AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene028410

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene028410.t1 MTR_7g100280 100.000 105 0 0 1 105 1 105 1.57e-71 208
MS.gene028410.t1 MTR_4g094308 100.000 105 0 0 1 105 1 105 1.57e-71 208
MS.gene028410.t1 MTR_2g008180 100.000 105 0 0 1 105 1 105 1.57e-71 208
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene028410.t1 AT4G14320 92.381 105 8 0 1 105 1 105 1.00e-66 196
MS.gene028410.t1 AT3G23390 92.381 105 8 0 1 105 1 105 1.00e-66 196
MS.gene028410.t1 AT4G14320 91.398 93 8 0 1 93 1 93 3.30e-57 174

Find 20 sgRNAs with CRISPR-Local

Find 45 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACAAACACGCTTACCTTAA+TGG 0.191393 4.2:+18670292 None:intergenic
CAAAGTTACCCAATACAAAA+AGG 0.271604 4.2:-18670573 MS.gene028410:CDS
CAAACCCGTCTTTCACAAAA+AGG 0.369511 4.2:-18670480 MS.gene028410:intron
TGTTTCACAACACGCCATTA+AGG 0.378293 4.2:-18670306 MS.gene028410:intron
TAAAGATTCCATCGCTGCTC+AGG 0.399194 4.2:-18670549 MS.gene028410:CDS
CGTTATGACCGCAAACAATC+TGG 0.415551 4.2:-18670518 MS.gene028410:CDS
GTATTGGGTAACTTTGTGTA+AGG 0.453756 4.2:+18670580 None:intergenic
CACCATAACCAGATTGTTTG+CGG 0.454458 4.2:+18670510 None:intergenic
GACCGCAAACAATCTGGTTA+TGG 0.454865 4.2:-18670512 MS.gene028410:CDS
AGGTGCAAGCACTTTGAGAT+TGG 0.462716 4.2:-18670191 MS.gene028410:CDS
TGAGATTGGTGGTGACAAGA+AGG 0.508837 4.2:-18670177 MS.gene028410:CDS
CGCAAACAATCTGGTTATGG+TGG 0.541862 4.2:-18670509 MS.gene028410:CDS
TGCAAGCACTTTGAGATTGG+TGG 0.545430 4.2:-18670188 MS.gene028410:CDS
GAGATTGGTGGTGACAAGAA+GGG 0.555011 4.2:-18670176 MS.gene028410:CDS
TGGTGGTGACAAGAAGGGAA+AGG 0.556835 4.2:-18670171 MS.gene028410:CDS
GGTGGTGACAAGAAGGGAAA+GGG 0.585073 4.2:-18670170 MS.gene028410:CDS
CTACTAAGAAAATTGTGTTG+AGG 0.599248 4.2:-18670352 MS.gene028410:CDS
AAAGATTCCATCGCTGCTCA+GGG 0.607025 4.2:-18670548 MS.gene028410:CDS
GAAAACCTACTGCAAAAGCA+AGG 0.613372 4.2:-18670618 MS.gene028410:CDS
GTGTTGAGGCTTCAGTGTCA+AGG 0.618711 4.2:-18670338 MS.gene028410:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATTCAATTTTTGTTGTTAT+AGG - chr4.2:18670247-18670266 MS.gene028410:intron 15.0%
!!! ATAAATGAAATTGTTGATAA+TGG + chr4.2:18670205-18670224 None:intergenic 15.0%
!!! TTTGTTTTTATTGTTGAATT+AGG - chr4.2:18670526-18670545 MS.gene028410:CDS 15.0%
!! ATCAAATTAAGAAAAACAGA+AGG + chr4.2:18670480-18670499 None:intergenic 20.0%
! AAAGTTACCCAATACAAAAA+GGG - chr4.2:18670335-18670354 MS.gene028410:CDS 25.0%
!! AATCTTTACCCTTTTTGTAT+TGG + chr4.2:18670346-18670365 None:intergenic 25.0%
!! ATCTTTACCCTTTTTGTATT+GGG + chr4.2:18670345-18670364 None:intergenic 25.0%
!!! GTGTAATTTGTTCTGTTTTT+GGG - chr4.2:18670654-18670673 MS.gene028410:intron 25.0%
!!! TGTGTAATTTGTTCTGTTTT+TGG - chr4.2:18670653-18670672 MS.gene028410:intron 25.0%
AAACAGAAGGTAAAGACTTA+AGG + chr4.2:18670467-18670486 None:intergenic 30.0%
CAAAGTTACCCAATACAAAA+AGG - chr4.2:18670334-18670353 MS.gene028410:CDS 30.0%
CTACTAAGAAAATTGTGTTG+AGG - chr4.2:18670555-18670574 MS.gene028410:CDS 30.0%
! TTGTACCTTTTTGTGAAAGA+CGG + chr4.2:18670435-18670454 None:intergenic 30.0%
!!! TTTTTTGTTTGTGTTTGCAG+AGG - chr4.2:18670696-18670715 MS.gene028410:intron 30.0%
AACAAACACGCTTACCTTAA+TGG + chr4.2:18670618-18670637 None:intergenic 35.0%
GTATTGGGTAACTTTGTGTA+AGG + chr4.2:18670330-18670349 None:intergenic 35.0%
! CAGTAGGTTTTCTTTGTCTT+TGG + chr4.2:18670281-18670300 None:intergenic 35.0%
! TGTACCTTTTTGTGAAAGAC+GGG + chr4.2:18670434-18670453 None:intergenic 35.0%
!! GATAATGGATGAAAGTGTTG+TGG + chr4.2:18670190-18670209 None:intergenic 35.0%
CAAACCCGTCTTTCACAAAA+AGG - chr4.2:18670427-18670446 MS.gene028410:intron 40.0%
CACCATAACCAGATTGTTTG+CGG + chr4.2:18670400-18670419 None:intergenic 40.0%
GAAAACCTACTGCAAAAGCA+AGG - chr4.2:18670289-18670308 MS.gene028410:intron 40.0%
TGTTGTGGAAGGTTAGATGA+GGG + chr4.2:18670175-18670194 None:intergenic 40.0%
TGTTTCACAACACGCCATTA+AGG - chr4.2:18670601-18670620 MS.gene028410:CDS 40.0%
!! ATGGATGAAAGTGTTGTGGA+AGG + chr4.2:18670186-18670205 None:intergenic 40.0%
!! CTTTTTGTGAAAGACGGGTT+TGG + chr4.2:18670429-18670448 None:intergenic 40.0%
!!! GTTCTGTTTTTGGGTTCTGT+GGG - chr4.2:18670663-18670682 MS.gene028410:intron 40.0%
!!! TGTTCTGTTTTTGGGTTCTG+TGG - chr4.2:18670662-18670681 MS.gene028410:intron 40.0%
!!! TTTTGGGTTCTGTGGGTAAT+GGG - chr4.2:18670670-18670689 MS.gene028410:intron 40.0%
!!! TTTTTGGGTTCTGTGGGTAA+TGG - chr4.2:18670669-18670688 MS.gene028410:intron 40.0%
AAAGATTCCATCGCTGCTCA+GGG - chr4.2:18670359-18670378 MS.gene028410:CDS 45.0%
CGCAAACAATCTGGTTATGG+TGG - chr4.2:18670398-18670417 MS.gene028410:intron 45.0%
CGTTATGACCGCAAACAATC+TGG - chr4.2:18670389-18670408 MS.gene028410:intron 45.0%
GACCGCAAACAATCTGGTTA+TGG - chr4.2:18670395-18670414 MS.gene028410:intron 45.0%
GTGTTGTGGAAGGTTAGATG+AGG + chr4.2:18670176-18670195 None:intergenic 45.0%
TAAAGATTCCATCGCTGCTC+AGG - chr4.2:18670358-18670377 MS.gene028410:CDS 45.0%
!! AGGTGCAAGCACTTTGAGAT+TGG - chr4.2:18670716-18670735 MS.gene028410:intron 45.0%
!! GAGATTGGTGGTGACAAGAA+GGG - chr4.2:18670731-18670750 MS.gene028410:intron 45.0%
!! TGAGATTGGTGGTGACAAGA+AGG - chr4.2:18670730-18670749 MS.gene028410:intron 45.0%
!! TGCAAGCACTTTGAGATTGG+TGG - chr4.2:18670719-18670738 MS.gene028410:intron 45.0%
GGTGGTGACAAGAAGGGAAA+GGG - chr4.2:18670737-18670756 MS.gene028410:intron 50.0%
GTGTTGAGGCTTCAGTGTCA+AGG - chr4.2:18670569-18670588 MS.gene028410:CDS 50.0%
! TGGTGGTGACAAGAAGGGAA+AGG - chr4.2:18670736-18670755 MS.gene028410:intron 50.0%
!! GCACTCCTTGCTTTTGCAGT+AGG + chr4.2:18670297-18670316 None:intergenic 50.0%
! ACGTTTTCCCTGAGCAGCGA+TGG + chr4.2:18670369-18670388 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 18670154 18670775 18670154 ID=MS.gene028410
chr4.2 mRNA 18670154 18670775 18670154 ID=MS.gene028410.t1;Parent=MS.gene028410
chr4.2 exon 18670773 18670775 18670773 ID=MS.gene028410.t1.exon1;Parent=MS.gene028410.t1
chr4.2 CDS 18670773 18670775 18670773 ID=cds.MS.gene028410.t1;Parent=MS.gene028410.t1
chr4.2 exon 18670481 18670660 18670481 ID=MS.gene028410.t1.exon2;Parent=MS.gene028410.t1
chr4.2 CDS 18670481 18670660 18670481 ID=cds.MS.gene028410.t1;Parent=MS.gene028410.t1
chr4.2 exon 18670307 18670381 18670307 ID=MS.gene028410.t1.exon3;Parent=MS.gene028410.t1
chr4.2 CDS 18670307 18670381 18670307 ID=cds.MS.gene028410.t1;Parent=MS.gene028410.t1
chr4.2 exon 18670154 18670213 18670154 ID=MS.gene028410.t1.exon4;Parent=MS.gene028410.t1
chr4.2 CDS 18670154 18670213 18670154 ID=cds.MS.gene028410.t1;Parent=MS.gene028410.t1
Gene Sequence

>MS.gene028410

ATGGTAAACTACTCATTTCCCTCATCTAACCTTCCACAACACTTTCATCCATTATCAACAATTTCATTTATAGATCTCACTTTATGTCAAATTAATTCAATTTTTGTTGTTATAGGTGAACGTTCCAAAGACAAAGAAAACCTACTGCAAAAGCAAGGAGTGCAAGAAGCACACCTTACACAAAGTTACCCAATACAAAAAGGGTAAAGATTCCATCGCTGCTCAGGGAAAACGTCGTTATGACCGCAAACAATCTGGTTATGGTGGACAGACCAAACCCGTCTTTCACAAAAAGGTACAATTGCTGTTACCTTAAGTCTTTACCTTCTGTTTTTCTTAATTTGATTAGTAATTAAGATGTTAATTAAGTTATTTGTTTTTATTGTTGAATTAGGCAAAAACTACTAAGAAAATTGTGTTGAGGCTTCAGTGTCAAGGTTGCAAGCATGTTTCACAACACGCCATTAAGGTAAGCGTGTTTGTTTATGTTGTTTTTTGATGTGTAATTTGTTCTGTTTTTGGGTTCTGTGGGTAATGGGATGTTTTTTGTTTGTGTTTGCAGAGGTGCAAGCACTTTGAGATTGGTGGTGACAAGAAGGGAAAGGGAACATCTCTGTTTTAG
Protein sequence

>MS.gene028410.t1

MVNVPKTKKTYCKSKECKKHTLHKVTQYKKGKDSIAAQGKRRYDRKQSGYGGQTKPVFHKKAKTTKKIVLRLQCQGCKHVSQHAIKRCKHFEIGGDKKGKGTSLF