AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1038320


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1038320 MtrunA17_Chr7g0274161 93.878 147 4 2 5 150 2 144 5.24e-92 263
Msa1038320 MtrunA17_Chr1g0190751 67.961 103 27 2 48 150 43 139 1.18e-41 135
Msa1038320 MtrunA17_Chr1g0194691 77.778 45 9 1 106 150 11 54 3.18e-14 63.2
Msa1038320 MtrunA17_Chr1g0202801 47.541 61 25 1 65 118 86 146 2.93e-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
Msa1038320 AT5G28750.1 66.337 101 34 0 50 150 47 147 4.97e-40 132
Msa1038320 AT5G52440.1 35.833 120 58 3 6 118 38 145 3.55e-13 65.1

Find 26 sgRNAs with CRISPR-Local

Find 142 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TACTGAGGTTTCTAGTTCTA+AGG 0.292945 7_1:-75138031 Msa1038320:CDS
GTTTGAGTCTGAGCTTAAAA+AGG 0.305627 7_1:-75138121 Msa1038320:CDS
CCTGAACTCGTTGTTATTGC+TGG 0.366575 7_1:-75140115 Msa1038320:CDS
GGTGTTGTGTTGATGCAATT+GGG 0.379796 7_1:+75140269 None:intergenic
AACTGTCAAAAGCTTTCAAC+AGG 0.389906 7_1:-75140032 Msa1038320:intron
CCGATACTGCGACCAACTTC+AGG 0.394518 7_1:+75140058 None:intergenic
AGAAGAAGAATAAACAATAA+TGG 0.400103 7_1:-75140172 Msa1038320:CDS
GGCTCCCCTCCTGAGGAATC+TGG 0.401880 7_1:+75138096 None:intergenic
AGGTGTTGTGTTGATGCAAT+TGG 0.404660 7_1:+75140268 None:intergenic
ATTGATAGAAACCCTTGAAA+TGG 0.413952 7_1:+75140216 None:intergenic
CTTCTTATTCTTCTTCTTCG+TGG 0.419513 7_1:+75140190 None:intergenic
TGTGTTGATGCAATTGGGGT+TGG 0.431544 7_1:+75140274 None:intergenic
CCAGCAATAACAACGAGTTC+AGG 0.481286 7_1:+75140115 None:intergenic
CCTGAAGTTGGTCGCAGTAT+CGG 0.502726 7_1:-75140058 Msa1038320:CDS
GTAAATCATGTAGGCAGCAA+AGG 0.522582 7_1:-75138145 Msa1038320:intron
ACAGCAATTGATTTCTCAGA+TGG 0.525895 7_1:+75138075 None:intergenic
ATGAAGAAGAAGAGAAAGCG+AGG 0.549986 7_1:+75140248 None:intergenic
CTCAGATGGCTCCCCTCCTG+AGG 0.577964 7_1:+75138089 None:intergenic
CTTATTCTTCTTCTTCGTGG+AGG 0.579523 7_1:+75140193 None:intergenic
GTGTTGTGTTGATGCAATTG+GGG 0.599012 7_1:+75140270 None:intergenic
GGAACCAGATTCCTCAGGAG+GGG 0.609899 7_1:-75138100 Msa1038320:CDS
AAGGAACCAGATTCCTCAGG+AGG 0.613287 7_1:-75138102 Msa1038320:CDS
AGGAACCAGATTCCTCAGGA+GGG 0.620434 7_1:-75138101 Msa1038320:CDS
ATAGATGTGATATGATGAGT+AGG 0.635858 7_1:-75137989 Msa1038320:three_prime_UTR
AGAGAAGAAGCAAGATACTG+AGG 0.643616 7_1:-75138046 Msa1038320:CDS
AAAGTAAAATCTAAACGCAG+TGG 0.668233 7_1:-75140372 Msa1038320:five_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTAAGTTGTTTATCTAAAT+AGG - chr7_1:75138529-75138548 Msa1038320:intron 15.0%
!!! TTAAGTTGTTTATCTAAATA+GGG - chr7_1:75138530-75138549 Msa1038320:intron 15.0%
!!! CCATAAACTTTATTTTAATT+AGG + chr7_1:75139129-75139148 None:intergenic 15.0%
!! CCTAATTAAAATAAAGTTTA+TGG - chr7_1:75139126-75139145 Msa1038320:intron 15.0%
!!! TTTATTTTACTTTTACAACA+CGG + chr7_1:75139587-75139606 None:intergenic 15.0%
!!! ATTCTCTTCTTTTTATATAA+AGG + chr7_1:75139681-75139700 None:intergenic 15.0%
!! TATATAAAAAGAAGAGAATT+TGG - chr7_1:75139682-75139701 Msa1038320:intron 15.0%
!!! ATATATTTTGTAAATCATGT+AGG - chr7_1:75140150-75140169 Msa1038320:CDS 15.0%
!!! TTTTTGAATATATATTGTCA+TGG + chr7_1:75140354-75140373 None:intergenic 15.0%
!! AGAAGAAGAATAAACAATAA+TGG - chr7_1:75138132-75138151 Msa1038320:CDS 20.0%
!! AATGAGAAGAAATAAAGAAA+GGG + chr7_1:75138304-75138323 None:intergenic 20.0%
!! AAAAGATAAATGTTTCTCTT+AGG + chr7_1:75138873-75138892 None:intergenic 20.0%
!! AACTTTATTGAGAAATACTA+GGG - chr7_1:75139057-75139076 Msa1038320:intron 20.0%
!! TAACTTGAAAAGCTTATATT+AGG - chr7_1:75139348-75139367 Msa1038320:intron 20.0%
!! ATCAAAATGTCAATCTTATT+TGG - chr7_1:75139400-75139419 Msa1038320:intron 20.0%
!!! CTAAAACATCACTTTTATTT+TGG + chr7_1:75139434-75139453 None:intergenic 20.0%
!!! GAAAATAGTTTTCAATCAAA+TGG - chr7_1:75139475-75139494 Msa1038320:intron 20.0%
!!! TTATTTTACTTTTACAACAC+GGG + chr7_1:75139586-75139605 None:intergenic 20.0%
!! TAAAATAAACAAGCAAAGAA+GGG - chr7_1:75139598-75139617 Msa1038320:intron 20.0%
!! ATCTTTTTGTTCCATTTCAA+GGG - chr7_1:75138077-75138096 Msa1038320:CDS 25.0%
! GAATGAGAAGAAATAAAGAA+AGG + chr7_1:75138305-75138324 None:intergenic 25.0%
!!! AACTCGTAACTTTAATTTGA+AGG + chr7_1:75138327-75138346 None:intergenic 25.0%
! AGTTTCAAATGTGTTTATGT+CGG + chr7_1:75138356-75138375 None:intergenic 25.0%
!!! GTATAAGATGTTTTAAGAGT+AGG - chr7_1:75138759-75138778 Msa1038320:intron 25.0%
!! GAAACATTTATCTTTTTGCT+TGG - chr7_1:75138877-75138896 Msa1038320:intron 25.0%
! GAACTTTATTGAGAAATACT+AGG - chr7_1:75139056-75139075 Msa1038320:intron 25.0%
! TGAAAAGCTTATATTAGGTT+TGG - chr7_1:75139353-75139372 Msa1038320:intron 25.0%
! GAAAAGCTTATATTAGGTTT+GGG - chr7_1:75139354-75139373 Msa1038320:intron 25.0%
!!! TATTTTACTTTTACAACACG+GGG + chr7_1:75139585-75139604 None:intergenic 25.0%
! GTAAAATAAACAAGCAAAGA+AGG - chr7_1:75139597-75139616 Msa1038320:intron 25.0%
! CACACAAATATTCTTTCAAA+TGG + chr7_1:75139867-75139886 None:intergenic 25.0%
! AAATAACCATATAAGCAATG+AGG + chr7_1:75140129-75140148 None:intergenic 25.0%
AAAGTAAAATCTAAACGCAG+TGG - chr7_1:75137932-75137951 Msa1038320:three_prime_UTR 30.0%
! CATCTTTTTGTTCCATTTCA+AGG - chr7_1:75138076-75138095 Msa1038320:CDS 30.0%
ATTGATAGAAACCCTTGAAA+TGG + chr7_1:75138091-75138110 None:intergenic 30.0%
!! GCTGTTTTCATAAGTTATCT+TGG + chr7_1:75138402-75138421 None:intergenic 30.0%
AATGACAATGTGATATTGCT+TGG + chr7_1:75138701-75138720 None:intergenic 30.0%
GTCATTTGAATTATGCCTTA+CGG - chr7_1:75138715-75138734 Msa1038320:intron 30.0%
ATAAAGTTCATGTGAAACAG+AGG + chr7_1:75139045-75139064 None:intergenic 30.0%
GAAATACTAGGGAAAAACAA+AGG - chr7_1:75139068-75139087 Msa1038320:intron 30.0%
ACTAGAAGCTAATCTACATT+AGG + chr7_1:75139094-75139113 None:intergenic 30.0%
TTAAATTTGAACGACTGGAT+CGG + chr7_1:75139331-75139350 None:intergenic 30.0%
TCAAGTTAAATTTGAACGAC+TGG + chr7_1:75139336-75139355 None:intergenic 30.0%
!! ATTTTACTTTTACAACACGG+GGG + chr7_1:75139584-75139603 None:intergenic 30.0%
!! AACTAATAGCTTCTAAAGCA+TGG - chr7_1:75139649-75139668 Msa1038320:intron 30.0%
ATGCAATACTTTCTTGCATT+TGG - chr7_1:75139767-75139786 Msa1038320:intron 30.0%
CAAAGTAATATGCTGTAATG+TGG + chr7_1:75139973-75139992 None:intergenic 30.0%
CACATTACAGCATATTACTT+TGG - chr7_1:75139971-75139990 Msa1038320:intron 30.0%
TACTTTCCTCATTGCTTATA+TGG - chr7_1:75140120-75140139 Msa1038320:CDS 30.0%
ATAGATGTGATATGATGAGT+AGG - chr7_1:75140315-75140334 Msa1038320:CDS 30.0%
CTTCTTATTCTTCTTCTTCG+TGG + chr7_1:75138117-75138136 None:intergenic 35.0%
!!! TTTTTTGGGACCAAAAACGA+TGG + chr7_1:75138223-75138242 None:intergenic 35.0%
!!! CCAACTTCAGGCAATTTTTT+GGG + chr7_1:75138237-75138256 None:intergenic 35.0%
!!! ACCAACTTCAGGCAATTTTT+TGG + chr7_1:75138238-75138257 None:intergenic 35.0%
AACTGTCAAAAGCTTTCAAC+AGG - chr7_1:75138272-75138291 Msa1038320:intron 35.0%
CTAATGCCAATACGTTTGTT+TGG + chr7_1:75138786-75138805 None:intergenic 35.0%
ACTCAGAGATATTTGTGTAG+TGG - chr7_1:75138842-75138861 Msa1038320:intron 35.0%
CATGCTTGAATTTCTCTATC+AGG + chr7_1:75138916-75138935 None:intergenic 35.0%
CTGATAGAGAAATTCAAGCA+TGG - chr7_1:75138914-75138933 Msa1038320:intron 35.0%
!! TGTTTTCGAGGGAGATTATA+CGG + chr7_1:75138986-75139005 None:intergenic 35.0%
! AATCCTGAGATGCTACTTAA+GGG + chr7_1:75139305-75139324 None:intergenic 35.0%
AATGGCCCCATAAACTATAT+TGG - chr7_1:75139493-75139512 Msa1038320:intron 35.0%
TGCCTCCAATATAGTTTATG+GGG + chr7_1:75139501-75139520 None:intergenic 35.0%
CTGCCTCCAATATAGTTTAT+GGG + chr7_1:75139502-75139521 None:intergenic 35.0%
TCTGCCTCCAATATAGTTTA+TGG + chr7_1:75139503-75139522 None:intergenic 35.0%
ATAAACTATATTGGAGGCAG+AGG - chr7_1:75139502-75139521 Msa1038320:intron 35.0%
! GTTTGGCTCATATAACTCAT+TGG - chr7_1:75139530-75139549 Msa1038320:intron 35.0%
AATAAACAAGCAAAGAAGGG+AGG - chr7_1:75139601-75139620 Msa1038320:intron 35.0%
!! ATAGCTTCTAAAGCATGGAA+AGG - chr7_1:75139654-75139673 Msa1038320:intron 35.0%
TATTGCATGCCATAGACTAA+CGG + chr7_1:75139755-75139774 None:intergenic 35.0%
TACTTTCTTGCATTTGGAAG+AGG - chr7_1:75139773-75139792 Msa1038320:intron 35.0%
CAACATCAGACATTGCTTTA+AGG - chr7_1:75139837-75139856 Msa1038320:intron 35.0%
TGTGTGAGAAAAATGCCATA+TGG - chr7_1:75139881-75139900 Msa1038320:intron 35.0%
ATTACAACAGTAGCACCATA+TGG + chr7_1:75139899-75139918 None:intergenic 35.0%
TATATCATCCCCTAATGTTC+AGG - chr7_1:75139939-75139958 Msa1038320:intron 35.0%
ACTCAAGCAGCCAAATAATT+TGG - chr7_1:75140027-75140046 Msa1038320:intron 35.0%
CAGCCAAATAATTTGGATTC+TGG - chr7_1:75140034-75140053 Msa1038320:CDS 35.0%
ACGCCAGAATCCAAATTATT+TGG + chr7_1:75140040-75140059 None:intergenic 35.0%
GTTTGAGTCTGAGCTTAAAA+AGG - chr7_1:75140183-75140202 Msa1038320:CDS 35.0%
! ACAGCAATTGATTTCTCAGA+TGG + chr7_1:75140232-75140251 None:intergenic 35.0%
!! TACTGAGGTTTCTAGTTCTA+AGG - chr7_1:75140273-75140292 Msa1038320:CDS 35.0%
! GTGTTGTGTTGATGCAATTG+GGG + chr7_1:75138037-75138056 None:intergenic 40.0%
! GGTGTTGTGTTGATGCAATT+GGG + chr7_1:75138038-75138057 None:intergenic 40.0%
! AGGTGTTGTGTTGATGCAAT+TGG + chr7_1:75138039-75138058 None:intergenic 40.0%
ATGAAGAAGAAGAGAAAGCG+AGG + chr7_1:75138059-75138078 None:intergenic 40.0%
CTTATTCTTCTTCTTCGTGG+AGG + chr7_1:75138114-75138133 None:intergenic 40.0%
! TTCACTTGCAACGCACTTTT+CGG - chr7_1:75138156-75138175 Msa1038320:intron 40.0%
CCCAAAAAATTGCCTGAAGT+TGG - chr7_1:75138234-75138253 Msa1038320:intron 40.0%
AAACTCACACACACGCAATT+GGG - chr7_1:75138640-75138659 Msa1038320:intron 40.0%
ACAATGTGATATTGCTTGGC+TGG + chr7_1:75138697-75138716 None:intergenic 40.0%
TGTAGTCATCTTTGTCCGTA+AGG + chr7_1:75138733-75138752 None:intergenic 40.0%
GTAGGACCAAACAAACGTAT+TGG - chr7_1:75138777-75138796 Msa1038320:intron 40.0%
GCTAAAGAAGTAGGCAGAAA+AGG + chr7_1:75139009-75139028 None:intergenic 40.0%
AGGAAGCTAGCTAAAGAAGT+AGG + chr7_1:75139018-75139037 None:intergenic 40.0%
TTTCCCTTAAGTAGCATCTC+AGG - chr7_1:75139299-75139318 Msa1038320:intron 40.0%
! GAATCCTGAGATGCTACTTA+AGG + chr7_1:75139306-75139325 None:intergenic 40.0%
ATAACTCATTGGATTGCTCC+AGG - chr7_1:75139541-75139560 Msa1038320:intron 40.0%
GAATAGTAAAACAGCATGCC+TGG + chr7_1:75139562-75139581 None:intergenic 40.0%
GTTACGTGACTCGAAAATCA+TGG + chr7_1:75139818-75139837 None:intergenic 40.0%
ATGCCAATCCTGAACATTAG+GGG + chr7_1:75139950-75139969 None:intergenic 40.0%
GATGCCAATCCTGAACATTA+GGG + chr7_1:75139951-75139970 None:intergenic 40.0%
GTAAATCATGTAGGCAGCAA+AGG - chr7_1:75140159-75140178 Msa1038320:CDS 40.0%
AAAAAGGAACCAGATTCCTC+AGG - chr7_1:75140199-75140218 Msa1038320:CDS 40.0%
AGAGAAGAAGCAAGATACTG+AGG - chr7_1:75140258-75140277 Msa1038320:CDS 40.0%
! TGTGTTGATGCAATTGGGGT+TGG + chr7_1:75138033-75138052 None:intergenic 45.0%
! TGCAACGCACTTTTCGGATT+AGG - chr7_1:75138162-75138181 Msa1038320:intron 45.0%
CCAGCAATAACAACGAGTTC+AGG + chr7_1:75138192-75138211 None:intergenic 45.0%
! CCTGAACTCGTTGTTATTGC+TGG - chr7_1:75138189-75138208 Msa1038320:intron 45.0%
TCTGTTGTCTGTAGACGAAG+TGG - chr7_1:75138604-75138623 Msa1038320:intron 45.0%
GAAACTCACACACACGCAAT+TGG - chr7_1:75138639-75138658 Msa1038320:intron 45.0%
!!! GGCAGAAAAGGTGTTTTCGA+GGG + chr7_1:75138997-75139016 None:intergenic 45.0%
!!! AGGCAGAAAAGGTGTTTTCG+AGG + chr7_1:75138998-75139017 None:intergenic 45.0%
AGTTCATGTGAAACAGAGGC+AGG + chr7_1:75139041-75139060 None:intergenic 45.0%
AATTTGAACGACTGGATCGG+TGG + chr7_1:75139328-75139347 None:intergenic 45.0%
GGCCCCATAAACTATATTGG+AGG - chr7_1:75139496-75139515 Msa1038320:intron 45.0%
GTTTCAACGCTCTTGACTCA+TGG - chr7_1:75139706-75139725 Msa1038320:intron 45.0%
TCATGGCAAGATCCAGGAAA+GGG - chr7_1:75139723-75139742 Msa1038320:intron 45.0%
CATCCCCTAATGTTCAGGAT+TGG - chr7_1:75139944-75139963 Msa1038320:intron 45.0%
GGATGCCAATCCTGAACATT+AGG + chr7_1:75139952-75139971 None:intergenic 45.0%
TATTTGGCTGCTTGAGTGCA+TGG + chr7_1:75140024-75140043 None:intergenic 45.0%
!!! GGTGTTGCTGCCATCGTTTT+TGG - chr7_1:75138210-75138229 Msa1038320:intron 50.0%
! CCTGAAGTTGGTCGCAGTAT+CGG - chr7_1:75138246-75138265 Msa1038320:intron 50.0%
GCGTGTGTGTGAGTTTCAAG+TGG + chr7_1:75138636-75138655 None:intergenic 50.0%
ACACGCAATTGGGAAGTCCT+GGG - chr7_1:75138650-75138669 Msa1038320:intron 50.0%
TTTCACTCGGGTTCAAACCC+AGG + chr7_1:75138670-75138689 None:intergenic 50.0%
TTGGCTGGACACTTTCACTC+GGG + chr7_1:75138682-75138701 None:intergenic 50.0%
CTTGGCTGGACACTTTCACT+CGG + chr7_1:75138683-75138702 None:intergenic 50.0%
TCATGTGAAACAGAGGCAGG+AGG + chr7_1:75139038-75139057 None:intergenic 50.0%
CTTGACTCATGGCAAGATCC+AGG - chr7_1:75139717-75139736 Msa1038320:intron 50.0%
CTCATGGCAAGATCCAGGAA+AGG - chr7_1:75139722-75139741 Msa1038320:intron 50.0%
AAGGAACCAGATTCCTCAGG+AGG - chr7_1:75140202-75140221 Msa1038320:CDS 50.0%
AGGAACCAGATTCCTCAGGA+GGG - chr7_1:75140203-75140222 Msa1038320:CDS 50.0%
CCGATACTGCGACCAACTTC+AGG + chr7_1:75138249-75138268 None:intergenic 55.0%
CACACGCAATTGGGAAGTCC+TGG - chr7_1:75138649-75138668 Msa1038320:intron 55.0%
!! TGGAGGCAGAGGCACTTGTT+TGG - chr7_1:75139513-75139532 Msa1038320:intron 55.0%
GGCAAGATCCAGGAAAGGGT+CGG - chr7_1:75139727-75139746 Msa1038320:intron 55.0%
GCAAGATCCAGGAAAGGGTC+GGG - chr7_1:75139728-75139747 Msa1038320:intron 55.0%
GGAACCAGATTCCTCAGGAG+GGG - chr7_1:75140204-75140223 Msa1038320:CDS 55.0%
! TAACGGACCCGACCCTTTCC+TGG + chr7_1:75139738-75139757 None:intergenic 60.0%
! GGGTCGGGTCCGTTAGTCTA+TGG - chr7_1:75139743-75139762 Msa1038320:intron 60.0%
GGCTCCCCTCCTGAGGAATC+TGG + chr7_1:75140211-75140230 None:intergenic 65.0%
CTCAGATGGCTCCCCTCCTG+AGG + chr7_1:75140218-75140237 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr7_1 gene 75137898 75140428 75137898 ID=Msa1038320;Name=Msa1038320
chr7_1 mRNA 75137898 75140428 75137898 ID=Msa1038320-mRNA-1;Parent=Msa1038320;Name=Msa1038320-mRNA-1;_AED=0.01;_eAED=0.01;_QI=78|1|1|1|1|1|2|122|150
chr7_1 exon 75137898 75138154 75137898 ID=Msa1038320-mRNA-1:exon:19120;Parent=Msa1038320-mRNA-1
chr7_1 exon 75140033 75140428 75140033 ID=Msa1038320-mRNA-1:exon:19119;Parent=Msa1038320-mRNA-1
chr7_1 five_prime_UTR 75140351 75140428 75140351 ID=Msa1038320-mRNA-1:five_prime_utr;Parent=Msa1038320-mRNA-1
chr7_1 CDS 75140033 75140350 75140033 ID=Msa1038320-mRNA-1:cds;Parent=Msa1038320-mRNA-1
chr7_1 CDS 75138020 75138154 75138020 ID=Msa1038320-mRNA-1:cds;Parent=Msa1038320-mRNA-1
chr7_1 three_prime_UTR 75137898 75138019 75137898 ID=Msa1038320-mRNA-1:three_prime_utr;Parent=Msa1038320-mRNA-1
Gene Sequence

>Msa1038320

ATGATGATGACGATGAACTGTGTTTCGTTTTGTTCGTCAATTTCAATTTCAATTCCAACCCCAATTGCATCAACACAACACCTCGCTTTCTCTTCTTCTTCATCTTTTTGTTCCATTTCAAGGGTTTCTATCAATCCTCCACGAAGAAGAAGAATAAGAAGAAGAATAAACAATAATGGTTTCACTTGCAACGCACTTTTCGGATTAGGTGTACCTGAACTCGTTGTTATTGCTGGTGTTGCTGCCATCGTTTTTGGTCCCAAAAAATTGCCTGAAGTTGGTCGCAGTATCGGTAAAACTGTCAAAAGCTTTCAACAGGCAGCAAAGGAGTTTGAGTCTGAGCTTAAAAAGGAACCAGATTCCTCAGGAGGGGAGCCATCTGAGAAATCAATTGCTGTTAGCGAAGAGAAGAAGCAAGATACTGAGGTTTCTAGTTCTAAGGACAGTGTATGA

Protein sequence

>Msa1038320

MMMTMNCVSFCSSISISIPTPIASTQHLAFSSSSSFCSISRVSINPPRRRRIRRRINNNGFTCNALFGLGVPELVVIAGVAAIVFGPKKLPEVGRSIGKTVKSFQQAAKEFESELKKEPDSSGGEPSEKSIAVSEEKKQDTEVSSSKDSV*