AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene000304

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene000304.t1 MTR_1g052885 99.099 111 1 0 1 111 1 111 3.88e-75 218
MS.gene000304.t1 MTR_2g089210 86.667 105 14 0 6 110 10 114 1.30e-60 181
MS.gene000304.t1 MTR_2g081580 69.444 108 33 0 6 113 10 117 4.40e-48 150
MS.gene000304.t1 MTR_8g466250 66.667 105 35 0 6 110 11 115 1.08e-44 141
MS.gene000304.t1 MTR_2g011400 60.396 101 40 0 6 106 14 114 2.09e-38 125
MS.gene000304.t1 MTR_8g027180 52.381 105 50 0 6 110 19 123 6.80e-35 117
MS.gene000304.t1 MTR_2g081300 62.637 91 33 1 6 96 5 94 7.23e-33 111
MS.gene000304.t1 MTR_2g081350 61.538 91 34 1 6 96 9 98 1.62e-31 108
MS.gene000304.t1 MTR_2g081440 61.538 91 34 1 6 96 9 98 2.96e-31 107
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene000304.t1 AT5G54490 66.981 106 34 1 6 110 19 124 1.93e-45 143
MS.gene000304.t1 AT4G27280 66.355 107 35 1 6 111 19 125 2.37e-43 138
MS.gene000304.t1 AT2G46600 54.054 111 51 0 6 116 22 132 1.01e-38 127

Find 22 sgRNAs with CRISPR-Local

Find 25 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAAGACTCTTCCATCAATTC+AGG 0.351816 4.4:+55264550 None:intergenic
TGATGGAAGAGTCTTGGTTT+TGG 0.354264 4.4:-55264543 MS.gene000304:CDS
AGGTGGTGAAGGTTTAATAA+AGG 0.428490 4.4:-55264773 MS.gene000304:CDS
CTGAATTGATGGAAGAGTCT+TGG 0.441368 4.4:-55264549 MS.gene000304:CDS
TTGAAGGAAGATGAACTTGT+TGG 0.457469 4.4:-55264652 MS.gene000304:CDS
TTGTTGATGGACAAAGAAAA+AGG 0.459319 4.4:-55264730 MS.gene000304:CDS
CCTAGCTTGTTTGCCATCAC+TGG 0.464938 4.4:+55264793 None:intergenic
TGAAGACTTGTTACCAGTGA+TGG 0.470070 4.4:-55264806 MS.gene000304:CDS
TTTGGGTTTACAAGATTTGA+AGG 0.473694 4.4:-55264668 MS.gene000304:CDS
TGATAACATTGGATAGTTTG+AGG 0.497485 4.4:-55264705 MS.gene000304:CDS
GAAGGTGATTTAGATAGAGA+TGG 0.504919 4.4:-55264619 MS.gene000304:CDS
TAGGTTGAGTCCTGAATTGA+TGG 0.511296 4.4:-55264560 MS.gene000304:CDS
TAACAAGTCTTCAAAACCAT+TGG 0.541959 4.4:+55264816 None:intergenic
GAAGCTCTTCAACATGAACT+TGG 0.544590 4.4:-55264514 MS.gene000304:CDS
TTAATAAAGGAGCTATGCAA+TGG 0.554583 4.4:-55264760 MS.gene000304:CDS
TCTTCAACAATGGCTACCAA+TGG 0.558273 4.4:-55264832 None:intergenic
GCAAACAAGCTAGGTGGTGA+AGG 0.561539 4.4:-55264784 MS.gene000304:CDS
CCAGTGATGGCAAACAAGCT+AGG 0.566082 4.4:-55264793 MS.gene000304:CDS
AGATGGAGCACTTACTCAGA+TGG 0.568398 4.4:-55264602 MS.gene000304:CDS
CTTGTTGGTATGATGAATGA+AGG 0.583851 4.4:-55264637 MS.gene000304:CDS
ATTGTTCCTAGGAAACTACA+AGG 0.600196 4.4:+55264477 None:intergenic
GTGATGGCAAACAAGCTAGG+TGG 0.738373 4.4:-55264790 MS.gene000304:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGTTTTGTGTTTTGATGTTT+AGG - chr4.4:55264736-55264755 MS.gene000304:CDS 25.0%
TAACAAGTCTTCAAAACCAT+TGG + chr4.4:55264502-55264521 None:intergenic 30.0%
TGATAACATTGGATAGTTTG+AGG - chr4.4:55264610-55264629 MS.gene000304:CDS 30.0%
TTAATAAAGGAGCTATGCAA+TGG - chr4.4:55264555-55264574 MS.gene000304:CDS 30.0%
! AGAAAAAGGTGTGATAACAT+TGG - chr4.4:55264599-55264618 MS.gene000304:CDS 30.0%
! TTGTTGATGGACAAAGAAAA+AGG - chr4.4:55264585-55264604 MS.gene000304:CDS 30.0%
! TTTGGGTTTACAAGATTTGA+AGG - chr4.4:55264647-55264666 MS.gene000304:CDS 30.0%
!!! CAATGGTTTTGAATTGTTGA+TGG - chr4.4:55264572-55264591 MS.gene000304:CDS 30.0%
AGGTGGTGAAGGTTTAATAA+AGG - chr4.4:55264542-55264561 MS.gene000304:CDS 35.0%
CTTGTTGGTATGATGAATGA+AGG - chr4.4:55264678-55264697 MS.gene000304:CDS 35.0%
GAAGGTGATTTAGATAGAGA+TGG - chr4.4:55264696-55264715 MS.gene000304:CDS 35.0%
TTGAAGGAAGATGAACTTGT+TGG - chr4.4:55264663-55264682 MS.gene000304:CDS 35.0%
CAAGACTCTTCCATCAATTC+AGG + chr4.4:55264768-55264787 None:intergenic 40.0%
CTGAATTGATGGAAGAGTCT+TGG - chr4.4:55264766-55264785 MS.gene000304:CDS 40.0%
GAAGCTCTTCAACATGAACT+TGG - chr4.4:55264801-55264820 MS.gene000304:CDS 40.0%
! TAGGTTGAGTCCTGAATTGA+TGG - chr4.4:55264755-55264774 MS.gene000304:CDS 40.0%
! TGATGGAAGAGTCTTGGTTT+TGG - chr4.4:55264772-55264791 MS.gene000304:CDS 40.0%
!! TGAAGACTTGTTACCAGTGA+TGG - chr4.4:55264509-55264528 MS.gene000304:CDS 40.0%
!!! AGGAAAAACGCTGCTGTTTT+GGG - chr4.4:55264630-55264649 MS.gene000304:CDS 40.0%
! AGATGGAGCACTTACTCAGA+TGG - chr4.4:55264713-55264732 MS.gene000304:CDS 45.0%
!! GAGGAAAAACGCTGCTGTTT+TGG - chr4.4:55264629-55264648 MS.gene000304:CDS 45.0%
CCAGTGATGGCAAACAAGCT+AGG - chr4.4:55264522-55264541 MS.gene000304:CDS 50.0%
GCAAACAAGCTAGGTGGTGA+AGG - chr4.4:55264531-55264550 MS.gene000304:CDS 50.0%
GTGATGGCAAACAAGCTAGG+TGG - chr4.4:55264525-55264544 MS.gene000304:CDS 50.0%
!! CCTAGCTTGTTTGCCATCAC+TGG + chr4.4:55264525-55264544 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr4.4 gene 55264492 55264845 55264492 ID=MS.gene000304
chr4.4 mRNA 55264492 55264845 55264492 ID=MS.gene000304.t1;Parent=MS.gene000304
chr4.4 exon 55264492 55264845 55264492 ID=MS.gene000304.t1.exon1;Parent=MS.gene000304.t1
chr4.4 CDS 55264492 55264845 55264492 ID=cds.MS.gene000304.t1;Parent=MS.gene000304.t1
Gene Sequence

>MS.gene000304

ATGGCTACCAATGGTTTTGAAGACTTGTTACCAGTGATGGCAAACAAGCTAGGTGGTGAAGGTTTAATAAAGGAGCTATGCAATGGTTTTGAATTGTTGATGGACAAAGAAAAAGGTGTGATAACATTGGATAGTTTGAGGAAAAACGCTGCTGTTTTGGGTTTACAAGATTTGAAGGAAGATGAACTTGTTGGTATGATGAATGAAGGTGATTTAGATAGAGATGGAGCACTTACTCAGATGGAGTTTTGTGTTTTGATGTTTAGGTTGAGTCCTGAATTGATGGAAGAGTCTTGGTTTTGGCTTGAAGAAGCTCTTCAACATGAACTTGGTGACAACAACTGTTCCTTGTAG
Protein sequence

>MS.gene000304.t1

MATNGFEDLLPVMANKLGGEGLIKELCNGFELLMDKEKGVITLDSLRKNAAVLGLQDLKEDELVGMMNEGDLDRDGALTQMEFCVLMFRLSPELMEESWFWLEEALQHELGDNNCSL