AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0784380


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 24 sgRNAs with CRISPR-Local

Find 116 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAAGTATCCAACGTCTAAAA+TGG 0.274637 5_2:-68985773 None:intergenic
CCGTGTAATGTTAATATCAT+TGG 0.275760 5_2:-68985556 None:intergenic
ATGGAAACATTCCAAATATT+AGG 0.313013 5_2:-68985754 None:intergenic
CAATGATGGCAACCTGATTT+CGG 0.357442 5_2:+68985391 Msa0784380:CDS
CGAAATCAGGTTGCCATCAT+TGG 0.368713 5_2:-68985390 None:intergenic
CAAATCGTTGTTTAATATAG+AGG 0.372797 5_2:+68985436 Msa0784380:CDS
GGAAATAGATGATGTTCTAT+AGG 0.418163 5_2:+68985522 Msa0784380:three_prime_UTR
AAAAGGGTGCTCGCAAAGGA+TGG 0.486096 5_2:+68985356 Msa0784380:CDS
GTTGTTTAATATAGAGGAAG+TGG 0.491868 5_2:+68985442 Msa0784380:CDS
GATTCTGTTGTTGCAACTTG+AGG 0.498939 5_2:-68985468 None:intergenic
GGGTGCCCTTCCACCAATGA+TGG 0.503752 5_2:+68985377 Msa0784380:CDS
AGAAAGAAAGAAAGAAGTGG+AGG 0.527740 5_2:+68985703 Msa0784380:three_prime_UTR
AATCAGGTTGCCATCATTGG+TGG 0.544019 5_2:-68985387 None:intergenic
AGAAGAAAGAAAGAAAGAAG+TGG 0.551674 5_2:+68985700 Msa0784380:three_prime_UTR
AGAGCTCTGTGTGACTGAAG+AGG 0.558782 5_2:+68985501 Msa0784380:three_prime_UTR
CCAATGATATTAACATTACA+CGG 0.560805 5_2:+68985556 Msa0784380:three_prime_UTR
ACATAAAAGGGTGCTCGCAA+AGG 0.565704 5_2:+68985352 Msa0784380:CDS
AGGTTGCCATCATTGGTGGA+AGG 0.587477 5_2:-68985383 None:intergenic
GGTTGCCATCATTGGTGGAA+GGG 0.589101 5_2:-68985382 None:intergenic
AAAGGGTGCTCGCAAAGGAT+GGG 0.600431 5_2:+68985357 Msa0784380:CDS
GTAATGTTAATATCATTGGA+TGG 0.606576 5_2:-68985552 None:intergenic
GATGGCAACCTGATTTCGGA+AGG 0.617035 5_2:+68985395 Msa0784380:CDS
ATAAGCACAAGATGCGCACA+AGG 0.633656 5_2:-68985845 None:intergenic
AATATGAAATGACACAAACA+AGG 0.695515 5_2:+68985599 Msa0784380:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGTAATTTCTTTGATTAAAT+AGG + chr5_2:68984884-68984903 Msa0784380:intron 15.0%
!! TGTAATTTCTTTGATTAAAT+AGG + chr5_2:68984884-68984903 Msa0784380:intron 15.0%
!!! CTACTGTTTATTTCATTTTT+TGG + chr5_2:68984981-68985000 Msa0784380:intron 20.0%
!!! AATATGTATACTACGTTTTT+TGG + chr5_2:68985004-68985023 Msa0784380:intron 20.0%
!!! ATATGTATACTACGTTTTTT+GGG + chr5_2:68985005-68985024 Msa0784380:intron 20.0%
!! AAAAGTTATTGAACAATCAT+GGG - chr5_2:68985161-68985180 None:intergenic 20.0%
!! AAAAAGTTATTGAACAATCA+TGG - chr5_2:68985162-68985181 None:intergenic 20.0%
!!! TTAATGCATAAGTTGATATA+TGG - chr5_2:68985300-68985319 None:intergenic 20.0%
!!! TTCTTCTTCATTTTTAATCA+AGG - chr5_2:68985675-68985694 None:intergenic 20.0%
!!! GAAAAAAAGGATTAGTATAT+AGG + chr5_2:68985725-68985744 Msa0784380:three_prime_UTR 20.0%
!!! TTGTATTTTGTGTTACATTT+TGG + chr5_2:68985797-68985816 Msa0784380:three_prime_UTR 20.0%
!!! CTACTGTTTATTTCATTTTT+TGG + chr5_2:68984981-68985000 Msa0784380:intron 20.0%
!!! AATATGTATACTACGTTTTT+TGG + chr5_2:68985004-68985023 Msa0784380:intron 20.0%
!!! ATATGTATACTACGTTTTTT+GGG + chr5_2:68985005-68985024 Msa0784380:intron 20.0%
!! AAAAGTTATTGAACAATCAT+GGG - chr5_2:68985161-68985180 None:intergenic 20.0%
!! AAAAAGTTATTGAACAATCA+TGG - chr5_2:68985162-68985181 None:intergenic 20.0%
!!! TTAATGCATAAGTTGATATA+TGG - chr5_2:68985300-68985319 None:intergenic 20.0%
!!! TTCTTCTTCATTTTTAATCA+AGG - chr5_2:68985675-68985694 None:intergenic 20.0%
!!! GAAAAAAAGGATTAGTATAT+AGG + chr5_2:68985725-68985744 Msa0784380:three_prime_UTR 20.0%
!!! TTGTATTTTGTGTTACATTT+TGG + chr5_2:68985797-68985816 Msa0784380:three_prime_UTR 20.0%
!!! TATGTATACTACGTTTTTTG+GGG + chr5_2:68985006-68985025 Msa0784380:intron 25.0%
! CTATGAAACGATGATAATAA+GGG - chr5_2:68985047-68985066 None:intergenic 25.0%
! ACTATGAAACGATGATAATA+AGG - chr5_2:68985048-68985067 None:intergenic 25.0%
! TTATTATCATCGTTTCATAG+TGG + chr5_2:68985047-68985066 Msa0784380:intron 25.0%
!!! TCATGATTTTGATTTGTTGT+TGG + chr5_2:68985083-68985102 Msa0784380:intron 25.0%
! CAAATCGTTGTTTAATATAG+AGG + chr5_2:68985436-68985455 Msa0784380:CDS 25.0%
! GTAATGTTAATATCATTGGA+TGG - chr5_2:68985555-68985574 None:intergenic 25.0%
! CCAATGATATTAACATTACA+CGG + chr5_2:68985556-68985575 Msa0784380:three_prime_UTR 25.0%
! AACATTACACGGAAAAAAAA+CGG + chr5_2:68985567-68985586 Msa0784380:three_prime_UTR 25.0%
! AATATGAAATGACACAAACA+AGG + chr5_2:68985599-68985618 Msa0784380:three_prime_UTR 25.0%
!! ATAGGCTTTTACCTAATATT+TGG + chr5_2:68985743-68985762 Msa0784380:three_prime_UTR 25.0%
! ATGGAAACATTCCAAATATT+AGG - chr5_2:68985757-68985776 None:intergenic 25.0%
!!! TATGTATACTACGTTTTTTG+GGG + chr5_2:68985006-68985025 Msa0784380:intron 25.0%
! CTATGAAACGATGATAATAA+GGG - chr5_2:68985047-68985066 None:intergenic 25.0%
! ACTATGAAACGATGATAATA+AGG - chr5_2:68985048-68985067 None:intergenic 25.0%
! TTATTATCATCGTTTCATAG+TGG + chr5_2:68985047-68985066 Msa0784380:intron 25.0%
!!! TCATGATTTTGATTTGTTGT+TGG + chr5_2:68985083-68985102 Msa0784380:intron 25.0%
! CAAATCGTTGTTTAATATAG+AGG + chr5_2:68985436-68985455 Msa0784380:CDS 25.0%
! GTAATGTTAATATCATTGGA+TGG - chr5_2:68985555-68985574 None:intergenic 25.0%
! CCAATGATATTAACATTACA+CGG + chr5_2:68985556-68985575 Msa0784380:three_prime_UTR 25.0%
! AACATTACACGGAAAAAAAA+CGG + chr5_2:68985567-68985586 Msa0784380:three_prime_UTR 25.0%
! AATATGAAATGACACAAACA+AGG + chr5_2:68985599-68985618 Msa0784380:three_prime_UTR 25.0%
!! ATAGGCTTTTACCTAATATT+TGG + chr5_2:68985743-68985762 Msa0784380:three_prime_UTR 25.0%
! ATGGAAACATTCCAAATATT+AGG - chr5_2:68985757-68985776 None:intergenic 25.0%
CTAACTAACTGAAAAAAGCA+AGG - chr5_2:68985261-68985280 None:intergenic 30.0%
!! TGTGATTCATTATTTTGCAG+TGG + chr5_2:68985323-68985342 Msa0784380:intron 30.0%
!! GTGATTCATTATTTTGCAGT+GGG + chr5_2:68985324-68985343 Msa0784380:intron 30.0%
CAGTGGGAAAAAACATAAAA+GGG + chr5_2:68985340-68985359 Msa0784380:intron 30.0%
GTTGTTTAATATAGAGGAAG+TGG + chr5_2:68985442-68985461 Msa0784380:CDS 30.0%
GGAAATAGATGATGTTCTAT+AGG + chr5_2:68985522-68985541 Msa0784380:three_prime_UTR 30.0%
CCGTGTAATGTTAATATCAT+TGG - chr5_2:68985559-68985578 None:intergenic 30.0%
AGAAGAAAGAAAGAAAGAAG+TGG + chr5_2:68985700-68985719 Msa0784380:three_prime_UTR 30.0%
! AATGTTTCCATTTTAGACGT+TGG + chr5_2:68985766-68985785 Msa0784380:three_prime_UTR 30.0%
TAAGTATCCAACGTCTAAAA+TGG - chr5_2:68985776-68985795 None:intergenic 30.0%
CTAACTAACTGAAAAAAGCA+AGG - chr5_2:68985261-68985280 None:intergenic 30.0%
!! TGTGATTCATTATTTTGCAG+TGG + chr5_2:68985323-68985342 Msa0784380:intron 30.0%
!! GTGATTCATTATTTTGCAGT+GGG + chr5_2:68985324-68985343 Msa0784380:intron 30.0%
CAGTGGGAAAAAACATAAAA+GGG + chr5_2:68985340-68985359 Msa0784380:intron 30.0%
GTTGTTTAATATAGAGGAAG+TGG + chr5_2:68985442-68985461 Msa0784380:CDS 30.0%
GGAAATAGATGATGTTCTAT+AGG + chr5_2:68985522-68985541 Msa0784380:three_prime_UTR 30.0%
CCGTGTAATGTTAATATCAT+TGG - chr5_2:68985559-68985578 None:intergenic 30.0%
AGAAGAAAGAAAGAAAGAAG+TGG + chr5_2:68985700-68985719 Msa0784380:three_prime_UTR 30.0%
! AATGTTTCCATTTTAGACGT+TGG + chr5_2:68985766-68985785 Msa0784380:three_prime_UTR 30.0%
TAAGTATCCAACGTCTAAAA+TGG - chr5_2:68985776-68985795 None:intergenic 30.0%
! TTGTTGGTCTATAGTACTGT+TGG + chr5_2:68985099-68985118 Msa0784380:intron 35.0%
! TACTTAAACTCGTTTTGCCT+AGG - chr5_2:68985220-68985239 None:intergenic 35.0%
GCAGTGGGAAAAAACATAAA+AGG + chr5_2:68985339-68985358 Msa0784380:intron 35.0%
TACACGGAAAAAAAACGGAA+CGG + chr5_2:68985572-68985591 Msa0784380:three_prime_UTR 35.0%
AGAAAGAAAGAAAGAAGTGG+AGG + chr5_2:68985703-68985722 Msa0784380:three_prime_UTR 35.0%
GAAAGAAGTGGAGGAAAAAA+AGG + chr5_2:68985712-68985731 Msa0784380:three_prime_UTR 35.0%
! TTGTTGGTCTATAGTACTGT+TGG + chr5_2:68985099-68985118 Msa0784380:intron 35.0%
! TACTTAAACTCGTTTTGCCT+AGG - chr5_2:68985220-68985239 None:intergenic 35.0%
GCAGTGGGAAAAAACATAAA+AGG + chr5_2:68985339-68985358 Msa0784380:intron 35.0%
TACACGGAAAAAAAACGGAA+CGG + chr5_2:68985572-68985591 Msa0784380:three_prime_UTR 35.0%
AGAAAGAAAGAAAGAAGTGG+AGG + chr5_2:68985703-68985722 Msa0784380:three_prime_UTR 35.0%
GAAAGAAGTGGAGGAAAAAA+AGG + chr5_2:68985712-68985731 Msa0784380:three_prime_UTR 35.0%
CATCGTTTCATAGTGGTGTT+TGG + chr5_2:68985054-68985073 Msa0784380:intron 40.0%
AATACAAGATGTGTTCCCAC+AGG - chr5_2:68985133-68985152 None:intergenic 40.0%
TTTACGAGTCGAGTTTACCT+AGG + chr5_2:68985200-68985219 Msa0784380:intron 40.0%
CAATGATGGCAACCTGATTT+CGG + chr5_2:68985391-68985410 Msa0784380:CDS 40.0%
! CTTCTTTTCCTTCCGAAATC+AGG - chr5_2:68985406-68985425 None:intergenic 40.0%
GATTCTGTTGTTGCAACTTG+AGG - chr5_2:68985471-68985490 None:intergenic 40.0%
ACACGGAAAAAAAACGGAAC+GGG + chr5_2:68985573-68985592 Msa0784380:three_prime_UTR 40.0%
CATCGTTTCATAGTGGTGTT+TGG + chr5_2:68985054-68985073 Msa0784380:intron 40.0%
AATACAAGATGTGTTCCCAC+AGG - chr5_2:68985133-68985152 None:intergenic 40.0%
TTTACGAGTCGAGTTTACCT+AGG + chr5_2:68985200-68985219 Msa0784380:intron 40.0%
CAATGATGGCAACCTGATTT+CGG + chr5_2:68985391-68985410 Msa0784380:CDS 40.0%
! CTTCTTTTCCTTCCGAAATC+AGG - chr5_2:68985406-68985425 None:intergenic 40.0%
GATTCTGTTGTTGCAACTTG+AGG - chr5_2:68985471-68985490 None:intergenic 40.0%
ACACGGAAAAAAAACGGAAC+GGG + chr5_2:68985573-68985592 Msa0784380:three_prime_UTR 40.0%
!! ACATAAAAGGGTGCTCGCAA+AGG + chr5_2:68985352-68985371 Msa0784380:CDS 45.0%
! AATCAGGTTGCCATCATTGG+TGG - chr5_2:68985390-68985409 None:intergenic 45.0%
! CGAAATCAGGTTGCCATCAT+TGG - chr5_2:68985393-68985412 None:intergenic 45.0%
ATAAGCACAAGATGCGCACA+AGG - chr5_2:68985848-68985867 None:intergenic 45.0%
!! ACATAAAAGGGTGCTCGCAA+AGG + chr5_2:68985352-68985371 Msa0784380:CDS 45.0%
! AATCAGGTTGCCATCATTGG+TGG - chr5_2:68985390-68985409 None:intergenic 45.0%
! CGAAATCAGGTTGCCATCAT+TGG - chr5_2:68985393-68985412 None:intergenic 45.0%
ATAAGCACAAGATGCGCACA+AGG - chr5_2:68985848-68985867 None:intergenic 45.0%
ACTGTTGGAGCTTGAACCTG+TGG + chr5_2:68985114-68985133 Msa0784380:intron 50.0%
CTGTTGGAGCTTGAACCTGT+GGG + chr5_2:68985115-68985134 Msa0784380:intron 50.0%
!! AAAAGGGTGCTCGCAAAGGA+TGG + chr5_2:68985356-68985375 Msa0784380:CDS 50.0%
!! AAAGGGTGCTCGCAAAGGAT+GGG + chr5_2:68985357-68985376 Msa0784380:CDS 50.0%
GGTTGCCATCATTGGTGGAA+GGG - chr5_2:68985385-68985404 None:intergenic 50.0%
AGGTTGCCATCATTGGTGGA+AGG - chr5_2:68985386-68985405 None:intergenic 50.0%
GATGGCAACCTGATTTCGGA+AGG + chr5_2:68985395-68985414 Msa0784380:CDS 50.0%
AGAGCTCTGTGTGACTGAAG+AGG + chr5_2:68985501-68985520 Msa0784380:three_prime_UTR 50.0%
ACTGTTGGAGCTTGAACCTG+TGG + chr5_2:68985114-68985133 Msa0784380:intron 50.0%
CTGTTGGAGCTTGAACCTGT+GGG + chr5_2:68985115-68985134 Msa0784380:intron 50.0%
!! AAAAGGGTGCTCGCAAAGGA+TGG + chr5_2:68985356-68985375 Msa0784380:CDS 50.0%
!! AAAGGGTGCTCGCAAAGGAT+GGG + chr5_2:68985357-68985376 Msa0784380:CDS 50.0%
GGTTGCCATCATTGGTGGAA+GGG - chr5_2:68985385-68985404 None:intergenic 50.0%
AGGTTGCCATCATTGGTGGA+AGG - chr5_2:68985386-68985405 None:intergenic 50.0%
GATGGCAACCTGATTTCGGA+AGG + chr5_2:68985395-68985414 Msa0784380:CDS 50.0%
AGAGCTCTGTGTGACTGAAG+AGG + chr5_2:68985501-68985520 Msa0784380:three_prime_UTR 50.0%
GGGTGCCCTTCCACCAATGA+TGG + chr5_2:68985377-68985396 Msa0784380:CDS 60.0%
GGGTGCCCTTCCACCAATGA+TGG + chr5_2:68985377-68985396 Msa0784380:CDS 60.0%
Chromosome Type Strat End Strand Name
chr5_2 gene 68984845 68985905 68984845 ID=Msa0784380;Name=Msa0784380
chr5_2 mRNA 68984845 68985905 68984845 ID=Msa0784380-mRNA-1;Parent=Msa0784380;Name=Msa0784380-mRNA-1;_AED=0.44;_eAED=0.47;_QI=0|0|0.5|1|0|0.5|2|412|59
chr5_2 exon 68984845 68984873 68984845 ID=Msa0784380-mRNA-1:exon:20696;Parent=Msa0784380-mRNA-1
chr5_2 exon 68985343 68985905 68985343 ID=Msa0784380-mRNA-1:exon:20697;Parent=Msa0784380-mRNA-1
chr5_2 CDS 68984845 68984873 68984845 ID=Msa0784380-mRNA-1:cds;Parent=Msa0784380-mRNA-1
chr5_2 CDS 68985343 68985493 68985343 ID=Msa0784380-mRNA-1:cds;Parent=Msa0784380-mRNA-1
chr5_2 three_prime_UTR 68985494 68985905 68985494 ID=Msa0784380-mRNA-1:three_prime_utr;Parent=Msa0784380-mRNA-1
Gene Sequence

>Msa0784380

ATGAGAGACACGTTTGCATCATCAATCATTGGGAAAAAACATAAAAGGGTGCTCGCAAAGGATGGGTGCCCTTCCACCAATGATGGCAACCTGATTTCGGAAGGAAAAGAAGATTACATTTACAAATCGTTGTTTAATATAGAGGAAGTGGTAACCTCAAGTTGCAACAACAGAATCTAA

Protein sequence

>Msa0784380

MRDTFASSIIGKKHKRVLAKDGCPSTNDGNLISEGKEDYIYKSLFNIEEVVTSSCNNRI*