AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0925020


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0925020 MtrunA17_CPg0492781 98.333 60 1 0 46 105 7 66 1.14e-38 124
Msa0925020 MtrunA17_Chr4g0015791 98.333 60 1 0 46 105 7 66 1.14e-38 124
Msa0925020 MtrunA17_Chr8g0355601 96.610 59 2 0 46 104 7 65 1.73e-37 120
Msa0925020 MtrunA17_Chr7g0224991 95.455 44 2 0 62 105 6 49 7.95e-26 90.9
Msa0925020 MtrunA17_CPg0492791 93.750 32 2 0 15 46 1 32 2.06e-15 64.3
Msa0925020 MtrunA17_Chr4g0015781 93.750 32 2 0 15 46 1 32 2.06e-15 64.3
Msa0925020 MtrunA17_Chr4g0028951 93.750 32 2 0 15 46 1 32 2.06e-15 64.3
Msa0925020 MtrunA17_Chr8g0355611 93.750 32 2 0 15 46 1 32 2.06e-15 64.3
Msa0925020 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
Msa0925020 ATCG00640.1 75.000 60 15 0 46 105 7 66 2.13e-29 100
Msa0925020 ATCG00630.1 84.375 32 5 0 15 46 1 32 8.57e-13 58.2

Find 13 sgRNAs with CRISPR-Local

Find 110 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATACGAATAACTGTTATTT+TGG 0.125276 6_2:-67573273 Msa0925020:CDS
AGAGTGTTAATAAGGAATCT+AGG 0.329597 6_2:-67573229 Msa0925020:CDS
AATCGTATGTTTGCAACAAA+AGG 0.396841 6_2:+67573133 None:intergenic
CACCAGTGGCAAGTACTCTA+TGG 0.426592 6_2:-67573910 Msa0925020:CDS
GAGTGTTAATAAGGAATCTA+GGG 0.452009 6_2:-67573228 Msa0925020:CDS
CTATGGTTCGCGGTTCTAGC+AGG 0.487956 6_2:-67573893 Msa0925020:CDS
ACACAATACACCTAGTCGAT+TGG 0.524208 6_2:-67573174 Msa0925020:CDS
GGCAAGTACTCTATGGTTCG+CGG 0.527936 6_2:-67573903 Msa0925020:CDS
ATCGTATGTTTGCAACAAAA+GGG 0.538893 6_2:+67573134 None:intergenic
TTTCTCAATTCCAATCGACT+AGG 0.574270 6_2:+67573164 None:intergenic
ATATCTCTCTGTGGCACCAG+TGG 0.585814 6_2:-67573924 Msa0925020:CDS
AACCATAGAGTACTTGCCAC+TGG 0.586013 6_2:+67573908 None:intergenic
AGTGTTAATAAGGAATCTAG+GGG 0.667965 6_2:-67573227 Msa0925020:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAATTAATATAAAATTAAT+TGG - chr6_2:67573658-67573677 Msa0925020:intron 0.0%
!! TAAATTAATATAAAATTAAT+TGG - chr6_2:67573658-67573677 Msa0925020:intron 0.0%
!! AATAACTAGAATCAAAAAAA+GGG + chr6_2:67573274-67573293 None:intergenic 15.0%
!! AGAGCAAATTAATTTAATAA+AGG - chr6_2:67573398-67573417 Msa0925020:intron 15.0%
!! TATTATTAAATTCATAGCAA+TGG + chr6_2:67573492-67573511 None:intergenic 15.0%
!! AATAACTAGAATCAAAAAAA+GGG + chr6_2:67573274-67573293 None:intergenic 15.0%
!! AGAGCAAATTAATTTAATAA+AGG - chr6_2:67573398-67573417 Msa0925020:intron 15.0%
!! TATTATTAAATTCATAGCAA+TGG + chr6_2:67573492-67573511 None:intergenic 15.0%
!!! TTCGTTTTTTTCTTGTAATT+TGG + chr6_2:67573122-67573141 None:intergenic 20.0%
!! AAATTACAAGAAAAAAACGA+AGG - chr6_2:67573121-67573140 Msa0925020:CDS 20.0%
!! ATAACTAGAATCAAAAAAAG+GGG + chr6_2:67573273-67573292 None:intergenic 20.0%
!! CAATAACTAGAATCAAAAAA+AGG + chr6_2:67573275-67573294 None:intergenic 20.0%
!!! CTTTTTTTGATTCTAGTTAT+TGG - chr6_2:67573273-67573292 Msa0925020:CDS 20.0%
!!! AGAGGGATTTAATATTTTAT+TGG + chr6_2:67573328-67573347 None:intergenic 20.0%
!! GCAAATTAATTTAATAAAGG+TGG - chr6_2:67573401-67573420 Msa0925020:intron 20.0%
!!! TAATTTAATAAAGGTGGATT+TGG - chr6_2:67573407-67573426 Msa0925020:intron 20.0%
!! TTCTATTACAATTCCATTTA+TGG + chr6_2:67573523-67573542 None:intergenic 20.0%
!!! TATACGAATAACTGTTATTT+TGG - chr6_2:67573822-67573841 Msa0925020:intron 20.0%
!!! TGATAAAAAGAGTGTTAATA+AGG - chr6_2:67573858-67573877 Msa0925020:intron 20.0%
!!! TTCGTTTTTTTCTTGTAATT+TGG + chr6_2:67573122-67573141 None:intergenic 20.0%
!! AAATTACAAGAAAAAAACGA+AGG - chr6_2:67573121-67573140 Msa0925020:CDS 20.0%
!! ATAACTAGAATCAAAAAAAG+GGG + chr6_2:67573273-67573292 None:intergenic 20.0%
!! CAATAACTAGAATCAAAAAA+AGG + chr6_2:67573275-67573294 None:intergenic 20.0%
!!! CTTTTTTTGATTCTAGTTAT+TGG - chr6_2:67573273-67573292 Msa0925020:CDS 20.0%
!!! AGAGGGATTTAATATTTTAT+TGG + chr6_2:67573328-67573347 None:intergenic 20.0%
!! GCAAATTAATTTAATAAAGG+TGG - chr6_2:67573401-67573420 Msa0925020:intron 20.0%
!!! TAATTTAATAAAGGTGGATT+TGG - chr6_2:67573407-67573426 Msa0925020:intron 20.0%
!! TTCTATTACAATTCCATTTA+TGG + chr6_2:67573523-67573542 None:intergenic 20.0%
!!! TATACGAATAACTGTTATTT+TGG - chr6_2:67573822-67573841 Msa0925020:intron 20.0%
!!! TGATAAAAAGAGTGTTAATA+AGG - chr6_2:67573858-67573877 Msa0925020:intron 20.0%
! AAAAAAAAAACGAACGAAGA+GGG + chr6_2:67573345-67573364 None:intergenic 25.0%
! AAAAAAAAAAACGAACGAAG+AGG + chr6_2:67573346-67573365 None:intergenic 25.0%
! TGGAATTGTAATAGAATACT+TGG - chr6_2:67573527-67573546 Msa0925020:intron 25.0%
! GGAATTGTAATAGAATACTT+GGG - chr6_2:67573528-67573547 Msa0925020:intron 25.0%
! AGTGAATCAAAAAAAACCAA+AGG - chr6_2:67573776-67573795 Msa0925020:intron 25.0%
! AAAAAAAAAACGAACGAAGA+GGG + chr6_2:67573345-67573364 None:intergenic 25.0%
! AAAAAAAAAAACGAACGAAG+AGG + chr6_2:67573346-67573365 None:intergenic 25.0%
! TGGAATTGTAATAGAATACT+TGG - chr6_2:67573527-67573546 Msa0925020:intron 25.0%
! GGAATTGTAATAGAATACTT+GGG - chr6_2:67573528-67573547 Msa0925020:intron 25.0%
! AGTGAATCAAAAAAAACCAA+AGG - chr6_2:67573776-67573795 Msa0925020:intron 25.0%
TTACAAGAAAAAAACGAAGG+AGG - chr6_2:67573124-67573143 Msa0925020:CDS 30.0%
TCTAAAAACATATCTCTCTG+TGG - chr6_2:67573162-67573181 Msa0925020:CDS 30.0%
AGAAATCAATCGTTTATTCC+CGG - chr6_2:67573234-67573253 Msa0925020:CDS 30.0%
! TTTGATTCTAGTTATTGGCA+CGG - chr6_2:67573278-67573297 Msa0925020:intron 30.0%
AAAAACTCCTAATTTCACTG+AGG + chr6_2:67573433-67573452 None:intergenic 30.0%
TAATAGAGTGAGACCATAAA+TGG - chr6_2:67573507-67573526 Msa0925020:intron 30.0%
GAATCAAAAAAAACCAAAGG+AGG - chr6_2:67573779-67573798 Msa0925020:intron 30.0%
TATTCGTATATCTTTACCCT+TGG + chr6_2:67573812-67573831 None:intergenic 30.0%
! AGAGTGTTAATAAGGAATCT+AGG - chr6_2:67573866-67573885 Msa0925020:intron 30.0%
GAGTGTTAATAAGGAATCTA+GGG - chr6_2:67573867-67573886 Msa0925020:intron 30.0%
AGTGTTAATAAGGAATCTAG+GGG - chr6_2:67573868-67573887 Msa0925020:intron 30.0%
ATCGTATGTTTGCAACAAAA+GGG + chr6_2:67573964-67573983 None:intergenic 30.0%
AATCGTATGTTTGCAACAAA+AGG + chr6_2:67573965-67573984 None:intergenic 30.0%
TTACAAGAAAAAAACGAAGG+AGG - chr6_2:67573124-67573143 Msa0925020:CDS 30.0%
TCTAAAAACATATCTCTCTG+TGG - chr6_2:67573162-67573181 Msa0925020:CDS 30.0%
AGAAATCAATCGTTTATTCC+CGG - chr6_2:67573234-67573253 Msa0925020:CDS 30.0%
! TTTGATTCTAGTTATTGGCA+CGG - chr6_2:67573278-67573297 Msa0925020:intron 30.0%
AAAAACTCCTAATTTCACTG+AGG + chr6_2:67573433-67573452 None:intergenic 30.0%
TAATAGAGTGAGACCATAAA+TGG - chr6_2:67573507-67573526 Msa0925020:intron 30.0%
GAATCAAAAAAAACCAAAGG+AGG - chr6_2:67573779-67573798 Msa0925020:intron 30.0%
TATTCGTATATCTTTACCCT+TGG + chr6_2:67573812-67573831 None:intergenic 30.0%
! AGAGTGTTAATAAGGAATCT+AGG - chr6_2:67573866-67573885 Msa0925020:intron 30.0%
GAGTGTTAATAAGGAATCTA+GGG - chr6_2:67573867-67573886 Msa0925020:intron 30.0%
AGTGTTAATAAGGAATCTAG+GGG - chr6_2:67573868-67573887 Msa0925020:intron 30.0%
ATCGTATGTTTGCAACAAAA+GGG + chr6_2:67573964-67573983 None:intergenic 30.0%
AATCGTATGTTTGCAACAAA+AGG + chr6_2:67573965-67573984 None:intergenic 30.0%
! TGAAATTAGGAGTTTTTCCC+AGG - chr6_2:67573436-67573455 Msa0925020:intron 35.0%
CTTCAATTCCATTGAAACCT+GGG + chr6_2:67573456-67573475 None:intergenic 35.0%
ACTTCAATTCCATTGAAACC+TGG + chr6_2:67573457-67573476 None:intergenic 35.0%
TTCGAAGCGAAGAAGAAAAA+AGG + chr6_2:67573737-67573756 None:intergenic 35.0%
AAAAAACCAAAGGAGGTTCA+TGG - chr6_2:67573786-67573805 Msa0925020:intron 35.0%
TTTCTCAATTCCAATCGACT+AGG + chr6_2:67573934-67573953 None:intergenic 35.0%
! TGAAATTAGGAGTTTTTCCC+AGG - chr6_2:67573436-67573455 Msa0925020:intron 35.0%
CTTCAATTCCATTGAAACCT+GGG + chr6_2:67573456-67573475 None:intergenic 35.0%
ACTTCAATTCCATTGAAACC+TGG + chr6_2:67573457-67573476 None:intergenic 35.0%
TTCGAAGCGAAGAAGAAAAA+AGG + chr6_2:67573737-67573756 None:intergenic 35.0%
AAAAAACCAAAGGAGGTTCA+TGG - chr6_2:67573786-67573805 Msa0925020:intron 35.0%
TTTCTCAATTCCAATCGACT+AGG + chr6_2:67573934-67573953 None:intergenic 35.0%
GATTTGGCCTCAGTGAAATT+AGG - chr6_2:67573423-67573442 Msa0925020:intron 40.0%
! GAGTTTTTCCCAGGTTTCAA+TGG - chr6_2:67573445-67573464 Msa0925020:intron 40.0%
ACACAATACACCTAGTCGAT+TGG - chr6_2:67573921-67573940 Msa0925020:CDS 40.0%
GATTTGGCCTCAGTGAAATT+AGG - chr6_2:67573423-67573442 Msa0925020:intron 40.0%
! GAGTTTTTCCCAGGTTTCAA+TGG - chr6_2:67573445-67573464 Msa0925020:intron 40.0%
ACACAATACACCTAGTCGAT+TGG - chr6_2:67573921-67573940 Msa0925020:CDS 40.0%
! AACCATAGAGTACTTGCCAC+TGG + chr6_2:67573190-67573209 None:intergenic 45.0%
AAGGGGAATGTCAATGCATC+CGG + chr6_2:67573256-67573275 None:intergenic 45.0%
! TTCTAGTTATTGGCACGGCA+AGG - chr6_2:67573283-67573302 Msa0925020:intron 45.0%
TCTAGTTATTGGCACGGCAA+GGG - chr6_2:67573284-67573303 Msa0925020:intron 45.0%
! AACCATAGAGTACTTGCCAC+TGG + chr6_2:67573190-67573209 None:intergenic 45.0%
AAGGGGAATGTCAATGCATC+CGG + chr6_2:67573256-67573275 None:intergenic 45.0%
! TTCTAGTTATTGGCACGGCA+AGG - chr6_2:67573283-67573302 Msa0925020:intron 45.0%
TCTAGTTATTGGCACGGCAA+GGG - chr6_2:67573284-67573303 Msa0925020:intron 45.0%
ATATCTCTCTGTGGCACCAG+TGG - chr6_2:67573171-67573190 Msa0925020:CDS 50.0%
CACCAGTGGCAAGTACTCTA+TGG - chr6_2:67573185-67573204 Msa0925020:CDS 50.0%
GGCAAGTACTCTATGGTTCG+CGG - chr6_2:67573192-67573211 Msa0925020:CDS 50.0%
AGGGGAATGTCAATGCATCC+GGG + chr6_2:67573255-67573274 None:intergenic 50.0%
CTAGTTATTGGCACGGCAAG+GGG - chr6_2:67573285-67573304 Msa0925020:intron 50.0%
CAAAGGAGGTTCATGGCCAA+GGG - chr6_2:67573793-67573812 Msa0925020:intron 50.0%
ATATCTCTCTGTGGCACCAG+TGG - chr6_2:67573171-67573190 Msa0925020:CDS 50.0%
CACCAGTGGCAAGTACTCTA+TGG - chr6_2:67573185-67573204 Msa0925020:CDS 50.0%
GGCAAGTACTCTATGGTTCG+CGG - chr6_2:67573192-67573211 Msa0925020:CDS 50.0%
AGGGGAATGTCAATGCATCC+GGG + chr6_2:67573255-67573274 None:intergenic 50.0%
CTAGTTATTGGCACGGCAAG+GGG - chr6_2:67573285-67573304 Msa0925020:intron 50.0%
CAAAGGAGGTTCATGGCCAA+GGG - chr6_2:67573793-67573812 Msa0925020:intron 50.0%
! CTATGGTTCGCGGTTCTAGC+AGG - chr6_2:67573202-67573221 Msa0925020:CDS 55.0%
CCTTGGCCATGAACCTCCTT+TGG + chr6_2:67573795-67573814 None:intergenic 55.0%
CCAAAGGAGGTTCATGGCCA+AGG - chr6_2:67573792-67573811 Msa0925020:intron 55.0%
! CTATGGTTCGCGGTTCTAGC+AGG - chr6_2:67573202-67573221 Msa0925020:CDS 55.0%
CCTTGGCCATGAACCTCCTT+TGG + chr6_2:67573795-67573814 None:intergenic 55.0%
CCAAAGGAGGTTCATGGCCA+AGG - chr6_2:67573792-67573811 Msa0925020:intron 55.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 67573112 67574005 67573112 ID=Msa0925020;Name=Msa0925020
chr6_2 mRNA 67573112 67574005 67573112 ID=Msa0925020-mRNA-1;Parent=Msa0925020;Name=Msa0925020-mRNA-1;_AED=0.45;_eAED=0.45;_QI=0|0|0|1|0|0|2|0|105
chr6_2 exon 67573873 67574005 67573873 ID=Msa0925020-mRNA-1:exon:10703;Parent=Msa0925020-mRNA-1
chr6_2 exon 67573112 67573296 67573112 ID=Msa0925020-mRNA-1:exon:10702;Parent=Msa0925020-mRNA-1
chr6_2 CDS 67573873 67574005 67573873 ID=Msa0925020-mRNA-1:cds;Parent=Msa0925020-mRNA-1
chr6_2 CDS 67573112 67573296 67573112 ID=Msa0925020-mRNA-1:cds;Parent=Msa0925020-mRNA-1
Gene Sequence

>Msa0925020

ATGTATTCCAAATTACAAGAAAAAAACGAAGGAGGATTTGAAATGCGAGATCTAAAAACATATCTCTCTGTGGCACCAGTGGCAAGTACTCTATGGTTCGCGGTTCTAGCAGGTCTCTTGATAGAAATCAATCATATACGAATAACTGTTATTTTGGAATGTAGCAGTTGTGATAAAAAGAGTGTTAATAAGGAATCTAGGGGTATTTCTAGATATATTACTCAAAAGAATCGACACAATACACCTAGTCGATTGGAATTGAGAAAATTCTGTCCCTTTTGTTGCAAACATACGATTCACGTCGAGATAAAGAAATAG

Protein sequence

>Msa0925020

MYSKLQEKNEGGFEMRDLKTYLSVAPVASTLWFAVLAGLLIEINHIRITVILECSSCDKKSVNKESRGISRYITQKNRHNTPSRLELRKFCPFCCKHTIHVEIKK*