AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0095140


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0095140 MtrunA17_CPg0492781 98.333 60 1 0 46 105 7 66 1.14e-38 124
Msa0095140 MtrunA17_Chr4g0015791 98.333 60 1 0 46 105 7 66 1.14e-38 124
Msa0095140 MtrunA17_Chr8g0355601 96.610 59 2 0 46 104 7 65 1.73e-37 120
Msa0095140 MtrunA17_Chr7g0224991 95.455 44 2 0 62 105 6 49 7.95e-26 90.9
Msa0095140 MtrunA17_CPg0492791 93.750 32 2 0 15 46 1 32 2.06e-15 64.3
Msa0095140 MtrunA17_Chr4g0015781 93.750 32 2 0 15 46 1 32 2.06e-15 64.3
Msa0095140 MtrunA17_Chr4g0028951 93.750 32 2 0 15 46 1 32 2.06e-15 64.3
Msa0095140 MtrunA17_Chr8g0355611 93.750 32 2 0 15 46 1 32 2.06e-15 64.3
Msa0095140 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
Msa0095140 ATCG00640.1 75.000 60 15 0 46 105 7 66 2.13e-29 100
Msa0095140 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 1_2:-79011577 Msa0095140:CDS
AGAGTGTTAATAAGGAATCT+AGG 0.329597 1_2:-79011533 Msa0095140:CDS
AATCGTATGTTTGCAACAAA+AGG 0.396841 1_2:+79011437 None:intergenic
CACCAGTGGCAAGTACTCTA+TGG 0.426592 1_2:-79012205 Msa0095140:CDS
GAGTGTTAATAAGGAATCTA+GGG 0.452009 1_2:-79011532 Msa0095140:CDS
CTATGGTTCGCGGTTCTAGC+AGG 0.487956 1_2:-79012188 Msa0095140:CDS
ACACAATACACCTAGTCGAT+TGG 0.524208 1_2:-79011478 Msa0095140:CDS
GGCAAGTACTCTATGGTTCG+CGG 0.527936 1_2:-79012198 Msa0095140:CDS
ATCGTATGTTTGCAACAAAA+GGG 0.538893 1_2:+79011438 None:intergenic
TTTCTCAATTCCAATCGACT+AGG 0.574270 1_2:+79011468 None:intergenic
ATATCTCTCTGTGGCACCAG+TGG 0.585814 1_2:-79012219 Msa0095140:CDS
AACCATAGAGTACTTGCCAC+TGG 0.586013 1_2:+79012203 None:intergenic
AGTGTTAATAAGGAATCTAG+GGG 0.667965 1_2:-79011531 Msa0095140:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAACTAGAATCAAAAAAA+GGG + chr1_2:79011578-79011597 None:intergenic 15.0%
!! AGAGCAAATTAATTTAATAA+AGG - chr1_2:79011703-79011722 Msa0095140:intron 15.0%
!! TATTATTAAATTCATAGCAA+TGG + chr1_2:79011797-79011816 None:intergenic 15.0%
!! CTGTACTATATAAAATTAAT+TGG - chr1_2:79011953-79011972 Msa0095140:intron 15.0%
!! AATAACTAGAATCAAAAAAA+GGG + chr1_2:79011578-79011597 None:intergenic 15.0%
!! AGAGCAAATTAATTTAATAA+AGG - chr1_2:79011703-79011722 Msa0095140:intron 15.0%
!! TATTATTAAATTCATAGCAA+TGG + chr1_2:79011797-79011816 None:intergenic 15.0%
!! CTGTACTATATAAAATTAAT+TGG - chr1_2:79011953-79011972 Msa0095140:intron 15.0%
!!! TTCGTTTTTTTCTTGTAATT+TGG + chr1_2:79011426-79011445 None:intergenic 20.0%
!! AAATTACAAGAAAAAAACGA+AGG - chr1_2:79011425-79011444 Msa0095140:CDS 20.0%
!! ATAACTAGAATCAAAAAAAG+GGG + chr1_2:79011577-79011596 None:intergenic 20.0%
!! CAATAACTAGAATCAAAAAA+AGG + chr1_2:79011579-79011598 None:intergenic 20.0%
!!! CTTTTTTTGATTCTAGTTAT+TGG - chr1_2:79011577-79011596 Msa0095140:CDS 20.0%
!!! AGAGGGATTTAATATTTTAT+TGG + chr1_2:79011632-79011651 None:intergenic 20.0%
!! GCAAATTAATTTAATAAAGG+TGG - chr1_2:79011706-79011725 Msa0095140:intron 20.0%
!!! TAATTTAATAAAGGTGGATT+TGG - chr1_2:79011712-79011731 Msa0095140:intron 20.0%
!! TTCTATTACAATTCCATTTA+TGG + chr1_2:79011828-79011847 None:intergenic 20.0%
!!! TATACGAATAACTGTTATTT+TGG - chr1_2:79012117-79012136 Msa0095140:intron 20.0%
!!! TGATAAAAAGAGTGTTAATA+AGG - chr1_2:79012153-79012172 Msa0095140:intron 20.0%
!!! TTCGTTTTTTTCTTGTAATT+TGG + chr1_2:79011426-79011445 None:intergenic 20.0%
!! AAATTACAAGAAAAAAACGA+AGG - chr1_2:79011425-79011444 Msa0095140:CDS 20.0%
!! ATAACTAGAATCAAAAAAAG+GGG + chr1_2:79011577-79011596 None:intergenic 20.0%
!! CAATAACTAGAATCAAAAAA+AGG + chr1_2:79011579-79011598 None:intergenic 20.0%
!!! CTTTTTTTGATTCTAGTTAT+TGG - chr1_2:79011577-79011596 Msa0095140:CDS 20.0%
!!! AGAGGGATTTAATATTTTAT+TGG + chr1_2:79011632-79011651 None:intergenic 20.0%
!! GCAAATTAATTTAATAAAGG+TGG - chr1_2:79011706-79011725 Msa0095140:intron 20.0%
!!! TAATTTAATAAAGGTGGATT+TGG - chr1_2:79011712-79011731 Msa0095140:intron 20.0%
!! TTCTATTACAATTCCATTTA+TGG + chr1_2:79011828-79011847 None:intergenic 20.0%
!!! TATACGAATAACTGTTATTT+TGG - chr1_2:79012117-79012136 Msa0095140:intron 20.0%
!!! TGATAAAAAGAGTGTTAATA+AGG - chr1_2:79012153-79012172 Msa0095140:intron 20.0%
! AAAAAAAAAACGAACGAAGA+GGG + chr1_2:79011649-79011668 None:intergenic 25.0%
! AAAAAAAAAAACGAACGAAG+AGG + chr1_2:79011650-79011669 None:intergenic 25.0%
! TGGAATTGTAATAGAATACT+TGG - chr1_2:79011832-79011851 Msa0095140:intron 25.0%
! GGAATTGTAATAGAATACTT+GGG - chr1_2:79011833-79011852 Msa0095140:intron 25.0%
! AGTGAATCAAAAAAAACCAA+AGG - chr1_2:79012071-79012090 Msa0095140:intron 25.0%
! AAAAAAAAAACGAACGAAGA+GGG + chr1_2:79011649-79011668 None:intergenic 25.0%
! AAAAAAAAAAACGAACGAAG+AGG + chr1_2:79011650-79011669 None:intergenic 25.0%
! TGGAATTGTAATAGAATACT+TGG - chr1_2:79011832-79011851 Msa0095140:intron 25.0%
! GGAATTGTAATAGAATACTT+GGG - chr1_2:79011833-79011852 Msa0095140:intron 25.0%
! AGTGAATCAAAAAAAACCAA+AGG - chr1_2:79012071-79012090 Msa0095140:intron 25.0%
TTACAAGAAAAAAACGAAGG+AGG - chr1_2:79011428-79011447 Msa0095140:CDS 30.0%
TCTAAAAACATATCTCTCTG+TGG - chr1_2:79011466-79011485 Msa0095140:CDS 30.0%
AGAAATCAATCGTTTATTCC+CGG - chr1_2:79011538-79011557 Msa0095140:CDS 30.0%
! TTTGATTCTAGTTATTGGCA+CGG - chr1_2:79011582-79011601 Msa0095140:intron 30.0%
AAAAACTCCTAATTTCACTG+AGG + chr1_2:79011738-79011757 None:intergenic 30.0%
TAATAGAGTGAGACCATAAA+TGG - chr1_2:79011812-79011831 Msa0095140:intron 30.0%
ATTGTAATAGAATACTTGGG+CGG - chr1_2:79011836-79011855 Msa0095140:intron 30.0%
GAATCAAAAAAAACCAAAGG+AGG - chr1_2:79012074-79012093 Msa0095140:intron 30.0%
TATTCGTATATCTTTACCCT+TGG + chr1_2:79012107-79012126 None:intergenic 30.0%
! AGAGTGTTAATAAGGAATCT+AGG - chr1_2:79012161-79012180 Msa0095140:intron 30.0%
GAGTGTTAATAAGGAATCTA+GGG - chr1_2:79012162-79012181 Msa0095140:intron 30.0%
AGTGTTAATAAGGAATCTAG+GGG - chr1_2:79012163-79012182 Msa0095140:intron 30.0%
ATCGTATGTTTGCAACAAAA+GGG + chr1_2:79012259-79012278 None:intergenic 30.0%
AATCGTATGTTTGCAACAAA+AGG + chr1_2:79012260-79012279 None:intergenic 30.0%
TTACAAGAAAAAAACGAAGG+AGG - chr1_2:79011428-79011447 Msa0095140:CDS 30.0%
TCTAAAAACATATCTCTCTG+TGG - chr1_2:79011466-79011485 Msa0095140:CDS 30.0%
AGAAATCAATCGTTTATTCC+CGG - chr1_2:79011538-79011557 Msa0095140:CDS 30.0%
! TTTGATTCTAGTTATTGGCA+CGG - chr1_2:79011582-79011601 Msa0095140:intron 30.0%
AAAAACTCCTAATTTCACTG+AGG + chr1_2:79011738-79011757 None:intergenic 30.0%
TAATAGAGTGAGACCATAAA+TGG - chr1_2:79011812-79011831 Msa0095140:intron 30.0%
ATTGTAATAGAATACTTGGG+CGG - chr1_2:79011836-79011855 Msa0095140:intron 30.0%
GAATCAAAAAAAACCAAAGG+AGG - chr1_2:79012074-79012093 Msa0095140:intron 30.0%
TATTCGTATATCTTTACCCT+TGG + chr1_2:79012107-79012126 None:intergenic 30.0%
! AGAGTGTTAATAAGGAATCT+AGG - chr1_2:79012161-79012180 Msa0095140:intron 30.0%
GAGTGTTAATAAGGAATCTA+GGG - chr1_2:79012162-79012181 Msa0095140:intron 30.0%
AGTGTTAATAAGGAATCTAG+GGG - chr1_2:79012163-79012182 Msa0095140:intron 30.0%
ATCGTATGTTTGCAACAAAA+GGG + chr1_2:79012259-79012278 None:intergenic 30.0%
AATCGTATGTTTGCAACAAA+AGG + chr1_2:79012260-79012279 None:intergenic 30.0%
! TGAAATTAGGAGTTTTTCCC+AGG - chr1_2:79011741-79011760 Msa0095140:intron 35.0%
CTTCAATTCCATTGAAACCT+GGG + chr1_2:79011761-79011780 None:intergenic 35.0%
ACTTCAATTCCATTGAAACC+TGG + chr1_2:79011762-79011781 None:intergenic 35.0%
TTGTAATAGAATACTTGGGC+GGG - chr1_2:79011837-79011856 Msa0095140:intron 35.0%
TTCGAAGCGAAGAAGAAAAA+AGG + chr1_2:79012032-79012051 None:intergenic 35.0%
AAAAAACCAAAGGAGGTTCA+TGG - chr1_2:79012081-79012100 Msa0095140:intron 35.0%
TTTCTCAATTCCAATCGACT+AGG + chr1_2:79012229-79012248 None:intergenic 35.0%
! TGAAATTAGGAGTTTTTCCC+AGG - chr1_2:79011741-79011760 Msa0095140:intron 35.0%
CTTCAATTCCATTGAAACCT+GGG + chr1_2:79011761-79011780 None:intergenic 35.0%
ACTTCAATTCCATTGAAACC+TGG + chr1_2:79011762-79011781 None:intergenic 35.0%
TTGTAATAGAATACTTGGGC+GGG - chr1_2:79011837-79011856 Msa0095140:intron 35.0%
TTCGAAGCGAAGAAGAAAAA+AGG + chr1_2:79012032-79012051 None:intergenic 35.0%
AAAAAACCAAAGGAGGTTCA+TGG - chr1_2:79012081-79012100 Msa0095140:intron 35.0%
TTTCTCAATTCCAATCGACT+AGG + chr1_2:79012229-79012248 None:intergenic 35.0%
GATTTGGCCTCAGTGAAATT+AGG - chr1_2:79011728-79011747 Msa0095140:intron 40.0%
! GAGTTTTTCCCAGGTTTCAA+TGG - chr1_2:79011750-79011769 Msa0095140:intron 40.0%
ACACAATACACCTAGTCGAT+TGG - chr1_2:79012216-79012235 Msa0095140:CDS 40.0%
GATTTGGCCTCAGTGAAATT+AGG - chr1_2:79011728-79011747 Msa0095140:intron 40.0%
! GAGTTTTTCCCAGGTTTCAA+TGG - chr1_2:79011750-79011769 Msa0095140:intron 40.0%
ACACAATACACCTAGTCGAT+TGG - chr1_2:79012216-79012235 Msa0095140:CDS 40.0%
! AACCATAGAGTACTTGCCAC+TGG + chr1_2:79011494-79011513 None:intergenic 45.0%
AAGGGGAATGTCAATGCATC+CGG + chr1_2:79011560-79011579 None:intergenic 45.0%
! TTCTAGTTATTGGCACGGCA+AGG - chr1_2:79011587-79011606 Msa0095140:intron 45.0%
TCTAGTTATTGGCACGGCAA+GGG - chr1_2:79011588-79011607 Msa0095140:intron 45.0%
! AACCATAGAGTACTTGCCAC+TGG + chr1_2:79011494-79011513 None:intergenic 45.0%
AAGGGGAATGTCAATGCATC+CGG + chr1_2:79011560-79011579 None:intergenic 45.0%
! TTCTAGTTATTGGCACGGCA+AGG - chr1_2:79011587-79011606 Msa0095140:intron 45.0%
TCTAGTTATTGGCACGGCAA+GGG - chr1_2:79011588-79011607 Msa0095140:intron 45.0%
ATATCTCTCTGTGGCACCAG+TGG - chr1_2:79011475-79011494 Msa0095140:CDS 50.0%
CACCAGTGGCAAGTACTCTA+TGG - chr1_2:79011489-79011508 Msa0095140:CDS 50.0%
GGCAAGTACTCTATGGTTCG+CGG - chr1_2:79011496-79011515 Msa0095140:CDS 50.0%
AGGGGAATGTCAATGCATCC+GGG + chr1_2:79011559-79011578 None:intergenic 50.0%
CTAGTTATTGGCACGGCAAG+GGG - chr1_2:79011589-79011608 Msa0095140:intron 50.0%
CAAAGGAGGTTCATGGCCAA+GGG - chr1_2:79012088-79012107 Msa0095140:intron 50.0%
ATATCTCTCTGTGGCACCAG+TGG - chr1_2:79011475-79011494 Msa0095140:CDS 50.0%
CACCAGTGGCAAGTACTCTA+TGG - chr1_2:79011489-79011508 Msa0095140:CDS 50.0%
GGCAAGTACTCTATGGTTCG+CGG - chr1_2:79011496-79011515 Msa0095140:CDS 50.0%
AGGGGAATGTCAATGCATCC+GGG + chr1_2:79011559-79011578 None:intergenic 50.0%
CTAGTTATTGGCACGGCAAG+GGG - chr1_2:79011589-79011608 Msa0095140:intron 50.0%
CAAAGGAGGTTCATGGCCAA+GGG - chr1_2:79012088-79012107 Msa0095140:intron 50.0%
! CTATGGTTCGCGGTTCTAGC+AGG - chr1_2:79011506-79011525 Msa0095140:CDS 55.0%
CCTTGGCCATGAACCTCCTT+TGG + chr1_2:79012090-79012109 None:intergenic 55.0%
CCAAAGGAGGTTCATGGCCA+AGG - chr1_2:79012087-79012106 Msa0095140:intron 55.0%
! CTATGGTTCGCGGTTCTAGC+AGG - chr1_2:79011506-79011525 Msa0095140:CDS 55.0%
CCTTGGCCATGAACCTCCTT+TGG + chr1_2:79012090-79012109 None:intergenic 55.0%
CCAAAGGAGGTTCATGGCCA+AGG - chr1_2:79012087-79012106 Msa0095140:intron 55.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 79011416 79012300 79011416 ID=Msa0095140;Name=Msa0095140
chr1_2 mRNA 79011416 79012300 79011416 ID=Msa0095140-mRNA-1;Parent=Msa0095140;Name=Msa0095140-mRNA-1;_AED=0.45;_eAED=0.45;_QI=0|0|0|1|0|0|2|0|105
chr1_2 exon 79012168 79012300 79012168 ID=Msa0095140-mRNA-1:exon:28077;Parent=Msa0095140-mRNA-1
chr1_2 exon 79011416 79011600 79011416 ID=Msa0095140-mRNA-1:exon:28076;Parent=Msa0095140-mRNA-1
chr1_2 CDS 79012168 79012300 79012168 ID=Msa0095140-mRNA-1:cds;Parent=Msa0095140-mRNA-1
chr1_2 CDS 79011416 79011600 79011416 ID=Msa0095140-mRNA-1:cds;Parent=Msa0095140-mRNA-1
Gene Sequence

>Msa0095140

ATGTATTCCAAATTACAAGAAAAAAACGAAGGAGGATTTGAAATGCGAGATCTAAAAACATATCTCTCTGTGGCACCAGTGGCAAGTACTCTATGGTTCGCGGTTCTAGCAGGTCTCTTGATAGAAATCAATCATATACGAATAACTGTTATTTTGGAATGTAGCAGTTGTGATAAAAAGAGTGTTAATAAGGAATCTAGGGGTATTTCTAGATATATTACTCAAAAGAATCGACACAATACACCTAGTCGATTGGAATTGAGAAAATTCTGTCCCTTTTGTTGCAAACATACGATTCACGTCGAGATAAAGAAATAG

Protein sequence

>Msa0095140

MYSKLQEKNEGGFEMRDLKTYLSVAPVASTLWFAVLAGLLIEINHIRITVILECSSCDKKSVNKESRGISRYITQKNRHNTPSRLELRKFCPFCCKHTIHVEIKK*