AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0712880


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0712880 MtrunA17_Chr5g0406131 95.455 154 6 1 1 154 1 153 4.10e-104 295
Msa0712880 MtrunA17_Chr8g0371181 54.658 161 60 7 1 154 1 155 4.62e-36 122
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 41 sgRNAs with CRISPR-Local

Find 43 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGTTCTGCTTTGGATTTCTA+AGG 0.172324 5_1:-4722821 Msa0712880:CDS
TTAGGAGAAGTGGGTTCTTT+TGG 0.237235 5_1:+4722940 None:intergenic
TGCTTTCTTCTAGCTTCCTT+AGG 0.309418 5_1:+4722985 None:intergenic
TCACCCATGCACGAGACTTT+AGG 0.317786 5_1:+4722922 None:intergenic
AAATTGTTACATTCACCTTT+CGG 0.403917 5_1:+4722666 None:intergenic
AAGGACAAGAAGTTACATAA+AGG 0.412042 5_1:-4722871 Msa0712880:CDS
GCTTTCTTCTAGCTTCCTTA+GGG 0.417399 5_1:+4722986 None:intergenic
AATGAAACCACATGTGTTGT+AGG 0.443488 5_1:+4723012 None:intergenic
AGGACAAGAAGTTACATAAA+GGG 0.488699 5_1:-4722870 Msa0712880:CDS
TCTAAGGGAAGTTATGAAGC+AGG 0.489058 5_1:-4722805 Msa0712880:CDS
TTCTCCTAAAGTCTCGTGCA+TGG 0.496688 5_1:-4722926 Msa0712880:CDS
ATCGACAAGGACTAAGAGTT+GGG 0.514111 5_1:+4723037 None:intergenic
AAGAAATTTACCAGTGGGAG+AGG 0.523630 5_1:-4722718 Msa0712880:CDS
GCACGAGACTTTAGGAGAAG+TGG 0.524552 5_1:+4722930 None:intergenic
TGTGGTTTCATTATTCCCTA+AGG 0.534785 5_1:-4723001 Msa0712880:CDS
CAACCACCAGTGTCTTTAGC+GGG 0.552346 5_1:-4723069 Msa0712880:CDS
AAGCTAGAAGAAAGCACAGA+AGG 0.555212 5_1:-4722978 Msa0712880:CDS
TCATAGAATCCAACGTTGGA+GGG 0.555841 5_1:+4722740 None:intergenic
AGCTAGAAGAAAGCACAGAA+GGG 0.558361 5_1:-4722977 Msa0712880:CDS
TTCATAGAATCCAACGTTGG+AGG 0.559594 5_1:+4722739 None:intergenic
GATCGACAAGGACTAAGAGT+TGG 0.560227 5_1:+4723036 None:intergenic
AGTGAATGTCCCTCCAACGT+TGG 0.563858 5_1:-4722749 Msa0712880:CDS
CACGAGACTTTAGGAGAAGT+GGG 0.567559 5_1:+4722931 None:intergenic
TCTCCTAAAGTCTCGTGCAT+GGG 0.572514 5_1:-4722925 Msa0712880:CDS
GTTCTGCTTTGGATTTCTAA+GGG 0.577860 5_1:-4722820 Msa0712880:CDS
CTAAGGGAAGTTATGAAGCA+GGG 0.583061 5_1:-4722804 Msa0712880:CDS
TGATATCCCGCTAAAGACAC+TGG 0.590824 5_1:+4723063 None:intergenic
ACAACCACCAGTGTCTTTAG+CGG 0.593632 5_1:-4723070 Msa0712880:CDS
GAGACAAGGTGGGAAAGAGA+AGG 0.596540 5_1:-4722782 Msa0712880:CDS
ACACAATGATCCTCTCCCAC+TGG 0.608376 5_1:+4722708 None:intergenic
AGTTATGAAGCAGGGAGACA+AGG 0.608744 5_1:-4722796 Msa0712880:CDS
CTATGAAGAAATTTACCAGT+GGG 0.611053 5_1:-4722723 Msa0712880:CDS
TTCTTCATAGAATCCAACGT+TGG 0.612106 5_1:+4722736 None:intergenic
TATGAAGCAGGGAGACAAGG+TGG 0.615974 5_1:-4722793 Msa0712880:CDS
TTGATGCAACACTATCCGAA+AGG 0.634236 5_1:-4722681 Msa0712880:CDS
GCTAGAAGAAAGCACAGAAG+GGG 0.641612 5_1:-4722976 Msa0712880:CDS
ATGAAGCAGGGAGACAAGGT+GGG 0.641635 5_1:-4722792 Msa0712880:CDS
TCGATCACCTACAACACATG+TGG 0.650680 5_1:-4723019 Msa0712880:CDS
TCTATGAAGAAATTTACCAG+TGG 0.673132 5_1:-4722724 Msa0712880:CDS
TATCCCGCTAAAGACACTGG+TGG 0.724982 5_1:+4723066 None:intergenic
TGTGTTGTAGGTGATCGACA+AGG 0.755971 5_1:+4723024 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
CAAGAAGAAGAAGAAAAAGA+AGG - chr5_1:4722908-4722927 Msa0712880:CDS 30.0%
AAGGACAAGAAGTTACATAA+AGG - chr5_1:4722927-4722946 Msa0712880:CDS 30.0%
AGGACAAGAAGTTACATAAA+GGG - chr5_1:4722928-4722947 Msa0712880:CDS 30.0%
TCTATGAAGAAATTTACCAG+TGG - chr5_1:4723074-4723093 Msa0712880:CDS 30.0%
CTATGAAGAAATTTACCAGT+GGG - chr5_1:4723075-4723094 Msa0712880:CDS 30.0%
AATGAAACCACATGTGTTGT+AGG + chr5_1:4722789-4722808 None:intergenic 35.0%
TGTGGTTTCATTATTCCCTA+AGG - chr5_1:4722797-4722816 Msa0712880:CDS 35.0%
! CAAAGCAGAACGTTTTTGTT+TGG + chr5_1:4722969-4722988 None:intergenic 35.0%
CAAACAAAAACGTTCTGCTT+TGG - chr5_1:4722967-4722986 Msa0712880:CDS 35.0%
! GTTCTGCTTTGGATTTCTAA+GGG - chr5_1:4722978-4722997 Msa0712880:CDS 35.0%
TTCTTCATAGAATCCAACGT+TGG + chr5_1:4723065-4723084 None:intergenic 35.0%
ATCGACAAGGACTAAGAGTT+GGG + chr5_1:4722764-4722783 None:intergenic 40.0%
!! GCTTTCTTCTAGCTTCCTTA+GGG + chr5_1:4722815-4722834 None:intergenic 40.0%
!! TGCTTTCTTCTAGCTTCCTT+AGG + chr5_1:4722816-4722835 None:intergenic 40.0%
! AAGCTAGAAGAAAGCACAGA+AGG - chr5_1:4722820-4722839 Msa0712880:CDS 40.0%
! AGCTAGAAGAAAGCACAGAA+GGG - chr5_1:4722821-4722840 Msa0712880:CDS 40.0%
!! TTAGGAGAAGTGGGTTCTTT+TGG + chr5_1:4722861-4722880 None:intergenic 40.0%
! CGTTCTGCTTTGGATTTCTA+AGG - chr5_1:4722977-4722996 Msa0712880:CDS 40.0%
TCTAAGGGAAGTTATGAAGC+AGG - chr5_1:4722993-4723012 Msa0712880:CDS 40.0%
CTAAGGGAAGTTATGAAGCA+GGG - chr5_1:4722994-4723013 Msa0712880:CDS 40.0%
TCATAGAATCCAACGTTGGA+GGG + chr5_1:4723061-4723080 None:intergenic 40.0%
TTCATAGAATCCAACGTTGG+AGG + chr5_1:4723062-4723081 None:intergenic 40.0%
AAGAAATTTACCAGTGGGAG+AGG - chr5_1:4723080-4723099 Msa0712880:CDS 40.0%
TTGATGCAACACTATCCGAA+AGG - chr5_1:4723117-4723136 Msa0712880:CDS 40.0%
ACAACCACCAGTGTCTTTAG+CGG - chr5_1:4722728-4722747 Msa0712880:CDS 45.0%
TGATATCCCGCTAAAGACAC+TGG + chr5_1:4722738-4722757 None:intergenic 45.0%
GATCGACAAGGACTAAGAGT+TGG + chr5_1:4722765-4722784 None:intergenic 45.0%
TGTGTTGTAGGTGATCGACA+AGG + chr5_1:4722777-4722796 None:intergenic 45.0%
TCGATCACCTACAACACATG+TGG - chr5_1:4722779-4722798 Msa0712880:CDS 45.0%
! GCTAGAAGAAAGCACAGAAG+GGG - chr5_1:4722822-4722841 Msa0712880:CDS 45.0%
! CACGAGACTTTAGGAGAAGT+GGG + chr5_1:4722870-4722889 None:intergenic 45.0%
TTCTCCTAAAGTCTCGTGCA+TGG - chr5_1:4722872-4722891 Msa0712880:CDS 45.0%
TCTCCTAAAGTCTCGTGCAT+GGG - chr5_1:4722873-4722892 Msa0712880:CDS 45.0%
AGTTATGAAGCAGGGAGACA+AGG - chr5_1:4723002-4723021 Msa0712880:CDS 45.0%
CAACCACCAGTGTCTTTAGC+GGG - chr5_1:4722729-4722748 Msa0712880:CDS 50.0%
TATCCCGCTAAAGACACTGG+TGG + chr5_1:4722735-4722754 None:intergenic 50.0%
! GCACGAGACTTTAGGAGAAG+TGG + chr5_1:4722871-4722890 None:intergenic 50.0%
TCACCCATGCACGAGACTTT+AGG + chr5_1:4722879-4722898 None:intergenic 50.0%
TATGAAGCAGGGAGACAAGG+TGG - chr5_1:4723005-4723024 Msa0712880:CDS 50.0%
ATGAAGCAGGGAGACAAGGT+GGG - chr5_1:4723006-4723025 Msa0712880:CDS 50.0%
GAGACAAGGTGGGAAAGAGA+AGG - chr5_1:4723016-4723035 Msa0712880:CDS 50.0%
AGTGAATGTCCCTCCAACGT+TGG - chr5_1:4723049-4723068 Msa0712880:CDS 50.0%
ACACAATGATCCTCTCCCAC+TGG + chr5_1:4723093-4723112 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr5_1 gene 4722678 4723142 4722678 ID=Msa0712880;Name=Msa0712880
chr5_1 mRNA 4722678 4723142 4722678 ID=Msa0712880-mRNA-1;Parent=Msa0712880;Name=Msa0712880-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|154
chr5_1 exon 4722678 4723142 4722678 ID=Msa0712880-mRNA-1:exon:1978;Parent=Msa0712880-mRNA-1
chr5_1 CDS 4722678 4723142 4722678 ID=Msa0712880-mRNA-1:cds;Parent=Msa0712880-mRNA-1
Gene Sequence

>Msa0712880

ATGGAGAAACTGTTTAAAATCAAAACAACGTTCTTGAAGTTTCTATCTAAACAACCACCAGTGTCTTTAGCGGGATATCAGAACCCAACTCTTAGTCCTTGTCGATCACCTACAACACATGTGGTTTCATTATTCCCTAAGGAAGCTAGAAGAAAGCACAGAAGGGGTATTAGTTTTAGTCCAAAAGAACCCACTTCTCCTAAAGTCTCGTGCATGGGTGAAATTAAGAGCAAGAAGAAGAAGAAAAAGAAGGACAAGAAGTTACATAAAGGGATTCAAGATGTTGTTCCAAACAAAAACGTTCTGCTTTGGATTTCTAAGGGAAGTTATGAAGCAGGGAGACAAGGTGGGAAAGAGAAGGAATCAGCTATAGTGAATGTCCCTCCAACGTTGGATTCTATGAAGAAATTTACCAGTGGGAGAGGATCATTGTGTGATTTTGATGCAACACTATCCGAAAGGTGA

Protein sequence

>Msa0712880

MEKLFKIKTTFLKFLSKQPPVSLAGYQNPTLSPCRSPTTHVVSLFPKEARRKHRRGISFSPKEPTSPKVSCMGEIKSKKKKKKKDKKLHKGIQDVVPNKNVLLWISKGSYEAGRQGGKEKESAIVNVPPTLDSMKKFTSGRGSLCDFDATLSER*