AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene66705

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene66705.t1 MTR_4g052060 93.407 182 11 1 1 181 1 182 4.65e-122 342
MS.gene66705.t1 MTR_4g052040 70.718 181 42 4 1 174 1 177 4.19e-75 223
MS.gene66705.t1 MTR_5g079710 44.720 161 83 4 4 163 6 161 6.76e-33 118
MS.gene66705.t1 MTR_7g105790 35.632 174 89 2 1 154 1 171 7.95e-22 88.2
MS.gene66705.t1 MTR_0907s0020 58.209 67 28 0 95 161 104 170 1.35e-20 84.3
MS.gene66705.t1 MTR_8g103520 41.558 77 45 0 86 162 217 293 2.57e-12 63.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene66705.t1 AT3G52525 57.576 66 27 1 89 153 61 126 4.04e-19 80.1
MS.gene66705.t1 AT2G36026 57.377 61 26 0 98 158 91 151 1.26e-17 76.6
MS.gene66705.t1 AT5G19650 44.776 67 37 0 92 158 153 219 4.96e-12 62.4
MS.gene66705.t1 AT5G22240 36.893 103 61 2 58 159 63 162 1.91e-11 60.5

Find 32 sgRNAs with CRISPR-Local

Find 35 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATTTGGCTAATGGAAATTT+TGG 0.176660 4.3:-47839907 None:intergenic
TGGACGAGGCCTTGCTAATT+TGG 0.263274 4.3:-47839923 None:intergenic
AGAGTGTTCTCAACAAATAT+TGG 0.365412 4.3:+47839828 MS.gene66705:CDS
GGCCTTGCTAATTTGGCTAA+TGG 0.370986 4.3:-47839916 None:intergenic
TCATAAACACGTATATTAGA+AGG 0.378322 4.3:-47840311 None:intergenic
GCCTCGTCCAACACAACTTT+AGG 0.401066 4.3:+47839936 MS.gene66705:CDS
ATGATCTTCTAGTTCTTCTT+CGG 0.414161 4.3:+47840171 MS.gene66705:CDS
GAGTGCTTGAAATCATGATA+TGG 0.426047 4.3:-47840107 None:intergenic
GTTTGATAGTGGGCTATGCT+TGG 0.435980 4.3:-47840054 None:intergenic
ACGACCACAGTGTTTGATAG+TGG 0.464120 4.3:-47840065 None:intergenic
AAACACTGTGGTCGTTGAAA+AGG 0.465908 4.3:+47840073 MS.gene66705:CDS
AGCTTCAGAGAAAGTGGTGG+TGG 0.499280 4.3:-47840006 None:intergenic
TATGCTTCAAATGATCTTCG+AGG 0.503327 4.3:+47840130 MS.gene66705:CDS
TCAACAAATATTGGAAGTTG+TGG 0.506051 4.3:+47839837 MS.gene66705:CDS
GTAGTAGTACAAACCTTGTC+GGG 0.514681 4.3:-47840272 None:intergenic
TGTTTCAGCTTCAGAGAAAG+TGG 0.518295 4.3:-47840012 None:intergenic
TTAGGTGAACGAAAGGGTGC+TGG 0.519534 4.3:+47839954 MS.gene66705:CDS
TTTGATAGTGGGCTATGCTT+GGG 0.527494 4.3:-47840053 None:intergenic
TTCCATTAGCCAAATTAGCA+AGG 0.533087 4.3:+47839914 MS.gene66705:CDS
AGTACACGAGCCTATTCAAA+AGG 0.546512 4.3:+47839884 MS.gene66705:CDS
CACAACTTTAGGTGAACGAA+AGG 0.552205 4.3:+47839947 MS.gene66705:CDS
ACCTAAAGTTGTGTTGGACG+AGG 0.553754 4.3:-47839937 None:intergenic
CTTCGAGGATGAGATCGATT+CGG 0.564919 4.3:+47840145 MS.gene66705:CDS
GATAGTGGGCTATGCTTGGG+TGG 0.571005 4.3:-47840050 None:intergenic
TCGTTCACCTAAAGTTGTGT+TGG 0.572809 4.3:-47839943 None:intergenic
CGACCACAGTGTTTGATAGT+GGG 0.594914 4.3:-47840064 None:intergenic
AGTAGTAGTACAAACCTTGT+CGG 0.598934 4.3:-47840273 None:intergenic
ACAACTTTAGGTGAACGAAA+GGG 0.627201 4.3:+47839948 MS.gene66705:CDS
TTCAGCTTCAGAGAAAGTGG+TGG 0.661349 4.3:-47840009 None:intergenic
CGAGGATGAGATCGATTCGG+AGG 0.665085 4.3:+47840148 MS.gene66705:CDS
TAAAGACTTTAACGATGACA+AGG 0.672661 4.3:-47840226 None:intergenic
TAGCCCACTATCAAACACTG+TGG 0.790071 4.3:+47840061 MS.gene66705:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TCATAAACACGTATATTAGA+AGG - chr4.3:47840314-47840333 None:intergenic 25.0%
!! AATTTGGCTAATGGAAATTT+TGG - chr4.3:47839910-47839929 None:intergenic 25.0%
TAAAGACTTTAACGATGACA+AGG - chr4.3:47840229-47840248 None:intergenic 30.0%
TCAACAAATATTGGAAGTTG+TGG + chr4.3:47839837-47839856 MS.gene66705:CDS 30.0%
! AGAGTGTTCTCAACAAATAT+TGG + chr4.3:47839828-47839847 MS.gene66705:CDS 30.0%
!! ATGATCTTCTAGTTCTTCTT+CGG + chr4.3:47840171-47840190 MS.gene66705:CDS 30.0%
!! GAAATTTTGGCCTTTTGAAT+AGG - chr4.3:47839897-47839916 None:intergenic 30.0%
ACAACTTTAGGTGAACGAAA+GGG + chr4.3:47839948-47839967 MS.gene66705:CDS 35.0%
AGTAGTAGTACAAACCTTGT+CGG - chr4.3:47840276-47840295 None:intergenic 35.0%
GAGTGCTTGAAATCATGATA+TGG - chr4.3:47840110-47840129 None:intergenic 35.0%
TATGCTTCAAATGATCTTCG+AGG + chr4.3:47840130-47840149 MS.gene66705:CDS 35.0%
TTCCATTAGCCAAATTAGCA+AGG + chr4.3:47839914-47839933 MS.gene66705:CDS 35.0%
! TCTCACAAGTCTTTTCTTGT+TGG - chr4.3:47839808-47839827 None:intergenic 35.0%
AAACACTGTGGTCGTTGAAA+AGG + chr4.3:47840073-47840092 MS.gene66705:CDS 40.0%
AGTACACGAGCCTATTCAAA+AGG + chr4.3:47839884-47839903 MS.gene66705:CDS 40.0%
CACAACTTTAGGTGAACGAA+AGG + chr4.3:47839947-47839966 MS.gene66705:CDS 40.0%
GTAGTAGTACAAACCTTGTC+GGG - chr4.3:47840275-47840294 None:intergenic 40.0%
TCGTTCACCTAAAGTTGTGT+TGG - chr4.3:47839946-47839965 None:intergenic 40.0%
TGTTTCAGCTTCAGAGAAAG+TGG - chr4.3:47840015-47840034 None:intergenic 40.0%
!! TTTGATAGTGGGCTATGCTT+GGG - chr4.3:47840056-47840075 None:intergenic 40.0%
ACCTAAAGTTGTGTTGGACG+AGG - chr4.3:47839940-47839959 None:intergenic 45.0%
ACGACCACAGTGTTTGATAG+TGG - chr4.3:47840068-47840087 None:intergenic 45.0%
CTTCGAGGATGAGATCGATT+CGG + chr4.3:47840145-47840164 MS.gene66705:CDS 45.0%
GGCCTTGCTAATTTGGCTAA+TGG - chr4.3:47839919-47839938 None:intergenic 45.0%
TAGCCCACTATCAAACACTG+TGG + chr4.3:47840061-47840080 MS.gene66705:CDS 45.0%
TTCAGCTTCAGAGAAAGTGG+TGG - chr4.3:47840012-47840031 None:intergenic 45.0%
! CGACCACAGTGTTTGATAGT+GGG - chr4.3:47840067-47840086 None:intergenic 45.0%
! TCATGAAGCTTTTCCCGACA+AGG + chr4.3:47840259-47840278 MS.gene66705:CDS 45.0%
!! GTTTGATAGTGGGCTATGCT+TGG - chr4.3:47840057-47840076 None:intergenic 45.0%
AGCTTCAGAGAAAGTGGTGG+TGG - chr4.3:47840009-47840028 None:intergenic 50.0%
GCCTCGTCCAACACAACTTT+AGG + chr4.3:47839936-47839955 MS.gene66705:CDS 50.0%
TGGACGAGGCCTTGCTAATT+TGG - chr4.3:47839926-47839945 None:intergenic 50.0%
! TTAGGTGAACGAAAGGGTGC+TGG + chr4.3:47839954-47839973 MS.gene66705:CDS 50.0%
!! CGAGGATGAGATCGATTCGG+AGG + chr4.3:47840148-47840167 MS.gene66705:CDS 55.0%
!! GATAGTGGGCTATGCTTGGG+TGG - chr4.3:47840053-47840072 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 47839798 47840343 47839798 ID=MS.gene66705
chr4.3 mRNA 47839798 47840343 47839798 ID=MS.gene66705.t1;Parent=MS.gene66705
chr4.3 exon 47839798 47840343 47839798 ID=MS.gene66705.t1.exon1;Parent=MS.gene66705.t1
chr4.3 CDS 47839798 47840343 47839798 ID=cds.MS.gene66705.t1;Parent=MS.gene66705.t1
Gene Sequence

>MS.gene66705

ATGTCTTCCAACAAGAAAAGACTTGTGAGAAGAGTGTTCTCAACAAATATTGGAAGTTGTGGCTGTGCAAAAAAGAAAGCAATTGTAGTACACGAGCCTATTCAAAAGGCCAAAATTTCCATTAGCCAAATTAGCAAGGCCTCGTCCAACACAACTTTAGGTGAACGAAAGGGTGCTGGTTGTAGCGTCGATCACAACGACGATTTCTCCACCACCACTTTCTCTGAAGCTGAAACAACTCAAAACTACTCTCCACCCAAGCATAGCCCACTATCAAACACTGTGGTCGTTGAAAAGGATTCTGATGATCCATATCATGATTTCAAGCACTCTATGCTTCAAATGATCTTCGAGGATGAGATCGATTCGGAGGATGATCTTCTAGTTCTTCTTCGGTGTTTTCTTCATCTCAATGATACTTATTATCACCTTGTCATCGTTAAAGTCTTTAATGATATATGTCATGAAGCTTTTCCCGACAAGGTTTGTACTACTACTTCGTCTGCTATCAAACCTTCTAATATACGTGTTTATGAAAATGAATAA
Protein sequence

>MS.gene66705.t1

MSSNKKRLVRRVFSTNIGSCGCAKKKAIVVHEPIQKAKISISQISKASSNTTLGERKGAGCSVDHNDDFSTTTFSEAETTQNYSPPKHSPLSNTVVVEKDSDDPYHDFKHSMLQMIFEDEIDSEDDLLVLLRCFLHLNDTYYHLVIVKVFNDICHEAFPDKVCTTTSSAIKPSNIRVYENE