AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene00312

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene00312.t1 MTR_8g040560 63.504 137 50 0 90 226 744 880 4.19e-53 184
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene00312.t1 AT3G12280 57.463 134 53 2 90 223 735 864 3.94e-42 152
MS.gene00312.t1 AT3G12280 57.463 134 53 2 90 223 735 864 3.95e-42 152

Find 43 sgRNAs with CRISPR-Local

Find 100 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCTGTAGAGCCACTGCTTT+TGG 0.167941 2.1:+56416038 MS.gene00312:CDS
TGTTGGGTGAAGTCAGAATT+AGG 0.300929 2.1:+56415599 MS.gene00312:CDS
GCTCGGAACATTGAGTTAAA+TGG 0.362997 2.1:-56415283 None:intergenic
TTTCTCCTAGATCATTATGT+TGG 0.375290 2.1:+56415582 MS.gene00312:intron
CGTATTTGTTGATTGGTCAT+TGG 0.390654 2.1:+56415933 MS.gene00312:CDS
TTGATAGCGTATTTGTTGAT+TGG 0.394006 2.1:+56415926 MS.gene00312:CDS
TTCATAGTGAATTTGTTGAT+TGG 0.400565 2.1:+56415130 MS.gene00312:CDS
GGCCATTGGCACGCATGGAC+TGG 0.408428 2.1:+56415151 MS.gene00312:CDS
TTCTCCTAGATCATTATGTT+GGG 0.426785 2.1:+56415583 MS.gene00312:intron
TCAGCATCTGGTAAAACAAT+AGG 0.429570 2.1:+56415967 MS.gene00312:CDS
GCATGCCAGGACTCAGCATC+TGG 0.452002 2.1:+56415955 MS.gene00312:CDS
TCTGTCGATGAAGAATTATC+TGG 0.461758 2.1:-56415681 None:intergenic
CTGTGGTTGCATTCTATAGC+TGG 0.465799 2.1:-56415091 None:intergenic
GCACGCATGGACTGGCCATA+TGG 0.467219 2.1:+56415159 MS.gene00312:CDS
TGATTGGTCATTGGCATGCC+AGG 0.482497 2.1:+56415942 MS.gene00312:CDS
TTATAACCTCCTTAAAAGTC+AGG 0.483868 2.1:-56415864 None:intergenic
AGGAGCGTGGTTGAAATGCT+AGG 0.502214 2.1:+56415619 MS.gene00312:CDS
CTATAATCTCTCGATAAGTT+AGG 0.506862 2.1:-56415068 None:intergenic
GGCCAGTCCATGCGTGCCAA+TGG 0.508439 2.1:-56415153 None:intergenic
AGAATTATCTCACAAGATAG+AGG 0.512835 2.1:+56414848 MS.gene00312:CDS
TAGGGTTATCTCAGCAGATA+AGG 0.519446 2.1:+56415638 MS.gene00312:CDS
TGATTGGCCATTGGCACGCA+TGG 0.524304 2.1:+56415146 MS.gene00312:CDS
CTATGCATGTGTCTCTCCAA+TGG 0.533378 2.1:+56415370 MS.gene00312:CDS
TATGCATGTGTCTCTCCAAT+GGG 0.533482 2.1:+56415371 MS.gene00312:CDS
ACCTCCTTAAAAGTCAGGCT+CGG 0.541985 2.1:-56415859 None:intergenic
AGGGTTATCTCAGCAGATAA+GGG 0.550907 2.1:+56415639 MS.gene00312:CDS
CAAAAGCAGTGGCTCTACAG+AGG 0.551471 2.1:-56416037 None:intergenic
TGAATTTGTTGATTGGCCAT+TGG 0.561366 2.1:+56415137 MS.gene00312:CDS
AAGCCTTTCTGTTATGTCTG+TGG 0.562011 2.1:+56415328 MS.gene00312:CDS
GGAGCGTGGTTGAAATGCTA+GGG 0.571354 2.1:+56415620 MS.gene00312:CDS
CTTCCACAGACATAACAGAA+AGG 0.576860 2.1:-56415331 None:intergenic
TTTGGAACTTGGCGTTGAAG+GGG 0.582633 2.1:+56416056 MS.gene00312:CDS
AAAAGCAGTGGCTCTACAGA+GGG 0.599947 2.1:-56416036 None:intergenic
AGTACCTCGGATGATCCCAT+TGG 0.608676 2.1:-56415386 None:intergenic
TTGCTTCTGTGCAGTCACAA+AGG 0.625881 2.1:+56415747 MS.gene00312:CDS
CTCTCCAATGGGATCATCCG+AGG 0.629524 2.1:+56415382 MS.gene00312:CDS
AAAACTCGTGGGTTGCATTG+CGG 0.634698 2.1:-56415904 None:intergenic
ACGCCAAGTTCCAAAAGCAG+TGG 0.646767 2.1:-56416048 None:intergenic
AGAAGCAACACACAATGATG+TGG 0.674691 2.1:-56415732 None:intergenic
CAATGATGTGGTCAATATGA+CGG 0.678181 2.1:-56415720 None:intergenic
TGAAGTCAGAATTAGGAGCG+TGG 0.693278 2.1:+56415606 MS.gene00312:CDS
AGAGACACATGCATAGTGTG+TGG 0.766106 2.1:-56415363 None:intergenic
AAAACTGGTGGTGTGCACTG+TGG 0.770580 2.1:-56415108 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATAAAAAGAATGAGAAAA+CGG - chr2.1:56415041-56415060 None:intergenic 15.0%
!!! TATAGATAATTTTATGTCAA+AGG + chr2.1:56415535-56415554 MS.gene00312:intron 15.0%
!! AATTAGGTCAATATGAAAAT+CGG - chr2.1:56414940-56414959 None:intergenic 20.0%
!! TTGTTTAAATTGAGAAACTT+GGG + chr2.1:56415773-56415792 MS.gene00312:intron 20.0%
!! TTTGTTTAAATTGAGAAACT+TGG + chr2.1:56415772-56415791 MS.gene00312:intron 20.0%
!!! CTTGTGAAAGTTAATATTTT+AGG - chr2.1:56415311-56415330 None:intergenic 20.0%
! ACAAATTCACTATGAAAAAC+TGG - chr2.1:56415126-56415145 None:intergenic 25.0%
! ACCAACTAGAAATAGTATAT+GGG - chr2.1:56415451-56415470 None:intergenic 25.0%
! ATACTAAAAACATAGTACCT+CGG - chr2.1:56415402-56415421 None:intergenic 25.0%
!! CTCATTCTTTTTATATTGCA+GGG + chr2.1:56415045-56415064 MS.gene00312:intron 25.0%
!! TATGTCAAAGGTTTACATTT+TGG + chr2.1:56415547-56415566 MS.gene00312:intron 25.0%
!! TCTCATTCTTTTTATATTGC+AGG + chr2.1:56415044-56415063 MS.gene00312:intron 25.0%
!!! GTGAAAGTTAATATTTTAGG+AGG - chr2.1:56415308-56415327 None:intergenic 25.0%
!!! TCAGTTTTAGTAATTTGAGA+GGG + chr2.1:56414999-56415018 MS.gene00312:intron 25.0%
!!! TTCAGTTTTAGTAATTTGAG+AGG + chr2.1:56414998-56415017 MS.gene00312:intron 25.0%
!!! TTCATAGTGAATTTGTTGAT+TGG + chr2.1:56415130-56415149 MS.gene00312:CDS 25.0%
AAAGAATAGGATGAGAAAAC+GGG - chr2.1:56415823-56415842 None:intergenic 30.0%
AATTCACTATGAAAAACTGG+TGG - chr2.1:56415123-56415142 None:intergenic 30.0%
AGAATTATCTCACAAGATAG+AGG + chr2.1:56414848-56414867 MS.gene00312:CDS 30.0%
CAATTGAAAGTAACTTAGCT+AGG - chr2.1:56415199-56415218 None:intergenic 30.0%
CACCAACTAGAAATAGTATA+TGG - chr2.1:56415452-56415471 None:intergenic 30.0%
CTATAATCTCTCGATAAGTT+AGG - chr2.1:56415071-56415090 None:intergenic 30.0%
GAAAGAATAGGATGAGAAAA+CGG - chr2.1:56415824-56415843 None:intergenic 30.0%
GGAAGCAACACAAAATAATT+AGG - chr2.1:56414956-56414975 None:intergenic 30.0%
TGAAATCTGCAAGAAAGAAT+AGG - chr2.1:56415836-56415855 None:intergenic 30.0%
TGAGTTAAATGGTCTGTAAA+TGG - chr2.1:56415275-56415294 None:intergenic 30.0%
TTATAACCTCCTTAAAAGTC+AGG - chr2.1:56415867-56415886 None:intergenic 30.0%
TTCTCCTAGATCATTATGTT+GGG + chr2.1:56415583-56415602 MS.gene00312:intron 30.0%
TTTCTCCTAGATCATTATGT+TGG + chr2.1:56415582-56415601 MS.gene00312:intron 30.0%
!! AGTTAATATTTTAGGAGGCT+CGG - chr2.1:56415303-56415322 None:intergenic 30.0%
!! TTGATAGCGTATTTGTTGAT+TGG + chr2.1:56415926-56415945 MS.gene00312:CDS 30.0%
!!! ATTATTTTGTGTTGCTTCCA+TGG + chr2.1:56414957-56414976 MS.gene00312:intron 30.0%
!!! GTTTTTAGTATGTCTTTCCT+TGG + chr2.1:56415411-56415430 MS.gene00312:intron 30.0%
AATACGCTATCAAAAACTCG+TGG - chr2.1:56415919-56415938 None:intergenic 35.0%
ACAAGATAGAGGTGAATGTA+GGG + chr2.1:56414859-56414878 MS.gene00312:intron 35.0%
ATACGCTATCAAAAACTCGT+GGG - chr2.1:56415918-56415937 None:intergenic 35.0%
ATGAAAATCGGAGAAGAGAT+GGG - chr2.1:56414928-56414947 None:intergenic 35.0%
CAATGATGTGGTCAATATGA+CGG - chr2.1:56415723-56415742 None:intergenic 35.0%
GCAAATGAACAAGTACCATA+TGG - chr2.1:56415177-56415196 None:intergenic 35.0%
TATGAAAATCGGAGAAGAGA+TGG - chr2.1:56414929-56414948 None:intergenic 35.0%
TCAGCATCTGGTAAAACAAT+AGG + chr2.1:56415967-56415986 MS.gene00312:CDS 35.0%
TCTGTCGATGAAGAATTATC+TGG - chr2.1:56415684-56415703 None:intergenic 35.0%
TTCACCCAACATAATGATCT+AGG - chr2.1:56415590-56415609 None:intergenic 35.0%
! CGTATTTGTTGATTGGTCAT+TGG + chr2.1:56415933-56415952 MS.gene00312:CDS 35.0%
!! GCCCATATACTATTTCTAGT+TGG + chr2.1:56415447-56415466 MS.gene00312:intron 35.0%
!! TGAATTTGTTGATTGGCCAT+TGG + chr2.1:56415137-56415156 MS.gene00312:CDS 35.0%
AAATGGAGCACACAAGTCAA+TGG - chr2.1:56415258-56415277 None:intergenic 40.0%
AAGCCTTTCTGTTATGTCTG+TGG + chr2.1:56415328-56415347 MS.gene00312:CDS 40.0%
AGAAGCAACACACAATGATG+TGG - chr2.1:56415735-56415754 None:intergenic 40.0%
AGGGTTATCTCAGCAGATAA+GGG + chr2.1:56415639-56415658 MS.gene00312:CDS 40.0%
CAAGATAGAGGTGAATGTAG+GGG + chr2.1:56414860-56414879 MS.gene00312:intron 40.0%
CACAAGATAGAGGTGAATGT+AGG + chr2.1:56414858-56414877 MS.gene00312:intron 40.0%
CTTCCACAGACATAACAGAA+AGG - chr2.1:56415334-56415353 None:intergenic 40.0%
CTTGCATAGAAATGGAAGTC+AGG - chr2.1:56415226-56415245 None:intergenic 40.0%
GCTCGGAACATTGAGTTAAA+TGG - chr2.1:56415286-56415305 None:intergenic 40.0%
GGGCAAAATGAAAAAGTCCA+AGG - chr2.1:56415431-56415450 None:intergenic 40.0%
TAGGGTTATCTCAGCAGATA+AGG + chr2.1:56415638-56415657 MS.gene00312:CDS 40.0%
TATGCATGTGTCTCTCCAAT+GGG + chr2.1:56415371-56415390 MS.gene00312:CDS 40.0%
TGAAAATCGGAGAAGAGATG+GGG - chr2.1:56414927-56414946 None:intergenic 40.0%
TGTTGGGTGAAGTCAGAATT+AGG + chr2.1:56415599-56415618 MS.gene00312:CDS 40.0%
TTGCAGGACTTGCATAGAAA+TGG - chr2.1:56415234-56415253 None:intergenic 40.0%
! AAAACCGAGCCTGACTTTTA+AGG + chr2.1:56415855-56415874 MS.gene00312:CDS 40.0%
!!! TTTTGGAACTTGGCGTTGAA+GGG + chr2.1:56416055-56416074 MS.gene00312:CDS 40.0%
ACCTCCTTAAAAGTCAGGCT+CGG - chr2.1:56415862-56415881 None:intergenic 45.0%
AGAGACACATGCATAGTGTG+TGG - chr2.1:56415366-56415385 None:intergenic 45.0%
CTATGCATGTGTCTCTCCAA+TGG + chr2.1:56415370-56415389 MS.gene00312:CDS 45.0%
CTGTGGTTGCATTCTATAGC+TGG - chr2.1:56415094-56415113 None:intergenic 45.0%
GAGAAACCTTTGCAACTCCA+TGG - chr2.1:56414977-56414996 None:intergenic 45.0%
GGATGAGAAAACGGGAATTG+AGG - chr2.1:56415815-56415834 None:intergenic 45.0%
GTTGGTGCAAAACACTCAAC+TGG + chr2.1:56415465-56415484 MS.gene00312:intron 45.0%
TGAAGTCAGAATTAGGAGCG+TGG + chr2.1:56415606-56415625 MS.gene00312:CDS 45.0%
TTGCTTCCATGGAGTTGCAA+AGG + chr2.1:56414968-56414987 MS.gene00312:intron 45.0%
TTGCTTCTGTGCAGTCACAA+AGG + chr2.1:56415747-56415766 MS.gene00312:CDS 45.0%
! AAAACTCGTGGGTTGCATTG+CGG - chr2.1:56415907-56415926 None:intergenic 45.0%
! AAAAGCAGTGGCTCTACAGA+GGG - chr2.1:56416039-56416058 None:intergenic 45.0%
! ACACTCAACTGGCATTTTCC+TGG + chr2.1:56415476-56415495 MS.gene00312:intron 45.0%
! TTTGGAACTTGGCGTTGAAG+GGG + chr2.1:56416056-56416075 MS.gene00312:CDS 45.0%
! TTTTACCAGATGCTGAGTCC+TGG - chr2.1:56415963-56415982 None:intergenic 45.0%
!! CACACAAGTCAATGGATTGC+AGG - chr2.1:56415250-56415269 None:intergenic 45.0%
!!! CTTTTGGAACTTGGCGTTGA+AGG + chr2.1:56416054-56416073 MS.gene00312:CDS 45.0%
ACGCCAAGTTCCAAAAGCAG+TGG - chr2.1:56416051-56416070 None:intergenic 50.0%
AGAGATGGGGCTGTTGAGTT+AGG - chr2.1:56414914-56414933 None:intergenic 50.0%
AGTACCTCGGATGATCCCAT+TGG - chr2.1:56415389-56415408 None:intergenic 50.0%
GCTGTTGAGTTAGGATTCGC+TGG - chr2.1:56414905-56414924 None:intergenic 50.0%
GGAGCGTGGTTGAAATGCTA+GGG + chr2.1:56415620-56415639 MS.gene00312:CDS 50.0%
! AAAACTGGTGGTGTGCACTG+TGG - chr2.1:56415111-56415130 None:intergenic 50.0%
! AGGAGCGTGGTTGAAATGCT+AGG + chr2.1:56415619-56415638 MS.gene00312:CDS 50.0%
! CAAAAGCAGTGGCTCTACAG+AGG - chr2.1:56416040-56416059 None:intergenic 50.0%
! CCTCGTGTACTTCTTTTGCC+AGG - chr2.1:56415497-56415516 None:intergenic 50.0%
! CCTGGCAAAAGAAGTACACG+AGG + chr2.1:56415494-56415513 MS.gene00312:intron 50.0%
! CTCTGTAGAGCCACTGCTTT+TGG + chr2.1:56416038-56416057 MS.gene00312:CDS 50.0%
! TGATTGGTCATTGGCATGCC+AGG + chr2.1:56415942-56415961 MS.gene00312:CDS 50.0%
!! ACCGAGCCTGACTTTTAAGG+AGG + chr2.1:56415858-56415877 MS.gene00312:CDS 50.0%
!!! GAGCCACTGCTTTTGGAACT+TGG + chr2.1:56416045-56416064 MS.gene00312:CDS 50.0%
CTCTCCAATGGGATCATCCG+AGG + chr2.1:56415382-56415401 MS.gene00312:CDS 55.0%
! TGATTGGCCATTGGCACGCA+TGG + chr2.1:56415146-56415165 MS.gene00312:CDS 55.0%
GCATGCCAGGACTCAGCATC+TGG + chr2.1:56415955-56415974 MS.gene00312:CDS 60.0%
!! GCACGCATGGACTGGCCATA+TGG + chr2.1:56415159-56415178 MS.gene00312:CDS 60.0%
GGCCAGTCCATGCGTGCCAA+TGG - chr2.1:56415156-56415175 None:intergenic 65.0%
GGCCATTGGCACGCATGGAC+TGG + chr2.1:56415151-56415170 MS.gene00312:CDS 65.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 56414834 56416089 56414834 ID=MS.gene00312
chr2.1 mRNA 56414834 56416089 56414834 ID=MS.gene00312.t1;Parent=MS.gene00312
chr2.1 exon 56414834 56414869 56414834 ID=MS.gene00312.t1.exon1;Parent=MS.gene00312.t1
chr2.1 CDS 56414834 56414869 56414834 ID=cds.MS.gene00312.t1;Parent=MS.gene00312.t1
chr2.1 exon 56415066 56415180 56415066 ID=MS.gene00312.t1.exon2;Parent=MS.gene00312.t1
chr2.1 CDS 56415066 56415180 56415066 ID=cds.MS.gene00312.t1;Parent=MS.gene00312.t1
chr2.1 exon 56415282 56415403 56415282 ID=MS.gene00312.t1.exon3;Parent=MS.gene00312.t1
chr2.1 CDS 56415282 56415403 56415282 ID=cds.MS.gene00312.t1;Parent=MS.gene00312.t1
chr2.1 exon 56415592 56415768 56415592 ID=MS.gene00312.t1.exon4;Parent=MS.gene00312.t1
chr2.1 CDS 56415592 56415768 56415592 ID=cds.MS.gene00312.t1;Parent=MS.gene00312.t1
chr2.1 exon 56415850 56416089 56415850 ID=MS.gene00312.t1.exon5;Parent=MS.gene00312.t1
chr2.1 CDS 56415850 56416089 56415850 ID=cds.MS.gene00312.t1;Parent=MS.gene00312.t1
Gene Sequence

>MS.gene00312

ATGGCTGAAAAGCTAGAATTATCTCACAAGATAGAGGTGAATGTAGGGGAGAATGTATACTATATTTTCCAGCGAATCCTAACTCAACAGCCCCATCTCTTCTCCGATTTTCATATTGACCTAATTATTTTGTGTTGCTTCCATGGAGTTGCAAAGGTTTCTCTTTCAGTTTTAGTAATTTGAGAGGGTAATGTTCTACAGTTGCCGTTTTCTCATTCTTTTTATATTGCAGGGCCTAACTTATCGAGAGATTATAGCCAGCTATAGAATGCAACCACAGTGCACACCACCAGTTTTTCATAGTGAATTTGTTGATTGGCCATTGGCACGCATGGACTGGCCATATGGTACTTGTTCATTTGCCTAGCTAAGTTACTTTCAATTGTTTTCCTGACTTCCATTTCTATGCAAGTCCTGCAATCCATTGACTTGTGTGCTCCATTTACAGACCATTTAACTCAATGTTCCGAGCCTCCTAAAATATTAACTTTCACAAGCCTTTCTGTTATGTCTGTGGAAGAAGTGTCTGCCACACACTATGCATGTGTCTCTCCAATGGGATCATCCGAGGTACTATGTTTTTAGTATGTCTTTCCTTGGACTTTTTCATTTTGCCCATATACTATTTCTAGTTGGTGCAAAACACTCAACTGGCATTTTCCTGGCAAAAGAAGTACACGAGGCTGTGACTCTCGTGCGCTTATAGATAATTTTATGTCAAAGGTTTACATTTTGGTTGCATTTCTTATTTCTCCTAGATCATTATGTTGGGTGAAGTCAGAATTAGGAGCGTGGTTGAAATGCTAGGGTTATCTCAGCAGATAAGGGAGAATGTATACAGTCTGTTCCAGATAATTCTTCATCGACAGACATCTCTCTTCTTCAACCGTCATATTGACCACATCATTGTGTGTTGCTTCTGTGCAGTCACAAAGGTTTTTGTTTAAATTGAGAAACTTGGGAGTATAAGTTTATGTGCCTCAATTCCCGTTTTCTCATCCTATTCTTTCTTGCAGATTTCAAAACCGAGCCTGACTTTTAAGGAGGTTATAAGCATCTATAAGAAGCAACCGCAATGCAACCCACGAGTTTTTGATAGCGTATTTGTTGATTGGTCATTGGCATGCCAGGACTCAGCATCTGGTAAAACAATAGGAAATGAGCATCTCGACATTATTACATTCTGCAATGATATATTTGTTCCCTCTGTAGAGCCACTGCTTTTGGAACTTGGCGTTGAAGGGGAGAAGCTGTGA
Protein sequence

>MS.gene00312.t1

MAEKLELSHKIEGLTYREIIASYRMQPQCTPPVFHSEFVDWPLARMDWPYDHLTQCSEPPKILTFTSLSVMSVEEVSATHYACVSPMGSSEIIMLGEVRIRSVVEMLGLSQQIRENVYSLFQIILHRQTSLFFNRHIDHIIVCCFCAVTKISKPSLTFKEVISIYKKQPQCNPRVFDSVFVDWSLACQDSASGKTIGNEHLDIITFCNDIFVPSVEPLLLELGVEGEKL