AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene90243

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene90243.t1 MTR_4g093510 81.905 105 19 0 6 110 70 174 2.09e-58 187
MS.gene90243.t1 MTR_4g093260 80.000 105 19 1 6 110 61 163 2.88e-56 184
MS.gene90243.t1 MTR_4g093260 80.000 105 19 1 6 110 70 172 2.95e-56 184
MS.gene90243.t1 MTR_4g093270 69.231 104 32 0 6 109 67 170 9.08e-53 168
MS.gene90243.t1 MTR_4g093280 73.786 103 27 0 6 108 70 172 2.32e-49 163
MS.gene90243.t1 MTR_4g093260 79.167 72 13 1 39 110 1 70 2.68e-35 127
MS.gene90243.t1 MTR_4g108350 40.000 80 40 2 8 82 68 144 4.49e-13 62.0
MS.gene90243.t1 MTR_4g108350 40.000 80 40 2 8 82 77 153 5.72e-13 62.0
MS.gene90243.t1 MTR_5g039530 37.079 89 46 3 8 86 74 162 2.90e-12 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene90243.t1 AT1G69700 39.130 92 49 3 6 90 74 165 4.38e-13 62.4
MS.gene90243.t1 AT1G74520 36.364 88 48 2 8 90 74 158 4.04e-11 57.4
MS.gene90243.t1 AT1G74520 36.364 88 48 2 8 90 74 158 4.04e-11 57.4

Find 26 sgRNAs with CRISPR-Local

Find 33 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTGACTACTTGCGGTTTCA+TGG 0.304620 4.2:-20112977 None:intergenic
TGAAGCGACAAATGAAATTA+TGG 0.324038 4.2:+20113323 MS.gene90243:CDS
TACATAGCTGTTTACCTTGT+TGG 0.357254 4.2:-20113112 None:intergenic
TTAAGCTAATGATCATCTTC+TGG 0.364058 4.2:+20112899 MS.gene90243:CDS
GTTGGCAATGAGTTTCTCTA+AGG 0.364553 4.2:-20113094 None:intergenic
TCATTTGTCGCTTCAGCATC+AGG 0.369557 4.2:-20113315 None:intergenic
GAGAAATATATGAAAGAGAA+TGG 0.445755 4.2:+20113063 MS.gene90243:CDS
TGGCTCATCATACCGGACTT+TGG 0.448937 4.2:+20112919 MS.gene90243:CDS
AAATGCTAAAGGCAAAGTTT+TGG 0.454006 4.2:+20113361 MS.gene90243:CDS
TCATTACCATGCGTGACATC+AGG 0.468355 4.2:+20112857 None:intergenic
CATGGAGGTTAAACAACTAC+TGG 0.497837 4.2:+20112998 MS.gene90243:CDS
AACCTCCATGTGACTACTTG+CGG 0.500472 4.2:-20112985 None:intergenic
TAAGAAGCTCGTCCAAAGTC+CGG 0.501414 4.2:-20112931 None:intergenic
TAAACAACTACTGGAGGAAG+TGG 0.507612 4.2:+20113007 MS.gene90243:CDS
TAGCATTTCTTTATTATCAG+TGG 0.509477 4.2:-20113346 None:intergenic
CATCTTCTGGCTCATCATAC+CGG 0.514317 4.2:+20112912 MS.gene90243:CDS
GTGACATCAGGTTTCACCTC+TGG 0.539831 4.2:+20112869 MS.gene90243:CDS
TGATAATAAAGAAATGCTAA+AGG 0.571675 4.2:+20113350 MS.gene90243:CDS
ATGATCATTAGCTTAACGTA+TGG 0.579799 4.2:-20112892 None:intergenic
AGAGAAACTCATTGCCAACA+AGG 0.624521 4.2:+20113098 MS.gene90243:CDS
TGAAACCGCAAGTAGTCACA+TGG 0.639727 4.2:+20112980 MS.gene90243:CDS
TATTGTAGAACACAATGTGT+AGG 0.642645 4.2:+20113292 MS.gene90243:intron
GGAGGTTAAACAACTACTGG+AGG 0.657523 4.2:+20113001 MS.gene90243:CDS
GTGAAACCTGATGTCACGCA+TGG 0.661268 4.2:-20112863 None:intergenic
TTAGCTTAACGTATGGCCAG+AGG 0.695704 4.2:-20112885 None:intergenic
AACCGCAAGTAGTCACATGG+AGG 0.759885 4.2:+20112983 MS.gene90243:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGATAATAAAGAAATGCTAA+AGG + chr4.2:20113350-20113369 MS.gene90243:CDS 20.0%
!!! GGACATTTTTATTTTATGTT+GGG - chr4.2:20113170-20113189 None:intergenic 20.0%
!!! TGGACATTTTTATTTTATGT+TGG - chr4.2:20113171-20113190 None:intergenic 20.0%
! GAGAAATATATGAAAGAGAA+TGG + chr4.2:20113063-20113082 MS.gene90243:CDS 25.0%
! TAGCATTTCTTTATTATCAG+TGG - chr4.2:20113349-20113368 None:intergenic 25.0%
! TATAAAAACATCCACATACT+TGG - chr4.2:20113227-20113246 None:intergenic 25.0%
!! AACTCTAGAAGAATTCTATA+GGG + chr4.2:20113199-20113218 MS.gene90243:intron 25.0%
CCTTATGCTGCATAAAAAAT+TGG + chr4.2:20113136-20113155 MS.gene90243:intron 30.0%
TATTGTAGAACACAATGTGT+AGG + chr4.2:20113292-20113311 MS.gene90243:intron 30.0%
TGAAGCGACAAATGAAATTA+TGG + chr4.2:20113323-20113342 MS.gene90243:CDS 30.0%
TTAAGCTAATGATCATCTTC+TGG + chr4.2:20112899-20112918 MS.gene90243:CDS 30.0%
! AAATGCTAAAGGCAAAGTTT+TGG + chr4.2:20113361-20113380 MS.gene90243:CDS 30.0%
! ATGATCATTAGCTTAACGTA+TGG - chr4.2:20112895-20112914 None:intergenic 30.0%
! GAACTCTAGAAGAATTCTAT+AGG + chr4.2:20113198-20113217 MS.gene90243:intron 30.0%
!!! CCAATTTTTTATGCAGCATA+AGG - chr4.2:20113139-20113158 None:intergenic 30.0%
TACATAGCTGTTTACCTTGT+TGG - chr4.2:20113115-20113134 None:intergenic 35.0%
!! TCTTCTAGAGTTCAAGTAGT+TGG - chr4.2:20113191-20113210 None:intergenic 35.0%
AGAGAAACTCATTGCCAACA+AGG + chr4.2:20113098-20113117 MS.gene90243:CDS 40.0%
CATGGAGGTTAAACAACTAC+TGG + chr4.2:20112998-20113017 MS.gene90243:CDS 40.0%
GTTGGCAATGAGTTTCTCTA+AGG - chr4.2:20113097-20113116 None:intergenic 40.0%
TAAACAACTACTGGAGGAAG+TGG + chr4.2:20113007-20113026 MS.gene90243:CDS 40.0%
TCTATAGGGAACCAAGTATG+TGG + chr4.2:20113213-20113232 MS.gene90243:intron 40.0%
AACCTCCATGTGACTACTTG+CGG - chr4.2:20112988-20113007 None:intergenic 45.0%
GGAGGTTAAACAACTACTGG+AGG + chr4.2:20113001-20113020 MS.gene90243:CDS 45.0%
TAAGAAGCTCGTCCAAAGTC+CGG - chr4.2:20112934-20112953 None:intergenic 45.0%
TGAAACCGCAAGTAGTCACA+TGG + chr4.2:20112980-20112999 MS.gene90243:CDS 45.0%
TGTGACTACTTGCGGTTTCA+TGG - chr4.2:20112980-20112999 None:intergenic 45.0%
TTAGCTTAACGTATGGCCAG+AGG - chr4.2:20112888-20112907 None:intergenic 45.0%
! TCATTTGTCGCTTCAGCATC+AGG - chr4.2:20113318-20113337 None:intergenic 45.0%
!! CATCTTCTGGCTCATCATAC+CGG + chr4.2:20112912-20112931 MS.gene90243:CDS 45.0%
AACCGCAAGTAGTCACATGG+AGG + chr4.2:20112983-20113002 MS.gene90243:CDS 50.0%
GTGACATCAGGTTTCACCTC+TGG + chr4.2:20112869-20112888 MS.gene90243:CDS 50.0%
TGGCTCATCATACCGGACTT+TGG + chr4.2:20112919-20112938 MS.gene90243:CDS 50.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 20112865 20113389 20112865 ID=MS.gene90243
chr4.2 mRNA 20112865 20113389 20112865 ID=MS.gene90243.t1;Parent=MS.gene90243
chr4.2 exon 20112865 20113119 20112865 ID=MS.gene90243.t1.exon1;Parent=MS.gene90243.t1
chr4.2 CDS 20112865 20113119 20112865 ID=cds.MS.gene90243.t1;Parent=MS.gene90243.t1
chr4.2 exon 20113300 20113389 20113300 ID=MS.gene90243.t1.exon2;Parent=MS.gene90243.t1
chr4.2 CDS 20113300 20113389 20113300 ID=cds.MS.gene90243.t1;Parent=MS.gene90243.t1
Gene Sequence

>MS.gene90243

ATGCGTGACATCAGGTTTCACCTCTGGCCATACGTTAAGCTAATGATCATCTTCTGGCTCATCATACCGGACTTTGGACGAGCTTCTTATATTTATAATAAGCTTATTAGTTCCATGAAACCGCAAGTAGTCACATGGAGGTTAAACAACTACTGGAGGAAGTGGTTTTGTAAGAAAGATAACTTTTTAATGCATGCAGAGAAATATATGAAAGAGAATGGAACTGAAGCCTTAGAGAAACTCATTGCCAACAAGGTAAACAGCTATGTAGCCTTATGCTGCATAAAAAATTGGAGTACAAACCCAACATAAAATAAAAATGTCCAACTACTTGAACTCTAGAAGAATTCTATAGGGAACCAAGTATGTGGATGTTTTTATATCTGCATCTGCAGTTGAAAATATTTGCTAATTCTTTGTTTTTTCGTATTGTAGAACACAATGTGTAGGCCTGATGCTGAAGCGACAAATGAAATTATGGCCACTGATAATAAAGAAATGCTAAAGGCAAAGTTTTGGTGTTAA
Protein sequence

>MS.gene90243.t1

MRDIRFHLWPYVKLMIIFWLIIPDFGRASYIYNKLISSMKPQVVTWRLNNYWRKWFCKKDNFLMHAEKYMKENGTEALEKLIANKNTMCRPDAEATNEIMATDNKEMLKAKFWC