AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene98606

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene98606.t1 MTR_4g052060 93.333 150 10 0 1 150 1 150 6.18e-101 288
MS.gene98606.t1 MTR_4g052040 67.470 166 46 3 1 159 1 165 2.95e-64 194
MS.gene98606.t1 MTR_5g079710 42.675 157 84 4 4 159 6 157 4.18e-29 107
MS.gene98606.t1 MTR_7g105790 35.294 170 87 2 1 150 1 167 1.56e-20 84.0
MS.gene98606.t1 MTR_0907s0020 62.500 56 21 0 95 150 104 159 9.88e-19 79.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene98606.t1 AT3G52525 57.143 63 26 1 89 150 61 123 6.30e-18 76.3
MS.gene98606.t1 AT2G36026 60.377 53 21 0 98 150 91 143 3.23e-16 72.4
MS.gene98606.t1 AT5G19650 41.791 67 39 0 92 158 153 219 3.16e-11 59.7

Find 32 sgRNAs with CRISPR-Local

Find 32 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATTTGGCTAATGGAAATTT+TGG 0.176660 4.2:-50089565 None:intergenic
TGGATGAAGCCTTGCTAATT+TGG 0.245892 4.2:-50089581 None:intergenic
GCTTCATCCAACACAACTTT+AGG 0.315005 4.2:+50089594 MS.gene98606:CDS
AGCCTTGCTAATTTGGCTAA+TGG 0.359333 4.2:-50089574 None:intergenic
AGAGTGTTCTCAACAAATAT+TGG 0.365412 4.2:+50089486 MS.gene98606:CDS
AAACACTGTGGTTGTTGAAA+AGG 0.406424 4.2:+50089731 MS.gene98606:CDS
GAGTGCTTGAAATCATGATA+TGG 0.426047 4.2:-50089765 None:intergenic
ATGATCTTCGAGTTCTTCTT+CGG 0.426591 4.2:+50089829 MS.gene98606:CDS
ACAACCACAGTGTTTGATAG+AGG 0.460583 4.2:-50089723 None:intergenic
CACAACTTTAGGTGAAAGAA+AGG 0.468235 4.2:+50089605 MS.gene98606:CDS
TCTTTCACCTAAAGTTGTGT+TGG 0.468817 4.2:-50089601 None:intergenic
GCTGTGGTCGACGCTACAAC+CGG 0.476684 4.2:-50089631 None:intergenic
TATGCTTCAAATGATCTTCG+AGG 0.503327 4.2:+50089788 MS.gene98606:CDS
TCAACAAATATTGGAAGTTG+TGG 0.506051 4.2:+50089495 MS.gene98606:CDS
GTAGTAGTACAAACCTTGTC+GGG 0.514681 4.2:-50089929 None:intergenic
GTTTGATAGAGGGCTATGCT+TGG 0.522411 4.2:-50089712 None:intergenic
AGCATCAGAGAAAGTGGTGG+TGG 0.530263 4.2:-50089664 None:intergenic
TTCCATTAGCCAAATTAGCA+AGG 0.533087 4.2:+50089572 MS.gene98606:CDS
TGTTTCAGCATCAGAGAAAG+TGG 0.542831 4.2:-50089670 None:intergenic
TTTGATAGAGGGCTATGCTT+GGG 0.544333 4.2:-50089711 None:intergenic
AGTACACGAGCCTATTCAAA+AGG 0.546512 4.2:+50089542 MS.gene98606:CDS
CTTCGAGGATGAGATCGATT+CGG 0.564919 4.2:+50089803 MS.gene98606:CDS
GATAGAGGGCTATGCTTGGG+TGG 0.581428 4.2:-50089708 None:intergenic
AGTAGTAGTACAAACCTTGT+CGG 0.598934 4.2:-50089930 None:intergenic
CAACCACAGTGTTTGATAGA+GGG 0.606410 4.2:-50089722 None:intergenic
TTAGGTGAAAGAAAGGGTGC+CGG 0.615123 4.2:+50089612 MS.gene98606:CDS
ACAACTTTAGGTGAAAGAAA+GGG 0.626599 4.2:+50089606 MS.gene98606:CDS
CGAGGATGAGATCGATTCGG+AGG 0.665085 4.2:+50089806 MS.gene98606:CDS
TTCAGCATCAGAGAAAGTGG+TGG 0.697803 4.2:-50089667 None:intergenic
TTAAGACTTTAACGATGACA+AGG 0.699227 4.2:-50089884 None:intergenic
TGGTGGAGAAATCGTCGCTG+TGG 0.708398 4.2:-50089647 None:intergenic
TAGCCCTCTATCAAACACTG+TGG 0.798981 4.2:+50089719 MS.gene98606:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTTGGCTAATGGAAATTT+TGG - chr4.2:50089568-50089587 None:intergenic 25.0%
ACAACTTTAGGTGAAAGAAA+GGG + chr4.2:50089606-50089625 MS.gene98606:CDS 30.0%
TCAACAAATATTGGAAGTTG+TGG + chr4.2:50089495-50089514 MS.gene98606:CDS 30.0%
TTAAGACTTTAACGATGACA+AGG - chr4.2:50089887-50089906 None:intergenic 30.0%
! AGAGTGTTCTCAACAAATAT+TGG + chr4.2:50089486-50089505 MS.gene98606:CDS 30.0%
!! GAAATTTTGGCCTTTTGAAT+AGG - chr4.2:50089555-50089574 None:intergenic 30.0%
AAACACTGTGGTTGTTGAAA+AGG + chr4.2:50089731-50089750 MS.gene98606:CDS 35.0%
CACAACTTTAGGTGAAAGAA+AGG + chr4.2:50089605-50089624 MS.gene98606:CDS 35.0%
GAGTGCTTGAAATCATGATA+TGG - chr4.2:50089768-50089787 None:intergenic 35.0%
TATGCTTCAAATGATCTTCG+AGG + chr4.2:50089788-50089807 MS.gene98606:CDS 35.0%
TCTTTCACCTAAAGTTGTGT+TGG - chr4.2:50089604-50089623 None:intergenic 35.0%
TTCCATTAGCCAAATTAGCA+AGG + chr4.2:50089572-50089591 MS.gene98606:CDS 35.0%
! ATGATCTTCGAGTTCTTCTT+CGG + chr4.2:50089829-50089848 MS.gene98606:CDS 35.0%
! TCTCACAAGTCTTTTCTTGT+TGG - chr4.2:50089466-50089485 None:intergenic 35.0%
ACAACCACAGTGTTTGATAG+AGG - chr4.2:50089726-50089745 None:intergenic 40.0%
AGCCTTGCTAATTTGGCTAA+TGG - chr4.2:50089577-50089596 None:intergenic 40.0%
AGTACACGAGCCTATTCAAA+AGG + chr4.2:50089542-50089561 MS.gene98606:CDS 40.0%
CAACCACAGTGTTTGATAGA+GGG - chr4.2:50089725-50089744 None:intergenic 40.0%
GCTTCATCCAACACAACTTT+AGG + chr4.2:50089594-50089613 MS.gene98606:CDS 40.0%
TGGATGAAGCCTTGCTAATT+TGG - chr4.2:50089584-50089603 None:intergenic 40.0%
TGTTTCAGCATCAGAGAAAG+TGG - chr4.2:50089673-50089692 None:intergenic 40.0%
TTTGATAGAGGGCTATGCTT+GGG - chr4.2:50089714-50089733 None:intergenic 40.0%
CTTCGAGGATGAGATCGATT+CGG + chr4.2:50089803-50089822 MS.gene98606:CDS 45.0%
GTTTGATAGAGGGCTATGCT+TGG - chr4.2:50089715-50089734 None:intergenic 45.0%
TAGCCCTCTATCAAACACTG+TGG + chr4.2:50089719-50089738 MS.gene98606:CDS 45.0%
TTCAGCATCAGAGAAAGTGG+TGG - chr4.2:50089670-50089689 None:intergenic 45.0%
! TTAGGTGAAAGAAAGGGTGC+CGG + chr4.2:50089612-50089631 MS.gene98606:CDS 45.0%
AGCATCAGAGAAAGTGGTGG+TGG - chr4.2:50089667-50089686 None:intergenic 50.0%
GATAGAGGGCTATGCTTGGG+TGG - chr4.2:50089711-50089730 None:intergenic 55.0%
TGGTGGAGAAATCGTCGCTG+TGG - chr4.2:50089650-50089669 None:intergenic 55.0%
!! CGAGGATGAGATCGATTCGG+AGG + chr4.2:50089806-50089825 MS.gene98606:CDS 55.0%
GCTGTGGTCGACGCTACAAC+CGG - chr4.2:50089634-50089653 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 50089456 50089937 50089456 ID=MS.gene98606
chr4.2 mRNA 50089456 50089937 50089456 ID=MS.gene98606.t1;Parent=MS.gene98606
chr4.2 exon 50089456 50089937 50089456 ID=MS.gene98606.t1.exon1;Parent=MS.gene98606.t1
chr4.2 CDS 50089456 50089937 50089456 ID=cds.MS.gene98606.t1;Parent=MS.gene98606.t1
Gene Sequence

>MS.gene98606

ATGTCTTCCAACAAGAAAAGACTTGTGAGAAGAGTGTTCTCAACAAATATTGGAAGTTGTGGCTGTGCAAAAAAGAAAGCAATTGTAGTACACGAGCCTATTCAAAAGGCCAAAATTTCCATTAGCCAAATTAGCAAGGCTTCATCCAACACAACTTTAGGTGAAAGAAAGGGTGCCGGTTGTAGCGTCGACCACAGCGACGATTTCTCCACCACCACTTTCTCTGATGCTGAAACAACTCAAAACTATTCTCCACCCAAGCATAGCCCTCTATCAAACACTGTGGTTGTTGAAAAGGATTCTGACGATCCATATCATGATTTCAAGCACTCTATGCTTCAAATGATCTTCGAGGATGAGATCGATTCGGAGGATGATCTTCGAGTTCTTCTTCGGTGTTTGCTTCATCTCAATGATACTTATTATCACCTTGTCATCGTTAAAGTCTTAATGATATATGTCATGAAGCTTTTCCCGACAAG
Protein sequence

>MS.gene98606.t1

MSSNKKRLVRRVFSTNIGSCGCAKKKAIVVHEPIQKAKISISQISKASSNTTLGERKGAGCSVDHSDDFSTTTFSDAETTQNYSPPKHSPLSNTVVVEKDSDDPYHDFKHSMLQMIFEDEIDSEDDLRVLLRCLLHLNDTYYHLVIVKVLMIYVMKLFPT