AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1463840

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1463840 MtrunA17_Chr3g0129901 96.429 56 2 0 1 56 1 56 3.04e-32 108
Msa1463840 MtrunA17_Chr8g0390801 89.286 56 6 0 1 56 1 56 4.57e-30 103
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1463840 AT5G09770.1 82.143 56 10 0 1 56 1 56 7.29e-28 97.8
Msa1463840 AT5G64650.1 82.143 56 10 0 1 56 1 56 1.02e-27 97.4

Find 28 sgRNAs with CRISPR-Local

Find 94 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTCTATTGTTTCTTGTTCT+TGG 0.106110 tig0043690:+8217 Msa1463840:three_prime_UTR
CTTCCTGAGCTTTGTCATTT+TGG 0.114761 tig0043690:-7715 None:intergenic
TAGAAGGCTTGCGGATAATA+TGG 0.358643 tig0043690:+8037 Msa1463840:CDS
TTTAGGCTAAGGAGGTTAGA+AGG 0.388038 tig0043690:+8021 Msa1463840:intron
TAGAACCATGGTCTCGCAAT+TGG 0.405067 tig0043690:+7872 Msa1463840:intron
CCTGTGAGAGTAATTGAATC+AGG 0.447262 tig0043690:+7540 Msa1463840:five_prime_UTR
ACAGTGTAAGAAAGAAAGCT+AGG 0.473644 tig0043690:+7668 Msa1463840:five_prime_UTR
TTAACCTGAGCATGGATAAC+CGG 0.473739 tig0043690:-7758 None:intergenic
AGGTTGGAAAGAAGAGAAGA+AGG 0.478059 tig0043690:-7508 None:intergenic
TCACAGGGTGCTTGTGAGGT+TGG 0.483232 tig0043690:-7524 None:intergenic
CCTGATTCAATTACTCTCAC+AGG 0.493849 tig0043690:-7540 None:intergenic
GGAAAGAAGAGAAGAAGGAA+AGG 0.504578 tig0043690:-7503 None:intergenic
TATGGTACAGCTTGGTAAAG+AGG 0.517654 tig0043690:+8055 Msa1463840:CDS
CTGCCAAAATGACAAAGCTC+AGG 0.541799 tig0043690:+7712 Msa1463840:exon
ACACTGTGCTATGCACAAAA+CGG 0.550922 tig0043690:-7652 None:intergenic
TTTAAATGGACTGTGAAATG+TGG 0.550934 tig0043690:+8153 Msa1463840:three_prime_UTR
CTGATTCAATTACTCTCACA+GGG 0.562821 tig0043690:-7539 None:intergenic
CTCACCGGTTATCCATGCTC+AGG 0.565167 tig0043690:+7754 Msa1463840:CDS
CAGTGTAAGAAAGAAAGCTA+GGG 0.568142 tig0043690:+7669 Msa1463840:five_prime_UTR
ACTCTCACAGGGTGCTTGTG+AGG 0.575600 tig0043690:-7528 None:intergenic
GCGGATAATATGGTACAGCT+TGG 0.582534 tig0043690:+8047 Msa1463840:CDS
CATTGAAACTACTATTACCA+AGG 0.585744 tig0043690:+7908 Msa1463840:CDS
AAAGCATGTTAACCTGAGCA+TGG 0.605726 tig0043690:-7766 None:intergenic
CCTCACCAATTGCGAGACCA+TGG 0.612029 tig0043690:-7877 None:intergenic
CCATGGTCTCGCAATTGGTG+AGG 0.620210 tig0043690:+7877 Msa1463840:CDS
TAAGGAGGTTAGAAGGCTTG+CGG 0.643881 tig0043690:+8028 Msa1463840:CDS
TCAATCGAGATACGTCTCAC+CGG 0.647896 tig0043690:+7739 Msa1463840:CDS
GAGAAGAAGGAAAGGAAACG+CGG 0.653078 tig0043690:-7495 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAAAAATAAAAAAAGGAAT+TGG - tig0043690:7804-7823 None:intergenic 10.0%
!! TTTGGATAAAAAATAAAAAA+AGG - tig0043690:7810-7829 None:intergenic 10.0%
!!! AAATTTTATTTATATTACCT+TGG - tig0043690:7928-7947 None:intergenic 10.0%
!! TAAAAAATAAAAAAAGGAAT+TGG - tig0043690:7804-7823 None:intergenic 10.0%
!! TTTGGATAAAAAATAAAAAA+AGG - tig0043690:7810-7829 None:intergenic 10.0%
!!! AAATTTTATTTATATTACCT+TGG - tig0043690:7928-7947 None:intergenic 10.0%
!!! TTATTTTTTATTTAGAACCA+TGG + tig0043690:7860-7879 Msa1463840:intron 15.0%
!!! TTATTTTTTATTTAGAACCA+TGG + tig0043690:7860-7879 Msa1463840:intron 15.0%
!! AAAATAAAAAAAGGAATTGG+AGG - tig0043690:7801-7820 None:intergenic 20.0%
!! TTTATCCAAATTCTGAATTA+TGG + tig0043690:7820-7839 Msa1463840:intron 20.0%
!! TTATCCAAATTCTGAATTAT+GGG + tig0043690:7821-7840 Msa1463840:intron 20.0%
!! TGTGAATTTCAATTAAAGTT+TGG + tig0043690:7982-8001 Msa1463840:intron 20.0%
!! AAAATAAAAAAAGGAATTGG+AGG - tig0043690:7801-7820 None:intergenic 20.0%
!! TTTATCCAAATTCTGAATTA+TGG + tig0043690:7820-7839 Msa1463840:intron 20.0%
!! TTATCCAAATTCTGAATTAT+GGG + tig0043690:7821-7840 Msa1463840:intron 20.0%
!! TGTGAATTTCAATTAAAGTT+TGG + tig0043690:7982-8001 Msa1463840:intron 20.0%
! GAATTTCAATTAAAGTTTGG+TGG + tig0043690:7985-8004 Msa1463840:intron 25.0%
!!! GTGGTTGTAATTTTGATTTT+AGG + tig0043690:8004-8023 Msa1463840:intron 25.0%
!!! GTAATTTTGATTTTAGGCTA+AGG + tig0043690:8010-8029 Msa1463840:intron 25.0%
!! TAGTTTAACTATTTTGCATC+TGG + tig0043690:8120-8139 Msa1463840:three_prime_UTR 25.0%
!! AGTTTAACTATTTTGCATCT+GGG + tig0043690:8121-8140 Msa1463840:three_prime_UTR 25.0%
!!! AGTGCATTTTTAGTTTCAAA+AGG + tig0043690:8188-8207 Msa1463840:three_prime_UTR 25.0%
! GAATTTCAATTAAAGTTTGG+TGG + tig0043690:7985-8004 Msa1463840:intron 25.0%
!!! GTGGTTGTAATTTTGATTTT+AGG + tig0043690:8004-8023 Msa1463840:intron 25.0%
!!! GTAATTTTGATTTTAGGCTA+AGG + tig0043690:8010-8029 Msa1463840:intron 25.0%
!! TAGTTTAACTATTTTGCATC+TGG + tig0043690:8120-8139 Msa1463840:three_prime_UTR 25.0%
!! AGTTTAACTATTTTGCATCT+GGG + tig0043690:8121-8140 Msa1463840:three_prime_UTR 25.0%
!!! AGTGCATTTTTAGTTTCAAA+AGG + tig0043690:8188-8207 Msa1463840:three_prime_UTR 25.0%
AAAAAAAGGAATTGGAGGAT+TGG - tig0043690:7796-7815 None:intergenic 30.0%
AGTACCCATAATTCAGAATT+TGG - tig0043690:7828-7847 None:intergenic 30.0%
CATTGAAACTACTATTACCA+AGG + tig0043690:7908-7927 Msa1463840:CDS 30.0%
! ATCGTAATCGTATGCATTTT+CGG + tig0043690:7949-7968 Msa1463840:intron 30.0%
!!! ATTTTGATTTTAGGCTAAGG+AGG + tig0043690:8013-8032 Msa1463840:intron 30.0%
! CTGGGTATGCAAATTTTAAA+TGG + tig0043690:8139-8158 Msa1463840:three_prime_UTR 30.0%
!! TTTAAATGGACTGTGAAATG+TGG + tig0043690:8153-8172 Msa1463840:three_prime_UTR 30.0%
! CTTCTATTGTTTCTTGTTCT+TGG + tig0043690:8217-8236 Msa1463840:three_prime_UTR 30.0%
AAAAAAAGGAATTGGAGGAT+TGG - tig0043690:7796-7815 None:intergenic 30.0%
AGTACCCATAATTCAGAATT+TGG - tig0043690:7828-7847 None:intergenic 30.0%
CATTGAAACTACTATTACCA+AGG + tig0043690:7908-7927 Msa1463840:CDS 30.0%
! ATCGTAATCGTATGCATTTT+CGG + tig0043690:7949-7968 Msa1463840:intron 30.0%
!!! ATTTTGATTTTAGGCTAAGG+AGG + tig0043690:8013-8032 Msa1463840:intron 30.0%
! CTGGGTATGCAAATTTTAAA+TGG + tig0043690:8139-8158 Msa1463840:three_prime_UTR 30.0%
!! TTTAAATGGACTGTGAAATG+TGG + tig0043690:8153-8172 Msa1463840:three_prime_UTR 30.0%
! CTTCTATTGTTTCTTGTTCT+TGG + tig0043690:8217-8236 Msa1463840:three_prime_UTR 30.0%
CTGATTCAATTACTCTCACA+GGG - tig0043690:7542-7561 None:intergenic 35.0%
ACAGTGTAAGAAAGAAAGCT+AGG + tig0043690:7668-7687 Msa1463840:five_prime_UTR 35.0%
CAGTGTAAGAAAGAAAGCTA+GGG + tig0043690:7669-7688 Msa1463840:five_prime_UTR 35.0%
CTGATTCAATTACTCTCACA+GGG - tig0043690:7542-7561 None:intergenic 35.0%
ACAGTGTAAGAAAGAAAGCT+AGG + tig0043690:7668-7687 Msa1463840:five_prime_UTR 35.0%
CAGTGTAAGAAAGAAAGCTA+GGG + tig0043690:7669-7688 Msa1463840:five_prime_UTR 35.0%
GGAAAGAAGAGAAGAAGGAA+AGG - tig0043690:7506-7525 None:intergenic 40.0%
AGGTTGGAAAGAAGAGAAGA+AGG - tig0043690:7511-7530 None:intergenic 40.0%
CCTGATTCAATTACTCTCAC+AGG - tig0043690:7543-7562 None:intergenic 40.0%
CCTGTGAGAGTAATTGAATC+AGG + tig0043690:7540-7559 Msa1463840:five_prime_UTR 40.0%
ACACTGTGCTATGCACAAAA+CGG - tig0043690:7655-7674 None:intergenic 40.0%
!! CTTCCTGAGCTTTGTCATTT+TGG - tig0043690:7718-7737 None:intergenic 40.0%
TTAACCTGAGCATGGATAAC+CGG - tig0043690:7761-7780 None:intergenic 40.0%
AAAGCATGTTAACCTGAGCA+TGG - tig0043690:7769-7788 None:intergenic 40.0%
TTTAGGCTAAGGAGGTTAGA+AGG + tig0043690:8021-8040 Msa1463840:intron 40.0%
TAGAAGGCTTGCGGATAATA+TGG + tig0043690:8037-8056 Msa1463840:CDS 40.0%
TATGGTACAGCTTGGTAAAG+AGG + tig0043690:8055-8074 Msa1463840:CDS 40.0%
GGAAAGAAGAGAAGAAGGAA+AGG - tig0043690:7506-7525 None:intergenic 40.0%
AGGTTGGAAAGAAGAGAAGA+AGG - tig0043690:7511-7530 None:intergenic 40.0%
CCTGATTCAATTACTCTCAC+AGG - tig0043690:7543-7562 None:intergenic 40.0%
CCTGTGAGAGTAATTGAATC+AGG + tig0043690:7540-7559 Msa1463840:five_prime_UTR 40.0%
ACACTGTGCTATGCACAAAA+CGG - tig0043690:7655-7674 None:intergenic 40.0%
!! CTTCCTGAGCTTTGTCATTT+TGG - tig0043690:7718-7737 None:intergenic 40.0%
TTAACCTGAGCATGGATAAC+CGG - tig0043690:7761-7780 None:intergenic 40.0%
AAAGCATGTTAACCTGAGCA+TGG - tig0043690:7769-7788 None:intergenic 40.0%
TTTAGGCTAAGGAGGTTAGA+AGG + tig0043690:8021-8040 Msa1463840:intron 40.0%
TAGAAGGCTTGCGGATAATA+TGG + tig0043690:8037-8056 Msa1463840:CDS 40.0%
TATGGTACAGCTTGGTAAAG+AGG + tig0043690:8055-8074 Msa1463840:CDS 40.0%
GAGAAGAAGGAAAGGAAACG+CGG - tig0043690:7498-7517 None:intergenic 45.0%
CTGCCAAAATGACAAAGCTC+AGG + tig0043690:7712-7731 Msa1463840:exon 45.0%
TCAATCGAGATACGTCTCAC+CGG + tig0043690:7739-7758 Msa1463840:CDS 45.0%
TAGAACCATGGTCTCGCAAT+TGG + tig0043690:7872-7891 Msa1463840:intron 45.0%
TAAGGAGGTTAGAAGGCTTG+CGG + tig0043690:8028-8047 Msa1463840:CDS 45.0%
GCGGATAATATGGTACAGCT+TGG + tig0043690:8047-8066 Msa1463840:CDS 45.0%
GAGAAGAAGGAAAGGAAACG+CGG - tig0043690:7498-7517 None:intergenic 45.0%
CTGCCAAAATGACAAAGCTC+AGG + tig0043690:7712-7731 Msa1463840:exon 45.0%
TCAATCGAGATACGTCTCAC+CGG + tig0043690:7739-7758 Msa1463840:CDS 45.0%
TAGAACCATGGTCTCGCAAT+TGG + tig0043690:7872-7891 Msa1463840:intron 45.0%
TAAGGAGGTTAGAAGGCTTG+CGG + tig0043690:8028-8047 Msa1463840:CDS 45.0%
GCGGATAATATGGTACAGCT+TGG + tig0043690:8047-8066 Msa1463840:CDS 45.0%
! TCACAGGGTGCTTGTGAGGT+TGG - tig0043690:7527-7546 None:intergenic 55.0%
! ACTCTCACAGGGTGCTTGTG+AGG - tig0043690:7531-7550 None:intergenic 55.0%
! CTCACCGGTTATCCATGCTC+AGG + tig0043690:7754-7773 Msa1463840:CDS 55.0%
CCTCACCAATTGCGAGACCA+TGG - tig0043690:7880-7899 None:intergenic 55.0%
CCATGGTCTCGCAATTGGTG+AGG + tig0043690:7877-7896 Msa1463840:CDS 55.0%
! TCACAGGGTGCTTGTGAGGT+TGG - tig0043690:7527-7546 None:intergenic 55.0%
! ACTCTCACAGGGTGCTTGTG+AGG - tig0043690:7531-7550 None:intergenic 55.0%
! CTCACCGGTTATCCATGCTC+AGG + tig0043690:7754-7773 Msa1463840:CDS 55.0%
CCTCACCAATTGCGAGACCA+TGG - tig0043690:7880-7899 None:intergenic 55.0%
CCATGGTCTCGCAATTGGTG+AGG + tig0043690:7877-7896 Msa1463840:CDS 55.0%
Chromosome Type Strat End Strand Name
tig0043690 gene 7490 8298 7490 ID=Msa1463840;Name=Msa1463840
tig0043690 mRNA 7490 8298 7490 ID=Msa1463840-mRNA-1;Parent=Msa1463840;Name=Msa1463840-mRNA-1;_AED=0.07;_eAED=0.07;_QI=230|1|1|1|1|1|3|189|64
tig0043690 exon 7490 7775 7490 ID=Msa1463840-mRNA-1:exon:24201;Parent=Msa1463840-mRNA-1
tig0043690 exon 7875 7929 7875 ID=Msa1463840-mRNA-1:exon:24202;Parent=Msa1463840-mRNA-1
tig0043690 exon 8026 8298 8026 ID=Msa1463840-mRNA-1:exon:24203;Parent=Msa1463840-mRNA-1
tig0043690 five_prime_UTR 7490 7719 7490 ID=Msa1463840-mRNA-1:five_prime_utr;Parent=Msa1463840-mRNA-1
tig0043690 CDS 7720 7775 7720 ID=Msa1463840-mRNA-1:cds;Parent=Msa1463840-mRNA-1
tig0043690 CDS 7875 7929 7875 ID=Msa1463840-mRNA-1:cds;Parent=Msa1463840-mRNA-1
tig0043690 CDS 8026 8109 8026 ID=Msa1463840-mRNA-1:cds;Parent=Msa1463840-mRNA-1
tig0043690 three_prime_UTR 8110 8298 8110 ID=Msa1463840-mRNA-1:three_prime_utr;Parent=Msa1463840-mRNA-1
Gene Sequence

>Msa1463840

ATGACAAAGCTCAGGAAGCTCAATCGAGATACGTCTCACCGGTTATCCATGCTCAGAACCATGGTCTCGCAATTGGTGAGGCATGAACGCATTGAAACTACTATTACCAAGGCTAAGGAGGTTAGAAGGCTTGCGGATAATATGGTACAGCTTGGTAAAGAGGTTAGTTCATTGTTTCATGTTGAATTGAATTGA
Protein sequence

>Msa1463840

MTKLRKLNRDTSHRLSMLRTMVSQLVRHERIETTITKAKEVRRLADNMVQLGKEVSSLFHVELN*