AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene79066

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene79066.t1 MTR_3g034200 34.058 138 81 3 5 134 21 156 1.24e-16 72.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene79066.t1 AT5G13780 32.800 125 74 3 17 133 33 155 1.40e-14 67.8

Find 38 sgRNAs with CRISPR-Local

Find 42 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAACAATGGTTATATCTTT+AGG 0.270166 3.1:+20698328 MS.gene79066:CDS
TTTCGAGCTTATTGTTTGTT+TGG 0.285966 3.1:+20698267 MS.gene79066:CDS
ACATCGATGATCGGCAGATT+TGG 0.298947 3.1:+20697841 None:intergenic
TGTTTGTTTGGAAAGACCTT+AGG 0.354964 3.1:+20698279 MS.gene79066:CDS
CGCTATTGAGGACTTGGAAC+GGG 0.400054 3.1:+20698074 MS.gene79066:CDS
TAAACAATCCTTCTGAGATC+AGG 0.411813 3.1:+20697872 MS.gene79066:CDS
TGTCAACTCTATAGTTCATA+AGG 0.425180 3.1:+20697957 MS.gene79066:CDS
GTTTGTTTGGAAAGACCTTA+GGG 0.452496 3.1:+20698280 MS.gene79066:CDS
GATGATCGGCAGATTTGGTC+TGG 0.455393 3.1:+20697846 None:intergenic
TAAGCTCGAAATTTCTTCCT+CGG 0.470115 3.1:-20698255 None:intergenic
AAGCTCGAAATTTCTTCCTC+GGG 0.485496 3.1:-20698254 None:intergenic
GACCGCCGCTATTGAGGACT+TGG 0.487277 3.1:+20698068 MS.gene79066:CDS
GCAGCTCATGCAGTGGTTGG+TGG 0.489191 3.1:-20697911 None:intergenic
ACCTTAGGGTACGATATTCA+TGG 0.489911 3.1:+20698294 MS.gene79066:CDS
TGCATTCTGAGGAGATCAAA+GGG 0.498730 3.1:+20698358 MS.gene79066:CDS
ACTTGTGACCGCCGCTATTG+AGG 0.499579 3.1:+20698062 MS.gene79066:CDS
GCCGCAGCTCATGCAGTGGT+TGG 0.537031 3.1:-20697914 None:intergenic
TGCGGCCGTGACAAAATTGT+CGG 0.540537 3.1:+20697931 MS.gene79066:CDS
TACGGAGAACCACGACGTGA+TGG 0.566601 3.1:-20698011 None:intergenic
CACGGCCGCAGCTCATGCAG+TGG 0.567631 3.1:-20697918 None:intergenic
ATGCATTCTGAGGAGATCAA+AGG 0.568832 3.1:+20698357 MS.gene79066:CDS
ACCAACCACTGCATGAGCTG+CGG 0.580426 3.1:+20697913 MS.gene79066:CDS
TGAAGAAGCCTGATCTCAGA+AGG 0.586919 3.1:-20697880 None:intergenic
AGCTATCATAGACGTGGTAT+CGG 0.590254 3.1:+20698033 MS.gene79066:CDS
ACATCTCAGCGCTCGTCCCG+AGG 0.601365 3.1:+20698238 MS.gene79066:CDS
ACCATGAATATCGTACCCTA+AGG 0.607373 3.1:-20698295 None:intergenic
TAGGAAGCAGATGCATTCTG+AGG 0.625836 3.1:+20698347 MS.gene79066:CDS
CATATAACGACATCGATGAT+CGG 0.625866 3.1:+20697832 None:intergenic
CTCCGTAGCTATCATAGACG+TGG 0.628264 3.1:+20698027 MS.gene79066:CDS
CCGCTATTGAGGACTTGGAA+CGG 0.633873 3.1:+20698073 MS.gene79066:CDS
ACGAGCGCTGAGATGTACTC+AGG 0.636447 3.1:-20698231 None:intergenic
CGCTAAAATCCATCACGTCG+TGG 0.646158 3.1:+20698002 MS.gene79066:CDS
TCTGAGGAGATCAAAGGGAA+CGG 0.649018 3.1:+20698363 MS.gene79066:CDS
TTCCAAGTCCTCAATAGCGG+CGG 0.666332 3.1:-20698070 None:intergenic
TACCACGTCTATGATAGCTA+CGG 0.686642 3.1:-20698029 None:intergenic
CCGTTCCAAGTCCTCAATAG+CGG 0.687217 3.1:-20698073 None:intergenic
GGTGCTGATGTTGAGAACAA+TGG 0.703960 3.1:+20698315 MS.gene79066:CDS
GAGGAGATCAAAGGGAACGG+TGG 0.705914 3.1:+20698366 MS.gene79066:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAGATTTATTCATAAACTT+TGG + chr3.1:20698159-20698178 MS.gene79066:intron 15.0%
!! GAATAATTGAAACAAACAAT+TGG - chr3.1:20698107-20698126 None:intergenic 20.0%
! AGAACAATGGTTATATCTTT+AGG + chr3.1:20698328-20698347 MS.gene79066:CDS 25.0%
!! TGTAACTCTATATGTTACTT+AGG + chr3.1:20698134-20698153 MS.gene79066:intron 25.0%
AACAAACACAGTAACATCAA+AGG - chr3.1:20698198-20698217 None:intergenic 30.0%
ACATATAGAGTTACAGAAGT+AGG - chr3.1:20698129-20698148 None:intergenic 30.0%
TGTCAACTCTATAGTTCATA+AGG + chr3.1:20697957-20697976 MS.gene79066:CDS 30.0%
TTTCGAGCTTATTGTTTGTT+TGG + chr3.1:20698267-20698286 MS.gene79066:CDS 30.0%
GTTTGTTTGGAAAGACCTTA+GGG + chr3.1:20698280-20698299 MS.gene79066:CDS 35.0%
TAAGCTCGAAATTTCTTCCT+CGG - chr3.1:20698258-20698277 None:intergenic 35.0%
TGTTTGTTTGGAAAGACCTT+AGG + chr3.1:20698279-20698298 MS.gene79066:CDS 35.0%
! CATAACCGACAATTTTGTCA+CGG - chr3.1:20697939-20697958 None:intergenic 35.0%
!! TAAACAATCCTTCTGAGATC+AGG + chr3.1:20697872-20697891 MS.gene79066:CDS 35.0%
AAGCTCGAAATTTCTTCCTC+GGG - chr3.1:20698257-20698276 None:intergenic 40.0%
ACCATGAATATCGTACCCTA+AGG - chr3.1:20698298-20698317 None:intergenic 40.0%
ACCTTAGGGTACGATATTCA+TGG + chr3.1:20698294-20698313 MS.gene79066:CDS 40.0%
AGCTATCATAGACGTGGTAT+CGG + chr3.1:20698033-20698052 MS.gene79066:CDS 40.0%
TACCACGTCTATGATAGCTA+CGG - chr3.1:20698032-20698051 None:intergenic 40.0%
! ATGCATTCTGAGGAGATCAA+AGG + chr3.1:20698357-20698376 MS.gene79066:CDS 40.0%
! TGCATTCTGAGGAGATCAAA+GGG + chr3.1:20698358-20698377 MS.gene79066:CDS 40.0%
TAGGAAGCAGATGCATTCTG+AGG + chr3.1:20698347-20698366 MS.gene79066:CDS 45.0%
TCTGAGGAGATCAAAGGGAA+CGG + chr3.1:20698363-20698382 MS.gene79066:CDS 45.0%
TGAAGAAGCCTGATCTCAGA+AGG - chr3.1:20697883-20697902 None:intergenic 45.0%
! CAGTAACATCAAAGGCGTAC+TGG - chr3.1:20698190-20698209 None:intergenic 45.0%
!! GGTGCTGATGTTGAGAACAA+TGG + chr3.1:20698315-20698334 MS.gene79066:CDS 45.0%
CCGCTATTGAGGACTTGGAA+CGG + chr3.1:20698073-20698092 MS.gene79066:CDS 50.0%
CCGTTCCAAGTCCTCAATAG+CGG - chr3.1:20698076-20698095 None:intergenic 50.0%
CGCTAAAATCCATCACGTCG+TGG + chr3.1:20698002-20698021 MS.gene79066:CDS 50.0%
CGCTATTGAGGACTTGGAAC+GGG + chr3.1:20698074-20698093 MS.gene79066:CDS 50.0%
CTCCGTAGCTATCATAGACG+TGG + chr3.1:20698027-20698046 MS.gene79066:CDS 50.0%
TGCGGCCGTGACAAAATTGT+CGG + chr3.1:20697931-20697950 MS.gene79066:CDS 50.0%
TTCCAAGTCCTCAATAGCGG+CGG - chr3.1:20698073-20698092 None:intergenic 50.0%
ACCAACCACTGCATGAGCTG+CGG + chr3.1:20697913-20697932 MS.gene79066:CDS 55.0%
ACTTGTGACCGCCGCTATTG+AGG + chr3.1:20698062-20698081 MS.gene79066:CDS 55.0%
GAGGAGATCAAAGGGAACGG+TGG + chr3.1:20698366-20698385 MS.gene79066:CDS 55.0%
TACGGAGAACCACGACGTGA+TGG - chr3.1:20698014-20698033 None:intergenic 55.0%
!! ACGAGCGCTGAGATGTACTC+AGG - chr3.1:20698234-20698253 None:intergenic 55.0%
GACCGCCGCTATTGAGGACT+TGG + chr3.1:20698068-20698087 MS.gene79066:CDS 60.0%
GCAGCTCATGCAGTGGTTGG+TGG - chr3.1:20697914-20697933 None:intergenic 60.0%
ACATCTCAGCGCTCGTCCCG+AGG + chr3.1:20698238-20698257 MS.gene79066:CDS 65.0%
GCCGCAGCTCATGCAGTGGT+TGG - chr3.1:20697917-20697936 None:intergenic 65.0%
CACGGCCGCAGCTCATGCAG+TGG - chr3.1:20697921-20697940 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr3.1 gene 20697847 20698398 20697847 ID=MS.gene79066
chr3.1 mRNA 20697847 20698398 20697847 ID=MS.gene79066.t1;Parent=MS.gene79066
chr3.1 exon 20697847 20698095 20697847 ID=MS.gene79066.t1.exon1;Parent=MS.gene79066.t1
chr3.1 CDS 20697847 20698095 20697847 ID=cds.MS.gene79066.t1;Parent=MS.gene79066.t1
chr3.1 exon 20698222 20698398 20698222 ID=MS.gene79066.t1.exon2;Parent=MS.gene79066.t1
chr3.1 CDS 20698222 20698398 20698222 ID=cds.MS.gene79066.t1;Parent=MS.gene79066.t1
Gene Sequence

>MS.gene79066

ATGATCGGCAGATTTGGTCTGGTTTTAAACAATCCTTCTGAGATCAGGCTTCTTCACGTCGCTGCCACCAACCACTGCATGAGCTGCGGCCGTGACAAAATTGTCGGTTATGTCAACTCTATAGTTCATAAGGAAACTAACGAGTGCAAGCATCACGCTAAAATCCATCACGTCGTGGTTCTCCGTAGCTATCATAGACGTGGTATCGGTACAAAACTTGTGACCGCCGCTATTGAGGACTTGGAACGGGTTTGTTACCAATTGTTTGTTTCAATTATTCCTACTTCTGTAACTCTATATGTTACTTAGGAGTTAGATTTATTCATAAACTTTGGTATAACCAGTACGCCTTTGATGTTACTGTGTTTGTTACAGATGTATCATCCTGAGTACATCTCAGCGCTCGTCCCGAGGAAGAAATTTCGAGCTTATTGTTTGTTTGGAAAGACCTTAGGGTACGATATTCATGGTGCTGATGTTGAGAACAATGGTTATATCTTTAGGAAGCAGATGCATTCTGAGGAGATCAAAGGGAACGGTGGTGCTTCTTGA
Protein sequence

>MS.gene79066.t1

MIGRFGLVLNNPSEIRLLHVAATNHCMSCGRDKIVGYVNSIVHKETNECKHHAKIHHVVVLRSYHRRGIGTKLVTAAIEDLERMYHPEYISALVPRKKFRAYCLFGKTLGYDIHGADVENNGYIFRKQMHSEEIKGNGGAS