AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1449600


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1449600 MtrunA17_Chr7g0274161 93.878 147 4 2 5 150 2 144 4.35e-92 263
Msa1449600 MtrunA17_Chr1g0190751 67.647 102 28 1 49 150 43 139 6.94e-42 136
Msa1449600 MtrunA17_Chr1g0194691 77.778 45 9 1 106 150 11 54 3.66e-14 63.2
Msa1449600 MtrunA17_Chr1g0202801 47.541 61 25 1 65 118 86 146 2.90e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1449600 AT5G28750.1 65.347 101 35 0 50 150 47 147 9.43e-39 129
Msa1449600 AT5G52440.1 35.833 120 58 3 6 118 38 145 8.05e-13 64.3

Find 24 sgRNAs with CRISPR-Local

Find 144 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TACTGAGGTTTCTAGTTCTA+AGG 0.292945 tig0032655:-22756 Msa1449600:CDS
GTTTGAGTCTGAGCTTAAAA+AGG 0.305627 tig0032655:-22846 Msa1449600:CDS
CCTGAACTCGTTGTTATTGC+TGG 0.366575 tig0032655:-24833 Msa1449600:CDS
GGTGTTGTGTTGATGCAATT+GGG 0.379796 tig0032655:+24987 None:intergenic
AACTGTCAAAAGCTTTCAAC+AGG 0.389906 tig0032655:-24750 Msa1449600:intron
CCGATACTGCGACCAACTTC+AGG 0.394518 tig0032655:+24776 None:intergenic
AGAAGAAGAATAAACAATAA+TGG 0.400103 tig0032655:-24890 Msa1449600:CDS
GGCTCCCCTCCTGAGGAATC+TGG 0.401880 tig0032655:+22821 None:intergenic
AGGTGTTGTGTTGATGCAAT+TGG 0.404660 tig0032655:+24986 None:intergenic
ATTGATAGAAACCCTTGAAA+TGG 0.413952 tig0032655:+24934 None:intergenic
TGTGTTGATGCAATTGGGGT+TGG 0.431544 tig0032655:+24992 None:intergenic
CCAGCAATAACAACGAGTTC+AGG 0.481286 tig0032655:+24833 None:intergenic
CCTGAAGTTGGTCGCAGTAT+CGG 0.502726 tig0032655:-24776 Msa1449600:CDS
GTAAATCATGTAGGCAGCAA+AGG 0.522582 tig0032655:-22870 Msa1449600:intron
ACAGCAATTGATTTCTCAGA+TGG 0.525895 tig0032655:+22800 None:intergenic
ATGAAGAAGAAGAGAAAGCG+AGG 0.549986 tig0032655:+24966 None:intergenic
CTCAGATGGCTCCCCTCCTG+AGG 0.577964 tig0032655:+22814 None:intergenic
GTGTTGTGTTGATGCAATTG+GGG 0.599012 tig0032655:+24988 None:intergenic
GGAACCAGATTCCTCAGGAG+GGG 0.609899 tig0032655:-22825 Msa1449600:CDS
AAGGAACCAGATTCCTCAGG+AGG 0.613287 tig0032655:-22827 Msa1449600:CDS
AGGAACCAGATTCCTCAGGA+GGG 0.620434 tig0032655:-22826 Msa1449600:CDS
ATAGATGTGATATGATGAGT+AGG 0.635858 tig0032655:-22714 Msa1449600:three_prime_UTR
AGAGAAGAAGCAAGATACTG+AGG 0.643616 tig0032655:-22771 Msa1449600:CDS
AAAGTAAAATCTAAACGCAG+TGG 0.668233 tig0032655:-25090 Msa1449600:five_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTAAGTTGTTTATCTAAAT+AGG - tig0032655:23253-23272 Msa1449600:intron 15.0%
!!! TTAAGTTGTTTATCTAAATA+GGG - tig0032655:23254-23273 Msa1449600:intron 15.0%
!!! CCATAAACTTTATTTTAATT+AGG + tig0032655:23847-23866 None:intergenic 15.0%
!! CCTAATTAAAATAAAGTTTA+TGG - tig0032655:23844-23863 Msa1449600:intron 15.0%
!!! TTTATTTTACTTTTACAACA+CGG + tig0032655:24305-24324 None:intergenic 15.0%
!!! ATTCTCTTCTTTTTATATAA+AGG + tig0032655:24399-24418 None:intergenic 15.0%
!! TATATAAAAAGAAGAGAATT+TGG - tig0032655:24400-24419 Msa1449600:intron 15.0%
!!! ATATATTTTGTAAATCATGT+AGG - tig0032655:24868-24887 Msa1449600:CDS 15.0%
!!! TTTTTGAATATATATTGTCA+TGG + tig0032655:25072-25091 None:intergenic 15.0%
!! AGAAGAAGAATAAACAATAA+TGG - tig0032655:22857-22876 Msa1449600:CDS 20.0%
!! AATGAGAAGAAATAAAGAAA+GGG + tig0032655:23029-23048 None:intergenic 20.0%
!! AAAAGATAAATGTTTCTCTT+AGG + tig0032655:23591-23610 None:intergenic 20.0%
!! AACTTTATTGAGAAATACTA+GGG - tig0032655:23775-23794 Msa1449600:intron 20.0%
!! TAACTTGAAAAGCTTATATT+AGG - tig0032655:24066-24085 Msa1449600:intron 20.0%
!! ATCAAAATGTCAATCTTATT+TGG - tig0032655:24118-24137 Msa1449600:intron 20.0%
!!! GAAAATAGTTTTCAATCAAA+TGG - tig0032655:24193-24212 Msa1449600:intron 20.0%
!!! TTATTTTACTTTTACAACAC+GGG + tig0032655:24304-24323 None:intergenic 20.0%
!! TAAAATAAACAAGCAAAGAA+GGG - tig0032655:24316-24335 Msa1449600:intron 20.0%
!! ATCTTTTTGTTCCATTTCAA+GGG - tig0032655:22802-22821 Msa1449600:CDS 25.0%
! GAATGAGAAGAAATAAAGAA+AGG + tig0032655:23030-23049 None:intergenic 25.0%
!!! AACTCGTAACTTTAATTTGA+AGG + tig0032655:23052-23071 None:intergenic 25.0%
! AGTTTCAAATGTGTTTATGT+CGG + tig0032655:23081-23100 None:intergenic 25.0%
!!! GTATAAGATGTTTTAAGAGT+AGG - tig0032655:23479-23498 Msa1449600:intron 25.0%
!! TGAAAAATGTGTTTTCTTTG+CGG - tig0032655:23536-23555 Msa1449600:intron 25.0%
!! GAAACATTTATCTTTTTGCT+TGG - tig0032655:23595-23614 Msa1449600:intron 25.0%
! GAACTTTATTGAGAAATACT+AGG - tig0032655:23774-23793 Msa1449600:intron 25.0%
! TGAAAAGCTTATATTAGGTT+TGG - tig0032655:24071-24090 Msa1449600:intron 25.0%
! GAAAAGCTTATATTAGGTTT+GGG - tig0032655:24072-24091 Msa1449600:intron 25.0%
!!! CTAAAACGTCACTTTTATTT+TGG + tig0032655:24152-24171 None:intergenic 25.0%
!!! TATTTTACTTTTACAACACG+GGG + tig0032655:24303-24322 None:intergenic 25.0%
! GTAAAATAAACAAGCAAAGA+AGG - tig0032655:24315-24334 Msa1449600:intron 25.0%
! CACACAAATATTCTTTCAAA+TGG + tig0032655:24585-24604 None:intergenic 25.0%
! AAATAACCATATAAGCAATG+AGG + tig0032655:24847-24866 None:intergenic 25.0%
AAAGTAAAATCTAAACGCAG+TGG - tig0032655:22657-22676 Msa1449600:three_prime_UTR 30.0%
! CATCTTTTTGTTCCATTTCA+AGG - tig0032655:22801-22820 Msa1449600:CDS 30.0%
ATTGATAGAAACCCTTGAAA+TGG + tig0032655:22816-22835 None:intergenic 30.0%
!! GCTGTTTTCATAAGTTATCT+TGG + tig0032655:23127-23146 None:intergenic 30.0%
CACTAATCATATAAGTGCTT+AGG + tig0032655:23214-23233 None:intergenic 30.0%
AATGACAATGTGATATTGCT+TGG + tig0032655:23421-23440 None:intergenic 30.0%
GTCATTTGAATTATGCCTTA+CGG - tig0032655:23435-23454 Msa1449600:intron 30.0%
ATAAAGTTCATGTGAAACAG+AGG + tig0032655:23763-23782 None:intergenic 30.0%
GAAATACTAGGGAAAAACAA+AGG - tig0032655:23786-23805 Msa1449600:intron 30.0%
ACTAGAAGCTAATCTACATT+AGG + tig0032655:23812-23831 None:intergenic 30.0%
TTAAATTTGAACGACTGGAT+CGG + tig0032655:24049-24068 None:intergenic 30.0%
TCAAGTTAAATTTGAACGAC+TGG + tig0032655:24054-24073 None:intergenic 30.0%
!! ATTTTACTTTTACAACACGG+GGG + tig0032655:24302-24321 None:intergenic 30.0%
ATGCAATACTTTCTTGCATT+TGG - tig0032655:24485-24504 Msa1449600:intron 30.0%
CAAAGTAATATGCTGTAATG+TGG + tig0032655:24691-24710 None:intergenic 30.0%
CACATTACAGCATATTACTT+TGG - tig0032655:24689-24708 Msa1449600:intron 30.0%
TACTTTCCTCATTGCTTATA+TGG - tig0032655:24838-24857 Msa1449600:CDS 30.0%
ATAGATGTGATATGATGAGT+AGG - tig0032655:25033-25052 Msa1449600:CDS 30.0%
!!! TTTTTTGGGACCAAAAACGA+TGG + tig0032655:22948-22967 None:intergenic 35.0%
!!! CCAACTTCAGGCAATTTTTT+GGG + tig0032655:22962-22981 None:intergenic 35.0%
!!! ACCAACTTCAGGCAATTTTT+TGG + tig0032655:22963-22982 None:intergenic 35.0%
AACTGTCAAAAGCTTTCAAC+AGG - tig0032655:22997-23016 Msa1449600:intron 35.0%
AATTGTGTGTGAGTTTCAAG+TGG + tig0032655:23360-23379 None:intergenic 35.0%
ACTTGAAACTCACACACAAT+TGG - tig0032655:23359-23378 Msa1449600:intron 35.0%
CTTGAAACTCACACACAATT+GGG - tig0032655:23360-23379 Msa1449600:intron 35.0%
CTAATGCCAATACGTTTGTT+TGG + tig0032655:23506-23525 None:intergenic 35.0%
AGACTCAGATATTTGTGTAG+TGG - tig0032655:23560-23579 Msa1449600:intron 35.0%
CATGCTTGAATTTCTCTATC+AGG + tig0032655:23634-23653 None:intergenic 35.0%
CTGATAGAGAAATTCAAGCA+TGG - tig0032655:23632-23651 Msa1449600:intron 35.0%
!! TGTTTTCGAGGGAGATTATA+CGG + tig0032655:23704-23723 None:intergenic 35.0%
! AATCCTGAGATGCTACTTAA+GGG + tig0032655:24023-24042 None:intergenic 35.0%
AATGGCCCCATAAACTATAT+TGG - tig0032655:24211-24230 Msa1449600:intron 35.0%
TGCCTCCAATATAGTTTATG+GGG + tig0032655:24219-24238 None:intergenic 35.0%
CTGCCTCCAATATAGTTTAT+GGG + tig0032655:24220-24239 None:intergenic 35.0%
TCTGCCTCCAATATAGTTTA+TGG + tig0032655:24221-24240 None:intergenic 35.0%
ATAAACTATATTGGAGGCAG+AGG - tig0032655:24220-24239 Msa1449600:intron 35.0%
! GTTTGGCTCATATAACTCAT+TGG - tig0032655:24248-24267 Msa1449600:intron 35.0%
ATAACTCATTGGATTGTTCC+AGG - tig0032655:24259-24278 Msa1449600:intron 35.0%
AATAAACAAGCAAAGAAGGG+AGG - tig0032655:24319-24338 Msa1449600:intron 35.0%
!! AACTAATAGCTTCTAAAGCG+TGG - tig0032655:24367-24386 Msa1449600:intron 35.0%
TATTGCATGCCATAGACTAA+CGG + tig0032655:24473-24492 None:intergenic 35.0%
TACTTTCTTGCATTTGGAAG+AGG - tig0032655:24491-24510 Msa1449600:intron 35.0%
CAACATCAGACATTGCTTTA+AGG - tig0032655:24555-24574 Msa1449600:intron 35.0%
TGTGTGAGAAAAATGCCATA+TGG - tig0032655:24599-24618 Msa1449600:intron 35.0%
ATTACAACAGTAGCACCATA+TGG + tig0032655:24617-24636 None:intergenic 35.0%
TATATCATCCCCTAATGTTC+AGG - tig0032655:24657-24676 Msa1449600:intron 35.0%
ACTCAAGCAGCCAAATAATT+TGG - tig0032655:24745-24764 Msa1449600:intron 35.0%
CAGCCAAATAATTTGGATTC+TGG - tig0032655:24752-24771 Msa1449600:CDS 35.0%
ACGCCAGAATCCAAATTATT+TGG + tig0032655:24758-24777 None:intergenic 35.0%
GTTTGAGTCTGAGCTTAAAA+AGG - tig0032655:24901-24920 Msa1449600:CDS 35.0%
! ACAGCAATTGATTTCTCAGA+TGG + tig0032655:24950-24969 None:intergenic 35.0%
!! TACTGAGGTTTCTAGTTCTA+AGG - tig0032655:24991-25010 Msa1449600:CDS 35.0%
! GTGTTGTGTTGATGCAATTG+GGG + tig0032655:22762-22781 None:intergenic 40.0%
! GGTGTTGTGTTGATGCAATT+GGG + tig0032655:22763-22782 None:intergenic 40.0%
! AGGTGTTGTGTTGATGCAAT+TGG + tig0032655:22764-22783 None:intergenic 40.0%
ATGAAGAAGAAGAGAAAGCG+AGG + tig0032655:22784-22803 None:intergenic 40.0%
CTTCTTCTTCTTCTTCTTCG+TGG + tig0032655:22842-22861 None:intergenic 40.0%
! TTCACTTGCAACGCACTTTT+CGG - tig0032655:22881-22900 Msa1449600:intron 40.0%
CCCAAAAAATTGCCTGAAGT+TGG - tig0032655:22959-22978 Msa1449600:intron 40.0%
ACAATGTGATATTGCTTGGC+TGG + tig0032655:23417-23436 None:intergenic 40.0%
TGTAGTCATCTTTGTCCGTA+AGG + tig0032655:23453-23472 None:intergenic 40.0%
GTAGGACCAAACAAACGTAT+TGG - tig0032655:23497-23516 Msa1449600:intron 40.0%
GCTAAAGAAGTAGGCAGAAA+AGG + tig0032655:23727-23746 None:intergenic 40.0%
AGGAAGCTAGCTAAAGAAGT+AGG + tig0032655:23736-23755 None:intergenic 40.0%
TTTCCCTTAAGTAGCATCTC+AGG - tig0032655:24017-24036 Msa1449600:intron 40.0%
! GAATCCTGAGATGCTACTTA+AGG + tig0032655:24024-24043 None:intergenic 40.0%
GAATAGTAAAACAGCATGCC+TGG + tig0032655:24280-24299 None:intergenic 40.0%
!! ATAGCTTCTAAAGCGTGGAA+AGG - tig0032655:24372-24391 Msa1449600:intron 40.0%
GTTACGTGACTCGAAAATCA+TGG + tig0032655:24536-24555 None:intergenic 40.0%
ATGCCAATCCTGAACATTAG+GGG + tig0032655:24668-24687 None:intergenic 40.0%
GATGCCAATCCTGAACATTA+GGG + tig0032655:24669-24688 None:intergenic 40.0%
GTAAATCATGTAGGCAGCAA+AGG - tig0032655:24877-24896 Msa1449600:CDS 40.0%
AAAAAGGAACCAGATTCCTC+AGG - tig0032655:24917-24936 Msa1449600:CDS 40.0%
AGAGAAGAAGCAAGATACTG+AGG - tig0032655:24976-24995 Msa1449600:CDS 40.0%
! TGTGTTGATGCAATTGGGGT+TGG + tig0032655:22758-22777 None:intergenic 45.0%
CTTCTTCTTCTTCTTCGTGG+AGG + tig0032655:22839-22858 None:intergenic 45.0%
! TGCAACGCACTTTTCGGATT+AGG - tig0032655:22887-22906 Msa1449600:intron 45.0%
CCAGCAATAACAACGAGTTC+AGG + tig0032655:22917-22936 None:intergenic 45.0%
! CCTGAACTCGTTGTTATTGC+TGG - tig0032655:22914-22933 Msa1449600:intron 45.0%
TCTGTTCTCTGTAGACGAAG+TGG - tig0032655:23328-23347 Msa1449600:intron 45.0%
ACACACAATTGGGAAGTCCT+GGG - tig0032655:23370-23389 Msa1449600:intron 45.0%
!!! GGCAGAAAAGGTGTTTTCGA+GGG + tig0032655:23715-23734 None:intergenic 45.0%
!!! AGGCAGAAAAGGTGTTTTCG+AGG + tig0032655:23716-23735 None:intergenic 45.0%
AGTTCATGTGAAACAGAGGC+AGG + tig0032655:23759-23778 None:intergenic 45.0%
AATTTGAACGACTGGATCGG+TGG + tig0032655:24046-24065 None:intergenic 45.0%
GGCCCCATAAACTATATTGG+AGG - tig0032655:24214-24233 Msa1449600:intron 45.0%
GTTTCAACGCTCTTGACTCA+TGG - tig0032655:24424-24443 Msa1449600:intron 45.0%
TCATGGCAAGATCCAGGAAA+GGG - tig0032655:24441-24460 Msa1449600:intron 45.0%
CATCCCCTAATGTTCAGGAT+TGG - tig0032655:24662-24681 Msa1449600:intron 45.0%
GGATGCCAATCCTGAACATT+AGG + tig0032655:24670-24689 None:intergenic 45.0%
TATTTGGCTGCTTGAGTGCA+TGG + tig0032655:24742-24761 None:intergenic 45.0%
!!! GGTGTTGCTGCCATCGTTTT+TGG - tig0032655:22935-22954 Msa1449600:intron 50.0%
! CCTGAAGTTGGTCGCAGTAT+CGG - tig0032655:22971-22990 Msa1449600:intron 50.0%
CACACACAATTGGGAAGTCC+TGG - tig0032655:23369-23388 Msa1449600:intron 50.0%
TTTCACTCGGGTTCAAACCC+AGG + tig0032655:23390-23409 None:intergenic 50.0%
TTGGCTGGACACTTTCACTC+GGG + tig0032655:23402-23421 None:intergenic 50.0%
CTTGGCTGGACACTTTCACT+CGG + tig0032655:23403-23422 None:intergenic 50.0%
TCATGTGAAACAGAGGCAGG+AGG + tig0032655:23756-23775 None:intergenic 50.0%
CTTGACTCATGGCAAGATCC+AGG - tig0032655:24435-24454 Msa1449600:intron 50.0%
CTCATGGCAAGATCCAGGAA+AGG - tig0032655:24440-24459 Msa1449600:intron 50.0%
AAGGAACCAGATTCCTCAGG+AGG - tig0032655:24920-24939 Msa1449600:CDS 50.0%
AGGAACCAGATTCCTCAGGA+GGG - tig0032655:24921-24940 Msa1449600:CDS 50.0%
CCGATACTGCGACCAACTTC+AGG + tig0032655:22974-22993 None:intergenic 55.0%
!! TGGAGGCAGAGGCACTTGTT+TGG - tig0032655:24231-24250 Msa1449600:intron 55.0%
GGCAAGATCCAGGAAAGGGT+CGG - tig0032655:24445-24464 Msa1449600:intron 55.0%
GCAAGATCCAGGAAAGGGTC+GGG - tig0032655:24446-24465 Msa1449600:intron 55.0%
GGAACCAGATTCCTCAGGAG+GGG - tig0032655:24922-24941 Msa1449600:CDS 55.0%
! TAACGGACCCGACCCTTTCC+TGG + tig0032655:24456-24475 None:intergenic 60.0%
! GGGTCGGGTCCGTTAGTCTA+TGG - tig0032655:24461-24480 Msa1449600:intron 60.0%
GGCTCCCCTCCTGAGGAATC+TGG + tig0032655:24929-24948 None:intergenic 65.0%
CTCAGATGGCTCCCCTCCTG+AGG + tig0032655:24936-24955 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
tig0032655 gene 22623 25146 22623 ID=Msa1449600;Name=Msa1449600
tig0032655 mRNA 22623 25146 22623 ID=Msa1449600-mRNA-1;Parent=Msa1449600;Name=Msa1449600-mRNA-1;_AED=0.01;_eAED=0.01;_QI=78|1|1|1|1|1|2|122|150
tig0032655 exon 22623 22879 22623 ID=Msa1449600-mRNA-1:exon:17019;Parent=Msa1449600-mRNA-1
tig0032655 exon 24751 25146 24751 ID=Msa1449600-mRNA-1:exon:17018;Parent=Msa1449600-mRNA-1
tig0032655 five_prime_UTR 25069 25146 25069 ID=Msa1449600-mRNA-1:five_prime_utr;Parent=Msa1449600-mRNA-1
tig0032655 CDS 24751 25068 24751 ID=Msa1449600-mRNA-1:cds;Parent=Msa1449600-mRNA-1
tig0032655 CDS 22745 22879 22745 ID=Msa1449600-mRNA-1:cds;Parent=Msa1449600-mRNA-1
tig0032655 three_prime_UTR 22623 22744 22623 ID=Msa1449600-mRNA-1:three_prime_utr;Parent=Msa1449600-mRNA-1
Gene Sequence

>Msa1449600

ATGACGATGACGATGAACTGTGTTTCGTTTTGTTCGTCAATTTCAATTTCAATTCCAACCCCAATTGCATCAACACAACACCTCGCTTTCTCTTCTTCTTCATCTTTTTGTTCCATTTCAAGGGTTTCTATCAATCCTCCACGAAGAAGAAGAAGAAGAAGAAGAATAAACAATAATGGTTTCACTTGCAACGCACTTTTCGGATTAGGTGTACCTGAACTCGTTGTTATTGCTGGTGTTGCTGCCATCGTTTTTGGTCCCAAAAAATTGCCTGAAGTTGGTCGCAGTATCGGTAAAACTGTCAAAAGCTTTCAACAGGCAGCAAAGGAGTTTGAGTCTGAGCTTAAAAAGGAACCAGATTCCTCAGGAGGGGAGCCATCTGAGAAATCAATTGCTGTTAGCGAAGAGAAGAAGCAAGATACTGAGGTTTCTAGTTCTAAGGACAGTGTATGA

Protein sequence

>Msa1449600

MTMTMNCVSFCSSISISIPTPIASTQHLAFSSSSSFCSISRVSINPPRRRRRRRRINNNGFTCNALFGLGVPELVVIAGVAAIVFGPKKLPEVGRSIGKTVKSFQQAAKEFESELKKEPDSSGGEPSEKSIAVSEEKKQDTEVSSSKDSV*