AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1086630


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1086630 MtrunA17_CPg0492781 98.333 60 1 0 46 105 7 66 1.14e-38 124
Msa1086630 MtrunA17_Chr4g0015791 98.333 60 1 0 46 105 7 66 1.14e-38 124
Msa1086630 MtrunA17_Chr8g0355601 96.610 59 2 0 46 104 7 65 1.73e-37 120
Msa1086630 MtrunA17_Chr7g0224991 95.455 44 2 0 62 105 6 49 7.95e-26 90.9
Msa1086630 MtrunA17_CPg0492791 93.750 32 2 0 15 46 1 32 2.06e-15 64.3
Msa1086630 MtrunA17_Chr4g0015781 93.750 32 2 0 15 46 1 32 2.06e-15 64.3
Msa1086630 MtrunA17_Chr4g0028951 93.750 32 2 0 15 46 1 32 2.06e-15 64.3
Msa1086630 MtrunA17_Chr8g0355611 93.750 32 2 0 15 46 1 32 2.06e-15 64.3
Msa1086630 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
Msa1086630 ATCG00640.1 75.000 60 15 0 46 105 7 66 2.13e-29 100
Msa1086630 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:-87491596 Msa1086630:CDS
AGAGTGTTAATAAGGAATCT+AGG 0.329597 7_2:-87491552 Msa1086630:CDS
AATCGTATGTTTGCAACAAA+AGG 0.396841 7_2:+87491456 None:intergenic
CACCAGTGGCAAGTACTCTA+TGG 0.426592 7_2:-87492223 Msa1086630:CDS
GAGTGTTAATAAGGAATCTA+GGG 0.452009 7_2:-87491551 Msa1086630:CDS
CTATGGTTCGCGGTTCTAGC+AGG 0.487956 7_2:-87492206 Msa1086630:CDS
ACACAATACACCTAGTCGAT+TGG 0.524208 7_2:-87491497 Msa1086630:CDS
GGCAAGTACTCTATGGTTCG+CGG 0.527936 7_2:-87492216 Msa1086630:CDS
ATCGTATGTTTGCAACAAAA+GGG 0.538893 7_2:+87491457 None:intergenic
TTTCTCAATTCCAATCGACT+AGG 0.574270 7_2:+87491487 None:intergenic
ATATCTCTCTGTGGCACCAG+TGG 0.585814 7_2:-87492237 Msa1086630:CDS
AACCATAGAGTACTTGCCAC+TGG 0.586013 7_2:+87492221 None:intergenic
AGTGTTAATAAGGAATCTAG+GGG 0.667965 7_2:-87491550 Msa1086630:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAACTAGAATCAAAAAAA+GGG + chr7_2:87491597-87491616 None:intergenic 15.0%
!! AGAGCAAATTAATTTAATAA+AGG - chr7_2:87491721-87491740 Msa1086630:intron 15.0%
!! TATTATTAAATTCATAGCAA+TGG + chr7_2:87491815-87491834 None:intergenic 15.0%
!! CTGTACTATATAAAATTAAT+TGG - chr7_2:87491971-87491990 Msa1086630:intron 15.0%
!! AATAACTAGAATCAAAAAAA+GGG + chr7_2:87491597-87491616 None:intergenic 15.0%
!! AGAGCAAATTAATTTAATAA+AGG - chr7_2:87491721-87491740 Msa1086630:intron 15.0%
!! TATTATTAAATTCATAGCAA+TGG + chr7_2:87491815-87491834 None:intergenic 15.0%
!! CTGTACTATATAAAATTAAT+TGG - chr7_2:87491971-87491990 Msa1086630:intron 15.0%
!!! TTCGTTTTTTTCTTGTAATT+TGG + chr7_2:87491445-87491464 None:intergenic 20.0%
!! AAATTACAAGAAAAAAACGA+AGG - chr7_2:87491444-87491463 Msa1086630:CDS 20.0%
!! ATAACTAGAATCAAAAAAAG+GGG + chr7_2:87491596-87491615 None:intergenic 20.0%
!! CAATAACTAGAATCAAAAAA+AGG + chr7_2:87491598-87491617 None:intergenic 20.0%
!!! CTTTTTTTGATTCTAGTTAT+TGG - chr7_2:87491596-87491615 Msa1086630:CDS 20.0%
!!! AGAGGGATTTAATATTTTAT+TGG + chr7_2:87491651-87491670 None:intergenic 20.0%
!! GCAAATTAATTTAATAAAGG+TGG - chr7_2:87491724-87491743 Msa1086630:intron 20.0%
!!! TAATTTAATAAAGGTGGATT+TGG - chr7_2:87491730-87491749 Msa1086630:intron 20.0%
!! TTCTATTACAATTCCATTTA+TGG + chr7_2:87491846-87491865 None:intergenic 20.0%
!!! TATACGAATAACTGTTATTT+TGG - chr7_2:87492135-87492154 Msa1086630:intron 20.0%
!!! TGATAAAAAGAGTGTTAATA+AGG - chr7_2:87492171-87492190 Msa1086630:intron 20.0%
!!! TTCGTTTTTTTCTTGTAATT+TGG + chr7_2:87491445-87491464 None:intergenic 20.0%
!! AAATTACAAGAAAAAAACGA+AGG - chr7_2:87491444-87491463 Msa1086630:CDS 20.0%
!! ATAACTAGAATCAAAAAAAG+GGG + chr7_2:87491596-87491615 None:intergenic 20.0%
!! CAATAACTAGAATCAAAAAA+AGG + chr7_2:87491598-87491617 None:intergenic 20.0%
!!! CTTTTTTTGATTCTAGTTAT+TGG - chr7_2:87491596-87491615 Msa1086630:CDS 20.0%
!!! AGAGGGATTTAATATTTTAT+TGG + chr7_2:87491651-87491670 None:intergenic 20.0%
!! GCAAATTAATTTAATAAAGG+TGG - chr7_2:87491724-87491743 Msa1086630:intron 20.0%
!!! TAATTTAATAAAGGTGGATT+TGG - chr7_2:87491730-87491749 Msa1086630:intron 20.0%
!! TTCTATTACAATTCCATTTA+TGG + chr7_2:87491846-87491865 None:intergenic 20.0%
!!! TATACGAATAACTGTTATTT+TGG - chr7_2:87492135-87492154 Msa1086630:intron 20.0%
!!! TGATAAAAAGAGTGTTAATA+AGG - chr7_2:87492171-87492190 Msa1086630:intron 20.0%
! AAAAAAAAAACGAACGAAGA+GGG + chr7_2:87491668-87491687 None:intergenic 25.0%
! AAAAAAAAAAACGAACGAAG+AGG + chr7_2:87491669-87491688 None:intergenic 25.0%
! TGGAATTGTAATAGAATACT+TGG - chr7_2:87491850-87491869 Msa1086630:intron 25.0%
! GGAATTGTAATAGAATACTT+GGG - chr7_2:87491851-87491870 Msa1086630:intron 25.0%
! AGTGAATCAAAAAAAACCAA+AGG - chr7_2:87492089-87492108 Msa1086630:intron 25.0%
! AAAAAAAAAACGAACGAAGA+GGG + chr7_2:87491668-87491687 None:intergenic 25.0%
! AAAAAAAAAAACGAACGAAG+AGG + chr7_2:87491669-87491688 None:intergenic 25.0%
! TGGAATTGTAATAGAATACT+TGG - chr7_2:87491850-87491869 Msa1086630:intron 25.0%
! GGAATTGTAATAGAATACTT+GGG - chr7_2:87491851-87491870 Msa1086630:intron 25.0%
! AGTGAATCAAAAAAAACCAA+AGG - chr7_2:87492089-87492108 Msa1086630:intron 25.0%
TTACAAGAAAAAAACGAAGG+AGG - chr7_2:87491447-87491466 Msa1086630:CDS 30.0%
TCTAAAAACATATCTCTCTG+TGG - chr7_2:87491485-87491504 Msa1086630:CDS 30.0%
AGAAATCAATCGTTTATTCC+CGG - chr7_2:87491557-87491576 Msa1086630:CDS 30.0%
! TTTGATTCTAGTTATTGGCA+CGG - chr7_2:87491601-87491620 Msa1086630:intron 30.0%
AAAAACTCCTAATTTCACTG+AGG + chr7_2:87491756-87491775 None:intergenic 30.0%
TAATAGAGTGAGACCATAAA+TGG - chr7_2:87491830-87491849 Msa1086630:intron 30.0%
ATTGTAATAGAATACTTGGG+CGG - chr7_2:87491854-87491873 Msa1086630:intron 30.0%
GAATCAAAAAAAACCAAAGG+AGG - chr7_2:87492092-87492111 Msa1086630:intron 30.0%
TATTCGTATATCTTTACCCT+TGG + chr7_2:87492125-87492144 None:intergenic 30.0%
! AGAGTGTTAATAAGGAATCT+AGG - chr7_2:87492179-87492198 Msa1086630:intron 30.0%
GAGTGTTAATAAGGAATCTA+GGG - chr7_2:87492180-87492199 Msa1086630:intron 30.0%
AGTGTTAATAAGGAATCTAG+GGG - chr7_2:87492181-87492200 Msa1086630:intron 30.0%
ATCGTATGTTTGCAACAAAA+GGG + chr7_2:87492277-87492296 None:intergenic 30.0%
AATCGTATGTTTGCAACAAA+AGG + chr7_2:87492278-87492297 None:intergenic 30.0%
TTACAAGAAAAAAACGAAGG+AGG - chr7_2:87491447-87491466 Msa1086630:CDS 30.0%
TCTAAAAACATATCTCTCTG+TGG - chr7_2:87491485-87491504 Msa1086630:CDS 30.0%
AGAAATCAATCGTTTATTCC+CGG - chr7_2:87491557-87491576 Msa1086630:CDS 30.0%
! TTTGATTCTAGTTATTGGCA+CGG - chr7_2:87491601-87491620 Msa1086630:intron 30.0%
AAAAACTCCTAATTTCACTG+AGG + chr7_2:87491756-87491775 None:intergenic 30.0%
TAATAGAGTGAGACCATAAA+TGG - chr7_2:87491830-87491849 Msa1086630:intron 30.0%
ATTGTAATAGAATACTTGGG+CGG - chr7_2:87491854-87491873 Msa1086630:intron 30.0%
GAATCAAAAAAAACCAAAGG+AGG - chr7_2:87492092-87492111 Msa1086630:intron 30.0%
TATTCGTATATCTTTACCCT+TGG + chr7_2:87492125-87492144 None:intergenic 30.0%
! AGAGTGTTAATAAGGAATCT+AGG - chr7_2:87492179-87492198 Msa1086630:intron 30.0%
GAGTGTTAATAAGGAATCTA+GGG - chr7_2:87492180-87492199 Msa1086630:intron 30.0%
AGTGTTAATAAGGAATCTAG+GGG - chr7_2:87492181-87492200 Msa1086630:intron 30.0%
ATCGTATGTTTGCAACAAAA+GGG + chr7_2:87492277-87492296 None:intergenic 30.0%
AATCGTATGTTTGCAACAAA+AGG + chr7_2:87492278-87492297 None:intergenic 30.0%
! TGAAATTAGGAGTTTTTCCC+AGG - chr7_2:87491759-87491778 Msa1086630:intron 35.0%
CTTCAATTCCATTGAAACCT+GGG + chr7_2:87491779-87491798 None:intergenic 35.0%
ACTTCAATTCCATTGAAACC+TGG + chr7_2:87491780-87491799 None:intergenic 35.0%
TTGTAATAGAATACTTGGGC+GGG - chr7_2:87491855-87491874 Msa1086630:intron 35.0%
TTCGAAGCGAAGAAGAAAAA+AGG + chr7_2:87492050-87492069 None:intergenic 35.0%
AAAAAACCAAAGGAGGTTCA+TGG - chr7_2:87492099-87492118 Msa1086630:intron 35.0%
TTTCTCAATTCCAATCGACT+AGG + chr7_2:87492247-87492266 None:intergenic 35.0%
! TGAAATTAGGAGTTTTTCCC+AGG - chr7_2:87491759-87491778 Msa1086630:intron 35.0%
CTTCAATTCCATTGAAACCT+GGG + chr7_2:87491779-87491798 None:intergenic 35.0%
ACTTCAATTCCATTGAAACC+TGG + chr7_2:87491780-87491799 None:intergenic 35.0%
TTGTAATAGAATACTTGGGC+GGG - chr7_2:87491855-87491874 Msa1086630:intron 35.0%
TTCGAAGCGAAGAAGAAAAA+AGG + chr7_2:87492050-87492069 None:intergenic 35.0%
AAAAAACCAAAGGAGGTTCA+TGG - chr7_2:87492099-87492118 Msa1086630:intron 35.0%
TTTCTCAATTCCAATCGACT+AGG + chr7_2:87492247-87492266 None:intergenic 35.0%
GATTTGGCCTCAGTGAAATT+AGG - chr7_2:87491746-87491765 Msa1086630:intron 40.0%
! GAGTTTTTCCCAGGTTTCAA+TGG - chr7_2:87491768-87491787 Msa1086630:intron 40.0%
ACACAATACACCTAGTCGAT+TGG - chr7_2:87492234-87492253 Msa1086630:CDS 40.0%
GATTTGGCCTCAGTGAAATT+AGG - chr7_2:87491746-87491765 Msa1086630:intron 40.0%
! GAGTTTTTCCCAGGTTTCAA+TGG - chr7_2:87491768-87491787 Msa1086630:intron 40.0%
ACACAATACACCTAGTCGAT+TGG - chr7_2:87492234-87492253 Msa1086630:CDS 40.0%
! AACCATAGAGTACTTGCCAC+TGG + chr7_2:87491513-87491532 None:intergenic 45.0%
AAGGGGAATGTCAATGCATC+CGG + chr7_2:87491579-87491598 None:intergenic 45.0%
! TTCTAGTTATTGGCACGGCA+AGG - chr7_2:87491606-87491625 Msa1086630:intron 45.0%
TCTAGTTATTGGCACGGCAA+GGG - chr7_2:87491607-87491626 Msa1086630:intron 45.0%
! AACCATAGAGTACTTGCCAC+TGG + chr7_2:87491513-87491532 None:intergenic 45.0%
AAGGGGAATGTCAATGCATC+CGG + chr7_2:87491579-87491598 None:intergenic 45.0%
! TTCTAGTTATTGGCACGGCA+AGG - chr7_2:87491606-87491625 Msa1086630:intron 45.0%
TCTAGTTATTGGCACGGCAA+GGG - chr7_2:87491607-87491626 Msa1086630:intron 45.0%
ATATCTCTCTGTGGCACCAG+TGG - chr7_2:87491494-87491513 Msa1086630:CDS 50.0%
CACCAGTGGCAAGTACTCTA+TGG - chr7_2:87491508-87491527 Msa1086630:CDS 50.0%
GGCAAGTACTCTATGGTTCG+CGG - chr7_2:87491515-87491534 Msa1086630:CDS 50.0%
AGGGGAATGTCAATGCATCC+GGG + chr7_2:87491578-87491597 None:intergenic 50.0%
CTAGTTATTGGCACGGCAAG+GGG - chr7_2:87491608-87491627 Msa1086630:intron 50.0%
CAAAGGAGGTTCATGGCCAA+GGG - chr7_2:87492106-87492125 Msa1086630:intron 50.0%
ATATCTCTCTGTGGCACCAG+TGG - chr7_2:87491494-87491513 Msa1086630:CDS 50.0%
CACCAGTGGCAAGTACTCTA+TGG - chr7_2:87491508-87491527 Msa1086630:CDS 50.0%
GGCAAGTACTCTATGGTTCG+CGG - chr7_2:87491515-87491534 Msa1086630:CDS 50.0%
AGGGGAATGTCAATGCATCC+GGG + chr7_2:87491578-87491597 None:intergenic 50.0%
CTAGTTATTGGCACGGCAAG+GGG - chr7_2:87491608-87491627 Msa1086630:intron 50.0%
CAAAGGAGGTTCATGGCCAA+GGG - chr7_2:87492106-87492125 Msa1086630:intron 50.0%
! CTATGGTTCGCGGTTCTAGC+AGG - chr7_2:87491525-87491544 Msa1086630:CDS 55.0%
CCTTGGCCATGAACCTCCTT+TGG + chr7_2:87492108-87492127 None:intergenic 55.0%
CCAAAGGAGGTTCATGGCCA+AGG - chr7_2:87492105-87492124 Msa1086630:intron 55.0%
! CTATGGTTCGCGGTTCTAGC+AGG - chr7_2:87491525-87491544 Msa1086630:CDS 55.0%
CCTTGGCCATGAACCTCCTT+TGG + chr7_2:87492108-87492127 None:intergenic 55.0%
CCAAAGGAGGTTCATGGCCA+AGG - chr7_2:87492105-87492124 Msa1086630:intron 55.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 87491435 87492318 87491435 ID=Msa1086630;Name=Msa1086630
chr7_2 mRNA 87491435 87492318 87491435 ID=Msa1086630-mRNA-1;Parent=Msa1086630;Name=Msa1086630-mRNA-1;_AED=0.45;_eAED=0.45;_QI=0|0|0|1|0|0|2|0|105
chr7_2 exon 87492186 87492318 87492186 ID=Msa1086630-mRNA-1:exon:23906;Parent=Msa1086630-mRNA-1
chr7_2 exon 87491435 87491619 87491435 ID=Msa1086630-mRNA-1:exon:23905;Parent=Msa1086630-mRNA-1
chr7_2 CDS 87492186 87492318 87492186 ID=Msa1086630-mRNA-1:cds;Parent=Msa1086630-mRNA-1
chr7_2 CDS 87491435 87491619 87491435 ID=Msa1086630-mRNA-1:cds;Parent=Msa1086630-mRNA-1
Gene Sequence

>Msa1086630

ATGTATTCCAAATTACAAGAAAAAAACGAAGGAGGATTTGAAATGCGAGATCTAAAAACATATCTCTCTGTGGCACCAGTGGCAAGTACTCTATGGTTCGCGGTTCTAGCAGGTCTCTTGATAGAAATCAATCATATACGAATAACTGTTATTTTGGAATGTAGCAGTTGTGATAAAAAGAGTGTTAATAAGGAATCTAGGGGTATTTCTAGATATATTACTCAAAAGAATCGACACAATACACCTAGTCGATTGGAATTGAGAAAATTCTGTCCCTTTTGTTGCAAACATACGATTCACGTCGAGATAAAGAAATAG

Protein sequence

>Msa1086630

MYSKLQEKNEGGFEMRDLKTYLSVAPVASTLWFAVLAGLLIEINHIRITVILECSSCDKKSVNKESRGISRYITQKNRHNTPSRLELRKFCPFCCKHTIHVEIKK*