AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene009424

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene009424.t1 MTR_3g408420 90.909 275 21 1 1 271 1 275 1.10e-178 493
MS.gene009424.t1 MTR_3g008310 62.909 275 98 2 1 271 1 275 1.23e-114 330
MS.gene009424.t1 MTR_3g408380 61.511 278 91 4 1 271 1 269 2.74e-112 324
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene009424.t1 AT1G02030 25.830 271 149 8 5 264 4 233 1.71e-12 66.2

Find 27 sgRNAs with CRISPR-Local

Find 45 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAGTCGTAGACAATTTAATT+TGG 0.296849 3.4:+3675689 MS.gene009424:CDS
AACAATCTATCTGAAGAAAT+TGG 0.300908 3.4:+3676014 MS.gene009424:CDS
TGAGAATACACAAGTTAAAT+TGG 0.302912 3.4:+3675788 MS.gene009424:CDS
ATACTATAGTGAGAAGAAAA+AGG 0.312924 3.4:+3675890 MS.gene009424:CDS
TAAATTGGTGTATAGTGATT+TGG 0.323391 3.4:+3675803 MS.gene009424:CDS
TCAGGTGCTTGGTTGTTGAT+TGG 0.373001 3.4:-3675474 None:intergenic
TATCATACCCTTGTAAACTT+TGG 0.403944 3.4:+3675609 MS.gene009424:CDS
CAACTGAGTGTTCAGGTGCT+TGG 0.424891 3.4:-3675485 None:intergenic
TCTGAAGAAATTGGTATAAG+TGG 0.426032 3.4:+3676023 MS.gene009424:CDS
CTATTATTTGTGTGAATGAA+TGG 0.435873 3.4:+3675850 MS.gene009424:CDS
AAGATCGAAGATTATGCATC+GGG 0.436213 3.4:-3675572 None:intergenic
GTTGACTCAACTGAGTGTTC+AGG 0.442669 3.4:-3675492 None:intergenic
AATAGAGAGAGTTTGATGTT+TGG 0.448411 3.4:-3675514 None:intergenic
TATTCTTACCAAAGTTTACA+AGG 0.477139 3.4:-3675617 None:intergenic
TCACAAGTGCACATATTGCT+TGG 0.480968 3.4:+3676076 MS.gene009424:CDS
CAATGCTTTCCCATTAGAAA+AGG 0.484168 3.4:-3675400 None:intergenic
TACAGAAGCTGCTGAAACAA+TGG 0.521106 3.4:+3675827 MS.gene009424:CDS
TGTACTTGAGGAACACAAAA+CGG 0.523616 3.4:+3676118 MS.gene009424:CDS
TGAATCTGATCATGTACTTG+AGG 0.537940 3.4:+3676106 MS.gene009424:CDS
ATAATCTTCGATCTTTGAAG+AGG 0.557615 3.4:+3675580 MS.gene009424:CDS
AGAAATTGGTATAAGTGGAA+AGG 0.574832 3.4:+3676028 MS.gene009424:CDS
AAAGATCGAAGATTATGCAT+CGG 0.580003 3.4:-3675573 None:intergenic
AGAGAATACAATATTTAATG+TGG 0.616169 3.4:+3675716 MS.gene009424:CDS
TGTGGCTGAAGAAAATGAAG+AGG 0.616323 3.4:+3675734 MS.gene009424:CDS
ATTCTTACCAAAGTTTACAA+GGG 0.625545 3.4:-3675616 None:intergenic
TCTAATGGGAAAGCATTGGG+AGG 0.669450 3.4:+3675405 MS.gene009424:CDS
GAATGAATGGAAACAAGTTG+AGG 0.698163 3.4:+3675863 MS.gene009424:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATAGATTGTTATTTTTCTTA+TGG - chr3.4:3676004-3676023 None:intergenic 15.0%
!! AGAGAATACAATATTTAATG+TGG + chr3.4:3675716-3675735 MS.gene009424:CDS 20.0%
! AACAATCTATCTGAAGAAAT+TGG + chr3.4:3676014-3676033 MS.gene009424:CDS 25.0%
! AAGAAAAAGGTTAGTGAAAA+TGG + chr3.4:3675903-3675922 MS.gene009424:CDS 25.0%
! ATACTATAGTGAGAAGAAAA+AGG + chr3.4:3675890-3675909 MS.gene009424:CDS 25.0%
! ATTCTTACCAAAGTTTACAA+GGG - chr3.4:3675619-3675638 None:intergenic 25.0%
! CTATTATTTGTGTGAATGAA+TGG + chr3.4:3675850-3675869 MS.gene009424:CDS 25.0%
! TAAATTGGTGTATAGTGATT+TGG + chr3.4:3675803-3675822 MS.gene009424:CDS 25.0%
! TATTCTTACCAAAGTTTACA+AGG - chr3.4:3675620-3675639 None:intergenic 25.0%
! TGAGAATACACAAGTTAAAT+TGG + chr3.4:3675788-3675807 MS.gene009424:CDS 25.0%
AAAGATCGAAGATTATGCAT+CGG - chr3.4:3675576-3675595 None:intergenic 30.0%
AATAGAGAGAGTTTGATGTT+TGG - chr3.4:3675517-3675536 None:intergenic 30.0%
AGAAATTGGTATAAGTGGAA+AGG + chr3.4:3676028-3676047 MS.gene009424:CDS 30.0%
CAGTCGTAGACAATTTAATT+TGG + chr3.4:3675689-3675708 MS.gene009424:CDS 30.0%
TATCATACCCTTGTAAACTT+TGG + chr3.4:3675609-3675628 MS.gene009424:CDS 30.0%
TCTGAAGAAATTGGTATAAG+TGG + chr3.4:3676023-3676042 MS.gene009424:CDS 30.0%
! ATAATCTTCGATCTTTGAAG+AGG + chr3.4:3675580-3675599 MS.gene009424:CDS 30.0%
! GTAACAAGTCCTTTTCTAAT+GGG + chr3.4:3675391-3675410 MS.gene009424:CDS 30.0%
! TGGGTTAGAATCAGAAAAAT+TGG - chr3.4:3676153-3676172 None:intergenic 30.0%
! TGTAACAAGTCCTTTTCTAA+TGG + chr3.4:3675390-3675409 MS.gene009424:CDS 30.0%
!! TGTTGATTGGAGATTTTAGA+GGG - chr3.4:3675464-3675483 None:intergenic 30.0%
!! TTGTTGATTGGAGATTTTAG+AGG - chr3.4:3675465-3675484 None:intergenic 30.0%
!! TTTTGGATTGGAAATTGATG+AGG - chr3.4:3675550-3675569 None:intergenic 30.0%
!!! TTTTCTAATGGGAAAGCATT+GGG + chr3.4:3675402-3675421 MS.gene009424:CDS 30.0%
AAGATCGAAGATTATGCATC+GGG - chr3.4:3675575-3675594 None:intergenic 35.0%
CAATGCTTTCCCATTAGAAA+AGG - chr3.4:3675403-3675422 None:intergenic 35.0%
GAATGAATGGAAACAAGTTG+AGG + chr3.4:3675863-3675882 MS.gene009424:CDS 35.0%
TGAATCTGATCATGTACTTG+AGG + chr3.4:3676106-3676125 MS.gene009424:CDS 35.0%
TGTACTTGAGGAACACAAAA+CGG + chr3.4:3676118-3676137 MS.gene009424:CDS 35.0%
! CTTTTTCCAGTTGGGTATTT+TGG - chr3.4:3675660-3675679 None:intergenic 35.0%
! GTTTCGATCTTTTTCCAGTT+GGG - chr3.4:3675668-3675687 None:intergenic 35.0%
! TAGCTAAGTGAGTTTTCATG+TGG - chr3.4:3675431-3675450 None:intergenic 35.0%
! TCTTTTCCAAAATACCCAAC+TGG + chr3.4:3675651-3675670 MS.gene009424:CDS 35.0%
!! ATTGGAGATTTTAGAGGGAT+TGG - chr3.4:3675459-3675478 None:intergenic 35.0%
!! CTTTTCTAATGGGAAAGCAT+TGG + chr3.4:3675401-3675420 MS.gene009424:CDS 35.0%
!!! AGATTATGCATCGGGTTTTT+TGG - chr3.4:3675567-3675586 None:intergenic 35.0%
TACAGAAGCTGCTGAAACAA+TGG + chr3.4:3675827-3675846 MS.gene009424:CDS 40.0%
TCACAAGTGCACATATTGCT+TGG + chr3.4:3676076-3676095 MS.gene009424:CDS 40.0%
TGTGGCTGAAGAAAATGAAG+AGG + chr3.4:3675734-3675753 MS.gene009424:CDS 40.0%
! CGTTTCGATCTTTTTCCAGT+TGG - chr3.4:3675669-3675688 None:intergenic 40.0%
!!! ATGCATCGGGTTTTTTGGAT+TGG - chr3.4:3675562-3675581 None:intergenic 40.0%
TCAGGTGCTTGGTTGTTGAT+TGG - chr3.4:3675477-3675496 None:intergenic 45.0%
! GTTGACTCAACTGAGTGTTC+AGG - chr3.4:3675495-3675514 None:intergenic 45.0%
!! TCTAATGGGAAAGCATTGGG+AGG + chr3.4:3675405-3675424 MS.gene009424:CDS 45.0%
CAACTGAGTGTTCAGGTGCT+TGG - chr3.4:3675488-3675507 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 3675360 3676175 3675360 ID=MS.gene009424
chr3.4 mRNA 3675360 3676175 3675360 ID=MS.gene009424.t1;Parent=MS.gene009424
chr3.4 exon 3675360 3676175 3675360 ID=MS.gene009424.t1.exon1;Parent=MS.gene009424.t1
chr3.4 CDS 3675360 3676175 3675360 ID=cds.MS.gene009424.t1;Parent=MS.gene009424.t1
Gene Sequence

>MS.gene009424

ATGGAGAACAATAGAAGAGAATGTCACATTTGTAACAAGTCCTTTTCTAATGGGAAAGCATTGGGAGGCCACATGAAAACTCACTTAGCTAAACTACCAATCCCTCTAAAATCTCCAATCAACAACCAAGCACCTGAACACTCAGTTGAGTCAACCAAACATCAAACTCTCTCTATTTCTACATCTTCCTCATCAATTTCCAATCCAAAAAACCCGATGCATAATCTTCGATCTTTGAAGAGGAACTTTTATCATACCCTTGTAAACTTTGGTAAGAATAGTGTGTTTGATTCTTTTCCAAAATACCCAACTGGAAAAAGATCGAAACGCAGTCGTAGACAATTTAATTTGGCTGAAGAGAATACAATATTTAATGTGGCTGAAGAAAATGAAGAGGATACACAATTTAATGCAGTTGAAGAAATAAATGAGAATACACAAGTTAAATTGGTGTATAGTGATTTGGATACAGAAGCTGCTGAAACAATGGCTATTATTTGTGTGAATGAATGGAAACAAGTTGAGGAGAAATACTATAGTGAGAAGAAAAAGGTTAGTGAAAATGGCAACATCATGTTTGAATGCGATATTTGTCATGAAGTGTTTCAATATTGCAAAGATCTTGTTAGACATGAAGCAATCCATAAGAAAAATAACAATCTATCTGAAGAAATTGGTATAAGTGGAAAGGAATATGATGTTGTAAATGAAGAAGTTCACAAGTGCACATATTGCTTGGAATTTTTTGAATCTGATCATGTACTTGAGGAACACAAAACGGTACACTTATCCAATTTTTCTGATTCTAACCCATAG
Protein sequence

>MS.gene009424.t1

MENNRRECHICNKSFSNGKALGGHMKTHLAKLPIPLKSPINNQAPEHSVESTKHQTLSISTSSSSISNPKNPMHNLRSLKRNFYHTLVNFGKNSVFDSFPKYPTGKRSKRSRRQFNLAEENTIFNVAEENEEDTQFNAVEEINENTQVKLVYSDLDTEAAETMAIICVNEWKQVEEKYYSEKKKVSENGNIMFECDICHEVFQYCKDLVRHEAIHKKNNNLSEEIGISGKEYDVVNEEVHKCTYCLEFFESDHVLEEHKTVHLSNFSDSNP