AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene003409

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene003409.t1 MTR_4g075450 99.342 152 1 0 1 152 1 152 2.04e-108 305
MS.gene003409.t1 MTR_1g070450 96.053 152 6 0 1 152 1 152 2.40e-104 295
MS.gene003409.t1 MTR_8g105110 93.506 154 8 1 1 152 1 154 3.53e-98 279
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene003409.t1 AT5G09500 88.816 152 15 1 1 152 1 150 1.62e-94 270
MS.gene003409.t1 AT5G09510 92.105 152 12 0 1 152 1 152 2.95e-92 264
MS.gene003409.t1 AT1G04270 92.105 152 12 0 1 152 1 152 3.48e-92 264
MS.gene003409.t1 AT5G09490 82.895 152 26 0 1 152 1 152 3.26e-91 261
MS.gene003409.t1 AT1G04270 91.447 152 12 1 1 152 1 151 1.13e-89 258
MS.gene003409.t1 AT5G43640 87.919 149 18 0 4 152 1 149 4.59e-85 246
MS.gene003409.t1 AT5G09510 93.220 118 8 0 35 152 1 118 4.73e-69 204
MS.gene003409.t1 AT5G63070 63.750 160 50 4 1 152 1 160 2.70e-62 189
MS.gene003409.t1 AT1G33850 79.104 67 14 0 4 70 1 67 1.15e-21 83.2

Find 47 sgRNAs with CRISPR-Local

Find 45 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGATAGTGGCCAATCATTTC+AGG 0.255429 4.1:-28504300 None:intergenic
GAGATGATTGGTAGCATTAT+TGG 0.295899 4.1:+28504237 MS.gene003409:CDS
AGGTGAGTCCTCACTGGTTC+TGG 0.312113 4.1:-28504192 None:intergenic
CCAGGCCTACCGTGCTTAAC+AGG 0.326778 4.1:-28504348 None:intergenic
GATCAGTGCCATAGGCTTGC+GGG 0.366809 4.1:-28504124 None:intergenic
GAAATTAAACCTGAAATGAT+TGG 0.389036 4.1:+28504291 MS.gene003409:CDS
TTTAATTTCAACCTGATTGA+AGG 0.413851 4.1:-28504277 None:intergenic
ACTGGTTCTGGCTTCTCACC+AGG 0.440200 4.1:-28504180 None:intergenic
ACTCCATGTGCTGCTACCTC+TGG 0.447556 4.1:-28503970 None:intergenic
AGTTGATCTCGATGCTCTCT+TGG 0.473380 4.1:+28504032 MS.gene003409:CDS
CAATGGAAAGACCTTCAATC+AGG 0.479116 4.1:+28504266 MS.gene003409:CDS
CCTGTTAAGCACGGTAGGCC+TGG 0.480548 4.1:+28504348 MS.gene003409:CDS
TGGTTTAACCCGCAAGCCTA+TGG 0.481267 4.1:+28504116 MS.gene003409:CDS
TCTCTGCACGTGCCCGACGA+AGG 0.500103 4.1:+28504085 MS.gene003409:CDS
TGATCAGTGCCATAGGCTTG+CGG 0.511355 4.1:-28504125 None:intergenic
TTGAGAATTCAGCAAGATAG+TGG 0.526209 4.1:-28504314 None:intergenic
CAGGCACAATGATCATGTTA+CGG 0.535956 4.1:-28504215 None:intergenic
TTCAAGAAGTTCAGTTTCCG+TGG 0.538808 4.1:+28504009 MS.gene003409:CDS
ATCATTGTGCCTGAGATGAT+TGG 0.552522 4.1:+28504225 MS.gene003409:CDS
ACCACGTCGAAACCTTCGTC+GGG 0.558631 4.1:-28504097 None:intergenic
GTGCCTCACGTTTCGCCTTG+CGG 0.558971 4.1:-28504155 None:intergenic
TTACGGAGGTGAGTCCTCAC+TGG 0.565975 4.1:-28504198 None:intergenic
GATGAGAGTCTTCACTTGAG+AGG 0.572177 4.1:-28504402 None:intergenic
TCGGTGCTACTAACTCCTCC+AGG 0.575536 4.1:+28504373 MS.gene003409:CDS
GAGTTAGTAGCACCGATACC+AGG 0.575818 4.1:-28504366 None:intergenic
AGCTTCACAAGTTCATCAGT+GGG 0.576252 4.1:-28504060 None:intergenic
ATAATGCTACCAATCATCTC+AGG 0.577641 4.1:-28504234 None:intergenic
AGCATTATTGGTGTCTACAA+TGG 0.579267 4.1:+28504249 MS.gene003409:CDS
AAGCACGGTAGGCCTGGTAT+CGG 0.593127 4.1:+28504354 MS.gene003409:CDS
GAACCAGAGGTAGCAGCACA+TGG 0.595234 4.1:+28503967 MS.gene003409:CDS
ACAAGCCTGTTAAGCACGGT+AGG 0.596494 4.1:+28504343 MS.gene003409:CDS
AGCTTCTTGATCAGTGCCAT+AGG 0.597848 4.1:-28504132 None:intergenic
GCGAAACGTGAGGCACCACC+TGG 0.605362 4.1:+28504162 MS.gene003409:CDS
AAGCTTCACAAGTTCATCAG+TGG 0.618110 4.1:-28504061 None:intergenic
AGAGGTAGCAGCACATGGAG+TGG 0.629988 4.1:+28503972 MS.gene003409:CDS
TCACTTGAGAGGAATAAACC+TGG 0.632316 4.1:-28504391 None:intergenic
AACCACGTCGAAACCTTCGT+CGG 0.635075 4.1:-28504098 None:intergenic
GGTTCTGGCTTCTCACCAGG+TGG 0.636958 4.1:-28504177 None:intergenic
TCTTACAAGCCTGTTAAGCA+CGG 0.639372 4.1:+28504339 MS.gene003409:CDS
GCTCCGCAAGGCGAAACGTG+AGG 0.649824 4.1:+28504152 MS.gene003409:CDS
ACTGATCAAGAAGCTCCGCA+AGG 0.663887 4.1:+28504140 MS.gene003409:CDS
CATGGCGGATGTTGAACCAG+AGG 0.672525 4.1:+28503954 None:intergenic
GAGCATCGAGATCAACTCCA+CGG 0.673689 4.1:-28504026 None:intergenic
GCCCGACGAAGGTTTCGACG+TGG 0.696172 4.1:+28504096 MS.gene003409:CDS
GTGAGAAGCCAGAACCAGTG+AGG 0.706617 4.1:+28504184 MS.gene003409:CDS
GCACAATGATCATGTTACGG+AGG 0.711118 4.1:-28504212 None:intergenic
CTTGAGAGGAATAAACCTGG+AGG 0.744280 4.1:-28504388 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! GAAATTAAACCTGAAATGAT+TGG + chr4.1:28504291-28504310 MS.gene003409:CDS 25.0%
!! TTTAATTTCAACCTGATTGA+AGG - chr4.1:28504280-28504299 None:intergenic 25.0%
ATAATGCTACCAATCATCTC+AGG - chr4.1:28504237-28504256 None:intergenic 35.0%
TTGAGAATTCAGCAAGATAG+TGG - chr4.1:28504317-28504336 None:intergenic 35.0%
! AGCATTATTGGTGTCTACAA+TGG + chr4.1:28504249-28504268 MS.gene003409:CDS 35.0%
! GAGATGATTGGTAGCATTAT+TGG + chr4.1:28504237-28504256 MS.gene003409:CDS 35.0%
AAGCTTCACAAGTTCATCAG+TGG - chr4.1:28504064-28504083 None:intergenic 40.0%
AGCTTCACAAGTTCATCAGT+GGG - chr4.1:28504063-28504082 None:intergenic 40.0%
ATCATTGTGCCTGAGATGAT+TGG + chr4.1:28504225-28504244 MS.gene003409:CDS 40.0%
CAATGGAAAGACCTTCAATC+AGG + chr4.1:28504266-28504285 MS.gene003409:CDS 40.0%
CAGGCACAATGATCATGTTA+CGG - chr4.1:28504218-28504237 None:intergenic 40.0%
TCACTTGAGAGGAATAAACC+TGG - chr4.1:28504394-28504413 None:intergenic 40.0%
TCTTACAAGCCTGTTAAGCA+CGG + chr4.1:28504339-28504358 MS.gene003409:CDS 40.0%
TTCAAGAAGTTCAGTTTCCG+TGG + chr4.1:28504009-28504028 MS.gene003409:CDS 40.0%
! AGATAGTGGCCAATCATTTC+AGG - chr4.1:28504303-28504322 None:intergenic 40.0%
AGCTTCTTGATCAGTGCCAT+AGG - chr4.1:28504135-28504154 None:intergenic 45.0%
AGTTGATCTCGATGCTCTCT+TGG + chr4.1:28504032-28504051 MS.gene003409:CDS 45.0%
CTTGAGAGGAATAAACCTGG+AGG - chr4.1:28504391-28504410 None:intergenic 45.0%
GCACAATGATCATGTTACGG+AGG - chr4.1:28504215-28504234 None:intergenic 45.0%
AACCACGTCGAAACCTTCGT+CGG - chr4.1:28504101-28504120 None:intergenic 50.0%
ACAAGCCTGTTAAGCACGGT+AGG + chr4.1:28504343-28504362 MS.gene003409:CDS 50.0%
ACTGATCAAGAAGCTCCGCA+AGG + chr4.1:28504140-28504159 MS.gene003409:CDS 50.0%
TGATCAGTGCCATAGGCTTG+CGG - chr4.1:28504128-28504147 None:intergenic 50.0%
TGGTTTAACCCGCAAGCCTA+TGG + chr4.1:28504116-28504135 MS.gene003409:CDS 50.0%
!! GAGCATCGAGATCAACTCCA+CGG - chr4.1:28504029-28504048 None:intergenic 50.0%
!! GAGTTAGTAGCACCGATACC+AGG - chr4.1:28504369-28504388 None:intergenic 50.0%
AAGCACGGTAGGCCTGGTAT+CGG + chr4.1:28504354-28504373 MS.gene003409:CDS 55.0%
ACCACGTCGAAACCTTCGTC+GGG - chr4.1:28504100-28504119 None:intergenic 55.0%
AGAGGTAGCAGCACATGGAG+TGG + chr4.1:28503972-28503991 MS.gene003409:CDS 55.0%
GAACCAGAGGTAGCAGCACA+TGG + chr4.1:28503967-28503986 MS.gene003409:CDS 55.0%
GATCAGTGCCATAGGCTTGC+GGG - chr4.1:28504127-28504146 None:intergenic 55.0%
GTGAGAAGCCAGAACCAGTG+AGG + chr4.1:28504184-28504203 MS.gene003409:CDS 55.0%
TTACGGAGGTGAGTCCTCAC+TGG - chr4.1:28504201-28504220 None:intergenic 55.0%
! ACTCCATGTGCTGCTACCTC+TGG - chr4.1:28503973-28503992 None:intergenic 55.0%
!! ACTGGTTCTGGCTTCTCACC+AGG - chr4.1:28504183-28504202 None:intergenic 55.0%
!! AGGTGAGTCCTCACTGGTTC+TGG - chr4.1:28504195-28504214 None:intergenic 55.0%
!! TCGGTGCTACTAACTCCTCC+AGG + chr4.1:28504373-28504392 MS.gene003409:CDS 55.0%
CCAGGCCTACCGTGCTTAAC+AGG - chr4.1:28504351-28504370 None:intergenic 60.0%
CCTGTTAAGCACGGTAGGCC+TGG + chr4.1:28504348-28504367 MS.gene003409:CDS 60.0%
GTGCCTCACGTTTCGCCTTG+CGG - chr4.1:28504158-28504177 None:intergenic 60.0%
!! GGTTCTGGCTTCTCACCAGG+TGG - chr4.1:28504180-28504199 None:intergenic 60.0%
GCCCGACGAAGGTTTCGACG+TGG + chr4.1:28504096-28504115 MS.gene003409:CDS 65.0%
GCTCCGCAAGGCGAAACGTG+AGG + chr4.1:28504152-28504171 MS.gene003409:CDS 65.0%
TCTCTGCACGTGCCCGACGA+AGG + chr4.1:28504085-28504104 MS.gene003409:CDS 65.0%
! GCGAAACGTGAGGCACCACC+TGG + chr4.1:28504162-28504181 MS.gene003409:CDS 65.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 28503955 28504413 28503955 ID=MS.gene003409
chr4.1 mRNA 28503955 28504413 28503955 ID=MS.gene003409.t1;Parent=MS.gene003409
chr4.1 exon 28503955 28504413 28503955 ID=MS.gene003409.t1.exon1;Parent=MS.gene003409.t1
chr4.1 CDS 28503955 28504413 28503955 ID=cds.MS.gene003409.t1;Parent=MS.gene003409.t1
Gene Sequence

>MS.gene003409

ATGGCGGATGTTGAACCAGAGGTAGCAGCACATGGAGTGGCAAAGAAGAGAACATTCAAGAAGTTCAGTTTCCGTGGAGTTGATCTCGATGCTCTCTTGGATATGCCCACTGATGAACTTGTGAAGCTTTTCTCTGCACGTGCCCGACGAAGGTTTCGACGTGGTTTAACCCGCAAGCCTATGGCACTGATCAAGAAGCTCCGCAAGGCGAAACGTGAGGCACCACCTGGTGAGAAGCCAGAACCAGTGAGGACTCACCTCCGTAACATGATCATTGTGCCTGAGATGATTGGTAGCATTATTGGTGTCTACAATGGAAAGACCTTCAATCAGGTTGAAATTAAACCTGAAATGATTGGCCACTATCTTGCTGAATTCTCAATCTCTTACAAGCCTGTTAAGCACGGTAGGCCTGGTATCGGTGCTACTAACTCCTCCAGGTTTATTCCTCTCAAGTGA
Protein sequence

>MS.gene003409.t1

MADVEPEVAAHGVAKKRTFKKFSFRGVDLDALLDMPTDELVKLFSARARRRFRRGLTRKPMALIKKLRKAKREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSISYKPVKHGRPGIGATNSSRFIPLK