AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene074031

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene074031.t1 MTR_5g039180 98.925 93 1 0 1 93 1 93 9.70e-61 180
MS.gene074031.t1 MTR_7g010120 72.826 92 24 1 1 92 1 91 1.01e-40 129
MS.gene074031.t1 MTR_6g011670 69.737 76 23 0 17 92 15 90 4.66e-34 112
MS.gene074031.t1 MTR_3g438070 74.026 77 18 1 17 93 17 91 4.82e-34 112
MS.gene074031.t1 MTR_7g059260 45.946 74 40 0 8 81 3 76 1.26e-11 55.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene074031.t1 AT1G26945 83.784 74 12 0 19 92 19 92 3.13e-39 125
MS.gene074031.t1 AT3G28857 64.894 94 30 2 1 93 1 92 3.72e-36 118
MS.gene074031.t1 AT3G47710 69.149 94 25 3 1 93 1 91 3.48e-35 115
MS.gene074031.t1 AT5G15160 73.333 75 19 1 19 92 18 92 3.25e-32 108
MS.gene074031.t1 AT1G74500 72.727 77 18 2 17 92 17 91 2.96e-31 105
MS.gene074031.t1 AT5G39860 65.385 78 26 1 17 93 15 92 1.73e-30 103

Find 16 sgRNAs with CRISPR-Local

Find 30 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGACCGATTGTCACAACTTT+TGG 0.275530 5.1:-29499988 MS.gene074031:CDS
GAGCGGCTAGCGCGAAGTTC+GGG 0.276939 5.1:+29500519 None:intergenic
GTGCTCAAGCAGCTATTATT+AGG 0.330670 5.1:-29499947 MS.gene074031:CDS
GGAGCGGCTAGCGCGAAGTT+CGG 0.362273 5.1:+29500518 None:intergenic
CTTATAGGTTTCAGCTACTA+AGG 0.382941 5.1:-29500069 MS.gene074031:intron
AGAGGAACCACCGGATTGTC+TGG 0.389390 5.1:+29500596 None:intergenic
GGGGATAAGTTGTTGTAACT+TGG 0.418381 5.1:+29500539 None:intergenic
AATAGCTGCTTGAGCACTGT+TGG 0.496664 5.1:+29499953 None:intergenic
AAGCCAAAAGTTGTGACAAT+CGG 0.524888 5.1:+29499985 None:intergenic
AGATCTCGTTCCAGACAATC+CGG 0.532260 5.1:-29500606 MS.gene074031:CDS
AAATAAATACCTTGTTGGAG+CGG 0.605762 5.1:+29500502 None:intergenic
TCGCGCTAGCCGCTCCAACA+AGG 0.613710 5.1:-29500511 MS.gene074031:intron
AGTGATCTCAGAGGAACCAC+CGG 0.628272 5.1:+29500587 None:intergenic
AGCGGCTAGCGCGAAGTTCG+GGG 0.650397 5.1:+29500520 None:intergenic
TCTCGTTCCAGACAATCCGG+TGG 0.728257 5.1:-29500603 MS.gene074031:CDS
TTGAGCATCAGTGATCTCAG+AGG 0.728981 5.1:+29500578 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTTTTTTATGGTCTTAT+AGG - chr5.1:29500466-29500485 MS.gene074031:intron 15.0%
!! TAGAAAAATAAATACCTTGT+TGG + chr5.1:29500056-29500075 None:intergenic 20.0%
AAATAAATACCTTGTTGGAG+CGG + chr5.1:29500051-29500070 None:intergenic 30.0%
ACAATACAATACACAAGTTG+TGG + chr5.1:29500313-29500332 None:intergenic 30.0%
CATAAAAAACTTGCATAGAG+AGG - chr5.1:29500526-29500545 MS.gene074031:CDS 30.0%
AAGCCAAAAGTTGTGACAAT+CGG + chr5.1:29500568-29500587 None:intergenic 35.0%
ATGCATGTGAATGATGACTT+GGG + chr5.1:29500199-29500218 None:intergenic 35.0%
CTTATAGGTTTCAGCTACTA+AGG - chr5.1:29500481-29500500 MS.gene074031:intron 35.0%
GATACAATGCACATATTGTG+TGG - chr5.1:29500230-29500249 MS.gene074031:intron 35.0%
TATGCATGTGAATGATGACT+TGG + chr5.1:29500200-29500219 None:intergenic 35.0%
! ATTTGTGAGAGTGTGTATGA+AGG + chr5.1:29500175-29500194 None:intergenic 35.0%
!! TGTGTGGACATTGTTAGTTT+TGG - chr5.1:29500246-29500265 MS.gene074031:intron 35.0%
CAAGTTGTGGCAAAGAATTG+AGG + chr5.1:29500300-29500319 None:intergenic 40.0%
GGGGATAAGTTGTTGTAACT+TGG + chr5.1:29500014-29500033 None:intergenic 40.0%
GTGCTCAAGCAGCTATTATT+AGG - chr5.1:29500603-29500622 MS.gene074031:CDS 40.0%
! TGACCGATTGTCACAACTTT+TGG - chr5.1:29500562-29500581 MS.gene074031:CDS 40.0%
AGATCTCGTTCCAGACAATC+CGG - chr5.1:29499944-29499963 MS.gene074031:CDS 45.0%
AGCTAGTTGCAACATGCAAG+TGG - chr5.1:29500379-29500398 MS.gene074031:intron 45.0%
GCTAGTTGCAACATGCAAGT+GGG - chr5.1:29500380-29500399 MS.gene074031:intron 45.0%
TTGAGCATCAGTGATCTCAG+AGG + chr5.1:29499975-29499994 None:intergenic 45.0%
! AATAGCTGCTTGAGCACTGT+TGG + chr5.1:29500600-29500619 None:intergenic 45.0%
!!! TTAATTTGTATTTTTTTTTA+TGG - chr5.1:29500457-29500476 MS.gene074031:intron 5.0%
AGTGATCTCAGAGGAACCAC+CGG + chr5.1:29499966-29499985 None:intergenic 50.0%
AGTTGCAACATGCAAGTGGG+TGG - chr5.1:29500383-29500402 MS.gene074031:intron 50.0%
AGAGGAACCACCGGATTGTC+TGG + chr5.1:29499957-29499976 None:intergenic 55.0%
TCTCGTTCCAGACAATCCGG+TGG - chr5.1:29499947-29499966 MS.gene074031:CDS 55.0%
AGCGGCTAGCGCGAAGTTCG+GGG + chr5.1:29500033-29500052 None:intergenic 65.0%
GAGCGGCTAGCGCGAAGTTC+GGG + chr5.1:29500034-29500053 None:intergenic 65.0%
GGAGCGGCTAGCGCGAAGTT+CGG + chr5.1:29500035-29500054 None:intergenic 65.0%
TCGCGCTAGCCGCTCCAACA+AGG - chr5.1:29500039-29500058 MS.gene074031:CDS 65.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 29499932 29500640 29499932 ID=MS.gene074031
chr5.1 mRNA 29499932 29500640 29499932 ID=MS.gene074031.t1;Parent=MS.gene074031
chr5.1 exon 29500512 29500640 29500512 ID=MS.gene074031.t1.exon1;Parent=MS.gene074031.t1
chr5.1 CDS 29500512 29500640 29500512 ID=cds.MS.gene074031.t1;Parent=MS.gene074031.t1
chr5.1 exon 29499932 29500084 29499932 ID=MS.gene074031.t1.exon2;Parent=MS.gene074031.t1
chr5.1 CDS 29499932 29500084 29499932 ID=cds.MS.gene074031.t1;Parent=MS.gene074031.t1
Gene Sequence

>MS.gene074031

ATGTCTAGCAGAAGATCTCGTTCCAGACAATCCGGTGGTTCCTCTGAGATCACTGATGCTCAAATCACTGATCTCATTTCCAAGTTACAACAACTTATCCCCGAACTTCGCGCTAGCCGCTCCAACAAGGTATTTATTTTTCTAAATATCGCTGTCTTCGTTCTTTAAACTGTCTGCAATTGTACGCAAATGATACTTAATTTATAAAAAATAAAATTATATTTTACTTATAAAACTTTTCCTTCATACACACTCTCACAAATTCCCAAGTCATCATTCACATGCATAATATAAGAATGATACAATGCACATATTGTGTGGACATTGTTAGTTTTGGTAGATAAACAATGTTTATTATGACTCTTCCTCAATTCTTTGCCACAACTTGTGTATTGTATTGTATTGTATTGTACTCATTTACTAATCATGCATTAATTACTAGCTTGTAGCTAGTTGCAACATGCAAGTGGGTGGTGTATAAAACTAAAAAAAGAATTAATTAAACTTTGACTCTAATAAAATTTATTAATTTGTATTTTTTTTTATGGTCTTATAGGTTTCAGCTACTAAGGTATTGCAAGAGACTTGCAACTACATAAAAAACTTGCATAGAGAGGTTGATGATTTAAGTGACCGATTGTCACAACTTTTGGCTTCTACAGATTCCAACAGTGCTCAAGCAGCTATTATTAGGAGCTTACTTATGTAA
Protein sequence

>MS.gene074031.t1

MSSRRSRSRQSGGSSEITDAQITDLISKLQQLIPELRASRSNKVSATKVLQETCNYIKNLHREVDDLSDRLSQLLASTDSNSAQAAIIRSLLM