AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1068290


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1068290 MtrunA17_Chr7g0249821 95.062 81 3 1 1 80 1 81 1.58e-54 164
Msa1068290 MtrunA17_Chr7g0249831 68.293 82 24 2 1 80 1 82 5.34e-33 110
Msa1068290 MtrunA17_Chr5g0396151 67.073 82 25 2 1 80 1 82 1.00e-32 109
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1068290 AT4G10040.1 68.293 82 24 2 1 80 1 82 1.08e-32 109
Msa1068290 AT1G22840.2 65.116 86 28 2 1 84 1 86 1.42e-31 106
Msa1068290 AT1G22840.1 65.854 82 26 2 1 80 1 82 8.16e-31 105

Find 28 sgRNAs with CRISPR-Local

Find 32 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCACCGGCAGCACGGTTTC+TGG 0.212914 7_2:-63268940 None:intergenic
ATGTGTTGTTTGTACCTTCT+TGG 0.279033 7_2:-63269304 None:intergenic
CCCAATCTGAATGGTTTGTT+TGG 0.305862 7_2:+63269180 Msa1068290:CDS
TGTGTTGTTTGTACCTTCTT+GGG 0.313440 7_2:-63269303 None:intergenic
ACAAGAACATGTCTATGAAT+TGG 0.322531 7_2:+63269247 Msa1068290:CDS
GCAAAACAATATGAATATTC+AGG 0.322686 7_2:-63269222 None:intergenic
GGTTTGTTTGGAAGTCAATC+TGG 0.344506 7_2:+63269192 Msa1068290:CDS
GTGCTGCCGGTGAGAAGTTC+AGG 0.352217 7_2:+63268949 Msa1068290:CDS
TCACCGGCAGCACGGTTTCT+GGG 0.386514 7_2:-63268939 None:intergenic
CAAGAACATGTCTATGAATT+GGG 0.403729 7_2:+63269248 Msa1068290:CDS
TCCAAACAAACCATTCAGAT+TGG 0.443064 7_2:-63269181 None:intergenic
GTACCTTCTTGGGGTTAAGC+AGG 0.468483 7_2:-63269293 None:intergenic
ACCTTAGGACCCAATCTGAA+TGG 0.493293 7_2:+63269171 Msa1068290:intron
CCAAACAAACCATTCAGATT+GGG 0.496498 7_2:-63269180 None:intergenic
TTTGTGAACGGCTCCTATGT+TGG 0.508283 7_2:-63268994 None:intergenic
TATTAAACCTTGTTTGTGAA+CGG 0.508923 7_2:-63269006 None:intergenic
CTTCCCAGAAACCGTGCTGC+CGG 0.509379 7_2:+63268936 Msa1068290:CDS
GTTTGTTTGGAAGTCAATCT+GGG 0.526603 7_2:+63269193 Msa1068290:CDS
GCTCAATGCCACACCAACAT+AGG 0.557024 7_2:+63268981 Msa1068290:CDS
GAATTGGGAGGAAAAGATCA+TGG 0.562314 7_2:+63269263 Msa1068290:CDS
GCACGGTTTCTGGGAAGTGT+CGG 0.562820 7_2:-63268930 None:intergenic
GTGTTGTTTGTACCTTCTTG+GGG 0.564448 7_2:-63269302 None:intergenic
ATAGGAGCCGTTCACAAACA+AGG 0.604312 7_2:+63268999 Msa1068290:CDS
TGAACTTCTCACCGGCAGCA+CGG 0.620657 7_2:-63268947 None:intergenic
ATCACTCCTGAACTTCTCAC+CGG 0.651892 7_2:-63268955 None:intergenic
GAACATGTCTATGAATTGGG+AGG 0.658810 7_2:+63269251 Msa1068290:CDS
TTACCTGCTTAACCCCAAGA+AGG 0.666741 7_2:+63269290 Msa1068290:CDS
GAACGGCTCCTATGTTGGTG+TGG 0.672356 7_2:-63268989 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATTAAACCTTGTTTGTGAA+CGG - chr7_2:63269009-63269028 None:intergenic 25.0%
! GTAAATCTGAGAGTTTATTT+AGG - chr7_2:63269048-63269067 None:intergenic 25.0%
!!! TTTTATTTGTTGTCAACCTT+AGG + chr7_2:63269156-63269175 Msa1068290:intron 25.0%
! GCAAAACAATATGAATATTC+AGG - chr7_2:63269225-63269244 None:intergenic 25.0%
ATGATGACATATATTCAAGC+AGG - chr7_2:63269106-63269125 None:intergenic 30.0%
ACAAGAACATGTCTATGAAT+TGG + chr7_2:63269247-63269266 Msa1068290:CDS 30.0%
CAAGAACATGTCTATGAATT+GGG + chr7_2:63269248-63269267 Msa1068290:CDS 30.0%
CCAAACAAACCATTCAGATT+GGG - chr7_2:63269183-63269202 None:intergenic 35.0%
TCCAAACAAACCATTCAGAT+TGG - chr7_2:63269184-63269203 None:intergenic 35.0%
GTTTGTTTGGAAGTCAATCT+GGG + chr7_2:63269193-63269212 Msa1068290:CDS 35.0%
!! TGTGTTGTTTGTACCTTCTT+GGG - chr7_2:63269306-63269325 None:intergenic 35.0%
!! ATGTGTTGTTTGTACCTTCT+TGG - chr7_2:63269307-63269326 None:intergenic 35.0%
!! CCCAATCTGAATGGTTTGTT+TGG + chr7_2:63269180-63269199 Msa1068290:CDS 40.0%
! GGTTTGTTTGGAAGTCAATC+TGG + chr7_2:63269192-63269211 Msa1068290:CDS 40.0%
GAACATGTCTATGAATTGGG+AGG + chr7_2:63269251-63269270 Msa1068290:CDS 40.0%
GAATTGGGAGGAAAAGATCA+TGG + chr7_2:63269263-63269282 Msa1068290:CDS 40.0%
!! GTGTTGTTTGTACCTTCTTG+GGG - chr7_2:63269305-63269324 None:intergenic 40.0%
ATCACTCCTGAACTTCTCAC+CGG - chr7_2:63268958-63268977 None:intergenic 45.0%
TTTGTGAACGGCTCCTATGT+TGG - chr7_2:63268997-63269016 None:intergenic 45.0%
ATAGGAGCCGTTCACAAACA+AGG + chr7_2:63268999-63269018 Msa1068290:CDS 45.0%
ACCTTAGGACCCAATCTGAA+TGG + chr7_2:63269171-63269190 Msa1068290:intron 45.0%
ACCATTCAGATTGGGTCCTA+AGG - chr7_2:63269175-63269194 None:intergenic 45.0%
TTACCTGCTTAACCCCAAGA+AGG + chr7_2:63269290-63269309 Msa1068290:CDS 45.0%
GCTCAATGCCACACCAACAT+AGG + chr7_2:63268981-63269000 Msa1068290:CDS 50.0%
GTACCTTCTTGGGGTTAAGC+AGG - chr7_2:63269296-63269315 None:intergenic 50.0%
! GCACGGTTTCTGGGAAGTGT+CGG - chr7_2:63268933-63268952 None:intergenic 55.0%
TGAACTTCTCACCGGCAGCA+CGG - chr7_2:63268950-63268969 None:intergenic 55.0%
GAACGGCTCCTATGTTGGTG+TGG - chr7_2:63268992-63269011 None:intergenic 55.0%
CTTCCCAGAAACCGTGCTGC+CGG + chr7_2:63268936-63268955 Msa1068290:CDS 60.0%
TCACCGGCAGCACGGTTTCT+GGG - chr7_2:63268942-63268961 None:intergenic 60.0%
GTGCTGCCGGTGAGAAGTTC+AGG + chr7_2:63268949-63268968 Msa1068290:CDS 60.0%
CTCACCGGCAGCACGGTTTC+TGG - chr7_2:63268943-63268962 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 63268915 63269329 63268915 ID=Msa1068290;Name=Msa1068290
chr7_2 mRNA 63268915 63269329 63268915 ID=Msa1068290-mRNA-1;Parent=Msa1068290;Name=Msa1068290-mRNA-1;_AED=0.04;_eAED=0.04;_QI=0|0|0|1|1|1|2|0|85
chr7_2 exon 63268915 63269020 63268915 ID=Msa1068290-mRNA-1:exon:13020;Parent=Msa1068290-mRNA-1
chr7_2 exon 63269178 63269329 63269178 ID=Msa1068290-mRNA-1:exon:13021;Parent=Msa1068290-mRNA-1
chr7_2 CDS 63268915 63269020 63268915 ID=Msa1068290-mRNA-1:cds;Parent=Msa1068290-mRNA-1
chr7_2 CDS 63269178 63269329 63269178 ID=Msa1068290-mRNA-1:cds;Parent=Msa1068290-mRNA-1
Gene Sequence

>Msa1068290

ATGGAGTTGTTCGAACCGACACTTCCCAGAAACCGTGCTGCCGGTGAGAAGTTCAGGAGTGATTGCGCTCAATGCCACACCAACATAGGAGCCGTTCACAAACAAGGACCCAATCTGAATGGTTTGTTTGGAAGTCAATCTGGGACAACTCCTGAATATTCATATTGTTTTGCTAACAAGAACATGTCTATGAATTGGGAGGAAAAGATCATGGATGATTACCTGCTTAACCCCAAGAAGGTACAAACAACACATTGA

Protein sequence

>Msa1068290

MELFEPTLPRNRAAGEKFRSDCAQCHTNIGAVHKQGPNLNGLFGSQSGTTPEYSYCFANKNMSMNWEEKIMDDYLLNPKKVQTTH*