AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene80846

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene80846.t1 MTR_6g084470 97.006 167 5 0 1 167 1 167 1.75e-109 309
MS.gene80846.t1 MTR_8g104210 63.218 174 50 7 3 167 4 172 8.57e-60 183
MS.gene80846.t1 MTR_8g104210 64.815 162 44 6 14 167 7 163 9.30e-58 178
MS.gene80846.t1 MTR_6g018430 42.286 175 86 6 1 167 1 168 1.48e-29 106
MS.gene80846.t1 MTR_1g110760 43.478 161 72 5 21 167 5 160 7.39e-22 86.7
MS.gene80846.t1 MTR_4g087400 37.267 161 67 7 1 153 1 135 2.15e-11 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene80846.t1 AT5G16110 47.283 184 74 8 1 167 67 244 7.98e-33 117
MS.gene80846.t1 AT3G02555 46.328 177 70 6 1 167 1 162 3.69e-32 113
MS.gene80846.t1 AT3G02555 46.328 177 70 6 1 167 1 162 3.69e-32 113
MS.gene80846.t1 AT1G68490 39.773 176 87 5 5 167 14 183 4.15e-26 98.2
MS.gene80846.t1 AT1G13390 37.912 182 91 9 1 167 2 176 1.11e-19 81.6
MS.gene80846.t1 AT1G13390 37.912 182 91 9 1 167 2 176 1.11e-19 81.6

Find 43 sgRNAs with CRISPR-Local

Find 84 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCAAAATTTGTGGCCTAAA+AGG 0.213971 6.2:-82905843 None:intergenic
AGACCAAATCGAATAGGTTT+AGG 0.280991 6.2:-82905798 None:intergenic
GTGGCCTAAAAGGTCTGATA+TGG 0.310493 6.2:-82905833 None:intergenic
CAATCAGAGGTTGAAGATTC+AGG 0.321864 6.2:+82905990 MS.gene80846:CDS
AGGTTGAAGATTCAGGTGTT+AGG 0.346664 6.2:+82905997 MS.gene80846:CDS
GTGATCCAAGATGAGCAATT+TGG 0.348409 6.2:+82906574 MS.gene80846:CDS
TGCCCTAAACCTATTCGATT+TGG 0.350421 6.2:+82905795 MS.gene80846:CDS
GAAGAGGGTGCCATGGAAAA+TGG 0.350699 6.2:-82906625 None:intergenic
AGGTGTTAGGGAAGATCTTC+TGG 0.363892 6.2:+82906010 MS.gene80846:CDS
CATTGCCAAATTGCTCATCT+TGG 0.383707 6.2:-82906579 None:intergenic
GACCAAATCGAATAGGTTTA+GGG 0.384037 6.2:-82905797 None:intergenic
TCAAAATACCTCAAAATTTG+TGG 0.413455 6.2:-82905852 None:intergenic
TTTGTGGATCTCCACCTAGC+AGG 0.415060 6.2:+82906539 MS.gene80846:CDS
TGTGCTCCAATGAAGAAGTT+TGG 0.423704 6.2:+82906670 MS.gene80846:CDS
GGTTGAAGATTCAGGTGTTA+GGG 0.425014 6.2:+82905998 MS.gene80846:CDS
AGAGATGAGGATGGAATCTC+TGG 0.450122 6.2:+82905770 MS.gene80846:CDS
CAAGCTGCAGTGAGGATTGA+AGG 0.451676 6.2:+82906700 MS.gene80846:CDS
GTGTGACCAAACTTCTTCAT+TGG 0.453010 6.2:-82906676 None:intergenic
TTTGGCAATGGCAATGGTCA+TGG 0.463708 6.2:+82906592 MS.gene80846:CDS
TTCATCAGACCAAATCGAAT+AGG 0.466136 6.2:-82905804 None:intergenic
AATTGCTCATCTTGGATCAC+AGG 0.470456 6.2:-82906571 None:intergenic
TTCTGGATATCATTCTCCCC+AGG 0.482476 6.2:+82906027 MS.gene80846:CDS
TTGTGGATCTCCACCTAGCA+GGG 0.495640 6.2:+82906540 MS.gene80846:CDS
TTGATTGTCTCAATAGGGAT+AGG 0.498503 6.2:+82906725 MS.gene80846:CDS
CATCTCTTCACAGCTTCTCA+TGG 0.503294 6.2:-82905754 None:intergenic
TCACCATCTTCCTCAGCTAG+AGG 0.554835 6.2:+82906646 MS.gene80846:CDS
TTGGCAATGGCAATGGTCAT+GGG 0.558206 6.2:+82906593 MS.gene80846:CDS
GAGCAATTTGGCAATGGCAA+TGG 0.565272 6.2:+82906586 MS.gene80846:CDS
CAACCTCTAGCTGAGGAAGA+TGG 0.571591 6.2:-82906649 None:intergenic
AAGCTGTGAAGAGATGAGGA+TGG 0.577435 6.2:+82905761 MS.gene80846:CDS
AGCTGAGGAAGATGGTGAAG+AGG 0.581033 6.2:-82906641 None:intergenic
AGATGGTGAAGAGGGTGCCA+TGG 0.590017 6.2:-82906632 None:intergenic
ACAGGGTTTGAAGCCCTGCT+AGG 0.591659 6.2:-82906553 None:intergenic
ATTGCTCATCTTGGATCACA+GGG 0.597595 6.2:-82906570 None:intergenic
CAAGATGAGCAATTTGGCAA+TGG 0.600303 6.2:+82906580 MS.gene80846:CDS
GGGTTTGAAGCCCTGCTAGG+TGG 0.606726 6.2:-82906550 None:intergenic
GCTGAGGAAGATGGTGAAGA+GGG 0.607679 6.2:-82906640 None:intergenic
TCTGGATATCATTCTCCCCA+GGG 0.618574 6.2:+82906028 MS.gene80846:CDS
AATAATCAGCTATCAATCAG+AGG 0.653539 6.2:+82905977 MS.gene80846:intron
TGGAGCACAACCTCTAGCTG+AGG 0.654183 6.2:-82906656 None:intergenic
TGAGAAGCTGTGAAGAGATG+AGG 0.665577 6.2:+82905757 MS.gene80846:CDS
GTCACACACAAGCTGCAGTG+AGG 0.704483 6.2:+82906692 MS.gene80846:CDS
TGTGAAAAGATGAATCACTG+TGG 0.839717 6.2:+82905714 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATAATTAAATATAAAATT+AGG - chr6.2:82905882-82905901 None:intergenic 0.0%
!! AATTGCTATAATGAAAAATT+TGG + chr6.2:82906484-82906503 MS.gene80846:CDS 15.0%
!! ATTGCTATAATGAAAAATTT+GGG + chr6.2:82906485-82906504 MS.gene80846:CDS 15.0%
!!! TCTTAATTTTTCATGAAAAA+AGG + chr6.2:82906068-82906087 MS.gene80846:intron 15.0%
!! TTGCTATAATGAAAAATTTG+GGG + chr6.2:82906486-82906505 MS.gene80846:CDS 20.0%
!!! TCAAATAAAATACCATGTTT+TGG + chr6.2:82906103-82906122 MS.gene80846:intron 20.0%
! ATGGTTAATGAACTTCATTA+AGG + chr6.2:82906226-82906245 MS.gene80846:intron 25.0%
! CCGAAATAAAGTAATAAAGT+CGG + chr6.2:82906308-82906327 MS.gene80846:intron 25.0%
! TCAAAATACCTCAAAATTTG+TGG - chr6.2:82905855-82905874 None:intergenic 25.0%
! TGTCTAATCTAACAATGATT+TGG + chr6.2:82906449-82906468 MS.gene80846:intron 25.0%
!! CCGACTTTATTACTTTATTT+CGG - chr6.2:82906311-82906330 None:intergenic 25.0%
AATAATCAGCTATCAATCAG+AGG + chr6.2:82905977-82905996 MS.gene80846:intron 30.0%
ATGATTGATGCACAATTACT+AGG + chr6.2:82906128-82906147 MS.gene80846:intron 30.0%
CATCAATCATAACCAAAACA+TGG - chr6.2:82906118-82906137 None:intergenic 30.0%
TGATTGATGCACAATTACTA+GGG + chr6.2:82906129-82906148 MS.gene80846:intron 30.0%
TTGACATAGAAATTTACCCT+GGG - chr6.2:82906047-82906066 None:intergenic 30.0%
TTTGACATAGAAATTTACCC+TGG - chr6.2:82906048-82906067 None:intergenic 30.0%
! ATCACTTGATTTGACTCAAA+TGG + chr6.2:82906207-82906226 MS.gene80846:intron 30.0%
! TTTCGGCCATTACTTTATTT+CGG - chr6.2:82906294-82906313 None:intergenic 30.0%
!! AACAATGATTTGGATTTTGC+AGG + chr6.2:82906459-82906478 MS.gene80846:intron 30.0%
!! ACAATGATTTGGATTTTGCA+GGG + chr6.2:82906460-82906479 MS.gene80846:intron 30.0%
!! GAATTTTAGTCCATTTTCCA+TGG + chr6.2:82906615-82906634 MS.gene80846:CDS 30.0%
!!! AAGGTTTTGATTGTCTCAAT+AGG + chr6.2:82906719-82906738 MS.gene80846:CDS 30.0%
!!! AGGTTTTGATTGTCTCAATA+GGG + chr6.2:82906720-82906739 MS.gene80846:CDS 30.0%
AGACCAAATCGAATAGGTTT+AGG - chr6.2:82905801-82905820 None:intergenic 35.0%
ATTCTCATGGAAAATCGTCA+TGG - chr6.2:82906361-82906380 None:intergenic 35.0%
CTCAAAATTTGTGGCCTAAA+AGG - chr6.2:82905846-82905865 None:intergenic 35.0%
GAAAAATTTGGGGAGCAATT+AGG + chr6.2:82906496-82906515 MS.gene80846:CDS 35.0%
GACCAAATCGAATAGGTTTA+GGG - chr6.2:82905800-82905819 None:intergenic 35.0%
TGACATAGAAATTTACCCTG+GGG - chr6.2:82906046-82906065 None:intergenic 35.0%
TTCATCAGACCAAATCGAAT+AGG - chr6.2:82905807-82905826 None:intergenic 35.0%
TTGATTGTCTCAATAGGGAT+AGG + chr6.2:82906725-82906744 MS.gene80846:CDS 35.0%
! ATTACTTTATTTCGGCCAGA+CGG - chr6.2:82906286-82906305 None:intergenic 35.0%
! CTTTTAGGCCACAAATTTTG+AGG + chr6.2:82905844-82905863 MS.gene80846:CDS 35.0%
! GAAACCATATCAGACCTTTT+AGG + chr6.2:82905829-82905848 MS.gene80846:CDS 35.0%
! GATTTTCCATGAGAATCAGA+GGG + chr6.2:82906365-82906384 MS.gene80846:intron 35.0%
AATTGCTCATCTTGGATCAC+AGG - chr6.2:82906574-82906593 None:intergenic 40.0%
AGGTTGAAGATTCAGGTGTT+AGG + chr6.2:82905997-82906016 MS.gene80846:CDS 40.0%
ATTGCTCATCTTGGATCACA+GGG - chr6.2:82906573-82906592 None:intergenic 40.0%
CAAGATGAGCAATTTGGCAA+TGG + chr6.2:82906580-82906599 MS.gene80846:CDS 40.0%
CAATCAGAGGTTGAAGATTC+AGG + chr6.2:82905990-82906009 MS.gene80846:CDS 40.0%
CATTGCCAAATTGCTCATCT+TGG - chr6.2:82906582-82906601 None:intergenic 40.0%
GATCCACAAAAAAATGGTGG+TGG - chr6.2:82906529-82906548 None:intergenic 40.0%
GGAAAATCGTCATGGTAATC+AGG - chr6.2:82906353-82906372 None:intergenic 40.0%
GGAGATCCACAAAAAAATGG+TGG - chr6.2:82906532-82906551 None:intergenic 40.0%
GGTGGAGATCCACAAAAAAA+TGG - chr6.2:82906535-82906554 None:intergenic 40.0%
GGTTGAAGATTCAGGTGTTA+GGG + chr6.2:82905998-82906017 MS.gene80846:CDS 40.0%
GTCTGGCCGAAATAAAGTAA+TGG + chr6.2:82906285-82906304 MS.gene80846:intron 40.0%
GTGATCCAAGATGAGCAATT+TGG + chr6.2:82906574-82906593 MS.gene80846:CDS 40.0%
GTGTGACCAAACTTCTTCAT+TGG - chr6.2:82906679-82906698 None:intergenic 40.0%
TAGGCTGGAAAAAAGAAGCT+TGG + chr6.2:82906390-82906409 MS.gene80846:intron 40.0%
TGCCCTAAACCTATTCGATT+TGG + chr6.2:82905795-82905814 MS.gene80846:CDS 40.0%
TGTGCTCCAATGAAGAAGTT+TGG + chr6.2:82906670-82906689 MS.gene80846:CDS 40.0%
! CGATTTTCCATGAGAATCAG+AGG + chr6.2:82906364-82906383 MS.gene80846:intron 40.0%
!!! TCACCACCACCATTTTTTTG+TGG + chr6.2:82906523-82906542 MS.gene80846:CDS 40.0%
AAGCTGTGAAGAGATGAGGA+TGG + chr6.2:82905761-82905780 MS.gene80846:CDS 45.0%
AGAGATGAGGATGGAATCTC+TGG + chr6.2:82905770-82905789 MS.gene80846:CDS 45.0%
AGGTGTTAGGGAAGATCTTC+TGG + chr6.2:82906010-82906029 MS.gene80846:CDS 45.0%
CATCTCTTCACAGCTTCTCA+TGG - chr6.2:82905757-82905776 None:intergenic 45.0%
CCATGAGAATCAGAGGGTTT+AGG + chr6.2:82906371-82906390 MS.gene80846:intron 45.0%
CCTAAACCCTCTGATTCTCA+TGG - chr6.2:82906374-82906393 None:intergenic 45.0%
GAGCAATTTGGCAATGGCAA+TGG + chr6.2:82906586-82906605 MS.gene80846:CDS 45.0%
GTGGCCTAAAAGGTCTGATA+TGG - chr6.2:82905836-82905855 None:intergenic 45.0%
TCTGGATATCATTCTCCCCA+GGG + chr6.2:82906028-82906047 MS.gene80846:CDS 45.0%
TGAGAAGCTGTGAAGAGATG+AGG + chr6.2:82905757-82905776 MS.gene80846:CDS 45.0%
TTCTGGATATCATTCTCCCC+AGG + chr6.2:82906027-82906046 MS.gene80846:CDS 45.0%
TTGGCAATGGCAATGGTCAT+GGG + chr6.2:82906593-82906612 MS.gene80846:CDS 45.0%
TTTGGCAATGGCAATGGTCA+TGG + chr6.2:82906592-82906611 MS.gene80846:CDS 45.0%
!! TTGCCGACTTTATTACCGTC+TGG + chr6.2:82906268-82906287 MS.gene80846:intron 45.0%
AGCTGAGGAAGATGGTGAAG+AGG - chr6.2:82906644-82906663 None:intergenic 50.0%
CAACCTCTAGCTGAGGAAGA+TGG - chr6.2:82906652-82906671 None:intergenic 50.0%
CAAGCTGCAGTGAGGATTGA+AGG + chr6.2:82906700-82906719 MS.gene80846:CDS 50.0%
CGGCCAGACGGTAATAAAGT+CGG - chr6.2:82906274-82906293 None:intergenic 50.0%
GAGAATCAGAGGGTTTAGGC+TGG + chr6.2:82906375-82906394 MS.gene80846:intron 50.0%
GCTGAGGAAGATGGTGAAGA+GGG - chr6.2:82906643-82906662 None:intergenic 50.0%
TCACCATCTTCCTCAGCTAG+AGG + chr6.2:82906646-82906665 MS.gene80846:CDS 50.0%
TTGTGGATCTCCACCTAGCA+GGG + chr6.2:82906540-82906559 MS.gene80846:CDS 50.0%
TTTGTGGATCTCCACCTAGC+AGG + chr6.2:82906539-82906558 MS.gene80846:CDS 50.0%
!! GAAGAGGGTGCCATGGAAAA+TGG - chr6.2:82906628-82906647 None:intergenic 50.0%
GTCACACACAAGCTGCAGTG+AGG + chr6.2:82906692-82906711 MS.gene80846:CDS 55.0%
TGGAGCACAACCTCTAGCTG+AGG - chr6.2:82906659-82906678 None:intergenic 55.0%
! ACAGGGTTTGAAGCCCTGCT+AGG - chr6.2:82906556-82906575 None:intergenic 55.0%
!! AGATGGTGAAGAGGGTGCCA+TGG - chr6.2:82906635-82906654 None:intergenic 55.0%
! GGGTTTGAAGCCCTGCTAGG+TGG - chr6.2:82906553-82906572 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 82905723 82906777 82905723 ID=MS.gene80846
chr6.2 mRNA 82905723 82906777 82905723 ID=MS.gene80846.t1;Parent=MS.gene80846
chr6.2 exon 82905723 82905865 82905723 ID=MS.gene80846.t1.exon1;Parent=MS.gene80846.t1
chr6.2 CDS 82905723 82905865 82905723 ID=cds.MS.gene80846.t1;Parent=MS.gene80846.t1
chr6.2 exon 82905986 82906049 82905986 ID=MS.gene80846.t1.exon2;Parent=MS.gene80846.t1
chr6.2 CDS 82905986 82906049 82905986 ID=cds.MS.gene80846.t1;Parent=MS.gene80846.t1
chr6.2 exon 82906481 82906777 82906481 ID=MS.gene80846.t1.exon3;Parent=MS.gene80846.t1
chr6.2 CDS 82906481 82906777 82906481 ID=cds.MS.gene80846.t1;Parent=MS.gene80846.t1
Gene Sequence

>MS.gene80846

ATGAATCACTGTGGCTATCAACAGAAGAACGCCATGAGAAGCTGTGAAGAGATGAGGATGGAATCTCTGGTTTGCCCTAAACCTATTCGATTTGGTCTGATGAACAGAAACCATATCAGACCTTTTAGGCCACAAATTTTGAGGTATTTTGATTTTCCTAATTTTATATTTAATTATTTTACACAATTGTTTTGTCAATTTTTTCAATCAATTTGTTTATGTAAAAATTCTAACTTTATTGTTTGTTCTTATGAAATAATCAGCTATCAATCAGAGGTTGAAGATTCAGGTGTTAGGGAAGATCTTCTGGATATCATTCTCCCCAGGGTAAATTTCTATGTCAAATCTTAATTTTTCATGAAAAAAGGTTAATACATGTTTCAAATAAAATACCATGTTTTGGTTATGATTGATGCACAATTACTAGGGAATTGTGAACATAACAACATCTATGATCTATTTCATCAAGTTTAGATGTTGTTGAATCACTTGATTTGACTCAAATGGTTAATGAACTTCATTAAGGACGAATCATTTAAGATCATTTGCCGACTTTATTACCGTCTGGCCGAAATAAAGTAATGGCCGAAATAAAGTAATAAAGTCGGCAAATGATCTTAAATGATTCCTGATTACCATGACGATTTTCCATGAGAATCAGAGGGTTTAGGCTGGAAAAAAGAAGCTTGGATGTTGTTGTTAATTGTTGATTGAAGTTAAATATGATGTCTAATCTAACAATGATTTGGATTTTGCAGGGAAATTGCTATAATGAAAAATTTGGGGAGCAATTAGGATCATCACCACCACCATTTTTTTGTGGATCTCCACCTAGCAGGGCTTCAAACCCTGTGATCCAAGATGAGCAATTTGGCAATGGCAATGGTCATGGGAATTTTAGTCCATTTTCCATGGCACCCTCTTCACCATCTTCCTCAGCTAGAGGTTGTGCTCCAATGAAGAAGTTTGGTCACACACAAGCTGCAGTGAGGATTGAAGGTTTTGATTGTCTCAATAGGGATAGGAGCAACTGCAGCATTTCAGCTGTTGCATAA
Protein sequence

>MS.gene80846.t1

MNHCGYQQKNAMRSCEEMRMESLVCPKPIRFGLMNRNHIRPFRPQILSYQSEVEDSGVREDLLDIILPRGNCYNEKFGEQLGSSPPPFFCGSPPSRASNPVIQDEQFGNGNGHGNFSPFSMAPSSPSSSARGCAPMKKFGHTQAAVRIEGFDCLNRDRSNCSISAVA