AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene060853

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060853.t1 MTR_1g098220 100.000 116 0 0 1 116 2 117 5.54e-83 238
MS.gene060853.t1 MTR_1g098170 100.000 116 0 0 1 116 2 117 5.91e-83 239
MS.gene060853.t1 MTR_1g098220 100.000 116 0 0 1 116 2 117 5.91e-83 239
MS.gene060853.t1 MTR_6g043210 98.276 116 2 0 1 116 2 117 4.65e-82 237
MS.gene060853.t1 MTR_1g492710 97.414 116 3 0 1 116 795 910 1.20e-73 236
MS.gene060853.t1 MTR_5g027650 94.937 79 4 0 38 116 11 89 6.43e-50 154
MS.gene060853.t1 MTR_5g027580 93.671 79 5 0 38 116 48 126 2.24e-49 154
MS.gene060853.t1 MTR_5g027670 95.455 66 3 0 51 116 1 66 4.18e-41 131
MS.gene060853.t1 MTR_5g027615 95.455 66 3 0 51 116 1 66 1.96e-40 129
MS.gene060853.t1 MTR_5g027605 95.455 66 3 0 51 116 1 66 1.96e-40 129
MS.gene060853.t1 MTR_5g027640 95.455 66 3 0 51 116 1 66 1.96e-40 129
MS.gene060853.t1 MTR_5g027600 95.455 66 3 0 51 116 1 66 1.96e-40 129
MS.gene060853.t1 MTR_1005s0010 95.238 63 3 0 54 116 2 64 5.51e-39 125
MS.gene060853.t1 MTR_4g015960 91.837 49 4 0 67 115 10 58 8.29e-26 100
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060853.t1 AT4G09800 90.517 116 11 0 1 116 2 117 1.93e-76 223
MS.gene060853.t1 AT1G34030 90.517 116 11 0 1 116 2 117 1.93e-76 223
MS.gene060853.t1 AT1G22780 90.517 116 11 0 1 116 2 117 1.93e-76 223

Find 23 sgRNAs with CRISPR-Local

Find 35 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAGCTTCATGTCAAGTTGAT+TGG 0.350481 1.1:-75241846 None:intergenic
CATGAAGCTGAGGGATGATT+TGG 0.353151 1.1:+75241859 MS.gene060853:CDS
TGATTGAGGTCATTGCGAAC+TGG 0.463060 1.1:-75241471 None:intergenic
GTTCGCAATGACCTCAATCA+AGG 0.484324 1.1:+75241474 MS.gene060853:CDS
ATGACCTCAATCAAGGGTAT+TGG 0.493197 1.1:+75241481 MS.gene060853:CDS
GTCAATTCAAGGTTCCAGAT+TGG 0.495981 1.1:+75241771 MS.gene060853:CDS
CGCTAACATCTGCTGTAAGA+AGG 0.503592 1.1:+75241513 MS.gene060853:CDS
TGCGAATCCTCGTCAATTCA+AGG 0.503849 1.1:+75241760 MS.gene060853:CDS
TGGAGAGACTCAAGAAGATC+CGG 0.515884 1.1:+75241879 MS.gene060853:CDS
GAACAGAAAGAAGGATTACA+AGG 0.525479 1.1:+75241799 MS.gene060853:CDS
AGAAAGAAGGATTACAAGGA+TGG 0.565673 1.1:+75241803 MS.gene060853:CDS
TGAATTGAGTGCCGCAGAGT+TGG 0.583506 1.1:+75241718 MS.gene060853:CDS
CCTACCAATACCCTTGATTG+AGG 0.590405 1.1:-75241485 None:intergenic
ATCAACTTGACATGAAGCTG+AGG 0.604543 1.1:+75241849 MS.gene060853:CDS
GTTGGATAATATTATGACAG+TGG 0.620536 1.1:+75241736 MS.gene060853:CDS
TTCGCAATGACCTCAATCAA+GGG 0.622158 1.1:+75241475 MS.gene060853:CDS
CCTCAATCAAGGGTATTGGT+AGG 0.631523 1.1:+75241485 MS.gene060853:CDS
GTGTTGAACACAAATGTCGA+TGG 0.634706 1.1:+75241436 MS.gene060853:CDS
TCAACTTGACATGAAGCTGA+GGG 0.637423 1.1:+75241850 MS.gene060853:CDS
CCTCTTGTTCATGTCAACAT+CGG 0.651019 1.1:-75241536 None:intergenic
CCGATGTTGACATGAACAAG+AGG 0.658386 1.1:+75241536 MS.gene060853:CDS
TCTGGAACCTTGAATTGACG+AGG 0.669518 1.1:-75241767 None:intergenic
CATAATATTATCCAACTCTG+CGG 0.698001 1.1:-75241729 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTTGTTGTTAAAATTAA+TGG + chr1.1:75241599-75241618 MS.gene060853:intron 10.0%
!!! TTTTTGTTGTTAAAATTAAT+GGG + chr1.1:75241600-75241619 MS.gene060853:intron 10.0%
!! TTTGATATTATTGTTGAAAT+GGG + chr1.1:75241663-75241682 MS.gene060853:intron 15.0%
!!! TTTTGATATTATTGTTGAAA+TGG + chr1.1:75241662-75241681 MS.gene060853:intron 15.0%
!!! AAATGACTGATTTATAAAAG+TGG - chr1.1:75241583-75241602 None:intergenic 20.0%
!!! AATGACTGATTTATAAAAGT+GGG - chr1.1:75241582-75241601 None:intergenic 20.0%
!!! TTTGTTGTTGGATTTTTTTA+GGG + chr1.1:75241691-75241710 MS.gene060853:intron 20.0%
!!! TTTTGTTGTTGGATTTTTTT+AGG + chr1.1:75241690-75241709 MS.gene060853:intron 20.0%
CATAATATTATCCAACTCTG+CGG - chr1.1:75241732-75241751 None:intergenic 30.0%
GTTGGATAATATTATGACAG+TGG + chr1.1:75241736-75241755 MS.gene060853:CDS 30.0%
TTTCTGTTCAAAAACCAATC+TGG - chr1.1:75241788-75241807 None:intergenic 30.0%
!! TTGGTTTTTGAACAGAAAGA+AGG + chr1.1:75241790-75241809 MS.gene060853:CDS 30.0%
!!! AAATGGGTTGTTTTTGTTGT+TGG + chr1.1:75241679-75241698 MS.gene060853:intron 30.0%
AGAAAGAAGGATTACAAGGA+TGG + chr1.1:75241803-75241822 MS.gene060853:CDS 35.0%
GAACAGAAAGAAGGATTACA+AGG + chr1.1:75241799-75241818 MS.gene060853:CDS 35.0%
!!! TTGTTGGATTTTTTTAGGGC+TGG + chr1.1:75241695-75241714 MS.gene060853:intron 35.0%
ATCAACTTGACATGAAGCTG+AGG + chr1.1:75241849-75241868 MS.gene060853:CDS 40.0%
CCTCTTGTTCATGTCAACAT+CGG - chr1.1:75241539-75241558 None:intergenic 40.0%
GTCAATTCAAGGTTCCAGAT+TGG + chr1.1:75241771-75241790 MS.gene060853:CDS 40.0%
GTGTTGAACACAAATGTCGA+TGG + chr1.1:75241436-75241455 MS.gene060853:CDS 40.0%
TCAACTTGACATGAAGCTGA+GGG + chr1.1:75241850-75241869 MS.gene060853:CDS 40.0%
TTCGCAATGACCTCAATCAA+GGG + chr1.1:75241475-75241494 MS.gene060853:CDS 40.0%
! ATGACCTCAATCAAGGGTAT+TGG + chr1.1:75241481-75241500 MS.gene060853:CDS 40.0%
!! CAGCTTCATGTCAAGTTGAT+TGG - chr1.1:75241849-75241868 None:intergenic 40.0%
CATGAAGCTGAGGGATGATT+TGG + chr1.1:75241859-75241878 MS.gene060853:CDS 45.0%
CCGATGTTGACATGAACAAG+AGG + chr1.1:75241536-75241555 MS.gene060853:CDS 45.0%
CCTACCAATACCCTTGATTG+AGG - chr1.1:75241488-75241507 None:intergenic 45.0%
CGCTAACATCTGCTGTAAGA+AGG + chr1.1:75241513-75241532 MS.gene060853:CDS 45.0%
GTTCGCAATGACCTCAATCA+AGG + chr1.1:75241474-75241493 MS.gene060853:CDS 45.0%
TCTTCGTTCGCAACCAAAGA+CGG - chr1.1:75241397-75241416 None:intergenic 45.0%
TGATTGAGGTCATTGCGAAC+TGG - chr1.1:75241474-75241493 None:intergenic 45.0%
TGCGAATCCTCGTCAATTCA+AGG + chr1.1:75241760-75241779 MS.gene060853:CDS 45.0%
! TCTGGAACCTTGAATTGACG+AGG - chr1.1:75241770-75241789 None:intergenic 45.0%
!! CCTCAATCAAGGGTATTGGT+AGG + chr1.1:75241485-75241504 MS.gene060853:CDS 45.0%
! TGAATTGAGTGCCGCAGAGT+TGG + chr1.1:75241718-75241737 MS.gene060853:CDS 50.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 75241397 75241900 75241397 ID=MS.gene060853
chr1.1 mRNA 75241397 75241900 75241397 ID=MS.gene060853.t1;Parent=MS.gene060853
chr1.1 exon 75241397 75241557 75241397 ID=MS.gene060853.t1.exon1;Parent=MS.gene060853.t1
chr1.1 CDS 75241397 75241557 75241397 ID=cds.MS.gene060853.t1;Parent=MS.gene060853.t1
chr1.1 exon 75241712 75241900 75241712 ID=MS.gene060853.t1.exon2;Parent=MS.gene060853.t1
chr1.1 CDS 75241712 75241900 75241712 ID=cds.MS.gene060853.t1;Parent=MS.gene060853.t1
Gene Sequence

>MS.gene060853

TCTTTGGTTGCGAACGAAGAATTTCAGCACATTTTGCGTGTGTTGAACACAAATGTCGATGGAAAGCAGAAGATCCAGTTCGCAATGACCTCAATCAAGGGTATTGGTAGGAGATTCGCTAACATCTGCTGTAAGAAGGCCGATGTTGACATGAACAAGAGGTTCGTTGTTCTGATTTTGCTCCCACTTTTATAAATCAGTCATTTTTGTTGTTAAAATTAATGGGTTTCTTGAGTTTAATTGATCTCACATTTAAAAATCAAATTTTTGATATTATTGTTGAAATGGGTTGTTTTTGTTGTTGGATTTTTTTAGGGCTGGTGAATTGAGTGCCGCAGAGTTGGATAATATTATGACAGTGGTTGCGAATCCTCGTCAATTCAAGGTTCCAGATTGGTTTTTGAACAGAAAGAAGGATTACAAGGATGGCAAATTCTCTCAAGTTGTATCCAATCAACTTGACATGAAGCTGAGGGATGATTTGGAGAGACTCAAGAAGATCCG
Protein sequence

>MS.gene060853.t1

SLVANEEFQHILRVLNTNVDGKQKIQFAMTSIKGIGRRFANICCKKADVDMNKRAGELSAAELDNIMTVVANPRQFKVPDWFLNRKKDYKDGKFSQVVSNQLDMKLRDDLERLKKI