AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0562940

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0562940 MtrunA17_Chr8g0376831 93.966 116 7 0 1 116 75 190 1.89e-64 193
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 33 sgRNAs with CRISPR-Local

Find 116 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCATTTGGTAGCCCCTTCT+TGG 0.192829 4_1:-63218034 None:intergenic
TCCTTTCATTCTCTCTAGAT+TGG 0.283756 4_1:-63218074 None:intergenic
CTAGATTGGTTTGCCGAGTT+TGG 0.294881 4_1:-63218060 None:intergenic
CTTACACAAGAAAGGTGATT+TGG 0.296388 4_1:-63217897 None:intergenic
AAGAGCAAACCTTGTCTTGT+TGG 0.327280 4_1:-63218212 None:intergenic
GAAGGGAGAAGGGGTGGAAC+TGG 0.369006 4_1:+63217773 Msa0562940:five_prime_UTR
GCCGAGTTTGGCACTGCATT+TGG 0.378393 4_1:-63218048 None:intergenic
CTTAATACATTCAAGTCAAA+AGG 0.425621 4_1:-63217846 None:intergenic
AGAATGAAAGGAAGAACAAA+AGG 0.442868 4_1:+63218085 Msa0562940:CDS
TAAGGTTATTTCTTGGAAGC+AGG 0.450938 4_1:+63217606 Msa0562940:five_prime_UTR
AGCTTTCCGTCTAAGAGAAA+TGG 0.454513 4_1:+63217872 Msa0562940:CDS
ATGTTCTATGCAGGCCAAGA+AGG 0.482623 4_1:+63218020 Msa0562940:intron
TTGGATCCATTTCTCTTAGA+CGG 0.482761 4_1:-63217878 None:intergenic
TGTTGGTTTGTCAACGGCGA+AGG 0.482817 4_1:-63218195 None:intergenic
TCGTAAGTCAATATAAGCTT+TGG 0.492221 4_1:+63217658 Msa0562940:five_prime_UTR
TGTTCTATGCAGGCCAAGAA+GGG 0.512387 4_1:+63218021 Msa0562940:intron
TTTGATCGCTTGCAAACAGA+AGG 0.523857 4_1:-63218403 None:intergenic
TTTCTTTCTTTCAGAAAAGG+AGG 0.524487 4_1:+63218362 Msa0562940:intron
ACCAAATGCAGTGCCAAACT+CGG 0.524803 4_1:+63218047 Msa0562940:CDS
GAAGCAGGCACTAGAGAACT+TGG 0.529673 4_1:+63217621 Msa0562940:five_prime_UTR
CACTATCTTCGCAATGTGGT+TGG 0.538774 4_1:+63217735 Msa0562940:five_prime_UTR
TTGTCTTGTTGGTTTGTCAA+CGG 0.539426 4_1:-63218201 None:intergenic
TTCTTTCTTTCAGAAAAGGA+GGG 0.543872 4_1:+63218363 Msa0562940:intron
ACCAATCTAGAGAGAATGAA+AGG 0.560310 4_1:+63218073 Msa0562940:CDS
ACTATGAATTCTTCTGCAAG+AGG 0.591142 4_1:+63217685 Msa0562940:five_prime_UTR
TTGCAGAAGAATTCATAGTA+CGG 0.598762 4_1:-63217681 None:intergenic
AATCAAGAAGGGAGAAGGGG+TGG 0.615870 4_1:+63217767 Msa0562940:five_prime_UTR
AAGTCAAAAGGAGATAAGCA+AGG 0.623892 4_1:-63217834 None:intergenic
TGTGTCTCTGAAATCGACAA+TGG 0.641607 4_1:-63217714 None:intergenic
GCAGGCACTAGAGAACTTGG+TGG 0.644607 4_1:+63217624 Msa0562940:five_prime_UTR
GTTCTATGCAGGCCAAGAAG+GGG 0.647685 4_1:+63218022 Msa0562940:intron
GTTGACAAACCAACAAGACA+AGG 0.663074 4_1:+63218203 Msa0562940:CDS
GACACACTATCTTCGCAATG+TGG 0.676741 4_1:+63217731 Msa0562940:five_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGTATAGAGAACTTTTAATA+AGG + chr4_1:63217588-63217607 Msa0562940:five_prime_UTR 20.0%
!!! CTTTTAATAAGGTTATTTCT+TGG + chr4_1:63217599-63217618 Msa0562940:five_prime_UTR 20.0%
!! TTAAAAATCTTACACAAGAA+AGG - chr4_1:63217908-63217927 None:intergenic 20.0%
!!! ATTTTTCTTTCTTTCAGAAA+AGG + chr4_1:63218359-63218378 Msa0562940:intron 20.0%
!!! AGTTCTTTTTTGTTTTGTTT+TGG + chr4_1:63218456-63218475 Msa0562940:three_prime_UTR 20.0%
!!! CTTTAAAAATGAACAAAGAA+CGG + chr4_1:63218543-63218562 Msa0562940:three_prime_UTR 20.0%
!!! TGTATAGAGAACTTTTAATA+AGG + chr4_1:63217588-63217607 Msa0562940:five_prime_UTR 20.0%
!!! CTTTTAATAAGGTTATTTCT+TGG + chr4_1:63217599-63217618 Msa0562940:five_prime_UTR 20.0%
!! TTAAAAATCTTACACAAGAA+AGG - chr4_1:63217908-63217927 None:intergenic 20.0%
!!! ATTTTTCTTTCTTTCAGAAA+AGG + chr4_1:63218359-63218378 Msa0562940:intron 20.0%
!!! AGTTCTTTTTTGTTTTGTTT+TGG + chr4_1:63218456-63218475 Msa0562940:three_prime_UTR 20.0%
!!! CTTTAAAAATGAACAAAGAA+CGG + chr4_1:63218543-63218562 Msa0562940:three_prime_UTR 20.0%
!!! AGGTTTTTTCTCATTCATTT+TGG - chr4_1:63217817-63217836 None:intergenic 25.0%
! CTTAATACATTCAAGTCAAA+AGG - chr4_1:63217849-63217868 None:intergenic 25.0%
! AAGCTACTACGAATTAAAAA+TGG + chr4_1:63218129-63218148 Msa0562940:CDS 25.0%
! ATAGACATTAAAAAGTCATG+TGG + chr4_1:63218292-63218311 Msa0562940:intron 25.0%
! AAAAAATAGAGTTTAGTGTC+GGG - chr4_1:63218502-63218521 None:intergenic 25.0%
! CAAAAAATAGAGTTTAGTGT+CGG - chr4_1:63218503-63218522 None:intergenic 25.0%
!!! AGGTTTTTTCTCATTCATTT+TGG - chr4_1:63217817-63217836 None:intergenic 25.0%
! CTTAATACATTCAAGTCAAA+AGG - chr4_1:63217849-63217868 None:intergenic 25.0%
! AAGCTACTACGAATTAAAAA+TGG + chr4_1:63218129-63218148 Msa0562940:CDS 25.0%
! ATAGACATTAAAAAGTCATG+TGG + chr4_1:63218292-63218311 Msa0562940:intron 25.0%
! AAAAAATAGAGTTTAGTGTC+GGG - chr4_1:63218502-63218521 None:intergenic 25.0%
! CAAAAAATAGAGTTTAGTGT+CGG - chr4_1:63218503-63218522 None:intergenic 25.0%
TCGTAAGTCAATATAAGCTT+TGG + chr4_1:63217658-63217677 Msa0562940:five_prime_UTR 30.0%
TTGCAGAAGAATTCATAGTA+CGG - chr4_1:63217684-63217703 None:intergenic 30.0%
! GATTTTTAAACTTCACTGTC+TGG + chr4_1:63217919-63217938 Msa0562940:intron 30.0%
AGAATGAAAGGAAGAACAAA+AGG + chr4_1:63218085-63218104 Msa0562940:CDS 30.0%
TTTCTTTCTTTCAGAAAAGG+AGG + chr4_1:63218362-63218381 Msa0562940:intron 30.0%
TTCTTTCTTTCAGAAAAGGA+GGG + chr4_1:63218363-63218382 Msa0562940:intron 30.0%
TCGTAAGTCAATATAAGCTT+TGG + chr4_1:63217658-63217677 Msa0562940:five_prime_UTR 30.0%
TTGCAGAAGAATTCATAGTA+CGG - chr4_1:63217684-63217703 None:intergenic 30.0%
! GATTTTTAAACTTCACTGTC+TGG + chr4_1:63217919-63217938 Msa0562940:intron 30.0%
AGAATGAAAGGAAGAACAAA+AGG + chr4_1:63218085-63218104 Msa0562940:CDS 30.0%
TTTCTTTCTTTCAGAAAAGG+AGG + chr4_1:63218362-63218381 Msa0562940:intron 30.0%
TTCTTTCTTTCAGAAAAGGA+GGG + chr4_1:63218363-63218382 Msa0562940:intron 30.0%
!! TAAGGTTATTTCTTGGAAGC+AGG + chr4_1:63217606-63217625 Msa0562940:five_prime_UTR 35.0%
ACTATGAATTCTTCTGCAAG+AGG + chr4_1:63217685-63217704 Msa0562940:five_prime_UTR 35.0%
TGGTGACACAAAAATCAAGA+AGG + chr4_1:63217755-63217774 Msa0562940:five_prime_UTR 35.0%
GGTGACACAAAAATCAAGAA+GGG + chr4_1:63217756-63217775 Msa0562940:five_prime_UTR 35.0%
ACAAAAATCAAGAAGGGAGA+AGG + chr4_1:63217762-63217781 Msa0562940:five_prime_UTR 35.0%
CAAAAATCAAGAAGGGAGAA+GGG + chr4_1:63217763-63217782 Msa0562940:five_prime_UTR 35.0%
AAAAATCAAGAAGGGAGAAG+GGG + chr4_1:63217764-63217783 Msa0562940:five_prime_UTR 35.0%
AAGTCAAAAGGAGATAAGCA+AGG - chr4_1:63217837-63217856 None:intergenic 35.0%
TTGGATCCATTTCTCTTAGA+CGG - chr4_1:63217881-63217900 None:intergenic 35.0%
CTTACACAAGAAAGGTGATT+TGG - chr4_1:63217900-63217919 None:intergenic 35.0%
! ATTTTGTCCTCATGTTTTGC+TGG + chr4_1:63217978-63217997 Msa0562940:intron 35.0%
CATTATACCAGCAAAACATG+AGG - chr4_1:63217988-63218007 None:intergenic 35.0%
ACCAATCTAGAGAGAATGAA+AGG + chr4_1:63218073-63218092 Msa0562940:CDS 35.0%
TCCTTTCATTCTCTCTAGAT+TGG - chr4_1:63218077-63218096 None:intergenic 35.0%
!! TTGTCTTGTTGGTTTGTCAA+CGG - chr4_1:63218204-63218223 None:intergenic 35.0%
!! TAAGGTTATTTCTTGGAAGC+AGG + chr4_1:63217606-63217625 Msa0562940:five_prime_UTR 35.0%
ACTATGAATTCTTCTGCAAG+AGG + chr4_1:63217685-63217704 Msa0562940:five_prime_UTR 35.0%
TGGTGACACAAAAATCAAGA+AGG + chr4_1:63217755-63217774 Msa0562940:five_prime_UTR 35.0%
GGTGACACAAAAATCAAGAA+GGG + chr4_1:63217756-63217775 Msa0562940:five_prime_UTR 35.0%
ACAAAAATCAAGAAGGGAGA+AGG + chr4_1:63217762-63217781 Msa0562940:five_prime_UTR 35.0%
CAAAAATCAAGAAGGGAGAA+GGG + chr4_1:63217763-63217782 Msa0562940:five_prime_UTR 35.0%
AAAAATCAAGAAGGGAGAAG+GGG + chr4_1:63217764-63217783 Msa0562940:five_prime_UTR 35.0%
AAGTCAAAAGGAGATAAGCA+AGG - chr4_1:63217837-63217856 None:intergenic 35.0%
TTGGATCCATTTCTCTTAGA+CGG - chr4_1:63217881-63217900 None:intergenic 35.0%
CTTACACAAGAAAGGTGATT+TGG - chr4_1:63217900-63217919 None:intergenic 35.0%
! ATTTTGTCCTCATGTTTTGC+TGG + chr4_1:63217978-63217997 Msa0562940:intron 35.0%
CATTATACCAGCAAAACATG+AGG - chr4_1:63217988-63218007 None:intergenic 35.0%
ACCAATCTAGAGAGAATGAA+AGG + chr4_1:63218073-63218092 Msa0562940:CDS 35.0%
TCCTTTCATTCTCTCTAGAT+TGG - chr4_1:63218077-63218096 None:intergenic 35.0%
!! TTGTCTTGTTGGTTTGTCAA+CGG - chr4_1:63218204-63218223 None:intergenic 35.0%
!! TGTGTCTCTGAAATCGACAA+TGG - chr4_1:63217717-63217736 None:intergenic 40.0%
AGCTTTCCGTCTAAGAGAAA+TGG + chr4_1:63217872-63217891 Msa0562940:CDS 40.0%
TTGGCCTGCATAGAACATAT+CGG - chr4_1:63218018-63218037 None:intergenic 40.0%
GTTGACAAACCAACAAGACA+AGG + chr4_1:63218203-63218222 Msa0562940:CDS 40.0%
AAGAGCAAACCTTGTCTTGT+TGG - chr4_1:63218215-63218234 None:intergenic 40.0%
CAGTGCATAACAATGGATGA+AGG - chr4_1:63218243-63218262 None:intergenic 40.0%
TGACACACAGTGCATAACAA+TGG - chr4_1:63218250-63218269 None:intergenic 40.0%
TCTCTCCTCAATGTAAGACA+CGG - chr4_1:63218273-63218292 None:intergenic 40.0%
TTTGATCGCTTGCAAACAGA+AGG - chr4_1:63218406-63218425 None:intergenic 40.0%
!! TGTGTCTCTGAAATCGACAA+TGG - chr4_1:63217717-63217736 None:intergenic 40.0%
AGCTTTCCGTCTAAGAGAAA+TGG + chr4_1:63217872-63217891 Msa0562940:CDS 40.0%
TTGGCCTGCATAGAACATAT+CGG - chr4_1:63218018-63218037 None:intergenic 40.0%
GTTGACAAACCAACAAGACA+AGG + chr4_1:63218203-63218222 Msa0562940:CDS 40.0%
AAGAGCAAACCTTGTCTTGT+TGG - chr4_1:63218215-63218234 None:intergenic 40.0%
CAGTGCATAACAATGGATGA+AGG - chr4_1:63218243-63218262 None:intergenic 40.0%
TGACACACAGTGCATAACAA+TGG - chr4_1:63218250-63218269 None:intergenic 40.0%
TCTCTCCTCAATGTAAGACA+CGG - chr4_1:63218273-63218292 None:intergenic 40.0%
TTTGATCGCTTGCAAACAGA+AGG - chr4_1:63218406-63218425 None:intergenic 40.0%
GACACACTATCTTCGCAATG+TGG + chr4_1:63217731-63217750 Msa0562940:five_prime_UTR 45.0%
CACTATCTTCGCAATGTGGT+TGG + chr4_1:63217735-63217754 Msa0562940:five_prime_UTR 45.0%
CACACCGATATGTTCTATGC+AGG + chr4_1:63218011-63218030 Msa0562940:intron 45.0%
ATGTTCTATGCAGGCCAAGA+AGG + chr4_1:63218020-63218039 Msa0562940:intron 45.0%
TGTTCTATGCAGGCCAAGAA+GGG + chr4_1:63218021-63218040 Msa0562940:intron 45.0%
ACCAAATGCAGTGCCAAACT+CGG + chr4_1:63218047-63218066 Msa0562940:CDS 45.0%
!! CTAGATTGGTTTGCCGAGTT+TGG - chr4_1:63218063-63218082 None:intergenic 45.0%
TGTCACCGTGTCTTACATTG+AGG + chr4_1:63218265-63218284 Msa0562940:intron 45.0%
GACACACTATCTTCGCAATG+TGG + chr4_1:63217731-63217750 Msa0562940:five_prime_UTR 45.0%
CACTATCTTCGCAATGTGGT+TGG + chr4_1:63217735-63217754 Msa0562940:five_prime_UTR 45.0%
CACACCGATATGTTCTATGC+AGG + chr4_1:63218011-63218030 Msa0562940:intron 45.0%
ATGTTCTATGCAGGCCAAGA+AGG + chr4_1:63218020-63218039 Msa0562940:intron 45.0%
TGTTCTATGCAGGCCAAGAA+GGG + chr4_1:63218021-63218040 Msa0562940:intron 45.0%
ACCAAATGCAGTGCCAAACT+CGG + chr4_1:63218047-63218066 Msa0562940:CDS 45.0%
!! CTAGATTGGTTTGCCGAGTT+TGG - chr4_1:63218063-63218082 None:intergenic 45.0%
TGTCACCGTGTCTTACATTG+AGG + chr4_1:63218265-63218284 Msa0562940:intron 45.0%
GAAGCAGGCACTAGAGAACT+TGG + chr4_1:63217621-63217640 Msa0562940:five_prime_UTR 50.0%
AATCAAGAAGGGAGAAGGGG+TGG + chr4_1:63217767-63217786 Msa0562940:five_prime_UTR 50.0%
GTTCTATGCAGGCCAAGAAG+GGG + chr4_1:63218022-63218041 Msa0562940:intron 50.0%
! TGCATTTGGTAGCCCCTTCT+TGG - chr4_1:63218037-63218056 None:intergenic 50.0%
!! TGTTGGTTTGTCAACGGCGA+AGG - chr4_1:63218198-63218217 None:intergenic 50.0%
GAAGCAGGCACTAGAGAACT+TGG + chr4_1:63217621-63217640 Msa0562940:five_prime_UTR 50.0%
AATCAAGAAGGGAGAAGGGG+TGG + chr4_1:63217767-63217786 Msa0562940:five_prime_UTR 50.0%
GTTCTATGCAGGCCAAGAAG+GGG + chr4_1:63218022-63218041 Msa0562940:intron 50.0%
! TGCATTTGGTAGCCCCTTCT+TGG - chr4_1:63218037-63218056 None:intergenic 50.0%
!! TGTTGGTTTGTCAACGGCGA+AGG - chr4_1:63218198-63218217 None:intergenic 50.0%
GCAGGCACTAGAGAACTTGG+TGG + chr4_1:63217624-63217643 Msa0562940:five_prime_UTR 55.0%
GCCGAGTTTGGCACTGCATT+TGG - chr4_1:63218051-63218070 None:intergenic 55.0%
GCAGGCACTAGAGAACTTGG+TGG + chr4_1:63217624-63217643 Msa0562940:five_prime_UTR 55.0%
GCCGAGTTTGGCACTGCATT+TGG - chr4_1:63218051-63218070 None:intergenic 55.0%
GAAGGGAGAAGGGGTGGAAC+TGG + chr4_1:63217773-63217792 Msa0562940:five_prime_UTR 60.0%
GAAGGGAGAAGGGGTGGAAC+TGG + chr4_1:63217773-63217792 Msa0562940:five_prime_UTR 60.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 63217545 63218573 63217545 ID=Msa0562940;Name=Msa0562940
chr4_1 mRNA 63217545 63218573 63217545 ID=Msa0562940-mRNA-1;Parent=Msa0562940;Name=Msa0562940-mRNA-1;_AED=0.05;_eAED=0.05;_QI=274|1|1|1|1|1|3|135|116
chr4_1 exon 63217545 63217914 63217545 ID=Msa0562940-mRNA-1:exon:20014;Parent=Msa0562940-mRNA-1
chr4_1 exon 63218033 63218224 63218033 ID=Msa0562940-mRNA-1:exon:20015;Parent=Msa0562940-mRNA-1
chr4_1 exon 63218376 63218573 63218376 ID=Msa0562940-mRNA-1:exon:20016;Parent=Msa0562940-mRNA-1
chr4_1 five_prime_UTR 63217545 63217818 63217545 ID=Msa0562940-mRNA-1:five_prime_utr;Parent=Msa0562940-mRNA-1
chr4_1 CDS 63217819 63217914 63217819 ID=Msa0562940-mRNA-1:cds;Parent=Msa0562940-mRNA-1
chr4_1 CDS 63218033 63218224 63218033 ID=Msa0562940-mRNA-1:cds;Parent=Msa0562940-mRNA-1
chr4_1 CDS 63218376 63218438 63218376 ID=Msa0562940-mRNA-1:cds;Parent=Msa0562940-mRNA-1
chr4_1 three_prime_UTR 63218439 63218573 63218439 ID=Msa0562940-mRNA-1:three_prime_utr;Parent=Msa0562940-mRNA-1
Gene Sequence

>Msa0562940

ATGAATGAGAAAAAACCTTGCTTATCTCCTTTTGACTTGAATGTATTAAGTGAAGCTTTCCGTCTAAGAGAAATGGATCCAAATCACCTTTCTTGTGCCAAGAAGGGGCTACCAAATGCAGTGCCAAACTCGGCAAACCAATCTAGAGAGAATGAAAGGAAGAACAAAAGGCATGAAAAACACGAGAAGCACAAGCTACTACGAATTAAAAATGGAAGTTGTGTTGATAATAACACAATTAGACACAATAATTCTCAGCCTTCGCCGTTGACAAACCAACAAGACAAGAAAAGGAGGGCTGAAACAAGCAACAATCCTTCTGTTTGCAAGCGATCAAATACTCGACAATGA
Protein sequence

>Msa0562940

MNEKKPCLSPFDLNVLSEAFRLREMDPNHLSCAKKGLPNAVPNSANQSRENERKNKRHEKHEKHKLLRIKNGSCVDNNTIRHNNSQPSPLTNQQDKKRRAETSNNPSVCKRSNTRQ*