AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene004838

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene004838.t1 MTR_1g075780 76.224 143 16 1 12 136 3 145 3.27e-75 220
MS.gene004838.t1 MTR_4g063510 31.977 172 63 4 17 136 13 182 1.48e-16 72.4
MS.gene004838.t1 MTR_1g075840 41.935 124 42 6 36 136 1 117 1.29e-14 65.9
MS.gene004838.t1 MTR_1g041455 31.646 158 70 7 14 136 13 167 2.29e-13 63.5
MS.gene004838.t1 MTR_5g056450 32.215 149 66 6 1 124 1 139 5.56e-12 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 25 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAATGACACATCAGTGAATT+TGG 0.236191 1.4:-62008934 MS.gene004838:CDS
TTATCCAACATGTTGATATA+TGG 0.260832 1.4:+62008990 None:intergenic
ATGGGAAAATTGGGTGGTAA+AGG 0.416030 1.4:+62009122 None:intergenic
TAAAGGGTTGGCCATTGATT+CGG 0.428827 1.4:+62009139 None:intergenic
TGGGAAAATTGGGTGGTAAA+GGG 0.468596 1.4:+62009123 None:intergenic
CAATCCTCAGGCCGAATCAA+TGG 0.469990 1.4:-62009150 MS.gene004838:CDS
CATTGATTCGGCCTGAGGAT+TGG 0.472364 1.4:+62009151 None:intergenic
CCACCAGTCCCTTGTTGTTG+TGG 0.476108 1.4:+62009044 None:intergenic
AAGCCACCTTGAGTCTCATA+TGG 0.484456 1.4:-62009210 MS.gene004838:CDS
CAAAATTATTGATATTGCTA+CGG 0.495293 1.4:+62009279 None:intergenic
ACAACAAGGGACTGGTGGTA+TGG 0.510630 1.4:-62009039 MS.gene004838:CDS
ATTCGGCCTGAGGATTGGTA+TGG 0.511741 1.4:+62009156 None:intergenic
TTGGCCATTGATTCGGCCTG+AGG 0.541375 1.4:+62009146 None:intergenic
CTTGAGCCATATGAGACTCA+AGG 0.558137 1.4:+62009204 None:intergenic
ATTAAACCATACCAATCCTC+AGG 0.560036 1.4:-62009162 MS.gene004838:CDS
ATGGAAGTCTCTCCGATCGA+TGG 0.567201 1.4:-62009020 MS.gene004838:CDS
TAAGCCATATATCAACATGT+TGG 0.587500 1.4:-62008994 MS.gene004838:CDS
TTTGGCATGGGAAAATTGGG+TGG 0.600647 1.4:+62009116 None:intergenic
AAAATTGGGTGGTAAAGGGT+TGG 0.611916 1.4:+62009127 None:intergenic
TTTCAGCAACCACAACAACA+AGG 0.614643 1.4:-62009053 MS.gene004838:CDS
CAACCACAACAACAAGGGAC+TGG 0.623235 1.4:-62009047 MS.gene004838:CDS
CCACAACAACAAGGGACTGG+TGG 0.623856 1.4:-62009044 MS.gene004838:CDS
TATGGCTTAGTTCCATCGAT+CGG 0.625287 1.4:+62009008 None:intergenic
TTCAGCAACCACAACAACAA+GGG 0.626204 1.4:-62009052 MS.gene004838:CDS
GAGCCATATGAGACTCAAGG+TGG 0.728487 1.4:+62009207 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATATCAATAATTTTGTATG+TGG - chr1.4:62008956-62008975 MS.gene004838:CDS 15.0%
!! CAAAATTATTGATATTGCTA+CGG + chr1.4:62008952-62008971 None:intergenic 20.0%
!!! TTGTTTTCATGTAATGATTT+TGG + chr1.4:62009133-62009152 None:intergenic 20.0%
! TTATCCAACATGTTGATATA+TGG + chr1.4:62009241-62009260 None:intergenic 25.0%
!!! AAATAACTTGCTTTTAACGA+AGG + chr1.4:62009158-62009177 None:intergenic 25.0%
TAAGCCATATATCAACATGT+TGG - chr1.4:62009234-62009253 MS.gene004838:CDS 30.0%
! AATGAAGACATTTTTCTCGA+TGG + chr1.4:62009266-62009285 None:intergenic 30.0%
! ATGAAGACATTTTTCTCGAT+GGG + chr1.4:62009265-62009284 None:intergenic 30.0%
!! TCATGTAATGATTTTGGCAT+GGG + chr1.4:62009127-62009146 None:intergenic 30.0%
!! TTCATGTAATGATTTTGGCA+TGG + chr1.4:62009128-62009147 None:intergenic 30.0%
ATTAAACCATACCAATCCTC+AGG - chr1.4:62009066-62009085 MS.gene004838:CDS 35.0%
CAATGACACATCAGTGAATT+TGG - chr1.4:62009294-62009313 MS.gene004838:CDS 35.0%
!! GATTTTGGCATGGGAAAATT+GGG + chr1.4:62009118-62009137 None:intergenic 35.0%
!! TGATTTTGGCATGGGAAAAT+TGG + chr1.4:62009119-62009138 None:intergenic 35.0%
AAAATTGGGTGGTAAAGGGT+TGG + chr1.4:62009104-62009123 None:intergenic 40.0%
ATGGGAAAATTGGGTGGTAA+AGG + chr1.4:62009109-62009128 None:intergenic 40.0%
TATGGCTTAGTTCCATCGAT+CGG + chr1.4:62009223-62009242 None:intergenic 40.0%
TGGGAAAATTGGGTGGTAAA+GGG + chr1.4:62009108-62009127 None:intergenic 40.0%
TTCAGCAACCACAACAACAA+GGG - chr1.4:62009176-62009195 MS.gene004838:CDS 40.0%
TTTCAGCAACCACAACAACA+AGG - chr1.4:62009175-62009194 MS.gene004838:CDS 40.0%
!! TAAAGGGTTGGCCATTGATT+CGG + chr1.4:62009092-62009111 None:intergenic 40.0%
AAGCCACCTTGAGTCTCATA+TGG - chr1.4:62009018-62009037 MS.gene004838:CDS 45.0%
CTTGAGCCATATGAGACTCA+AGG + chr1.4:62009027-62009046 None:intergenic 45.0%
TTTGGCATGGGAAAATTGGG+TGG + chr1.4:62009115-62009134 None:intergenic 45.0%
ATGGAAGTCTCTCCGATCGA+TGG - chr1.4:62009208-62009227 MS.gene004838:CDS 50.0%
CAACCACAACAACAAGGGAC+TGG - chr1.4:62009181-62009200 MS.gene004838:CDS 50.0%
CAATCCTCAGGCCGAATCAA+TGG - chr1.4:62009078-62009097 MS.gene004838:CDS 50.0%
GAGCCATATGAGACTCAAGG+TGG + chr1.4:62009024-62009043 None:intergenic 50.0%
! ACAACAAGGGACTGGTGGTA+TGG - chr1.4:62009189-62009208 MS.gene004838:CDS 50.0%
! ATTCGGCCTGAGGATTGGTA+TGG + chr1.4:62009075-62009094 None:intergenic 50.0%
!! CATTGATTCGGCCTGAGGAT+TGG + chr1.4:62009080-62009099 None:intergenic 50.0%
CCACAACAACAAGGGACTGG+TGG - chr1.4:62009184-62009203 MS.gene004838:CDS 55.0%
!! CCACCAGTCCCTTGTTGTTG+TGG + chr1.4:62009187-62009206 None:intergenic 55.0%
!! TTGGCCATTGATTCGGCCTG+AGG + chr1.4:62009085-62009104 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 62008920 62009330 62008920 ID=MS.gene004838
chr1.4 mRNA 62008920 62009330 62008920 ID=MS.gene004838.t1;Parent=MS.gene004838
chr1.4 exon 62008920 62009330 62008920 ID=MS.gene004838.t1.exon1;Parent=MS.gene004838.t1
chr1.4 CDS 62008920 62009330 62008920 ID=cds.MS.gene004838.t1;Parent=MS.gene004838.t1
Gene Sequence

>MS.gene004838

ATGGGTGACGATTTCGCTCAAGAGAACAACCGTAGCAATATCAATAATTTTGTATGTGGATTGTGCAATCATGATTGCACAAACTTCGAATCACTCATAAGCCACCTTGAGTCTCATATGGCTCAAGAAAATCTTGCTATTGCAAGATTAAACCATACCAATCCTCAGGCCGAATCAATGGCCAACCCTTTACCACCCAATTTTCCCATGCCAAAATCATTACATGAAAACAAAACCTTCGTTAAAAGCAAGTTATTTCAGCAACCACAACAACAAGGGACTGGTGGTATGGAAGTCTCTCCGATCGATGGAACTAAGCCATATATCAACATGTTGGATAAACCCATCGAGAAAAATGTCTTCATTAACATCATCAATGACACATCAGTGAATTTGGAGTTAAAGCTCTAG
Protein sequence

>MS.gene004838.t1

MGDDFAQENNRSNINNFVCGLCNHDCTNFESLISHLESHMAQENLAIARLNHTNPQAESMANPLPPNFPMPKSLHENKTFVKSKLFQQPQQQGTGGMEVSPIDGTKPYINMLDKPIEKNVFINIINDTSVNLELKL