AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene56037

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene56037.t1 MTR_1g008220 99.083 218 2 0 3 220 36 253 1.37e-159 441
MS.gene56037.t1 MTR_1g008220 99.083 218 2 0 3 220 36 253 2.32e-159 442
MS.gene56037.t1 MTR_3g091340 72.973 222 52 4 1 220 7 222 1.38e-101 295
MS.gene56037.t1 MTR_3g091340 72.727 220 52 4 3 220 2 215 5.11e-100 290
MS.gene56037.t1 MTR_3g091340 72.727 220 52 4 3 220 38 251 3.29e-99 290
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene56037.t1 AT5G53420 49.550 222 93 8 1 220 35 239 2.76e-60 190
MS.gene56037.t1 AT4G27900 46.957 230 90 6 4 220 25 235 1.19e-56 181
MS.gene56037.t1 AT4G27900 46.957 230 90 6 4 220 25 235 1.19e-56 181
MS.gene56037.t1 AT5G53420 51.412 177 67 8 46 220 1 160 3.64e-46 151
MS.gene56037.t1 AT5G53420 51.412 177 67 8 46 220 1 160 3.64e-46 151
MS.gene56037.t1 AT5G53420 51.412 177 67 8 46 220 1 160 3.64e-46 151
MS.gene56037.t1 AT5G53420 45.763 177 82 6 1 175 35 199 1.82e-40 137

Find 48 sgRNAs with CRISPR-Local

Find 77 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTCTTCTTATTCCTATATC+TGG 0.246824 1.2:+37054200 None:intergenic
TTCAGGAAATTTGAGTTCAA+TGG 0.350069 1.2:-37054843 MS.gene56037:CDS
GATAATAGTACATCAGGAAT+TGG 0.361584 1.2:+37054878 None:intergenic
CCTGCTTTCCTTGATTTCCC+TGG 0.370726 1.2:-37054794 MS.gene56037:CDS
AAGAAGACAAGGAGAAACTT+TGG 0.387483 1.2:-37054186 MS.gene56037:CDS
AGGAAAGCAGGCTTCATTGC+AGG 0.402149 1.2:+37054806 None:intergenic
ACCGCGTTAAAATCAATTCC+AGG 0.422111 1.2:+37054776 None:intergenic
GAAATTTGAGTTCAATGGAT+TGG 0.431971 1.2:-37054838 MS.gene56037:CDS
TTATCAAAGAGTGTCAGTTC+AGG 0.440427 1.2:-37054860 MS.gene56037:CDS
GAGCAGGAATCTTGATTTCA+AGG 0.444374 1.2:+37054936 None:intergenic
CTCTTTGATAATAGTACATC+AGG 0.447091 1.2:+37054872 None:intergenic
AGAAGACAAGGAGAAACTTT+GGG 0.461172 1.2:-37054185 MS.gene56037:CDS
GTGCAGTTGCTGAGAAGAAA+AGG 0.470162 1.2:+37054249 None:intergenic
AATCAATTCCAGGGAAATCA+AGG 0.470610 1.2:+37054786 None:intergenic
TGGGGAAGACATGTCGTCGC+AGG 0.471749 1.2:-37055080 MS.gene56037:CDS
ATTTAGTGAAGGAGATATAA+AGG 0.474162 1.2:-37054735 MS.gene56037:intron
CGGTTCTTCAATAATCGTCT+CGG 0.477444 1.2:+37055150 None:intergenic
CGAGACGATTATTGAAGAAC+CGG 0.482715 1.2:-37055149 MS.gene56037:CDS
TGGCTGCTTGCATTTGATCA+AGG 0.489809 1.2:+37055119 None:intergenic
GTCGCAGGGTCTAAAATCTT+CGG 0.499847 1.2:-37055065 MS.gene56037:CDS
TTGTTTGTATAACAGACTCT+TGG 0.509295 1.2:-37054312 MS.gene56037:intron
AGAATTTGATTTATTTGTAG+AGG 0.514069 1.2:-37055191 MS.gene56037:CDS
TTCTCGTCAATGTTCAGAGC+AGG 0.527138 1.2:+37054920 None:intergenic
ATTTGATCAAGGTCCATCTC+CGG 0.536269 1.2:+37055130 None:intergenic
CCAGGGAAATCAAGGAAAGC+AGG 0.538494 1.2:+37054794 None:intergenic
GAATTTGATTTATTTGTAGA+GGG 0.539422 1.2:-37055190 MS.gene56037:CDS
AGTTCAATGGATTGGATGCA+TGG 0.542974 1.2:-37054830 MS.gene56037:CDS
ATTTCAAGGATTTCAGAAAG+AGG 0.543254 1.2:+37054950 None:intergenic
GCAGCCATGTCAATGATGTC+TGG 0.545025 1.2:-37055103 MS.gene56037:CDS
GATTATTGAAGAACCGGAGA+TGG 0.549985 1.2:-37055143 MS.gene56037:CDS
GGTTCTTCAATAATCGTCTC+GGG 0.551243 1.2:+37055151 None:intergenic
CCGCGTTAAAATCAATTCCA+GGG 0.559154 1.2:+37054777 None:intergenic
AAGGCCTCTCTAGAGTGGAT+TGG 0.563933 1.2:+37054268 None:intergenic
AAACTTTGGGAGGAAAATCA+AGG 0.564099 1.2:-37054172 None:intergenic
GGGGAAGACATGTCGTCGCA+GGG 0.576526 1.2:-37055079 MS.gene56037:CDS
AAGAAAAGGCCTCTCTAGAG+TGG 0.578670 1.2:+37054263 None:intergenic
CCATGTCAATGATGTCTGGT+GGG 0.605089 1.2:-37055099 MS.gene56037:CDS
GTATAACAGACTCTTGGCAA+TGG 0.606169 1.2:-37054306 MS.gene56037:intron
GGCAATGGTAACATGAGTGT+TGG 0.622717 1.2:-37054291 MS.gene56037:CDS
CCCACCAGACATCATTGACA+TGG 0.626711 1.2:+37055099 None:intergenic
GCCATGTCAATGATGTCTGG+TGG 0.631276 1.2:-37055100 MS.gene56037:CDS
GATATAGGAATAAGAAGACA+AGG 0.632233 1.2:-37054197 MS.gene56037:CDS
ATGCGAAGAGCATTTAGTGA+AGG 0.636958 1.2:-37054746 MS.gene56037:CDS
AGAAAGAGGTGATTCTATAG+CGG 0.645696 1.2:+37054964 None:intergenic
TTGGCCAATCCACTCTAGAG+AGG 0.651640 1.2:-37054272 MS.gene56037:CDS
ACATCGCATATGATTGAACA+AGG 0.660417 1.2:+37055215 None:intergenic
CATGTCAATGATGTCTGGTG+GGG 0.675165 1.2:-37055098 MS.gene56037:CDS
AGACAAGGAGAAACTTTGGG+AGG 0.688525 1.2:-37054182 MS.gene56037:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATAAATTAAATAACATCTA+TGG - chr1.2:37054725-37054744 MS.gene56037:intron 10.0%
!! TTAAACATTATATGTTGTAT+TGG - chr1.2:37054756-37054775 MS.gene56037:CDS 15.0%
!! ACATATAATGTTTAACAAAG+TGG + chr1.2:37054751-37054770 None:intergenic 20.0%
!! TATAAATTAAGTAACATCCA+TGG + chr1.2:37055004-37055023 None:intergenic 20.0%
!!! AGAATTTGATTTATTTGTAG+AGG - chr1.2:37054208-37054227 MS.gene56037:CDS 20.0%
!!! GAATTTGATTTATTTGTAGA+GGG - chr1.2:37054209-37054228 MS.gene56037:CDS 20.0%
!!! TTAAATTTTTATATTGGACC+TGG + chr1.2:37054879-37054898 None:intergenic 20.0%
! AGATATAAAGGTCAACTTAA+AGG - chr1.2:37054676-37054695 MS.gene56037:intron 25.0%
! ATTTAGTGAAGGAGATATAA+AGG - chr1.2:37054664-37054683 MS.gene56037:intron 25.0%
! CAAAAAAGATCTCTTAGAAA+AGG - chr1.2:37054412-37054431 MS.gene56037:intron 25.0%
! TTTGCCATATCAAAATGATT+TGG - chr1.2:37055051-37055070 MS.gene56037:CDS 25.0%
!! ATATAATGTCTAAGACAAAG+AGG - chr1.2:37054978-37054997 MS.gene56037:CDS 25.0%
!! TCTTACAAAACTAGTTTGTA+AGG + chr1.2:37054851-37054870 None:intergenic 25.0%
!!! ATCATTTTGATATGGCAAAT+AGG + chr1.2:37055050-37055069 None:intergenic 25.0%
!!! TACACCAAATCATTTTGATA+TGG + chr1.2:37055058-37055077 None:intergenic 25.0%
AAGAAAAACTCTCCAGATAT+AGG - chr1.2:37055187-37055206 MS.gene56037:CDS 30.0%
ATTTCAAGGATTTCAGAAAG+AGG + chr1.2:37054452-37054471 None:intergenic 30.0%
GATAATAGTACATCAGGAAT+TGG + chr1.2:37054524-37054543 None:intergenic 30.0%
GATATAGGAATAAGAAGACA+AGG - chr1.2:37055202-37055221 MS.gene56037:CDS 30.0%
TATGTTGATGTATCTAGACT+CGG - chr1.2:37054899-37054918 MS.gene56037:CDS 30.0%
TGTCTTCTTATTCCTATATC+TGG + chr1.2:37055202-37055221 None:intergenic 30.0%
TTGTTTGTATAACAGACTCT+TGG - chr1.2:37055087-37055106 MS.gene56037:CDS 30.0%
! AAAACTAGTTTGTAAGGTGA+GGG + chr1.2:37054845-37054864 None:intergenic 30.0%
! CTCTTTGATAATAGTACATC+AGG + chr1.2:37054530-37054549 None:intergenic 30.0%
! GAAATTTGAGTTCAATGGAT+TGG - chr1.2:37054561-37054580 MS.gene56037:intron 30.0%
! TTCAGGAAATTTGAGTTCAA+TGG - chr1.2:37054556-37054575 MS.gene56037:intron 30.0%
!! ATTGATTTTAACGCGGTTTA+TGG - chr1.2:37054629-37054648 MS.gene56037:intron 30.0%
AAGAAGACAAGGAGAAACTT+TGG - chr1.2:37055213-37055232 MS.gene56037:CDS 35.0%
AATCAATTCCAGGGAAATCA+AGG + chr1.2:37054616-37054635 None:intergenic 35.0%
ACATCGCATATGATTGAACA+AGG + chr1.2:37054187-37054206 None:intergenic 35.0%
AGAAAGAGGTGATTCTATAG+CGG + chr1.2:37054438-37054457 None:intergenic 35.0%
AGAAGACAAGGAGAAACTTT+GGG - chr1.2:37055214-37055233 MS.gene56037:CDS 35.0%
ATGTTGATGTATCTAGACTC+GGG - chr1.2:37054900-37054919 MS.gene56037:CDS 35.0%
! AAACTAGTTTGTAAGGTGAG+GGG + chr1.2:37054844-37054863 None:intergenic 35.0%
! CAAAACTAGTTTGTAAGGTG+AGG + chr1.2:37054846-37054865 None:intergenic 35.0%
!! TTATCAAAGAGTGTCAGTTC+AGG - chr1.2:37054539-37054558 MS.gene56037:intron 35.0%
!!! TAGTTTTGTAAGAATGAGCC+AGG - chr1.2:37054858-37054877 MS.gene56037:CDS 35.0%
ACCGCGTTAAAATCAATTCC+AGG + chr1.2:37054626-37054645 None:intergenic 40.0%
ATTTGATCAAGGTCCATCTC+CGG + chr1.2:37054272-37054291 None:intergenic 40.0%
CCGCGTTAAAATCAATTCCA+GGG + chr1.2:37054625-37054644 None:intergenic 40.0%
CGAGACGATTATTGAAGAAC+CGG - chr1.2:37054250-37054269 MS.gene56037:CDS 40.0%
CGGTTCTTCAATAATCGTCT+CGG + chr1.2:37054252-37054271 None:intergenic 40.0%
CGTTGAGAAGAGATAAGACT+TGG - chr1.2:37054796-37054815 MS.gene56037:CDS 40.0%
GAGCAGGAATCTTGATTTCA+AGG + chr1.2:37054466-37054485 None:intergenic 40.0%
GATTATTGAAGAACCGGAGA+TGG - chr1.2:37054256-37054275 MS.gene56037:CDS 40.0%
GGTTCTTCAATAATCGTCTC+GGG + chr1.2:37054251-37054270 None:intergenic 40.0%
GTATAACAGACTCTTGGCAA+TGG - chr1.2:37055093-37055112 MS.gene56037:CDS 40.0%
GTCTTATCTCTTCTCAACGT+GGG + chr1.2:37054795-37054814 None:intergenic 40.0%
! AGTCTTATCTCTTCTCAACG+TGG + chr1.2:37054796-37054815 None:intergenic 40.0%
!! AAGCGAACAACTTTTGAGTG+AGG - chr1.2:37054376-37054395 MS.gene56037:intron 40.0%
!! AGTTCAATGGATTGGATGCA+TGG - chr1.2:37054569-37054588 MS.gene56037:intron 40.0%
!! ATGCGAAGAGCATTTAGTGA+AGG - chr1.2:37054653-37054672 MS.gene56037:intron 40.0%
!! CCCTGGAATTGATTTTAACG+CGG - chr1.2:37054622-37054641 MS.gene56037:intron 40.0%
AGACAAGGAGAAACTTTGGG+AGG - chr1.2:37055217-37055236 MS.gene56037:CDS 45.0%
CATGTCAATGATGTCTGGTG+GGG - chr1.2:37054301-37054320 MS.gene56037:intron 45.0%
CCATGTCAATGATGTCTGGT+GGG - chr1.2:37054300-37054319 MS.gene56037:CDS 45.0%
GGCAATGGTAACATGAGTGT+TGG - chr1.2:37055108-37055127 MS.gene56037:CDS 45.0%
GTGCAGTTGCTGAGAAGAAA+AGG + chr1.2:37055153-37055172 None:intergenic 45.0%
TGGCTGCTTGCATTTGATCA+AGG + chr1.2:37054283-37054302 None:intergenic 45.0%
TTCTCGTCAATGTTCAGAGC+AGG + chr1.2:37054482-37054501 None:intergenic 45.0%
! AAGAAAAGGCCTCTCTAGAG+TGG + chr1.2:37055139-37055158 None:intergenic 45.0%
! GTCGCAGGGTCTAAAATCTT+CGG - chr1.2:37054334-37054353 MS.gene56037:intron 45.0%
! TGTCTAAGACAAAGAGGCCA+TGG - chr1.2:37054984-37055003 MS.gene56037:CDS 45.0%
!!! AACATATTAAATTTTTATAT+TGG + chr1.2:37054885-37054904 None:intergenic 5.0%
AGGAAAGCAGGCTTCATTGC+AGG + chr1.2:37054596-37054615 None:intergenic 50.0%
CCAGGGAAATCAAGGAAAGC+AGG + chr1.2:37054608-37054627 None:intergenic 50.0%
CCCACCAGACATCATTGACA+TGG + chr1.2:37054303-37054322 None:intergenic 50.0%
CCTGCTTTCCTTGATTTCCC+TGG - chr1.2:37054605-37054624 MS.gene56037:intron 50.0%
GCAGCCATGTCAATGATGTC+TGG - chr1.2:37054296-37054315 MS.gene56037:CDS 50.0%
GCCATGTCAATGATGTCTGG+TGG - chr1.2:37054299-37054318 MS.gene56037:CDS 50.0%
! TTGGCCAATCCACTCTAGAG+AGG - chr1.2:37055127-37055146 MS.gene56037:CDS 50.0%
!! AAGGCCTCTCTAGAGTGGAT+TGG + chr1.2:37055134-37055153 None:intergenic 50.0%
GTCCTCTTTAGCGCTGCACA+CGG - chr1.2:37054922-37054941 MS.gene56037:CDS 55.0%
TTAGCGCTGCACACGGTGAA+CGG - chr1.2:37054929-37054948 MS.gene56037:CDS 55.0%
CACCGTGTGCAGCGCTAAAG+AGG + chr1.2:37054927-37054946 None:intergenic 60.0%
GGGGAAGACATGTCGTCGCA+GGG - chr1.2:37054320-37054339 MS.gene56037:intron 60.0%
TGGGGAAGACATGTCGTCGC+AGG - chr1.2:37054319-37054338 MS.gene56037:intron 60.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 37054173 37055248 37054173 ID=MS.gene56037
chr1.2 mRNA 37054173 37055248 37054173 ID=MS.gene56037.t1;Parent=MS.gene56037
chr1.2 exon 37054736 37055248 37054736 ID=MS.gene56037.t1.exon1;Parent=MS.gene56037.t1
chr1.2 CDS 37054736 37055248 37054736 ID=cds.MS.gene56037.t1;Parent=MS.gene56037.t1
chr1.2 exon 37054173 37054319 37054173 ID=MS.gene56037.t1.exon2;Parent=MS.gene56037.t1
chr1.2 CDS 37054173 37054319 37054173 ID=cds.MS.gene56037.t1;Parent=MS.gene56037.t1
Gene Sequence

>MS.gene56037

ATGCAGAGTGACCTTGTTCAATCATATGCGATGTCAGAATTTGATTTATTTGTAGAGGGAGATCTGTTCAAAGCACCCGAGACGATTATTGAAGAACCGGAGATGGACCTTGATCAAATGCAAGCAGCCATGTCAATGATGTCTGGTGGGGAAGACATGTCGTCGCAGGGTCTAAAATCTTCGGATATTGATGATGTGCTTCAAAGCGAACAACTTTTGAGTGAGGTCTACTATGATTGCAAAAAAGATCTCTTAGAAAAGGCCGCTATAGAATCACCTCTTTCTGAAATCCTTGAAATCAAGATTCCTGCTCTGAACATTGACGAGAATTCGATTCAAGAAAACAAACCAATTCCTGATGTACTATTATCAAAGAGTGTCAGTTCAGGAAATTTGAGTTCAATGGATTGGATGCATGGTCCTGCAATGAAGCCTGCTTTCCTTGATTTCCCTGGAATTGATTTTAACGCGGTTTATGGCATGCGAAGAGCATTTAGTGAAGGAGATATAAAGGTCAACTTAAAGGAATTCATGTATTTTGCGTGTTCTTCTTATAAATTAAATAACATCTATGGCCACTTTGTTAAACATTATATGTTGTATTGGAAAAAATCTAAGTCCCACGTTGAGAAGAGATAAGACTTGGATATAGTTTCTAAAGAAAGACACCCCTCACCTTACAAACTAGTTTTGTAAGAATGAGCCAGGTCCAATATAAAAATTTAATATGTTGATGTATCTAGACTCGGGTCCTCTTTAGCGCTGCACACGGTGAACGGATGTTACTAAGTTCAGATACATCAACATATAATGTCTAAGACAAAGAGGCCATGGATGTTACTTAATTTATATAGACTGAGAAATATACTGTATACCTATTTGCCATATCAAAATGATTTGGTGTATGATTAATATTGTTTGTATAACAGACTCTTGGCAATGGTAACATGAGTGTTGGCCAATCCACTCTAGAGAGGCCTTTTCTTCTCAGCAACTGCACGAGTGAGCAACGTCAAGAAAAACTCTCCAGATATAGGAATAAGAAGACAAGGAGAAACTTTGGGAGGAAAATCAAG
Protein sequence

>MS.gene56037.t1

MQSDLVQSYAMSEFDLFVEGDLFKAPETIIEEPEMDLDQMQAAMSMMSGGEDMSSQGLKSSDIDDVLQSEQLLSEVYYDCKKDLLEKAAIESPLSEILEIKIPALNIDENSIQENKPIPDVLLSKSVSSGNLSSMDWMHGPAMKPAFLDFPGIDFNAVYGMRRAFSEGDIKTLGNGNMSVGQSTLERPFLLSNCTSEQRQEKLSRYRNKKTRRNFGRKIK