AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene051551


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene051551.t1 MTR_1g015290 96.800 125 4 0 1 125 1 125 2.02e-82 237
MS.gene051551.t1 MTR_3g104950 63.710 124 40 2 1 124 1 119 9.06e-47 147
MS.gene051551.t1 MTR_4g125600 58.730 126 40 6 1 124 1 116 1.20e-34 116
MS.gene051551.t1 MTR_2g041260 54.400 125 50 3 1 124 1 119 3.13e-22 85.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene051551.t1 AT2G06520 56.604 106 44 2 20 125 13 116 1.54e-27 98.6

Find 25 sgRNAs with CRISPR-Local

Find 31 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTAATTAAGTTCTCTTAAC+AGG 0.244780 1.3:+6960028 None:intergenic
TTGTGGGTTGCTTGGGTTAG+TGG 0.297198 1.3:+6960358 None:intergenic
TGTTGTTCTTACAGCTATAT+TGG 0.300493 1.3:-6960080 MS.gene051551:CDS
GTTGTTCTTACAGCTATATT+GGG 0.346937 1.3:-6960079 MS.gene051551:CDS
GTCTTCTTTGCTTGTGGAAA+GGG 0.350437 1.3:+6960292 None:intergenic
GCTATATTGGGTGCTGTTGT+TGG 0.379016 1.3:-6960067 MS.gene051551:CDS
ACTTCAAAATCCAACCTTGT+TGG 0.385727 1.3:-6960253 MS.gene051551:CDS
TTTGCTTGTGGAAAGGGTAA+TGG 0.395127 1.3:+6960298 None:intergenic
ACTAGTGTCTTCTTTGCTTG+TGG 0.430477 1.3:+6960286 None:intergenic
CCAGATGTTGCTCATGCAGC+TGG 0.445643 1.3:-6960157 MS.gene051551:CDS
TGTCTTCTTTGCTTGTGGAA+AGG 0.459779 1.3:+6960291 None:intergenic
TCTCTTAACAGGATCAAAGT+TGG 0.467747 1.3:+6960039 None:intergenic
TGCTTGAATTCCAACAAGGT+TGG 0.477724 1.3:+6960243 None:intergenic
TTCAAGAAGGGTGTGGTGGA+AGG 0.483812 1.3:+6960322 None:intergenic
ATTGAAAGACAAAACAATGA+AGG 0.486165 1.3:-6960218 MS.gene051551:CDS
CCAGCTGCATGAGCAACATC+TGG 0.490868 1.3:+6960157 None:intergenic
AAGGGTAATGGTTTCAAGAA+GGG 0.543271 1.3:+6960310 None:intergenic
TTGCTTAGCATTGCTGCTGG+TGG 0.565122 1.3:-6960103 MS.gene051551:CDS
TTGAAAGACAAAACAATGAA+GGG 0.567767 1.3:-6960217 MS.gene051551:CDS
TGGTTTCAAGAAGGGTGTGG+TGG 0.576256 1.3:+6960318 None:intergenic
AAAGGGTAATGGTTTCAAGA+AGG 0.589420 1.3:+6960309 None:intergenic
GTGTGGTGGAAGGATTGTGA+AGG 0.617280 1.3:+6960332 None:intergenic
TAATGGTTTCAAGAAGGGTG+TGG 0.623935 1.3:+6960315 None:intergenic
AACATCTGGTAACACCATAG+AGG 0.635135 1.3:+6960171 None:intergenic
ATGATGCTTGAATTCCAACA+AGG 0.644146 1.3:+6960239 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ATTGAAAGACAAAACAATGA+AGG - chr1.3:6960203-6960222 MS.gene051551:CDS 25.0%
! TTGAAAGACAAAACAATGAA+GGG - chr1.3:6960204-6960223 MS.gene051551:CDS 25.0%
!!! AGCAAAAAGTTTTTAAGAGA+TGG + chr1.3:6960303-6960322 None:intergenic 25.0%
GTTGTTCTTACAGCTATATT+GGG - chr1.3:6960342-6960361 MS.gene051551:CDS 30.0%
TGTTGTTCTTACAGCTATAT+TGG - chr1.3:6960341-6960360 MS.gene051551:CDS 30.0%
ACTTCAAAATCCAACCTTGT+TGG - chr1.3:6960168-6960187 MS.gene051551:CDS 35.0%
ATGATGCTTGAATTCCAACA+AGG + chr1.3:6960185-6960204 None:intergenic 35.0%
TCTCTTAACAGGATCAAAGT+TGG + chr1.3:6960385-6960404 None:intergenic 35.0%
! AAAGGGTAATGGTTTCAAGA+AGG + chr1.3:6960115-6960134 None:intergenic 35.0%
! AAGGATTGTGAAGGTTTTTG+TGG + chr1.3:6960083-6960102 None:intergenic 35.0%
! AAGGGTAATGGTTTCAAGAA+GGG + chr1.3:6960114-6960133 None:intergenic 35.0%
! AGGATTGTGAAGGTTTTTGT+GGG + chr1.3:6960082-6960101 None:intergenic 35.0%
! TTTTGCATTAACAGCCTCTA+TGG - chr1.3:6960236-6960255 MS.gene051551:CDS 35.0%
AACATCTGGTAACACCATAG+AGG + chr1.3:6960253-6960272 None:intergenic 40.0%
ACTAGTGTCTTCTTTGCTTG+TGG + chr1.3:6960138-6960157 None:intergenic 40.0%
GTCTTCTTTGCTTGTGGAAA+GGG + chr1.3:6960132-6960151 None:intergenic 40.0%
TAATGGTTTCAAGAAGGGTG+TGG + chr1.3:6960109-6960128 None:intergenic 40.0%
TGCTTGAATTCCAACAAGGT+TGG + chr1.3:6960181-6960200 None:intergenic 40.0%
TGTCTTCTTTGCTTGTGGAA+AGG + chr1.3:6960133-6960152 None:intergenic 40.0%
TTTGCTTGTGGAAAGGGTAA+TGG + chr1.3:6960126-6960145 None:intergenic 40.0%
! TTTTTGCTTAGCATTGCTGC+TGG - chr1.3:6960315-6960334 MS.gene051551:CDS 40.0%
!! AAGGTTTTTGTGGGTTGCTT+GGG + chr1.3:6960073-6960092 None:intergenic 40.0%
!! GAAGGTTTTTGTGGGTTGCT+TGG + chr1.3:6960074-6960093 None:intergenic 45.0%
!! GCTATATTGGGTGCTGTTGT+TGG - chr1.3:6960354-6960373 MS.gene051551:CDS 45.0%
TTGCTTAGCATTGCTGCTGG+TGG - chr1.3:6960318-6960337 MS.gene051551:CDS 50.0%
! GTGTGGTGGAAGGATTGTGA+AGG + chr1.3:6960092-6960111 None:intergenic 50.0%
! TGGTTTCAAGAAGGGTGTGG+TGG + chr1.3:6960106-6960125 None:intergenic 50.0%
! TTCAAGAAGGGTGTGGTGGA+AGG + chr1.3:6960102-6960121 None:intergenic 50.0%
! TTGTGGGTTGCTTGGGTTAG+TGG + chr1.3:6960066-6960085 None:intergenic 50.0%
CCAGATGTTGCTCATGCAGC+TGG - chr1.3:6960264-6960283 MS.gene051551:CDS 55.0%
CCAGCTGCATGAGCAACATC+TGG + chr1.3:6960267-6960286 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 6960033 6960410 6960033 ID=MS.gene051551
chr1.3 mRNA 6960033 6960410 6960033 ID=MS.gene051551.t1;Parent=MS.gene051551
chr1.3 exon 6960033 6960410 6960033 ID=MS.gene051551.t1.exon1;Parent=MS.gene051551.t1
chr1.3 CDS 6960033 6960410 6960033 ID=cds.MS.gene051551.t1;Parent=MS.gene051551.t1
Gene Sequence

>MS.gene051551

ATGGCTTCAGCTTCTGTTTCAATGTCTTTACCACTAACCCAAGCAACCCACAAAAACCTTCACAATCCTTCCACCACACCCTTCTTGAAACCATTACCCTTTCCACAAGCAAAGAAGACACTAGTCAACAAGTCAACTTCAAAATCCAACCTTGTTGGAATTCAAGCATCATTGAAAGACAAAACAATGAAGGGTCTAACTGCTTTTGCATTAACAGCCTCTATGGTGTTACCAGATGTTGCTCATGCAGCTGGAAATGATTTTTCACCATCTCTTAAAAACTTTTTGCTTAGCATTGCTGCTGGTGGTGTTGTTCTTACAGCTATATTGGGTGCTGTTGTTGGTGTTTCCAACTTTGATCCTGTTAAGAGAACTTAA

Protein sequence

>MS.gene051551.t1

MASASVSMSLPLTQATHKNLHNPSTTPFLKPLPFPQAKKTLVNKSTSKSNLVGIQASLKDKTMKGLTAFALTASMVLPDVAHAAGNDFSPSLKNFLLSIAAGGVVLTAILGAVVGVSNFDPVKRT