AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene03515

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene03515.t1 MTR_1g101810 66.667 117 38 1 2 117 43 159 2.23e-48 157
MS.gene03515.t1 MTR_1g101810 66.667 117 38 1 2 117 73 189 4.85e-48 157
MS.gene03515.t1 MTR_8g033070 67.391 92 29 1 22 113 80 170 6.82e-38 130
MS.gene03515.t1 MTR_7g028160 57.143 91 39 0 10 100 38 128 1.59e-31 112
MS.gene03515.t1 MTR_1g038650 63.014 73 27 0 12 84 22 94 1.08e-28 104
MS.gene03515.t1 MTR_1g114380 62.338 77 28 1 9 84 19 95 1.69e-27 102
MS.gene03515.t1 MTR_2g006150 58.242 91 38 0 19 109 127 217 1.98e-27 105
MS.gene03515.t1 MTR_2g006150 58.242 91 38 0 19 109 127 217 3.06e-27 103
MS.gene03515.t1 MTR_1g063870 69.841 63 19 0 22 84 49 111 1.22e-26 98.2
MS.gene03515.t1 MTR_5g039600 53.191 94 44 0 10 103 55 148 2.30e-26 101
MS.gene03515.t1 MTR_4g108370 65.000 80 22 1 11 84 80 159 1.08e-25 99.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene03515.t1 AT5G51910 65.000 100 34 1 1 99 35 134 2.78e-38 130
MS.gene03515.t1 AT5G51910 65.000 100 34 1 1 99 35 134 2.78e-38 130
MS.gene03515.t1 AT2G45680 67.010 97 31 1 22 117 75 171 6.45e-38 131
MS.gene03515.t1 AT1G69690 74.603 63 16 0 22 84 52 114 3.73e-29 107
MS.gene03515.t1 AT1G58100 71.212 66 19 0 19 84 57 122 1.44e-28 107
MS.gene03515.t1 AT1G35560 72.727 66 18 0 19 84 52 117 1.61e-28 106
MS.gene03515.t1 AT3G27010 63.750 80 23 1 4 83 66 139 2.03e-28 105
MS.gene03515.t1 AT3G27010 63.750 80 23 1 4 83 66 139 2.03e-28 105
MS.gene03515.t1 AT3G47620 59.091 88 31 1 2 84 92 179 2.45e-28 107
MS.gene03515.t1 AT5G23280 61.842 76 29 0 9 84 26 101 2.75e-28 103
MS.gene03515.t1 AT1G72010 73.913 69 18 0 16 84 57 125 8.20e-28 104
MS.gene03515.t1 AT5G08330 65.217 69 24 0 16 84 25 93 2.93e-27 100
MS.gene03515.t1 AT5G41030 62.319 69 26 0 19 87 65 133 2.44e-25 95.9
MS.gene03515.t1 AT2G37000 71.186 59 17 0 22 80 43 101 1.50e-24 92.4
MS.gene03515.t1 AT3G45150 52.542 59 28 0 23 81 18 76 6.30e-18 75.1

Find 41 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCGGTGGCTTTGATGATTGC+AGG 0.311422 6.2:+37993774 None:intergenic
AGAAACAATTGGGTGGTTAC+TGG 0.359195 6.2:-37993808 MS.gene03515:CDS
GGCTATGGCCGGAATTATTC+CGG 0.369975 6.2:+37993749 None:intergenic
CAACTTTCCGCCCTCTGAAA+TGG 0.397867 6.2:+37993728 None:intergenic
CACCGGCACCGGAATAATTC+CGG 0.398178 6.2:-37993757 MS.gene03515:CDS
GACCAAGATCTCTCGTCAAC+TGG 0.398427 6.2:+37993844 None:intergenic
TTCCAGTTGACGAGAGATCT+TGG 0.406107 6.2:-37993846 MS.gene03515:CDS
GGTCTAGCTGCCGATGTTGT+TGG 0.412258 6.2:+37993699 None:intergenic
CTGTCCTTTGTGGTTCCAGC+GGG 0.431388 6.2:+37993964 None:intergenic
AAGTCTGATGGAGAAACAAT+TGG 0.436411 6.2:-37993819 MS.gene03515:CDS
TCGGCCGACACTGTCCTTTG+TGG 0.438494 6.2:+37993954 None:intergenic
TTCAGAGGGCGGAAAGTTGA+AGG 0.466569 6.2:-37993724 MS.gene03515:CDS
TTGCTGACAGTGTGACTCTT+CGG 0.478708 6.2:+37993886 None:intergenic
ATCCACAAATTAACCAATTG+AGG 0.488844 6.2:+37993638 None:intergenic
TTCGTGTGACGGTCTTCTGA+TGG 0.489473 6.2:+37993924 None:intergenic
ATCATCAAAGCCACCGGCAC+CGG 0.497106 6.2:-37993768 MS.gene03515:CDS
CCCTCTGAAATGGCTATGGC+CGG 0.502325 6.2:+37993738 None:intergenic
TGTCAGCAACATGTGCATCT+AGG 0.504146 6.2:-37993872 MS.gene03515:CDS
AAAAGCAAGAGAGCCTCAAT+TGG 0.505951 6.2:-37993651 MS.gene03515:CDS
GGCCGGAATTATTCCGGTGC+CGG 0.511782 6.2:+37993755 None:intergenic
AGCTAGACCAGACGACCAAA+AGG 0.513397 6.2:-37993685 MS.gene03515:CDS
TCCGCCCTCTGAAATGGCTA+TGG 0.528278 6.2:+37993734 None:intergenic
CGGAATTATTCCGGTGCCGG+TGG 0.529649 6.2:+37993758 None:intergenic
AAAACAGACGTTGAACCCGC+TGG 0.542316 6.2:-37993979 MS.gene03515:CDS
GTCCCTCCACCTTCGTGTGA+CGG 0.543321 6.2:+37993913 None:intergenic
AGTCTGATGGAGAAACAATT+GGG 0.550554 6.2:-37993818 MS.gene03515:CDS
GATCTTGGTCACAAGTCTGA+TGG 0.556205 6.2:-37993831 MS.gene03515:CDS
AGACCGTCACACGAAGGTGG+AGG 0.561466 6.2:-37993916 MS.gene03515:CDS
GACCGTCACACGAAGGTGGA+GGG 0.603506 6.2:-37993915 MS.gene03515:CDS
CAGACGACCAAAAGGCCCCA+AGG 0.608467 6.2:-37993677 MS.gene03515:CDS
TCCGGCCATAGCCATTTCAG+AGG 0.619818 6.2:-37993739 MS.gene03515:CDS
GCCATAGCCATTTCAGAGGG+CGG 0.621097 6.2:-37993735 MS.gene03515:CDS
AGAAGACCGTCACACGAAGG+TGG 0.622175 6.2:-37993919 MS.gene03515:CDS
ACTGTCCTTTGTGGTTCCAG+CGG 0.626132 6.2:+37993963 None:intergenic
CCTGCAATCATCAAAGCCAC+CGG 0.628378 6.2:-37993774 MS.gene03515:CDS
CCGGCCATAGCCATTTCAGA+GGG 0.636688 6.2:-37993738 MS.gene03515:CDS
GTTGAAGGTTCCAACAACAT+CGG 0.665250 6.2:-37993709 MS.gene03515:CDS
GGAACCACAAAGGACAGTGT+CGG 0.666432 6.2:-37993958 MS.gene03515:CDS
ATCAGAAGACCGTCACACGA+AGG 0.685962 6.2:-37993922 MS.gene03515:CDS
TGAACCCGCTGGAACCACAA+AGG 0.689031 6.2:-37993968 MS.gene03515:CDS
CTGATGGAGAAACAATTGGG+TGG 0.698165 6.2:-37993815 MS.gene03515:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGTCTGATGGAGAAACAAT+TGG - chr6.2:37993812-37993831 MS.gene03515:CDS 35.0%
AGTCTGATGGAGAAACAATT+GGG - chr6.2:37993813-37993832 MS.gene03515:CDS 35.0%
! GTCTTCTGATGGTTTCTTTT+CGG + chr6.2:37993699-37993718 None:intergenic 35.0%
AAAAGCAAGAGAGCCTCAAT+TGG - chr6.2:37993980-37993999 MS.gene03515:CDS 40.0%
AGAAACAATTGGGTGGTTAC+TGG - chr6.2:37993823-37993842 MS.gene03515:CDS 40.0%
GTTGAAGGTTCCAACAACAT+CGG - chr6.2:37993922-37993941 MS.gene03515:CDS 40.0%
!! CTCTCTTGCTTTTCTTCCTT+GGG + chr6.2:37993973-37993992 None:intergenic 40.0%
!! TCTCTTGCTTTTCTTCCTTG+GGG + chr6.2:37993972-37993991 None:intergenic 40.0%
CTGATGGAGAAACAATTGGG+TGG - chr6.2:37993816-37993835 MS.gene03515:CDS 45.0%
GATCTTGGTCACAAGTCTGA+TGG - chr6.2:37993800-37993819 MS.gene03515:CDS 45.0%
TGTCAGCAACATGTGCATCT+AGG - chr6.2:37993759-37993778 MS.gene03515:CDS 45.0%
TTCCAGTTGACGAGAGATCT+TGG - chr6.2:37993785-37993804 MS.gene03515:CDS 45.0%
TTGCTGACAGTGTGACTCTT+CGG + chr6.2:37993748-37993767 None:intergenic 45.0%
! TTTTCTTCCTTGGGGCCTTT+TGG + chr6.2:37993964-37993983 None:intergenic 45.0%
!! GCTCTCTTGCTTTTCTTCCT+TGG + chr6.2:37993974-37993993 None:intergenic 45.0%
AAAACAGACGTTGAACCCGC+TGG - chr6.2:37993652-37993671 MS.gene03515:CDS 50.0%
ACTGTCCTTTGTGGTTCCAG+CGG + chr6.2:37993671-37993690 None:intergenic 50.0%
AGCTAGACCAGACGACCAAA+AGG - chr6.2:37993946-37993965 MS.gene03515:CDS 50.0%
ATCAGAAGACCGTCACACGA+AGG - chr6.2:37993709-37993728 MS.gene03515:CDS 50.0%
CCTGCAATCATCAAAGCCAC+CGG - chr6.2:37993857-37993876 MS.gene03515:CDS 50.0%
GACCAAGATCTCTCGTCAAC+TGG + chr6.2:37993790-37993809 None:intergenic 50.0%
GGAACCACAAAGGACAGTGT+CGG - chr6.2:37993673-37993692 MS.gene03515:CDS 50.0%
GGCTATGGCCGGAATTATTC+CGG + chr6.2:37993885-37993904 None:intergenic 50.0%
TTCAGAGGGCGGAAAGTTGA+AGG - chr6.2:37993907-37993926 MS.gene03515:CDS 50.0%
TTCGTGTGACGGTCTTCTGA+TGG + chr6.2:37993710-37993729 None:intergenic 50.0%
! CAACTTTCCGCCCTCTGAAA+TGG + chr6.2:37993906-37993925 None:intergenic 50.0%
AGAAGACCGTCACACGAAGG+TGG - chr6.2:37993712-37993731 MS.gene03515:CDS 55.0%
ATCATCAAAGCCACCGGCAC+CGG - chr6.2:37993863-37993882 MS.gene03515:CDS 55.0%
CCGGCCATAGCCATTTCAGA+GGG - chr6.2:37993893-37993912 MS.gene03515:CDS 55.0%
CTGTCCTTTGTGGTTCCAGC+GGG + chr6.2:37993670-37993689 None:intergenic 55.0%
GCCATAGCCATTTCAGAGGG+CGG - chr6.2:37993896-37993915 MS.gene03515:CDS 55.0%
GGTCTAGCTGCCGATGTTGT+TGG + chr6.2:37993935-37993954 None:intergenic 55.0%
TCCGGCCATAGCCATTTCAG+AGG - chr6.2:37993892-37993911 MS.gene03515:CDS 55.0%
TGAACCCGCTGGAACCACAA+AGG - chr6.2:37993663-37993682 MS.gene03515:CDS 55.0%
! CACCGGCACCGGAATAATTC+CGG - chr6.2:37993874-37993893 MS.gene03515:CDS 55.0%
!! CCCTCTGAAATGGCTATGGC+CGG + chr6.2:37993896-37993915 None:intergenic 55.0%
!! CCGGTGGCTTTGATGATTGC+AGG + chr6.2:37993860-37993879 None:intergenic 55.0%
!! TCCGCCCTCTGAAATGGCTA+TGG + chr6.2:37993900-37993919 None:intergenic 55.0%
AGACCGTCACACGAAGGTGG+AGG - chr6.2:37993715-37993734 MS.gene03515:CDS 60.0%
CAGACGACCAAAAGGCCCCA+AGG - chr6.2:37993954-37993973 MS.gene03515:CDS 60.0%
GACCGTCACACGAAGGTGGA+GGG - chr6.2:37993716-37993735 MS.gene03515:CDS 60.0%
GGCCGGAATTATTCCGGTGC+CGG + chr6.2:37993879-37993898 None:intergenic 60.0%
GTCCCTCCACCTTCGTGTGA+CGG + chr6.2:37993721-37993740 None:intergenic 60.0%
TCGGCCGACACTGTCCTTTG+TGG + chr6.2:37993680-37993699 None:intergenic 60.0%
! CGGAATTATTCCGGTGCCGG+TGG + chr6.2:37993876-37993895 None:intergenic 60.0%
! CTTGGGGCCTTTTGGTCGTC+TGG + chr6.2:37993956-37993975 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 37993647 37994006 37993647 ID=MS.gene03515
chr6.2 mRNA 37993647 37994006 37993647 ID=MS.gene03515.t1;Parent=MS.gene03515
chr6.2 exon 37993647 37994006 37993647 ID=MS.gene03515.t1.exon1;Parent=MS.gene03515.t1
chr6.2 CDS 37993647 37994006 37993647 ID=cds.MS.gene03515.t1;Parent=MS.gene03515.t1
Gene Sequence

>MS.gene03515

ATGGAAAAACAGACGTTGAACCCGCTGGAACCACAAAGGACAGTGTCGGCCGAAAAGAAACCATCAGAAGACCGTCACACGAAGGTGGAGGGACGTGTCCGAAGAGTCACACTGTCAGCAACATGTGCATCTAGGATCTTCCAGTTGACGAGAGATCTTGGTCACAAGTCTGATGGAGAAACAATTGGGTGGTTACTGGAACAAGCTGAACCTGCAATCATCAAAGCCACCGGCACCGGAATAATTCCGGCCATAGCCATTTCAGAGGGCGGAAAGTTGAAGGTTCCAACAACATCGGCAGCTAGACCAGACGACCAAAAGGCCCCAAGGAAGAAAAGCAAGAGAGCCTCAATTGGTTAA
Protein sequence

>MS.gene03515.t1

MEKQTLNPLEPQRTVSAEKKPSEDRHTKVEGRVRRVTLSATCASRIFQLTRDLGHKSDGETIGWLLEQAEPAIIKATGTGIIPAIAISEGGKLKVPTTSAARPDDQKAPRKKSKRASIG