AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene06431

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene06431.t1 MTR_3g095830 94.872 117 6 0 1 117 1 117 2.17e-79 229
MS.gene06431.t1 MTR_3g095840 59.292 113 38 2 3 107 8 120 3.86e-38 132
MS.gene06431.t1 MTR_1g007670 45.312 64 35 0 44 107 10 73 2.59e-15 70.5
MS.gene06431.t1 MTR_5g010300 36.842 95 57 1 18 109 197 291 4.92e-14 67.4
MS.gene06431.t1 MTR_5g010300 36.842 95 57 1 18 109 197 291 5.16e-14 67.4
MS.gene06431.t1 MTR_5g010300 36.842 95 57 1 18 109 197 291 5.35e-14 67.0
MS.gene06431.t1 MTR_5g010300 36.842 95 57 1 18 109 197 291 5.55e-14 67.0
MS.gene06431.t1 MTR_1g007700 50.000 48 20 1 60 107 258 301 2.57e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene06431.t1 AT5G09790 50.000 100 42 2 16 110 18 114 3.73e-25 97.8
MS.gene06431.t1 AT5G09790 50.000 100 42 2 16 110 18 114 4.01e-25 97.8
MS.gene06431.t1 AT5G24330 69.565 46 14 0 62 107 34 79 1.14e-18 79.7
MS.gene06431.t1 AT1G63490 41.772 79 43 1 31 109 213 288 6.60e-13 63.9
MS.gene06431.t1 AT1G63490 41.772 79 43 1 31 109 213 288 6.73e-13 63.9

Find 36 sgRNAs with CRISPR-Local

Find 39 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTAGAGTTCCTATTGGTTCA+TGG 0.294500 3.2:+79997926 MS.gene06431:CDS
AGTCTGTTGGCTTCTTCTTT+CGG 0.305637 3.2:-79997711 None:intergenic
GAAGTGTCTGAGACCGGTTC+TGG 0.362102 3.2:+79997903 MS.gene06431:CDS
CCCCAAGTGTTGTTCTGAGC+TGG 0.393884 3.2:+79997954 MS.gene06431:CDS
GGGCAAATCCATGAACCAAT+AGG 0.417784 3.2:-79997934 None:intergenic
GGCTTCTTCTTTCGGTGGCA+CGG 0.431024 3.2:-79997703 None:intergenic
ATGTGTGCGGCGGGTGAAGC+TGG 0.451472 3.2:-79997677 None:intergenic
TAGGACGATGACTAATATAA+TGG 0.454899 3.2:+79997756 MS.gene06431:CDS
CTCCAGCTCAGAACAACACT+TGG 0.460665 3.2:-79997956 None:intergenic
GCACGGTGCATGTGTGCGGC+GGG 0.463261 3.2:-79997686 None:intergenic
GTTCTGGCTAGAGTTCCTAT+TGG 0.469825 3.2:+79997919 MS.gene06431:CDS
GTGAAGCTGGTTAGCTTACG+AGG 0.474210 3.2:-79997664 None:intergenic
ATGTGTGAGCGATGTGGATC+TGG 0.479905 3.2:+79997826 MS.gene06431:CDS
CATCGCGGGTGACGAAGTAT+AGG 0.492844 3.2:+79997737 MS.gene06431:CDS
ATAGGAACTCTAGCCAGAAC+CGG 0.497595 3.2:-79997916 None:intergenic
TCACACAACAAAAGCTCCTC+AGG 0.503103 3.2:-79997856 None:intergenic
CTGTTGGCTTCTTCTTTCGG+TGG 0.523013 3.2:-79997708 None:intergenic
TCATATGAAGTGTCTGAGAC+CGG 0.525057 3.2:+79997897 MS.gene06431:CDS
GGCACGGTGCATGTGTGCGG+CGG 0.525820 3.2:-79997687 None:intergenic
GCCAACAGACTCGTCATCGC+GGG 0.543998 3.2:+79997723 MS.gene06431:CDS
TCCAGCTCAGAACAACACTT+GGG 0.544872 3.2:-79997955 None:intergenic
ATATGCAGTGGTTGAGAAGG+AGG 0.563550 3.2:+79997789 MS.gene06431:CDS
TAAATATGCAGTGGTTGAGA+AGG 0.574113 3.2:+79997786 MS.gene06431:CDS
ACCCGCGATGACGAGTCTGT+TGG 0.610544 3.2:-79997724 None:intergenic
TTGTGTGACAAATGCGACAA+AGG 0.628248 3.2:+79997871 MS.gene06431:CDS
CGATGACTAATATAATGGCG+AGG 0.630890 3.2:+79997761 MS.gene06431:CDS
GATGACTAATATAATGGCGA+GGG 0.645664 3.2:+79997762 MS.gene06431:CDS
GGTGGCACGGTGCATGTGTG+CGG 0.648842 3.2:-79997690 None:intergenic
AGCCAACAGACTCGTCATCG+CGG 0.654231 3.2:+79997722 MS.gene06431:CDS
TGAAGCTGGTTAGCTTACGA+GGG 0.657884 3.2:-79997663 None:intergenic
GGCGAGGGCTAAATATGCAG+TGG 0.659115 3.2:+79997777 MS.gene06431:CDS
CCAGCTCAGAACAACACTTG+GGG 0.668343 3.2:-79997954 None:intergenic
GACTGCATGTGTGAGCGATG+TGG 0.685024 3.2:+79997820 MS.gene06431:CDS
GAAGCTGGTTAGCTTACGAG+GGG 0.692874 3.2:-79997662 None:intergenic
TGGATCTGGTGAACAACCTG+AGG 0.697540 3.2:+79997840 MS.gene06431:CDS
AAGCTGGTTAGCTTACGAGG+GGG 0.759841 3.2:-79997661 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
TAGGACGATGACTAATATAA+TGG + chr3.2:79997756-79997775 MS.gene06431:CDS 30.0%
GATGACTAATATAATGGCGA+GGG + chr3.2:79997762-79997781 MS.gene06431:CDS 35.0%
TAAATATGCAGTGGTTGAGA+AGG + chr3.2:79997786-79997805 MS.gene06431:CDS 35.0%
CGATGACTAATATAATGGCG+AGG + chr3.2:79997761-79997780 MS.gene06431:CDS 40.0%
TTGTGTGACAAATGCGACAA+AGG + chr3.2:79997871-79997890 MS.gene06431:CDS 40.0%
! TCATATGAAGTGTCTGAGAC+CGG + chr3.2:79997897-79997916 MS.gene06431:CDS 40.0%
!! AGTCTGTTGGCTTCTTCTTT+CGG - chr3.2:79997714-79997733 None:intergenic 40.0%
!! CTAGAGTTCCTATTGGTTCA+TGG + chr3.2:79997926-79997945 MS.gene06431:CDS 40.0%
ATAGGAACTCTAGCCAGAAC+CGG - chr3.2:79997919-79997938 None:intergenic 45.0%
ATATGCAGTGGTTGAGAAGG+AGG + chr3.2:79997789-79997808 MS.gene06431:CDS 45.0%
GGGCAAATCCATGAACCAAT+AGG - chr3.2:79997937-79997956 None:intergenic 45.0%
TCACACAACAAAAGCTCCTC+AGG - chr3.2:79997859-79997878 None:intergenic 45.0%
TCCAGCTCAGAACAACACTT+GGG - chr3.2:79997958-79997977 None:intergenic 45.0%
! GTTCTGGCTAGAGTTCCTAT+TGG + chr3.2:79997919-79997938 MS.gene06431:CDS 45.0%
!! TGAAGCTGGTTAGCTTACGA+GGG - chr3.2:79997666-79997685 None:intergenic 45.0%
ATGTGTGAGCGATGTGGATC+TGG + chr3.2:79997826-79997845 MS.gene06431:CDS 50.0%
CCAGCTCAGAACAACACTTG+GGG - chr3.2:79997957-79997976 None:intergenic 50.0%
CTCCAGCTCAGAACAACACT+TGG - chr3.2:79997959-79997978 None:intergenic 50.0%
TGGATCTGGTGAACAACCTG+AGG + chr3.2:79997840-79997859 MS.gene06431:CDS 50.0%
!! AAGCTGGTTAGCTTACGAGG+GGG - chr3.2:79997664-79997683 None:intergenic 50.0%
!! CTGTTGGCTTCTTCTTTCGG+TGG - chr3.2:79997711-79997730 None:intergenic 50.0%
!! GAAGCTGGTTAGCTTACGAG+GGG - chr3.2:79997665-79997684 None:intergenic 50.0%
!! GTGAAGCTGGTTAGCTTACG+AGG - chr3.2:79997667-79997686 None:intergenic 50.0%
AGCCAACAGACTCGTCATCG+CGG + chr3.2:79997722-79997741 MS.gene06431:CDS 55.0%
CATCGCGGGTGACGAAGTAT+AGG + chr3.2:79997737-79997756 MS.gene06431:CDS 55.0%
GACTGCATGTGTGAGCGATG+TGG + chr3.2:79997820-79997839 MS.gene06431:CDS 55.0%
GGCGAGGGCTAAATATGCAG+TGG + chr3.2:79997777-79997796 MS.gene06431:CDS 55.0%
GGCTTCTTCTTTCGGTGGCA+CGG - chr3.2:79997706-79997725 None:intergenic 55.0%
! CCCCAAGTGTTGTTCTGAGC+TGG + chr3.2:79997954-79997973 MS.gene06431:CDS 55.0%
! GAAGTGTCTGAGACCGGTTC+TGG + chr3.2:79997903-79997922 MS.gene06431:CDS 55.0%
ACCCGCGATGACGAGTCTGT+TGG - chr3.2:79997727-79997746 None:intergenic 60.0%
GCCAACAGACTCGTCATCGC+GGG + chr3.2:79997723-79997742 MS.gene06431:CDS 60.0%
! GTTAGCTTACGAGGGGGAGG+TGG - chr3.2:79997658-79997677 None:intergenic 60.0%
!! CTGGTTAGCTTACGAGGGGG+AGG - chr3.2:79997661-79997680 None:intergenic 60.0%
ATGTGTGCGGCGGGTGAAGC+TGG - chr3.2:79997680-79997699 None:intergenic 65.0%
GGTGGCACGGTGCATGTGTG+CGG - chr3.2:79997693-79997712 None:intergenic 65.0%
CTTACGAGGGGGAGGTGGCG+AGG - chr3.2:79997653-79997672 None:intergenic 70.0%
GCACGGTGCATGTGTGCGGC+GGG - chr3.2:79997689-79997708 None:intergenic 70.0%
GGCACGGTGCATGTGTGCGG+CGG - chr3.2:79997690-79997709 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr3.2 gene 79997643 79997996 79997643 ID=MS.gene06431
chr3.2 mRNA 79997643 79997996 79997643 ID=MS.gene06431.t1;Parent=MS.gene06431
chr3.2 exon 79997643 79997996 79997643 ID=MS.gene06431.t1.exon1;Parent=MS.gene06431.t1
chr3.2 CDS 79997643 79997996 79997643 ID=cds.MS.gene06431.t1;Parent=MS.gene06431.t1
Gene Sequence

>MS.gene06431

ATGTATTCCTCGCCACCTCCCCCTCGTAAGCTAACCAGCTTCACCCGCCGCACACATGCACCGTGCCACCGAAAGAAGAAGCCAACAGACTCGTCATCGCGGGTGACGAAGTATAGGACGATGACTAATATAATGGCGAGGGCTAAATATGCAGTGGTTGAGAAGGAGGATTACAGTGACTGCATGTGTGAGCGATGTGGATCTGGTGAACAACCTGAGGAGCTTTTGTTGTGTGACAAATGCGACAAAGGTTTTCATATGAAGTGTCTGAGACCGGTTCTGGCTAGAGTTCCTATTGGTTCATGGATTTGCCCCAAGTGTTGTTCTGAGCTGGAGAGAGTGAAAAGTAAGTGA
Protein sequence

>MS.gene06431.t1

MYSSPPPPRKLTSFTRRTHAPCHRKKKPTDSSSRVTKYRTMTNIMARAKYAVVEKEDYSDCMCERCGSGEQPEELLLCDKCDKGFHMKCLRPVLARVPIGSWICPKCCSELERVKSK