AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0014710


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0014710 MtrunA17_Chr4g0001231 91.071 56 5 0 33 88 288 343 2.87e-26 101
Msa0014710 MtrunA17_Chr4g0074301 91.071 56 5 0 33 88 290 345 6.65e-26 100
Msa0014710 MtrunA17_Chr4g0070931 91.071 56 5 0 33 88 290 345 6.79e-26 100
Msa0014710 MtrunA17_Chr4g0074271 89.286 56 6 0 33 88 289 344 1.24e-25 99.4
Msa0014710 MtrunA17_Chr4g0045381 72.727 44 12 0 1 44 2331 2374 6.00e-14 66.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0014710 AT1G80790.3 50.000 64 32 0 33 96 298 361 3.28e-13 64.7
Msa0014710 AT1G80790.1 50.000 64 32 0 33 96 298 361 4.31e-13 64.7
Msa0014710 AT1G80790.2 50.000 64 32 0 33 96 298 361 4.31e-13 64.7

Find 19 sgRNAs with CRISPR-Local

Find 30 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTAATACCTCACGCTTATTT+AGG 0.249515 1_1:+23506673 None:intergenic
TGAGGAGGTACGAAGTATAT+TGG 0.387120 1_1:-23506763 Msa0014710:CDS
CTTATTTAGGTCTCTGCTCC+AGG 0.431017 1_1:+23506686 None:intergenic
AGAGCTAAATTTGAATGCTA+AGG 0.432495 1_1:-23507005 Msa0014710:CDS
GAGCAACCAAGGACATTAGT+AGG 0.462611 1_1:+23506485 None:intergenic
AAATTTGAATGCTAAGGAAC+AGG 0.469593 1_1:-23506999 Msa0014710:CDS
AGAGAAGTTGAGTAATGAGT+TGG 0.478671 1_1:-23506733 Msa0014710:CDS
TGGTCTCCTACTAATGTCCT+TGG 0.511467 1_1:-23506491 Msa0014710:three_prime_UTR
ACTAGAAGAGGACAAGAAGA+AGG 0.546755 1_1:-23506631 Msa0014710:CDS
AAATGCGGAAGCTTGATACC+TGG 0.551489 1_1:-23506704 Msa0014710:CDS
ATTTGATCTGTCTTTCTCTG+TGG 0.585123 1_1:-23506511 Msa0014710:three_prime_UTR
ATTCAAATCAAGAGCAACCA+AGG 0.610599 1_1:+23506474 None:intergenic
TATAGCAGGAAAAGATGCAG+AGG 0.611609 1_1:-23507139 Msa0014710:intron
CATGCAGCGTAAAGCTCGTG+AGG 0.627326 1_1:-23506781 Msa0014710:CDS
AGGTATTAACTGATCAAGAG+AGG 0.653894 1_1:-23506659 Msa0014710:CDS
AGAGAGGCAGAAACTAGAAG+AGG 0.669695 1_1:-23506643 Msa0014710:CDS
GTTCTGAAGAGTGATATAGC+AGG 0.673495 1_1:-23507153 Msa0014710:CDS
CAGAGACCTAAATAAGCGTG+AGG 0.681605 1_1:-23506679 Msa0014710:CDS
GCAGCGTAAAGCTCGTGAGG+AGG 0.682044 1_1:-23506778 Msa0014710:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CAATAAAAAATCTTTAAAAT+AGG + chr1_1:23507058-23507077 None:intergenic 10.0%
!!! AAAAAAATGAGACATTTTTG+TGG + chr1_1:23506812-23506831 None:intergenic 20.0%
! ACGATATATACAATTACCAA+TGG + chr1_1:23506751-23506770 None:intergenic 25.0%
! ACTTTGTTTCGTTTCTTTGT+TGG - chr1_1:23506564-23506583 Msa0014710:exon 30.0%
AGAGCTAAATTTGAATGCTA+AGG - chr1_1:23506623-23506642 Msa0014710:CDS 30.0%
AAATTTGAATGCTAAGGAAC+AGG - chr1_1:23506629-23506648 Msa0014710:CDS 30.0%
TTGCATCGAATAAAATGTCT+TGG - chr1_1:23506685-23506704 Msa0014710:CDS 30.0%
!!! TCATTTTTTTGTCAGAGTCA+AGG - chr1_1:23506822-23506841 Msa0014710:intron 30.0%
! ATGAGTTGGATGAAAAAATG+CGG - chr1_1:23506909-23506928 Msa0014710:intron 30.0%
TTAATACCTCACGCTTATTT+AGG + chr1_1:23506958-23506977 None:intergenic 30.0%
!!! CAAATTTTTTGCAAGCACAA+TGG + chr1_1:23507102-23507121 None:intergenic 30.0%
TTTCTTTGTTGGACTCTGAT+AGG - chr1_1:23506575-23506594 Msa0014710:CDS 35.0%
AAATGTCTTGGACGTCATAT+TGG - chr1_1:23506697-23506716 Msa0014710:CDS 35.0%
TTAAAGCTTAGCACTACCAT+TGG - chr1_1:23506732-23506751 Msa0014710:CDS 35.0%
AGAGAAGTTGAGTAATGAGT+TGG - chr1_1:23506895-23506914 Msa0014710:intron 35.0%
AGGTATTAACTGATCAAGAG+AGG - chr1_1:23506969-23506988 Msa0014710:intron 35.0%
ATTTGATCTGTCTTTCTCTG+TGG - chr1_1:23507117-23507136 Msa0014710:intron 35.0%
TATAGCAGGAAAAGATGCAG+AGG - chr1_1:23506489-23506508 Msa0014710:three_prime_UTR 40.0%
! AGATGCAGAGGTAGGATTTT+CGG - chr1_1:23506501-23506520 Msa0014710:three_prime_UTR 40.0%
! TGAGGAGGTACGAAGTATAT+TGG - chr1_1:23506865-23506884 Msa0014710:intron 40.0%
ACTAGAAGAGGACAAGAAGA+AGG - chr1_1:23506997-23507016 Msa0014710:CDS 40.0%
AAATGCGGAAGCTTGATACC+TGG - chr1_1:23506924-23506943 Msa0014710:intron 45.0%
CTTATTTAGGTCTCTGCTCC+AGG + chr1_1:23506945-23506964 None:intergenic 45.0%
CAGAGACCTAAATAAGCGTG+AGG - chr1_1:23506949-23506968 Msa0014710:intron 45.0%
AGAGAGGCAGAAACTAGAAG+AGG - chr1_1:23506985-23507004 Msa0014710:CDS 45.0%
TGGTCTCCTACTAATGTCCT+TGG - chr1_1:23507137-23507156 Msa0014710:intron 45.0%
GAGCAACCAAGGACATTAGT+AGG + chr1_1:23507146-23507165 None:intergenic 45.0%
GCAGGAAAAGATGCAGAGGT+AGG - chr1_1:23506493-23506512 Msa0014710:three_prime_UTR 50.0%
CATGCAGCGTAAAGCTCGTG+AGG - chr1_1:23506847-23506866 Msa0014710:intron 55.0%
GCAGCGTAAAGCTCGTGAGG+AGG - chr1_1:23506850-23506869 Msa0014710:intron 60.0%
Chromosome Type Strat End Strand Name
chr1_1 gene 23506478 23507172 23506478 ID=Msa0014710;Name=Msa0014710
chr1_1 mRNA 23506478 23507172 23506478 ID=Msa0014710-mRNA-1;Parent=Msa0014710;Name=Msa0014710-mRNA-1;_AED=0.08;_eAED=0.08;_QI=0|0|0|0.66|1|0.66|3|91|116
chr1_1 exon 23506478 23506811 23506478 ID=Msa0014710-mRNA-1:exon:8197;Parent=Msa0014710-mRNA-1
chr1_1 exon 23506979 23507053 23506979 ID=Msa0014710-mRNA-1:exon:8196;Parent=Msa0014710-mRNA-1
chr1_1 exon 23507140 23507172 23507140 ID=Msa0014710-mRNA-1:exon:8195;Parent=Msa0014710-mRNA-1
chr1_1 CDS 23507140 23507172 23507140 ID=Msa0014710-mRNA-1:cds;Parent=Msa0014710-mRNA-1
chr1_1 CDS 23506979 23507053 23506979 ID=Msa0014710-mRNA-1:cds;Parent=Msa0014710-mRNA-1
chr1_1 CDS 23506569 23506811 23506569 ID=Msa0014710-mRNA-1:cds;Parent=Msa0014710-mRNA-1
chr1_1 three_prime_UTR 23506478 23506568 23506478 ID=Msa0014710-mRNA-1:three_prime_utr;Parent=Msa0014710-mRNA-1
Gene Sequence

>Msa0014710

CTGAAGAGTGATATAGCAGGAAAAGATGCAGAGGTTGCACAGATGAAAGTTCATATTTCAGAGCTAAATTTGAATGCTAAGGAACAGGCAATTGAGTATAAAGAGAAATCAAGGAGCATGCAGCGTAAAGCTCGTGAGGAGGTACGAAGTATATTGGAAGAACAAGAGAAGTTGAGTAATGAGTTGGATGAAAAAATGCGGAAGCTTGATACCTGGAGCAGAGACCTAAATAAGCGTGAGGTATTAACTGATCAAGAGAGGCAGAAACTAGAAGAGGACAAGAAGAAGGTAATGTATATTACATTTTTTAGCAATCAGTATATGCCTATTTTAAAGATTTTTTATTGCTAA

Protein sequence

>Msa0014710

LKSDIAGKDAEVAQMKVHISELNLNAKEQAIEYKEKSRSMQRKAREEVRSILEEQEKLSNELDEKMRKLDTWSRDLNKREVLTDQERQKLEEDKKKVMYITFFSNQYMPILKIFYC*