AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0923460


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0923460 MtrunA17_Chr6g0482371 54.701 117 34 1 1 98 8 124 7.38e-34 113
Msa0923460 MtrunA17_Chr6g0482501 38.889 144 41 1 1 97 388 531 5.71e-20 83.2
Msa0923460 MtrunA17_Chr1g0172551 58.929 56 23 0 2 57 91 146 7.42e-15 65.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 32 sgRNAs with CRISPR-Local

Find 118 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAATTTACACTCGTCTTCTT+TGG 0.265768 6_2:+63937959 None:intergenic
TTTCCTCAAAGGATTGATTA+AGG 0.300302 6_2:+63938499 None:intergenic
AGAATATCCTTTGCCAGGTT+TGG 0.313974 6_2:+63938743 None:intergenic
CATCAAGAATGCGTCAGATT+TGG 0.343857 6_2:-63938015 Msa0923460:CDS
GTCCGAATTATCACTGCATT+TGG 0.381704 6_2:+63938782 None:intergenic
CACCAAATGCAGTGATAATT+CGG 0.387621 6_2:-63938784 Msa0923460:five_prime_UTR
TGATTCCATTTCCCTGCCTC+AGG 0.390409 6_2:-63938703 Msa0923460:CDS
GGATAACAATCTTTCATCAT+TGG 0.397150 6_2:-63938445 Msa0923460:intron
CAATGTAGATCAAACTGGTT+TGG 0.399242 6_2:-63938475 Msa0923460:CDS
TACCTCCTGAGGCAGGGAAA+TGG 0.417978 6_2:+63938698 None:intergenic
AAGCCTTAATCAATCCTTTG+AGG 0.420274 6_2:-63938502 Msa0923460:CDS
CCCTCAGAATATCCTTTGCC+AGG 0.426000 6_2:+63938738 None:intergenic
ACCTTCTTGCAAGGTCAGTC+TGG 0.427797 6_2:+63938277 None:intergenic
GAAACCAATGTAGATCAAAC+TGG 0.445612 6_2:-63938480 Msa0923460:CDS
TCAAACTGGTTTGGATGAAT+CGG 0.469296 6_2:-63938466 Msa0923460:CDS
GAAGGTATACCTCCTGAGGC+AGG 0.477144 6_2:+63938691 None:intergenic
CAAACCAGTTTGATCTACAT+TGG 0.479317 6_2:+63938476 None:intergenic
CTCTCAGGTGTTGACTGTGC+AGG 0.482350 6_2:+63938902 None:intergenic
ATCTACATTGGTTTCCTCAA+AGG 0.486879 6_2:+63938488 None:intergenic
GAACCGAGCAACAATCTCTC+AGG 0.525201 6_2:+63938887 None:intergenic
ACTCGTCTTCTTTGGTCACA+TGG 0.531127 6_2:+63937967 None:intergenic
TTCCATTTCCCTGCCTCAGG+AGG 0.537186 6_2:-63938700 Msa0923460:intron
AGTGTAGACATGTCCAAACC+TGG 0.561902 6_2:-63938756 Msa0923460:exon
GACATGTCCAAACCTGGCAA+AGG 0.587270 6_2:-63938750 Msa0923460:CDS
GAAGATACCACCTTCTTGCA+AGG 0.602323 6_2:+63938268 None:intergenic
ACCTGGCAAAGGATATTCTG+AGG 0.611952 6_2:-63938739 Msa0923460:CDS
AAGGTATACCTCCTGAGGCA+GGG 0.624468 6_2:+63938692 None:intergenic
AGACTGACCTTGCAAGAAGG+TGG 0.638902 6_2:-63938275 Msa0923460:intron
CCTGGCAAAGGATATTCTGA+GGG 0.645926 6_2:-63938738 Msa0923460:CDS
ACACCTGAGAGATTGTTGCT+CGG 0.646918 6_2:-63938890 Msa0923460:five_prime_UTR
GATGGAAGGTATACCTCCTG+AGG 0.662058 6_2:+63938687 None:intergenic
GCCAGACTGACCTTGCAAGA+AGG 0.667163 6_2:-63938278 Msa0923460:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTATGTTTGTTATCTATTA+TGG - chr6_2:63938755-63938774 Msa0923460:exon 15.0%
!!! TTATGTTTGTTATCTATTAT+GGG - chr6_2:63938756-63938775 Msa0923460:exon 15.0%
!!! TTTATGTTTGTTATCTATTA+TGG - chr6_2:63938755-63938774 Msa0923460:exon 15.0%
!!! TTATGTTTGTTATCTATTAT+GGG - chr6_2:63938756-63938775 Msa0923460:exon 15.0%
!! AAATTAAAACCAAAACAAGA+TGG + chr6_2:63938223-63938242 None:intergenic 20.0%
!!! TCTTGTTTTGGTTTTAATTT+TGG - chr6_2:63938223-63938242 Msa0923460:intron 20.0%
!!! ACAATAAAATTGCTTTTGAA+AGG + chr6_2:63938299-63938318 None:intergenic 20.0%
!! AGAAGAATAAGAACTAAATA+AGG + chr6_2:63938827-63938846 None:intergenic 20.0%
!! AAATTAAAACCAAAACAAGA+TGG + chr6_2:63938223-63938242 None:intergenic 20.0%
!!! TCTTGTTTTGGTTTTAATTT+TGG - chr6_2:63938223-63938242 Msa0923460:intron 20.0%
!!! ACAATAAAATTGCTTTTGAA+AGG + chr6_2:63938299-63938318 None:intergenic 20.0%
!! AGAAGAATAAGAACTAAATA+AGG + chr6_2:63938827-63938846 None:intergenic 20.0%
!! GTAATTGCTTTCTTGATAAT+TGG - chr6_2:63938343-63938362 Msa0923460:intron 25.0%
! ATAAACACAGAATTCTAACT+CGG + chr6_2:63938740-63938759 None:intergenic 25.0%
!! GTAATTGCTTTCTTGATAAT+TGG - chr6_2:63938343-63938362 Msa0923460:intron 25.0%
! ATAAACACAGAATTCTAACT+CGG + chr6_2:63938740-63938759 None:intergenic 25.0%
TAAAACCAAAACAAGATGGA+AGG + chr6_2:63938219-63938238 None:intergenic 30.0%
TTTCCTCAAAGGATTGATTA+AGG + chr6_2:63938393-63938412 None:intergenic 30.0%
GGATAACAATCTTTCATCAT+TGG - chr6_2:63938444-63938463 Msa0923460:intron 30.0%
ACTAATCTTATCCTCTCAAT+AGG - chr6_2:63938549-63938568 Msa0923460:intron 30.0%
!! TTGGAGTATCAGTCTATTTT+AGG - chr6_2:63938703-63938722 Msa0923460:CDS 30.0%
!! TGGAGTATCAGTCTATTTTA+GGG - chr6_2:63938704-63938723 Msa0923460:CDS 30.0%
! TACAACATCAGAACTTTTGA+TGG - chr6_2:63938801-63938820 Msa0923460:five_prime_UTR 30.0%
GCTGCAAATATAACATGTTA+TGG + chr6_2:63938855-63938874 None:intergenic 30.0%
TAAAACCAAAACAAGATGGA+AGG + chr6_2:63938219-63938238 None:intergenic 30.0%
TTTCCTCAAAGGATTGATTA+AGG + chr6_2:63938393-63938412 None:intergenic 30.0%
GGATAACAATCTTTCATCAT+TGG - chr6_2:63938444-63938463 Msa0923460:intron 30.0%
ACTAATCTTATCCTCTCAAT+AGG - chr6_2:63938549-63938568 Msa0923460:intron 30.0%
!! TTGGAGTATCAGTCTATTTT+AGG - chr6_2:63938703-63938722 Msa0923460:CDS 30.0%
!! TGGAGTATCAGTCTATTTTA+GGG - chr6_2:63938704-63938723 Msa0923460:CDS 30.0%
! TACAACATCAGAACTTTTGA+TGG - chr6_2:63938801-63938820 Msa0923460:five_prime_UTR 30.0%
GCTGCAAATATAACATGTTA+TGG + chr6_2:63938855-63938874 None:intergenic 30.0%
! CTTTTGACAGTCAAATTCTG+AGG + chr6_2:63938038-63938057 None:intergenic 35.0%
CACCAAATGCAGTGATAATT+CGG - chr6_2:63938105-63938124 Msa0923460:intron 35.0%
!! GTATACCTTCCATCTTGTTT+TGG - chr6_2:63938211-63938230 Msa0923460:intron 35.0%
! GATAATTGGTTTCTCAATGC+AGG - chr6_2:63938357-63938376 Msa0923460:intron 35.0%
AAGCCTTAATCAATCCTTTG+AGG - chr6_2:63938387-63938406 Msa0923460:intron 35.0%
!! ATCTACATTGGTTTCCTCAA+AGG + chr6_2:63938404-63938423 None:intergenic 35.0%
GAAACCAATGTAGATCAAAC+TGG - chr6_2:63938409-63938428 Msa0923460:intron 35.0%
CAAACCAGTTTGATCTACAT+TGG + chr6_2:63938416-63938435 None:intergenic 35.0%
CAATGTAGATCAAACTGGTT+TGG - chr6_2:63938414-63938433 Msa0923460:intron 35.0%
!! TCAAACTGGTTTGGATGAAT+CGG - chr6_2:63938423-63938442 Msa0923460:intron 35.0%
! GGTGTGATTGACTCTATATT+TGG - chr6_2:63938465-63938484 Msa0923460:CDS 35.0%
! CTGATCAACTGTTGTTCTTT+TGG - chr6_2:63938684-63938703 Msa0923460:intron 35.0%
CAATTTACACTCGTCTTCTT+TGG + chr6_2:63938933-63938952 None:intergenic 35.0%
! CTTTTGACAGTCAAATTCTG+AGG + chr6_2:63938038-63938057 None:intergenic 35.0%
CACCAAATGCAGTGATAATT+CGG - chr6_2:63938105-63938124 Msa0923460:intron 35.0%
!! GTATACCTTCCATCTTGTTT+TGG - chr6_2:63938211-63938230 Msa0923460:intron 35.0%
! GATAATTGGTTTCTCAATGC+AGG - chr6_2:63938357-63938376 Msa0923460:intron 35.0%
AAGCCTTAATCAATCCTTTG+AGG - chr6_2:63938387-63938406 Msa0923460:intron 35.0%
!! ATCTACATTGGTTTCCTCAA+AGG + chr6_2:63938404-63938423 None:intergenic 35.0%
GAAACCAATGTAGATCAAAC+TGG - chr6_2:63938409-63938428 Msa0923460:intron 35.0%
CAAACCAGTTTGATCTACAT+TGG + chr6_2:63938416-63938435 None:intergenic 35.0%
CAATGTAGATCAAACTGGTT+TGG - chr6_2:63938414-63938433 Msa0923460:intron 35.0%
!! TCAAACTGGTTTGGATGAAT+CGG - chr6_2:63938423-63938442 Msa0923460:intron 35.0%
! GGTGTGATTGACTCTATATT+TGG - chr6_2:63938465-63938484 Msa0923460:CDS 35.0%
! CTGATCAACTGTTGTTCTTT+TGG - chr6_2:63938684-63938703 Msa0923460:intron 35.0%
CAATTTACACTCGTCTTCTT+TGG + chr6_2:63938933-63938952 None:intergenic 35.0%
! AAGTCGAGCAATCTTTTTGC+AGG + chr6_2:63938079-63938098 None:intergenic 40.0%
GTCCGAATTATCACTGCATT+TGG + chr6_2:63938110-63938129 None:intergenic 40.0%
AGAATATCCTTTGCCAGGTT+TGG + chr6_2:63938149-63938168 None:intergenic 40.0%
TTTCAGCTTCTCCTATTGAG+AGG + chr6_2:63938563-63938582 None:intergenic 40.0%
TGATGTTGTACCAAACTGCT+AGG + chr6_2:63938791-63938810 None:intergenic 40.0%
CATCAAGAATGCGTCAGATT+TGG - chr6_2:63938874-63938893 Msa0923460:five_prime_UTR 40.0%
! AAGTCGAGCAATCTTTTTGC+AGG + chr6_2:63938079-63938098 None:intergenic 40.0%
GTCCGAATTATCACTGCATT+TGG + chr6_2:63938110-63938129 None:intergenic 40.0%
AGAATATCCTTTGCCAGGTT+TGG + chr6_2:63938149-63938168 None:intergenic 40.0%
TTTCAGCTTCTCCTATTGAG+AGG + chr6_2:63938563-63938582 None:intergenic 40.0%
TGATGTTGTACCAAACTGCT+AGG + chr6_2:63938791-63938810 None:intergenic 40.0%
CATCAAGAATGCGTCAGATT+TGG - chr6_2:63938874-63938893 Msa0923460:five_prime_UTR 40.0%
ACACCTGAGAGATTGTTGCT+CGG - chr6_2:63937999-63938018 Msa0923460:CDS 45.0%
AGTGTAGACATGTCCAAACC+TGG - chr6_2:63938133-63938152 Msa0923460:intron 45.0%
ACCTGGCAAAGGATATTCTG+AGG - chr6_2:63938150-63938169 Msa0923460:intron 45.0%
CCTGGCAAAGGATATTCTGA+GGG - chr6_2:63938151-63938170 Msa0923460:intron 45.0%
GAAGATACCACCTTCTTGCA+AGG + chr6_2:63938624-63938643 None:intergenic 45.0%
TGCAAGAAGGTGGTATCTTC+TGG - chr6_2:63938624-63938643 Msa0923460:intron 45.0%
GATAGCAGAACCTAGCAGTT+TGG - chr6_2:63938778-63938797 Msa0923460:five_prime_UTR 45.0%
ACTCGTCTTCTTTGGTCACA+TGG + chr6_2:63938925-63938944 None:intergenic 45.0%
ACACCTGAGAGATTGTTGCT+CGG - chr6_2:63937999-63938018 Msa0923460:CDS 45.0%
AGTGTAGACATGTCCAAACC+TGG - chr6_2:63938133-63938152 Msa0923460:intron 45.0%
ACCTGGCAAAGGATATTCTG+AGG - chr6_2:63938150-63938169 Msa0923460:intron 45.0%
CCTGGCAAAGGATATTCTGA+GGG - chr6_2:63938151-63938170 Msa0923460:intron 45.0%
GAAGATACCACCTTCTTGCA+AGG + chr6_2:63938624-63938643 None:intergenic 45.0%
TGCAAGAAGGTGGTATCTTC+TGG - chr6_2:63938624-63938643 Msa0923460:intron 45.0%
GATAGCAGAACCTAGCAGTT+TGG - chr6_2:63938778-63938797 Msa0923460:five_prime_UTR 45.0%
ACTCGTCTTCTTTGGTCACA+TGG + chr6_2:63938925-63938944 None:intergenic 45.0%
GAACCGAGCAACAATCTCTC+AGG + chr6_2:63938005-63938024 None:intergenic 50.0%
GACATGTCCAAACCTGGCAA+AGG - chr6_2:63938139-63938158 Msa0923460:intron 50.0%
CCCTCAGAATATCCTTTGCC+AGG + chr6_2:63938154-63938173 None:intergenic 50.0%
TGATTCCATTTCCCTGCCTC+AGG - chr6_2:63938186-63938205 Msa0923460:intron 50.0%
AAGGTATACCTCCTGAGGCA+GGG + chr6_2:63938200-63938219 None:intergenic 50.0%
! GATGGAAGGTATACCTCCTG+AGG + chr6_2:63938205-63938224 None:intergenic 50.0%
ACCTTCTTGCAAGGTCAGTC+TGG + chr6_2:63938615-63938634 None:intergenic 50.0%
AGACTGACCTTGCAAGAAGG+TGG - chr6_2:63938614-63938633 Msa0923460:intron 50.0%
! CTTCTGGAGACACTGTGTAC+TGG - chr6_2:63938640-63938659 Msa0923460:intron 50.0%
! TGGAGACACTGTGTACTGGT+GGG - chr6_2:63938644-63938663 Msa0923460:intron 50.0%
GAACCGAGCAACAATCTCTC+AGG + chr6_2:63938005-63938024 None:intergenic 50.0%
GACATGTCCAAACCTGGCAA+AGG - chr6_2:63938139-63938158 Msa0923460:intron 50.0%
CCCTCAGAATATCCTTTGCC+AGG + chr6_2:63938154-63938173 None:intergenic 50.0%
TGATTCCATTTCCCTGCCTC+AGG - chr6_2:63938186-63938205 Msa0923460:intron 50.0%
AAGGTATACCTCCTGAGGCA+GGG + chr6_2:63938200-63938219 None:intergenic 50.0%
! GATGGAAGGTATACCTCCTG+AGG + chr6_2:63938205-63938224 None:intergenic 50.0%
ACCTTCTTGCAAGGTCAGTC+TGG + chr6_2:63938615-63938634 None:intergenic 50.0%
AGACTGACCTTGCAAGAAGG+TGG - chr6_2:63938614-63938633 Msa0923460:intron 50.0%
! CTTCTGGAGACACTGTGTAC+TGG - chr6_2:63938640-63938659 Msa0923460:intron 50.0%
! TGGAGACACTGTGTACTGGT+GGG - chr6_2:63938644-63938663 Msa0923460:intron 50.0%
!! CTCTCAGGTGTTGACTGTGC+AGG + chr6_2:63937990-63938009 None:intergenic 55.0%
TTCCATTTCCCTGCCTCAGG+AGG - chr6_2:63938189-63938208 Msa0923460:intron 55.0%
TACCTCCTGAGGCAGGGAAA+TGG + chr6_2:63938194-63938213 None:intergenic 55.0%
! GAAGGTATACCTCCTGAGGC+AGG + chr6_2:63938201-63938220 None:intergenic 55.0%
GCCAGACTGACCTTGCAAGA+AGG - chr6_2:63938611-63938630 Msa0923460:intron 55.0%
CTGGAGACACTGTGTACTGG+TGG - chr6_2:63938643-63938662 Msa0923460:intron 55.0%
!! CTCTCAGGTGTTGACTGTGC+AGG + chr6_2:63937990-63938009 None:intergenic 55.0%
TTCCATTTCCCTGCCTCAGG+AGG - chr6_2:63938189-63938208 Msa0923460:intron 55.0%
TACCTCCTGAGGCAGGGAAA+TGG + chr6_2:63938194-63938213 None:intergenic 55.0%
! GAAGGTATACCTCCTGAGGC+AGG + chr6_2:63938201-63938220 None:intergenic 55.0%
GCCAGACTGACCTTGCAAGA+AGG - chr6_2:63938611-63938630 Msa0923460:intron 55.0%
CTGGAGACACTGTGTACTGG+TGG - chr6_2:63938643-63938662 Msa0923460:intron 55.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 63937944 63938967 63937944 ID=Msa0923460;Name=Msa0923460
chr6_2 mRNA 63937944 63938967 63937944 ID=Msa0923460-mRNA-1;Parent=Msa0923460;Name=Msa0923460-mRNA-1;_AED=0.35;_eAED=0.44;_QI=198|0.33|0.25|1|0.66|0.75|4|0|104
chr6_2 exon 63937944 63938037 63937944 ID=Msa0923460-mRNA-1:exon:9987;Parent=Msa0923460-mRNA-1
chr6_2 exon 63938276 63938340 63938276 ID=Msa0923460-mRNA-1:exon:9986;Parent=Msa0923460-mRNA-1
chr6_2 exon 63938446 63938532 63938446 ID=Msa0923460-mRNA-1:exon:9985;Parent=Msa0923460-mRNA-1
chr6_2 exon 63938701 63938967 63938701 ID=Msa0923460-mRNA-1:exon:9984;Parent=Msa0923460-mRNA-1
chr6_2 five_prime_UTR 63938770 63938967 63938770 ID=Msa0923460-mRNA-1:five_prime_utr;Parent=Msa0923460-mRNA-1
chr6_2 CDS 63938701 63938769 63938701 ID=Msa0923460-mRNA-1:cds;Parent=Msa0923460-mRNA-1
chr6_2 CDS 63938446 63938532 63938446 ID=Msa0923460-mRNA-1:cds;Parent=Msa0923460-mRNA-1
chr6_2 CDS 63938276 63938340 63938276 ID=Msa0923460-mRNA-1:cds;Parent=Msa0923460-mRNA-1
chr6_2 CDS 63937944 63938037 63937944 ID=Msa0923460-mRNA-1:cds;Parent=Msa0923460-mRNA-1
Gene Sequence

>Msa0923460

ATGTCCAAACCTGGCAAAGGATATTCTGAGGGTCTCAAATCTTTTGATTCCATTTCCCTGCCTCAGGAGGTAGAAGAAAGCCTTAATCAATCCTTTGAGGAAACCAATGTAGATCAAACTGGTTTGGATGAATCGGATAACAATCTTTCATCATTGGAGAAGCTGAAAAACAGATTGAGATTTTGCAAAAGATTGTGCCAGACTGACCTTGCAAGAAGGTGCATCAAGAATGCGTCAGATTTGGACTCAGTTCGATCAAGACTTCTCAGCCATGTGACCAAAGAAGACGAGTGTAAATTGCATTGTTGCAAATGA

Protein sequence

>Msa0923460

MSKPGKGYSEGLKSFDSISLPQEVEESLNQSFEETNVDQTGLDESDNNLSSLEKLKNRLRFCKRLCQTDLARRCIKNASDLDSVRSRLLSHVTKEDECKLHCCK*