AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene88356

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene88356.t1 MTR_7g080390 74.242 132 32 1 1 132 1 130 3.08e-66 197
MS.gene88356.t1 MTR_7g080760 44.538 119 58 2 18 131 3 118 7.23e-27 97.1
MS.gene88356.t1 MTR_4g133928 36.290 124 66 2 18 132 4 123 8.76e-18 73.9
MS.gene88356.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.gene88356.t1 AT1G65290 62.121 132 44 3 1 132 1 126 1.46e-48 152
MS.gene88356.t1 AT2G44620 43.939 132 62 5 1 131 1 121 6.23e-26 94.7
MS.gene88356.t1 AT5G47630 38.750 80 49 0 53 132 48 127 2.53e-13 62.8
MS.gene88356.t1 AT5G47630 38.750 80 49 0 53 132 48 127 2.53e-13 62.8
MS.gene88356.t1 AT5G47630 38.750 80 49 0 53 132 48 127 2.53e-13 62.8
MS.gene88356.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:-17141201 MS.gene88356:CDS
GGCGGCTCGGGGAAGCGGTT+TGG 0.290380 5.1:-17141202 MS.gene88356:CDS
TGACAATGTTGATCCTTCTA+AGG 0.294761 5.1:-17141004 MS.gene88356:intron
ATGGATCTTGATACAGAGTT+TGG 0.311699 5.1:-17140140 MS.gene88356:CDS
ATCAACAACAATGGCGGCTC+GGG 0.345626 5.1:-17141214 None:intergenic
AAGCACGAACCTCAACTCTT+AGG 0.392906 5.1:+17141166 None:intergenic
GAAATCAACAGCTTGATTAA+CGG 0.409809 5.1:+17140079 None:intergenic
ATGGAAGTGAAAACCTTAGA+AGG 0.418506 5.1:+17140991 None:intergenic
TTTCTATGATGACCTTGGAT+TGG 0.444522 5.1:-17140189 MS.gene88356:CDS
AAGATCCATACAGATCTCTA+TGG 0.455448 5.1:+17140154 None:intergenic
GTCGCTTCAGCGAAGAGATC+AGG 0.457126 5.1:-17141086 MS.gene88356:CDS
ACAATGGCGGCTCGGGGAAG+CGG 0.466910 5.1:-17141207 MS.gene88356:CDS
GAGGAGTACGCAAAGGAGAT+TGG 0.466971 5.1:+17141130 None:intergenic
CAGCGACGAAGGAAGGAATT+CGG 0.467889 5.1:+17141108 None:intergenic
CATCATAGAAATGAGCAGTT+GGG 0.468087 5.1:+17140201 None:intergenic
TTTCATTGCATCTCATCCTC+AGG 0.474149 5.1:-17140060 MS.gene88356:CDS
GCTCATTTCTATGATGACCT+TGG 0.491539 5.1:-17140194 MS.gene88356:CDS
TATCAACAACAATGGCGGCT+CGG 0.529312 5.1:-17141215 None:intergenic
TCATCATAGAAATGAGCAGT+TGG 0.537450 5.1:+17140200 None:intergenic
GAAGCGACAGCGACGAAGGA+AGG 0.545017 5.1:+17141101 None:intergenic
CGCTGAAGCGACAGCGACGA+AGG 0.552195 5.1:+17141097 None:intergenic
AGACGCCATAGAGATCTGTA+TGG 0.564613 5.1:-17140159 MS.gene88356:CDS
ATCATAGAAATGAGCAGTTG+GGG 0.586456 5.1:+17140202 None:intergenic
GATGAATTACCTAAGAGTTG+AGG 0.587013 5.1:-17141175 MS.gene88356:CDS
CGTCTAAACTATCCAATCCA+AGG 0.606873 5.1:+17140177 None:intergenic
GAGTACGCAAAGGAGATTGG+TGG 0.606939 5.1:+17141133 None:intergenic
TCAACAACAATGGCGGCTCG+GGG 0.630083 5.1:-17141213 None:intergenic
GAATTCGGAGGAGTACGCAA+AGG 0.668596 5.1:+17141123 None:intergenic
AGGTTAGACTACTTCGCCTG+AGG 0.672291 5.1:+17140044 None:intergenic
CGACGAAGGAAGGAATTCGG+AGG 0.686278 5.1:+17141111 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGAAAATAAATGAAGAAATT+AGG + chr5.1:17140297-17140316 None:intergenic 15.0%
!!! CTATTTTCAATCTTTAATTT+AGG - chr5.1:17140333-17140352 MS.gene88356:intron 15.0%
!! AAGCCAAAGATATAATATAA+CGG + chr5.1:17140981-17141000 None:intergenic 20.0%
!! TAAATGAAGAAATTAGGTTA+AGG + chr5.1:17140291-17140310 None:intergenic 20.0%
! GTACCGTTATATTATATCTT+TGG - chr5.1:17140975-17140994 MS.gene88356:intron 25.0%
!! ATAAGTTGTCTTTTCAAACA+TGG + chr5.1:17140674-17140693 None:intergenic 25.0%
!! TTATCCTTTTATGTTGTGTT+TGG + chr5.1:17140514-17140533 None:intergenic 25.0%
GAAATCAACAGCTTGATTAA+CGG + chr5.1:17141180-17141199 None:intergenic 30.0%
GTTTATCTGAGCTTATTTAC+TGG + chr5.1:17140864-17140883 None:intergenic 30.0%
TAAAGTAAAAGTCTACACTG+AGG + chr5.1:17140900-17140919 None:intergenic 30.0%
TGAAGAAATTAGGTTAAGGA+TGG + chr5.1:17140287-17140306 None:intergenic 30.0%
TGATCCAAACACAACATAAA+AGG - chr5.1:17140507-17140526 MS.gene88356:intron 30.0%
! ATCTTGTCTACTTCATTTTC+AGG + chr5.1:17141152-17141171 None:intergenic 30.0%
! GCTAAGTGAAGACTATATTT+TGG - chr5.1:17140638-17140657 MS.gene88356:intron 30.0%
! TGACCAATTCTTGTAAGTTT+TGG - chr5.1:17140378-17140397 MS.gene88356:intron 30.0%
!! AAGTGAAGACTATATTTTGG+AGG - chr5.1:17140641-17140660 MS.gene88356:intron 30.0%
!!! ATTGTCAAATTTTTTGACGC+AGG + chr5.1:17140239-17140258 None:intergenic 30.0%
AACTGACACAAGCACATTAA+AGG + chr5.1:17140923-17140942 None:intergenic 35.0%
AAGATCCATACAGATCTCTA+TGG + chr5.1:17141105-17141124 None:intergenic 35.0%
AGGCCAAAACTTACAAGAAT+TGG + chr5.1:17140384-17140403 None:intergenic 35.0%
ATATAACGGTACACAAATGC+TGG + chr5.1:17140967-17140986 None:intergenic 35.0%
ATCATAGAAATGAGCAGTTG+GGG + chr5.1:17141057-17141076 None:intergenic 35.0%
ATGGAAGTGAAAACCTTAGA+AGG + chr5.1:17140268-17140287 None:intergenic 35.0%
ATGGATCTTGATACAGAGTT+TGG - chr5.1:17141116-17141135 MS.gene88356:CDS 35.0%
CATCATAGAAATGAGCAGTT+GGG + chr5.1:17141058-17141077 None:intergenic 35.0%
GATGAATTACCTAAGAGTTG+AGG - chr5.1:17140081-17140100 MS.gene88356:CDS 35.0%
GTACAATAAACCCAAAAGTG+CGG - chr5.1:17140592-17140611 MS.gene88356:intron 35.0%
TCATCATAGAAATGAGCAGT+TGG + chr5.1:17141059-17141078 None:intergenic 35.0%
TGACAATGTTGATCCTTCTA+AGG - chr5.1:17140252-17140271 MS.gene88356:intron 35.0%
TTAATGTGCTTGTGTCAGTT+TGG - chr5.1:17140923-17140942 MS.gene88356:intron 35.0%
TTATTTCCGTAAGCTATCCT+AGG + chr5.1:17140766-17140785 None:intergenic 35.0%
TTTCTATGATGACCTTGGAT+TGG - chr5.1:17141067-17141086 MS.gene88356:CDS 35.0%
! AAGTTCTAGTCCTCGAAATA+GGG - chr5.1:17140560-17140579 MS.gene88356:intron 35.0%
! CTGTTTTCATAAGCTATCCT+AGG - chr5.1:17140746-17140765 MS.gene88356:intron 35.0%
! GAGAACTTTTCTCGACAAAT+CGG - chr5.1:17140192-17140211 MS.gene88356:CDS 35.0%
! TTGTGTTTGGATCAGTGTTT+TGG + chr5.1:17140501-17140520 None:intergenic 35.0%
AGCTATCCTAGGATAGCTTA+CGG - chr5.1:17140757-17140776 MS.gene88356:intron 40.0%
CGTCTAAACTATCCAATCCA+AGG + chr5.1:17141082-17141101 None:intergenic 40.0%
GCTCATTTCTATGATGACCT+TGG - chr5.1:17141062-17141081 MS.gene88356:CDS 40.0%
GGAAACAGCTTATGACATGT+AGG + chr5.1:17140802-17140821 None:intergenic 40.0%
TTTCATTGCATCTCATCCTC+AGG - chr5.1:17141196-17141215 MS.gene88356:CDS 40.0%
! AACTTTTCTCGACAAATCGG+AGG - chr5.1:17140195-17140214 MS.gene88356:CDS 40.0%
! CAAGTTCTAGTCCTCGAAAT+AGG - chr5.1:17140559-17140578 MS.gene88356:intron 40.0%
! CATAGTCTTACCCTATTTCG+AGG + chr5.1:17140573-17140592 None:intergenic 40.0%
! TGACAAAAGCAAAGAAGCAC+AGG + chr5.1:17141029-17141048 None:intergenic 40.0%
!! TGTGCTTCTTTGCTTTTGTC+AGG - chr5.1:17141028-17141047 MS.gene88356:CDS 40.0%
AAGCACGAACCTCAACTCTT+AGG + chr5.1:17140093-17140112 None:intergenic 45.0%
AAGTTGTTGTCACCTGACTG+AGG - chr5.1:17140533-17140552 MS.gene88356:intron 45.0%
AGACGCCATAGAGATCTGTA+TGG - chr5.1:17141097-17141116 MS.gene88356:CDS 45.0%
AGACTGTGTGATAGAGCTTG+TGG + chr5.1:17140823-17140842 None:intergenic 45.0%
ATCAGCTCAAACGCACGTTT+GGG + chr5.1:17140432-17140451 None:intergenic 45.0%
TAGAACTTGTGACCTCAGTC+AGG + chr5.1:17140548-17140567 None:intergenic 45.0%
TTTGCCGCAGAAACAAACAG+AGG + chr5.1:17140404-17140423 None:intergenic 45.0%
!! TTGGCCTCTGTTTGTTTCTG+CGG - chr5.1:17140397-17140416 MS.gene88356:intron 45.0%
CAGCGACGAAGGAAGGAATT+CGG + chr5.1:17140151-17140170 None:intergenic 50.0%
CATCAGCTCAAACGCACGTT+TGG + chr5.1:17140433-17140452 None:intergenic 50.0%
GAGTACGCAAAGGAGATTGG+TGG + chr5.1:17140126-17140145 None:intergenic 50.0%
GGTACACAAATGCTGGCAGA+GGG + chr5.1:17140960-17140979 None:intergenic 50.0%
GTCTACACTGAGGCTCTGTT+TGG + chr5.1:17140890-17140909 None:intergenic 50.0%
! ATAAACCCAAAAGTGCGGCG+CGG - chr5.1:17140597-17140616 MS.gene88356:intron 50.0%
! GAATTCGGAGGAGTACGCAA+AGG + chr5.1:17140136-17140155 None:intergenic 50.0%
! GAGGAGTACGCAAAGGAGAT+TGG + chr5.1:17140129-17140148 None:intergenic 50.0%
CGACGAAGGAAGGAATTCGG+AGG + chr5.1:17140148-17140167 None:intergenic 55.0%
CGGTACACAAATGCTGGCAG+AGG + chr5.1:17140961-17140980 None:intergenic 55.0%
GTCGCTTCAGCGAAGAGATC+AGG - chr5.1:17140170-17140189 MS.gene88356:CDS 55.0%
GAAGCGACAGCGACGAAGGA+AGG + chr5.1:17140158-17140177 None:intergenic 60.0%
! AAGCTACCGCGCCGCACTTT+TGG + chr5.1:17140606-17140625 None:intergenic 60.0%
! AGCTACCGCGCCGCACTTTT+GGG + chr5.1:17140605-17140624 None:intergenic 60.0%
CGCTGAAGCGACAGCGACGA+AGG + chr5.1:17140162-17140181 None:intergenic 65.0%
! GCGGCTCGGGGAAGCGGTTT+GGG - chr5.1:17140055-17140074 MS.gene88356:CDS 70.0%
! GGCGGCTCGGGGAAGCGGTT+TGG - chr5.1:17140054-17140073 MS.gene88356:CDS 75.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 17140052 17141226 17140052 ID=MS.gene88356
chr5.1 mRNA 17140052 17141226 17140052 ID=MS.gene88356.t1;Parent=MS.gene88356
chr5.1 exon 17141005 17141226 17141005 ID=MS.gene88356.t1.exon1;Parent=MS.gene88356.t1
chr5.1 CDS 17141005 17141226 17141005 ID=cds.MS.gene88356.t1;Parent=MS.gene88356.t1
chr5.1 exon 17140052 17140228 17140052 ID=MS.gene88356.t1.exon2;Parent=MS.gene88356.t1
chr5.1 CDS 17140052 17140228 17140052 ID=cds.MS.gene88356.t1;Parent=MS.gene88356.t1
Gene Sequence

>MS.gene88356

ATGGCGGCTCGGGGAAGCGGTTTGGGTCTGATGAATTACCTAAGAGTTGAGGTTCGTGCTTCTGCTCTCAACCACCAATCTCCTTTGCGTACTCCTCCGAATTCCTTCCTTCGTCGCTGTCGCTTCAGCGAAGAGATCAGGAGAACTTTTCTCGACAAATCGGAGGTCACTGATCGCGTCATTTCCTGCGTCAAAAAATTTGACAATGTTGATCCTTCTAAGGTTTTCACTTCCATCCTTAACCTAATTTCTTCATTTATTTTCATTTATTTTACAAATTTCTATTTTCAATCTTTAATTTAGGTCATATTTAGTATCTTAATTAATGACCAATTCTTGTAAGTTTTGGCCTCTGTTTGTTTCTGCGGCAAAACAAGCCCAAACGTGCGTTTGAGCTGATGCTACTAGTTGTAGCTTCTTAAAAATCAAGTTTATTTGATAGAAAACCAAAACACTGATCCAAACACAACATAAAAGGATAAAGTTGTTGTCACCTGACTGAGGTCACAAGTTCTAGTCCTCGAAATAGGGTAAGACTATGTACAATAAACCCAAAAGTGCGGCGCGGTAGCTTTATTGTATGAAAGCTAAGTGAAGACTATATTTTGGAGGATTAAGACCATGTTTGAAAAGACAACTTATTTAAGCGTTTTGTGTAAGCTATTTCTTTAACAAAAAATAAAATAAAATCAAACTGTTTTCATAAGCTATCCTAGGATAGCTTACGGAAATAAGTTTAAACATTTACCTACATGTCATAAGCTGTTTCCACAAGCTCTATCACACAGTCTCACTCACAATTTTCTTTTCCAGTAAATAAGCTCAGATAAACAATCCAAACAGAGCCTCAGTGTAGACTTTTACTTTACCTTTAATGTGCTTGTGTCAGTTTGGAGAATTTAAATCCCTCTGCCAGCATTTGTGTACCGTTATATTATATCTTTGGCTTATGTTATTTTGATAATAACACAGAACCTGTGCTTCTTTGCTTTTGTCAGGTTACCCCAACTGCTCATTTCTATGATGACCTTGGATTGGATAGTTTAGACGCCATAGAGATCTGTATGGATCTTGATACAGAGTTTGGATTTGAGATTCCTGAAAATGAAGTAGACAAGATCGTCTCCGTTAATCAAGCTGTTGATTTCATTGCATCTCATCCTCAGGCGAAGTAG
Protein sequence

>MS.gene88356.t1

MAARGSGLGLMNYLRVEVRASALNHQSPLRTPPNSFLRRCRFSEEIRRTFLDKSEVTDRVISCVKKFDNVDPSKVTPTAHFYDDLGLDSLDAIEICMDLDTEFGFEIPENEVDKIVSVNQAVDFIASHPQAK