AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene82126

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene82126.t1 MTR_7g080390 74.242 132 32 1 1 132 1 130 3.08e-66 197
MS.gene82126.t1 MTR_7g080760 44.538 119 58 2 18 131 3 118 7.23e-27 97.1
MS.gene82126.t1 MTR_4g133928 36.290 124 66 2 18 132 4 123 8.76e-18 73.9
MS.gene82126.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.gene82126.t1 AT1G65290 62.121 132 44 3 1 132 1 126 1.46e-48 152
MS.gene82126.t1 AT2G44620 43.939 132 62 5 1 131 1 121 6.23e-26 94.7
MS.gene82126.t1 AT5G47630 38.750 80 49 0 53 132 48 127 2.53e-13 62.8
MS.gene82126.t1 AT5G47630 38.750 80 49 0 53 132 48 127 2.53e-13 62.8
MS.gene82126.t1 AT5G47630 38.750 80 49 0 53 132 48 127 2.53e-13 62.8
MS.gene82126.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 5.2:+17274778 MS.gene82126:CDS
GGCGGCTCGGGGAAGCGGTT+TGG 0.290380 5.2:+17274777 MS.gene82126:CDS
TGACAATGTTGATCCTTCTA+AGG 0.294761 5.2:+17274975 MS.gene82126:CDS
ATGGATCTTGATACAGAGTT+TGG 0.311699 5.2:+17275839 MS.gene82126:CDS
ATCAACAACAATGGCGGCTC+GGG 0.345626 5.2:+17274765 None:intergenic
AAGCACGAACCTCAACTCTT+AGG 0.392906 5.2:-17274813 None:intergenic
GAAATCAACAGCTTGATTAA+CGG 0.409809 5.2:-17275900 None:intergenic
ATGGAAGTGAAAACCTTAGA+AGG 0.418506 5.2:-17274988 None:intergenic
TTTCTATGATGACCTTGGAT+TGG 0.444522 5.2:+17275790 MS.gene82126:CDS
AAGATCCATACAGATCTCTA+TGG 0.455448 5.2:-17275825 None:intergenic
GTCGCTTCAGCGAAGAGATC+AGG 0.457126 5.2:+17274893 MS.gene82126:CDS
ACAATGGCGGCTCGGGGAAG+CGG 0.466910 5.2:+17274772 None:intergenic
GAGGAGTACGCAAAGGAGAT+TGG 0.466971 5.2:-17274849 None:intergenic
CAGCGACGAAGGAAGGAATT+CGG 0.467889 5.2:-17274871 None:intergenic
CATCATAGAAATGAGCAGTT+GGG 0.468087 5.2:-17275778 None:intergenic
TTTCATTGCATCTCATCCTC+AGG 0.474149 5.2:+17275919 MS.gene82126:CDS
GCTCATTTCTATGATGACCT+TGG 0.491539 5.2:+17275785 MS.gene82126:CDS
TATCAACAACAATGGCGGCT+CGG 0.529312 5.2:+17274764 None:intergenic
TCATCATAGAAATGAGCAGT+TGG 0.537450 5.2:-17275779 None:intergenic
GAAGCGACAGCGACGAAGGA+AGG 0.545017 5.2:-17274878 None:intergenic
CGCTGAAGCGACAGCGACGA+AGG 0.552195 5.2:-17274882 None:intergenic
AGACGCCATAGAGATCTGTA+TGG 0.564613 5.2:+17275820 MS.gene82126:CDS
ATCATAGAAATGAGCAGTTG+GGG 0.586456 5.2:-17275777 None:intergenic
GATGAATTACCTAAGAGTTG+AGG 0.587013 5.2:+17274804 MS.gene82126:CDS
CGTCTAAACTATCCAATCCA+AGG 0.606873 5.2:-17275802 None:intergenic
GAGTACGCAAAGGAGATTGG+TGG 0.606939 5.2:-17274846 None:intergenic
TCAACAACAATGGCGGCTCG+GGG 0.630083 5.2:+17274766 None:intergenic
GAATTCGGAGGAGTACGCAA+AGG 0.668596 5.2:-17274856 None:intergenic
AGGTTAGACTACTTCGCCTG+AGG 0.672291 5.2:-17275935 None:intergenic
CGACGAAGGAAGGAATTCGG+AGG 0.686278 5.2:-17274868 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGAAAATAAATGAAGAAATT+AGG - chr5.2:17275020-17275039 None:intergenic 15.0%
!!! CTATTTTCAATCTTTAATTT+AGG + chr5.2:17275056-17275075 MS.gene82126:intron 15.0%
!! AAGCCAAAGATATAATATAA+CGG - chr5.2:17275704-17275723 None:intergenic 20.0%
!! TAAATGAAGAAATTAGGTTA+AGG - chr5.2:17275014-17275033 None:intergenic 20.0%
! GTACCGTTATATTATATCTT+TGG + chr5.2:17275698-17275717 MS.gene82126:intron 25.0%
!! ATAAGTTGTCTTTTCAAACA+TGG - chr5.2:17275397-17275416 None:intergenic 25.0%
!! TTATCCTTTTATGTTGTGTT+TGG - chr5.2:17275237-17275256 None:intergenic 25.0%
GAAATCAACAGCTTGATTAA+CGG - chr5.2:17275903-17275922 None:intergenic 30.0%
GTTTATCTGAGCTTATTTAC+TGG - chr5.2:17275587-17275606 None:intergenic 30.0%
TAAAGTAAAAGTCTACACTG+AGG - chr5.2:17275623-17275642 None:intergenic 30.0%
TGAAGAAATTAGGTTAAGGA+TGG - chr5.2:17275010-17275029 None:intergenic 30.0%
TGATCCAAACACAACATAAA+AGG + chr5.2:17275230-17275249 MS.gene82126:intron 30.0%
! ATCTTGTCTACTTCATTTTC+AGG - chr5.2:17275875-17275894 None:intergenic 30.0%
! GCTAAGTGAAGACTATATTT+TGG + chr5.2:17275361-17275380 MS.gene82126:intron 30.0%
! TGACCAATTCTTGTAAGTTT+TGG + chr5.2:17275101-17275120 MS.gene82126:intron 30.0%
!! AAGTGAAGACTATATTTTGG+AGG + chr5.2:17275364-17275383 MS.gene82126:intron 30.0%
!!! ATTGTCAAATTTTTTGACGC+AGG - chr5.2:17274962-17274981 None:intergenic 30.0%
AACTGACACAAGCACATTAA+AGG - chr5.2:17275646-17275665 None:intergenic 35.0%
AAGATCCATACAGATCTCTA+TGG - chr5.2:17275828-17275847 None:intergenic 35.0%
AGGCCAAAACTTACAAGAAT+TGG - chr5.2:17275107-17275126 None:intergenic 35.0%
ATATAACGGTACACAAATGC+TGG - chr5.2:17275690-17275709 None:intergenic 35.0%
ATCATAGAAATGAGCAGTTG+GGG - chr5.2:17275780-17275799 None:intergenic 35.0%
ATGGAAGTGAAAACCTTAGA+AGG - chr5.2:17274991-17275010 None:intergenic 35.0%
ATGGATCTTGATACAGAGTT+TGG + chr5.2:17275839-17275858 MS.gene82126:CDS 35.0%
CATCATAGAAATGAGCAGTT+GGG - chr5.2:17275781-17275800 None:intergenic 35.0%
GATGAATTACCTAAGAGTTG+AGG + chr5.2:17274804-17274823 MS.gene82126:CDS 35.0%
GTACAATAAACCCAAAAGTG+CGG + chr5.2:17275315-17275334 MS.gene82126:intron 35.0%
TCATCATAGAAATGAGCAGT+TGG - chr5.2:17275782-17275801 None:intergenic 35.0%
TGACAATGTTGATCCTTCTA+AGG + chr5.2:17274975-17274994 MS.gene82126:CDS 35.0%
TTAATGTGCTTGTGTCAGTT+TGG + chr5.2:17275646-17275665 MS.gene82126:intron 35.0%
TTATTTCCGTAAGCTATCCT+AGG - chr5.2:17275489-17275508 None:intergenic 35.0%
TTTCTATGATGACCTTGGAT+TGG + chr5.2:17275790-17275809 MS.gene82126:CDS 35.0%
! AAGTTCTAGTCCTCGAAATA+GGG + chr5.2:17275283-17275302 MS.gene82126:intron 35.0%
! CTGTTTTCATAAGCTATCCT+AGG + chr5.2:17275469-17275488 MS.gene82126:intron 35.0%
! GAGAACTTTTCTCGACAAAT+CGG + chr5.2:17274915-17274934 MS.gene82126:CDS 35.0%
! TTGTGTTTGGATCAGTGTTT+TGG - chr5.2:17275224-17275243 None:intergenic 35.0%
AGCTATCCTAGGATAGCTTA+CGG + chr5.2:17275480-17275499 MS.gene82126:intron 40.0%
CGTCTAAACTATCCAATCCA+AGG - chr5.2:17275805-17275824 None:intergenic 40.0%
GCTCATTTCTATGATGACCT+TGG + chr5.2:17275785-17275804 MS.gene82126:CDS 40.0%
GGAAACAGCTTATGACATGT+AGG - chr5.2:17275525-17275544 None:intergenic 40.0%
TTTCATTGCATCTCATCCTC+AGG + chr5.2:17275919-17275938 MS.gene82126:CDS 40.0%
! AACTTTTCTCGACAAATCGG+AGG + chr5.2:17274918-17274937 MS.gene82126:CDS 40.0%
! CAAGTTCTAGTCCTCGAAAT+AGG + chr5.2:17275282-17275301 MS.gene82126:intron 40.0%
! CATAGTCTTACCCTATTTCG+AGG - chr5.2:17275296-17275315 None:intergenic 40.0%
! TGACAAAAGCAAAGAAGCAC+AGG - chr5.2:17275752-17275771 None:intergenic 40.0%
!! TGTGCTTCTTTGCTTTTGTC+AGG + chr5.2:17275751-17275770 MS.gene82126:intron 40.0%
AAGCACGAACCTCAACTCTT+AGG - chr5.2:17274816-17274835 None:intergenic 45.0%
AAGTTGTTGTCACCTGACTG+AGG + chr5.2:17275256-17275275 MS.gene82126:intron 45.0%
AGACGCCATAGAGATCTGTA+TGG + chr5.2:17275820-17275839 MS.gene82126:CDS 45.0%
AGACTGTGTGATAGAGCTTG+TGG - chr5.2:17275546-17275565 None:intergenic 45.0%
ATCAGCTCAAACGCACGTTT+GGG - chr5.2:17275155-17275174 None:intergenic 45.0%
TAGAACTTGTGACCTCAGTC+AGG - chr5.2:17275271-17275290 None:intergenic 45.0%
TTTGCCGCAGAAACAAACAG+AGG - chr5.2:17275127-17275146 None:intergenic 45.0%
!! TTGGCCTCTGTTTGTTTCTG+CGG + chr5.2:17275120-17275139 MS.gene82126:intron 45.0%
CAGCGACGAAGGAAGGAATT+CGG - chr5.2:17274874-17274893 None:intergenic 50.0%
CATCAGCTCAAACGCACGTT+TGG - chr5.2:17275156-17275175 None:intergenic 50.0%
GAGTACGCAAAGGAGATTGG+TGG - chr5.2:17274849-17274868 None:intergenic 50.0%
GGTACACAAATGCTGGCAGA+GGG - chr5.2:17275683-17275702 None:intergenic 50.0%
GTCTACACTGAGGCTCTGTT+TGG - chr5.2:17275613-17275632 None:intergenic 50.0%
! ATAAACCCAAAAGTGCGGCG+CGG + chr5.2:17275320-17275339 MS.gene82126:intron 50.0%
! GAATTCGGAGGAGTACGCAA+AGG - chr5.2:17274859-17274878 None:intergenic 50.0%
! GAGGAGTACGCAAAGGAGAT+TGG - chr5.2:17274852-17274871 None:intergenic 50.0%
CGACGAAGGAAGGAATTCGG+AGG - chr5.2:17274871-17274890 None:intergenic 55.0%
CGGTACACAAATGCTGGCAG+AGG - chr5.2:17275684-17275703 None:intergenic 55.0%
GTCGCTTCAGCGAAGAGATC+AGG + chr5.2:17274893-17274912 MS.gene82126:CDS 55.0%
GAAGCGACAGCGACGAAGGA+AGG - chr5.2:17274881-17274900 None:intergenic 60.0%
! AAGCTACCGCGCCGCACTTT+TGG - chr5.2:17275329-17275348 None:intergenic 60.0%
! AGCTACCGCGCCGCACTTTT+GGG - chr5.2:17275328-17275347 None:intergenic 60.0%
CGCTGAAGCGACAGCGACGA+AGG - chr5.2:17274885-17274904 None:intergenic 65.0%
! GCGGCTCGGGGAAGCGGTTT+GGG + chr5.2:17274778-17274797 MS.gene82126:CDS 70.0%
! GGCGGCTCGGGGAAGCGGTT+TGG + chr5.2:17274777-17274796 MS.gene82126:CDS 75.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 17274775 17275949 17274775 ID=MS.gene82126
chr5.2 mRNA 17274775 17275949 17274775 ID=MS.gene82126.t1;Parent=MS.gene82126
chr5.2 exon 17274775 17274996 17274775 ID=MS.gene82126.t1.exon1;Parent=MS.gene82126.t1
chr5.2 CDS 17274775 17274996 17274775 ID=cds.MS.gene82126.t1;Parent=MS.gene82126.t1
chr5.2 exon 17275773 17275949 17275773 ID=MS.gene82126.t1.exon2;Parent=MS.gene82126.t1
chr5.2 CDS 17275773 17275949 17275773 ID=cds.MS.gene82126.t1;Parent=MS.gene82126.t1
Gene Sequence

>MS.gene82126

ATGGCGGCTCGGGGAAGCGGTTTGGGTCTGATGAATTACCTAAGAGTTGAGGTTCGTGCTTCTGCTCTCAACCACCAATCTCCTTTGCGTACTCCTCCGAATTCCTTCCTTCGTCGCTGTCGCTTCAGCGAAGAGATCAGGAGAACTTTTCTCGACAAATCGGAGGTCACTGATCGCGTCATTTCCTGCGTCAAAAAATTTGACAATGTTGATCCTTCTAAGGTTTTCACTTCCATCCTTAACCTAATTTCTTCATTTATTTTCATTTATTTTACAAATTTCTATTTTCAATCTTTAATTTAGGTCATATTTAGTATCTTAATTAATGACCAATTCTTGTAAGTTTTGGCCTCTGTTTGTTTCTGCGGCAAAACAAGCCCAAACGTGCGTTTGAGCTGATGCTACTAGTTGTAGCTTCTTAAAAATCAAGTTTATTTGATAGAAAACCAAAACACTGATCCAAACACAACATAAAAGGATAAAGTTGTTGTCACCTGACTGAGGTCACAAGTTCTAGTCCTCGAAATAGGGTAAGACTATGTACAATAAACCCAAAAGTGCGGCGCGGTAGCTTTATTGTATGAAAGCTAAGTGAAGACTATATTTTGGAGGATTAAGACCATGTTTGAAAAGACAACTTATTTAAGCGTTTTGTGTAAGCTATTTCTTTAACAAAAAATAAAATAAAATCAAACTGTTTTCATAAGCTATCCTAGGATAGCTTACGGAAATAAGTTTAAACATTTACCTACATGTCATAAGCTGTTTCCACAAGCTCTATCACACAGTCTCACTCACAATTTTCTTTTCCAGTAAATAAGCTCAGATAAACAATCCAAACAGAGCCTCAGTGTAGACTTTTACTTTACCTTTAATGTGCTTGTGTCAGTTTGGAGAATTTAAATCCCTCTGCCAGCATTTGTGTACCGTTATATTATATCTTTGGCTTATGTTATTTTGATAATAACACAGAACCTGTGCTTCTTTGCTTTTGTCAGGTTACCCCAACTGCTCATTTCTATGATGACCTTGGATTGGATAGTTTAGACGCCATAGAGATCTGTATGGATCTTGATACAGAGTTTGGATTTGAGATTCCTGAAAATGAAGTAGACAAGATCGTCTCCGTTAATCAAGCTGTTGATTTCATTGCATCTCATCCTCAGGCGAAGTAG
Protein sequence

>MS.gene82126.t1

MAARGSGLGLMNYLRVEVRASALNHQSPLRTPPNSFLRRCRFSEEIRRTFLDKSEVTDRVISCVKKFDNVDPSKVTPTAHFYDDLGLDSLDAIEICMDLDTEFGFEIPENEVDKIVSVNQAVDFIASHPQAK