AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene073056

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene073056.t1 MTR_3g109420 93.373 166 5 1 1 160 1 166 2.86e-114 321
MS.gene073056.t1 MTR_1g008700 75.301 166 33 3 1 158 1 166 1.52e-85 248
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene073056.t1 AT4G32690 69.591 171 39 2 1 158 1 171 4.18e-81 237

Find 37 sgRNAs with CRISPR-Local

Find 55 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAAAACCAGTACGAATTCT+TGG 0.289012 3.3:+89655074 MS.gene073056:CDS
ATAGAACCTGTTGTAGAAAT+TGG 0.299176 3.3:-89654905 None:intergenic
AAAGTTAATCAACATTATCT+TGG 0.353946 3.3:-89655680 None:intergenic
GCTTCATGTGTCACAGGAAA+TGG 0.391868 3.3:-89655592 None:intergenic
GAGGAGGACCTCCCATTCTC+TGG 0.415467 3.3:-89655098 None:intergenic
TGCTTTGTCTTTATCAGACT+TGG 0.418611 3.3:-89655049 None:intergenic
CGAATTCTTGGTCCAGAGAA+TGG 0.418706 3.3:+89655086 MS.gene073056:CDS
TTTCCACCAATTTCTACAAC+AGG 0.420675 3.3:+89654899 MS.gene073056:CDS
CTTCCAGCTGCATCCTTGCA+AGG 0.423236 3.3:-89655847 None:intergenic
AAACAAGTTGGTGTCATCAA+TGG 0.436122 3.3:-89654845 None:intergenic
AAAGGTTAATGAAAGTTTGA+AGG 0.487596 3.3:-89654879 None:intergenic
ACTTCATATGCAACAAGCAT+TGG 0.490000 3.3:+89655630 MS.gene073056:CDS
TTCCAGCTGCATCCTTGCAA+GGG 0.503260 3.3:-89655846 None:intergenic
GAATTCTTGGTCCAGAGAAT+GGG 0.505694 3.3:+89655087 MS.gene073056:CDS
CACCCTTGCAAGGATGCAGC+TGG 0.514180 3.3:+89655844 MS.gene073056:CDS
TCTGGACCAAGAATTCGTAC+TGG 0.524772 3.3:-89655080 None:intergenic
TGTTGTAGAAATTGGTGGAA+AGG 0.527682 3.3:-89654897 None:intergenic
CTGCATCCTTGCAAGGGTGA+AGG 0.528329 3.3:-89655840 None:intergenic
TGCAAGAGAAGGCTTCTGAA+TGG 0.530466 3.3:+89654794 MS.gene073056:CDS
TCGGCAGCTTCATGTGTCAC+AGG 0.536702 3.3:-89655598 None:intergenic
GAACCTGTTGTAGAAATTGG+TGG 0.539038 3.3:-89654902 None:intergenic
GATGACGATGAGGAGTGGTT+TGG 0.563976 3.3:+89655015 MS.gene073056:CDS
CGATGTCTAGTAATTAGAGC+AGG 0.568423 3.3:-89655568 None:intergenic
CACATGAAGCTGCCGAGAGG+TGG 0.582503 3.3:+89655605 MS.gene073056:CDS
CCTCTGTATTCTCAGAGAAG+AGG 0.592545 3.3:+89655117 MS.gene073056:CDS
TCAAAGCCTTCACCCTTGCA+AGG 0.595706 3.3:+89655834 MS.gene073056:CDS
ACCAACTTGTTTCAAAAGCT+AGG 0.598000 3.3:+89654856 MS.gene073056:CDS
CTTGCAAGGATGCAGCTGGA+AGG 0.604226 3.3:+89655848 MS.gene073056:CDS
GATGCAGAATCTGCAAGAGA+AGG 0.605698 3.3:+89654783 None:intergenic
TTCTTGGTCCAGAGAATGGG+AGG 0.632605 3.3:+89655090 MS.gene073056:CDS
CATATGAAGTAACCACCTCT+CGG 0.635321 3.3:-89655617 None:intergenic
TAGAGTGTATGATGACGATG+AGG 0.661998 3.3:+89655005 MS.gene073056:intron
GAGAAGGCTTCTGAATGGAG+TGG 0.664521 3.3:+89654799 MS.gene073056:CDS
TGTATGATGACGATGAGGAG+TGG 0.684110 3.3:+89655010 MS.gene073056:CDS
CCTCTTCTCTGAGAATACAG+AGG 0.698670 3.3:-89655117 None:intergenic
CTTCTCTGAGAATACAGAGG+AGG 0.701310 3.3:-89655114 None:intergenic
TGACACATGAAGCTGCCGAG+AGG 0.786257 3.3:+89655602 MS.gene073056:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGTCAATAATATTCTTTATT+TGG + chr3.3:89655387-89655406 MS.gene073056:intron 15.0%
!! TATATGACCTAAATATATAT+AGG - chr3.3:89655489-89655508 None:intergenic 15.0%
!!! CTTTTAGATTTTTAACTTTT+CGG + chr3.3:89655184-89655203 MS.gene073056:intron 15.0%
!!! GTCAATAATATTCTTTATTT+GGG + chr3.3:89655388-89655407 MS.gene073056:intron 15.0%
!!! TCAATAATATTCTTTATTTG+GGG + chr3.3:89655389-89655408 MS.gene073056:intron 15.0%
!!! TTTGAAACCTATATATATTT+AGG + chr3.3:89655479-89655498 MS.gene073056:intron 15.0%
!! AAAGTTAATCAACATTATCT+TGG - chr3.3:89655683-89655702 None:intergenic 20.0%
!! ATATATCTCTAATAAATGTG+TGG + chr3.3:89655506-89655525 MS.gene073056:intron 20.0%
! AAAGGTTAATGAAAGTTTGA+AGG - chr3.3:89654882-89654901 None:intergenic 25.0%
! ACTAAGTTCATGACAATTAA+TGG + chr3.3:89654971-89654990 MS.gene073056:intron 25.0%
! ATATATAGGTTTCAAAGCTT+AGG - chr3.3:89655475-89655494 None:intergenic 25.0%
!! TAATATTCTTTATTTGGGGA+TGG + chr3.3:89655393-89655412 MS.gene073056:intron 25.0%
!!! AACCTGTGTTTTTACTTTTT+AGG + chr3.3:89655770-89655789 MS.gene073056:intron 25.0%
ATAGAACCTGTTGTAGAAAT+TGG - chr3.3:89654908-89654927 None:intergenic 30.0%
GTCATGAACTTAGTAAAGAA+AGG - chr3.3:89654965-89654984 None:intergenic 30.0%
TGCCTAAAAAGTAAAAACAC+AGG - chr3.3:89655775-89655794 None:intergenic 30.0%
! TTGATTCTTCTTTTCAACTC+CGG - chr3.3:89655818-89655837 None:intergenic 30.0%
ACTTCATATGCAACAAGCAT+TGG + chr3.3:89655630-89655649 MS.gene073056:CDS 35.0%
ATGTCCTGTAATGTGAAGTA+CGG - chr3.3:89655548-89655567 None:intergenic 35.0%
TCAAAACCAGTACGAATTCT+TGG + chr3.3:89655074-89655093 MS.gene073056:CDS 35.0%
TGCTTTGTCTTTATCAGACT+TGG - chr3.3:89655052-89655071 None:intergenic 35.0%
TGTTGTAGAAATTGGTGGAA+AGG - chr3.3:89654900-89654919 None:intergenic 35.0%
TTTCCACCAATTTCTACAAC+AGG + chr3.3:89654899-89654918 MS.gene073056:CDS 35.0%
! ACCAACTTGTTTCAAAAGCT+AGG + chr3.3:89654856-89654875 MS.gene073056:CDS 35.0%
! ACTGCATATTTTCTTGTTGC+CGG + chr3.3:89655796-89655815 MS.gene073056:CDS 35.0%
!! AAACAAGTTGGTGTCATCAA+TGG - chr3.3:89654848-89654867 None:intergenic 35.0%
CATATGAAGTAACCACCTCT+CGG - chr3.3:89655620-89655639 None:intergenic 40.0%
CGATGTCTAGTAATTAGAGC+AGG - chr3.3:89655571-89655590 None:intergenic 40.0%
GAACCTGTTGTAGAAATTGG+TGG - chr3.3:89654905-89654924 None:intergenic 40.0%
GAATTCTTGGTCCAGAGAAT+GGG + chr3.3:89655087-89655106 MS.gene073056:CDS 40.0%
GGGATGGTTAGTAAAATGAC+AGG + chr3.3:89655409-89655428 MS.gene073056:intron 40.0%
! TAGAGTGTATGATGACGATG+AGG + chr3.3:89655005-89655024 MS.gene073056:intron 40.0%
!!! GCCTAGCTTTTGAAACAAGT+TGG - chr3.3:89654860-89654879 None:intergenic 40.0%
CCTCTGTATTCTCAGAGAAG+AGG + chr3.3:89655117-89655136 MS.gene073056:CDS 45.0%
CGAATTCTTGGTCCAGAGAA+TGG + chr3.3:89655086-89655105 MS.gene073056:CDS 45.0%
GCTACCGTACTTCACATTAC+AGG + chr3.3:89655541-89655560 MS.gene073056:intron 45.0%
GCTTCATGTGTCACAGGAAA+TGG - chr3.3:89655595-89655614 None:intergenic 45.0%
TCTGGACCAAGAATTCGTAC+TGG - chr3.3:89655083-89655102 None:intergenic 45.0%
TGCAAGAGAAGGCTTCTGAA+TGG + chr3.3:89654794-89654813 MS.gene073056:CDS 45.0%
! CCTCTTCTCTGAGAATACAG+AGG - chr3.3:89655120-89655139 None:intergenic 45.0%
! CTTCTCTGAGAATACAGAGG+AGG - chr3.3:89655117-89655136 None:intergenic 45.0%
! TGTATGATGACGATGAGGAG+TGG + chr3.3:89655010-89655029 MS.gene073056:CDS 45.0%
GAGAAGGCTTCTGAATGGAG+TGG + chr3.3:89654799-89654818 MS.gene073056:CDS 50.0%
GATGACGATGAGGAGTGGTT+TGG + chr3.3:89655015-89655034 MS.gene073056:CDS 50.0%
TCAAAGCCTTCACCCTTGCA+AGG + chr3.3:89655834-89655853 MS.gene073056:CDS 50.0%
TTCCAGCTGCATCCTTGCAA+GGG - chr3.3:89655849-89655868 None:intergenic 50.0%
TTCTTGGTCCAGAGAATGGG+AGG + chr3.3:89655090-89655109 MS.gene073056:CDS 50.0%
CTGCATCCTTGCAAGGGTGA+AGG - chr3.3:89655843-89655862 None:intergenic 55.0%
CTTCCAGCTGCATCCTTGCA+AGG - chr3.3:89655850-89655869 None:intergenic 55.0%
CTTGCAAGGATGCAGCTGGA+AGG + chr3.3:89655848-89655867 MS.gene073056:CDS 55.0%
TCGGCAGCTTCATGTGTCAC+AGG - chr3.3:89655601-89655620 None:intergenic 55.0%
TGACACATGAAGCTGCCGAG+AGG + chr3.3:89655602-89655621 MS.gene073056:CDS 55.0%
CACATGAAGCTGCCGAGAGG+TGG + chr3.3:89655605-89655624 MS.gene073056:CDS 60.0%
CACCCTTGCAAGGATGCAGC+TGG + chr3.3:89655844-89655863 MS.gene073056:CDS 60.0%
GAGGAGGACCTCCCATTCTC+TGG - chr3.3:89655101-89655120 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 89654784 89655877 89654784 ID=MS.gene073056
chr3.3 mRNA 89654784 89655877 89654784 ID=MS.gene073056.t1;Parent=MS.gene073056
chr3.3 exon 89654784 89654920 89654784 ID=MS.gene073056.t1.exon1;Parent=MS.gene073056.t1
chr3.3 CDS 89654784 89654920 89654784 ID=cds.MS.gene073056.t1;Parent=MS.gene073056.t1
chr3.3 exon 89655008 89655138 89655008 ID=MS.gene073056.t1.exon2;Parent=MS.gene073056.t1
chr3.3 CDS 89655008 89655138 89655008 ID=cds.MS.gene073056.t1;Parent=MS.gene073056.t1
chr3.3 exon 89655563 89655689 89655563 ID=MS.gene073056.t1.exon3;Parent=MS.gene073056.t1
chr3.3 CDS 89655563 89655689 89655563 ID=cds.MS.gene073056.t1;Parent=MS.gene073056.t1
chr3.3 exon 89655792 89655877 89655792 ID=MS.gene073056.t1.exon4;Parent=MS.gene073056.t1
chr3.3 CDS 89655792 89655877 89655792 ID=cds.MS.gene073056.t1;Parent=MS.gene073056.t1
Gene Sequence

>MS.gene073056

ATGCAGAATCTGCAAGAGAAGGCTTCTGAATGGAGTGGTGTTGAGACAAATCATGCTTTTGCCATTGATGACACCAACTTGTTTCAAAAGCTAGGCCTTCAAACTTTCATTAACCTTTCCACCAATTTCTACAACAGGTTCTATATATATTCAACTTATATATTTCAATATTAAATAACCTTTCTTTACTAAGTTCATGACAATTAATGGTTGTGCTATAATAGAGTGTATGATGACGATGAGGAGTGGTTTGGTTCAATATTTGCCAAGTCTGATAAAGACAAAGCAATTCAAAACCAGTACGAATTCTTGGTCCAGAGAATGGGAGGTCCTCCTCTGTATTCTCAGAGAAGAGGTCAATATTCTTTATTTTATTTTTATTTCACTTTTCATAGAAACACTTTTAGATTTTTAACTTTTCGGAAAAATACTTCTAATTAGTGATTACTATTTTACTGATTTTTTTGTACTCAAGTAAGCAAACAATATGATAGATTTTTTTCAAAAAATAAATAAATACTATTATAGATATATTTTGAAAAATGCTATTAATTCTTGATTAATTTAACACTACTAACAATTTTTTTTTAGTGTATGTGATTTAGTCAATAATATTCTTTATTTGGGGATGGTTAGTAAAATGACAGGTTTTGAACTTACTACACAATGAGTTTATAAGTGATTATTGCCTAAGCTTTGAAACCTATATATATTTAGGTCATATATATCTCTAATAAATGTGTGGCTTAGTTCATTTGCTACCGTACTTCACATTACAGGACATCCTGCTCTAATTACTAGACATCGACCATTTCCTGTGACACATGAAGCTGCCGAGAGGTGGTTACTTCATATGCAACAAGCATTGGACAATATTTCAGATATAGATCATGATTCCAAGATAATGTTGATTAACTTTTTCAGATTTATTATCTTCACTTTGCAGAAATCAAATCAATAAAAATAAATAATGTTCATGATATAACAACCTGTGTTTTTACTTTTTAGGCACACTGCATATTTTCTTGTTGCCGGAGTTGAAAAGAAGAATCAAAGCCTTCACCCTTGCAAGGATGCAGCTGGAAGGCATCCAT
Protein sequence

>MS.gene073056.t1

MQNLQEKASEWSGVETNHAFAIDDTNLFQKLGLQTFINLSTNFYNRVYDDDEEWFGSIFAKSDKDKAIQNQYEFLVQRMGGPPLYSQRRGHPALITRHRPFPVTHEAAERWLLHMQQALDNISDIDHDSKIMHTAYFLVAGVEKKNQSLHPCKDAAGRHP