AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene010900

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene010900.t1 MTR_3g050860 81.290 155 28 1 1 154 1 155 4.31e-87 259
MS.gene010900.t1 MTR_0439s0020 79.720 143 27 1 1 141 1 143 3.20e-79 231
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 37 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGCGTCAGTGTTGGTCTTC+GGG 0.301799 7.2:+53024890 None:intergenic
GGTTTCATCGTCTTTGATAT+TGG 0.310497 7.2:-53025181 MS.gene010900:CDS
AACCTTGTCCAAGTCCATTT+CGG 0.354048 7.2:+53025063 None:intergenic
AATGCGTCAGTGTTGGTCTT+CGG 0.376239 7.2:+53024889 None:intergenic
ACTTATGACCATGGCCGAAA+TGG 0.377990 7.2:-53025077 MS.gene010900:CDS
TCTTCGTTAATCCTATCTTT+CGG 0.388459 7.2:-53025120 MS.gene010900:CDS
CATCCACAAGAATCTTAAAT+AGG 0.405177 7.2:+53025290 None:intergenic
GTGAAGAGCAATAATATTGA+TGG 0.429245 7.2:-53024832 MS.gene010900:CDS
AGAATCTTAAATAGGTCAAC+AGG 0.430459 7.2:+53025298 None:intergenic
TGACGTGGATGCTAAAAGTT+TGG 0.430756 7.2:-53025257 MS.gene010900:CDS
AATCCTATCTTTCGGAGAAA+AGG 0.435079 7.2:-53025112 MS.gene010900:CDS
GTCCAAGTCCATTTCGGCCA+TGG 0.446272 7.2:+53025069 None:intergenic
GACCATGGCCGAAATGGACT+TGG 0.476008 7.2:-53025071 MS.gene010900:CDS
GATCTGAAGCATACTGGTTA+TGG 0.504056 7.2:-53025157 MS.gene010900:CDS
TGACCTATTTAAGATTCTTG+TGG 0.505182 7.2:-53025293 MS.gene010900:CDS
GAGCAATAATATTGATGGGA+AGG 0.524325 7.2:-53024827 MS.gene010900:CDS
ATTGGTGATCTGAAGCATAC+TGG 0.528676 7.2:-53025163 MS.gene010900:CDS
GTCGCCGAGGATAAACTCCT+AGG 0.541691 7.2:-53025214 MS.gene010900:CDS
GGCCGAAATGGACTTGGACA+AGG 0.545609 7.2:-53025065 MS.gene010900:intron
TGAAGAGCAATAATATTGAT+GGG 0.562579 7.2:-53024831 MS.gene010900:CDS
GCATCTCTTACGACCACATG+TGG 0.566352 7.2:+53025325 None:intergenic
AAACTCCTAGGGTTTATCCT+CGG 0.580594 7.2:-53025202 MS.gene010900:CDS
ATCATGACGAAGAAGCTCGA+GGG 0.582010 7.2:-53024790 MS.gene010900:CDS
TAAGAGTAATGCGTCAGTGT+TGG 0.594559 7.2:+53024882 None:intergenic
TCGCCGAGGATAAACTCCTA+GGG 0.604901 7.2:-53025213 MS.gene010900:CDS
AAACCCTAGGAGTTTATCCT+CGG 0.607628 7.2:+53025210 None:intergenic
GTCAGTGTTGGTCTTCGGGA+CGG 0.627712 7.2:+53024894 None:intergenic
ATCTCTTACGACCACATGTG+GGG 0.629012 7.2:+53025327 None:intergenic
TGAAACCGAGGATAAACCCT+AGG 0.631949 7.2:+53025197 None:intergenic
CATCTCTTACGACCACATGT+GGG 0.632600 7.2:+53025326 None:intergenic
GATGCTAAAAGTTTGGCGAA+TGG 0.635951 7.2:-53025250 MS.gene010900:CDS
CATCATGACGAAGAAGCTCG+AGG 0.646448 7.2:-53024791 MS.gene010900:CDS
TCATGACGAAGAAGCTCGAG+GGG 0.655307 7.2:-53024789 MS.gene010900:CDS
AAAGATGGAGTCCCCACATG+TGG 0.657747 7.2:-53025338 None:intergenic
CGCTACTCGACTTATGACCA+TGG 0.665656 7.2:-53025086 MS.gene010900:CDS
TATCAAAGACGATGAAACCG+AGG 0.669702 7.2:+53025185 None:intergenic
TAAGATTCTTCAAGTCGCCG+AGG 0.715340 7.2:-53025227 MS.gene010900:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGTGTCTTCTTTTAATTTAA+TGG - chr7.2:53025111-53025130 MS.gene010900:CDS 20.0%
! AAAATTATGACAGAGTCAAT+AGG + chr7.2:53025078-53025097 None:intergenic 25.0%
! ATTCAAAAAGATGAAGTATG+AGG - chr7.2:53025242-53025261 MS.gene010900:CDS 25.0%
! TGAAGAGCAATAATATTGAT+GGG - chr7.2:53025271-53025290 MS.gene010900:CDS 25.0%
!!! TTTTAATTTAATGGCGTGAT+TGG - chr7.2:53025120-53025139 MS.gene010900:CDS 25.0%
AGAATCTTAAATAGGTCAAC+AGG + chr7.2:53024807-53024826 None:intergenic 30.0%
CATCCACAAGAATCTTAAAT+AGG + chr7.2:53024815-53024834 None:intergenic 30.0%
GTGAAGAGCAATAATATTGA+TGG - chr7.2:53025270-53025289 MS.gene010900:CDS 30.0%
TCTTCGTTAATCCTATCTTT+CGG - chr7.2:53024982-53025001 MS.gene010900:intron 30.0%
! GATTGGTGTAGTTTGTAATA+TGG - chr7.2:53025137-53025156 MS.gene010900:CDS 30.0%
! TGACCTATTTAAGATTCTTG+TGG - chr7.2:53024809-53024828 MS.gene010900:CDS 30.0%
AATCCTATCTTTCGGAGAAA+AGG - chr7.2:53024990-53025009 MS.gene010900:intron 35.0%
CAAAAAGATGAAGTATGAGG+AGG - chr7.2:53025245-53025264 MS.gene010900:CDS 35.0%
GAGCAATAATATTGATGGGA+AGG - chr7.2:53025275-53025294 MS.gene010900:CDS 35.0%
GGTTTCATCGTCTTTGATAT+TGG - chr7.2:53024921-53024940 MS.gene010900:CDS 35.0%
AAACCCTAGGAGTTTATCCT+CGG + chr7.2:53024895-53024914 None:intergenic 40.0%
AAACTCCTAGGGTTTATCCT+CGG - chr7.2:53024900-53024919 MS.gene010900:CDS 40.0%
AACCTTGTCCAAGTCCATTT+CGG + chr7.2:53025042-53025061 None:intergenic 40.0%
CTGTTACTGTGTTTGTAGCA+AGG - chr7.2:53025165-53025184 MS.gene010900:CDS 40.0%
GATGCTAAAAGTTTGGCGAA+TGG - chr7.2:53024852-53024871 MS.gene010900:CDS 40.0%
TAAGAGTAATGCGTCAGTGT+TGG + chr7.2:53025223-53025242 None:intergenic 40.0%
TATCAAAGACGATGAAACCG+AGG + chr7.2:53024920-53024939 None:intergenic 40.0%
TGACGTGGATGCTAAAAGTT+TGG - chr7.2:53024845-53024864 MS.gene010900:CDS 40.0%
TGCTACAAACACAGTAACAG+AGG + chr7.2:53025165-53025184 None:intergenic 40.0%
! AAACTTTTAGCATCCACGTC+AGG + chr7.2:53024846-53024865 None:intergenic 40.0%
! ATTGGTGATCTGAAGCATAC+TGG - chr7.2:53024939-53024958 MS.gene010900:intron 40.0%
! GATCTGAAGCATACTGGTTA+TGG - chr7.2:53024945-53024964 MS.gene010900:intron 40.0%
! TGTCCTTTTCTCCGAAAGAT+AGG + chr7.2:53024996-53025015 None:intergenic 40.0%
ACTTATGACCATGGCCGAAA+TGG - chr7.2:53025025-53025044 MS.gene010900:intron 45.0%
ATCATGACGAAGAAGCTCGA+GGG - chr7.2:53025312-53025331 MS.gene010900:CDS 45.0%
ATCTCTTACGACCACATGTG+GGG + chr7.2:53024778-53024797 None:intergenic 45.0%
CATCTCTTACGACCACATGT+GGG + chr7.2:53024779-53024798 None:intergenic 45.0%
TAAGATTCTTCAAGTCGCCG+AGG - chr7.2:53024875-53024894 MS.gene010900:CDS 45.0%
TGAAACCGAGGATAAACCCT+AGG + chr7.2:53024908-53024927 None:intergenic 45.0%
!! AATGCGTCAGTGTTGGTCTT+CGG + chr7.2:53025216-53025235 None:intergenic 45.0%
CATCATGACGAAGAAGCTCG+AGG - chr7.2:53025311-53025330 MS.gene010900:CDS 50.0%
CGCTACTCGACTTATGACCA+TGG - chr7.2:53025016-53025035 MS.gene010900:intron 50.0%
GCATCTCTTACGACCACATG+TGG + chr7.2:53024780-53024799 None:intergenic 50.0%
TCATGACGAAGAAGCTCGAG+GGG - chr7.2:53025313-53025332 MS.gene010900:CDS 50.0%
TCGCCGAGGATAAACTCCTA+GGG - chr7.2:53024889-53024908 MS.gene010900:CDS 50.0%
!! ATGCGTCAGTGTTGGTCTTC+GGG + chr7.2:53025215-53025234 None:intergenic 50.0%
!!! GGATGCTGTTTTACCTGACG+TGG - chr7.2:53024830-53024849 MS.gene010900:CDS 50.0%
GTCCAAGTCCATTTCGGCCA+TGG + chr7.2:53025036-53025055 None:intergenic 55.0%
GTCGCCGAGGATAAACTCCT+AGG - chr7.2:53024888-53024907 MS.gene010900:CDS 55.0%
! GACCATGGCCGAAATGGACT+TGG - chr7.2:53025031-53025050 MS.gene010900:intron 55.0%
! GGCCGAAATGGACTTGGACA+AGG - chr7.2:53025037-53025056 MS.gene010900:intron 55.0%
!! GTCAGTGTTGGTCTTCGGGA+CGG + chr7.2:53025211-53025230 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr7.2 gene 53024768 53025356 53024768 ID=MS.gene010900
chr7.2 mRNA 53024768 53025356 53024768 ID=MS.gene010900.t1;Parent=MS.gene010900
chr7.2 exon 53025066 53025356 53025066 ID=MS.gene010900.t1.exon1;Parent=MS.gene010900.t1
chr7.2 CDS 53025066 53025356 53025066 ID=cds.MS.gene010900.t1;Parent=MS.gene010900.t1
chr7.2 exon 53024768 53024941 53024768 ID=MS.gene010900.t1.exon2;Parent=MS.gene010900.t1
chr7.2 CDS 53024768 53024941 53024768 ID=cds.MS.gene010900.t1;Parent=MS.gene010900.t1
Gene Sequence

>MS.gene010900

ATGGAGTCCCCACATGTGGTCGTAAGAGATGCAACACCTGTTGACCTATTTAAGATTCTTGTGGATGCTGTTTTACCTGACGTGGATGCTAAAAGTTTGGCGAATGGTAAGATTCTTCAAGTCGCCGAGGATAAACTCCTAGGGTTTATCCTCGGTTTCATCGTCTTTGATATTGGTGATCTGAAGCATACTGGTTATGGTCATATCACTTCTCTCTTCGTTAATCCTATCTTTCGGAGAAAAGGACACGCTACTCGACTTATGACCATGGCCGAAATGGACTTGGACAAGGTTTGTTTGTTTTCTACCTATTGACTCTGTCATAATTTTGTTTGTTAACAATTGTGTCTTCTTTTAATTTAATGGCGTGATTGGTGTAGTTTGTAATATGGTTCCTCTGTTACTGTGTTTGTAGCAAGGTGCTGCTTACGTCTCAGTGACCGTCCCGAAGACCAACACTGACGCATTACTCTTATTCAAAAAGATGAAGTATGAGGAGGCTGTGAAGAGCAATAATATTGATGGGAAGGATGATGCTAATGTCATCATGACGAAGAAGCTCGAGGGGAAGCAGATGCATTCTGCGTAG
Protein sequence

>MS.gene010900.t1

MESPHVVVRDATPVDLFKILVDAVLPDVDAKSLANGKILQVAEDKLLGFILGFIVFDIGDLKHTGYGHITSLFVNPIFRRKGHATRLMTMAEMDLDKQGAAYVSVTVPKTNTDALLLFKKMKYEEAVKSNNIDGKDDANVIMTKKLEGKQMHSA