AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1345320

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1345320 MtrunA17_Chr2g0287961 97.391 115 3 0 1 115 1 115 3.05e-80 231
Msa1345320 MtrunA17_Chr4g0074501 70.370 108 30 2 1 106 1 108 2.43e-52 160
Msa1345320 MtrunA17_Chr0c30g0494111 68.657 67 19 2 42 106 1 67 8.30e-27 94.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1345320 AT5G19190.1 41.905 105 50 4 1 98 1 101 1.92e-16 70.9
Msa1345320 AT3G06070.1 39.773 88 48 3 1 83 1 88 8.06e-15 66.6

Find 40 sgRNAs with CRISPR-Local

Find 116 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTTTCTTGTACCTCCTTCT+TGG 0.149558 tig0007116:+17749 None:intergenic
CTTCATCTTCATCCATTATT+AGG 0.195790 tig0007116:+18213 None:intergenic
ATTTAGGTGTATATAATATA+TGG 0.250639 tig0007116:+17448 None:intergenic
ATACATGATGACTAATATTT+AGG 0.266098 tig0007116:+17432 None:intergenic
TTAATATCATTAACAGAAAA+AGG 0.277524 tig0007116:+17326 None:intergenic
CTAGAAACTAAATACACTTT+TGG 0.281635 tig0007116:-18332 Msa1345320:five_prime_UTR
TAATTAATTCTTTAGCCTTT+AGG 0.283220 tig0007116:-17540 Msa1345320:three_prime_UTR
TTCTATTCTTATTTATATAA+AGG 0.283430 tig0007116:-17491 Msa1345320:three_prime_UTR
TTCTTGGCTGTGTTGCTTGT+GGG 0.315774 tig0007116:+17765 None:intergenic
GGAAATTGCTCTCCTAATAA+TGG 0.320698 tig0007116:-18225 Msa1345320:CDS
TCAACCTGCAAACTCTCTTC+AGG 0.344380 tig0007116:-18177 Msa1345320:intron
TGTTTGATAGAATTCTTGTT+AGG 0.386930 tig0007116:+17662 None:intergenic
GCCTTTAGGCAATAATTGTA+TGG 0.401046 tig0007116:-17526 Msa1345320:three_prime_UTR
TATGGAGGTTGCTATGGAAA+TGG 0.408929 tig0007116:-18279 Msa1345320:CDS
AGAAGAGAAAGCAAAGGAAC+AGG 0.411669 tig0007116:-17797 Msa1345320:CDS
CTTCTTGGCTGTGTTGCTTG+TGG 0.415079 tig0007116:+17764 None:intergenic
ATCACACAGCTTTAACTAGA+AGG 0.419335 tig0007116:+17614 None:intergenic
AATTAATATGGAGGTTGCTA+TGG 0.431362 tig0007116:-18285 Msa1345320:exon
AGAACCTGAAGAGAGTTTGC+AGG 0.436707 tig0007116:+18173 None:intergenic
AGTGGAGGTTGCAAAACCTT+TGG 0.437819 tig0007116:+17397 None:intergenic
AAATATTAGTCATCATGTAT+AGG 0.461723 tig0007116:-17429 Msa1345320:three_prime_UTR
AATTCTATCAAACAGTGAAA+TGG 0.469397 tig0007116:-17653 Msa1345320:exon
GCCATACAATTATTGCCTAA+AGG 0.474343 tig0007116:+17525 None:intergenic
CACAAGCAACACAGCCAAGA+AGG 0.493229 tig0007116:-17763 Msa1345320:CDS
TATAAAGGTGGATATGTACA+TGG 0.524484 tig0007116:-17476 Msa1345320:three_prime_UTR
AAGAAATCAAACTGTGGAGG+AGG 0.531737 tig0007116:+17839 None:intergenic
TATTCTTATTTATATAAAGG+TGG 0.546547 tig0007116:-17488 Msa1345320:three_prime_UTR
CCAAGAAGGAGGTACAAGAA+AGG 0.549607 tig0007116:-17749 Msa1345320:CDS
GATACATACGCACAATTGAA+AGG 0.556467 tig0007116:-18359 Msa1345320:five_prime_UTR
TTTATATTGAATTAATATGG+AGG 0.566576 tig0007116:-18294 Msa1345320:exon
GTATAGGAGGATTCAACCAA+AGG 0.585124 tig0007116:-17413 Msa1345320:three_prime_UTR
TATTAGTCATCATGTATAGG+AGG 0.591401 tig0007116:-17426 Msa1345320:three_prime_UTR
TTGATTAGAAGAGAAAGCAA+AGG 0.610534 tig0007116:-17803 Msa1345320:CDS
TTTGCAGGTTGAGAAGCAAG+TGG 0.620205 tig0007116:+18188 None:intergenic
ATAAAGGTGGATATGTACAT+GGG 0.623401 tig0007116:-17475 Msa1345320:three_prime_UTR
TAGAAGAAATCAAACTGTGG+AGG 0.634181 tig0007116:+17836 None:intergenic
AAGCAACACAGCCAAGAAGG+AGG 0.682199 tig0007116:-17760 Msa1345320:CDS
AATGCTTGTCCACACAGTGG+AGG 0.692722 tig0007116:+17382 None:intergenic
CAAAATGCTTGTCCACACAG+TGG 0.720567 tig0007116:+17379 None:intergenic
TCATAGAAGAAATCAAACTG+TGG 0.762193 tig0007116:+17833 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TCTTTTATATTGAATTAATA+TGG - tig0007116:17381-17400 Msa1345320:three_prime_UTR 10.0%
!!! TTAAACTAATTTTATTTTGT+AGG - tig0007116:17796-17815 Msa1345320:CDS 10.0%
!!! TTCTATTCTTATTTATATAA+AGG - tig0007116:18187-18206 Msa1345320:CDS 10.0%
!!! TCTTTTATATTGAATTAATA+TGG - tig0007116:17381-17400 Msa1345320:three_prime_UTR 10.0%
!!! TTAAACTAATTTTATTTTGT+AGG - tig0007116:17796-17815 Msa1345320:CDS 10.0%
!!! TTCTATTCTTATTTATATAA+AGG - tig0007116:18187-18206 Msa1345320:CDS 10.0%
!! TTTATATTGAATTAATATGG+AGG - tig0007116:17384-17403 Msa1345320:three_prime_UTR 15.0%
!!! CTTTAAAAAAATTTCATGAT+TGG + tig0007116:17670-17689 None:intergenic 15.0%
!!! TATTCTTATTTATATAAAGG+TGG - tig0007116:18190-18209 Msa1345320:CDS 15.0%
!! ATTTAGGTGTATATAATATA+TGG + tig0007116:18233-18252 None:intergenic 15.0%
!! TTAATATCATTAACAGAAAA+AGG + tig0007116:18355-18374 None:intergenic 15.0%
!! TTTATATTGAATTAATATGG+AGG - tig0007116:17384-17403 Msa1345320:three_prime_UTR 15.0%
!!! CTTTAAAAAAATTTCATGAT+TGG + tig0007116:17670-17689 None:intergenic 15.0%
!!! TATTCTTATTTATATAAAGG+TGG - tig0007116:18190-18209 Msa1345320:CDS 15.0%
!! ATTTAGGTGTATATAATATA+TGG + tig0007116:18233-18252 None:intergenic 15.0%
!! TTAATATCATTAACAGAAAA+AGG + tig0007116:18355-18374 None:intergenic 15.0%
!!! TTTAAAAAAAGTGTCATGAT+TGG + tig0007116:17625-17644 None:intergenic 20.0%
!!! TTAAAGAATTTATTTCTGCA+TGG - tig0007116:17684-17703 Msa1345320:CDS 20.0%
!!! TAATTAATTCTTTAGCCTTT+AGG - tig0007116:18138-18157 Msa1345320:intron 20.0%
!! ATACATGATGACTAATATTT+AGG + tig0007116:18249-18268 None:intergenic 20.0%
!! AAATATTAGTCATCATGTAT+AGG - tig0007116:18249-18268 Msa1345320:CDS 20.0%
!!! TTTAAAAAAAGTGTCATGAT+TGG + tig0007116:17625-17644 None:intergenic 20.0%
!!! TTAAAGAATTTATTTCTGCA+TGG - tig0007116:17684-17703 Msa1345320:CDS 20.0%
!!! TAATTAATTCTTTAGCCTTT+AGG - tig0007116:18138-18157 Msa1345320:intron 20.0%
!! ATACATGATGACTAATATTT+AGG + tig0007116:18249-18268 None:intergenic 20.0%
!! AAATATTAGTCATCATGTAT+AGG - tig0007116:18249-18268 Msa1345320:CDS 20.0%
!! CTAGAAACTAAATACACTTT+TGG - tig0007116:17346-17365 Msa1345320:three_prime_UTR 25.0%
!!! ATTTTTTGCAAATTTGAGCA+AGG - tig0007116:17432-17451 Msa1345320:three_prime_UTR 25.0%
! TGTTTGATAGAATTCTTGTT+AGG + tig0007116:18019-18038 None:intergenic 25.0%
! AATTCTATCAAACAGTGAAA+TGG - tig0007116:18025-18044 Msa1345320:intron 25.0%
!! CTAGAAACTAAATACACTTT+TGG - tig0007116:17346-17365 Msa1345320:three_prime_UTR 25.0%
!!! ATTTTTTGCAAATTTGAGCA+AGG - tig0007116:17432-17451 Msa1345320:three_prime_UTR 25.0%
! TGTTTGATAGAATTCTTGTT+AGG + tig0007116:18019-18038 None:intergenic 25.0%
! AATTCTATCAAACAGTGAAA+TGG - tig0007116:18025-18044 Msa1345320:intron 25.0%
AATTAATATGGAGGTTGCTA+TGG - tig0007116:17393-17412 Msa1345320:three_prime_UTR 30.0%
CTTCATCTTCATCCATTATT+AGG + tig0007116:17468-17487 None:intergenic 30.0%
AGTATGTAACTATGACTATG+AGG + tig0007116:17565-17584 None:intergenic 30.0%
AACTTGGAAGAAGGATAAAA+GGG + tig0007116:17602-17621 None:intergenic 30.0%
! ATTTTGCATGTAGAGAAGAA+GGG + tig0007116:17768-17787 None:intergenic 30.0%
! TATTTTGCATGTAGAGAAGA+AGG + tig0007116:17769-17788 None:intergenic 30.0%
TCATAGAAGAAATCAAACTG+TGG + tig0007116:17848-17867 None:intergenic 30.0%
TTGATTAGAAGAGAAAGCAA+AGG - tig0007116:17875-17894 Msa1345320:intron 30.0%
TATAAAGGTGGATATGTACA+TGG - tig0007116:18202-18221 Msa1345320:CDS 30.0%
ATAAAGGTGGATATGTACAT+GGG - tig0007116:18203-18222 Msa1345320:CDS 30.0%
TATTAGTCATCATGTATAGG+AGG - tig0007116:18252-18271 Msa1345320:CDS 30.0%
AATTAATATGGAGGTTGCTA+TGG - tig0007116:17393-17412 Msa1345320:three_prime_UTR 30.0%
CTTCATCTTCATCCATTATT+AGG + tig0007116:17468-17487 None:intergenic 30.0%
AGTATGTAACTATGACTATG+AGG + tig0007116:17565-17584 None:intergenic 30.0%
AACTTGGAAGAAGGATAAAA+GGG + tig0007116:17602-17621 None:intergenic 30.0%
! ATTTTGCATGTAGAGAAGAA+GGG + tig0007116:17768-17787 None:intergenic 30.0%
! TATTTTGCATGTAGAGAAGA+AGG + tig0007116:17769-17788 None:intergenic 30.0%
TCATAGAAGAAATCAAACTG+TGG + tig0007116:17848-17867 None:intergenic 30.0%
TTGATTAGAAGAGAAAGCAA+AGG - tig0007116:17875-17894 Msa1345320:intron 30.0%
TATAAAGGTGGATATGTACA+TGG - tig0007116:18202-18221 Msa1345320:CDS 30.0%
ATAAAGGTGGATATGTACAT+GGG - tig0007116:18203-18222 Msa1345320:CDS 30.0%
TATTAGTCATCATGTATAGG+AGG - tig0007116:18252-18271 Msa1345320:CDS 30.0%
GATACATACGCACAATTGAA+AGG - tig0007116:17319-17338 Msa1345320:three_prime_UTR 35.0%
GGAAATTGCTCTCCTAATAA+TGG - tig0007116:17453-17472 Msa1345320:three_prime_UTR 35.0%
GTGCATGTATTTACTTAAGG+AGG + tig0007116:17543-17562 None:intergenic 35.0%
GAGGTGCATGTATTTACTTA+AGG + tig0007116:17546-17565 None:intergenic 35.0%
GAACTTGGAAGAAGGATAAA+AGG + tig0007116:17603-17622 None:intergenic 35.0%
! AAAGTGTCATGATTGGAACT+TGG + tig0007116:17618-17637 None:intergenic 35.0%
TAGAAGAAATCAAACTGTGG+AGG + tig0007116:17845-17864 None:intergenic 35.0%
! ATCACACAGCTTTAACTAGA+AGG + tig0007116:18067-18086 None:intergenic 35.0%
GCCTTTAGGCAATAATTGTA+TGG - tig0007116:18152-18171 Msa1345320:intron 35.0%
GCCATACAATTATTGCCTAA+AGG + tig0007116:18156-18175 None:intergenic 35.0%
GATACATACGCACAATTGAA+AGG - tig0007116:17319-17338 Msa1345320:three_prime_UTR 35.0%
GGAAATTGCTCTCCTAATAA+TGG - tig0007116:17453-17472 Msa1345320:three_prime_UTR 35.0%
GTGCATGTATTTACTTAAGG+AGG + tig0007116:17543-17562 None:intergenic 35.0%
GAGGTGCATGTATTTACTTA+AGG + tig0007116:17546-17565 None:intergenic 35.0%
GAACTTGGAAGAAGGATAAA+AGG + tig0007116:17603-17622 None:intergenic 35.0%
! AAAGTGTCATGATTGGAACT+TGG + tig0007116:17618-17637 None:intergenic 35.0%
TAGAAGAAATCAAACTGTGG+AGG + tig0007116:17845-17864 None:intergenic 35.0%
! ATCACACAGCTTTAACTAGA+AGG + tig0007116:18067-18086 None:intergenic 35.0%
GCCTTTAGGCAATAATTGTA+TGG - tig0007116:18152-18171 Msa1345320:intron 35.0%
GCCATACAATTATTGCCTAA+AGG + tig0007116:18156-18175 None:intergenic 35.0%
TATGGAGGTTGCTATGGAAA+TGG - tig0007116:17399-17418 Msa1345320:three_prime_UTR 40.0%
CATGATTGGAACTTGGAAGA+AGG + tig0007116:17611-17630 None:intergenic 40.0%
AAGAAATCAAACTGTGGAGG+AGG + tig0007116:17842-17861 None:intergenic 40.0%
AGAAGAGAAAGCAAAGGAAC+AGG - tig0007116:17881-17900 Msa1345320:intron 40.0%
GTATAGGAGGATTCAACCAA+AGG - tig0007116:18265-18284 Msa1345320:CDS 40.0%
TATGGAGGTTGCTATGGAAA+TGG - tig0007116:17399-17418 Msa1345320:three_prime_UTR 40.0%
CATGATTGGAACTTGGAAGA+AGG + tig0007116:17611-17630 None:intergenic 40.0%
AAGAAATCAAACTGTGGAGG+AGG + tig0007116:17842-17861 None:intergenic 40.0%
AGAAGAGAAAGCAAAGGAAC+AGG - tig0007116:17881-17900 Msa1345320:intron 40.0%
GTATAGGAGGATTCAACCAA+AGG - tig0007116:18265-18284 Msa1345320:CDS 40.0%
! TTTGCAGGTTGAGAAGCAAG+TGG + tig0007116:17493-17512 None:intergenic 45.0%
TCAACCTGCAAACTCTCTTC+AGG - tig0007116:17501-17520 Msa1345320:three_prime_UTR 45.0%
AGAACCTGAAGAGAGTTTGC+AGG + tig0007116:17508-17527 None:intergenic 45.0%
ATTTCTGCATGGCAGTTCAG+TGG - tig0007116:17695-17714 Msa1345320:CDS 45.0%
!! TTCTTGGCTGTGTTGCTTGT+GGG + tig0007116:17916-17935 None:intergenic 45.0%
CCTTTCTTGTACCTCCTTCT+TGG + tig0007116:17932-17951 None:intergenic 45.0%
! CCAAGAAGGAGGTACAAGAA+AGG - tig0007116:17929-17948 Msa1345320:intron 45.0%
AGTGGAGGTTGCAAAACCTT+TGG + tig0007116:18284-18303 None:intergenic 45.0%
CAAAATGCTTGTCCACACAG+TGG + tig0007116:18302-18321 None:intergenic 45.0%
! CTGTGTGGACAAGCATTTTG+TGG - tig0007116:18302-18321 Msa1345320:five_prime_UTR 45.0%
! TTTGCAGGTTGAGAAGCAAG+TGG + tig0007116:17493-17512 None:intergenic 45.0%
TCAACCTGCAAACTCTCTTC+AGG - tig0007116:17501-17520 Msa1345320:three_prime_UTR 45.0%
AGAACCTGAAGAGAGTTTGC+AGG + tig0007116:17508-17527 None:intergenic 45.0%
ATTTCTGCATGGCAGTTCAG+TGG - tig0007116:17695-17714 Msa1345320:CDS 45.0%
!! TTCTTGGCTGTGTTGCTTGT+GGG + tig0007116:17916-17935 None:intergenic 45.0%
CCTTTCTTGTACCTCCTTCT+TGG + tig0007116:17932-17951 None:intergenic 45.0%
! CCAAGAAGGAGGTACAAGAA+AGG - tig0007116:17929-17948 Msa1345320:intron 45.0%
AGTGGAGGTTGCAAAACCTT+TGG + tig0007116:18284-18303 None:intergenic 45.0%
CAAAATGCTTGTCCACACAG+TGG + tig0007116:18302-18321 None:intergenic 45.0%
! CTGTGTGGACAAGCATTTTG+TGG - tig0007116:18302-18321 Msa1345320:five_prime_UTR 45.0%
!! CTTCTTGGCTGTGTTGCTTG+TGG + tig0007116:17917-17936 None:intergenic 50.0%
CACAAGCAACACAGCCAAGA+AGG - tig0007116:17915-17934 Msa1345320:intron 50.0%
AAGCAACACAGCCAAGAAGG+AGG - tig0007116:17918-17937 Msa1345320:intron 50.0%
! GTTTTGCAACCTCCACTGTG+TGG - tig0007116:18287-18306 Msa1345320:exon 50.0%
AATGCTTGTCCACACAGTGG+AGG + tig0007116:18299-18318 None:intergenic 50.0%
!! CTTCTTGGCTGTGTTGCTTG+TGG + tig0007116:17917-17936 None:intergenic 50.0%
CACAAGCAACACAGCCAAGA+AGG - tig0007116:17915-17934 Msa1345320:intron 50.0%
AAGCAACACAGCCAAGAAGG+AGG - tig0007116:17918-17937 Msa1345320:intron 50.0%
! GTTTTGCAACCTCCACTGTG+TGG - tig0007116:18287-18306 Msa1345320:exon 50.0%
AATGCTTGTCCACACAGTGG+AGG + tig0007116:18299-18318 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
tig0007116 gene 17307 18393 17307 ID=Msa1345320;Name=Msa1345320
tig0007116 mRNA 17307 18393 17307 ID=Msa1345320-mRNA-1;Parent=Msa1345320;Name=Msa1345320-mRNA-1;_AED=0.03;_eAED=0.03;_QI=93|1|1|1|1|1|2|351|115
tig0007116 exon 17307 17882 17307 ID=Msa1345320-mRNA-1:exon:4940;Parent=Msa1345320-mRNA-1
tig0007116 exon 18178 18393 18178 ID=Msa1345320-mRNA-1:exon:4939;Parent=Msa1345320-mRNA-1
tig0007116 five_prime_UTR 18301 18393 18301 ID=Msa1345320-mRNA-1:five_prime_utr;Parent=Msa1345320-mRNA-1
tig0007116 CDS 18178 18300 18178 ID=Msa1345320-mRNA-1:cds;Parent=Msa1345320-mRNA-1
tig0007116 CDS 17658 17882 17658 ID=Msa1345320-mRNA-1:cds;Parent=Msa1345320-mRNA-1
tig0007116 three_prime_UTR 17307 17657 17307 ID=Msa1345320-mRNA-1:three_prime_utr;Parent=Msa1345320-mRNA-1
Gene Sequence

>Msa1345320

ATGGAGGTTGCTATGGAAATGGAAGATGAGTTATTTTTTGCAAATTTGAGCAAGGAAATTGCTCTCCTAATAATGGATGAAGATGAAGATCCACTTGCTTCTCAACCTGCAAACTCTCTTCAGGATTTCTCTAGAGCAATTCATCCTCCTCCACAGTTTGATTTCTTCTATGAGCAAGCTTTGATTAGAAGAGAAAGCAAAGGAACAGGAGTGTTTATCCCACAAGCAACACAGCCAAGAAGGAGGTACAAGAAAGGAAGATCTAATTCATTCTCAAAATATCAAAAGCAGTCTCAAGACACAAGAATGATTTCTCAAGTTCCTAACAAGAATTCTATCAAACAGTGA
Protein sequence

>Msa1345320

MEVAMEMEDELFFANLSKEIALLIMDEDEDPLASQPANSLQDFSRAIHPPPQFDFFYEQALIRRESKGTGVFIPQATQPRRRYKKGRSNSFSKYQKQSQDTRMISQVPNKNSIKQ*