AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene82841

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene82841.t1 MTR_4g014360 99.029 103 1 0 1 103 1 103 2.78e-72 210
MS.gene82841.t1 MTR_6g005030 97.087 103 3 0 1 103 52 154 8.12e-70 205
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene82841.t1 AT3G18880 70.526 95 28 0 1 95 1 95 2.48e-47 147
MS.gene82841.t1 AT3G18880 70.526 95 28 0 1 95 1 95 2.48e-47 147
MS.gene82841.t1 AT1G49400 79.518 83 17 0 1 83 1 83 1.25e-46 145
MS.gene82841.t1 AT1G79850 39.744 78 47 0 1 78 50 127 4.21e-13 61.6

Find 20 sgRNAs with CRISPR-Local

Find 31 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAAGCGCACTTCCAAGTTTA+TGG 0.135840 6.1:+1079331 MS.gene82841:CDS
AGGTTCGATTGGATTCTTCT+AGG 0.331841 6.1:+1079672 MS.gene82841:intron
TGGAAGTGCGCTTAATATAT+CGG 0.362502 6.1:-1079322 None:intergenic
CTTGTCATTTCAGGTTCGAT+TGG 0.439317 6.1:+1079661 MS.gene82841:intron
TTCGAATAAGATGCAGAAAT+CGG 0.439794 6.1:+1079256 MS.gene82841:CDS
GAGAAGATGAAGCAAGTAGT+AGG 0.480871 6.1:+1079224 None:intergenic
GATGAAGCAAGTAGTAGGAA+TGG 0.481818 6.1:+1079229 None:intergenic
TCTGAGCAAGCGTAAACATT+GGG 0.508662 6.1:+1079697 MS.gene82841:CDS
TTCATCATGAGCCATAAACT+TGG 0.509537 6.1:-1079342 None:intergenic
CAAATTTATGATGTAGATGT+AGG 0.528358 6.1:-1079806 None:intergenic
CTCTGAGCAAGCGTAAACAT+TGG 0.545204 6.1:+1079696 MS.gene82841:CDS
TAAGATGCAGAAATCGGTTG+TGG 0.553827 6.1:+1079262 MS.gene82841:CDS
TTCTCAGACACCGTTGCAGA+GGG 0.577883 6.1:-1079761 None:intergenic
GAAGCAAGTAGTAGGAATGG+TGG 0.579237 6.1:+1079232 MS.gene82841:CDS
ATATGTTCCTCCCTCTGCAA+CGG 0.584593 6.1:+1079751 MS.gene82841:CDS
AATGCGAGCTCGAACTCTGT+AGG 0.604238 6.1:+1079782 MS.gene82841:CDS
GAAAACAATCTTTGCAACAT+CGG 0.608322 6.1:+1079362 MS.gene82841:CDS
ATTCTCAGACACCGTTGCAG+AGG 0.611069 6.1:-1079762 None:intergenic
TCAGACACCGTTGCAGAGGG+AGG 0.631588 6.1:-1079758 None:intergenic
CAATGTTTACGCTTGCTCAG+AGG 0.639617 6.1:-1079695 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTATTCACAATACTAACT+CGG - chr6.1:1079391-1079410 None:intergenic 20.0%
! TAACAACAATGGTAAAAGAT+AGG - chr6.1:1079416-1079435 None:intergenic 25.0%
GAAAACAATCTTTGCAACAT+CGG + chr6.1:1079362-1079381 MS.gene82841:CDS 30.0%
TTAACAAAACCAAGAACACA+CGG - chr6.1:1079613-1079632 None:intergenic 30.0%
TTCGAATAAGATGCAGAAAT+CGG + chr6.1:1079256-1079275 MS.gene82841:CDS 30.0%
! AACAGTGTCTTGTACAATTT+TGG + chr6.1:1079582-1079601 MS.gene82841:intron 30.0%
! TTACCATTGTTGTTAAACAG+CGG + chr6.1:1079421-1079440 MS.gene82841:intron 30.0%
!! TATATCGGTTGAACATTTTG+TGG - chr6.1:1079310-1079329 None:intergenic 30.0%
!!! TTTGATCAAACTGCTGTTTT+TGG + chr6.1:1079551-1079570 MS.gene82841:intron 30.0%
AGGCAACAATTTGTGCTAAA+TGG - chr6.1:1079497-1079516 None:intergenic 35.0%
TTCATCATGAGCCATAAACT+TGG - chr6.1:1079345-1079364 None:intergenic 35.0%
! TGGAAGTGCGCTTAATATAT+CGG - chr6.1:1079325-1079344 None:intergenic 35.0%
AGGTTCGATTGGATTCTTCT+AGG + chr6.1:1079672-1079691 MS.gene82841:intron 40.0%
TAAGATGCAGAAATCGGTTG+TGG + chr6.1:1079262-1079281 MS.gene82841:CDS 40.0%
TAAGCGCACTTCCAAGTTTA+TGG + chr6.1:1079331-1079350 MS.gene82841:CDS 40.0%
TCTGAGCAAGCGTAAACATT+GGG + chr6.1:1079697-1079716 MS.gene82841:CDS 40.0%
! ATCGGTTGAACATTTTGTGG+TGG - chr6.1:1079307-1079326 None:intergenic 40.0%
!! CTTGTCATTTCAGGTTCGAT+TGG + chr6.1:1079661-1079680 MS.gene82841:intron 40.0%
!! GCTTTTGTGCTTGTCATTTC+AGG + chr6.1:1079652-1079671 MS.gene82841:intron 40.0%
ATATGTTCCTCCCTCTGCAA+CGG + chr6.1:1079751-1079770 MS.gene82841:CDS 45.0%
CAATGTTTACGCTTGCTCAG+AGG - chr6.1:1079698-1079717 None:intergenic 45.0%
CTCTGAGCAAGCGTAAACAT+TGG + chr6.1:1079696-1079715 MS.gene82841:CDS 45.0%
GAAGCAAGTAGTAGGAATGG+TGG + chr6.1:1079232-1079251 MS.gene82841:CDS 45.0%
GCACAAATTGTTGCCTCTAG+TGG + chr6.1:1079501-1079520 MS.gene82841:intron 45.0%
TTGGATTTGCCGTGTGTTCT+TGG + chr6.1:1079601-1079620 MS.gene82841:intron 45.0%
AATGCGAGCTCGAACTCTGT+AGG + chr6.1:1079782-1079801 MS.gene82841:CDS 50.0%
ATTCTCAGACACCGTTGCAG+AGG - chr6.1:1079765-1079784 None:intergenic 50.0%
GCGCCGCTGTTTAACAACAA+TGG - chr6.1:1079427-1079446 None:intergenic 50.0%
TTCTCAGACACCGTTGCAGA+GGG - chr6.1:1079764-1079783 None:intergenic 50.0%
! AGTGCTGCTATAGCCACTAG+AGG - chr6.1:1079517-1079536 None:intergenic 50.0%
TCAGACACCGTTGCAGAGGG+AGG - chr6.1:1079761-1079780 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr6.1 gene 1079230 1079823 1079230 ID=MS.gene82841
chr6.1 mRNA 1079230 1079823 1079230 ID=MS.gene82841.t1;Parent=MS.gene82841
chr6.1 exon 1079230 1079391 1079230 ID=MS.gene82841.t1.exon1;Parent=MS.gene82841.t1
chr6.1 CDS 1079230 1079391 1079230 ID=cds.MS.gene82841.t1;Parent=MS.gene82841.t1
chr6.1 exon 1079674 1079823 1079674 ID=MS.gene82841.t1.exon2;Parent=MS.gene82841.t1
chr6.1 CDS 1079674 1079823 1079674 ID=cds.MS.gene82841.t1;Parent=MS.gene82841.t1
Gene Sequence

>MS.gene82841

ATGAAGCAAGTAGTAGGAATGGTGGTTTCGAATAAGATGCAGAAATCGGTTGTGGTAGCAGTTGATAGATTGTTCCACCACAAAATGTTCAACCGATATATTAAGCGCACTTCCAAGTTTATGGCTCATGATGAAAACAATCTTTGCAACATCGGTGACCGAGTTAGTATTGTGAATAATTTACCTATCTTTTACCATTGTTGTTAAACAGCGGCGCTACAGCGTAGCTGAATTTTTAATAAATTACTATTATTTTGCAATACGCCATTTAGCACAAATTGTTGCCTCTAGTGGCTATAGCAGCACTATTGTGTAGCTAAATTTGATCAAACTGCTGTTTTTGGTGATCGACAACAGTGTCTTGTACAATTTTGGATTTGCCGTGTGTTCTTGGTTTTGTTAAGATAACTAAACAAGCATATGCTTTTGTGCTTGTCATTTCAGGTTCGATTGGATTCTTCTAGGCCTCTGAGCAAGCGTAAACATTGGGTTGTTGCTGAAATTCTCAAGAAAGCACGCATATATGTTCCTCCCTCTGCAACGGTGTCTGAGAATGCGAGCTCGAACTCTGTAGGACCTACATCTACATCATAA
Protein sequence

>MS.gene82841.t1

MKQVVGMVVSNKMQKSVVVAVDRLFHHKMFNRYIKRTSKFMAHDENNLCNIGDRVRLDSSRPLSKRKHWVVAEILKKARIYVPPSATVSENASSNSVGPTSTS