AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0119850


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0119850 MtrunA17_Chr1g0170791 98.810 84 1 0 3 86 323 406 4.66e-54 172
Msa0119850 MtrunA17_Chr5g0418301 67.500 80 26 0 3 82 329 408 2.02e-34 121
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0119850 AT5G13610.1 76.250 80 19 0 3 82 322 401 7.99e-38 130
Msa0119850 AT1G69380.1 59.259 81 33 0 3 83 289 369 2.22e-31 112

Find 24 sgRNAs with CRISPR-Local

Find 92 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCCCATATCTGACCATATT+TGG 0.221053 1_3:+44264502 None:intergenic
GGTGCTACTCATCAAGATTT+TGG 0.237523 1_3:-44263912 Msa0119850:three_prime_UTR
ACCATATTTGGCATCTTTCC+AGG 0.288418 1_3:+44264514 None:intergenic
GCAAAGTGATGAAACAATTA+TGG 0.342063 1_3:-44264052 Msa0119850:three_prime_UTR
TACAAGAAATTCTTCAAAAC+AGG 0.343403 1_3:-44264285 Msa0119850:CDS
ATGCCAAATATGGTCAGATA+TGG 0.351572 1_3:-44264505 Msa0119850:CDS
GGTCTTACATGCCACCATAA+AGG 0.371821 1_3:+44263980 None:intergenic
GTCAGATATGGGAGTATCTC+AGG 0.391860 1_3:-44264493 Msa0119850:CDS
GCCTGGAAAGATGCCAAATA+TGG 0.392620 1_3:-44264515 Msa0119850:CDS
GTCTTACATGCCACCATAAA+GGG 0.393914 1_3:+44263981 None:intergenic
TTTAACAGCATTGTTTCTAC+TGG 0.397693 1_3:-44264168 Msa0119850:exon
TGGCTCATTATTGCATTGAT+TGG 0.416590 1_3:-44264244 Msa0119850:CDS
TGATTTCAAGTTGAAATTTG+TGG 0.429980 1_3:-44264435 Msa0119850:CDS
GGTTGTATTGATGCAAGCTT+TGG 0.436791 1_3:-44264031 Msa0119850:three_prime_UTR
GATTGTAGAATAAGAGAACT+TGG 0.526182 1_3:-44263933 Msa0119850:three_prime_UTR
TTTACAGATCAGATATCGCC+TGG 0.534883 1_3:-44264532 Msa0119850:intron
TGCCAAATATGGTCAGATAT+GGG 0.539187 1_3:-44264504 Msa0119850:CDS
CTCTATATGACATTGTTCAA+AGG 0.569742 1_3:-44264204 Msa0119850:CDS
GGAAATCTGATTTCCTTGAG+TGG 0.592677 1_3:-44264264 Msa0119850:CDS
ATGCAATAATGAGCCACTCA+AGG 0.594797 1_3:+44264251 None:intergenic
TTTCAAGTTGAAATTTGTGG+AGG 0.601208 1_3:-44264432 Msa0119850:intron
ATGTCAAATGAACAAATCAA+CGG 0.630464 1_3:-44264113 Msa0119850:three_prime_UTR
TCAGATATGGGAGTATCTCA+GGG 0.654645 1_3:-44264492 Msa0119850:CDS
TCAAATGAACAAATCAACGG+AGG 0.702502 1_3:-44264110 Msa0119850:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAGTAATGTAATTAATGT+TGG - chr1_3:44263935-44263954 Msa0119850:three_prime_UTR 15.0%
!!! TCAACTTAAAAAGTTTTAAA+TGG - chr1_3:44264082-44264101 Msa0119850:three_prime_UTR 15.0%
!!! TCAACTTAAAAAGTTTTAAA+TGG - chr1_3:44264082-44264101 Msa0119850:three_prime_UTR 15.0%
!! AATAGTAATGTAATTAATGT+TGG - chr1_3:44263935-44263954 Msa0119850:three_prime_UTR 15.0%
!!! TCAACTTAAAAAGTTTTAAA+TGG - chr1_3:44264082-44264101 Msa0119850:three_prime_UTR 15.0%
!!! TCAACTTAAAAAGTTTTAAA+TGG - chr1_3:44264082-44264101 Msa0119850:three_prime_UTR 15.0%
!! TGAAAGAGACATATAATATT+TGG + chr1_3:44264065-44264084 None:intergenic 20.0%
!! TGAAAGAGACATATAATATT+TGG + chr1_3:44264065-44264084 None:intergenic 20.0%
!! ATTGTGCTGTAAAATTAAAA+AGG + chr1_3:44264421-44264440 None:intergenic 20.0%
!!! TCATATTTATTTTCCCTTTA+TGG - chr1_3:44264742-44264761 Msa0119850:intron 20.0%
!! TGAAAGAGACATATAATATT+TGG + chr1_3:44264065-44264084 None:intergenic 20.0%
!! TGAAAGAGACATATAATATT+TGG + chr1_3:44264065-44264084 None:intergenic 20.0%
!! ATTGTGCTGTAAAATTAAAA+AGG + chr1_3:44264421-44264440 None:intergenic 20.0%
!!! TCATATTTATTTTCCCTTTA+TGG - chr1_3:44264742-44264761 Msa0119850:intron 20.0%
! TTGGTAAACATAATGACAAA+AGG - chr1_3:44263954-44263973 Msa0119850:three_prime_UTR 25.0%
!!! AAGTTTTAAATGGTGTTTAC+AGG - chr1_3:44264092-44264111 Msa0119850:three_prime_UTR 25.0%
!!! AGTTTTAAATGGTGTTTACA+GGG - chr1_3:44264093-44264112 Msa0119850:three_prime_UTR 25.0%
!!! TGATTTCAAGTTGAAATTTG+TGG - chr1_3:44264301-44264320 Msa0119850:CDS 25.0%
! TACAAGAAATTCTTCAAAAC+AGG - chr1_3:44264451-44264470 Msa0119850:CDS 25.0%
! ATGTCAAATGAACAAATCAA+CGG - chr1_3:44264623-44264642 Msa0119850:intron 25.0%
!!! TATTTATTTTCCCTTTATGG+TGG - chr1_3:44264745-44264764 Msa0119850:intron 25.0%
! TTGGTAAACATAATGACAAA+AGG - chr1_3:44263954-44263973 Msa0119850:three_prime_UTR 25.0%
!!! AAGTTTTAAATGGTGTTTAC+AGG - chr1_3:44264092-44264111 Msa0119850:three_prime_UTR 25.0%
!!! AGTTTTAAATGGTGTTTACA+GGG - chr1_3:44264093-44264112 Msa0119850:three_prime_UTR 25.0%
!!! TGATTTCAAGTTGAAATTTG+TGG - chr1_3:44264301-44264320 Msa0119850:CDS 25.0%
! TACAAGAAATTCTTCAAAAC+AGG - chr1_3:44264451-44264470 Msa0119850:CDS 25.0%
! ATGTCAAATGAACAAATCAA+CGG - chr1_3:44264623-44264642 Msa0119850:intron 25.0%
!!! TATTTATTTTCCCTTTATGG+TGG - chr1_3:44264745-44264764 Msa0119850:intron 25.0%
TGTGTGTCTTTACTTTCTTT+CGG - chr1_3:44263992-44264011 Msa0119850:three_prime_UTR 30.0%
!! TTTCAAGTTGAAATTTGTGG+AGG - chr1_3:44264304-44264323 Msa0119850:CDS 30.0%
! TTCTCACTTCATTTTCTATC+CGG - chr1_3:44264357-44264376 Msa0119850:intron 30.0%
GATAAATTTGTAGAGATGTC+CGG + chr1_3:44264379-44264398 None:intergenic 30.0%
CTCTATATGACATTGTTCAA+AGG - chr1_3:44264532-44264551 Msa0119850:intron 30.0%
!! TTTAACAGCATTGTTTCTAC+TGG - chr1_3:44264568-44264587 Msa0119850:intron 30.0%
GCAAAGTGATGAAACAATTA+TGG - chr1_3:44264684-44264703 Msa0119850:intron 30.0%
GATTGTAGAATAAGAGAACT+TGG - chr1_3:44264803-44264822 Msa0119850:intron 30.0%
TGTGTGTCTTTACTTTCTTT+CGG - chr1_3:44263992-44264011 Msa0119850:three_prime_UTR 30.0%
!! TTTCAAGTTGAAATTTGTGG+AGG - chr1_3:44264304-44264323 Msa0119850:CDS 30.0%
! TTCTCACTTCATTTTCTATC+CGG - chr1_3:44264357-44264376 Msa0119850:intron 30.0%
GATAAATTTGTAGAGATGTC+CGG + chr1_3:44264379-44264398 None:intergenic 30.0%
CTCTATATGACATTGTTCAA+AGG - chr1_3:44264532-44264551 Msa0119850:intron 30.0%
!! TTTAACAGCATTGTTTCTAC+TGG - chr1_3:44264568-44264587 Msa0119850:intron 30.0%
GCAAAGTGATGAAACAATTA+TGG - chr1_3:44264684-44264703 Msa0119850:intron 30.0%
GATTGTAGAATAAGAGAACT+TGG - chr1_3:44264803-44264822 Msa0119850:intron 30.0%
TGTCTTTACTTTCTTTCGGT+TGG - chr1_3:44263996-44264015 Msa0119850:three_prime_UTR 35.0%
TTCTTTCGGTTGGATCATAT+TGG - chr1_3:44264006-44264025 Msa0119850:three_prime_UTR 35.0%
ATGCCAAATATGGTCAGATA+TGG - chr1_3:44264231-44264250 Msa0119850:CDS 35.0%
TGCCAAATATGGTCAGATAT+GGG - chr1_3:44264232-44264251 Msa0119850:CDS 35.0%
! TGGCTCATTATTGCATTGAT+TGG - chr1_3:44264492-44264511 Msa0119850:CDS 35.0%
TCAAATGAACAAATCAACGG+AGG - chr1_3:44264626-44264645 Msa0119850:intron 35.0%
TGTCTTTACTTTCTTTCGGT+TGG - chr1_3:44263996-44264015 Msa0119850:three_prime_UTR 35.0%
TTCTTTCGGTTGGATCATAT+TGG - chr1_3:44264006-44264025 Msa0119850:three_prime_UTR 35.0%
ATGCCAAATATGGTCAGATA+TGG - chr1_3:44264231-44264250 Msa0119850:CDS 35.0%
TGCCAAATATGGTCAGATAT+GGG - chr1_3:44264232-44264251 Msa0119850:CDS 35.0%
! TGGCTCATTATTGCATTGAT+TGG - chr1_3:44264492-44264511 Msa0119850:CDS 35.0%
TCAAATGAACAAATCAACGG+AGG - chr1_3:44264626-44264645 Msa0119850:intron 35.0%
GGTGTTTACAGGGATCATAT+TGG - chr1_3:44264103-44264122 Msa0119850:three_prime_UTR 40.0%
TTTACAGATCAGATATCGCC+TGG - chr1_3:44264204-44264223 Msa0119850:CDS 40.0%
ACCATATTTGGCATCTTTCC+AGG + chr1_3:44264225-44264244 None:intergenic 40.0%
CTCCCATATCTGACCATATT+TGG + chr1_3:44264237-44264256 None:intergenic 40.0%
!! TCAGATATGGGAGTATCTCA+GGG - chr1_3:44264244-44264263 Msa0119850:CDS 40.0%
GGAAATCTGATTTCCTTGAG+TGG - chr1_3:44264472-44264491 Msa0119850:CDS 40.0%
ATGCAATAATGAGCCACTCA+AGG + chr1_3:44264488-44264507 None:intergenic 40.0%
! GGTTGTATTGATGCAAGCTT+TGG - chr1_3:44264705-44264724 Msa0119850:intron 40.0%
GTCTTACATGCCACCATAAA+GGG + chr1_3:44264758-44264777 None:intergenic 40.0%
!!! GGTGCTACTCATCAAGATTT+TGG - chr1_3:44264824-44264843 Msa0119850:intron 40.0%
! GCTACTCATCAAGATTTTGG+TGG - chr1_3:44264827-44264846 Msa0119850:intron 40.0%
GGTGTTTACAGGGATCATAT+TGG - chr1_3:44264103-44264122 Msa0119850:three_prime_UTR 40.0%
TTTACAGATCAGATATCGCC+TGG - chr1_3:44264204-44264223 Msa0119850:CDS 40.0%
ACCATATTTGGCATCTTTCC+AGG + chr1_3:44264225-44264244 None:intergenic 40.0%
CTCCCATATCTGACCATATT+TGG + chr1_3:44264237-44264256 None:intergenic 40.0%
!! TCAGATATGGGAGTATCTCA+GGG - chr1_3:44264244-44264263 Msa0119850:CDS 40.0%
GGAAATCTGATTTCCTTGAG+TGG - chr1_3:44264472-44264491 Msa0119850:CDS 40.0%
ATGCAATAATGAGCCACTCA+AGG + chr1_3:44264488-44264507 None:intergenic 40.0%
! GGTTGTATTGATGCAAGCTT+TGG - chr1_3:44264705-44264724 Msa0119850:intron 40.0%
GTCTTACATGCCACCATAAA+GGG + chr1_3:44264758-44264777 None:intergenic 40.0%
!!! GGTGCTACTCATCAAGATTT+TGG - chr1_3:44264824-44264843 Msa0119850:intron 40.0%
! GCTACTCATCAAGATTTTGG+TGG - chr1_3:44264827-44264846 Msa0119850:intron 40.0%
AGTCAGTGAGTTGCACTGTT+TGG - chr1_3:44263894-44263913 Msa0119850:three_prime_UTR 45.0%
TTGCACTGTTTGGCAGAAGA+GGG - chr1_3:44263904-44263923 Msa0119850:three_prime_UTR 45.0%
GCCTGGAAAGATGCCAAATA+TGG - chr1_3:44264221-44264240 Msa0119850:CDS 45.0%
!! GTCAGATATGGGAGTATCTC+AGG - chr1_3:44264243-44264262 Msa0119850:CDS 45.0%
GGTCTTACATGCCACCATAA+AGG + chr1_3:44264759-44264778 None:intergenic 45.0%
AGTCAGTGAGTTGCACTGTT+TGG - chr1_3:44263894-44263913 Msa0119850:three_prime_UTR 45.0%
TTGCACTGTTTGGCAGAAGA+GGG - chr1_3:44263904-44263923 Msa0119850:three_prime_UTR 45.0%
GCCTGGAAAGATGCCAAATA+TGG - chr1_3:44264221-44264240 Msa0119850:CDS 45.0%
!! GTCAGATATGGGAGTATCTC+AGG - chr1_3:44264243-44264262 Msa0119850:CDS 45.0%
GGTCTTACATGCCACCATAA+AGG + chr1_3:44264759-44264778 None:intergenic 45.0%
!! AAAAAATAAAAAATAAAAAC+TGG + chr1_3:44264780-44264799 None:intergenic 5.0%
!! AAAAAATAAAAAATAAAAAC+TGG + chr1_3:44264780-44264799 None:intergenic 5.0%
GTTGCACTGTTTGGCAGAAG+AGG - chr1_3:44263903-44263922 Msa0119850:three_prime_UTR 50.0%
GTTGCACTGTTTGGCAGAAG+AGG - chr1_3:44263903-44263922 Msa0119850:three_prime_UTR 50.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 44263891 44264867 44263891 ID=Msa0119850;Name=Msa0119850
chr1_3 mRNA 44263891 44264867 44263891 ID=Msa0119850-mRNA-1;Parent=Msa0119850;Name=Msa0119850-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|0.5|0.33|0.66|1|1|3|295|86
chr1_3 exon 44263891 44264323 44263891 ID=Msa0119850-mRNA-1:exon:13202;Parent=Msa0119850-mRNA-1
chr1_3 exon 44264433 44264547 44264433 ID=Msa0119850-mRNA-1:exon:13201;Parent=Msa0119850-mRNA-1
chr1_3 exon 44264860 44264867 44264860 ID=Msa0119850-mRNA-1:exon:13200;Parent=Msa0119850-mRNA-1
chr1_3 CDS 44264860 44264867 44264860 ID=Msa0119850-mRNA-1:cds;Parent=Msa0119850-mRNA-1
chr1_3 CDS 44264433 44264547 44264433 ID=Msa0119850-mRNA-1:cds;Parent=Msa0119850-mRNA-1
chr1_3 CDS 44264186 44264323 44264186 ID=Msa0119850-mRNA-1:cds;Parent=Msa0119850-mRNA-1
chr1_3 three_prime_UTR 44263891 44264185 44263891 ID=Msa0119850-mRNA-1:three_prime_utr;Parent=Msa0119850-mRNA-1
Gene Sequence

>Msa0119850

ATGAGTCAATCAGATATCGCCTGGAAAGATGCCAAATATGGTCAGATATGGGAGTATCTCAGGGACGAATTTGAGTTAACTCAGAGATTTGCAAGTCTTGATTTCAAGTTGAAATTTGTGGAGCACAATATTCGATTTCTACAAGAAATTCTTCAAAACAGGAAATCTGATTTCCTTGAGTGGCTCATTATTGCATTGATTGGTGCTGAAATTCTGCTGTCTCTATATGACATTGTTCAAAGGTCTGCGATGAATCTTTAA

Protein sequence

>Msa0119850

MSQSDIAWKDAKYGQIWEYLRDEFELTQRFASLDFKLKFVEHNIRFLQEILQNRKSDFLEWLIIALIGAEILLSLYDIVQRSAMNL*