AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0101910

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0101910 MtrunA17_Chr1g0153841 88.462 104 12 0 1 104 1 104 7.87e-67 196
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 26 sgRNAs with CRISPR-Local

Find 31 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGTCGCCAACATGTGGATTC+TGG 0.218060 1_3:+8582060 None:intergenic
TGGTGTCCATGGGGATTGTT+GGG 0.291649 1_3:+8581967 None:intergenic
TTGGTGTCCATGGGGATTGT+TGG 0.338734 1_3:+8581966 None:intergenic
TGGAGGCACGTTGGTGTCCA+TGG 0.365721 1_3:+8581956 None:intergenic
TGGGGATTGTTGGGGTTGAA+TGG 0.408417 1_3:+8581976 None:intergenic
GTCGCCAACATGTGGATTCT+GGG 0.412404 1_3:+8582061 None:intergenic
CACCTAATTAATTAACGCCT+TGG 0.435077 1_3:+8581936 None:intergenic
CATATGAAAACATAGTCATT+TGG 0.452470 1_3:-8582127 Msa0101910:CDS
TATGTTTCTCAACCCTTGCT+AGG 0.462334 1_3:-8582190 Msa0101910:CDS
TGGGGTTGAATGGCCAGCAC+CGG 0.464105 1_3:+8581986 None:intergenic
GGAGGCACGTTGGTGTCCAT+GGG 0.465448 1_3:+8581957 None:intergenic
CTAATTAATTAACGCCTTGG+AGG 0.484883 1_3:+8581939 None:intergenic
CCAGGTCATAGTCCCGGTGC+TGG 0.508743 1_3:-8581999 Msa0101910:CDS
GGGGTTGAATGGCCAGCACC+GGG 0.545577 1_3:+8581987 None:intergenic
TGGACACCAACGTGCCTCCA+AGG 0.558768 1_3:-8581953 Msa0101910:CDS
GGACTATGACCTGGATCCGT+TGG 0.561199 1_3:+8582008 None:intergenic
TCAGCTTCGTCGCCAACATG+TGG 0.570493 1_3:+8582053 None:intergenic
ATGAAAACATAGTCATTTGG+CGG 0.581045 1_3:-8582124 Msa0101910:CDS
CCAGCACCGGGACTATGACC+TGG 0.585779 1_3:+8581999 None:intergenic
GGTGTCCATGGGGATTGTTG+GGG 0.593694 1_3:+8581968 None:intergenic
ACGGATCCAGGTCATAGTCC+CGG 0.595399 1_3:-8582005 Msa0101910:CDS
GATTCCCAGAATCCACATGT+TGG 0.624961 1_3:-8582065 Msa0101910:CDS
TTCAACCCCAACAATCCCCA+TGG 0.630589 1_3:-8581973 Msa0101910:CDS
GAGGCACGTTGGTGTCCATG+GGG 0.682384 1_3:+8581958 None:intergenic
TTAACGCCTTGGAGGCACGT+TGG 0.691422 1_3:+8581947 None:intergenic
GAAAAGTAGAATTGAACACA+AGG 0.697977 1_3:+8582234 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTGTTCTCTCTTTTTACTA+GGG + chr1_3:8582032-8582051 None:intergenic 25.0%
!! ATTTGTTCTCTCTTTTTACT+AGG + chr1_3:8582033-8582052 None:intergenic 25.0%
! CATATGAAAACATAGTCATT+TGG - chr1_3:8582068-8582087 Msa0101910:CDS 25.0%
GAAAAGTAGAATTGAACACA+AGG + chr1_3:8581964-8581983 None:intergenic 30.0%
! TTGTTCTCTCTTTTTACTAG+GGG + chr1_3:8582031-8582050 None:intergenic 30.0%
ATGAAAACATAGTCATTTGG+CGG - chr1_3:8582071-8582090 Msa0101910:CDS 30.0%
TATGTTTCTCAACCCTTGCT+AGG - chr1_3:8582005-8582024 Msa0101910:CDS 40.0%
! TTTTACTAGGGGCCTAGCAA+GGG + chr1_3:8582020-8582039 None:intergenic 45.0%
! TTTTTACTAGGGGCCTAGCA+AGG + chr1_3:8582021-8582040 None:intergenic 45.0%
GATTCCCAGAATCCACATGT+TGG - chr1_3:8582130-8582149 Msa0101910:CDS 45.0%
! GATCGACGATTTTCGACCAA+CGG - chr1_3:8582171-8582190 Msa0101910:CDS 45.0%
GTCGCCAACATGTGGATTCT+GGG + chr1_3:8582137-8582156 None:intergenic 50.0%
! GATTTTCGACCAACGGATCC+AGG - chr1_3:8582178-8582197 Msa0101910:CDS 50.0%
TGGGGATTGTTGGGGTTGAA+TGG + chr1_3:8582222-8582241 None:intergenic 50.0%
TTCAACCCCAACAATCCCCA+TGG - chr1_3:8582222-8582241 Msa0101910:CDS 50.0%
TGGTGTCCATGGGGATTGTT+GGG + chr1_3:8582231-8582250 None:intergenic 50.0%
! TTGGTGTCCATGGGGATTGT+TGG + chr1_3:8582232-8582251 None:intergenic 50.0%
CGTCGCCAACATGTGGATTC+TGG + chr1_3:8582138-8582157 None:intergenic 55.0%
TCAGCTTCGTCGCCAACATG+TGG + chr1_3:8582145-8582164 None:intergenic 55.0%
GGACTATGACCTGGATCCGT+TGG + chr1_3:8582190-8582209 None:intergenic 55.0%
ACGGATCCAGGTCATAGTCC+CGG - chr1_3:8582190-8582209 Msa0101910:CDS 55.0%
GGTGTCCATGGGGATTGTTG+GGG + chr1_3:8582230-8582249 None:intergenic 55.0%
! TTAACGCCTTGGAGGCACGT+TGG + chr1_3:8582251-8582270 None:intergenic 55.0%
TGGGGTTGAATGGCCAGCAC+CGG + chr1_3:8582212-8582231 None:intergenic 60.0%
! GAGGCACGTTGGTGTCCATG+GGG + chr1_3:8582240-8582259 None:intergenic 60.0%
! GGAGGCACGTTGGTGTCCAT+GGG + chr1_3:8582241-8582260 None:intergenic 60.0%
! TGGAGGCACGTTGGTGTCCA+TGG + chr1_3:8582242-8582261 None:intergenic 60.0%
TGGACACCAACGTGCCTCCA+AGG - chr1_3:8582242-8582261 Msa0101910:CDS 60.0%
! CCAGCACCGGGACTATGACC+TGG + chr1_3:8582199-8582218 None:intergenic 65.0%
CCAGGTCATAGTCCCGGTGC+TGG - chr1_3:8582196-8582215 Msa0101910:CDS 65.0%
GGGGTTGAATGGCCAGCACC+GGG + chr1_3:8582211-8582230 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 8581947 8582270 8581947 ID=Msa0101910;Name=Msa0101910
chr1_3 mRNA 8581947 8582270 8581947 ID=Msa0101910-mRNA-1;Parent=Msa0101910;Name=Msa0101910-mRNA-1;_AED=0.02;_eAED=0.02;_QI=0|-1|0|1|-1|1|1|0|107
chr1_3 exon 8581947 8582270 8581947 ID=Msa0101910-mRNA-1:exon:3404;Parent=Msa0101910-mRNA-1
chr1_3 CDS 8581947 8582270 8581947 ID=Msa0101910-mRNA-1:cds;Parent=Msa0101910-mRNA-1
Gene Sequence

>Msa0101910

ATGGCAAATTCTAACCTTGTGTTCAATTCTACTTTTCTAGTCTTAATTATTTTCAATTTATGTTTCTCAACCCTTGCTAGGCCCCTAGTAAAAAGAGAGAACAAATTAGAGTACACATCAACATATGAAAACATAGTCATTTGGCGGCGTAACATTTTAGAGAAAGAAGCTGCGACAACATTAGATTCCCAGAATCCACATGTTGGCGACGAAGCTGAAAAATTGATCGACGATTTTCGACCAACGGATCCAGGTCATAGTCCCGGTGCTGGCCATTCAACCCCAACAATCCCCATGGACACCAACGTGCCTCCAAGGCGTTAA
Protein sequence

>Msa0101910

MANSNLVFNSTFLVLIIFNLCFSTLARPLVKRENKLEYTSTYENIVIWRRNILEKEAATTLDSQNPHVGDEAEKLIDDFRPTDPGHSPGAGHSTPTIPMDTNVPPRR*