AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene060221

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060221.t1 MTR_7g117040 93.678 174 11 0 1 174 1 174 6.69e-123 343
MS.gene060221.t1 MTR_7g117040 91.379 174 11 1 1 174 1 170 1.68e-117 330
MS.gene060221.t1 MTR_7g117040 89.655 174 11 1 1 174 1 167 4.50e-115 323
MS.gene060221.t1 MTR_3g034200 35.185 162 100 2 1 161 1 158 1.14e-28 105
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060221.t1 AT1G03150 90.230 174 17 0 1 174 1 174 1.29e-119 335
MS.gene060221.t1 AT5G13780 37.179 156 97 1 1 155 1 156 1.33e-28 105

Find 39 sgRNAs with CRISPR-Local

Find 84 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGAGTGCTACGTTATTATTC+TGG 0.239936 2.3:-21049232 MS.gene060221:CDS
GTAACCCATGATTCGATTTC+CGG 0.242250 2.3:+21049977 None:intergenic
TGATTCGATTTCCGGGGCCT+TGG 0.300853 2.3:+21049985 None:intergenic
GTCAGGCCATCTTGCTAAAT+AGG 0.361124 2.3:+21050022 None:intergenic
TTCCGGGGCCTTGGGCGACT+TGG 0.382516 2.3:+21049994 None:intergenic
GATTCGATTTCCGGGGCCTT+GGG 0.386942 2.3:+21049986 None:intergenic
TAACCCATGATTCGATTTCC+GGG 0.408074 2.3:+21049978 None:intergenic
TAGTCGTATTCTAATTCATC+AGG 0.411545 2.3:+21049030 None:intergenic
TTCTGGGGAAGAAGATGGAT+TGG 0.420903 2.3:-21049215 MS.gene060221:CDS
TATTATTCTGGGGAAGAAGA+TGG 0.447212 2.3:-21049220 MS.gene060221:CDS
TGCTAAATAGGTCATGTAGA+AGG 0.454880 2.3:+21050034 None:intergenic
AGTCCGTCAGCCCTCTTAAA+CGG 0.466234 2.3:-21049062 MS.gene060221:CDS
GAGTGCTACGTTATTATTCT+GGG 0.470429 2.3:-21049231 MS.gene060221:CDS
TCTGGGGAAGAAGATGGATT+GGG 0.475034 2.3:-21049214 MS.gene060221:intron
TTCCAAGTCGCCCAAGGCCC+CGG 0.485170 2.3:-21049996 MS.gene060221:CDS
TGACATTTGTAAAACGAAGA+AGG 0.486544 2.3:+21050185 None:intergenic
GGAGTGACATGCCGTTTAAG+AGG 0.496131 2.3:+21049051 None:intergenic
TAGAGGGGCAAGGAGAATCT+TGG 0.499019 2.3:-21049864 MS.gene060221:CDS
TGGGCGACTTGGAAATAGTC+AGG 0.503036 2.3:+21050005 None:intergenic
AGCCATCAAGATGTATGAAA+AGG 0.514376 2.3:-21049626 MS.gene060221:intron
AGGCCCCGGAAATCGAATCA+TGG 0.515528 2.3:-21049982 MS.gene060221:CDS
AACGTGAGTACGTACAGTTT+CGG 0.540046 2.3:+21050147 None:intergenic
ACATGACCTATTTAGCAAGA+TGG 0.544945 2.3:-21050028 MS.gene060221:CDS
GCAGTTATGGGTAAAGTAGA+GGG 0.544970 2.3:-21049880 MS.gene060221:intron
GGCCCCGGAAATCGAATCAT+GGG 0.555258 2.3:-21049981 MS.gene060221:CDS
GACTATTTCCAAGTCGCCCA+AGG 0.565815 2.3:-21050002 MS.gene060221:CDS
AACTGCAGTAACCGTTGCTA+CGG 0.572799 2.3:-21049830 MS.gene060221:CDS
ATGGGTAAAGTAGAGGGGCA+AGG 0.572891 2.3:-21049874 MS.gene060221:CDS
TGCAGTTATGGGTAAAGTAG+AGG 0.579669 2.3:-21049881 MS.gene060221:intron
GAGTGACATGCCGTTTAAGA+GGG 0.585815 2.3:+21049052 None:intergenic
CCGTTGCTACGGAGTATCGC+AGG 0.596977 2.3:-21049819 MS.gene060221:CDS
AATAATAACGTAGCACTCGT+CGG 0.603392 2.3:+21049236 None:intergenic
AACCCATGATTCGATTTCCG+GGG 0.619081 2.3:+21049979 None:intergenic
ATGCCGTTTAAGAGGGCTGA+CGG 0.621153 2.3:+21049059 None:intergenic
GGGCAAGGAGAATCTTGGCA+TGG 0.661266 2.3:-21049859 MS.gene060221:CDS
AGTGCTACGTTATTATTCTG+GGG 0.665106 2.3:-21049230 MS.gene060221:CDS
CAGTTATGGGTAAAGTAGAG+GGG 0.668038 2.3:-21049879 MS.gene060221:CDS
CCTGCGATACTCCGTAGCAA+CGG 0.679156 2.3:+21049819 None:intergenic
AAGAGATGACGACAATACGT+AGG 0.724152 2.3:-21050222 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAATGTATAACTTAATCAT+TGG - chr2.3:21049861-21049880 MS.gene060221:CDS 15.0%
!! AAAAAACCCTATTAGAATTT+GGG + chr2.3:21049802-21049821 None:intergenic 20.0%
!! AGATTACTTATCAATAGTTT+AGG - chr2.3:21049835-21049854 MS.gene060221:CDS 20.0%
!! TAAAAAACCCTATTAGAATT+TGG + chr2.3:21049803-21049822 None:intergenic 20.0%
!! TATAACTTAATCATTGGATA+TGG - chr2.3:21049867-21049886 MS.gene060221:CDS 20.0%
!!! GATATGTTTTCTTTTAGATT+AGG - chr2.3:21049910-21049929 MS.gene060221:intron 20.0%
! AATATCATTCATGCAGTTAT+GGG - chr2.3:21049354-21049373 MS.gene060221:intron 25.0%
! ACAGCAAATAAATAGTGATA+CGG + chr2.3:21050107-21050126 None:intergenic 25.0%
! TCCTCATATCTGAAAATAAA+GGG + chr2.3:21050137-21050156 None:intergenic 25.0%
! TGTGTAAAAGACTATACTAT+GGG - chr2.3:21049317-21049336 MS.gene060221:intron 25.0%
! TTCCTCATATCTGAAAATAA+AGG + chr2.3:21050138-21050157 None:intergenic 25.0%
! TTGTGTAAAAGACTATACTA+TGG - chr2.3:21049316-21049335 MS.gene060221:intron 25.0%
!!! ACACAAGGTTTGTTTTAAAT+CGG - chr2.3:21049702-21049721 MS.gene060221:intron 25.0%
!!! TTTATTTTCAGATATGAGGA+AGG - chr2.3:21050137-21050156 MS.gene060221:intron 25.0%
ACATATCCTAATCCAACAAA+TGG + chr2.3:21049897-21049916 None:intergenic 30.0%
ATCCAACCCAAATTCTAATA+GGG - chr2.3:21049793-21049812 MS.gene060221:CDS 30.0%
CAAGCTATAAGATGTCAAAA+AGG + chr2.3:21049977-21049996 None:intergenic 30.0%
CAATATCATTCATGCAGTTA+TGG - chr2.3:21049353-21049372 MS.gene060221:intron 30.0%
CATAACTGCATGAATGATAT+TGG + chr2.3:21049355-21049374 None:intergenic 30.0%
TAGTCGTATTCTAATTCATC+AGG + chr2.3:21050219-21050238 None:intergenic 30.0%
TGACATTTGTAAAACGAAGA+AGG + chr2.3:21049064-21049083 None:intergenic 30.0%
! CTTTTTGACATCTTATAGCT+TGG - chr2.3:21049975-21049994 MS.gene060221:intron 30.0%
! TACCTTTTCATACATCTTGA+TGG + chr2.3:21049625-21049644 None:intergenic 30.0%
!! CATAAAGTGAATTGAGTTGA+GGG + chr2.3:21049147-21049166 None:intergenic 30.0%
!!! TCCCTTTATTTTCAGATATG+AGG - chr2.3:21050133-21050152 MS.gene060221:intron 30.0%
AACCCTATTAGAATTTGGGT+TGG + chr2.3:21049798-21049817 None:intergenic 35.0%
AACTGCATGAATGATATTGG+TGG + chr2.3:21049352-21049371 None:intergenic 35.0%
AATAATAACGTAGCACTCGT+CGG + chr2.3:21050013-21050032 None:intergenic 35.0%
ACATGACCTATTTAGCAAGA+TGG - chr2.3:21049218-21049237 MS.gene060221:CDS 35.0%
AGCCATCAAGATGTATGAAA+AGG - chr2.3:21049620-21049639 MS.gene060221:intron 35.0%
AGTGACAATATGTAAGGCAT+CGG - chr2.3:21049492-21049511 MS.gene060221:intron 35.0%
AGTGCTACGTTATTATTCTG+GGG - chr2.3:21050016-21050035 MS.gene060221:CDS 35.0%
AGTGGAAGGTTTAATCTGAA+AGG + chr2.3:21049664-21049683 None:intergenic 35.0%
GACATCAGTGACAATATGTA+AGG - chr2.3:21049486-21049505 MS.gene060221:intron 35.0%
GAGTGCTACGTTATTATTCT+GGG - chr2.3:21050015-21050034 MS.gene060221:CDS 35.0%
GATCCAACCCAAATTCTAAT+AGG - chr2.3:21049792-21049811 MS.gene060221:CDS 35.0%
TGCTAAATAGGTCATGTAGA+AGG + chr2.3:21049215-21049234 None:intergenic 35.0%
! GCATAAAGTGAATTGAGTTG+AGG + chr2.3:21049148-21049167 None:intergenic 35.0%
! TATTATTCTGGGGAAGAAGA+TGG - chr2.3:21050026-21050045 MS.gene060221:CDS 35.0%
!! TGAATTGAGTTGAGGGTTTA+GGG + chr2.3:21049140-21049159 None:intergenic 35.0%
!! TTTTCATACATCTTGATGGC+TGG + chr2.3:21049621-21049640 None:intergenic 35.0%
AACGTGAGTACGTACAGTTT+CGG + chr2.3:21049102-21049121 None:intergenic 40.0%
ACCTTGTGTACAAACCTACA+AGG + chr2.3:21049691-21049710 None:intergenic 40.0%
CAGTTATGGGTAAAGTAGAG+GGG - chr2.3:21049367-21049386 MS.gene060221:intron 40.0%
CGAGTGCTACGTTATTATTC+TGG - chr2.3:21050014-21050033 MS.gene060221:CDS 40.0%
GCAGTTATGGGTAAAGTAGA+GGG - chr2.3:21049366-21049385 MS.gene060221:intron 40.0%
GGATATGGACTTCCATTTGT+TGG - chr2.3:21049882-21049901 MS.gene060221:intron 40.0%
GTAACCCATGATTCGATTTC+CGG + chr2.3:21049272-21049291 None:intergenic 40.0%
TAACCCATGATTCGATTTCC+GGG + chr2.3:21049271-21049290 None:intergenic 40.0%
TATGTGTGTTTGTCTCTGTG+TGG - chr2.3:21049515-21049534 MS.gene060221:intron 40.0%
TCCTTGTAGGTTTGTACACA+AGG - chr2.3:21049687-21049706 MS.gene060221:intron 40.0%
TGCAGTTATGGGTAAAGTAG+AGG - chr2.3:21049365-21049384 MS.gene060221:intron 40.0%
! GGACTTCCATTTGTTGGATT+AGG - chr2.3:21049888-21049907 MS.gene060221:intron 40.0%
!! GTGAATTGAGTTGAGGGTTT+AGG + chr2.3:21049141-21049160 None:intergenic 40.0%
AACCCATGATTCGATTTCCG+GGG + chr2.3:21049270-21049289 None:intergenic 45.0%
AACTGCAGTAACCGTTGCTA+CGG - chr2.3:21049416-21049435 MS.gene060221:intron 45.0%
ACAAACCTACAAGGAAGCAG+TGG + chr2.3:21049682-21049701 None:intergenic 45.0%
CCCTACAAAATCAGCTTGTG+CGG + chr2.3:21049764-21049783 None:intergenic 45.0%
GTCAGGCCATCTTGCTAAAT+AGG + chr2.3:21049227-21049246 None:intergenic 45.0%
! GAGTGACATGCCGTTTAAGA+GGG + chr2.3:21050197-21050216 None:intergenic 45.0%
! TCTGGGGAAGAAGATGGATT+GGG - chr2.3:21050032-21050051 MS.gene060221:CDS 45.0%
! TTCTGGGGAAGAAGATGGAT+TGG - chr2.3:21050031-21050050 MS.gene060221:CDS 45.0%
!! ACCGCACAAGCTGATTTTGT+AGG - chr2.3:21049760-21049779 MS.gene060221:intron 45.0%
!! CCGCACAAGCTGATTTTGTA+GGG - chr2.3:21049761-21049780 MS.gene060221:intron 45.0%
!! GGAAGAAGATGGATTGGGTA+TGG - chr2.3:21050037-21050056 MS.gene060221:CDS 45.0%
ACCTACAAGGAAGCAGTGGA+AGG + chr2.3:21049678-21049697 None:intergenic 50.0%
ACCTTCCACTGCTTCCTTGT+AGG - chr2.3:21049674-21049693 MS.gene060221:CDS 50.0%
AGTCCGTCAGCCCTCTTAAA+CGG - chr2.3:21050184-21050203 MS.gene060221:CDS 50.0%
ATGGGTAAAGTAGAGGGGCA+AGG - chr2.3:21049372-21049391 MS.gene060221:intron 50.0%
GACTATTTCCAAGTCGCCCA+AGG - chr2.3:21049244-21049263 MS.gene060221:CDS 50.0%
GTGTGTTTGTCTCTGTGTGG+AGG - chr2.3:21049518-21049537 MS.gene060221:intron 50.0%
TAGAGGGGCAAGGAGAATCT+TGG - chr2.3:21049382-21049401 MS.gene060221:intron 50.0%
! ATGCCGTTTAAGAGGGCTGA+CGG + chr2.3:21050190-21050209 None:intergenic 50.0%
! GGAGTGACATGCCGTTTAAG+AGG + chr2.3:21050198-21050217 None:intergenic 50.0%
! TGGGCGACTTGGAAATAGTC+AGG + chr2.3:21049244-21049263 None:intergenic 50.0%
AGGCCCCGGAAATCGAATCA+TGG - chr2.3:21049264-21049283 MS.gene060221:intron 55.0%
CCTGCGATACTCCGTAGCAA+CGG + chr2.3:21049430-21049449 None:intergenic 55.0%
GATTCGATTTCCGGGGCCTT+GGG + chr2.3:21049263-21049282 None:intergenic 55.0%
GGCCCCGGAAATCGAATCAT+GGG - chr2.3:21049265-21049284 MS.gene060221:intron 55.0%
GGGCAAGGAGAATCTTGGCA+TGG - chr2.3:21049387-21049406 MS.gene060221:intron 55.0%
TGATTCGATTTCCGGGGCCT+TGG + chr2.3:21049264-21049283 None:intergenic 55.0%
!! CCGTTGCTACGGAGTATCGC+AGG - chr2.3:21049427-21049446 MS.gene060221:intron 60.0%
TTCCAAGTCGCCCAAGGCCC+CGG - chr2.3:21049250-21049269 MS.gene060221:CDS 65.0%
TTCCGGGGCCTTGGGCGACT+TGG + chr2.3:21049255-21049274 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 21049029 21050239 21049029 ID=MS.gene060221
chr2.3 mRNA 21049029 21050239 21049029 ID=MS.gene060221.t1;Parent=MS.gene060221
chr2.3 exon 21050162 21050239 21050162 ID=MS.gene060221.t1.exon1;Parent=MS.gene060221.t1
chr2.3 CDS 21050162 21050239 21050162 ID=cds.MS.gene060221.t1;Parent=MS.gene060221.t1
chr2.3 exon 21049976 21050066 21049976 ID=MS.gene060221.t1.exon2;Parent=MS.gene060221.t1
chr2.3 CDS 21049976 21050066 21049976 ID=cds.MS.gene060221.t1;Parent=MS.gene060221.t1
chr2.3 exon 21049766 21049898 21049766 ID=MS.gene060221.t1.exon3;Parent=MS.gene060221.t1
chr2.3 CDS 21049766 21049898 21049766 ID=cds.MS.gene060221.t1;Parent=MS.gene060221.t1
chr2.3 exon 21049627 21049696 21049627 ID=MS.gene060221.t1.exon4;Parent=MS.gene060221.t1
chr2.3 CDS 21049627 21049696 21049627 ID=cds.MS.gene060221.t1;Parent=MS.gene060221.t1
chr2.3 exon 21049215 21049275 21049215 ID=MS.gene060221.t1.exon5;Parent=MS.gene060221.t1
chr2.3 CDS 21049215 21049275 21049215 ID=cds.MS.gene060221.t1;Parent=MS.gene060221.t1
chr2.3 exon 21049029 21049120 21049029 ID=MS.gene060221.t1.exon6;Parent=MS.gene060221.t1
chr2.3 CDS 21049029 21049120 21049029 ID=cds.MS.gene060221.t1;Parent=MS.gene060221.t1
Gene Sequence

>MS.gene060221

ATGACGACAATACGTAGGTTTTGCTGCAAAGACCTTCTTCGTTTTACAAATGTCAATCTTGATCATCTTACCGAAACTGTACGTACTCACGTTTTTCTTTCTTCTAAACCCTAAACCCTCAACTCAATTCACTTTATGCTTTCGTTCTTAATAAGTTGTTCATTCTGTTTCAGTTTAACATGTCCTTCTACATGACCTATTTAGCAAGATGGCCTGACTATTTCCAAGTCGCCCAAGGCCCCGGAAATCGAATCATGGGTTACAGTAAGTCTTTTTCTTCATCTTTTTTGTGTAAAAGACTATACTATGGGATATTAACACCACCAATATCATTCATGCAGTTATGGGTAAAGTAGAGGGGCAAGGAGAATCTTGGCATGGTCATGTAACTGCAGTAACCGTTGCTACGGAGTATCGCAGGCAACAGTTAGCAAACAAACTAATGAATATTCTCGAAGACATCAGTGACAATATGTAAGGCATCGGTATGTGTGTTTGTCTCTGTGTGGAGGTTTTGATATAATTTAGAATTGAATTTTGCAGTGACAAAGCATACTTTGTTGATCTATTTGTGAGAGCATCAAATGCACCAGCCATCAAGATGTATGAAAAGGTAATGATTTTGTACTTTTCCTTTCAGATTAAACCTTCCACTGCTTCCTTGTAGGTTTGTACACAAGGTTTGTTTTAAATCGGTTTCTTTGTTAGACATCTGTGAAATTAAATAAGACACCGCACAAGCTGATTTTGTAGGGTTGAGTTAGATCCAACCCAAATTCTAATAGGGTTTTTTATCGAGAATTTACAGATTACTTATCAATAGTTTAGGAATTTAATGTATAACTTAATCATTGGATATGGACTTCCATTTGTTGGATTAGGATATGTTTTCTTTTAGATTAGGATTTTCTGATTTTCAAGCTTAAATTGCTAACTAATTATTTTCCTTTTTGACATCTTATAGCTTGGATATGTGATTTACCGACGAGTGCTACGTTATTATTCTGGGGAAGAAGATGGATTGGGTATGGTTTCTTTTTTTTTTTTTGTACTTCTCTAACTCTTTGAACAAAGTCCGTATCACTATTTATTTGCTGTCGTTTTTCCCTTTATTTTCAGATATGAGGAAGGCGTTATCTCGTGATGTTAATAAGAAGTCCGTCAGCCCTCTTAAACGGCATGTCACTCCTGATGAATTAGAATACGACTAA
Protein sequence

>MS.gene060221.t1

MTTIRRFCCKDLLRFTNVNLDHLTETFNMSFYMTYLARWPDYFQVAQGPGNRIMGYIMGKVEGQGESWHGHVTAVTVATEYRRQQLANKLMNILEDISDNIDKAYFVDLFVRASNAPAIKMYEKLGYVIYRRVLRYYSGEEDGLDMRKALSRDVNKKSVSPLKRHVTPDELEYD