AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene44027

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene44027.t1 MTR_1g081580 48.630 146 32 2 1 103 1 146 6.46e-37 128
MS.gene44027.t1 MTR_7g114600 56.250 80 31 1 27 102 80 159 2.45e-22 89.7
MS.gene44027.t1 MTR_1g081570 51.948 77 9 1 19 95 15 63 1.70e-18 73.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene44027.t1 AT3G04930 47.253 91 39 4 21 102 98 188 7.88e-18 77.0
MS.gene44027.t1 AT3G04930 47.253 91 39 4 21 102 98 188 9.40e-18 77.0
MS.gene44027.t1 AT5G28040 47.312 93 38 5 21 103 85 176 8.73e-14 65.9
MS.gene44027.t1 AT5G28040 47.312 93 38 5 21 103 85 176 8.73e-14 65.9
MS.gene44027.t1 AT1G44810 50.000 56 28 0 47 102 115 170 2.33e-13 64.3
MS.gene44027.t1 AT1G61730 48.980 49 25 0 54 102 155 203 5.28e-11 57.8
MS.gene44027.t1 AT4G00390 49.020 51 26 0 53 103 156 206 7.43e-11 57.4

Find 18 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTTCCATTTGCTCCCATTT+TGG 0.158841 1.3:+57569391 None:intergenic
ACGACTCCCTTGAACCAAAA+TGG 0.287269 1.3:-57569405 MS.gene44027:CDS
TCTTCTTATCATAATGATAC+TGG 0.348077 1.3:-57569268 MS.gene44027:CDS
GTCAGCGTAATCATCTTGAT+TGG 0.417428 1.3:+57569600 None:intergenic
TCAGCGTAATCATCTTGATT+GGG 0.435610 1.3:+57569601 None:intergenic
TTTGATGTTGCAGCGGTGTT+TGG 0.438701 1.3:+57569436 None:intergenic
TGAACCAAAATGGGAGCAAA+TGG 0.444622 1.3:-57569395 MS.gene44027:CDS
CGACTCCCTTGAACCAAAAT+GGG 0.455745 1.3:-57569404 MS.gene44027:CDS
ATCGTTCTACGATCAAATTA+AGG 0.483787 1.3:-57569245 MS.gene44027:CDS
CTTCTTTAGTCCAGAGACAT+TGG 0.490028 1.3:+57569341 None:intergenic
CTCGATTACAACGCCAATCG+TGG 0.500789 1.3:-57569292 MS.gene44027:CDS
CTTATCAACAAGCTAGCTCT+TGG 0.516531 1.3:+57569201 None:intergenic
GACGAGATTACGATCTTGCA+AGG 0.547606 1.3:-57569319 MS.gene44027:CDS
TGTTGCAGCGGTGTTTGGTA+AGG 0.547867 1.3:+57569441 None:intergenic
ATGATAAGAAGATCCACGAT+TGG 0.603760 1.3:+57569279 None:intergenic
GATGATTACGCTGACATCGA+AGG 0.605803 1.3:-57569592 MS.gene44027:intron
CAGCGTAATCATCTTGATTG+GGG 0.618177 1.3:+57569602 None:intergenic
GACAATGTTTGATGTTGCAG+CGG 0.648384 1.3:+57569429 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TCTTCTTATCATAATGATAC+TGG - chr1.3:57569576-57569595 MS.gene44027:intron 25.0%
! TTGACAAAGATTGTTTAGTT+TGG + chr1.3:57569341-57569360 None:intergenic 25.0%
ATCGTTCTACGATCAAATTA+AGG - chr1.3:57569599-57569618 MS.gene44027:CDS 30.0%
!! GTTTGGTAGTTTTTGATGTT+TGG + chr1.3:57569324-57569343 None:intergenic 30.0%
ATGATAAGAAGATCCACGAT+TGG + chr1.3:57569568-57569587 None:intergenic 35.0%
TCAGCGTAATCATCTTGATT+GGG + chr1.3:57569246-57569265 None:intergenic 35.0%
TGATGTTTGGTTGGACAAAA+TGG + chr1.3:57569311-57569330 None:intergenic 35.0%
! GGTAGTTTTTGATGTTTGGT+TGG + chr1.3:57569320-57569339 None:intergenic 35.0%
CAGCGTAATCATCTTGATTG+GGG + chr1.3:57569245-57569264 None:intergenic 40.0%
CTTCTTTAGTCCAGAGACAT+TGG + chr1.3:57569506-57569525 None:intergenic 40.0%
GACAATGTTTGATGTTGCAG+CGG + chr1.3:57569418-57569437 None:intergenic 40.0%
GTCAGCGTAATCATCTTGAT+TGG + chr1.3:57569247-57569266 None:intergenic 40.0%
GTTTGGTAAGGCTAAGATGA+TGG + chr1.3:57569394-57569413 None:intergenic 40.0%
TGAACCAAAATGGGAGCAAA+TGG - chr1.3:57569449-57569468 MS.gene44027:intron 40.0%
! AGAAGCTTTTCCAATGTCTC+TGG - chr1.3:57569493-57569512 MS.gene44027:intron 40.0%
! TCTTCCATTTGCTCCCATTT+TGG + chr1.3:57569456-57569475 None:intergenic 40.0%
!!! TTGCTCCCATTTTGGTTCAA+GGG + chr1.3:57569448-57569467 None:intergenic 40.0%
!!! TTTGCTCCCATTTTGGTTCA+AGG + chr1.3:57569449-57569468 None:intergenic 40.0%
ACGACTCCCTTGAACCAAAA+TGG - chr1.3:57569439-57569458 MS.gene44027:CDS 45.0%
CGACTCCCTTGAACCAAAAT+GGG - chr1.3:57569440-57569459 MS.gene44027:CDS 45.0%
GACGAGATTACGATCTTGCA+AGG - chr1.3:57569525-57569544 MS.gene44027:intron 45.0%
GATGATTACGCTGACATCGA+AGG - chr1.3:57569252-57569271 MS.gene44027:CDS 45.0%
TTTGATGTTGCAGCGGTGTT+TGG + chr1.3:57569411-57569430 None:intergenic 45.0%
! TGGTAAGGCTAAGATGATGG+TGG + chr1.3:57569391-57569410 None:intergenic 45.0%
!! AAGGCTAAGATGATGGTGGT+GGG + chr1.3:57569387-57569406 None:intergenic 45.0%
!! TAAGGCTAAGATGATGGTGG+TGG + chr1.3:57569388-57569407 None:intergenic 45.0%
CTCGATTACAACGCCAATCG+TGG - chr1.3:57569552-57569571 MS.gene44027:intron 50.0%
TGTTGCAGCGGTGTTTGGTA+AGG + chr1.3:57569406-57569425 None:intergenic 50.0%
!! AGGCTAAGATGATGGTGGTG+GGG + chr1.3:57569386-57569405 None:intergenic 50.0%
!! TAAGATGATGGTGGTGGGGA+TGG + chr1.3:57569382-57569401 None:intergenic 50.0%
! GATGGTGGCAGTGGTGGTGA+AGG + chr1.3:57569364-57569383 None:intergenic 60.0%
!! GATGATGGTGGTGGGGATGG+TGG + chr1.3:57569379-57569398 None:intergenic 60.0%
! GGTGGGGATGGTGGCAGTGG+TGG + chr1.3:57569370-57569389 None:intergenic 70.0%
!! GGTGGTGGGGATGGTGGCAG+TGG + chr1.3:57569373-57569392 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 57569213 57569653 57569213 ID=MS.gene44027
chr1.3 mRNA 57569213 57569653 57569213 ID=MS.gene44027.t1;Parent=MS.gene44027
chr1.3 exon 57569593 57569653 57569593 ID=MS.gene44027.t1.exon1;Parent=MS.gene44027.t1
chr1.3 CDS 57569593 57569653 57569593 ID=cds.MS.gene44027.t1;Parent=MS.gene44027.t1
chr1.3 exon 57569213 57569463 57569213 ID=MS.gene44027.t1.exon2;Parent=MS.gene44027.t1
chr1.3 CDS 57569213 57569463 57569213 ID=cds.MS.gene44027.t1;Parent=MS.gene44027.t1
Gene Sequence

>MS.gene44027

ATGGCATTCTCTCGAAACGACATCGTTATCCCCAATCAAGATGATTACGCTGACATCGAAGGTGAAGACAATGACAAATTAGAAGAATAAGACAACCATTTTGTCCAACCAAACATCAAAAACTACCAAACTAAACAATCTTTGTCAACCTTCACCACCACTGCCACCATCCCCACCACCATCATCTTAGCCTTACCAAACACCGCTGCAACATCAAACATTGTCGACGACTCCCTTGAACCAAAATGGGAGCAAATGGAAGAGAAGAACAATGATTCACAGAAGCTTTTCCAATGTCTCTGGACTAAAGAAGACGAGATTACGATCTTGCAAGGTTTGCTCGATTACAACGCCAATCGTGGATCTTCTTATCATAATGATACTGGATCGTTCTACGATCAAATTAAGGCAAAGATTCAACTCGATGTCACCAAGAGCTAG
Protein sequence

>MS.gene44027.t1

MAFSRNDIVIPNQDDYADIEALPNTAATSNIVDDSLEPKWEQMEEKNNDSQKLFQCLWTKEDEITILQGLLDYNANRGSSYHNDTGSFYDQIKAKIQLDVTKS