27938788-27938807 MS.gene53533:CDS 40.0%
! TGATTTTGCTGGGATGTCTT+CGG - chr1.2:27938833-27938852 None:intergenic 40.0%
! TGCTTGTGGACTACATTTCA+AGG + chr1.2:27938781-27938800 MS.gene53533:CDS 40.0%
!! GGTCTGATAACTGATTTTGC+TGG - chr1.2:27938844-27938863 None:intergenic 40.0%
!! TGGAGATTGGTTTGAAAGCT+CGG - chr1.2:27938897-27938916 None:intergenic 40.0%
GAGCTTTCAAACCAATCTCC+AGG + chr1.2:27938896-27938915 MS.gene53533:CDS 45.0%
!! GGAGATTGGTTTGAAAGCTC+GGG - chr1.2:27938896-27938915 None:intergenic 45.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 27938719 27939398 27938719 ID=MS.gene53533
chr1.2 mRNA 27938719 27939398 27938719 ID=MS.gene53533.t1;Parent=MS.gene53533
chr1.2 exon 27938719 27938917 27938719 ID=MS.gene53533.t1.exon1;Parent=MS.gene53533.t1
chr1.2 CDS 27938719 27938917 27938719 ID=cds.MS.gene53533.t1;Parent=MS.gene53533.t1
chr1.2 exon 27939334 27939398 27939334 ID=MS.gene53533.t1.exon2;Parent=MS.gene53533.t1
chr1.2 CDS 27939334 27939398 27939334 ID=cds.MS.gene53533.t1;Parent=MS.gene53533.t1
Gene Sequence

>MS.gene53533

ATGGTTTTGACAGAAACTAAACTTTGGCGTAAAGGACCGTATGAGAAGCCAATACTATGTAATGCTTGTGGACTACATTTCAAGGCTAAAGGAACCCTTGATAACTATCTTCCGAAGACATCCCAGCAAAATCAGTTATCAGACCTTGACATTGAAAAGGAATCTGAAAGTGATCCCGAGCTTTCAAACCAATCTCCAGGTAATAAAAAATGCAATAAGTTAATTAACTATTCACCCCATTTTTCAACAAATATAAAGCACAATTTATACAAGAAGAGTGAGCGAGAAAGTTATTGTAAGAATTTTCTTAAGAGGTACAATTTAGGAGTATTGTTATGATATAAACACTACTATTTATATATGAGGTGTAACATGTCAACCCTAATTCCTTTCATTGTCAATAAGAGCATTCATTTGAGTAGACACGGTATTAGGTTTTGAATGAATTGTATTGATGGGGATTAGGTGACATACATACAACTCCACATTCATACATTTATGGATATATTTTTTTCAAATAATAGCATATATTTTTTCAAATAATACATATAAATGATTATCCATTGATATGTACCGTGTATGATGTATACATATAAACTTTTAATTTTTTTGTAGAAAGGACACCATCGATTGTGAAGAATCAAATGGAGGAGTTTCAACAAAAGCTTCAAAGTCTATGA
Protein sequence

>MS.gene53533.t1

MVLTETKLWRKGPYEKPILCNACGLHFKAKGTLDNYLPKTSQQNQLSDLDIEKESESDPELSNQSPERTPSIVKNQMEEFQQKLQSL