AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene72802

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene72802.t1 MTR_7g080390 74.242 132 32 1 1 132 1 130 3.08e-66 197
MS.gene72802.t1 MTR_7g080760 44.538 119 58 2 18 131 3 118 7.23e-27 97.1
MS.gene72802.t1 MTR_4g133928 36.290 124 66 2 18 132 4 123 8.76e-18 73.9
MS.gene72802.t1 MTR_0446s0010 37.500 104 52 2 18 112 4 103 4.87e-13 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene72802.t1 AT1G65290 62.121 132 44 3 1 132 1 126 1.46e-48 152
MS.gene72802.t1 AT2G44620 43.939 132 62 5 1 131 1 121 6.23e-26 94.7
MS.gene72802.t1 AT5G47630 38.750 80 49 0 53 132 48 127 2.53e-13 62.8
MS.gene72802.t1 AT5G47630 38.750 80 49 0 53 132 48 127 2.53e-13 62.8
MS.gene72802.t1 AT5G47630 38.750 80 49 0 53 132 48 127 2.53e-13 62.8
MS.gene72802.t1 AT3G05020 35.955 89 57 0 37 125 41 129 3.77e-11 57.0

Find 30 sgRNAs with CRISPR-Local

Find 71 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCGGCTCGGGGAAGCGGTTT+GGG 0.283525 5.1:+17113951 MS.gene72802:CDS
GGCGGCTCGGGGAAGCGGTT+TGG 0.290380 5.1:+17113950 MS.gene72802:CDS
TGACAATGTTGATCCTTCTA+AGG 0.294761 5.1:+17114148 MS.gene72802:CDS
ATGGATCTTGATACAGAGTT+TGG 0.311699 5.1:+17115012 MS.gene72802:CDS
ATCAACAACAATGGCGGCTC+GGG 0.345626 5.1:+17113938 None:intergenic
AAGCACGAACCTCAACTCTT+AGG 0.392906 5.1:-17113986 None:intergenic
GAAATCAACAGCTTGATTAA+CGG 0.409809 5.1:-17115073 None:intergenic
ATGGAAGTGAAAACCTTAGA+AGG 0.418506 5.1:-17114161 None:intergenic
TTTCTATGATGACCTTGGAT+TGG 0.444522 5.1:+17114963 MS.gene72802:CDS
AAGATCCATACAGATCTCTA+TGG 0.455448 5.1:-17114998 None:intergenic
GTCGCTTCAGCGAAGAGATC+AGG 0.457126 5.1:+17114066 MS.gene72802:CDS
ACAATGGCGGCTCGGGGAAG+CGG 0.466910 5.1:+17113945 None:intergenic
GAGGAGTACGCAAAGGAGAT+TGG 0.466971 5.1:-17114022 None:intergenic
CAGCGACGAAGGAAGGAATT+CGG 0.467889 5.1:-17114044 None:intergenic
CATCATAGAAATGAGCAGTT+GGG 0.468087 5.1:-17114951 None:intergenic
TTTCATTGCATCTCATCCTC+AGG 0.474149 5.1:+17115092 MS.gene72802:CDS
GCTCATTTCTATGATGACCT+TGG 0.491539 5.1:+17114958 MS.gene72802:CDS
TATCAACAACAATGGCGGCT+CGG 0.529312 5.1:+17113937 None:intergenic
TCATCATAGAAATGAGCAGT+TGG 0.537450 5.1:-17114952 None:intergenic
GAAGCGACAGCGACGAAGGA+AGG 0.545017 5.1:-17114051 None:intergenic
CGCTGAAGCGACAGCGACGA+AGG 0.552195 5.1:-17114055 None:intergenic
AGACGCCATAGAGATCTGTA+TGG 0.564613 5.1:+17114993 MS.gene72802:CDS
ATCATAGAAATGAGCAGTTG+GGG 0.586456 5.1:-17114950 None:intergenic
GATGAATTACCTAAGAGTTG+AGG 0.587013 5.1:+17113977 MS.gene72802:CDS
CGTCTAAACTATCCAATCCA+AGG 0.606873 5.1:-17114975 None:intergenic
GAGTACGCAAAGGAGATTGG+TGG 0.606939 5.1:-17114019 None:intergenic
TCAACAACAATGGCGGCTCG+GGG 0.630083 5.1:+17113939 None:intergenic
GAATTCGGAGGAGTACGCAA+AGG 0.668596 5.1:-17114029 None:intergenic
AGGTTAGACTACTTCGCCTG+AGG 0.672291 5.1:-17115108 None:intergenic
CGACGAAGGAAGGAATTCGG+AGG 0.686278 5.1:-17114041 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGAAAATAAATGAAGAAATT+AGG - chr5.1:17114193-17114212 None:intergenic 15.0%
!!! CTATTTTCAATCTTTAATTT+AGG + chr5.1:17114229-17114248 MS.gene72802:intron 15.0%
!! AAGCCAAAGATATAATATAA+CGG - chr5.1:17114877-17114896 None:intergenic 20.0%
!! TAAATGAAGAAATTAGGTTA+AGG - chr5.1:17114187-17114206 None:intergenic 20.0%
! GTACCGTTATATTATATCTT+TGG + chr5.1:17114871-17114890 MS.gene72802:intron 25.0%
!! ATAAGTTGTCTTTTCAAACA+TGG - chr5.1:17114570-17114589 None:intergenic 25.0%
!! TTATCCTTTTATGTTGTGTT+TGG - chr5.1:17114410-17114429 None:intergenic 25.0%
GAAATCAACAGCTTGATTAA+CGG - chr5.1:17115076-17115095 None:intergenic 30.0%
GTTTATCTGAGCTTATTTAC+TGG - chr5.1:17114760-17114779 None:intergenic 30.0%
TAAAGTAAAAGTCTACACTG+AGG - chr5.1:17114796-17114815 None:intergenic 30.0%
TGAAGAAATTAGGTTAAGGA+TGG - chr5.1:17114183-17114202 None:intergenic 30.0%
TGATCCAAACACAACATAAA+AGG + chr5.1:17114403-17114422 MS.gene72802:intron 30.0%
! ATCTTGTCTACTTCATTTTC+AGG - chr5.1:17115048-17115067 None:intergenic 30.0%
! GCTAAGTGAAGACTATATTT+TGG + chr5.1:17114534-17114553 MS.gene72802:intron 30.0%
! TGACCAATTCTTGTAAGTTT+TGG + chr5.1:17114274-17114293 MS.gene72802:intron 30.0%
!! AAGTGAAGACTATATTTTGG+AGG + chr5.1:17114537-17114556 MS.gene72802:intron 30.0%
!!! ATTGTCAAATTTTTTGACGC+AGG - chr5.1:17114135-17114154 None:intergenic 30.0%
AACTGACACAAGCACATTAA+AGG - chr5.1:17114819-17114838 None:intergenic 35.0%
AAGATCCATACAGATCTCTA+TGG - chr5.1:17115001-17115020 None:intergenic 35.0%
AGGCCAAAACTTACAAGAAT+TGG - chr5.1:17114280-17114299 None:intergenic 35.0%
ATATAACGGTACACAAATGC+TGG - chr5.1:17114863-17114882 None:intergenic 35.0%
ATCATAGAAATGAGCAGTTG+GGG - chr5.1:17114953-17114972 None:intergenic 35.0%
ATGGAAGTGAAAACCTTAGA+AGG - chr5.1:17114164-17114183 None:intergenic 35.0%
ATGGATCTTGATACAGAGTT+TGG + chr5.1:17115012-17115031 MS.gene72802:CDS 35.0%
CATCATAGAAATGAGCAGTT+GGG - chr5.1:17114954-17114973 None:intergenic 35.0%
GATGAATTACCTAAGAGTTG+AGG + chr5.1:17113977-17113996 MS.gene72802:CDS 35.0%
GTACAATAAACCCAAAAGTG+CGG + chr5.1:17114488-17114507 MS.gene72802:intron 35.0%
TCATCATAGAAATGAGCAGT+TGG - chr5.1:17114955-17114974 None:intergenic 35.0%
TGACAATGTTGATCCTTCTA+AGG + chr5.1:17114148-17114167 MS.gene72802:CDS 35.0%
TTAATGTGCTTGTGTCAGTT+TGG + chr5.1:17114819-17114838 MS.gene72802:intron 35.0%
TTATTTCCGTAAGCTATCCT+AGG - chr5.1:17114662-17114681 None:intergenic 35.0%
TTTCTATGATGACCTTGGAT+TGG + chr5.1:17114963-17114982 MS.gene72802:CDS 35.0%
! AAGTTCTAGTCCTCGAAATA+GGG + chr5.1:17114456-17114475 MS.gene72802:intron 35.0%
! CTGTTTTCATAAGCTATCCT+AGG + chr5.1:17114642-17114661 MS.gene72802:intron 35.0%
! GAGAACTTTTCTCGACAAAT+CGG + chr5.1:17114088-17114107 MS.gene72802:CDS 35.0%
! TTGTGTTTGGATCAGTGTTT+TGG - chr5.1:17114397-17114416 None:intergenic 35.0%
AGCTATCCTAGGATAGCTTA+CGG + chr5.1:17114653-17114672 MS.gene72802:intron 40.0%
CGTCTAAACTATCCAATCCA+AGG - chr5.1:17114978-17114997 None:intergenic 40.0%
GCTCATTTCTATGATGACCT+TGG + chr5.1:17114958-17114977 MS.gene72802:CDS 40.0%
GGAAACAGCTTATGACATGT+AGG - chr5.1:17114698-17114717 None:intergenic 40.0%
TTTCATTGCATCTCATCCTC+AGG + chr5.1:17115092-17115111 MS.gene72802:CDS 40.0%
! AACTTTTCTCGACAAATCGG+AGG + chr5.1:17114091-17114110 MS.gene72802:CDS 40.0%
! CAAGTTCTAGTCCTCGAAAT+AGG + chr5.1:17114455-17114474 MS.gene72802:intron 40.0%
! CATAGTCTTACCCTATTTCG+AGG - chr5.1:17114469-17114488 None:intergenic 40.0%
! TGACAAAAGCAAAGAAGCAC+AGG - chr5.1:17114925-17114944 None:intergenic 40.0%
!! TGTGCTTCTTTGCTTTTGTC+AGG + chr5.1:17114924-17114943 MS.gene72802:intron 40.0%
AAGCACGAACCTCAACTCTT+AGG - chr5.1:17113989-17114008 None:intergenic 45.0%
AAGTTGTTGTCACCTGACTG+AGG + chr5.1:17114429-17114448 MS.gene72802:intron 45.0%
AGACGCCATAGAGATCTGTA+TGG + chr5.1:17114993-17115012 MS.gene72802:CDS 45.0%
AGACTGTGTGATAGAGCTTG+TGG - chr5.1:17114719-17114738 None:intergenic 45.0%
ATCAGCTCAAACGCACGTTT+GGG - chr5.1:17114328-17114347 None:intergenic 45.0%
TAGAACTTGTGACCTCAGTC+AGG - chr5.1:17114444-17114463 None:intergenic 45.0%
TTTGCCGCAGAAACAAACAG+AGG - chr5.1:17114300-17114319 None:intergenic 45.0%
!! TTGGCCTCTGTTTGTTTCTG+CGG + chr5.1:17114293-17114312 MS.gene72802:intron 45.0%
CAGCGACGAAGGAAGGAATT+CGG - chr5.1:17114047-17114066 None:intergenic 50.0%
CATCAGCTCAAACGCACGTT+TGG - chr5.1:17114329-17114348 None:intergenic 50.0%
GAGTACGCAAAGGAGATTGG+TGG - chr5.1:17114022-17114041 None:intergenic 50.0%
GGTACACAAATGCTGGCAGA+GGG - chr5.1:17114856-17114875 None:intergenic 50.0%
GTCTACACTGAGGCTCTGTT+TGG - chr5.1:17114786-17114805 None:intergenic 50.0%
! ATAAACCCAAAAGTGCGGCG+CGG + chr5.1:17114493-17114512 MS.gene72802:intron 50.0%
! GAATTCGGAGGAGTACGCAA+AGG - chr5.1:17114032-17114051 None:intergenic 50.0%
! GAGGAGTACGCAAAGGAGAT+TGG - chr5.1:17114025-17114044 None:intergenic 50.0%
CGACGAAGGAAGGAATTCGG+AGG - chr5.1:17114044-17114063 None:intergenic 55.0%
CGGTACACAAATGCTGGCAG+AGG - chr5.1:17114857-17114876 None:intergenic 55.0%
GTCGCTTCAGCGAAGAGATC+AGG + chr5.1:17114066-17114085 MS.gene72802:CDS 55.0%
GAAGCGACAGCGACGAAGGA+AGG - chr5.1:17114054-17114073 None:intergenic 60.0%
! AAGCTACCGCGCCGCACTTT+TGG - chr5.1:17114502-17114521 None:intergenic 60.0%
! AGCTACCGCGCCGCACTTTT+GGG - chr5.1:17114501-17114520 None:intergenic 60.0%
CGCTGAAGCGACAGCGACGA+AGG - chr5.1:17114058-17114077 None:intergenic 65.0%
! GCGGCTCGGGGAAGCGGTTT+GGG + chr5.1:17113951-17113970 MS.gene72802:CDS 70.0%
! GGCGGCTCGGGGAAGCGGTT+TGG + chr5.1:17113950-17113969 MS.gene72802:CDS 75.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 17113948 17115122 17113948 ID=MS.gene72802
chr5.1 mRNA 17113948 17115122 17113948 ID=MS.gene72802.t1;Parent=MS.gene72802
chr5.1 exon 17113948 17114169 17113948 ID=MS.gene72802.t1.exon1;Parent=MS.gene72802.t1
chr5.1 CDS 17113948 17114169 17113948 ID=cds.MS.gene72802.t1;Parent=MS.gene72802.t1
chr5.1 exon 17114946 17115122 17114946 ID=MS.gene72802.t1.exon2;Parent=MS.gene72802.t1
chr5.1 CDS 17114946 17115122 17114946 ID=cds.MS.gene72802.t1;Parent=MS.gene72802.t1
Gene Sequence

>MS.gene72802

ATGGCGGCTCGGGGAAGCGGTTTGGGTCTGATGAATTACCTAAGAGTTGAGGTTCGTGCTTCTGCTCTCAACCACCAATCTCCTTTGCGTACTCCTCCGAATTCCTTCCTTCGTCGCTGTCGCTTCAGCGAAGAGATCAGGAGAACTTTTCTCGACAAATCGGAGGTCACTGATCGCGTCATTTCCTGCGTCAAAAAATTTGACAATGTTGATCCTTCTAAGGTTTTCACTTCCATCCTTAACCTAATTTCTTCATTTATTTTCATTTATTTTACAAATTTCTATTTTCAATCTTTAATTTAGGTCATATTTAGTATCTTAATTAATGACCAATTCTTGTAAGTTTTGGCCTCTGTTTGTTTCTGCGGCAAAACAAGCCCAAACGTGCGTTTGAGCTGATGCTACTAGTTGTAGCTTCTTAAAAATCAAGTTTATTTGATAGAAAACCAAAACACTGATCCAAACACAACATAAAAGGATAAAGTTGTTGTCACCTGACTGAGGTCACAAGTTCTAGTCCTCGAAATAGGGTAAGACTATGTACAATAAACCCAAAAGTGCGGCGCGGTAGCTTTATTGTATGAAAGCTAAGTGAAGACTATATTTTGGAGGATTAAGACCATGTTTGAAAAGACAACTTATTTAAGCGTTTTGTGTAAGCTATTTCTTTAACAAAAAATAAAATAAAATCAAACTGTTTTCATAAGCTATCCTAGGATAGCTTACGGAAATAAGTTTAAACATTTACCTACATGTCATAAGCTGTTTCCACAAGCTCTATCACACAGTCTCACTCACAATTTTCTTTTCCAGTAAATAAGCTCAGATAAACAATCCAAACAGAGCCTCAGTGTAGACTTTTACTTTACCTTTAATGTGCTTGTGTCAGTTTGGAGAATTTAAATCCCTCTGCCAGCATTTGTGTACCGTTATATTATATCTTTGGCTTATGTTATTTTGATAATAACACAGAACCTGTGCTTCTTTGCTTTTGTCAGGTTACCCCAACTGCTCATTTCTATGATGACCTTGGATTGGATAGTTTAGACGCCATAGAGATCTGTATGGATCTTGATACAGAGTTTGGATTTGAGATTCCTGAAAATGAAGTAGACAAGATCGTCTCCGTTAATCAAGCTGTTGATTTCATTGCATCTCATCCTCAGGCGAAGTAG
Protein sequence

>MS.gene72802.t1

MAARGSGLGLMNYLRVEVRASALNHQSPLRTPPNSFLRRCRFSEEIRRTFLDKSEVTDRVISCVKKFDNVDPSKVTPTAHFYDDLGLDSLDAIEICMDLDTEFGFEIPENEVDKIVSVNQAVDFIASHPQAK