AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene24564

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24564.t1 MTR_1g016200 55.357 112 35 4 9 114 2 104 1.77e-25 93.2
MS.gene24564.t1 MTR_1g016170 43.158 95 45 2 29 114 140 234 2.91e-14 67.8
MS.gene24564.t1 MTR_7g112330 44.068 59 33 0 70 128 22 80 2.59e-11 57.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24564.t1 AT4G36620 47.368 57 30 0 70 126 75 131 8.77e-12 60.1
MS.gene24564.t1 AT5G26930 48.980 49 25 0 66 114 22 70 1.93e-11 57.4
MS.gene24564.t1 AT2G18380 49.123 57 29 0 70 126 92 148 9.02e-11 57.4
MS.gene24564.t1 AT5G56860 70.588 34 10 0 70 103 230 263 9.73e-11 58.2

Find 30 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCAGTGTCAAGACCCTTAT+TGG 0.213155 1.2:-6289190 None:intergenic
TTCCTCTTTGTGACTGGAAT+TGG 0.242970 1.2:-6288742 None:intergenic
AGTATTCGCCATTGCCCTTT+TGG 0.253039 1.2:-6288859 None:intergenic
GGAAGAGGCAAAAGCCAATA+AGG 0.316264 1.2:+6289176 MS.gene24564:CDS
GAATACTATATCCAAGGAAT+TGG 0.396437 1.2:+6288875 MS.gene24564:CDS
ATACGAACACTACTCCTCTT+TGG 0.428715 1.2:+6288947 MS.gene24564:CDS
TAAGGGTCTTGACACTGAAA+AGG 0.459357 1.2:+6289194 MS.gene24564:CDS
TTGCCTCTTCCCTTCTTCGT+CGG 0.477939 1.2:-6289164 None:intergenic
ACTGAAAAGGGAAAGGGAAA+TGG 0.483033 1.2:+6289207 MS.gene24564:CDS
TCTTTGGCGGAGTGATCCTA+CGG 0.514022 1.2:+6288963 MS.gene24564:CDS
ACTGAATACGAATACCCAAA+AGG 0.514268 1.2:+6288844 MS.gene24564:CDS
GGAGGGCTGAACCAATTCCT+TGG 0.517307 1.2:-6288886 None:intergenic
AAGGGTCTTGACACTGAAAA+GGG 0.524508 1.2:+6289195 MS.gene24564:CDS
GAAGAGGCAAAAGCCAATAA+GGG 0.527753 1.2:+6289177 MS.gene24564:CDS
CTGAATACGAATACCCAAAA+GGG 0.530093 1.2:+6288845 MS.gene24564:CDS
ATGTGGACTCCGACGAAGAA+GGG 0.540307 1.2:+6289155 MS.gene24564:CDS
CATGTGGACTCCGACGAAGA+AGG 0.573346 1.2:+6289154 MS.gene24564:CDS
GAGTGATCCTACGGGTTCCA+AGG 0.575967 1.2:+6288972 MS.gene24564:CDS
CGAACACTACTCCTCTTTGG+CGG 0.584168 1.2:+6288950 MS.gene24564:CDS
CTTTGGCGGAGTGATCCTAC+GGG 0.586116 1.2:+6288964 MS.gene24564:CDS
ACTCCGACGAAGAAGGGAAG+AGG 0.589069 1.2:+6289161 MS.gene24564:CDS
ATCCAATTCCAGTCACAAAG+AGG 0.594857 1.2:+6288740 MS.gene24564:CDS
TCTTGACACTGAAAAGGGAA+AGG 0.595440 1.2:+6289200 MS.gene24564:CDS
CTTGACACTGAAAAGGGAAA+GGG 0.607329 1.2:+6289201 MS.gene24564:CDS
CAGTCGTTGTGCAATGCATG+TGG 0.610062 1.2:+6289138 MS.gene24564:intron
ACGAATACCCAAAAGGGCAA+TGG 0.610371 1.2:+6288851 MS.gene24564:CDS
AATGGCGAATACTATATCCA+AGG 0.653439 1.2:+6288869 MS.gene24564:CDS
ATCGCAATCGAAACAAACCC+TGG 0.664892 1.2:-6288926 None:intergenic
GTAGGATCACTCCGCCAAAG+AGG 0.691241 1.2:-6288961 None:intergenic
AGTAATACCTTGGAACCCGT+AGG 0.710916 1.2:-6288979 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAATCAATATGTATAAGTA+TGG - chr1.2:6289071-6289090 None:intergenic 15.0%
!! ATAGTTAACAAGAAATATGT+TGG + chr1.2:6289113-6289132 MS.gene24564:intron 20.0%
!!! AGCAGTTTTTATTTTCTTTT+TGG - chr1.2:6288824-6288843 None:intergenic 20.0%
!!! ATTTGATAGTAAATAAGTTG+TGG - chr1.2:6289018-6289037 None:intergenic 20.0%
!!! TTACTATCAAATTTCACTTT+TGG + chr1.2:6289026-6289045 MS.gene24564:intron 20.0%
!!! TAAAACTTTTTCACATTCTC+AGG - chr1.2:6289246-6289265 None:intergenic 25.0%
AGACAGATTAAGTAATACCT+TGG - chr1.2:6288992-6289011 None:intergenic 30.0%
GAATACTATATCCAAGGAAT+TGG + chr1.2:6288875-6288894 MS.gene24564:CDS 30.0%
AATGGCGAATACTATATCCA+AGG + chr1.2:6288869-6288888 MS.gene24564:CDS 35.0%
ACTGAATACGAATACCCAAA+AGG + chr1.2:6288844-6288863 MS.gene24564:CDS 35.0%
CTGAATACGAATACCCAAAA+GGG + chr1.2:6288845-6288864 MS.gene24564:CDS 35.0%
TCCTAGTAAAAACACAACCA+GGG + chr1.2:6288909-6288928 MS.gene24564:CDS 35.0%
!! TTGTGTTTTTACTAGGAGGA+GGG - chr1.2:6288906-6288925 None:intergenic 35.0%
AAGGGTCTTGACACTGAAAA+GGG + chr1.2:6289195-6289214 MS.gene24564:CDS 40.0%
ACTGAAAAGGGAAAGGGAAA+TGG + chr1.2:6289207-6289226 MS.gene24564:CDS 40.0%
ATACGAACACTACTCCTCTT+TGG + chr1.2:6288947-6288966 MS.gene24564:CDS 40.0%
ATCCAATTCCAGTCACAAAG+AGG + chr1.2:6288740-6288759 MS.gene24564:CDS 40.0%
CTCCTAGTAAAAACACAACC+AGG + chr1.2:6288908-6288927 MS.gene24564:CDS 40.0%
CTTGACACTGAAAAGGGAAA+GGG + chr1.2:6289201-6289220 MS.gene24564:CDS 40.0%
GAAGAGGCAAAAGCCAATAA+GGG + chr1.2:6289177-6289196 MS.gene24564:CDS 40.0%
TAAGGGTCTTGACACTGAAA+AGG + chr1.2:6289194-6289213 MS.gene24564:CDS 40.0%
TCTTGACACTGAAAAGGGAA+AGG + chr1.2:6289200-6289219 MS.gene24564:CDS 40.0%
TTCAGTGTCAAGACCCTTAT+TGG - chr1.2:6289193-6289212 None:intergenic 40.0%
TTCCTCTTTGTGACTGGAAT+TGG - chr1.2:6288745-6288764 None:intergenic 40.0%
!! ACCCTGGTTGTGTTTTTACT+AGG - chr1.2:6288913-6288932 None:intergenic 40.0%
!! CTGGTTGTGTTTTTACTAGG+AGG - chr1.2:6288910-6288929 None:intergenic 40.0%
!! GTTGTGTTTTTACTAGGAGG+AGG - chr1.2:6288907-6288926 None:intergenic 40.0%
!!! GCTTTTTTCCTCTTTGTGAC+TGG - chr1.2:6288751-6288770 None:intergenic 40.0%
ACGAATACCCAAAAGGGCAA+TGG + chr1.2:6288851-6288870 MS.gene24564:CDS 45.0%
AGAGGAAAAAAGCTGCTGCT+AGG + chr1.2:6288758-6288777 MS.gene24564:CDS 45.0%
AGTAATACCTTGGAACCCGT+AGG - chr1.2:6288982-6289001 None:intergenic 45.0%
ATCGCAATCGAAACAAACCC+TGG - chr1.2:6288929-6288948 None:intergenic 45.0%
GAGGAAAAAAGCTGCTGCTA+GGG + chr1.2:6288759-6288778 MS.gene24564:CDS 45.0%
GGAAGAGGCAAAAGCCAATA+AGG + chr1.2:6289176-6289195 MS.gene24564:CDS 45.0%
! AGTATTCGCCATTGCCCTTT+TGG - chr1.2:6288862-6288881 None:intergenic 45.0%
! GTATTCGCCATTGCCCTTTT+GGG - chr1.2:6288861-6288880 None:intergenic 45.0%
ATGTGGACTCCGACGAAGAA+GGG + chr1.2:6289155-6289174 MS.gene24564:CDS 50.0%
CAGTCGTTGTGCAATGCATG+TGG + chr1.2:6289138-6289157 MS.gene24564:intron 50.0%
CGAACACTACTCCTCTTTGG+CGG + chr1.2:6288950-6288969 MS.gene24564:CDS 50.0%
TCTTTGGCGGAGTGATCCTA+CGG + chr1.2:6288963-6288982 MS.gene24564:CDS 50.0%
TTGCCTCTTCCCTTCTTCGT+CGG - chr1.2:6289167-6289186 None:intergenic 50.0%
ACTCCGACGAAGAAGGGAAG+AGG + chr1.2:6289161-6289180 MS.gene24564:CDS 55.0%
CATGTGGACTCCGACGAAGA+AGG + chr1.2:6289154-6289173 MS.gene24564:CDS 55.0%
CTTTGGCGGAGTGATCCTAC+GGG + chr1.2:6288964-6288983 MS.gene24564:CDS 55.0%
GAGTGATCCTACGGGTTCCA+AGG + chr1.2:6288972-6288991 MS.gene24564:CDS 55.0%
GGAGGGCTGAACCAATTCCT+TGG - chr1.2:6288889-6288908 None:intergenic 55.0%
GTAGGATCACTCCGCCAAAG+AGG - chr1.2:6288964-6288983 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 6288721 6289266 6288721 ID=MS.gene24564
chr1.2 mRNA 6288721 6289266 6288721 ID=MS.gene24564.t1;Parent=MS.gene24564
chr1.2 exon 6288721 6288993 6288721 ID=MS.gene24564.t1.exon1;Parent=MS.gene24564.t1
chr1.2 CDS 6288721 6288993 6288721 ID=cds.MS.gene24564.t1;Parent=MS.gene24564.t1
chr1.2 exon 6289141 6289266 6289141 ID=MS.gene24564.t1.exon2;Parent=MS.gene24564.t1
chr1.2 CDS 6289141 6289266 6289141 ID=cds.MS.gene24564.t1;Parent=MS.gene24564.t1
Gene Sequence

>MS.gene24564

ATGAGAGTATGTAACGATGATCCAATTCCAGTCACAAAGAGGAAAAAAGCTGCTGCTAGGGCTACAAAAAAGAAGAAAACAGCTGCTACTGCTAGTGCTGCCAAAAAGAAAATAAAAACTGCTACTGAATACGAATACCCAAAAGGGCAATGGCGAATACTATATCCAAGGAATTGGTTCAGCCCTCCTCCTAGTAAAAACACAACCAGGGTTTGTTTCGATTGCGATACGAACACTACTCCTCTTTGGCGGAGTGATCCTACGGGTTCCAAGGTATTACTTAATCTGTCTTCTCCACAACTTATTTACTATCAAATTTCACTTTTGGTTCATTCAAAAGTGTTATTCCATACTTATACATATTGATTAATAATTTGAATATCTAGTTATATATAGTTAACAAGAAATATGTTGGTGCAGTCGTTGTGCAATGCATGTGGACTCCGACGAAGAAGGGAAGAGGCAAAAGCCAATAAGGGTCTTGACACTGAAAAGGGAAAGGGAAATGGCGAAAGCTCATCACCTGAGAATGTGAAAAAGTTTTAA
Protein sequence

>MS.gene24564.t1

MRVCNDDPIPVTKRKKAAARATKKKKTAATASAAKKKIKTATEYEYPKGQWRILYPRNWFSPPPSKNTTRVCFDCDTNTTPLWRSDPTGSKSLCNACGLRRRREEAKANKGLDTEKGKGNGESSSPENVKKF