AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene54023

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene54023.t1 MTR_2g095290 100.000 129 0 0 1 129 1 129 4.38e-93 265
MS.gene54023.t1 MTR_2g026695 45.545 101 54 1 24 123 187 287 6.09e-22 88.2
MS.gene54023.t1 MTR_5g088270 46.465 99 51 2 25 123 180 276 1.33e-21 87.0
MS.gene54023.t1 MTR_0446s0050 45.545 101 54 1 24 123 8 108 3.27e-20 79.7
MS.gene54023.t1 MTR_4g133970 45.545 101 54 1 24 123 139 239 4.62e-19 79.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene54023.t1 AT2G28060 58.879 107 41 1 23 129 11 114 2.87e-40 130
MS.gene54023.t1 AT2G28060 58.879 107 41 1 23 129 11 114 2.87e-40 130
MS.gene54023.t1 AT2G28060 58.879 107 41 1 23 129 11 114 2.87e-40 130
MS.gene54023.t1 AT2G28060 58.879 107 41 1 23 129 11 114 2.87e-40 130
MS.gene54023.t1 AT5G21170 40.404 99 56 1 25 123 144 239 8.35e-20 82.0
MS.gene54023.t1 AT5G21170 40.404 99 56 1 25 123 188 283 2.04e-19 81.6
MS.gene54023.t1 AT5G21170 40.404 99 56 1 25 123 225 320 2.21e-19 82.0

Find 27 sgRNAs with CRISPR-Local

Find 32 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTACAGGGTTTGCAGCATA+TGG 0.311228 2.3:-6961910 None:intergenic
GTGGCTCCTCTTCTTTGAAC+TGG 0.318379 2.3:-6962297 None:intergenic
GAGCACTGCGGTAACAAATT+TGG 0.334556 2.3:-6962268 None:intergenic
ACAAAGATCTGTGGTAGCTT+TGG 0.363636 2.3:+6962224 MS.gene54023:CDS
CAAAGATCTGTGGTAGCTTT+GGG 0.386108 2.3:+6962225 MS.gene54023:CDS
TGCAATTGTGGAGGAATCTC+CGG 0.451213 2.3:-6962099 None:intergenic
AGGGTATGCATTATTGTAAC+CGG 0.453451 2.3:-6962049 None:intergenic
AAAGCTACCACAGATCTTTG+TGG 0.495424 2.3:-6962222 None:intergenic
CTAAAACTATCGACGTTAGC+AGG 0.500591 2.3:-6962141 None:intergenic
CGTGCCTCGTCTTCATTCAA+AGG 0.509032 2.3:-6962069 None:intergenic
TGCATTATTGTAACCGGAGT+CGG 0.515469 2.3:-6962043 None:intergenic
GTCAGCACATCAAATGTTTG+TGG 0.524550 2.3:-6962316 None:intergenic
CAGGGTGAAGCAACTGTCAT+GGG 0.531491 2.3:+6962000 MS.gene54023:intron
ATTGATGAATTCACAACTAG+TGG 0.549979 2.3:+6961861 None:intergenic
GCAGGGTGAAGCAACTGTCA+TGG 0.551840 2.3:+6961999 MS.gene54023:intron
CAATTGCAAAACACCTTGGT+CGG 0.554828 2.3:+6962114 MS.gene54023:CDS
GTGCCTCGTCTTCATTCAAA+GGG 0.556952 2.3:-6962068 None:intergenic
TCCACAATTGCAAAACACCT+TGG 0.563433 2.3:+6962110 MS.gene54023:CDS
TACAAACCAGTTCAAAGAAG+AGG 0.566713 2.3:+6962291 MS.gene54023:CDS
AGACGAGGCACGTGATCCAC+CGG 0.579131 2.3:+6962080 MS.gene54023:CDS
TGATTTAGAATCGCGTTCTG+AGG 0.592686 2.3:-6962177 None:intergenic
AGAATCGCGTTCTGAGGCAA+TGG 0.601841 2.3:-6962171 None:intergenic
TAGAGAGCCACAAAGATCTG+TGG 0.633970 2.3:+6962215 MS.gene54023:CDS
GTTAGCAGGATAGCCGACCA+AGG 0.693637 2.3:-6962127 None:intergenic
AATTGTGGAGGAATCTCCGG+TGG 0.706339 2.3:-6962096 None:intergenic
AACTGGTTTGTAGAGCACTG+CGG 0.723124 2.3:-6962280 None:intergenic
ATACCCTTTGAATGAAGACG+AGG 0.726906 2.3:+6962065 MS.gene54023:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TGTTACATGAATTACTTACA+GGG - chr2.3:6961927-6961946 None:intergenic 25.0%
! TTGTTACATGAATTACTTAC+AGG - chr2.3:6961928-6961947 None:intergenic 25.0%
AAATTTACAATCTGCATGCA+GGG + chr2.3:6961982-6962001 MS.gene54023:intron 30.0%
TAAATTTACAATCTGCATGC+AGG + chr2.3:6961981-6962000 MS.gene54023:intron 30.0%
AGGGTATGCATTATTGTAAC+CGG - chr2.3:6962052-6962071 None:intergenic 35.0%
TACAAACCAGTTCAAAGAAG+AGG + chr2.3:6962291-6962310 MS.gene54023:CDS 35.0%
!! ATTTTGAAAACATCCGACTC+CGG + chr2.3:6962030-6962049 MS.gene54023:CDS 35.0%
AAAGCTACCACAGATCTTTG+TGG - chr2.3:6962225-6962244 None:intergenic 40.0%
ACAAAGATCTGTGGTAGCTT+TGG + chr2.3:6962224-6962243 MS.gene54023:CDS 40.0%
ATACCCTTTGAATGAAGACG+AGG + chr2.3:6962065-6962084 MS.gene54023:CDS 40.0%
CAAAGATCTGTGGTAGCTTT+GGG + chr2.3:6962225-6962244 MS.gene54023:CDS 40.0%
CAATTGCAAAACACCTTGGT+CGG + chr2.3:6962114-6962133 MS.gene54023:CDS 40.0%
CTAAAACTATCGACGTTAGC+AGG - chr2.3:6962144-6962163 None:intergenic 40.0%
TCCACAATTGCAAAACACCT+TGG + chr2.3:6962110-6962129 MS.gene54023:CDS 40.0%
TGCATTATTGTAACCGGAGT+CGG - chr2.3:6962046-6962065 None:intergenic 40.0%
! TGATTTAGAATCGCGTTCTG+AGG - chr2.3:6962180-6962199 None:intergenic 40.0%
!! AAGGTGTTTTGCAATTGTGG+AGG - chr2.3:6962111-6962130 None:intergenic 40.0%
!! ACCAAGGTGTTTTGCAATTG+TGG - chr2.3:6962114-6962133 None:intergenic 40.0%
CTTACAGGGTTTGCAGCATA+TGG - chr2.3:6961913-6961932 None:intergenic 45.0%
GTGCCTCGTCTTCATTCAAA+GGG - chr2.3:6962071-6962090 None:intergenic 45.0%
TAGAGAGCCACAAAGATCTG+TGG + chr2.3:6962215-6962234 MS.gene54023:CDS 45.0%
TGCAATTGTGGAGGAATCTC+CGG - chr2.3:6962102-6962121 None:intergenic 45.0%
! GAGCACTGCGGTAACAAATT+TGG - chr2.3:6962271-6962290 None:intergenic 45.0%
!! AACTGGTTTGTAGAGCACTG+CGG - chr2.3:6962283-6962302 None:intergenic 45.0%
AATTGTGGAGGAATCTCCGG+TGG - chr2.3:6962099-6962118 None:intergenic 50.0%
CAGGGTGAAGCAACTGTCAT+GGG + chr2.3:6962000-6962019 MS.gene54023:intron 50.0%
CGTGCCTCGTCTTCATTCAA+AGG - chr2.3:6962072-6962091 None:intergenic 50.0%
GTGGCTCCTCTTCTTTGAAC+TGG - chr2.3:6962300-6962319 None:intergenic 50.0%
!! AGAATCGCGTTCTGAGGCAA+TGG - chr2.3:6962174-6962193 None:intergenic 50.0%
GCAGGGTGAAGCAACTGTCA+TGG + chr2.3:6961999-6962018 MS.gene54023:intron 55.0%
GTTAGCAGGATAGCCGACCA+AGG - chr2.3:6962130-6962149 None:intergenic 55.0%
AGACGAGGCACGTGATCCAC+CGG + chr2.3:6962080-6962099 MS.gene54023:CDS 60.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 6961865 6962329 6961865 ID=MS.gene54023
chr2.3 mRNA 6961865 6962329 6961865 ID=MS.gene54023.t1;Parent=MS.gene54023
chr2.3 exon 6961865 6961927 6961865 ID=MS.gene54023.t1.exon1;Parent=MS.gene54023.t1
chr2.3 CDS 6961865 6961927 6961865 ID=cds.MS.gene54023.t1;Parent=MS.gene54023.t1
chr2.3 exon 6962003 6962329 6962003 ID=MS.gene54023.t1.exon2;Parent=MS.gene54023.t1
chr2.3 CDS 6962003 6962329 6962003 ID=cds.MS.gene54023.t1;Parent=MS.gene54023.t1
Gene Sequence

>MS.gene54023

ATGAATTCACAACTAGTGGTTGACTTGAATAGCAAGATGAATAATCCATATGCTGCAAACCCTGTAAGTAATTCATGTAACAAATAATAACATCTATTACTTGTCATTAGTAAGTCTAAATTTACAATCTGCATGCAGGGTGAAGCAACTGTCATGGGATTTGAAATTTTGAAAACATCCGACTCCGGTTACAATAATGCATACCCTTTGAATGAAGACGAGGCACGTGATCCACCGGAGATTCCTCCACAATTGCAAAACACCTTGGTCGGCTATCCTGCTAACGTCGATAGTTTTAGTTCTCTTCCATTGCCTCAGAACGCGATTCTAAATCATCTTTATATTGAGAATAGAGAGCCACAAAGATCTGTGGTAGCTTTGGGATACACTCATCGCTTTCGTACCAAATTTGTTACCGCAGTGCTCTACAAACCAGTTCAAAGAAGAGGAGCCACAAACATTTGA
Protein sequence

>MS.gene54023.t1

MNSQLVVDLNSKMNNPYAANPGEATVMGFEILKTSDSGYNNAYPLNEDEARDPPEIPPQLQNTLVGYPANVDSFSSLPLPQNAILNHLYIENREPQRSVVALGYTHRFRTKFVTAVLYKPVQRRGATNI