AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene073917

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene073917.t1 MTR_2g006150 78.378 111 20 1 1 111 91 197 5.42e-55 178
MS.gene073917.t1 MTR_2g006150 78.378 111 20 1 1 111 91 197 1.02e-54 179
MS.gene073917.t1 MTR_4g108370 59.048 105 41 1 9 111 60 164 2.19e-34 124
MS.gene073917.t1 MTR_5g039600 74.324 74 18 1 39 111 61 134 2.83e-32 118
MS.gene073917.t1 MTR_1g101810 60.920 87 30 1 20 106 44 126 6.37e-31 113
MS.gene073917.t1 MTR_1g101810 60.920 87 30 1 20 106 74 156 1.25e-30 113
MS.gene073917.t1 MTR_8g033070 69.014 71 22 0 41 111 77 147 9.68e-30 110
MS.gene073917.t1 MTR_7g028160 66.667 69 23 0 39 107 45 113 6.86e-29 107
MS.gene073917.t1 MTR_1g038650 57.471 87 34 1 29 115 20 103 4.68e-28 103
MS.gene073917.t1 MTR_1g063870 63.889 72 26 0 36 107 41 112 5.54e-28 102
MS.gene073917.t1 MTR_1g114380 63.636 77 25 1 35 111 27 100 1.29e-27 103
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene073917.t1 AT1G58100 74.648 71 18 0 41 111 57 127 1.10e-31 116
MS.gene073917.t1 AT2G45680 56.075 107 42 2 10 111 36 142 1.58e-31 115
MS.gene073917.t1 AT1G69690 72.973 74 19 1 39 111 46 119 2.21e-31 114
MS.gene073917.t1 AT3G47620 66.265 83 26 1 31 111 102 184 3.24e-31 116
MS.gene073917.t1 AT1G72010 71.831 71 20 0 41 111 60 130 7.79e-31 114
MS.gene073917.t1 AT5G51910 73.529 68 17 1 40 106 52 119 5.07e-29 107
MS.gene073917.t1 AT5G51910 73.529 68 17 1 40 106 52 119 5.07e-29 107
MS.gene073917.t1 AT3G27010 74.242 66 16 1 40 104 73 138 6.51e-29 107
MS.gene073917.t1 AT3G27010 74.242 66 16 1 40 104 73 138 6.51e-29 107
MS.gene073917.t1 AT1G35560 69.014 71 22 0 41 111 52 122 1.69e-28 107
MS.gene073917.t1 AT5G08330 53.061 98 40 2 14 108 1 95 7.53e-28 103
MS.gene073917.t1 AT5G23280 63.014 73 24 1 36 108 34 103 2.67e-26 99.8
MS.gene073917.t1 AT5G41030 67.273 55 18 0 41 95 65 119 7.61e-24 93.2
MS.gene073917.t1 AT2G37000 73.077 52 14 0 44 95 43 94 4.53e-23 89.7
MS.gene073917.t1 AT3G45150 56.250 64 27 1 41 104 14 76 5.35e-20 81.3
MS.gene073917.t1 AT1G58100 94.444 36 2 0 41 76 57 92 7.00e-17 76.3

Find 39 sgRNAs with CRISPR-Local

Find 37 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGAAGAAAATGGTTGAATT+TGG 0.273936 1.1:+28536956 None:intergenic
CCGATGGTGAAACAATTAAA+TGG 0.306505 1.1:-28536783 MS.gene073917:CDS
TTCCAGTTGACCAGAGAATT+AGG 0.308053 1.1:-28536814 MS.gene073917:CDS
TACCAACACGCGCCTTTGTT+AGG 0.309870 1.1:-28536608 None:intergenic
GCGGTTGAAGTTGAAGAAAA+TGG 0.393103 1.1:+28536946 None:intergenic
GGCCTAATTCTCTGGTCAAC+TGG 0.396838 1.1:+28536812 None:intergenic
GGATTTGTGGCCTAATTCTC+TGG 0.401966 1.1:+28536804 None:intergenic
CTGTCCTTCGTGGATCGTTT+CGG 0.405314 1.1:+28536901 None:intergenic
TTGTTTCACCATCGGATTTG+TGG 0.413051 1.1:+28536791 None:intergenic
ACCAACACGCGCCTTTGTTA+GGG 0.449441 1.1:-28536607 None:intergenic
ACTCTTGATGCGCATGTCGC+TGG 0.455067 1.1:+28536838 None:intergenic
TTGTTGTTGTCGGATACATC+TGG 0.477775 1.1:+28536985 None:intergenic
CCATTTAATTGTTTCACCAT+CGG 0.483763 1.1:+28536783 None:intergenic
AGAGTGTAGAGCCGCTGCTA+CGG 0.485412 1.1:+28536711 None:intergenic
AGGATTTGCAACCGCGGTGA+CGG 0.494209 1.1:+28536924 None:intergenic
CAAAAGTTGACGGCCGTGGC+CGG 0.517328 1.1:-28536873 MS.gene073917:CDS
GCTTCTTCAACAAGCGAAGC+CGG 0.522046 1.1:-28536761 MS.gene073917:CDS
TTGTCGGATACATCTGGAAA+AGG 0.527954 1.1:+28536991 None:intergenic
GCATTCGAATTCTCCGGCCA+CGG 0.536590 1.1:+28536860 None:intergenic
CGAAACGATCCACGAAGGAC+AGG 0.538494 1.1:-28536900 MS.gene073917:CDS
CACACAAAAGTTGACGGCCG+TGG 0.538934 1.1:-28536877 MS.gene073917:CDS
TGGAAAAGGAGGTTCAGATC+TGG 0.540562 1.1:+28537005 None:intergenic
GACAGGCACACAAAAGTTGA+CGG 0.553080 1.1:-28536883 MS.gene073917:CDS
ACCCTAACAAAGGCGCGTGT+TGG 0.563265 1.1:+28536606 None:intergenic
AGATCTGGTGGCAATTGCCA+TGG 0.568346 1.1:+28537020 None:intergenic
TCGCTGGCATTCGAATTCTC+CGG 0.573987 1.1:+28536854 None:intergenic
ATTTGCAACCGCGGTGACGG+CGG 0.577827 1.1:+28536927 None:intergenic
TCCTTCGTGGATCGTTTCGG+AGG 0.590579 1.1:+28536904 None:intergenic
GTTGAGCATTGAGAAATCGC+CGG 0.615988 1.1:+28536742 None:intergenic
AACTTCAACCGCCGTCACCG+CGG 0.629301 1.1:-28536935 MS.gene073917:CDS
AAAAGGAGGTTCAGATCTGG+TGG 0.633145 1.1:+28537008 None:intergenic
AACGTCTCACTCCGTAGCAG+CGG 0.639266 1.1:-28536722 MS.gene073917:CDS
GAATTAGGCCACAAATCCGA+TGG 0.643115 1.1:-28536799 MS.gene073917:CDS
AGAGGAGTTGATTTCGACGA+CGG 0.646957 1.1:+28536683 None:intergenic
TCGGATACATCTGGAAAAGG+AGG 0.647309 1.1:+28536994 None:intergenic
TGAGGATGAAACCCTAACAA+AGG 0.670241 1.1:+28536596 None:intergenic
TTTCGGAGGATTTGCAACCG+CGG 0.679872 1.1:+28536918 None:intergenic
TCCTCCGAAACGATCCACGA+AGG 0.689266 1.1:-28536905 MS.gene073917:CDS
AGCGCGCTATGAAAACTGAG+AGG 0.728294 1.1:+28536665 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TTGAAGAAAATGGTTGAATT+TGG + chr1.1:28536674-28536693 None:intergenic 25.0%
CCATTTAATTGTTTCACCAT+CGG + chr1.1:28536847-28536866 None:intergenic 30.0%
CCGATGGTGAAACAATTAAA+TGG - chr1.1:28536844-28536863 MS.gene073917:CDS 35.0%
! TTGGTTGTTGTTGTTGTTGT+CGG + chr1.1:28536655-28536674 None:intergenic 35.0%
GCGGTTGAAGTTGAAGAAAA+TGG + chr1.1:28536684-28536703 None:intergenic 40.0%
TTCCAGTTGACCAGAGAATT+AGG - chr1.1:28536813-28536832 MS.gene073917:CDS 40.0%
TTGTCGGATACATCTGGAAA+AGG + chr1.1:28536639-28536658 None:intergenic 40.0%
TTGTTTCACCATCGGATTTG+TGG + chr1.1:28536839-28536858 None:intergenic 40.0%
! TTGTTGTTGTCGGATACATC+TGG + chr1.1:28536645-28536664 None:intergenic 40.0%
AAAAGGAGGTTCAGATCTGG+TGG + chr1.1:28536622-28536641 None:intergenic 45.0%
GAATTAGGCCACAAATCCGA+TGG - chr1.1:28536828-28536847 MS.gene073917:CDS 45.0%
GACAGGCACACAAAAGTTGA+CGG - chr1.1:28536744-28536763 MS.gene073917:CDS 45.0%
GGATTTGTGGCCTAATTCTC+TGG + chr1.1:28536826-28536845 None:intergenic 45.0%
TCGGATACATCTGGAAAAGG+AGG + chr1.1:28536636-28536655 None:intergenic 45.0%
TGGAAAAGGAGGTTCAGATC+TGG + chr1.1:28536625-28536644 None:intergenic 45.0%
! AGAGGAGTTGATTTCGACGA+CGG + chr1.1:28536947-28536966 None:intergenic 45.0%
!! GTTGAGCATTGAGAAATCGC+CGG + chr1.1:28536888-28536907 None:intergenic 45.0%
AGCGCGCTATGAAAACTGAG+AGG + chr1.1:28536965-28536984 None:intergenic 50.0%
CTGTCCTTCGTGGATCGTTT+CGG + chr1.1:28536729-28536748 None:intergenic 50.0%
GCTTCTTCAACAAGCGAAGC+CGG - chr1.1:28536866-28536885 MS.gene073917:CDS 50.0%
GGCCTAATTCTCTGGTCAAC+TGG + chr1.1:28536818-28536837 None:intergenic 50.0%
TCGCTGGCATTCGAATTCTC+CGG + chr1.1:28536776-28536795 None:intergenic 50.0%
TTTCGGAGGATTTGCAACCG+CGG + chr1.1:28536712-28536731 None:intergenic 50.0%
! TTTTCATAGCGCGCTTGCAC+TGG - chr1.1:28536970-28536989 MS.gene073917:CDS 50.0%
! TTTTGTGTGCCTGTCCTTCG+TGG + chr1.1:28536739-28536758 None:intergenic 50.0%
AACGTCTCACTCCGTAGCAG+CGG - chr1.1:28536905-28536924 MS.gene073917:CDS 55.0%
ACTCTTGATGCGCATGTCGC+TGG + chr1.1:28536792-28536811 None:intergenic 55.0%
AGAGTGTAGAGCCGCTGCTA+CGG + chr1.1:28536919-28536938 None:intergenic 55.0%
AGGATTTGCAACCGCGGTGA+CGG + chr1.1:28536706-28536725 None:intergenic 55.0%
CACACAAAAGTTGACGGCCG+TGG - chr1.1:28536750-28536769 MS.gene073917:CDS 55.0%
CGAAACGATCCACGAAGGAC+AGG - chr1.1:28536727-28536746 MS.gene073917:CDS 55.0%
GCATTCGAATTCTCCGGCCA+CGG + chr1.1:28536770-28536789 None:intergenic 55.0%
TCCTCCGAAACGATCCACGA+AGG - chr1.1:28536722-28536741 MS.gene073917:CDS 55.0%
TCCTTCGTGGATCGTTTCGG+AGG + chr1.1:28536726-28536745 None:intergenic 55.0%
AACTTCAACCGCCGTCACCG+CGG - chr1.1:28536692-28536711 MS.gene073917:CDS 60.0%
CAAAAGTTGACGGCCGTGGC+CGG - chr1.1:28536754-28536773 MS.gene073917:CDS 60.0%
! ATTTGCAACCGCGGTGACGG+CGG + chr1.1:28536703-28536722 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 28536609 28537040 28536609 ID=MS.gene073917
chr1.1 mRNA 28536609 28537040 28536609 ID=MS.gene073917.t1;Parent=MS.gene073917
chr1.1 exon 28536609 28537040 28536609 ID=MS.gene073917.t1.exon1;Parent=MS.gene073917.t1
chr1.1 CDS 28536609 28537040 28536609 ID=cds.MS.gene073917.t1;Parent=MS.gene073917.t1
Gene Sequence

>MS.gene073917

ATGGCAATTGCCACCAGATCTGAACCTCCTTTTCCAGATGTATCCGACAACAACAACAACAACCAAATTCAACCATTTTCTTCAACTTCAACCGCCGTCACCGCGGTTGCAAATCCTCCGAAACGATCCACGAAGGACAGGCACACAAAAGTTGACGGCCGTGGCCGGAGAATTCGAATGCCAGCGACATGCGCATCAAGAGTTTTCCAGTTGACCAGAGAATTAGGCCACAAATCCGATGGTGAAACAATTAAATGGCTTCTTCAACAAGCGAAGCCGGCGATTTCTCAATGCTCAACGTCTCACTCCGTAGCAGCGGCTCTACACTCTCTGCGCCGTCGTCGAAATCAACTCCTCTCAGTTTTCATAGCGCGCTTGCACTGGCTCATCATCTTTACGAAGAAGCTGCGTACCAACACGCGCCTTTGTTAG
Protein sequence

>MS.gene073917.t1

MAIATRSEPPFPDVSDNNNNNQIQPFSSTSTAVTAVANPPKRSTKDRHTKVDGRGRRIRMPATCASRVFQLTRELGHKSDGETIKWLLQQAKPAISQCSTSHSVAAALHSLRRRRNQLLSVFIARLHWLIIFTKKLRTNTRLC