AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene039071

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene039071.t1 MTR_2g068760 90.909 88 1 2 1 82 73 159 1.12e-50 156
MS.gene039071.t1 MTR_4g083680 59.036 83 23 2 1 78 75 151 1.10e-24 90.9
MS.gene039071.t1 MTR_4g060950 72.917 48 13 0 1 48 85 132 1.02e-18 75.9
MS.gene039071.t1 MTR_1g095850 72.917 48 13 0 1 48 132 179 5.93e-18 74.7
MS.gene039071.t1 MTR_2g093310 48.718 78 33 2 1 71 93 170 6.99e-18 73.9
MS.gene039071.t1 MTR_3g031660 66.667 51 17 0 1 51 67 117 4.78e-17 71.2
MS.gene039071.t1 MTR_5g083230 73.913 46 12 0 1 46 66 111 5.76e-17 70.9
MS.gene039071.t1 MTR_3g071590 71.739 46 13 0 1 46 68 113 1.49e-16 69.7
MS.gene039071.t1 MTR_3g094690 56.250 48 21 0 1 48 106 153 9.41e-14 63.9
MS.gene039071.t1 MTR_3g094690 56.250 48 21 0 1 48 107 154 9.82e-14 63.9
MS.gene039071.t1 MTR_3g077240 56.250 48 21 0 1 48 70 117 1.10e-12 60.5
MS.gene039071.t1 MTR_5g083960 50.820 61 27 1 1 61 99 156 2.72e-12 59.3
MS.gene039071.t1 MTR_6g005070 43.836 73 36 2 1 73 69 136 3.96e-12 58.2
MS.gene039071.t1 MTR_4g105170 54.000 50 23 0 1 50 71 120 4.16e-12 58.9
MS.gene039071.t1 MTR_7g096530 58.140 43 18 0 1 43 75 117 5.75e-11 56.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene039071.t1 AT1G16530 47.312 93 34 4 1 81 75 164 6.97e-20 78.6
MS.gene039071.t1 AT1G31320 85.417 48 7 0 1 48 73 120 2.71e-17 72.0
MS.gene039071.t1 AT2G30130 63.158 57 19 1 1 55 68 124 2.67e-16 69.7
MS.gene039071.t1 AT1G07900 64.583 48 17 0 1 48 93 140 2.17e-15 67.4
MS.gene039071.t1 AT2G28500 62.000 50 19 0 1 50 115 164 1.57e-14 65.9
MS.gene039071.t1 AT5G63090 60.870 46 18 0 1 46 71 116 5.09e-13 61.2
MS.gene039071.t1 AT5G63090 60.870 46 18 0 1 46 71 116 5.09e-13 61.2
MS.gene039071.t1 AT5G63090 60.870 46 18 0 1 46 71 116 5.09e-13 61.2
MS.gene039071.t1 AT5G63090 60.870 46 18 0 1 46 71 116 5.09e-13 61.2
MS.gene039071.t1 AT2G30340 45.098 51 28 0 1 51 112 162 4.88e-12 59.7
MS.gene039071.t1 AT2G30340 45.098 51 28 0 1 51 113 163 5.17e-12 59.3

Find 17 sgRNAs with CRISPR-Local

Find 19 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGCTTGTGCTTGAGCTAAT+TGG 0.150837 2.4:-26682051 None:intergenic
TTCTTCACCAAACAACAAAA+TGG 0.216907 2.4:+26682159 MS.gene039071:CDS
TGCTTGTGCTTGAGCTAATT+GGG 0.350545 2.4:-26682050 None:intergenic
AAGAAAAGAACCTGCTTGAT+TGG 0.406684 2.4:-26682141 None:intergenic
TCTTCACCAAACAACAAAAT+GGG 0.425696 2.4:+26682160 MS.gene039071:CDS
ATGAAGCAAATGCAAGAGTA+AGG 0.428990 2.4:+26681963 MS.gene039071:CDS
GATGATGATCAGATGAGAAT+TGG 0.476334 2.4:-26682096 None:intergenic
AGAGTAAGGGATCCTGTGTA+TGG 0.521523 2.4:+26681977 MS.gene039071:CDS
TGAAGCAAATGCAAGAGTAA+GGG 0.570272 2.4:+26681964 MS.gene039071:CDS
AAAATGTGTACCAATCAAGC+AGG 0.584103 2.4:+26682131 MS.gene039071:CDS
GGATCCTGTGTATGGATGTG+TGG 0.591101 2.4:+26681985 MS.gene039071:CDS
AGCTAGCTAGTAAGACCACA+AGG 0.627089 2.4:-26682188 None:intergenic
GATCCTGTGTATGGATGTGT+GGG 0.634230 2.4:+26681986 MS.gene039071:CDS
ATTAGCTCAAGCACAAGCAG+AGG 0.647477 2.4:+26682054 MS.gene039071:CDS
ATCTACTTGTTGCTGCAGAG+AGG 0.672706 2.4:-26682017 None:intergenic
GCTCCCACACATCCATACAC+AGG 0.680929 2.4:-26681989 None:intergenic
ACAAAATGGGACAATCCTTG+TGG 0.683389 2.4:+26682173 MS.gene039071:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
TCTTCACCAAACAACAAAAT+GGG + chr2.4:26682160-26682179 MS.gene039071:CDS 30.0%
TTCTTCACCAAACAACAAAA+TGG + chr2.4:26682159-26682178 MS.gene039071:CDS 30.0%
AAAATGTGTACCAATCAAGC+AGG + chr2.4:26682131-26682150 MS.gene039071:CDS 35.0%
AAGAAAAGAACCTGCTTGAT+TGG - chr2.4:26682144-26682163 None:intergenic 35.0%
ATGAAGCAAATGCAAGAGTA+AGG + chr2.4:26681963-26681982 MS.gene039071:CDS 35.0%
GATGATGATCAGATGAGAAT+TGG - chr2.4:26682099-26682118 None:intergenic 35.0%
TGAAGCAAATGCAAGAGTAA+GGG + chr2.4:26681964-26681983 MS.gene039071:CDS 35.0%
! GATTGGTACACATTTTCTGA+TGG - chr2.4:26682127-26682146 None:intergenic 35.0%
!!! GATTGTCCCATTTTGTTGTT+TGG - chr2.4:26682169-26682188 None:intergenic 35.0%
ACAAAATGGGACAATCCTTG+TGG + chr2.4:26682173-26682192 MS.gene039071:CDS 40.0%
TGCTTGTGCTTGAGCTAATT+GGG - chr2.4:26682053-26682072 None:intergenic 40.0%
! TGGTACACATTTTCTGATGG+TGG - chr2.4:26682124-26682143 None:intergenic 40.0%
AGAGTAAGGGATCCTGTGTA+TGG + chr2.4:26681977-26681996 MS.gene039071:CDS 45.0%
ATTAGCTCAAGCACAAGCAG+AGG + chr2.4:26682054-26682073 MS.gene039071:CDS 45.0%
CTGCTTGTGCTTGAGCTAAT+TGG - chr2.4:26682054-26682073 None:intergenic 45.0%
GATCCTGTGTATGGATGTGT+GGG + chr2.4:26681986-26682005 MS.gene039071:CDS 45.0%
! ATCTACTTGTTGCTGCAGAG+AGG - chr2.4:26682020-26682039 None:intergenic 45.0%
GGATCCTGTGTATGGATGTG+TGG + chr2.4:26681985-26682004 MS.gene039071:CDS 50.0%
GCTCCCACACATCCATACAC+AGG - chr2.4:26681992-26682011 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 26681956 26682204 26681956 ID=MS.gene039071
chr2.4 mRNA 26681956 26682204 26681956 ID=MS.gene039071.t1;Parent=MS.gene039071
chr2.4 exon 26681956 26682204 26681956 ID=MS.gene039071.t1.exon1;Parent=MS.gene039071.t1
chr2.4 CDS 26681956 26682204 26681956 ID=cds.MS.gene039071.t1;Parent=MS.gene039071.t1
Gene Sequence

>MS.gene039071

ATGGTATATGAAGCAAATGCAAGAGTAAGGGATCCTGTGTATGGATGTGTGGGAGCTATATCCTCTCTGCAGCAACAAGTAGATGTGCTACAAACCCAATTAGCTCAAGCACAAGCAGAGGTTGTGCATATGAAGATGCACCAATTCTCATCTGATCATCATCAACCACCATCAGAAAATGTGTACCAATCAAGCAGGTTCTTTTCTTCACCAAACAACAAAATGGGACAATCCTTGTGGTCTTACTAG
Protein sequence

>MS.gene039071.t1

MVYEANARVRDPVYGCVGAISSLQQQVDVLQTQLAQAQAEVVHMKMHQFSSDHHQPPSENVYQSSRFFSSPNNKMGQSLWSY