AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0201160

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0201160 MtrunA17_Chr6g0482481 89.516 124 11 1 1 122 64 187 9.36e-75 219
Msa0201160 MtrunA17_Chr6g0482501 91.803 122 10 0 2 123 410 531 1.73e-73 227
Msa0201160 MtrunA17_Chr6g0482371 58.678 121 22 1 3 123 31 123 5.24e-39 127
Msa0201160 MtrunA17_Chr6g0482341 88.235 68 7 1 2 69 25 91 2.07e-34 114
Msa0201160 MtrunA17_Chr1g0172551 85.366 41 6 0 2 42 112 152 1.73e-17 73.6
Msa0201160 MtrunA17_Chr1g0184201 41.860 86 50 0 29 114 551 636 8.40e-11 57.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0201160 AT3G54710.1 42.857 84 48 0 31 114 391 474 1.42e-16 74.7
Msa0201160 AT2G31270.1 41.667 84 49 0 31 114 475 558 1.51e-15 72.0

Find 26 sgRNAs with CRISPR-Local

Find 102 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAATGTAGATCAACATTATT+TGG 0.136054 2_1:-22082636 Msa0201160:CDS
TGAAGAACAGATTGAGATTT+TGG 0.155235 2_1:-22082379 Msa0201160:CDS
TGCAAGAAGTTGGTTTCTTC+TGG 0.236168 2_1:-22082333 Msa0201160:CDS
TCCTTCATCATTGGTGGAAC+TGG 0.334230 2_1:-22082597 Msa0201160:CDS
TGTCAAGAATGTGTTAGATT+TGG 0.348709 2_1:-22081984 Msa0201160:CDS
AACTTCTTGCAAAGCCAGTC+TGG 0.423623 2_1:+22082345 None:intergenic
TGCTCTGCGCATGCATTGCT+TGG 0.426565 2_1:-22081883 Msa0201160:three_prime_UTR
TGGAAAAGATTGTGCCAGAC+TGG 0.443412 2_1:-22082359 Msa0201160:CDS
ATGCATTGCTTGGTAATTGT+TGG 0.459448 2_1:-22081873 Msa0201160:three_prime_UTR
ATTTGGACTCAGTTCGATCA+AGG 0.466721 2_1:-22081967 Msa0201160:CDS
ACCAGTTCCACCAATGATGA+AGG 0.470890 2_1:+22082596 None:intergenic
AGACTGGCTTTGCAAGAAGT+TGG 0.482751 2_1:-22082343 Msa0201160:CDS
ACCAGCTATAGTGAATATCT+TGG 0.485587 2_1:-22081816 Msa0201160:three_prime_UTR
GGATGACAATCCTTCATCAT+TGG 0.498702 2_1:-22082606 Msa0201160:CDS
GCCAAGATATTCACTATAGC+TGG 0.499828 2_1:+22081815 None:intergenic
AAGAACTTCAATCACAAAAG+AGG 0.504889 2_1:-22082540 Msa0201160:CDS
ACATATTGTATTCTCTGTCT+CGG 0.509486 2_1:-22081729 Msa0201160:three_prime_UTR
CTTCTGGAGACACTATGTAC+TGG 0.511897 2_1:-22082317 Msa0201160:intron
ACATATGAGACTGTAAGAAC+AGG 0.517455 2_1:-22081788 Msa0201160:three_prime_UTR
TCAACATTATTTGGATGCAT+CGG 0.535332 2_1:-22082627 Msa0201160:CDS
TGACAATCCTTCATCATTGG+TGG 0.549380 2_1:-22082603 Msa0201160:CDS
GCTATAGTGAATATCTTGGC+TGG 0.565487 2_1:-22081812 Msa0201160:three_prime_UTR
ATTGCTTGGTAATTGTTGGT+TGG 0.578319 2_1:-22081869 Msa0201160:three_prime_UTR
GAACAAAGGAGATGAGTGAA+AGG 0.614241 2_1:-22081930 Msa0201160:exon
ATGCAGGTAGATGAGAACCT+TGG 0.622672 2_1:-22082677 Msa0201160:CDS
CTTCTCAGCAATGTGAACAA+AGG 0.638405 2_1:-22081944 Msa0201160:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ACAAAATTTTACATATATCA+TGG - chr2_1:22082204-22082223 Msa0201160:intron 15.0%
!!! ACAAAATTTTACATATATCA+TGG - chr2_1:22082204-22082223 Msa0201160:intron 15.0%
!! TTTCTTAGTAATAAACATTC+TGG - chr2_1:22081943-22081962 Msa0201160:CDS 20.0%
!! GTTTAATCATAAATACAAAG+AGG + chr2_1:22082090-22082109 None:intergenic 20.0%
!!! TGAAATTTCATGTTTTAAGT+TGG + chr2_1:22082163-22082182 None:intergenic 20.0%
!! TACATATATCATGGATATAA+TGG - chr2_1:22082213-22082232 Msa0201160:intron 20.0%
!! TTTCTTAGTAATAAACATTC+TGG - chr2_1:22081943-22081962 Msa0201160:CDS 20.0%
!! GTTTAATCATAAATACAAAG+AGG + chr2_1:22082090-22082109 None:intergenic 20.0%
!!! TGAAATTTCATGTTTTAAGT+TGG + chr2_1:22082163-22082182 None:intergenic 20.0%
!! TACATATATCATGGATATAA+TGG - chr2_1:22082213-22082232 Msa0201160:intron 20.0%
! CAATGTAGATCAACATTATT+TGG - chr2_1:22081741-22081760 Msa0201160:three_prime_UTR 25.0%
! CAATGTAGATCAACATTATT+TGG - chr2_1:22081741-22081760 Msa0201160:three_prime_UTR 25.0%
!! TTTTCTGAAAAGAATGACCA+AGG + chr2_1:22081720-22081739 None:intergenic 30.0%
TCAACATTATTTGGATGCAT+CGG - chr2_1:22081750-22081769 Msa0201160:three_prime_UTR 30.0%
AAGAACTTCAATCACAAAAG+AGG - chr2_1:22081837-22081856 Msa0201160:three_prime_UTR 30.0%
! TGAAGAACAGATTGAGATTT+TGG - chr2_1:22081998-22082017 Msa0201160:intron 30.0%
ACATGAAATTTCAGTCTCTT+CGG - chr2_1:22082170-22082189 Msa0201160:intron 30.0%
AAAAGAACTTAGCAGTTTGA+TGG - chr2_1:22082239-22082258 Msa0201160:intron 30.0%
! AGCAGAACTTTTGATGTTAT+TGG - chr2_1:22082265-22082284 Msa0201160:intron 30.0%
TGTCAAGAATGTGTTAGATT+TGG - chr2_1:22082393-22082412 Msa0201160:intron 30.0%
ACATATTGTATTCTCTGTCT+CGG - chr2_1:22082648-22082667 Msa0201160:CDS 30.0%
!! TTTTCTGAAAAGAATGACCA+AGG + chr2_1:22081720-22081739 None:intergenic 30.0%
TCAACATTATTTGGATGCAT+CGG - chr2_1:22081750-22081769 Msa0201160:three_prime_UTR 30.0%
AAGAACTTCAATCACAAAAG+AGG - chr2_1:22081837-22081856 Msa0201160:three_prime_UTR 30.0%
! TGAAGAACAGATTGAGATTT+TGG - chr2_1:22081998-22082017 Msa0201160:intron 30.0%
ACATGAAATTTCAGTCTCTT+CGG - chr2_1:22082170-22082189 Msa0201160:intron 30.0%
AAAAGAACTTAGCAGTTTGA+TGG - chr2_1:22082239-22082258 Msa0201160:intron 30.0%
! AGCAGAACTTTTGATGTTAT+TGG - chr2_1:22082265-22082284 Msa0201160:intron 30.0%
TGTCAAGAATGTGTTAGATT+TGG - chr2_1:22082393-22082412 Msa0201160:intron 30.0%
ACATATTGTATTCTCTGTCT+CGG - chr2_1:22082648-22082667 Msa0201160:CDS 30.0%
!! ACAGAGTATCAGTCTCTTTT+AGG - chr2_1:22082120-22082139 Msa0201160:intron 35.0%
!! CAGAGTATCAGTCTCTTTTA+GGG - chr2_1:22082121-22082140 Msa0201160:intron 35.0%
CATGAAATTTCAGTCTCTTC+GGG - chr2_1:22082171-22082190 Msa0201160:intron 35.0%
!! TACTTTGAAGTCAACACCAA+GGG + chr2_1:22082314-22082333 None:intergenic 35.0%
CTTGACACTGCAAATATAAC+AGG + chr2_1:22082380-22082399 None:intergenic 35.0%
! ATGCATTGCTTGGTAATTGT+TGG - chr2_1:22082504-22082523 Msa0201160:CDS 35.0%
! ATTGCTTGGTAATTGTTGGT+TGG - chr2_1:22082508-22082527 Msa0201160:CDS 35.0%
ACCAGCTATAGTGAATATCT+TGG - chr2_1:22082561-22082580 Msa0201160:CDS 35.0%
ACATATGAGACTGTAAGAAC+AGG - chr2_1:22082589-22082608 Msa0201160:CDS 35.0%
!! ACAGAGTATCAGTCTCTTTT+AGG - chr2_1:22082120-22082139 Msa0201160:intron 35.0%
!! CAGAGTATCAGTCTCTTTTA+GGG - chr2_1:22082121-22082140 Msa0201160:intron 35.0%
CATGAAATTTCAGTCTCTTC+GGG - chr2_1:22082171-22082190 Msa0201160:intron 35.0%
!! TACTTTGAAGTCAACACCAA+GGG + chr2_1:22082314-22082333 None:intergenic 35.0%
CTTGACACTGCAAATATAAC+AGG + chr2_1:22082380-22082399 None:intergenic 35.0%
! ATGCATTGCTTGGTAATTGT+TGG - chr2_1:22082504-22082523 Msa0201160:CDS 35.0%
! ATTGCTTGGTAATTGTTGGT+TGG - chr2_1:22082508-22082527 Msa0201160:CDS 35.0%
ACCAGCTATAGTGAATATCT+TGG - chr2_1:22082561-22082580 Msa0201160:CDS 35.0%
ACATATGAGACTGTAAGAAC+AGG - chr2_1:22082589-22082608 Msa0201160:CDS 35.0%
GGATGACAATCCTTCATCAT+TGG - chr2_1:22081771-22081790 Msa0201160:three_prime_UTR 40.0%
TGACAATCCTTCATCATTGG+TGG - chr2_1:22081774-22081793 Msa0201160:three_prime_UTR 40.0%
ACTAATCTTGTCCTCCCAAT+AGG - chr2_1:22081969-22081988 Msa0201160:CDS 40.0%
GTTCTTCAGCTTCTCCTATT+GGG + chr2_1:22081986-22082005 None:intergenic 40.0%
TGTTCTTCAGCTTCTCCTAT+TGG + chr2_1:22081987-22082006 None:intergenic 40.0%
! TGCAAGAAGTTGGTTTCTTC+TGG - chr2_1:22082044-22082063 Msa0201160:intron 40.0%
CTGATACTCTGTAAGCATGA+AGG + chr2_1:22082112-22082131 None:intergenic 40.0%
TATTGTGAGCCAAAATCCCT+TGG - chr2_1:22082295-22082314 Msa0201160:intron 40.0%
! AAGTCAACACCAAGGGATTT+TGG + chr2_1:22082307-22082326 None:intergenic 40.0%
!! CTACTTTGAAGTCAACACCA+AGG + chr2_1:22082315-22082334 None:intergenic 40.0%
ATTTGGACTCAGTTCGATCA+AGG - chr2_1:22082410-22082429 Msa0201160:intron 40.0%
CTTCTCAGCAATGTGAACAA+AGG - chr2_1:22082433-22082452 Msa0201160:intron 40.0%
GAACAAAGGAGATGAGTGAA+AGG - chr2_1:22082447-22082466 Msa0201160:intron 40.0%
GCCAAGATATTCACTATAGC+TGG + chr2_1:22082565-22082584 None:intergenic 40.0%
GCTATAGTGAATATCTTGGC+TGG - chr2_1:22082565-22082584 Msa0201160:CDS 40.0%
!!! CTCTGTCTCGGTTTCTTTTT+TGG - chr2_1:22082660-22082679 Msa0201160:CDS 40.0%
GGATGACAATCCTTCATCAT+TGG - chr2_1:22081771-22081790 Msa0201160:three_prime_UTR 40.0%
TGACAATCCTTCATCATTGG+TGG - chr2_1:22081774-22081793 Msa0201160:three_prime_UTR 40.0%
ACTAATCTTGTCCTCCCAAT+AGG - chr2_1:22081969-22081988 Msa0201160:CDS 40.0%
GTTCTTCAGCTTCTCCTATT+GGG + chr2_1:22081986-22082005 None:intergenic 40.0%
TGTTCTTCAGCTTCTCCTAT+TGG + chr2_1:22081987-22082006 None:intergenic 40.0%
! TGCAAGAAGTTGGTTTCTTC+TGG - chr2_1:22082044-22082063 Msa0201160:intron 40.0%
CTGATACTCTGTAAGCATGA+AGG + chr2_1:22082112-22082131 None:intergenic 40.0%
TATTGTGAGCCAAAATCCCT+TGG - chr2_1:22082295-22082314 Msa0201160:intron 40.0%
! AAGTCAACACCAAGGGATTT+TGG + chr2_1:22082307-22082326 None:intergenic 40.0%
!! CTACTTTGAAGTCAACACCA+AGG + chr2_1:22082315-22082334 None:intergenic 40.0%
ATTTGGACTCAGTTCGATCA+AGG - chr2_1:22082410-22082429 Msa0201160:intron 40.0%
CTTCTCAGCAATGTGAACAA+AGG - chr2_1:22082433-22082452 Msa0201160:intron 40.0%
GAACAAAGGAGATGAGTGAA+AGG - chr2_1:22082447-22082466 Msa0201160:intron 40.0%
GCCAAGATATTCACTATAGC+TGG + chr2_1:22082565-22082584 None:intergenic 40.0%
GCTATAGTGAATATCTTGGC+TGG - chr2_1:22082565-22082584 Msa0201160:CDS 40.0%
!!! CTCTGTCTCGGTTTCTTTTT+TGG - chr2_1:22082660-22082679 Msa0201160:CDS 40.0%
ATGCAGGTAGATGAGAACCT+TGG - chr2_1:22081700-22081719 Msa0201160:three_prime_UTR 45.0%
TCCTTCATCATTGGTGGAAC+TGG - chr2_1:22081780-22081799 Msa0201160:three_prime_UTR 45.0%
ACCAGTTCCACCAATGATGA+AGG + chr2_1:22081784-22081803 None:intergenic 45.0%
TGGAAAAGATTGTGCCAGAC+TGG - chr2_1:22082018-22082037 Msa0201160:intron 45.0%
AACTTCTTGCAAAGCCAGTC+TGG + chr2_1:22082035-22082054 None:intergenic 45.0%
!! AGACTGGCTTTGCAAGAAGT+TGG - chr2_1:22082034-22082053 Msa0201160:intron 45.0%
! CTTCTGGAGACACTATGTAC+TGG - chr2_1:22082060-22082079 Msa0201160:intron 45.0%
! TGGAGACACTATGTACTGGT+GGG - chr2_1:22082064-22082083 Msa0201160:intron 45.0%
ATGCAGGTAGATGAGAACCT+TGG - chr2_1:22081700-22081719 Msa0201160:three_prime_UTR 45.0%
TCCTTCATCATTGGTGGAAC+TGG - chr2_1:22081780-22081799 Msa0201160:three_prime_UTR 45.0%
ACCAGTTCCACCAATGATGA+AGG + chr2_1:22081784-22081803 None:intergenic 45.0%
TGGAAAAGATTGTGCCAGAC+TGG - chr2_1:22082018-22082037 Msa0201160:intron 45.0%
AACTTCTTGCAAAGCCAGTC+TGG + chr2_1:22082035-22082054 None:intergenic 45.0%
!! AGACTGGCTTTGCAAGAAGT+TGG - chr2_1:22082034-22082053 Msa0201160:intron 45.0%
! CTTCTGGAGACACTATGTAC+TGG - chr2_1:22082060-22082079 Msa0201160:intron 45.0%
! TGGAGACACTATGTACTGGT+GGG - chr2_1:22082064-22082083 Msa0201160:intron 45.0%
CTTCAGCTTCTCCTATTGGG+AGG + chr2_1:22081983-22082002 None:intergenic 50.0%
CTGGAGACACTATGTACTGG+TGG - chr2_1:22082063-22082082 Msa0201160:intron 50.0%
CTTCAGCTTCTCCTATTGGG+AGG + chr2_1:22081983-22082002 None:intergenic 50.0%
CTGGAGACACTATGTACTGG+TGG - chr2_1:22082063-22082082 Msa0201160:intron 50.0%
TGCTCTGCGCATGCATTGCT+TGG - chr2_1:22082494-22082513 Msa0201160:CDS 55.0%
TGCTCTGCGCATGCATTGCT+TGG - chr2_1:22082494-22082513 Msa0201160:CDS 55.0%
Chromosome Type Strat End Strand Name
chr2_1 gene 22081700 22082699 22081700 ID=Msa0201160;Name=Msa0201160
chr2_1 mRNA 22081700 22082699 22081700 ID=Msa0201160-mRNA-1;Parent=Msa0201160;Name=Msa0201160-mRNA-1;_AED=0.45;_eAED=0.45;_QI=0|1|0.66|1|1|1|3|234|123
chr2_1 exon 22081700 22082006 22081700 ID=Msa0201160-mRNA-1:exon:8890;Parent=Msa0201160-mRNA-1
chr2_1 exon 22082318 22082408 22082318 ID=Msa0201160-mRNA-1:exon:8889;Parent=Msa0201160-mRNA-1
chr2_1 exon 22082492 22082699 22082492 ID=Msa0201160-mRNA-1:exon:8888;Parent=Msa0201160-mRNA-1
chr2_1 CDS 22082492 22082699 22082492 ID=Msa0201160-mRNA-1:cds;Parent=Msa0201160-mRNA-1
chr2_1 CDS 22082318 22082408 22082318 ID=Msa0201160-mRNA-1:cds;Parent=Msa0201160-mRNA-1
chr2_1 CDS 22081934 22082006 22081934 ID=Msa0201160-mRNA-1:cds;Parent=Msa0201160-mRNA-1
chr2_1 three_prime_UTR 22081700 22081933 22081700 ID=Msa0201160-mRNA-1:three_prime_utr;Parent=Msa0201160-mRNA-1
Gene Sequence

>Msa0201160

ATGCAGGTAGATGAGAACCTTGGTCATTCTTTTCAGAAAATCAATGTAGATCAACATTATTTGGATGCATCGGATGACAATCCTTCATCATTGGTGGAACTGGTTAATGTGATTGACTCTATATTTGACTCTGTCAAAAGAACTTCAATCACAAAAGAGGAGCTCTTGCAAAAGATAATGATGAACTGTTTAGATTTTGTTGAGATTAGAGAAGCTGAAGAACAGATTGAGATTTTGGAAAAGATTGTGCCAGACTGGCTTTGCAAGAAGTTGGTTTCTTCTGGAGACACTATGTACTGTGTCAAGAATGTGTTAGATTTGGACTCAGTTCGATCAAGGCTTCTCAGCAATGTGAACAAAGGAGATGAGTGA
Protein sequence

>Msa0201160

MQVDENLGHSFQKINVDQHYLDASDDNPSSLVELVNVIDSIFDSVKRTSITKEELLQKIMMNCLDFVEIREAEEQIEILEKIVPDWLCKKLVSSGDTMYCVKNVLDLDSVRSRLLSNVNKGDE*