AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0180000129.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 20 sgRNAs with CRISPR-Local

Find 51 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGTAGATCTTCGTAGAATT+TGG 0.177361 1:+1870564 None:intergenic
GGTGAATTGTCGCAGATATT+TGG 0.236061 1:-1870390 MsG0180000129.01.T01:intron
TTGGAGATTCCCGTGCTTAA+AGG 0.276086 1:-1870371 MsG0180000129.01.T01:CDS
TGTAGATCTTCGTAGAATTT+GGG 0.362572 1:+1870565 None:intergenic
TTAATCCCTTTACGTCTAGA+AGG 0.369196 1:+1870335 None:intergenic
TTATTCCTTCTAGACGTAAA+GGG 0.415844 1:-1870340 MsG0180000129.01.T01:CDS
GTTATTCCTTCTAGACGTAA+AGG 0.445368 1:-1870341 MsG0180000129.01.T01:CDS
GCGCAGTGCATCACCATACC+TGG 0.521524 1:-1870799 MsG0180000129.01.T01:CDS
GCATCACCATACCTGGTTCA+AGG 0.523106 1:-1870792 MsG0180000129.01.T01:CDS
AACAATCTCACCTTTAAGCA+CGG 0.530428 1:+1870361 None:intergenic
AAAGGGATTAAAAGTGGTGG+AGG 0.538533 1:-1870323 MsG0180000129.01.T01:CDS
ACAATCTCACCTTTAAGCAC+GGG 0.566321 1:+1870362 None:intergenic
AGACGTAAAGGGATTAAAAG+TGG 0.579688 1:-1870329 MsG0180000129.01.T01:CDS
CGTAAAGGGATTAAAAGTGG+TGG 0.606986 1:-1870326 MsG0180000129.01.T01:CDS
GAATTTGAGATTGTGTGGTG+TGG 0.608337 1:+1870850 None:intergenic
TATGAGAATTTGAGATTGTG+TGG 0.613739 1:+1870845 None:intergenic
GTGTTGGTGCAGACTCAACA+AGG 0.624217 1:-1870635 MsG0180000129.01.T01:intron
AAGGGATTAAAAGTGGTGGA+GGG 0.644540 1:-1870322 MsG0180000129.01.T01:CDS
CGAGCTTGTGATGACAATGG+TGG 0.702358 1:-1870526 MsG0180000129.01.T01:CDS
CAACGAGCTTGTGATGACAA+TGG 0.721779 1:-1870529 MsG0180000129.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGAAAACAATAATATGATAA+TGG + Chr1:1870461-1870480 None:intergenic 15.0%
!! AAACAAAACAAAAAACATGT+TGG + Chr1:1870496-1870515 None:intergenic 20.0%
!!! ATATGATAATGGAAATGATA+AGG + Chr1:1870450-1870469 None:intergenic 20.0%
! CTAATCTCATCTGAAAAAAT+GGG - Chr1:1870343-1870362 MsG0180000129.01.T01:CDS 25.0%
! TCTAATCTCATCTGAAAAAA+TGG - Chr1:1870342-1870361 MsG0180000129.01.T01:CDS 25.0%
ACTCAACAAGGAAAAAAAGT+GGG - Chr1:1870541-1870560 MsG0180000129.01.T01:CDS 30.0%
TAGAGAAGTTTCGTAAGATT+CGG - Chr1:1870753-1870772 MsG0180000129.01.T01:intron 30.0%
TGTAGATCTTCGTAGAATTT+GGG + Chr1:1870602-1870621 None:intergenic 30.0%
TTATTCCTTCTAGACGTAAA+GGG - Chr1:1870824-1870843 MsG0180000129.01.T01:CDS 30.0%
TTGTAGATCTTCGTAGAATT+TGG + Chr1:1870603-1870622 None:intergenic 30.0%
! TATGAGAATTTGAGATTGTG+TGG + Chr1:1870322-1870341 None:intergenic 30.0%
!! AAAGAGTATGTGGTTGATTT+TGG - Chr1:1870669-1870688 MsG0180000129.01.T01:intron 30.0%
!!! TACTACAGTACGTTTTTTGT+GGG + Chr1:1870416-1870435 None:intergenic 30.0%
!!! TTACTACAGTACGTTTTTTG+TGG + Chr1:1870417-1870436 None:intergenic 30.0%
!!! TTTTTTGTGTGTGTTTGTGT+TGG - Chr1:1870513-1870532 MsG0180000129.01.T01:CDS 30.0%
AACAATCTCACCTTTAAGCA+CGG + Chr1:1870806-1870825 None:intergenic 35.0%
AATGGAAATGATAAGGAACG+TGG + Chr1:1870443-1870462 None:intergenic 35.0%
AGACGTAAAGGGATTAAAAG+TGG - Chr1:1870835-1870854 MsG0180000129.01.T01:CDS 35.0%
GACTCAACAAGGAAAAAAAG+TGG - Chr1:1870540-1870559 MsG0180000129.01.T01:CDS 35.0%
GGAAAAAAAGTGGGCAATTT+CGG - Chr1:1870550-1870569 MsG0180000129.01.T01:CDS 35.0%
GTTATTCCTTCTAGACGTAA+AGG - Chr1:1870823-1870842 MsG0180000129.01.T01:CDS 35.0%
TGTTACCTAGGTAAAATGGA+TGG + Chr1:1870703-1870722 None:intergenic 35.0%
TTAATCCCTTTACGTCTAGA+AGG + Chr1:1870832-1870851 None:intergenic 35.0%
! ATCAACCACATACTCTTTTC+TGG + Chr1:1870667-1870686 None:intergenic 35.0%
! ATCCATTTTACCTAGGTAAC+AGG - Chr1:1870702-1870721 MsG0180000129.01.T01:intron 35.0%
! TCAACCACATACTCTTTTCT+GGG + Chr1:1870666-1870685 None:intergenic 35.0%
!! TATGTGGTTGATTTTGGTCT+GGG - Chr1:1870675-1870694 MsG0180000129.01.T01:intron 35.0%
AAAGGGATTAAAAGTGGTGG+AGG - Chr1:1870841-1870860 MsG0180000129.01.T01:CDS 40.0%
ACAATCTCACCTTTAAGCAC+GGG + Chr1:1870805-1870824 None:intergenic 40.0%
CGTAAAGGGATTAAAAGTGG+TGG - Chr1:1870838-1870857 MsG0180000129.01.T01:CDS 40.0%
GACCTGTTACCTAGGTAAAA+TGG + Chr1:1870707-1870726 None:intergenic 40.0%
GGTGAATTGTCGCAGATATT+TGG - Chr1:1870774-1870793 MsG0180000129.01.T01:CDS 40.0%
TCTTATGGTGAGTGATGATC+AGG - Chr1:1870730-1870749 MsG0180000129.01.T01:intron 40.0%
! AAGGGATTAAAAGTGGTGGA+GGG - Chr1:1870842-1870861 MsG0180000129.01.T01:CDS 40.0%
! AGAATGGTTTTCCTTGAACC+AGG + Chr1:1870386-1870405 None:intergenic 40.0%
! GAATTTGAGATTGTGTGGTG+TGG + Chr1:1870317-1870336 None:intergenic 40.0%
! TTTTGTGGGAAGTGGAAGAA+TGG + Chr1:1870402-1870421 None:intergenic 40.0%
!! GTATGTGGTTGATTTTGGTC+TGG - Chr1:1870674-1870693 MsG0180000129.01.T01:intron 40.0%
!!! AGTACGTTTTTTGTGGGAAG+TGG + Chr1:1870410-1870429 None:intergenic 40.0%
AGGTAACAGGTCTGCTCTTA+TGG - Chr1:1870715-1870734 MsG0180000129.01.T01:intron 45.0%
CAACGAGCTTGTGATGACAA+TGG - Chr1:1870635-1870654 MsG0180000129.01.T01:intron 45.0%
GGAAATGATAAGGAACGTGG+TGG + Chr1:1870440-1870459 None:intergenic 45.0%
TAAGAGCAGACCTGTTACCT+AGG + Chr1:1870715-1870734 None:intergenic 45.0%
TTGGAGATTCCCGTGCTTAA+AGG - Chr1:1870793-1870812 MsG0180000129.01.T01:CDS 45.0%
! GGAACCCAGAAAAGAGTATG+TGG - Chr1:1870659-1870678 MsG0180000129.01.T01:intron 45.0%
! GGGAACCATCCATTTTACCT+AGG - Chr1:1870695-1870714 MsG0180000129.01.T01:intron 45.0%
! GGTTTTCCTTGAACCAGGTA+TGG + Chr1:1870381-1870400 None:intergenic 45.0%
CGAGCTTGTGATGACAATGG+TGG - Chr1:1870638-1870657 MsG0180000129.01.T01:intron 50.0%
GCATCACCATACCTGGTTCA+AGG - Chr1:1870372-1870391 MsG0180000129.01.T01:CDS 50.0%
! GTGTTGGTGCAGACTCAACA+AGG - Chr1:1870529-1870548 MsG0180000129.01.T01:CDS 50.0%
GCGCAGTGCATCACCATACC+TGG - Chr1:1870365-1870384 MsG0180000129.01.T01:CDS 60.0%
Chromosome Type Strat End Strand Name
Chr1 gene 1870310 1870876 1870310 ID=MsG0180000129.01;Name=MsG0180000129.01
Chr1 mRNA 1870310 1870876 1870310 ID=MsG0180000129.01.T01;Parent=MsG0180000129.01;Name=MsG0180000129.01.T01;_AED=0.54;_eAED=0.54;_QI=0|0.5|0|1|0|0|3|0|111
Chr1 exon 1870762 1870876 1870762 ID=MsG0180000129.01.T01:exon:6986;Parent=MsG0180000129.01.T01
Chr1 exon 1870513 1870645 1870513 ID=MsG0180000129.01.T01:exon:6987;Parent=MsG0180000129.01.T01
Chr1 exon 1870310 1870397 1870310 ID=MsG0180000129.01.T01:exon:6988;Parent=MsG0180000129.01.T01
Chr1 CDS 1870762 1870876 1870762 ID=MsG0180000129.01.T01:cds;Parent=MsG0180000129.01.T01
Chr1 CDS 1870513 1870645 1870513 ID=MsG0180000129.01.T01:cds;Parent=MsG0180000129.01.T01
Chr1 CDS 1870310 1870397 1870310 ID=MsG0180000129.01.T01:cds;Parent=MsG0180000129.01.T01
Gene Sequence

>MsG0180000129.01.T01

ATGTCCACACCACACAATCTCAAATTCTCATATCTAATCTCATCTGAAAAAATGGGCGCAGTGCATCACCATACCTGGTTCAAGGAAAACCATTCTTCCACTTCCCACAAAAAACACTCAACAAGGAAAAAAAGTGGGCAATTTCGGAGTGTATTGCAAGAAGAAGACATACACCCAAATTCTACGAAGATCTACAAGTTTTACTGTAACAACGAGCTTGTGATGACAATGGTGGAACCCAGAAAAGAATATTTGGAGATTCCCGTGCTTAAAGGTGAGATTGTTATTCCTTCTAGACGTAAAGGGATTAAAAGTGGTGGAGGGAAGAAGAAGTGA

Protein sequence

>MsG0180000129.01.T01

MSTPHNLKFSYLISSEKMGAVHHHTWFKENHSSTSHKKHSTRKKSGQFRSVLQEEDIHPNSTKIYKFYCNNELVMTMVEPRKEYLEIPVLKGEIVIPSRRKGIKSGGGKKK*