AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1005380


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1005380 MtrunA17_Chr7g0214291 77.570 107 11 3 91 197 1 94 2.02e-40 135
Msa1005380 MtrunA17_Chr4g0066741 32.710 107 64 2 80 182 196 298 8.05e-13 66.2
Msa1005380 MtrunA17_Chr2g0286291 27.869 122 77 3 80 197 199 313 7.15e-12 63.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1005380 AT5G18620.1 30.328 122 74 3 80 197 202 316 2.19e-13 68.6
Msa1005380 AT5G18620.2 30.328 122 74 3 80 197 202 316 2.19e-13 68.6
Msa1005380 AT3G06400.3 30.328 122 74 3 80 197 197 311 3.68e-13 67.8
Msa1005380 AT3G06400.1 30.328 122 74 3 80 197 197 311 3.79e-13 67.8
Msa1005380 AT3G06400.2 30.328 122 74 3 80 197 197 311 3.79e-13 67.8

Find 40 sgRNAs with CRISPR-Local

Find 112 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTCCATCACCATTTAATTT+TGG 0.165025 7_1:-3036338 None:intergenic
ATGATACTTTAAGCCTTAAT+TGG 0.191299 7_1:+3035914 Msa1005380:CDS
TTAAACTCTCCAAAATTAAA+TGG 0.244854 7_1:+3036329 Msa1005380:CDS
AGAAATCGATTAACCAAGTT+TGG 0.260666 7_1:-3035357 None:intergenic
AGTGAAATATCATGATTTAA+AGG 0.299376 7_1:+3036219 Msa1005380:CDS
GAAGGTATTAACTATTGTTA+TGG 0.305658 7_1:+3035984 Msa1005380:CDS
CAACAACTCAGGAGAATTAA+TGG 0.337925 7_1:+3036115 Msa1005380:CDS
AAATATCAATCAGCCAATTA+AGG 0.350978 7_1:-3035927 None:intergenic
ACCATATCTTTACCACCTTC+AGG 0.371491 7_1:-3035540 None:intergenic
GAAGGATTCCTTTCCATCCT+AGG 0.377685 7_1:-3035636 None:intergenic
AAGGTATTAACTATTGTTAT+GGG 0.388633 7_1:+3035985 Msa1005380:CDS
AAATACCTTCGATTGATAGA+AGG 0.404032 7_1:-3035654 None:intergenic
CCAATGGTCCATCATCAACT+TGG 0.427516 7_1:-3036158 None:intergenic
TTTAAAGGAAGTTGATTTGA+AGG 0.435712 7_1:+3036234 Msa1005380:CDS
TGTTGCAAACAATGTTGAAA+AGG 0.480563 7_1:+3036303 Msa1005380:CDS
AATAGGCAGTAACATGGCGC+TGG 0.498728 7_1:+3035885 Msa1005380:intron
TTGCCATTGTCGTTGCTCCT+AGG 0.498730 7_1:+3035619 Msa1005380:CDS
TCCTGAAGGTGGTAAAGATA+TGG 0.515727 7_1:+3035539 Msa1005380:CDS
TCTCCAAAATTAAATGGTGA+TGG 0.515919 7_1:+3036335 Msa1005380:CDS
GCTGATGATGATGGTGGGAG+TGG 0.523385 7_1:+3035591 Msa1005380:CDS
TCTCACGCCCAAGTTGATGA+TGG 0.528994 7_1:+3036150 Msa1005380:CDS
CATTGTCGTTGCTCCTAGGA+TGG 0.538312 7_1:+3035623 Msa1005380:CDS
CCAAGTTGATGATGGACCAT+TGG 0.554041 7_1:+3036158 Msa1005380:CDS
TATTAATCTTATCAATCCAA+TGG 0.563475 7_1:-3036174 None:intergenic
AAGCTAATATCATCCAAACT+TGG 0.565067 7_1:+3035344 Msa1005380:CDS
CAATGGTCCATCATCAACTT+GGG 0.577723 7_1:-3036157 None:intergenic
AAAGTTGCTGCTGATGATGA+TGG 0.585831 7_1:+3035582 Msa1005380:CDS
TATCATACTTGCAACAACTC+AGG 0.593179 7_1:+3036104 Msa1005380:CDS
ATAGGCAGTAACATGGCGCT+GGG 0.596708 7_1:+3035886 Msa1005380:intron
TTGTTCAATAGGCAGTAACA+TGG 0.605014 7_1:+3035879 Msa1005380:intron
TCGTTGCTCCTAGGATGGAA+AGG 0.616152 7_1:+3035628 Msa1005380:CDS
GGAATCCTTCTATCAATCGA+AGG 0.618500 7_1:+3035649 Msa1005380:CDS
CATCCTAGGAGCAACGACAA+TGG 0.624587 7_1:-3035622 None:intergenic
TGGAGTCTTAGCATACGAGA+AGG 0.658530 7_1:+3035966 Msa1005380:CDS
GATAATGTTGTTGATCCTGA+AGG 0.664854 7_1:+3035525 Msa1005380:CDS
TTGCTGCTGATGATGATGGT+GGG 0.685686 7_1:+3035586 Msa1005380:CDS
TTGGGCGTGAGAATCAAATG+AGG 0.687571 7_1:-3036139 None:intergenic
GTTGCTGCTGATGATGATGG+TGG 0.691465 7_1:+3035585 Msa1005380:CDS
AATGTTGTTGATCCTGAAGG+TGG 0.708685 7_1:+3035528 Msa1005380:CDS
ATGGTCGTTGATCTTGAACG+TGG 0.746664 7_1:+3035558 Msa1005380:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTAAGTTTTCTTTTATTTC+AGG + chr7_1:3035742-3035761 Msa1005380:intron 15.0%
!!! TTTAAGTTTTCTTTTATTTC+AGG + chr7_1:3035742-3035761 Msa1005380:intron 15.0%
!!! AAGGTATTAACTATTGTTAT+GGG + chr7_1:3035985-3036004 Msa1005380:CDS 20.0%
!! TATTAATCTTATCAATCCAA+TGG - chr7_1:3036177-3036196 None:intergenic 20.0%
!! AGTGAAATATCATGATTTAA+AGG + chr7_1:3036219-3036238 Msa1005380:CDS 20.0%
!! TTAAACTCTCCAAAATTAAA+TGG + chr7_1:3036329-3036348 Msa1005380:CDS 20.0%
!!! AAGGTATTAACTATTGTTAT+GGG + chr7_1:3035985-3036004 Msa1005380:CDS 20.0%
!! TATTAATCTTATCAATCCAA+TGG - chr7_1:3036177-3036196 None:intergenic 20.0%
!! AGTGAAATATCATGATTTAA+AGG + chr7_1:3036219-3036238 Msa1005380:CDS 20.0%
!! TTAAACTCTCCAAAATTAAA+TGG + chr7_1:3036329-3036348 Msa1005380:CDS 20.0%
!!! TGAACATGTTGATTGTTTTT+TGG + chr7_1:3035428-3035447 Msa1005380:intron 25.0%
!!! GAACATGTTGATTGTTTTTT+GGG + chr7_1:3035429-3035448 Msa1005380:intron 25.0%
!! TATTTAATGAACCTTGTTGT+TGG + chr7_1:3035453-3035472 Msa1005380:intron 25.0%
! AGTTTCTTTAATCCATTGAA+TGG + chr7_1:3035823-3035842 Msa1005380:intron 25.0%
! ATGATACTTTAAGCCTTAAT+TGG + chr7_1:3035914-3035933 Msa1005380:CDS 25.0%
! AAATATCAATCAGCCAATTA+AGG - chr7_1:3035930-3035949 None:intergenic 25.0%
!!! GAAGGTATTAACTATTGTTA+TGG + chr7_1:3035984-3036003 Msa1005380:CDS 25.0%
!!! TTTAAAGGAAGTTGATTTGA+AGG + chr7_1:3036234-3036253 Msa1005380:CDS 25.0%
!!! TGAACATGTTGATTGTTTTT+TGG + chr7_1:3035428-3035447 Msa1005380:intron 25.0%
!!! GAACATGTTGATTGTTTTTT+GGG + chr7_1:3035429-3035448 Msa1005380:intron 25.0%
!! TATTTAATGAACCTTGTTGT+TGG + chr7_1:3035453-3035472 Msa1005380:intron 25.0%
! AGTTTCTTTAATCCATTGAA+TGG + chr7_1:3035823-3035842 Msa1005380:intron 25.0%
! ATGATACTTTAAGCCTTAAT+TGG + chr7_1:3035914-3035933 Msa1005380:CDS 25.0%
! AAATATCAATCAGCCAATTA+AGG - chr7_1:3035930-3035949 None:intergenic 25.0%
!!! GAAGGTATTAACTATTGTTA+TGG + chr7_1:3035984-3036003 Msa1005380:CDS 25.0%
!!! TTTAAAGGAAGTTGATTTGA+AGG + chr7_1:3036234-3036253 Msa1005380:CDS 25.0%
AAGCTAATATCATCCAAACT+TGG + chr7_1:3035344-3035363 Msa1005380:CDS 30.0%
AGAAATCGATTAACCAAGTT+TGG - chr7_1:3035360-3035379 None:intergenic 30.0%
AGAGACTCAAACTAATTAGA+TGG - chr7_1:3035393-3035412 None:intergenic 30.0%
! ATCTAATTAGTTTGAGTCTC+TGG + chr7_1:3035392-3035411 Msa1005380:intron 30.0%
AAATACCTTCGATTGATAGA+AGG - chr7_1:3035657-3035676 None:intergenic 30.0%
AGATTAATGCAACCATTCAA+TGG - chr7_1:3035838-3035857 None:intergenic 30.0%
TTGCCCATTATTTGTTCAAT+AGG + chr7_1:3035868-3035887 Msa1005380:intron 30.0%
CTGCCTATTGAACAAATAAT+GGG - chr7_1:3035874-3035893 None:intergenic 30.0%
ACTGCCTATTGAACAAATAA+TGG - chr7_1:3035875-3035894 None:intergenic 30.0%
! ATTTTCGATCGATCTATGAA+TGG + chr7_1:3035946-3035965 Msa1005380:CDS 30.0%
TGTTGCAAACAATGTTGAAA+AGG + chr7_1:3036303-3036322 Msa1005380:CDS 30.0%
AAGCTAATATCATCCAAACT+TGG + chr7_1:3035344-3035363 Msa1005380:CDS 30.0%
AGAAATCGATTAACCAAGTT+TGG - chr7_1:3035360-3035379 None:intergenic 30.0%
AGAGACTCAAACTAATTAGA+TGG - chr7_1:3035393-3035412 None:intergenic 30.0%
! ATCTAATTAGTTTGAGTCTC+TGG + chr7_1:3035392-3035411 Msa1005380:intron 30.0%
AAATACCTTCGATTGATAGA+AGG - chr7_1:3035657-3035676 None:intergenic 30.0%
AGATTAATGCAACCATTCAA+TGG - chr7_1:3035838-3035857 None:intergenic 30.0%
TTGCCCATTATTTGTTCAAT+AGG + chr7_1:3035868-3035887 Msa1005380:intron 30.0%
CTGCCTATTGAACAAATAAT+GGG - chr7_1:3035874-3035893 None:intergenic 30.0%
ACTGCCTATTGAACAAATAA+TGG - chr7_1:3035875-3035894 None:intergenic 30.0%
! ATTTTCGATCGATCTATGAA+TGG + chr7_1:3035946-3035965 Msa1005380:CDS 30.0%
TGTTGCAAACAATGTTGAAA+AGG + chr7_1:3036303-3036322 Msa1005380:CDS 30.0%
!! TTAATGAACCTTGTTGTTGG+TGG + chr7_1:3035456-3035475 Msa1005380:intron 35.0%
!! TGAAAAGTTGTTGGTGTTGA+AGG + chr7_1:3035480-3035499 Msa1005380:intron 35.0%
GATAATGTTGTTGATCCTGA+AGG + chr7_1:3035525-3035544 Msa1005380:CDS 35.0%
!!! CAATCGAAGGTATTTTACCA+AGG + chr7_1:3035662-3035681 Msa1005380:intron 35.0%
TTGTTCAATAGGCAGTAACA+TGG + chr7_1:3035879-3035898 Msa1005380:intron 35.0%
TATCATACTTGCAACAACTC+AGG + chr7_1:3036104-3036123 Msa1005380:CDS 35.0%
CAACAACTCAGGAGAATTAA+TGG + chr7_1:3036115-3036134 Msa1005380:CDS 35.0%
!! TTAATGAACCTTGTTGTTGG+TGG + chr7_1:3035456-3035475 Msa1005380:intron 35.0%
!! TGAAAAGTTGTTGGTGTTGA+AGG + chr7_1:3035480-3035499 Msa1005380:intron 35.0%
GATAATGTTGTTGATCCTGA+AGG + chr7_1:3035525-3035544 Msa1005380:CDS 35.0%
!!! CAATCGAAGGTATTTTACCA+AGG + chr7_1:3035662-3035681 Msa1005380:intron 35.0%
TTGTTCAATAGGCAGTAACA+TGG + chr7_1:3035879-3035898 Msa1005380:intron 35.0%
TATCATACTTGCAACAACTC+AGG + chr7_1:3036104-3036123 Msa1005380:CDS 35.0%
CAACAACTCAGGAGAATTAA+TGG + chr7_1:3036115-3036134 Msa1005380:CDS 35.0%
! CTTTTCAACCACCAACAACA+AGG - chr7_1:3035467-3035486 None:intergenic 40.0%
!! GTTGGTGGTTGAAAAGTTGT+TGG + chr7_1:3035471-3035490 Msa1005380:intron 40.0%
AATGTTGTTGATCCTGAAGG+TGG + chr7_1:3035528-3035547 Msa1005380:CDS 40.0%
TCCTGAAGGTGGTAAAGATA+TGG + chr7_1:3035539-3035558 Msa1005380:CDS 40.0%
ACCATATCTTTACCACCTTC+AGG - chr7_1:3035543-3035562 None:intergenic 40.0%
! AAAGTTGCTGCTGATGATGA+TGG + chr7_1:3035582-3035601 Msa1005380:CDS 40.0%
GGAATCCTTCTATCAATCGA+AGG + chr7_1:3035649-3035668 Msa1005380:CDS 40.0%
CAATGGTCCATCATCAACTT+GGG - chr7_1:3036160-3036179 None:intergenic 40.0%
! CTTTTCAACCACCAACAACA+AGG - chr7_1:3035467-3035486 None:intergenic 40.0%
!! GTTGGTGGTTGAAAAGTTGT+TGG + chr7_1:3035471-3035490 Msa1005380:intron 40.0%
AATGTTGTTGATCCTGAAGG+TGG + chr7_1:3035528-3035547 Msa1005380:CDS 40.0%
TCCTGAAGGTGGTAAAGATA+TGG + chr7_1:3035539-3035558 Msa1005380:CDS 40.0%
ACCATATCTTTACCACCTTC+AGG - chr7_1:3035543-3035562 None:intergenic 40.0%
! AAAGTTGCTGCTGATGATGA+TGG + chr7_1:3035582-3035601 Msa1005380:CDS 40.0%
GGAATCCTTCTATCAATCGA+AGG + chr7_1:3035649-3035668 Msa1005380:CDS 40.0%
CAATGGTCCATCATCAACTT+GGG - chr7_1:3036160-3036179 None:intergenic 40.0%
ATGGTCGTTGATCTTGAACG+TGG + chr7_1:3035558-3035577 Msa1005380:CDS 45.0%
!! TTGCTGCTGATGATGATGGT+GGG + chr7_1:3035586-3035605 Msa1005380:CDS 45.0%
GAAGGATTCCTTTCCATCCT+AGG - chr7_1:3035639-3035658 None:intergenic 45.0%
TCAATCACGATTTGCGTCCT+TGG - chr7_1:3035682-3035701 None:intergenic 45.0%
TGGAGTCTTAGCATACGAGA+AGG + chr7_1:3035966-3035985 Msa1005380:CDS 45.0%
TTGGGCGTGAGAATCAAATG+AGG - chr7_1:3036142-3036161 None:intergenic 45.0%
CCAATGGTCCATCATCAACT+TGG - chr7_1:3036161-3036180 None:intergenic 45.0%
!! CCAAGTTGATGATGGACCAT+TGG + chr7_1:3036158-3036177 Msa1005380:CDS 45.0%
ATGGTCGTTGATCTTGAACG+TGG + chr7_1:3035558-3035577 Msa1005380:CDS 45.0%
!! TTGCTGCTGATGATGATGGT+GGG + chr7_1:3035586-3035605 Msa1005380:CDS 45.0%
GAAGGATTCCTTTCCATCCT+AGG - chr7_1:3035639-3035658 None:intergenic 45.0%
TCAATCACGATTTGCGTCCT+TGG - chr7_1:3035682-3035701 None:intergenic 45.0%
TGGAGTCTTAGCATACGAGA+AGG + chr7_1:3035966-3035985 Msa1005380:CDS 45.0%
TTGGGCGTGAGAATCAAATG+AGG - chr7_1:3036142-3036161 None:intergenic 45.0%
CCAATGGTCCATCATCAACT+TGG - chr7_1:3036161-3036180 None:intergenic 45.0%
!! CCAAGTTGATGATGGACCAT+TGG + chr7_1:3036158-3036177 Msa1005380:CDS 45.0%
!! GTTGCTGCTGATGATGATGG+TGG + chr7_1:3035585-3035604 Msa1005380:CDS 50.0%
TTGCCATTGTCGTTGCTCCT+AGG + chr7_1:3035619-3035638 Msa1005380:CDS 50.0%
CATCCTAGGAGCAACGACAA+TGG - chr7_1:3035625-3035644 None:intergenic 50.0%
CATTGTCGTTGCTCCTAGGA+TGG + chr7_1:3035623-3035642 Msa1005380:CDS 50.0%
TCGTTGCTCCTAGGATGGAA+AGG + chr7_1:3035628-3035647 Msa1005380:CDS 50.0%
AATAGGCAGTAACATGGCGC+TGG + chr7_1:3035885-3035904 Msa1005380:intron 50.0%
ATAGGCAGTAACATGGCGCT+GGG + chr7_1:3035886-3035905 Msa1005380:intron 50.0%
!! TCTCACGCCCAAGTTGATGA+TGG + chr7_1:3036150-3036169 Msa1005380:CDS 50.0%
!! GTTGCTGCTGATGATGATGG+TGG + chr7_1:3035585-3035604 Msa1005380:CDS 50.0%
TTGCCATTGTCGTTGCTCCT+AGG + chr7_1:3035619-3035638 Msa1005380:CDS 50.0%
CATCCTAGGAGCAACGACAA+TGG - chr7_1:3035625-3035644 None:intergenic 50.0%
CATTGTCGTTGCTCCTAGGA+TGG + chr7_1:3035623-3035642 Msa1005380:CDS 50.0%
TCGTTGCTCCTAGGATGGAA+AGG + chr7_1:3035628-3035647 Msa1005380:CDS 50.0%
AATAGGCAGTAACATGGCGC+TGG + chr7_1:3035885-3035904 Msa1005380:intron 50.0%
ATAGGCAGTAACATGGCGCT+GGG + chr7_1:3035886-3035905 Msa1005380:intron 50.0%
!! TCTCACGCCCAAGTTGATGA+TGG + chr7_1:3036150-3036169 Msa1005380:CDS 50.0%
!! GCTGATGATGATGGTGGGAG+TGG + chr7_1:3035591-3035610 Msa1005380:CDS 55.0%
!! GCTGATGATGATGGTGGGAG+TGG + chr7_1:3035591-3035610 Msa1005380:CDS 55.0%
Chromosome Type Strat End Strand Name
chr7_1 gene 3035323 3036354 3035323 ID=Msa1005380;Name=Msa1005380
chr7_1 mRNA 3035323 3036354 3035323 ID=Msa1005380-mRNA-1;Parent=Msa1005380;Name=Msa1005380-mRNA-1;_AED=0.43;_eAED=0.48;_QI=0|0|0|0.5|1|1|4|0|197
chr7_1 exon 3035323 3035365 3035323 ID=Msa1005380-mRNA-1:exon:1308;Parent=Msa1005380-mRNA-1
chr7_1 exon 3035511 3035670 3035511 ID=Msa1005380-mRNA-1:exon:1309;Parent=Msa1005380-mRNA-1
chr7_1 exon 3035894 3036006 3035894 ID=Msa1005380-mRNA-1:exon:1310;Parent=Msa1005380-mRNA-1
chr7_1 exon 3036077 3036354 3036077 ID=Msa1005380-mRNA-1:exon:1311;Parent=Msa1005380-mRNA-1
chr7_1 CDS 3035323 3035365 3035323 ID=Msa1005380-mRNA-1:cds;Parent=Msa1005380-mRNA-1
chr7_1 CDS 3035511 3035670 3035511 ID=Msa1005380-mRNA-1:cds;Parent=Msa1005380-mRNA-1
chr7_1 CDS 3035894 3036006 3035894 ID=Msa1005380-mRNA-1:cds;Parent=Msa1005380-mRNA-1
chr7_1 CDS 3036077 3036354 3036077 ID=Msa1005380-mRNA-1:cds;Parent=Msa1005380-mRNA-1
Gene Sequence

>Msa1005380

ATGACATATTATTATTTAATAAAGCTAATATCATCCAAACTTGTTTCTGTTGTTGATGATAATGTTGTTGATCCTGAAGGTGGTAAAGATATGGTCGTTGATCTTGAACGTGGTAAAGTTGCTGCTGATGATGATGGTGGGAGTGGACACATTGCCATTGTCGTTGCTCCTAGGATGGAAAGGAATCCTTCTATCAATCGAAGTAACATGGCGCTGGGATATCATGATACTTTAAGCCTTAATTGGCTGATTGATATTTTCGATCGATCTATGAATGGAGTCTTAGCATACGAGAAGGTATTAACTATTGTTATGGAAAACATTGATAAAATTATATATCTTCTATCATACTTGCAACAACTCAGGAGAATTAATGGTCCTCATTTGATTCTCACGCCCAAGTTGATGATGGACCATTGGATTGATAAGATTAATAGAATTGTTTCAGAGCTAAATACAGTGAAATATCATGATTTAAAGGAAGTTGATTTGAAGGAAGCTAGCTTATCACATTTACATATATGTATAGCTAGTTTTGAAGATGTTGCAAACAATGTTGAAAAGGAATTTAAACTCTCCAAAATTAAATGGTGA

Protein sequence

>Msa1005380

MTYYYLIKLISSKLVSVVDDNVVDPEGGKDMVVDLERGKVAADDDGGSGHIAIVVAPRMERNPSINRSNMALGYHDTLSLNWLIDIFDRSMNGVLAYEKVLTIVMENIDKIIYLLSYLQQLRRINGPHLILTPKLMMDHWIDKINRIVSELNTVKYHDLKEVDLKEASLSHLHICIASFEDVANNVEKEFKLSKIKW*