AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1394280


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1394280 MtrunA17_CPg0492781 98.333 60 1 0 46 105 7 66 1.14e-38 124
Msa1394280 MtrunA17_Chr4g0015791 98.333 60 1 0 46 105 7 66 1.14e-38 124
Msa1394280 MtrunA17_Chr8g0355601 96.610 59 2 0 46 104 7 65 1.73e-37 120
Msa1394280 MtrunA17_Chr7g0224991 95.455 44 2 0 62 105 6 49 7.95e-26 90.9
Msa1394280 MtrunA17_CPg0492791 93.750 32 2 0 15 46 1 32 2.06e-15 64.3
Msa1394280 MtrunA17_Chr4g0015781 93.750 32 2 0 15 46 1 32 2.06e-15 64.3
Msa1394280 MtrunA17_Chr4g0028951 93.750 32 2 0 15 46 1 32 2.06e-15 64.3
Msa1394280 MtrunA17_Chr8g0355611 93.750 32 2 0 15 46 1 32 2.06e-15 64.3
Msa1394280 MtrunA17_Chr4g0016881 96.774 31 1 0 15 45 1 31 5.83e-15 63.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1394280 ATCG00640.1 75.000 60 15 0 46 105 7 66 2.13e-29 100
Msa1394280 ATCG00630.1 84.375 32 5 0 15 46 1 32 8.57e-13 58.2

Find 13 sgRNAs with CRISPR-Local

Find 114 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATACGAATAACTGTTATTT+TGG 0.125276 tig0021785:+101230 Msa1394280:CDS
AGAGTGTTAATAAGGAATCT+AGG 0.329597 tig0021785:+101274 Msa1394280:CDS
AATCGTATGTTTGCAACAAA+AGG 0.396841 tig0021785:-101370 None:intergenic
CACCAGTGGCAAGTACTCTA+TGG 0.426592 tig0021785:+100603 Msa1394280:CDS
GAGTGTTAATAAGGAATCTA+GGG 0.452009 tig0021785:+101275 Msa1394280:CDS
CTATGGTTCGCGGTTCTAGC+AGG 0.487956 tig0021785:+100620 Msa1394280:CDS
ACACAATACACCTAGTCGAT+TGG 0.524208 tig0021785:+101329 Msa1394280:CDS
GGCAAGTACTCTATGGTTCG+CGG 0.527936 tig0021785:+100610 Msa1394280:CDS
ATCGTATGTTTGCAACAAAA+GGG 0.538893 tig0021785:-101369 None:intergenic
TTTCTCAATTCCAATCGACT+AGG 0.574270 tig0021785:-101339 None:intergenic
ATATCTCTCTGTGGCACCAG+TGG 0.585814 tig0021785:+100589 Msa1394280:CDS
AACCATAGAGTACTTGCCAC+TGG 0.586013 tig0021785:-100605 None:intergenic
AGTGTTAATAAGGAATCTAG+GGG 0.667965 tig0021785:+101276 Msa1394280:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAACTAGAATCAAAAAAA+GGG - tig0021785:100692-100711 None:intergenic 15.0%
!! AGAGCAAATTAATTTAATAA+AGG + tig0021785:100816-100835 Msa1394280:intron 15.0%
!! TATTATTAAATTCATAGCAA+TGG - tig0021785:100910-100929 None:intergenic 15.0%
!! CTGTACTATATAAAATTAAT+TGG + tig0021785:101066-101085 Msa1394280:intron 15.0%
!! AATAACTAGAATCAAAAAAA+GGG - tig0021785:100692-100711 None:intergenic 15.0%
!! AGAGCAAATTAATTTAATAA+AGG + tig0021785:100816-100835 Msa1394280:intron 15.0%
!! TATTATTAAATTCATAGCAA+TGG - tig0021785:100910-100929 None:intergenic 15.0%
!! CTGTACTATATAAAATTAAT+TGG + tig0021785:101066-101085 Msa1394280:intron 15.0%
!!! TTCGTTTTTTTCTTGTAATT+TGG - tig0021785:100540-100559 None:intergenic 20.0%
!! AAATTACAAGAAAAAAACGA+AGG + tig0021785:100539-100558 Msa1394280:CDS 20.0%
!! ATAACTAGAATCAAAAAAAG+GGG - tig0021785:100691-100710 None:intergenic 20.0%
!! CAATAACTAGAATCAAAAAA+AGG - tig0021785:100693-100712 None:intergenic 20.0%
!!! CTTTTTTTGATTCTAGTTAT+TGG + tig0021785:100691-100710 Msa1394280:intron 20.0%
!!! AGAGGGATTTAATATTTTAT+TGG - tig0021785:100746-100765 None:intergenic 20.0%
!! GCAAATTAATTTAATAAAGG+TGG + tig0021785:100819-100838 Msa1394280:intron 20.0%
!!! TAATTTAATAAAGGTGGATT+TGG + tig0021785:100825-100844 Msa1394280:intron 20.0%
!! TTCTATTACAATTCCATTTA+TGG - tig0021785:100941-100960 None:intergenic 20.0%
!!! TATACGAATAACTGTTATTT+TGG + tig0021785:101230-101249 Msa1394280:CDS 20.0%
!!! TGATAAAAAGAGTGTTAATA+AGG + tig0021785:101266-101285 Msa1394280:CDS 20.0%
!!! TTCGTTTTTTTCTTGTAATT+TGG - tig0021785:100540-100559 None:intergenic 20.0%
!! AAATTACAAGAAAAAAACGA+AGG + tig0021785:100539-100558 Msa1394280:CDS 20.0%
!! ATAACTAGAATCAAAAAAAG+GGG - tig0021785:100691-100710 None:intergenic 20.0%
!! CAATAACTAGAATCAAAAAA+AGG - tig0021785:100693-100712 None:intergenic 20.0%
!!! CTTTTTTTGATTCTAGTTAT+TGG + tig0021785:100691-100710 Msa1394280:intron 20.0%
!!! AGAGGGATTTAATATTTTAT+TGG - tig0021785:100746-100765 None:intergenic 20.0%
!! GCAAATTAATTTAATAAAGG+TGG + tig0021785:100819-100838 Msa1394280:intron 20.0%
!!! TAATTTAATAAAGGTGGATT+TGG + tig0021785:100825-100844 Msa1394280:intron 20.0%
!! TTCTATTACAATTCCATTTA+TGG - tig0021785:100941-100960 None:intergenic 20.0%
!!! TATACGAATAACTGTTATTT+TGG + tig0021785:101230-101249 Msa1394280:CDS 20.0%
!!! TGATAAAAAGAGTGTTAATA+AGG + tig0021785:101266-101285 Msa1394280:CDS 20.0%
! AAAAAAAAAACGAACGAAGA+GGG - tig0021785:100763-100782 None:intergenic 25.0%
! AAAAAAAAAAACGAACGAAG+AGG - tig0021785:100764-100783 None:intergenic 25.0%
! TGGAATTGTAATAGAATACT+TGG + tig0021785:100945-100964 Msa1394280:intron 25.0%
! GGAATTGTAATAGAATACTT+GGG + tig0021785:100946-100965 Msa1394280:intron 25.0%
! AGTGAATCAAAAAAAACCAA+AGG + tig0021785:101184-101203 Msa1394280:intron 25.0%
! AAAAAAAAAACGAACGAAGA+GGG - tig0021785:100763-100782 None:intergenic 25.0%
! AAAAAAAAAAACGAACGAAG+AGG - tig0021785:100764-100783 None:intergenic 25.0%
! TGGAATTGTAATAGAATACT+TGG + tig0021785:100945-100964 Msa1394280:intron 25.0%
! GGAATTGTAATAGAATACTT+GGG + tig0021785:100946-100965 Msa1394280:intron 25.0%
! AGTGAATCAAAAAAAACCAA+AGG + tig0021785:101184-101203 Msa1394280:intron 25.0%
TTACAAGAAAAAAACGAAGG+AGG + tig0021785:100542-100561 Msa1394280:CDS 30.0%
TCTAAAAACATATCTCTCTG+TGG + tig0021785:100580-100599 Msa1394280:CDS 30.0%
AGAAATCAATCGTTTATTCC+CGG + tig0021785:100652-100671 Msa1394280:intron 30.0%
! TTTGATTCTAGTTATTGGCA+CGG + tig0021785:100696-100715 Msa1394280:intron 30.0%
AAAAACTCCTAATTTCACTG+AGG - tig0021785:100851-100870 None:intergenic 30.0%
TAATAGAGTGAGACCATAAA+TGG + tig0021785:100925-100944 Msa1394280:intron 30.0%
ATTGTAATAGAATACTTGGG+CGG + tig0021785:100949-100968 Msa1394280:intron 30.0%
GAATCAAAAAAAACCAAAGG+AGG + tig0021785:101187-101206 Msa1394280:intron 30.0%
TATTCGTATATCTTTACCCT+TGG - tig0021785:101220-101239 None:intergenic 30.0%
! AGAGTGTTAATAAGGAATCT+AGG + tig0021785:101274-101293 Msa1394280:CDS 30.0%
GAGTGTTAATAAGGAATCTA+GGG + tig0021785:101275-101294 Msa1394280:CDS 30.0%
AGTGTTAATAAGGAATCTAG+GGG + tig0021785:101276-101295 Msa1394280:CDS 30.0%
ATCGTATGTTTGCAACAAAA+GGG - tig0021785:101372-101391 None:intergenic 30.0%
AATCGTATGTTTGCAACAAA+AGG - tig0021785:101373-101392 None:intergenic 30.0%
TTACAAGAAAAAAACGAAGG+AGG + tig0021785:100542-100561 Msa1394280:CDS 30.0%
TCTAAAAACATATCTCTCTG+TGG + tig0021785:100580-100599 Msa1394280:CDS 30.0%
AGAAATCAATCGTTTATTCC+CGG + tig0021785:100652-100671 Msa1394280:intron 30.0%
! TTTGATTCTAGTTATTGGCA+CGG + tig0021785:100696-100715 Msa1394280:intron 30.0%
AAAAACTCCTAATTTCACTG+AGG - tig0021785:100851-100870 None:intergenic 30.0%
TAATAGAGTGAGACCATAAA+TGG + tig0021785:100925-100944 Msa1394280:intron 30.0%
ATTGTAATAGAATACTTGGG+CGG + tig0021785:100949-100968 Msa1394280:intron 30.0%
GAATCAAAAAAAACCAAAGG+AGG + tig0021785:101187-101206 Msa1394280:intron 30.0%
TATTCGTATATCTTTACCCT+TGG - tig0021785:101220-101239 None:intergenic 30.0%
! AGAGTGTTAATAAGGAATCT+AGG + tig0021785:101274-101293 Msa1394280:CDS 30.0%
GAGTGTTAATAAGGAATCTA+GGG + tig0021785:101275-101294 Msa1394280:CDS 30.0%
AGTGTTAATAAGGAATCTAG+GGG + tig0021785:101276-101295 Msa1394280:CDS 30.0%
ATCGTATGTTTGCAACAAAA+GGG - tig0021785:101372-101391 None:intergenic 30.0%
AATCGTATGTTTGCAACAAA+AGG - tig0021785:101373-101392 None:intergenic 30.0%
! TGAAATTAGGAGTTTTTCCC+AGG + tig0021785:100854-100873 Msa1394280:intron 35.0%
CTTCAATTCCATTGAAACCT+GGG - tig0021785:100874-100893 None:intergenic 35.0%
ACTTCAATTCCATTGAAACC+TGG - tig0021785:100875-100894 None:intergenic 35.0%
TTGTAATAGAATACTTGGGC+GGG + tig0021785:100950-100969 Msa1394280:intron 35.0%
TTCGAAGCGAAGAAGAAAAA+AGG - tig0021785:101145-101164 None:intergenic 35.0%
AAAAAACCAAAGGAGGTTCA+TGG + tig0021785:101194-101213 Msa1394280:intron 35.0%
TTTCTCAATTCCAATCGACT+AGG - tig0021785:101342-101361 None:intergenic 35.0%
! TGAAATTAGGAGTTTTTCCC+AGG + tig0021785:100854-100873 Msa1394280:intron 35.0%
CTTCAATTCCATTGAAACCT+GGG - tig0021785:100874-100893 None:intergenic 35.0%
ACTTCAATTCCATTGAAACC+TGG - tig0021785:100875-100894 None:intergenic 35.0%
TTGTAATAGAATACTTGGGC+GGG + tig0021785:100950-100969 Msa1394280:intron 35.0%
TTCGAAGCGAAGAAGAAAAA+AGG - tig0021785:101145-101164 None:intergenic 35.0%
AAAAAACCAAAGGAGGTTCA+TGG + tig0021785:101194-101213 Msa1394280:intron 35.0%
TTTCTCAATTCCAATCGACT+AGG - tig0021785:101342-101361 None:intergenic 35.0%
GATTTGGCCTCAGTGAAATT+AGG + tig0021785:100841-100860 Msa1394280:intron 40.0%
! GAGTTTTTCCCAGGTTTCAA+TGG + tig0021785:100863-100882 Msa1394280:intron 40.0%
ACACAATACACCTAGTCGAT+TGG + tig0021785:101329-101348 Msa1394280:CDS 40.0%
GATTTGGCCTCAGTGAAATT+AGG + tig0021785:100841-100860 Msa1394280:intron 40.0%
! GAGTTTTTCCCAGGTTTCAA+TGG + tig0021785:100863-100882 Msa1394280:intron 40.0%
ACACAATACACCTAGTCGAT+TGG + tig0021785:101329-101348 Msa1394280:CDS 40.0%
! AACCATAGAGTACTTGCCAC+TGG - tig0021785:100608-100627 None:intergenic 45.0%
AAGGGGAATGTCAATGCATC+CGG - tig0021785:100674-100693 None:intergenic 45.0%
! TTCTAGTTATTGGCACGGCA+AGG + tig0021785:100701-100720 Msa1394280:intron 45.0%
TCTAGTTATTGGCACGGCAA+GGG + tig0021785:100702-100721 Msa1394280:intron 45.0%
! AACCATAGAGTACTTGCCAC+TGG - tig0021785:100608-100627 None:intergenic 45.0%
AAGGGGAATGTCAATGCATC+CGG - tig0021785:100674-100693 None:intergenic 45.0%
! TTCTAGTTATTGGCACGGCA+AGG + tig0021785:100701-100720 Msa1394280:intron 45.0%
TCTAGTTATTGGCACGGCAA+GGG + tig0021785:100702-100721 Msa1394280:intron 45.0%
ATATCTCTCTGTGGCACCAG+TGG + tig0021785:100589-100608 Msa1394280:CDS 50.0%
CACCAGTGGCAAGTACTCTA+TGG + tig0021785:100603-100622 Msa1394280:CDS 50.0%
GGCAAGTACTCTATGGTTCG+CGG + tig0021785:100610-100629 Msa1394280:CDS 50.0%
AGGGGAATGTCAATGCATCC+GGG - tig0021785:100673-100692 None:intergenic 50.0%
CTAGTTATTGGCACGGCAAG+GGG + tig0021785:100703-100722 Msa1394280:intron 50.0%
CAAAGGAGGTTCATGGCCAA+GGG + tig0021785:101201-101220 Msa1394280:intron 50.0%
ATATCTCTCTGTGGCACCAG+TGG + tig0021785:100589-100608 Msa1394280:CDS 50.0%
CACCAGTGGCAAGTACTCTA+TGG + tig0021785:100603-100622 Msa1394280:CDS 50.0%
GGCAAGTACTCTATGGTTCG+CGG + tig0021785:100610-100629 Msa1394280:CDS 50.0%
AGGGGAATGTCAATGCATCC+GGG - tig0021785:100673-100692 None:intergenic 50.0%
CTAGTTATTGGCACGGCAAG+GGG + tig0021785:100703-100722 Msa1394280:intron 50.0%
CAAAGGAGGTTCATGGCCAA+GGG + tig0021785:101201-101220 Msa1394280:intron 50.0%
! CTATGGTTCGCGGTTCTAGC+AGG + tig0021785:100620-100639 Msa1394280:CDS 55.0%
CCTTGGCCATGAACCTCCTT+TGG - tig0021785:101203-101222 None:intergenic 55.0%
CCAAAGGAGGTTCATGGCCA+AGG + tig0021785:101200-101219 Msa1394280:intron 55.0%
! CTATGGTTCGCGGTTCTAGC+AGG + tig0021785:100620-100639 Msa1394280:CDS 55.0%
CCTTGGCCATGAACCTCCTT+TGG - tig0021785:101203-101222 None:intergenic 55.0%
CCAAAGGAGGTTCATGGCCA+AGG + tig0021785:101200-101219 Msa1394280:intron 55.0%
Chromosome Type Strat End Strand Name
tig0021785 gene 100530 101413 100530 ID=Msa1394280;Name=Msa1394280
tig0021785 mRNA 100530 101413 100530 ID=Msa1394280-mRNA-1;Parent=Msa1394280;Name=Msa1394280-mRNA-1;_AED=0.45;_eAED=0.46;_QI=0|0|0|1|0|0|2|0|105
tig0021785 exon 100530 100662 100530 ID=Msa1394280-mRNA-1:exon:14240;Parent=Msa1394280-mRNA-1
tig0021785 exon 101229 101413 101229 ID=Msa1394280-mRNA-1:exon:14241;Parent=Msa1394280-mRNA-1
tig0021785 CDS 100530 100662 100530 ID=Msa1394280-mRNA-1:cds;Parent=Msa1394280-mRNA-1
tig0021785 CDS 101229 101413 101229 ID=Msa1394280-mRNA-1:cds;Parent=Msa1394280-mRNA-1
Gene Sequence

>Msa1394280

ATGTATTCCAAATTACAAGAAAAAAACGAAGGAGGATTTGAAATGCGAGATCTAAAAACATATCTCTCTGTGGCACCAGTGGCAAGTACTCTATGGTTCGCGGTTCTAGCAGGTCTCTTGATAGAAATCAATCATATACGAATAACTGTTATTTTGGAATGTAGCAGTTGTGATAAAAAGAGTGTTAATAAGGAATCTAGGGGTATTTCTAGATATATTACTCAAAAGAATCGACACAATACACCTAGTCGATTGGAATTGAGAAAATTCTGTCCCTTTTGTTGCAAACATACGATTCACGTCGAGATAAAGAAATAG

Protein sequence

>Msa1394280

MYSKLQEKNEGGFEMRDLKTYLSVAPVASTLWFAVLAGLLIEINHIRITVILECSSCDKKSVNKESRGISRYITQKNRHNTPSRLELRKFCPFCCKHTIHVEIKK*