AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0663090


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0663090 MtrunA17_Chr4g0021011 97.357 227 2 1 1 227 12 234 4.96e-162 447
Msa0663090 MtrunA17_Chr1g0154661 32.444 225 143 4 11 227 37 260 2.27e-31 115
Msa0663090 MtrunA17_Chr7g0246721 25.991 227 147 8 8 226 14 227 3.13e-11 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0663090 AT3G47430.1 74.222 225 57 1 3 227 4 227 5.76e-117 333
Msa0663090 AT1G47750.1 30.342 234 152 6 3 227 16 247 1.18e-24 98.2

Find 35 sgRNAs with CRISPR-Local

Find 48 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTAGCAGTGCTTTCTAATTC+AGG 0.262558 4_4:-1355553 Msa0663090:CDS
TTGAACCTCTTGGATATATC+AGG 0.291987 4_4:+1355688 None:intergenic
CACACGCCAGTTTGCAAGCT+TGG 0.301187 4_4:+1355723 None:intergenic
CTGGTTCTACTCTCACTTTA+AGG 0.302972 4_4:-1355579 Msa0663090:CDS
ATGAGTTTCATATCAGCTTT+TGG 0.313454 4_4:-1355451 Msa0663090:CDS
TTGCAAGCTTGGAAACATAT+TGG 0.323667 4_4:+1355734 None:intergenic
TTTCTTTGGTTATCAAGAAT+TGG 0.329320 4_4:-1355502 Msa0663090:CDS
ACTGTTTCTCTTGGTATTAG+TGG 0.331245 4_4:-1355193 Msa0663090:CDS
TTTGTCCACTGTGTCATTCA+TGG 0.336012 4_4:+1355810 None:intergenic
GGGCTGGTTGGTATAGAAAT+TGG 0.339600 4_4:-1355156 Msa0663090:CDS
GTGTGATTGCAGAAAGGATT+TGG 0.354377 4_4:+1355214 None:intergenic
AGAACTGGAAGATTTCTTAC+TGG 0.354482 4_4:-1355625 Msa0663090:CDS
TTCTCTTGGTATTAGTGGAT+TGG 0.370396 4_4:-1355188 Msa0663090:CDS
TTCTTGATAACCAAAGAAAA+TGG 0.395137 4_4:+1355506 None:intergenic
TGCAATCACACTGTTTCTCT+TGG 0.395141 4_4:-1355202 Msa0663090:CDS
GCTTTCTAATTCAGGAGAAA+TGG 0.401761 4_4:-1355545 Msa0663090:CDS
GAATGACACAGTGGACAAAT+TGG 0.413926 4_4:-1355806 Msa0663090:CDS
TGATAGAATAATGAGGCTTA+TGG 0.438357 4_4:-1355287 Msa0663090:CDS
TGGAACTGTGGATGCAAACT+TGG 0.446439 4_4:-1355482 Msa0663090:CDS
ATGTTTCCAAGCTTGCAAAC+TGG 0.447747 4_4:-1355729 Msa0663090:CDS
GGAATTAATTGACTTTATGA+AGG 0.456415 4_4:+1355133 None:intergenic
AGCAGAAAAGCATTCAGAAC+TGG 0.460756 4_4:-1355640 Msa0663090:CDS
TGGTTTCTGCATGGGCTGGT+TGG 0.463961 4_4:-1355168 Msa0663090:CDS
TAGTGGATTGGTTTCTGCAT+GGG 0.486842 4_4:-1355176 Msa0663090:CDS
TGCAGATTTGATTATAGCAT+TGG 0.487810 4_4:-1355248 Msa0663090:CDS
GGATTGGTTTCTGCATGGGC+TGG 0.505965 4_4:-1355172 Msa0663090:CDS
TTAGTGGATTGGTTTCTGCA+TGG 0.506709 4_4:-1355177 Msa0663090:CDS
TTTGTTGAATGAAGGGTTGA+AGG 0.511768 4_4:-1355386 Msa0663090:CDS
AATGCTCTTAGAAGAAATCC+TGG 0.530140 4_4:-1355598 Msa0663090:CDS
CAAGCTTGCAAACTGGCGTG+TGG 0.589710 4_4:-1355722 Msa0663090:CDS
CTTAAAGTGAGAGTAGAACC+AGG 0.591365 4_4:+1355580 None:intergenic
GAAACAGTGTGATTGCAGAA+AGG 0.592768 4_4:+1355208 None:intergenic
GTTATCAAGAATTGGAACTG+TGG 0.648703 4_4:-1355494 Msa0663090:CDS
CTCATCCTGATATATCCAAG+AGG 0.684877 4_4:-1355693 Msa0663090:CDS
TTCTACCATGAATGACACAG+TGG 0.746124 4_4:-1355815 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTCATTTTGTTGAATGAA+GGG - chr4_4:1355562-1355581 Msa0663090:CDS 20.0%
!! TAAAAAGTGATAGAATAATG+AGG - chr4_4:1355661-1355680 Msa0663090:CDS 20.0%
!! TTCTTGATAACCAAAGAAAA+TGG + chr4_4:1355452-1355471 None:intergenic 25.0%
! TTTCTTTGGTTATCAAGAAT+TGG - chr4_4:1355453-1355472 Msa0663090:CDS 25.0%
!! GATTTCATTTTGTTGAATGA+AGG - chr4_4:1355561-1355580 Msa0663090:CDS 25.0%
TATCCAAGAGGTTCAAAAAT+TGG - chr4_4:1355274-1355293 Msa0663090:CDS 30.0%
ATCCAAGAGGTTCAAAAATT+GGG - chr4_4:1355275-1355294 Msa0663090:CDS 30.0%
! TCTTCTTTGACCATTTTCTT+TGG - chr4_4:1355439-1355458 Msa0663090:CDS 30.0%
! ATGAGTTTCATATCAGCTTT+TGG - chr4_4:1355504-1355523 Msa0663090:CDS 30.0%
AAAAAGCTTAGAAGTTCAGA+GGG - chr4_4:1355597-1355616 Msa0663090:CDS 30.0%
TGATAGAATAATGAGGCTTA+TGG - chr4_4:1355668-1355687 Msa0663090:CDS 30.0%
TGCAGATTTGATTATAGCAT+TGG - chr4_4:1355707-1355726 Msa0663090:CDS 30.0%
ATCTTCCTAGCAAAAAGAGA+TGG - chr4_4:1355174-1355193 Msa0663090:CDS 35.0%
TTGCAAGCTTGGAAACATAT+TGG + chr4_4:1355224-1355243 None:intergenic 35.0%
TTGAACCTCTTGGATATATC+AGG + chr4_4:1355270-1355289 None:intergenic 35.0%
! TTCCCAATTTTTGAACCTCT+TGG + chr4_4:1355280-1355299 None:intergenic 35.0%
AGAACTGGAAGATTTCTTAC+TGG - chr4_4:1355330-1355349 Msa0663090:CDS 35.0%
AATGCTCTTAGAAGAAATCC+TGG - chr4_4:1355357-1355376 Msa0663090:CDS 35.0%
GCTTTCTAATTCAGGAGAAA+TGG - chr4_4:1355410-1355429 Msa0663090:CDS 35.0%
GTTATCAAGAATTGGAACTG+TGG - chr4_4:1355461-1355480 Msa0663090:CDS 35.0%
! TTTCATATCAGCTTTTGGTG+AGG - chr4_4:1355509-1355528 Msa0663090:CDS 35.0%
TTTGTTGAATGAAGGGTTGA+AGG - chr4_4:1355569-1355588 Msa0663090:CDS 35.0%
GAAAAAGCTTAGAAGTTCAG+AGG - chr4_4:1355596-1355615 Msa0663090:CDS 35.0%
! ACTGTTTCTCTTGGTATTAG+TGG - chr4_4:1355762-1355781 Msa0663090:CDS 35.0%
! TTCTCTTGGTATTAGTGGAT+TGG - chr4_4:1355767-1355786 Msa0663090:CDS 35.0%
GAATGACACAGTGGACAAAT+TGG - chr4_4:1355149-1355168 Msa0663090:CDS 40.0%
! CTATGCCATCTCTTTTTGCT+AGG + chr4_4:1355182-1355201 None:intergenic 40.0%
ATGTTTCCAAGCTTGCAAAC+TGG - chr4_4:1355226-1355245 Msa0663090:CDS 40.0%
CTCATCCTGATATATCCAAG+AGG - chr4_4:1355262-1355281 Msa0663090:CDS 40.0%
AAAAATTGGGAAGTAGCCTC+TGG - chr4_4:1355288-1355307 Msa0663090:CDS 40.0%
!! AGCAGAAAAGCATTCAGAAC+TGG - chr4_4:1355315-1355334 Msa0663090:CDS 40.0%
CTTAAAGTGAGAGTAGAACC+AGG + chr4_4:1355378-1355397 None:intergenic 40.0%
!! CTGGTTCTACTCTCACTTTA+AGG - chr4_4:1355376-1355395 Msa0663090:CDS 40.0%
CTAGCAGTGCTTTCTAATTC+AGG - chr4_4:1355402-1355421 Msa0663090:CDS 40.0%
GTGTGATTGCAGAAAGGATT+TGG + chr4_4:1355744-1355763 None:intergenic 40.0%
GAAACAGTGTGATTGCAGAA+AGG + chr4_4:1355750-1355769 None:intergenic 40.0%
! TGCAATCACACTGTTTCTCT+TGG - chr4_4:1355753-1355772 Msa0663090:CDS 40.0%
!! TTAGTGGATTGGTTTCTGCA+TGG - chr4_4:1355778-1355797 Msa0663090:CDS 40.0%
!! TAGTGGATTGGTTTCTGCAT+GGG - chr4_4:1355779-1355798 Msa0663090:CDS 40.0%
TGGAACTGTGGATGCAAACT+TGG - chr4_4:1355473-1355492 Msa0663090:CDS 45.0%
!! GGGCTGGTTGGTATAGAAAT+TGG - chr4_4:1355799-1355818 Msa0663090:CDS 45.0%
! TGCTTTTCTGCTGAGACCAG+AGG + chr4_4:1355307-1355326 None:intergenic 50.0%
! ATCAGCTTTTGGTGAGGCTG+TGG - chr4_4:1355515-1355534 Msa0663090:CDS 50.0%
! TCAGCTTTTGGTGAGGCTGT+GGG - chr4_4:1355516-1355535 Msa0663090:CDS 50.0%
CACACGCCAGTTTGCAAGCT+TGG + chr4_4:1355235-1355254 None:intergenic 55.0%
CAAGCTTGCAAACTGGCGTG+TGG - chr4_4:1355233-1355252 Msa0663090:CDS 55.0%
!! GGATTGGTTTCTGCATGGGC+TGG - chr4_4:1355783-1355802 Msa0663090:CDS 55.0%
!! TGGTTTCTGCATGGGCTGGT+TGG - chr4_4:1355787-1355806 Msa0663090:CDS 55.0%
Chromosome Type Strat End Strand Name
chr4_4 gene 1355147 1355830 1355147 ID=Msa0663090;Name=Msa0663090
chr4_4 mRNA 1355147 1355830 1355147 ID=Msa0663090-mRNA-1;Parent=Msa0663090;Name=Msa0663090-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|227
chr4_4 exon 1355147 1355830 1355147 ID=Msa0663090-mRNA-1:exon:436;Parent=Msa0663090-mRNA-1
chr4_4 CDS 1355147 1355830 1355147 ID=Msa0663090-mRNA-1:cds;Parent=Msa0663090-mRNA-1
Gene Sequence

>Msa0663090

ATGAATGACACAGTGGACAAATTGGTGATCTTCCTAGCAAAAAGAGATGGCATAGACAAGCTTGTGAAGACATTCCAATATGTTTCCAAGCTTGCAAACTGGCGTGTGGAAGTCACTCATCCTGATATATCCAAGAGGTTCAAAAATTGGGAAGTAGCCTCTGGTCTCAGCAGAAAAGCATTCAGAACTGGAAGATTTCTTACTGGATTCAATGCTCTTAGAAGAAATCCTGGTTCTACTCTCACTTTAAGGCTACTAGCAGTGCTTTCTAATTCAGGAGAAATGGTTTATTTCTTCTTTGACCATTTTCTTTGGTTATCAAGAATTGGAACTGTGGATGCAAACTTGGCAAAGAAGATGAGTTTCATATCAGCTTTTGGTGAGGCTGTGGGATATGTTTTCTTCATTATAGCTGATTTCATTTTGTTGAATGAAGGGTTGAAGGCTGAGAAAAAGCTTAGAAGTTCAGAGGGAAAAGAAAAATCAGAAAATAATGAAAAAGAGATTCAGAAATTAAAAAGTGATAGAATAATGAGGCTTATGGCTGTTGCTGCTAATGTTGCAGATTTGATTATAGCATTGGCTGAAATTGAGCCAAATCCTTTCTGCAATCACACTGTTTCTCTTGGTATTAGTGGATTGGTTTCTGCATGGGCTGGTTGGTATAGAAATTGGCCTTCATAA

Protein sequence

>Msa0663090

MNDTVDKLVIFLAKRDGIDKLVKTFQYVSKLANWRVEVTHPDISKRFKNWEVASGLSRKAFRTGRFLTGFNALRRNPGSTLTLRLLAVLSNSGEMVYFFFDHFLWLSRIGTVDANLAKKMSFISAFGEAVGYVFFIIADFILLNEGLKAEKKLRSSEGKEKSENNEKEIQKLKSDRIMRLMAVAANVADLIIALAEIEPNPFCNHTVSLGISGLVSAWAGWYRNWPS*