AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1234070

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1234070 MtrunA17_Chr8g0353741 99.038 104 1 0 1 104 246 349 1.02e-71 219
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 40 sgRNAs with CRISPR-Local

Find 120 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGTGGTTACATGGTCTAAC+TGG 0.224137 8_2:-11241909 Msa1234070:five_prime_UTR
TGACAAATGGCTCGAGAAAA+AGG 0.250141 8_2:-11241953 Msa1234070:five_prime_UTR
CTGTTAGCTGGATCAACTTA+AGG 0.272045 8_2:-11241735 Msa1234070:intron
CTTGTAAGCACTTGGTTGTT+CGG 0.324737 8_2:+11241492 None:intergenic
GTTCCTTTCAGTGAGGTATT+TGG 0.330408 8_2:-11241712 Msa1234070:CDS
TTGTAAGCACTTGGTTGTTC+GGG 0.331399 8_2:+11241493 None:intergenic
AGCATTTACCGGTTGAAATA+AGG 0.337859 8_2:+11241832 None:intergenic
GATAGCAGGCTTGGCATGGC+AGG 0.353519 8_2:-11241656 Msa1234070:CDS
TGTTAGCTGGATCAACTTAA+GGG 0.364997 8_2:-11241734 Msa1234070:intron
CTGCTGATCGATCACTGATA+TGG 0.379826 8_2:-11241525 Msa1234070:CDS
ATCAGCAGTCTGCCACATAA+TGG 0.411049 8_2:+11241540 None:intergenic
GCTGGCACTGCTCATGCATA+GGG 0.413949 8_2:-11241587 Msa1234070:CDS
CCAACTTTGCTGTGGTTACA+TGG 0.432008 8_2:-11241918 Msa1234070:five_prime_UTR
TGCTGGCACTGCTCATGCAT+AGG 0.451328 8_2:-11241588 Msa1234070:CDS
CCACATAATGGAGTTGGTAA+TGG 0.454379 8_2:+11241552 None:intergenic
GGCTGTTGAGATAGCAGGCT+TGG 0.474217 8_2:-11241665 Msa1234070:CDS
CCATGTAACCACAGCAAAGT+TGG 0.477162 8_2:+11241918 None:intergenic
CATTGAGTGAAGCTCTACTT+AGG 0.486355 8_2:-11241978 Msa1234070:five_prime_UTR
GAAAGCCACCTTATTTCAAC+CGG 0.492823 8_2:-11241840 Msa1234070:intron
TTCTGTGAGGTGCAATCTAA+AGG 0.503920 8_2:-11241689 Msa1234070:CDS
TATCTTAACTTGTAAGCACT+TGG 0.518187 8_2:+11241484 None:intergenic
CTCTACTTAGGCATGACAAA+TGG 0.520429 8_2:-11241966 Msa1234070:five_prime_UTR
CCATTACCAACTCCATTATG+TGG 0.523018 8_2:-11241552 Msa1234070:CDS
AAGGAGGCTGTTGAGATAGC+AGG 0.526134 8_2:-11241670 Msa1234070:CDS
TTGAGATAGCAGGCTTGGCA+TGG 0.531721 8_2:-11241660 Msa1234070:CDS
TGTGGTTACATGGTCTAACT+GGG 0.550055 8_2:-11241908 Msa1234070:five_prime_UTR
TAAATAAAGAACCTTCACTT+AGG 0.560908 8_2:-11242232 None:intergenic
ATAGCAGGCTTGGCATGGCA+GGG 0.561447 8_2:-11241655 Msa1234070:CDS
ATTTACCGGTTGAAATAAGG+TGG 0.581719 8_2:+11241835 None:intergenic
AGTCTGCCACATAATGGAGT+TGG 0.588727 8_2:+11241546 None:intergenic
GAACCAAATACCTCACTGAA+AGG 0.590238 8_2:+11241709 None:intergenic
AAAGAATGCCAACTTTGCTG+TGG 0.610380 8_2:-11241926 Msa1234070:five_prime_UTR
TGGCAGGGCCGTGCTCATTG+TGG 0.610622 8_2:-11241640 Msa1234070:CDS
CATCAAGACCACAATGAGCA+CGG 0.626290 8_2:+11241632 None:intergenic
CTGGCACTGCTCATGCATAG+GGG 0.636374 8_2:-11241586 Msa1234070:CDS
CTGAGCCCATACCTAAGTGA+AGG 0.651802 8_2:+11242221 None:intergenic
CTTAAGGGTTCCTTTCAGTG+AGG 0.652944 8_2:-11241719 Msa1234070:CDS
GTGAGGTATTTGGTTCTGTG+AGG 0.653734 8_2:-11241702 Msa1234070:CDS
TGTGAGGTGCAATCTAAAGG+AGG 0.669292 8_2:-11241686 Msa1234070:CDS
TATATGGTTCAGGTGGACAG+AGG 0.693553 8_2:-11242006 Msa1234070:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATCGTATTTCTTATTGTATA+TGG - chr8_2:11241680-11241699 Msa1234070:CDS 20.0%
!! ATCGTATTTCTTATTGTATA+TGG - chr8_2:11241680-11241699 Msa1234070:CDS 20.0%
!! CAAAGTATTTCTGTCATTAA+AGG + chr8_2:11241573-11241592 None:intergenic 25.0%
! TAGTATTTGACAAGCAAAAT+AGG + chr8_2:11241620-11241639 None:intergenic 25.0%
! TTTCTTATTGTATATGGTTC+AGG - chr8_2:11241686-11241705 Msa1234070:CDS 25.0%
! AATGATAACCTATGTTTATC+AGG - chr8_2:11241903-11241922 Msa1234070:five_prime_UTR 25.0%
! AATGAAATCCTGATAAACAT+AGG + chr8_2:11241914-11241933 None:intergenic 25.0%
!! CAAAGTATTTCTGTCATTAA+AGG + chr8_2:11241573-11241592 None:intergenic 25.0%
! TAGTATTTGACAAGCAAAAT+AGG + chr8_2:11241620-11241639 None:intergenic 25.0%
! TTTCTTATTGTATATGGTTC+AGG - chr8_2:11241686-11241705 Msa1234070:CDS 25.0%
! AATGATAACCTATGTTTATC+AGG - chr8_2:11241903-11241922 Msa1234070:five_prime_UTR 25.0%
! AATGAAATCCTGATAAACAT+AGG + chr8_2:11241914-11241933 None:intergenic 25.0%
TCAAAAGAGATTGTCTGTAA+GGG + chr8_2:11241520-11241539 None:intergenic 30.0%
TTCAAAAGAGATTGTCTGTA+AGG + chr8_2:11241521-11241540 None:intergenic 30.0%
TTGCTTGTCAAATACTACTT+TGG - chr8_2:11241623-11241642 Msa1234070:CDS 30.0%
! GCTTTCGAATTTTCTTGAAA+CGG + chr8_2:11241848-11241867 None:intergenic 30.0%
!! TATCTTAACTTGTAAGCACT+TGG + chr8_2:11242221-11242240 None:intergenic 30.0%
TCAAAAGAGATTGTCTGTAA+GGG + chr8_2:11241520-11241539 None:intergenic 30.0%
TTCAAAAGAGATTGTCTGTA+AGG + chr8_2:11241521-11241540 None:intergenic 30.0%
TTGCTTGTCAAATACTACTT+TGG - chr8_2:11241623-11241642 Msa1234070:CDS 30.0%
! GCTTTCGAATTTTCTTGAAA+CGG + chr8_2:11241848-11241867 None:intergenic 30.0%
!! TATCTTAACTTGTAAGCACT+TGG + chr8_2:11242221-11242240 None:intergenic 30.0%
CTGTCATTAAAGGTCAGTTT+GGG + chr8_2:11241563-11241582 None:intergenic 35.0%
TCTGTCATTAAAGGTCAGTT+TGG + chr8_2:11241564-11241583 None:intergenic 35.0%
GATTAACAATCTTCACCCAA+AGG + chr8_2:11241663-11241682 None:intergenic 35.0%
CTTATTGTATATGGTTCAGG+TGG - chr8_2:11241689-11241708 Msa1234070:CDS 35.0%
! ATTTACCGGTTGAAATAAGG+TGG + chr8_2:11241870-11241889 None:intergenic 35.0%
! AGCATTTACCGGTTGAAATA+AGG + chr8_2:11241873-11241892 None:intergenic 35.0%
TTATACTGTGCAGCATTTAC+CGG + chr8_2:11241884-11241903 None:intergenic 35.0%
TGTTAGCTGGATCAACTTAA+GGG - chr8_2:11241968-11241987 Msa1234070:five_prime_UTR 35.0%
CTGTCATTAAAGGTCAGTTT+GGG + chr8_2:11241563-11241582 None:intergenic 35.0%
TCTGTCATTAAAGGTCAGTT+TGG + chr8_2:11241564-11241583 None:intergenic 35.0%
GATTAACAATCTTCACCCAA+AGG + chr8_2:11241663-11241682 None:intergenic 35.0%
CTTATTGTATATGGTTCAGG+TGG - chr8_2:11241689-11241708 Msa1234070:CDS 35.0%
! ATTTACCGGTTGAAATAAGG+TGG + chr8_2:11241870-11241889 None:intergenic 35.0%
! AGCATTTACCGGTTGAAATA+AGG + chr8_2:11241873-11241892 None:intergenic 35.0%
TTATACTGTGCAGCATTTAC+CGG + chr8_2:11241884-11241903 None:intergenic 35.0%
TGTTAGCTGGATCAACTTAA+GGG - chr8_2:11241968-11241987 Msa1234070:five_prime_UTR 35.0%
GCTTGTTCATTCTTGCCTTT+GGG - chr8_2:11241645-11241664 Msa1234070:CDS 40.0%
CATTGAGTGAAGCTCTACTT+AGG - chr8_2:11241724-11241743 Msa1234070:CDS 40.0%
CTCTACTTAGGCATGACAAA+TGG - chr8_2:11241736-11241755 Msa1234070:intron 40.0%
TGACAAATGGCTCGAGAAAA+AGG - chr8_2:11241749-11241768 Msa1234070:intron 40.0%
GACAAATGGCTCGAGAAAAA+GGG - chr8_2:11241750-11241769 Msa1234070:intron 40.0%
AAAGAATGCCAACTTTGCTG+TGG - chr8_2:11241776-11241795 Msa1234070:intron 40.0%
TGTGGTTACATGGTCTAACT+GGG - chr8_2:11241794-11241813 Msa1234070:intron 40.0%
! GAAAGCCACCTTATTTCAAC+CGG - chr8_2:11241862-11241881 Msa1234070:CDS 40.0%
! GCTTTTGAACTTCTGTTAGC+TGG - chr8_2:11241955-11241974 Msa1234070:five_prime_UTR 40.0%
CTGTTAGCTGGATCAACTTA+AGG - chr8_2:11241967-11241986 Msa1234070:five_prime_UTR 40.0%
! GTTCCTTTCAGTGAGGTATT+TGG - chr8_2:11241990-11242009 Msa1234070:five_prime_UTR 40.0%
GAACCAAATACCTCACTGAA+AGG + chr8_2:11241996-11242015 None:intergenic 40.0%
TTCTGTGAGGTGCAATCTAA+AGG - chr8_2:11242013-11242032 Msa1234070:intron 40.0%
!! CCACATAATGGAGTTGGTAA+TGG + chr8_2:11242153-11242172 None:intergenic 40.0%
CCATTACCAACTCCATTATG+TGG - chr8_2:11242150-11242169 Msa1234070:intron 40.0%
TTGTAAGCACTTGGTTGTTC+GGG + chr8_2:11242212-11242231 None:intergenic 40.0%
CTTGTAAGCACTTGGTTGTT+CGG + chr8_2:11242213-11242232 None:intergenic 40.0%
GCTTGTTCATTCTTGCCTTT+GGG - chr8_2:11241645-11241664 Msa1234070:CDS 40.0%
CATTGAGTGAAGCTCTACTT+AGG - chr8_2:11241724-11241743 Msa1234070:CDS 40.0%
CTCTACTTAGGCATGACAAA+TGG - chr8_2:11241736-11241755 Msa1234070:intron 40.0%
TGACAAATGGCTCGAGAAAA+AGG - chr8_2:11241749-11241768 Msa1234070:intron 40.0%
GACAAATGGCTCGAGAAAAA+GGG - chr8_2:11241750-11241769 Msa1234070:intron 40.0%
AAAGAATGCCAACTTTGCTG+TGG - chr8_2:11241776-11241795 Msa1234070:intron 40.0%
TGTGGTTACATGGTCTAACT+GGG - chr8_2:11241794-11241813 Msa1234070:intron 40.0%
! GAAAGCCACCTTATTTCAAC+CGG - chr8_2:11241862-11241881 Msa1234070:CDS 40.0%
! GCTTTTGAACTTCTGTTAGC+TGG - chr8_2:11241955-11241974 Msa1234070:five_prime_UTR 40.0%
CTGTTAGCTGGATCAACTTA+AGG - chr8_2:11241967-11241986 Msa1234070:five_prime_UTR 40.0%
! GTTCCTTTCAGTGAGGTATT+TGG - chr8_2:11241990-11242009 Msa1234070:five_prime_UTR 40.0%
GAACCAAATACCTCACTGAA+AGG + chr8_2:11241996-11242015 None:intergenic 40.0%
TTCTGTGAGGTGCAATCTAA+AGG - chr8_2:11242013-11242032 Msa1234070:intron 40.0%
!! CCACATAATGGAGTTGGTAA+TGG + chr8_2:11242153-11242172 None:intergenic 40.0%
CCATTACCAACTCCATTATG+TGG - chr8_2:11242150-11242169 Msa1234070:intron 40.0%
TTGTAAGCACTTGGTTGTTC+GGG + chr8_2:11242212-11242231 None:intergenic 40.0%
CTTGTAAGCACTTGGTTGTT+CGG + chr8_2:11242213-11242232 None:intergenic 40.0%
! GGCTTGTTCATTCTTGCCTT+TGG - chr8_2:11241644-11241663 Msa1234070:CDS 45.0%
TATATGGTTCAGGTGGACAG+AGG - chr8_2:11241696-11241715 Msa1234070:CDS 45.0%
CCATGTAACCACAGCAAAGT+TGG + chr8_2:11241787-11241806 None:intergenic 45.0%
! CCAACTTTGCTGTGGTTACA+TGG - chr8_2:11241784-11241803 Msa1234070:intron 45.0%
CTGTGGTTACATGGTCTAAC+TGG - chr8_2:11241793-11241812 Msa1234070:intron 45.0%
CTTAAGGGTTCCTTTCAGTG+AGG - chr8_2:11241983-11242002 Msa1234070:five_prime_UTR 45.0%
!! GTGAGGTATTTGGTTCTGTG+AGG - chr8_2:11242000-11242019 Msa1234070:intron 45.0%
TGTGAGGTGCAATCTAAAGG+AGG - chr8_2:11242016-11242035 Msa1234070:intron 45.0%
CATCAAGACCACAATGAGCA+CGG + chr8_2:11242073-11242092 None:intergenic 45.0%
! CAGCAGACGAGCAGTATTTT+TGG + chr8_2:11242099-11242118 None:intergenic 45.0%
CAAAAATACTGCTCGTCTGC+TGG - chr8_2:11242097-11242116 Msa1234070:intron 45.0%
! AGTCTGCCACATAATGGAGT+TGG + chr8_2:11242159-11242178 None:intergenic 45.0%
ATCAGCAGTCTGCCACATAA+TGG + chr8_2:11242165-11242184 None:intergenic 45.0%
CTGCTGATCGATCACTGATA+TGG - chr8_2:11242177-11242196 Msa1234070:intron 45.0%
! GGCTTGTTCATTCTTGCCTT+TGG - chr8_2:11241644-11241663 Msa1234070:CDS 45.0%
TATATGGTTCAGGTGGACAG+AGG - chr8_2:11241696-11241715 Msa1234070:CDS 45.0%
CCATGTAACCACAGCAAAGT+TGG + chr8_2:11241787-11241806 None:intergenic 45.0%
! CCAACTTTGCTGTGGTTACA+TGG - chr8_2:11241784-11241803 Msa1234070:intron 45.0%
CTGTGGTTACATGGTCTAAC+TGG - chr8_2:11241793-11241812 Msa1234070:intron 45.0%
CTTAAGGGTTCCTTTCAGTG+AGG - chr8_2:11241983-11242002 Msa1234070:five_prime_UTR 45.0%
!! GTGAGGTATTTGGTTCTGTG+AGG - chr8_2:11242000-11242019 Msa1234070:intron 45.0%
TGTGAGGTGCAATCTAAAGG+AGG - chr8_2:11242016-11242035 Msa1234070:intron 45.0%
CATCAAGACCACAATGAGCA+CGG + chr8_2:11242073-11242092 None:intergenic 45.0%
! CAGCAGACGAGCAGTATTTT+TGG + chr8_2:11242099-11242118 None:intergenic 45.0%
CAAAAATACTGCTCGTCTGC+TGG - chr8_2:11242097-11242116 Msa1234070:intron 45.0%
! AGTCTGCCACATAATGGAGT+TGG + chr8_2:11242159-11242178 None:intergenic 45.0%
ATCAGCAGTCTGCCACATAA+TGG + chr8_2:11242165-11242184 None:intergenic 45.0%
CTGCTGATCGATCACTGATA+TGG - chr8_2:11242177-11242196 Msa1234070:intron 45.0%
CTGAGCCCATACCTAAGTGA+AGG + chr8_2:11241484-11241503 None:intergenic 50.0%
AAGGAGGCTGTTGAGATAGC+AGG - chr8_2:11242032-11242051 Msa1234070:intron 50.0%
TTGAGATAGCAGGCTTGGCA+TGG - chr8_2:11242042-11242061 Msa1234070:intron 50.0%
CTGAGCCCATACCTAAGTGA+AGG + chr8_2:11241484-11241503 None:intergenic 50.0%
AAGGAGGCTGTTGAGATAGC+AGG - chr8_2:11242032-11242051 Msa1234070:intron 50.0%
TTGAGATAGCAGGCTTGGCA+TGG - chr8_2:11242042-11242061 Msa1234070:intron 50.0%
GGCTGTTGAGATAGCAGGCT+TGG - chr8_2:11242037-11242056 Msa1234070:intron 55.0%
ATAGCAGGCTTGGCATGGCA+GGG - chr8_2:11242047-11242066 Msa1234070:intron 55.0%
TGCTGGCACTGCTCATGCAT+AGG - chr8_2:11242114-11242133 Msa1234070:intron 55.0%
GCTGGCACTGCTCATGCATA+GGG - chr8_2:11242115-11242134 Msa1234070:intron 55.0%
CTGGCACTGCTCATGCATAG+GGG - chr8_2:11242116-11242135 Msa1234070:intron 55.0%
GGCTGTTGAGATAGCAGGCT+TGG - chr8_2:11242037-11242056 Msa1234070:intron 55.0%
ATAGCAGGCTTGGCATGGCA+GGG - chr8_2:11242047-11242066 Msa1234070:intron 55.0%
TGCTGGCACTGCTCATGCAT+AGG - chr8_2:11242114-11242133 Msa1234070:intron 55.0%
GCTGGCACTGCTCATGCATA+GGG - chr8_2:11242115-11242134 Msa1234070:intron 55.0%
CTGGCACTGCTCATGCATAG+GGG - chr8_2:11242116-11242135 Msa1234070:intron 55.0%
GATAGCAGGCTTGGCATGGC+AGG - chr8_2:11242046-11242065 Msa1234070:intron 60.0%
GATAGCAGGCTTGGCATGGC+AGG - chr8_2:11242046-11242065 Msa1234070:intron 60.0%
TGGCAGGGCCGTGCTCATTG+TGG - chr8_2:11242062-11242081 Msa1234070:intron 65.0%
TGGCAGGGCCGTGCTCATTG+TGG - chr8_2:11242062-11242081 Msa1234070:intron 65.0%
Chromosome Type Strat End Strand Name
chr8_2 gene 11241477 11242247 11241477 ID=Msa1234070;Name=Msa1234070
chr8_2 mRNA 11241477 11242247 11241477 ID=Msa1234070-mRNA-1;Parent=Msa1234070;Name=Msa1234070-mRNA-1;_AED=0.02;_eAED=0.02;_QI=135|1|0.66|1|0.5|0.33|3|0|109
chr8_2 exon 11241477 11241750 11241477 ID=Msa1234070-mRNA-1:exon:4391;Parent=Msa1234070-mRNA-1
chr8_2 exon 11241841 11242016 11241841 ID=Msa1234070-mRNA-1:exon:4390;Parent=Msa1234070-mRNA-1
chr8_2 exon 11242233 11242247 11242233 ID=Msa1234070-mRNA-1:exon:4389;Parent=Msa1234070-mRNA-1
chr8_2 five_prime_UTR 11242233 11242247 11242233 ID=Msa1234070-mRNA-1:five_prime_utr;Parent=Msa1234070-mRNA-1
chr8_2 five_prime_UTR 11241897 11242016 11241897 ID=Msa1234070-mRNA-1:five_prime_utr;Parent=Msa1234070-mRNA-1
chr8_2 CDS 11241841 11241896 11241841 ID=Msa1234070-mRNA-1:cds;Parent=Msa1234070-mRNA-1
chr8_2 CDS 11241477 11241750 11241477 ID=Msa1234070-mRNA-1:cds;Parent=Msa1234070-mRNA-1
Gene Sequence

>Msa1234070

ATGCTTGAATCTGAGTGCCGTTTCAAGAAAATTCGAAAGCCACCTTATTTCAACCGCTGGATCAACTTAAGGGTTCCTTTCAGTGAGGTATTTGGTTCTGTGAGGTGCAATCTAAAGGAGGCTGTTGAGATAGCAGGCTTGGCATGGCAGGGCCGTGCTCATTGTGGTCTTGATGATGCCAAAAATACTGCTCGTCTGCTGGCACTGCTCATGCATAGGGGTTTTAAGTTTTCCATTACCAACTCCATTATGTGGCAGACTGCTGATCGATCACTGATATGGAAGCAGTCTCCCGAACAACCAAGTGCTTACAAGTTAAGATATTTTTAG
Protein sequence

>Msa1234070

MLESECRFKKIRKPPYFNRWINLRVPFSEVFGSVRCNLKEAVEIAGLAWQGRAHCGLDDAKNTARLLALLMHRGFKFSITNSIMWQTADRSLIWKQSPEQPSAYKLRYF*