AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene009422

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene009422.t1 MTR_3g408420 90.545 275 22 1 1 271 1 275 1.08e-175 485
MS.gene009422.t1 MTR_3g008310 63.273 275 97 2 1 271 1 275 1.09e-114 331
MS.gene009422.t1 MTR_3g408380 62.230 278 89 4 1 271 1 269 6.58e-114 328
MS.gene009422.t1 MTR_0160s0030 25.392 319 168 11 4 263 2 309 6.18e-12 65.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene009422.t1 AT1G02030 25.830 271 149 8 5 264 4 233 5.73e-12 64.7
MS.gene009422.t1 AT3G60580 26.354 277 148 10 7 262 5 246 1.43e-11 63.9

Find 27 sgRNAs with CRISPR-Local

Find 45 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGGTCGTAGACAATTTAATT+TGG 0.272723 3.4:+3663973 MS.gene009422:CDS
AACAATCTATCTGAAGAAAT+TGG 0.300908 3.4:+3664298 MS.gene009422:CDS
TGAGAATACACAAGTTAAAT+TGG 0.302912 3.4:+3664072 MS.gene009422:CDS
ATACTATAGTGAGAAGAAAA+AGG 0.312924 3.4:+3664174 MS.gene009422:CDS
TAAATTGGTGTATAGTGATT+TGG 0.323391 3.4:+3664087 MS.gene009422:CDS
CTATTATTTGTGTGAATGAA+TGG 0.399412 3.4:+3664134 MS.gene009422:CDS
TCACGTGCTTGGTTGTTGAT+TGG 0.399497 3.4:-3663758 None:intergenic
TATCATACCCATGTAAACTT+TGG 0.417954 3.4:+3663893 MS.gene009422:CDS
TCTGAAGAAATTGGTATAAG+TGG 0.426032 3.4:+3664307 MS.gene009422:CDS
TATTCTTACCAAAGTTTACA+TGG 0.428708 3.4:-3663901 None:intergenic
AATAGAGAGAGTTTGATGTT+TGG 0.448411 3.4:-3663798 None:intergenic
TACAGAAGCTGCTGAAACAT+TGG 0.473334 3.4:+3664111 MS.gene009422:CDS
TCACAAGTGCACATATTGCT+TGG 0.480968 3.4:+3664360 MS.gene009422:CDS
CAATGCTTTCCCATTAGAAA+AGG 0.484168 3.4:-3663684 None:intergenic
AAGACCGAAGATTATGCATA+GGG 0.490172 3.4:-3663856 None:intergenic
AAAACCCTATGCATAATCTT+CGG 0.502900 3.4:+3663852 MS.gene009422:CDS
TGTACTTGAGGAACACAAAA+CGG 0.523616 3.4:+3664402 MS.gene009422:CDS
CAACTGAGTGTTCACGTGCT+TGG 0.533072 3.4:-3663769 None:intergenic
TGAATCTGATCATGTACTTG+AGG 0.537940 3.4:+3664390 MS.gene009422:CDS
AAAGACCGAAGATTATGCAT+AGG 0.573672 3.4:-3663857 None:intergenic
AGAAATTGGTATAAGTGGAA+AGG 0.574832 3.4:+3664312 MS.gene009422:CDS
ATAATCTTCGGTCTTTGAAG+AGG 0.587392 3.4:+3663864 MS.gene009422:CDS
ATTCTTACCAAAGTTTACAT+GGG 0.598735 3.4:-3663900 None:intergenic
AGAGAATACAATATTTAATG+TGG 0.616169 3.4:+3664000 MS.gene009422:CDS
TGTGGCTGAAGAAAATGAAG+AGG 0.616323 3.4:+3664018 MS.gene009422:CDS
TCTAATGGGAAAGCATTGGG+AGG 0.669450 3.4:+3663689 MS.gene009422:CDS
GAATGAATGGAAACAAGTTG+AGG 0.698163 3.4:+3664147 MS.gene009422:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATAGATTGTTATTTTTCTTA+TGG - chr3.4:3664288-3664307 None:intergenic 15.0%
!! AGAGAATACAATATTTAATG+TGG + chr3.4:3664000-3664019 MS.gene009422:CDS 20.0%
! AACAATCTATCTGAAGAAAT+TGG + chr3.4:3664298-3664317 MS.gene009422:CDS 25.0%
! AAGAAAAAGGTTAGTGAAAA+TGG + chr3.4:3664187-3664206 MS.gene009422:CDS 25.0%
! ATACTATAGTGAGAAGAAAA+AGG + chr3.4:3664174-3664193 MS.gene009422:CDS 25.0%
! ATTCTTACCAAAGTTTACAT+GGG - chr3.4:3663903-3663922 None:intergenic 25.0%
! CTATTATTTGTGTGAATGAA+TGG + chr3.4:3664134-3664153 MS.gene009422:CDS 25.0%
! TAAATTGGTGTATAGTGATT+TGG + chr3.4:3664087-3664106 MS.gene009422:CDS 25.0%
! TATTCTTACCAAAGTTTACA+TGG - chr3.4:3663904-3663923 None:intergenic 25.0%
! TGAGAATACACAAGTTAAAT+TGG + chr3.4:3664072-3664091 MS.gene009422:CDS 25.0%
!! TGGGTTAGAATCATAAAAAT+TGG - chr3.4:3664437-3664456 None:intergenic 25.0%
AAAACCCTATGCATAATCTT+CGG + chr3.4:3663852-3663871 MS.gene009422:CDS 30.0%
AATAGAGAGAGTTTGATGTT+TGG - chr3.4:3663801-3663820 None:intergenic 30.0%
AGAAATTGGTATAAGTGGAA+AGG + chr3.4:3664312-3664331 MS.gene009422:CDS 30.0%
TATCATACCCATGTAAACTT+TGG + chr3.4:3663893-3663912 MS.gene009422:CDS 30.0%
TCTGAAGAAATTGGTATAAG+TGG + chr3.4:3664307-3664326 MS.gene009422:CDS 30.0%
! GTAACAAGTCCTTTTCTAAT+GGG + chr3.4:3663675-3663694 MS.gene009422:CDS 30.0%
! TGTAACAAGTCCTTTTCTAA+TGG + chr3.4:3663674-3663693 MS.gene009422:CDS 30.0%
!! TGTTGATTGGAGATTTTAGA+GGG - chr3.4:3663748-3663767 None:intergenic 30.0%
!! TTGTTGATTGGAGATTTTAG+AGG - chr3.4:3663749-3663768 None:intergenic 30.0%
!! TTTTGGATTGGAAATTGATG+AGG - chr3.4:3663834-3663853 None:intergenic 30.0%
!!! AGATTATGCATAGGGTTTTT+TGG - chr3.4:3663851-3663870 None:intergenic 30.0%
!!! TTTTCTAATGGGAAAGCATT+GGG + chr3.4:3663686-3663705 MS.gene009422:CDS 30.0%
AAAGACCGAAGATTATGCAT+AGG - chr3.4:3663860-3663879 None:intergenic 35.0%
AAGACCGAAGATTATGCATA+GGG - chr3.4:3663859-3663878 None:intergenic 35.0%
CAATGCTTTCCCATTAGAAA+AGG - chr3.4:3663687-3663706 None:intergenic 35.0%
CGGTCGTAGACAATTTAATT+TGG + chr3.4:3663973-3663992 MS.gene009422:CDS 35.0%
GAATGAATGGAAACAAGTTG+AGG + chr3.4:3664147-3664166 MS.gene009422:CDS 35.0%
TGAATCTGATCATGTACTTG+AGG + chr3.4:3664390-3664409 MS.gene009422:CDS 35.0%
TGTACTTGAGGAACACAAAA+CGG + chr3.4:3664402-3664421 MS.gene009422:CDS 35.0%
! ATAATCTTCGGTCTTTGAAG+AGG + chr3.4:3663864-3663883 MS.gene009422:CDS 35.0%
! CTTTTTCCAGTTGGGTTTTT+TGG - chr3.4:3663944-3663963 None:intergenic 35.0%
! GTTTCGATCTTTTTCCAGTT+GGG - chr3.4:3663952-3663971 None:intergenic 35.0%
! TAGCTAAGTGAGTTTTCATG+TGG - chr3.4:3663715-3663734 None:intergenic 35.0%
! TCTTTTCCAAAAAACCCAAC+TGG + chr3.4:3663935-3663954 MS.gene009422:CDS 35.0%
!! CTTTTCTAATGGGAAAGCAT+TGG + chr3.4:3663685-3663704 MS.gene009422:CDS 35.0%
!!! ATGCATAGGGTTTTTTGGAT+TGG - chr3.4:3663846-3663865 None:intergenic 35.0%
ACTGGAAAAAGATCGAAACG+CGG + chr3.4:3663953-3663972 MS.gene009422:CDS 40.0%
TACAGAAGCTGCTGAAACAT+TGG + chr3.4:3664111-3664130 MS.gene009422:CDS 40.0%
TCACAAGTGCACATATTGCT+TGG + chr3.4:3664360-3664379 MS.gene009422:CDS 40.0%
TGTGGCTGAAGAAAATGAAG+AGG + chr3.4:3664018-3664037 MS.gene009422:CDS 40.0%
! CGTTTCGATCTTTTTCCAGT+TGG - chr3.4:3663953-3663972 None:intergenic 40.0%
TCACGTGCTTGGTTGTTGAT+TGG - chr3.4:3663761-3663780 None:intergenic 45.0%
!! TCTAATGGGAAAGCATTGGG+AGG + chr3.4:3663689-3663708 MS.gene009422:CDS 45.0%
CAACTGAGTGTTCACGTGCT+TGG - chr3.4:3663772-3663791 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 3663644 3664459 3663644 ID=MS.gene009422
chr3.4 mRNA 3663644 3664459 3663644 ID=MS.gene009422.t1;Parent=MS.gene009422
chr3.4 exon 3663644 3664459 3663644 ID=MS.gene009422.t1.exon1;Parent=MS.gene009422.t1
chr3.4 CDS 3663644 3664459 3663644 ID=cds.MS.gene009422.t1;Parent=MS.gene009422.t1
Gene Sequence

>MS.gene009422

ATGGAGAACAATAGAAGAGAATGTCACATTTGTAACAAGTCCTTTTCTAATGGGAAAGCATTGGGAGGCCACATGAAAACTCACTTAGCTAAACTACTAATCCCTCTAAAATCTCCAATCAACAACCAAGCACGTGAACACTCAGTTGAGTCAACCAAACATCAAACTCTCTCTATTTCTACATCTTCCTCATCAATTTCCAATCCAAAAAACCCTATGCATAATCTTCGGTCTTTGAAGAGGAATTTTTATCATACCCATGTAAACTTTGGTAAGAATAGTGTGTTTGATTCTTTTCCAAAAAACCCAACTGGAAAAAGATCGAAACGCGGTCGTAGACAATTTAATTTGGCTGAAGAGAATACAATATTTAATGTGGCTGAAGAAAATGAAGAGGATACACAATTTAATGCAGTTGAAGAAATAAATGAGAATACACAAGTTAAATTGGTGTATAGTGATTTGGATACAGAAGCTGCTGAAACATTGGCTATTATTTGTGTGAATGAATGGAAACAAGTTGAGGAGAAATACTATAGTGAGAAGAAAAAGGTTAGTGAAAATGGCAACATCATGTTTGAATGCGATATTTGTCATGAAGTGTTTCAATATTGCAAAGATCTTGTTAGACATGAAGCAATCCATAAGAAAAATAACAATCTATCTGAAGAAATTGGTATAAGTGGAAAGGAATATGATGTTGTAAATGAAGAAGTTCACAAGTGCACATATTGCTTGGAATTTTTTGAATCTGATCATGTACTTGAGGAACACAAAACGGTACACTTATCCAATTTTTATGATTCTAACCCATAG
Protein sequence

>MS.gene009422.t1

MENNRRECHICNKSFSNGKALGGHMKTHLAKLLIPLKSPINNQAREHSVESTKHQTLSISTSSSSISNPKNPMHNLRSLKRNFYHTHVNFGKNSVFDSFPKNPTGKRSKRGRRQFNLAEENTIFNVAEENEEDTQFNAVEEINENTQVKLVYSDLDTEAAETLAIICVNEWKQVEEKYYSEKKKVSENGNIMFECDICHEVFQYCKDLVRHEAIHKKNNNLSEEIGISGKEYDVVNEEVHKCTYCLEFFESDHVLEEHKTVHLSNFYDSNP