AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0148930

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0148930 MtrunA17_Chr3g0137181 100.000 51 0 0 37 87 1 51 6.66e-33 108
Msa0148930 MtrunA17_Chr1g0149761 100.000 51 0 0 37 87 1 51 6.66e-33 108
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0148930 AT4G31985.1 90.196 51 5 0 37 87 1 51 9.56e-30 100
Msa0148930 AT3G02190.1 88.235 51 6 0 37 87 1 51 2.51e-28 97.1
Msa0148930 AT2G25210.1 90.909 44 4 0 44 87 1 44 3.46e-24 86.3

Find 33 sgRNAs with CRISPR-Local

Find 100 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAGATCACTGTTGTTATTTA+AGG 0.147633 1_4:-9376726 Msa0148930:three_prime_UTR
TCCCACATTTGAGCTGATTT+TGG 0.157358 1_4:-9376543 Msa0148930:three_prime_UTR
CCTTCTTCTTCGGCTGCGTC+TGG 0.331724 1_4:+9377224 None:intergenic
AATAAGTTGTTTACCTAGAC+AGG 0.348405 1_4:+9376497 None:intergenic
AGAGGTCGAGTAAGCCATTA+GGG 0.372730 1_4:-9377279 Msa0148930:CDS
TCTTCTTCTTCCTTCTTCTT+CGG 0.378925 1_4:+9377214 None:intergenic
GTTCTCATACGGATCCAATA+AGG 0.402869 1_4:+9377006 None:intergenic
AAGAGGTCGAGTAAGCCATT+AGG 0.405044 1_4:-9377280 Msa0148930:CDS
AGAACAGACCCATCCCTTAT+TGG 0.418161 1_4:-9377020 Msa0148930:CDS
TCGAGTAAGCCATTAGGGTT+TGG 0.465477 1_4:-9377274 Msa0148930:CDS
TTCTCATACGGATCCAATAA+GGG 0.468482 1_4:+9377007 None:intergenic
AATTAACCTGATGGTGTTGT+CGG 0.494295 1_4:+9376984 None:intergenic
TTGTTATAATAGCCCTGTCT+AGG 0.497081 1_4:-9376510 Msa0148930:three_prime_UTR
TTAGGGTTTGGTATCGCCGT+TGG 0.497744 1_4:-9377262 Msa0148930:CDS
CACTGGCGTCGTACCAAGCT+CGG 0.498772 1_4:-9376853 Msa0148930:CDS
ACGGCGATACCAAACCCTAA+TGG 0.499172 1_4:+9377265 None:intergenic
TGAGAACCGACAACACCATC+AGG 0.505441 1_4:-9376990 Msa0148930:intron
GTTATTTAAGGATGTAATTG+TGG 0.507108 1_4:-9376714 Msa0148930:three_prime_UTR
CGTACCAAGCTCGGATTCTG+AGG 0.516160 1_4:-9376844 Msa0148930:exon
CCCCAAAATCAGCTCAAATG+TGG 0.522629 1_4:+9376541 None:intergenic
AAAACCTCAGAATCCGAGCT+TGG 0.535716 1_4:+9376840 None:intergenic
TGGTGTTGTCGGTTCTCATA+CGG 0.540409 1_4:+9376995 None:intergenic
ACAATGCTAAGCGTCGTCAC+TGG 0.548403 1_4:-9376870 Msa0148930:CDS
CCAGACGCAGCCGAAGAAGA+AGG 0.553197 1_4:-9377224 Msa0148930:CDS
CCCAAAATCAGCTCAAATGT+GGG 0.561607 1_4:+9376542 None:intergenic
AACAACAGTGATCTCAATCT+CGG 0.564640 1_4:+9376734 None:intergenic
AGAAGCTCGCGAAGAAGATG+AGG 0.578712 1_4:-9377044 Msa0148930:CDS
CATACGGATCCAATAAGGGA+TGG 0.584103 1_4:+9377011 None:intergenic
ATGACGAATGTCTTGTGTGA+AGG 0.588940 1_4:+9377072 None:intergenic
ATACGGATCCAATAAGGGAT+GGG 0.595390 1_4:+9377012 None:intergenic
CCACTAAATGAAACAAAATG+TGG 0.627125 1_4:+9376683 None:intergenic
ATAAGTTGTTTACCTAGACA+GGG 0.631721 1_4:+9376498 None:intergenic
GAGATGAAATGCTGAACCAA+CGG 0.639403 1_4:+9377246 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATGTTTTTTCATTTGATTTT+AGG - chr1_4:9376864-9376883 Msa0148930:CDS 15.0%
!!! ATGTTTTTTCATTTGATTTT+AGG - chr1_4:9376864-9376883 Msa0148930:CDS 15.0%
! ATAGATAGAAATTAACCTGA+TGG + chr1_4:9376786-9376805 None:intergenic 25.0%
! TAATCGTGTTAAATCATGTT+TGG - chr1_4:9376831-9376850 Msa0148930:exon 25.0%
!!! TTCTGAGGTTTTTTAGTTTA+TGG - chr1_4:9376929-9376948 Msa0148930:intron 25.0%
!!! TCTGAGGTTTTTTAGTTTAT+GGG - chr1_4:9376930-9376949 Msa0148930:intron 25.0%
! GTTATTTAAGGATGTAATTG+TGG - chr1_4:9377044-9377063 Msa0148930:CDS 25.0%
!!! CTCATGATTTTGATTTTGTT+AGG - chr1_4:9377123-9377142 Msa0148930:intron 25.0%
!! ATTTTGTTAGGTAGAATGAA+TGG - chr1_4:9377135-9377154 Msa0148930:intron 25.0%
! ATAGATAGAAATTAACCTGA+TGG + chr1_4:9376786-9376805 None:intergenic 25.0%
! TAATCGTGTTAAATCATGTT+TGG - chr1_4:9376831-9376850 Msa0148930:exon 25.0%
!!! TTCTGAGGTTTTTTAGTTTA+TGG - chr1_4:9376929-9376948 Msa0148930:intron 25.0%
!!! TCTGAGGTTTTTTAGTTTAT+GGG - chr1_4:9376930-9376949 Msa0148930:intron 25.0%
! GTTATTTAAGGATGTAATTG+TGG - chr1_4:9377044-9377063 Msa0148930:CDS 25.0%
!!! CTCATGATTTTGATTTTGTT+AGG - chr1_4:9377123-9377142 Msa0148930:intron 25.0%
!! ATTTTGTTAGGTAGAATGAA+TGG - chr1_4:9377135-9377154 Msa0148930:intron 25.0%
AGAATAGTGAAATTAGGAGT+GGG + chr1_4:9376622-9376641 None:intergenic 30.0%
GAATCGAGAATAGTGAAATT+AGG + chr1_4:9376628-9376647 None:intergenic 30.0%
!! GAGATCACTGTTGTTATTTA+AGG - chr1_4:9377032-9377051 Msa0148930:CDS 30.0%
CCACTAAATGAAACAAAATG+TGG + chr1_4:9377078-9377097 None:intergenic 30.0%
!! CCACATTTTGTTTCATTTAG+TGG - chr1_4:9377075-9377094 Msa0148930:CDS 30.0%
ATAAGTTGTTTACCTAGACA+GGG + chr1_4:9377263-9377282 None:intergenic 30.0%
AATAAGTTGTTTACCTAGAC+AGG + chr1_4:9377264-9377283 None:intergenic 30.0%
AGAATAGTGAAATTAGGAGT+GGG + chr1_4:9376622-9376641 None:intergenic 30.0%
GAATCGAGAATAGTGAAATT+AGG + chr1_4:9376628-9376647 None:intergenic 30.0%
!! GAGATCACTGTTGTTATTTA+AGG - chr1_4:9377032-9377051 Msa0148930:CDS 30.0%
CCACTAAATGAAACAAAATG+TGG + chr1_4:9377078-9377097 None:intergenic 30.0%
!! CCACATTTTGTTTCATTTAG+TGG - chr1_4:9377075-9377094 Msa0148930:CDS 30.0%
ATAAGTTGTTTACCTAGACA+GGG + chr1_4:9377263-9377282 None:intergenic 30.0%
AATAAGTTGTTTACCTAGAC+AGG + chr1_4:9377264-9377283 None:intergenic 30.0%
TCTTCTTCTTCCTTCTTCTT+CGG + chr1_4:9376547-9376566 None:intergenic 35.0%
AGAAGAAGAAGCTGCAAAAA+TGG - chr1_4:9376564-9376583 Msa0148930:three_prime_UTR 35.0%
TGAAATTAGGAGTGGGAATT+TGG + chr1_4:9376615-9376634 None:intergenic 35.0%
GAGAATAGTGAAATTAGGAG+TGG + chr1_4:9376623-9376642 None:intergenic 35.0%
TTCTCATACGGATCCAATAA+GGG + chr1_4:9376754-9376773 None:intergenic 35.0%
!! AATTAACCTGATGGTGTTGT+CGG + chr1_4:9376777-9376796 None:intergenic 35.0%
TTAACAGTACAACGTTGTTG+TGG + chr1_4:9376814-9376833 None:intergenic 35.0%
AACAACAGTGATCTCAATCT+CGG + chr1_4:9377027-9377046 None:intergenic 35.0%
TTGTTATAATAGCCCTGTCT+AGG - chr1_4:9377248-9377267 Msa0148930:CDS 35.0%
TCTTCTTCTTCCTTCTTCTT+CGG + chr1_4:9376547-9376566 None:intergenic 35.0%
AGAAGAAGAAGCTGCAAAAA+TGG - chr1_4:9376564-9376583 Msa0148930:three_prime_UTR 35.0%
TGAAATTAGGAGTGGGAATT+TGG + chr1_4:9376615-9376634 None:intergenic 35.0%
GAGAATAGTGAAATTAGGAG+TGG + chr1_4:9376623-9376642 None:intergenic 35.0%
TTCTCATACGGATCCAATAA+GGG + chr1_4:9376754-9376773 None:intergenic 35.0%
!! AATTAACCTGATGGTGTTGT+CGG + chr1_4:9376777-9376796 None:intergenic 35.0%
TTAACAGTACAACGTTGTTG+TGG + chr1_4:9376814-9376833 None:intergenic 35.0%
AACAACAGTGATCTCAATCT+CGG + chr1_4:9377027-9377046 None:intergenic 35.0%
TTGTTATAATAGCCCTGTCT+AGG - chr1_4:9377248-9377267 Msa0148930:CDS 35.0%
GAGATGAAATGCTGAACCAA+CGG + chr1_4:9376515-9376534 None:intergenic 40.0%
ATGACGAATGTCTTGTGTGA+AGG + chr1_4:9376689-9376708 None:intergenic 40.0%
ATACGGATCCAATAAGGGAT+GGG + chr1_4:9376749-9376768 None:intergenic 40.0%
GTTCTCATACGGATCCAATA+AGG + chr1_4:9376755-9376774 None:intergenic 40.0%
!!! GACAGTGACTTTTGCTGTTT+TGG - chr1_4:9376974-9376993 Msa0148930:intron 40.0%
!! TCCCACATTTGAGCTGATTT+TGG - chr1_4:9377215-9377234 Msa0148930:CDS 40.0%
CCCAAAATCAGCTCAAATGT+GGG + chr1_4:9377219-9377238 None:intergenic 40.0%
!! CCCACATTTGAGCTGATTTT+GGG - chr1_4:9377216-9377235 Msa0148930:CDS 40.0%
!! CCACATTTGAGCTGATTTTG+GGG - chr1_4:9377217-9377236 Msa0148930:CDS 40.0%
GAGATGAAATGCTGAACCAA+CGG + chr1_4:9376515-9376534 None:intergenic 40.0%
ATGACGAATGTCTTGTGTGA+AGG + chr1_4:9376689-9376708 None:intergenic 40.0%
ATACGGATCCAATAAGGGAT+GGG + chr1_4:9376749-9376768 None:intergenic 40.0%
GTTCTCATACGGATCCAATA+AGG + chr1_4:9376755-9376774 None:intergenic 40.0%
!!! GACAGTGACTTTTGCTGTTT+TGG - chr1_4:9376974-9376993 Msa0148930:intron 40.0%
!! TCCCACATTTGAGCTGATTT+TGG - chr1_4:9377215-9377234 Msa0148930:CDS 40.0%
CCCAAAATCAGCTCAAATGT+GGG + chr1_4:9377219-9377238 None:intergenic 40.0%
!! CCCACATTTGAGCTGATTTT+GGG - chr1_4:9377216-9377235 Msa0148930:CDS 40.0%
!! CCACATTTGAGCTGATTTTG+GGG - chr1_4:9377217-9377236 Msa0148930:CDS 40.0%
AAGAGGTCGAGTAAGCCATT+AGG - chr1_4:9376478-9376497 Msa0148930:three_prime_UTR 45.0%
AGAGGTCGAGTAAGCCATTA+GGG - chr1_4:9376479-9376498 Msa0148930:three_prime_UTR 45.0%
TCGAGTAAGCCATTAGGGTT+TGG - chr1_4:9376484-9376503 Msa0148930:three_prime_UTR 45.0%
AGAACAGACCCATCCCTTAT+TGG - chr1_4:9376738-9376757 Msa0148930:three_prime_UTR 45.0%
CATACGGATCCAATAAGGGA+TGG + chr1_4:9376750-9376769 None:intergenic 45.0%
!! TGGTGTTGTCGGTTCTCATA+CGG + chr1_4:9376766-9376785 None:intergenic 45.0%
AAAACCTCAGAATCCGAGCT+TGG + chr1_4:9376921-9376940 None:intergenic 45.0%
CCCCAAAATCAGCTCAAATG+TGG + chr1_4:9377220-9377239 None:intergenic 45.0%
AAGAGGTCGAGTAAGCCATT+AGG - chr1_4:9376478-9376497 Msa0148930:three_prime_UTR 45.0%
AGAGGTCGAGTAAGCCATTA+GGG - chr1_4:9376479-9376498 Msa0148930:three_prime_UTR 45.0%
TCGAGTAAGCCATTAGGGTT+TGG - chr1_4:9376484-9376503 Msa0148930:three_prime_UTR 45.0%
AGAACAGACCCATCCCTTAT+TGG - chr1_4:9376738-9376757 Msa0148930:three_prime_UTR 45.0%
CATACGGATCCAATAAGGGA+TGG + chr1_4:9376750-9376769 None:intergenic 45.0%
!! TGGTGTTGTCGGTTCTCATA+CGG + chr1_4:9376766-9376785 None:intergenic 45.0%
AAAACCTCAGAATCCGAGCT+TGG + chr1_4:9376921-9376940 None:intergenic 45.0%
CCCCAAAATCAGCTCAAATG+TGG + chr1_4:9377220-9377239 None:intergenic 45.0%
ACGGCGATACCAAACCCTAA+TGG + chr1_4:9376496-9376515 None:intergenic 50.0%
! TTAGGGTTTGGTATCGCCGT+TGG - chr1_4:9376496-9376515 Msa0148930:three_prime_UTR 50.0%
AGAAGCTCGCGAAGAAGATG+AGG - chr1_4:9376714-9376733 Msa0148930:three_prime_UTR 50.0%
TGAGAACCGACAACACCATC+AGG - chr1_4:9376768-9376787 Msa0148930:three_prime_UTR 50.0%
! ACAATGCTAAGCGTCGTCAC+TGG - chr1_4:9376888-9376907 Msa0148930:intron 50.0%
ACGGCGATACCAAACCCTAA+TGG + chr1_4:9376496-9376515 None:intergenic 50.0%
! TTAGGGTTTGGTATCGCCGT+TGG - chr1_4:9376496-9376515 Msa0148930:three_prime_UTR 50.0%
AGAAGCTCGCGAAGAAGATG+AGG - chr1_4:9376714-9376733 Msa0148930:three_prime_UTR 50.0%
TGAGAACCGACAACACCATC+AGG - chr1_4:9376768-9376787 Msa0148930:three_prime_UTR 50.0%
! ACAATGCTAAGCGTCGTCAC+TGG - chr1_4:9376888-9376907 Msa0148930:intron 50.0%
CGTACCAAGCTCGGATTCTG+AGG - chr1_4:9376914-9376933 Msa0148930:intron 55.0%
CGTACCAAGCTCGGATTCTG+AGG - chr1_4:9376914-9376933 Msa0148930:intron 55.0%
CCTTCTTCTTCGGCTGCGTC+TGG + chr1_4:9376537-9376556 None:intergenic 60.0%
CCAGACGCAGCCGAAGAAGA+AGG - chr1_4:9376534-9376553 Msa0148930:three_prime_UTR 60.0%
CACTGGCGTCGTACCAAGCT+CGG - chr1_4:9376905-9376924 Msa0148930:intron 60.0%
CCTTCTTCTTCGGCTGCGTC+TGG + chr1_4:9376537-9376556 None:intergenic 60.0%
CCAGACGCAGCCGAAGAAGA+AGG - chr1_4:9376534-9376553 Msa0148930:three_prime_UTR 60.0%
CACTGGCGTCGTACCAAGCT+CGG - chr1_4:9376905-9376924 Msa0148930:intron 60.0%
Chromosome Type Strat End Strand Name
chr1_4 gene 9376475 9377305 9376475 ID=Msa0148930;Name=Msa0148930
chr1_4 mRNA 9376475 9377305 9376475 ID=Msa0148930-mRNA-1;Parent=Msa0148930;Name=Msa0148930-mRNA-1;_AED=0.07;_eAED=0.07;_QI=0|1|1|1|0|0.33|3|371|87
chr1_4 exon 9376475 9376894 9376475 ID=Msa0148930-mRNA-1:exon:3920;Parent=Msa0148930-mRNA-1
chr1_4 exon 9376991 9377094 9376991 ID=Msa0148930-mRNA-1:exon:3919;Parent=Msa0148930-mRNA-1
chr1_4 exon 9377195 9377305 9377195 ID=Msa0148930-mRNA-1:exon:3918;Parent=Msa0148930-mRNA-1
chr1_4 CDS 9377195 9377305 9377195 ID=Msa0148930-mRNA-1:cds;Parent=Msa0148930-mRNA-1
chr1_4 CDS 9376991 9377094 9376991 ID=Msa0148930-mRNA-1:cds;Parent=Msa0148930-mRNA-1
chr1_4 CDS 9376846 9376894 9376846 ID=Msa0148930-mRNA-1:cds;Parent=Msa0148930-mRNA-1
chr1_4 three_prime_UTR 9376475 9376845 9376475 ID=Msa0148930-mRNA-1:three_prime_utr;Parent=Msa0148930-mRNA-1
Gene Sequence

>Msa0148930

AAAAAGAGGTCGAGTAAGCCATTAGGGTTTGGTATCGCCGTTGGTTCAGCATTTCATCTCCAGACGCAGCCGAAGAAGAAGGAAGAAGAAGAAGAAGAAGCTGCAAAAATGCCTTCACACAAGACATTCGTCATCAAGAAGAAGCTCGCGAAGAAGATGAGGCAGAACAGACCCATCCCTTATTGGATCCGTATGAGAACCGACAACACCATCAGGTACAATGCTAAGCGTCGTCACTGGCGTCGTACCAAGCTCGGATTCTGA
Protein sequence

>Msa0148930

KKRSSKPLGFGIAVGSAFHLQTQPKKKEEEEEEAAKMPSHKTFVIKKKLAKKMRQNRPIPYWIRMRTDNTIRYNAKRRHWRRTKLGF*