AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1086830


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1086830 MtrunA17_CPg0492781 98.333 60 1 0 46 105 7 66 1.14e-38 124
Msa1086830 MtrunA17_Chr4g0015791 98.333 60 1 0 46 105 7 66 1.14e-38 124
Msa1086830 MtrunA17_Chr8g0355601 96.610 59 2 0 46 104 7 65 1.73e-37 120
Msa1086830 MtrunA17_Chr7g0224991 95.455 44 2 0 62 105 6 49 7.95e-26 90.9
Msa1086830 MtrunA17_CPg0492791 93.750 32 2 0 15 46 1 32 2.06e-15 64.3
Msa1086830 MtrunA17_Chr4g0015781 93.750 32 2 0 15 46 1 32 2.06e-15 64.3
Msa1086830 MtrunA17_Chr4g0028951 93.750 32 2 0 15 46 1 32 2.06e-15 64.3
Msa1086830 MtrunA17_Chr8g0355611 93.750 32 2 0 15 46 1 32 2.06e-15 64.3
Msa1086830 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
Msa1086830 ATCG00640.1 75.000 60 15 0 46 105 7 66 2.13e-29 100
Msa1086830 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 7_2:-87591766 Msa1086830:CDS
AGAGTGTTAATAAGGAATCT+AGG 0.329597 7_2:-87591722 Msa1086830:CDS
AATCGTATGTTTGCAACAAA+AGG 0.396841 7_2:+87591626 None:intergenic
CACCAGTGGCAAGTACTCTA+TGG 0.426592 7_2:-87592393 Msa1086830:CDS
GAGTGTTAATAAGGAATCTA+GGG 0.452009 7_2:-87591721 Msa1086830:CDS
CTATGGTTCGCGGTTCTAGC+AGG 0.487956 7_2:-87592376 Msa1086830:CDS
ACACAATACACCTAGTCGAT+TGG 0.524208 7_2:-87591667 Msa1086830:CDS
GGCAAGTACTCTATGGTTCG+CGG 0.527936 7_2:-87592386 Msa1086830:CDS
ATCGTATGTTTGCAACAAAA+GGG 0.538893 7_2:+87591627 None:intergenic
TTTCTCAATTCCAATCGACT+AGG 0.574270 7_2:+87591657 None:intergenic
ATATCTCTCTGTGGCACCAG+TGG 0.585814 7_2:-87592407 Msa1086830:CDS
AACCATAGAGTACTTGCCAC+TGG 0.586013 7_2:+87592391 None:intergenic
AGTGTTAATAAGGAATCTAG+GGG 0.667965 7_2:-87591720 Msa1086830:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAACTAGAATCAAAAAAA+GGG + chr7_2:87591767-87591786 None:intergenic 15.0%
!! AGAGCAAATTAATTTAATAA+AGG - chr7_2:87591891-87591910 Msa1086830:intron 15.0%
!! TATTATTAAATTCATAGCAA+TGG + chr7_2:87591985-87592004 None:intergenic 15.0%
!! CTGTACTATATAAAATTAAT+TGG - chr7_2:87592141-87592160 Msa1086830:intron 15.0%
!! AATAACTAGAATCAAAAAAA+GGG + chr7_2:87591767-87591786 None:intergenic 15.0%
!! AGAGCAAATTAATTTAATAA+AGG - chr7_2:87591891-87591910 Msa1086830:intron 15.0%
!! TATTATTAAATTCATAGCAA+TGG + chr7_2:87591985-87592004 None:intergenic 15.0%
!! CTGTACTATATAAAATTAAT+TGG - chr7_2:87592141-87592160 Msa1086830:intron 15.0%
!!! TTCGTTTTTTTCTTGTAATT+TGG + chr7_2:87591615-87591634 None:intergenic 20.0%
!! AAATTACAAGAAAAAAACGA+AGG - chr7_2:87591614-87591633 Msa1086830:CDS 20.0%
!! ATAACTAGAATCAAAAAAAG+GGG + chr7_2:87591766-87591785 None:intergenic 20.0%
!! CAATAACTAGAATCAAAAAA+AGG + chr7_2:87591768-87591787 None:intergenic 20.0%
!!! CTTTTTTTGATTCTAGTTAT+TGG - chr7_2:87591766-87591785 Msa1086830:CDS 20.0%
!!! AGAGGGATTTAATATTTTAT+TGG + chr7_2:87591821-87591840 None:intergenic 20.0%
!! GCAAATTAATTTAATAAAGG+TGG - chr7_2:87591894-87591913 Msa1086830:intron 20.0%
!!! TAATTTAATAAAGGTGGATT+TGG - chr7_2:87591900-87591919 Msa1086830:intron 20.0%
!! TTCTATTACAATTCCATTTA+TGG + chr7_2:87592016-87592035 None:intergenic 20.0%
!!! TATACGAATAACTGTTATTT+TGG - chr7_2:87592305-87592324 Msa1086830:intron 20.0%
!!! TGATAAAAAGAGTGTTAATA+AGG - chr7_2:87592341-87592360 Msa1086830:intron 20.0%
!!! TTCGTTTTTTTCTTGTAATT+TGG + chr7_2:87591615-87591634 None:intergenic 20.0%
!! AAATTACAAGAAAAAAACGA+AGG - chr7_2:87591614-87591633 Msa1086830:CDS 20.0%
!! ATAACTAGAATCAAAAAAAG+GGG + chr7_2:87591766-87591785 None:intergenic 20.0%
!! CAATAACTAGAATCAAAAAA+AGG + chr7_2:87591768-87591787 None:intergenic 20.0%
!!! CTTTTTTTGATTCTAGTTAT+TGG - chr7_2:87591766-87591785 Msa1086830:CDS 20.0%
!!! AGAGGGATTTAATATTTTAT+TGG + chr7_2:87591821-87591840 None:intergenic 20.0%
!! GCAAATTAATTTAATAAAGG+TGG - chr7_2:87591894-87591913 Msa1086830:intron 20.0%
!!! TAATTTAATAAAGGTGGATT+TGG - chr7_2:87591900-87591919 Msa1086830:intron 20.0%
!! TTCTATTACAATTCCATTTA+TGG + chr7_2:87592016-87592035 None:intergenic 20.0%
!!! TATACGAATAACTGTTATTT+TGG - chr7_2:87592305-87592324 Msa1086830:intron 20.0%
!!! TGATAAAAAGAGTGTTAATA+AGG - chr7_2:87592341-87592360 Msa1086830:intron 20.0%
! AAAAAAAAAACGAACGAAGA+GGG + chr7_2:87591838-87591857 None:intergenic 25.0%
! AAAAAAAAAAACGAACGAAG+AGG + chr7_2:87591839-87591858 None:intergenic 25.0%
! TGGAATTGTAATAGAATACT+TGG - chr7_2:87592020-87592039 Msa1086830:intron 25.0%
! GGAATTGTAATAGAATACTT+GGG - chr7_2:87592021-87592040 Msa1086830:intron 25.0%
! AGTGAATCAAAAAAAACCAA+AGG - chr7_2:87592259-87592278 Msa1086830:intron 25.0%
! AAAAAAAAAACGAACGAAGA+GGG + chr7_2:87591838-87591857 None:intergenic 25.0%
! AAAAAAAAAAACGAACGAAG+AGG + chr7_2:87591839-87591858 None:intergenic 25.0%
! TGGAATTGTAATAGAATACT+TGG - chr7_2:87592020-87592039 Msa1086830:intron 25.0%
! GGAATTGTAATAGAATACTT+GGG - chr7_2:87592021-87592040 Msa1086830:intron 25.0%
! AGTGAATCAAAAAAAACCAA+AGG - chr7_2:87592259-87592278 Msa1086830:intron 25.0%
TTACAAGAAAAAAACGAAGG+AGG - chr7_2:87591617-87591636 Msa1086830:CDS 30.0%
TCTAAAAACATATCTCTCTG+TGG - chr7_2:87591655-87591674 Msa1086830:CDS 30.0%
AGAAATCAATCGTTTATTCC+CGG - chr7_2:87591727-87591746 Msa1086830:CDS 30.0%
! TTTGATTCTAGTTATTGGCA+CGG - chr7_2:87591771-87591790 Msa1086830:intron 30.0%
AAAAACTCCTAATTTCACTG+AGG + chr7_2:87591926-87591945 None:intergenic 30.0%
TAATAGAGTGAGACCATAAA+TGG - chr7_2:87592000-87592019 Msa1086830:intron 30.0%
ATTGTAATAGAATACTTGGG+CGG - chr7_2:87592024-87592043 Msa1086830:intron 30.0%
GAATCAAAAAAAACCAAAGG+AGG - chr7_2:87592262-87592281 Msa1086830:intron 30.0%
TATTCGTATATCTTTACCCT+TGG + chr7_2:87592295-87592314 None:intergenic 30.0%
! AGAGTGTTAATAAGGAATCT+AGG - chr7_2:87592349-87592368 Msa1086830:intron 30.0%
GAGTGTTAATAAGGAATCTA+GGG - chr7_2:87592350-87592369 Msa1086830:intron 30.0%
AGTGTTAATAAGGAATCTAG+GGG - chr7_2:87592351-87592370 Msa1086830:intron 30.0%
ATCGTATGTTTGCAACAAAA+GGG + chr7_2:87592447-87592466 None:intergenic 30.0%
AATCGTATGTTTGCAACAAA+AGG + chr7_2:87592448-87592467 None:intergenic 30.0%
TTACAAGAAAAAAACGAAGG+AGG - chr7_2:87591617-87591636 Msa1086830:CDS 30.0%
TCTAAAAACATATCTCTCTG+TGG - chr7_2:87591655-87591674 Msa1086830:CDS 30.0%
AGAAATCAATCGTTTATTCC+CGG - chr7_2:87591727-87591746 Msa1086830:CDS 30.0%
! TTTGATTCTAGTTATTGGCA+CGG - chr7_2:87591771-87591790 Msa1086830:intron 30.0%
AAAAACTCCTAATTTCACTG+AGG + chr7_2:87591926-87591945 None:intergenic 30.0%
TAATAGAGTGAGACCATAAA+TGG - chr7_2:87592000-87592019 Msa1086830:intron 30.0%
ATTGTAATAGAATACTTGGG+CGG - chr7_2:87592024-87592043 Msa1086830:intron 30.0%
GAATCAAAAAAAACCAAAGG+AGG - chr7_2:87592262-87592281 Msa1086830:intron 30.0%
TATTCGTATATCTTTACCCT+TGG + chr7_2:87592295-87592314 None:intergenic 30.0%
! AGAGTGTTAATAAGGAATCT+AGG - chr7_2:87592349-87592368 Msa1086830:intron 30.0%
GAGTGTTAATAAGGAATCTA+GGG - chr7_2:87592350-87592369 Msa1086830:intron 30.0%
AGTGTTAATAAGGAATCTAG+GGG - chr7_2:87592351-87592370 Msa1086830:intron 30.0%
ATCGTATGTTTGCAACAAAA+GGG + chr7_2:87592447-87592466 None:intergenic 30.0%
AATCGTATGTTTGCAACAAA+AGG + chr7_2:87592448-87592467 None:intergenic 30.0%
! TGAAATTAGGAGTTTTTCCC+AGG - chr7_2:87591929-87591948 Msa1086830:intron 35.0%
CTTCAATTCCATTGAAACCT+GGG + chr7_2:87591949-87591968 None:intergenic 35.0%
ACTTCAATTCCATTGAAACC+TGG + chr7_2:87591950-87591969 None:intergenic 35.0%
TTGTAATAGAATACTTGGGC+GGG - chr7_2:87592025-87592044 Msa1086830:intron 35.0%
TTCGAAGCGAAGAAGAAAAA+AGG + chr7_2:87592220-87592239 None:intergenic 35.0%
AAAAAACCAAAGGAGGTTCA+TGG - chr7_2:87592269-87592288 Msa1086830:intron 35.0%
TTTCTCAATTCCAATCGACT+AGG + chr7_2:87592417-87592436 None:intergenic 35.0%
! TGAAATTAGGAGTTTTTCCC+AGG - chr7_2:87591929-87591948 Msa1086830:intron 35.0%
CTTCAATTCCATTGAAACCT+GGG + chr7_2:87591949-87591968 None:intergenic 35.0%
ACTTCAATTCCATTGAAACC+TGG + chr7_2:87591950-87591969 None:intergenic 35.0%
TTGTAATAGAATACTTGGGC+GGG - chr7_2:87592025-87592044 Msa1086830:intron 35.0%
TTCGAAGCGAAGAAGAAAAA+AGG + chr7_2:87592220-87592239 None:intergenic 35.0%
AAAAAACCAAAGGAGGTTCA+TGG - chr7_2:87592269-87592288 Msa1086830:intron 35.0%
TTTCTCAATTCCAATCGACT+AGG + chr7_2:87592417-87592436 None:intergenic 35.0%
GATTTGGCCTCAGTGAAATT+AGG - chr7_2:87591916-87591935 Msa1086830:intron 40.0%
! GAGTTTTTCCCAGGTTTCAA+TGG - chr7_2:87591938-87591957 Msa1086830:intron 40.0%
ACACAATACACCTAGTCGAT+TGG - chr7_2:87592404-87592423 Msa1086830:CDS 40.0%
GATTTGGCCTCAGTGAAATT+AGG - chr7_2:87591916-87591935 Msa1086830:intron 40.0%
! GAGTTTTTCCCAGGTTTCAA+TGG - chr7_2:87591938-87591957 Msa1086830:intron 40.0%
ACACAATACACCTAGTCGAT+TGG - chr7_2:87592404-87592423 Msa1086830:CDS 40.0%
! AACCATAGAGTACTTGCCAC+TGG + chr7_2:87591683-87591702 None:intergenic 45.0%
AAGGGGAATGTCAATGCATC+CGG + chr7_2:87591749-87591768 None:intergenic 45.0%
! TTCTAGTTATTGGCACGGCA+AGG - chr7_2:87591776-87591795 Msa1086830:intron 45.0%
TCTAGTTATTGGCACGGCAA+GGG - chr7_2:87591777-87591796 Msa1086830:intron 45.0%
! AACCATAGAGTACTTGCCAC+TGG + chr7_2:87591683-87591702 None:intergenic 45.0%
AAGGGGAATGTCAATGCATC+CGG + chr7_2:87591749-87591768 None:intergenic 45.0%
! TTCTAGTTATTGGCACGGCA+AGG - chr7_2:87591776-87591795 Msa1086830:intron 45.0%
TCTAGTTATTGGCACGGCAA+GGG - chr7_2:87591777-87591796 Msa1086830:intron 45.0%
ATATCTCTCTGTGGCACCAG+TGG - chr7_2:87591664-87591683 Msa1086830:CDS 50.0%
CACCAGTGGCAAGTACTCTA+TGG - chr7_2:87591678-87591697 Msa1086830:CDS 50.0%
GGCAAGTACTCTATGGTTCG+CGG - chr7_2:87591685-87591704 Msa1086830:CDS 50.0%
AGGGGAATGTCAATGCATCC+GGG + chr7_2:87591748-87591767 None:intergenic 50.0%
CTAGTTATTGGCACGGCAAG+GGG - chr7_2:87591778-87591797 Msa1086830:intron 50.0%
CAAAGGAGGTTCATGGCCAA+GGG - chr7_2:87592276-87592295 Msa1086830:intron 50.0%
ATATCTCTCTGTGGCACCAG+TGG - chr7_2:87591664-87591683 Msa1086830:CDS 50.0%
CACCAGTGGCAAGTACTCTA+TGG - chr7_2:87591678-87591697 Msa1086830:CDS 50.0%
GGCAAGTACTCTATGGTTCG+CGG - chr7_2:87591685-87591704 Msa1086830:CDS 50.0%
AGGGGAATGTCAATGCATCC+GGG + chr7_2:87591748-87591767 None:intergenic 50.0%
CTAGTTATTGGCACGGCAAG+GGG - chr7_2:87591778-87591797 Msa1086830:intron 50.0%
CAAAGGAGGTTCATGGCCAA+GGG - chr7_2:87592276-87592295 Msa1086830:intron 50.0%
! CTATGGTTCGCGGTTCTAGC+AGG - chr7_2:87591695-87591714 Msa1086830:CDS 55.0%
CCTTGGCCATGAACCTCCTT+TGG + chr7_2:87592278-87592297 None:intergenic 55.0%
CCAAAGGAGGTTCATGGCCA+AGG - chr7_2:87592275-87592294 Msa1086830:intron 55.0%
! CTATGGTTCGCGGTTCTAGC+AGG - chr7_2:87591695-87591714 Msa1086830:CDS 55.0%
CCTTGGCCATGAACCTCCTT+TGG + chr7_2:87592278-87592297 None:intergenic 55.0%
CCAAAGGAGGTTCATGGCCA+AGG - chr7_2:87592275-87592294 Msa1086830:intron 55.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 87591605 87592488 87591605 ID=Msa1086830;Name=Msa1086830
chr7_2 mRNA 87591605 87592488 87591605 ID=Msa1086830-mRNA-1;Parent=Msa1086830;Name=Msa1086830-mRNA-1;_AED=0.45;_eAED=0.45;_QI=0|0|0|1|0|0|2|0|105
chr7_2 exon 87592356 87592488 87592356 ID=Msa1086830-mRNA-1:exon:23960;Parent=Msa1086830-mRNA-1
chr7_2 exon 87591605 87591789 87591605 ID=Msa1086830-mRNA-1:exon:23959;Parent=Msa1086830-mRNA-1
chr7_2 CDS 87592356 87592488 87592356 ID=Msa1086830-mRNA-1:cds;Parent=Msa1086830-mRNA-1
chr7_2 CDS 87591605 87591789 87591605 ID=Msa1086830-mRNA-1:cds;Parent=Msa1086830-mRNA-1
Gene Sequence

>Msa1086830

ATGTATTCCAAATTACAAGAAAAAAACGAAGGAGGATTTGAAATGCGAGATCTAAAAACATATCTCTCTGTGGCACCAGTGGCAAGTACTCTATGGTTCGCGGTTCTAGCAGGTCTCTTGATAGAAATCAATCATATACGAATAACTGTTATTTTGGAATGTAGCAGTTGTGATAAAAAGAGTGTTAATAAGGAATCTAGGGGTATTTCTAGATATATTACTCAAAAGAATCGACACAATACACCTAGTCGATTGGAATTGAGAAAATTCTGTCCCTTTTGTTGCAAACATACGATTCACGTCGAGATAAAGAAATAG

Protein sequence

>Msa1086830

MYSKLQEKNEGGFEMRDLKTYLSVAPVASTLWFAVLAGLLIEINHIRITVILECSSCDKKSVNKESRGISRYITQKNRHNTPSRLELRKFCPFCCKHTIHVEIKK*