AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0478860


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0478860 MtrunA17_Chr3g0141701 63.115 122 8 2 1 85 1 122 1.32e-42 135
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 17 sgRNAs with CRISPR-Local

Find 110 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAATTCCAACATTTGTGTTC+TGG 0.239933 3_3:-83676561 Msa0478860:CDS
AATTCCAACATTTGTGTTCT+GGG 0.279236 3_3:-83676560 Msa0478860:CDS
TTTGACTTGGACTTGTACTT+TGG 0.409420 3_3:+83673884 None:intergenic
CTCATGTATCTTGTTTGACT+TGG 0.410489 3_3:+83673871 None:intergenic
ACCACTGACTTGGCAGGTGG+CGG 0.515445 3_3:+83676285 None:intergenic
TTTACTATTTGATGCAAGGT+CGG 0.516012 3_3:+83676483 None:intergenic
TTGTACTTTGGAAGCATCAT+CGG 0.516399 3_3:+83673896 None:intergenic
TCTACAACCACTGACTTGGC+AGG 0.516779 3_3:+83676279 None:intergenic
ATTCTTTACTATTTGATGCA+AGG 0.520583 3_3:+83676479 None:intergenic
GTGTTGGTGTGATTATTGTA+AGG 0.522525 3_3:+83676533 None:intergenic
AAAGCCCAGAACACAAATGT+TGG 0.544379 3_3:+83676556 None:intergenic
ATGAAGGTAAGAAGAATGAT+CGG 0.544526 3_3:-83676339 Msa0478860:CDS
TGAAGGTAAGAAGAATGATC+GGG 0.567599 3_3:-83676338 Msa0478860:CDS
AAATATAACAGAGACAATGA+AGG 0.611259 3_3:-83676355 Msa0478860:CDS
TACTTTGGAAGCATCATCGG+TGG 0.630715 3_3:+83673899 None:intergenic
ACAACCACTGACTTGGCAGG+TGG 0.640558 3_3:+83676282 None:intergenic
TCGGACAAGAGAATTAGTGT+TGG 0.641471 3_3:+83676517 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAAATTAATTGTATCAATTT+TGG + chr3_3:83674030-83674049 None:intergenic 10.0%
!!! AATTAATTTTCTCTTTAATT+AGG - chr3_3:83674040-83674059 Msa0478860:intron 10.0%
!!! TGAATAAGTTATTTTGAAAA+AGG + chr3_3:83675399-83675418 None:intergenic 15.0%
!! TCAAAAAAAACTTATTCAAA+AGG + chr3_3:83674612-83674631 None:intergenic 15.0%
!!! TGAATAAGTTATTTTGAAAA+AGG - chr3_3:83675399-83675418 Msa0478860:intron 15.0%
!!! TGAATAAGTTATTTTGAAAA+AGG - chr3_3:83675399-83675418 Msa0478860:intron 15.0%
!!! TGAATAAGTTATTTTGAAAA+AGG - chr3_3:83675399-83675418 Msa0478860:intron 15.0%
!!! TAATTAAGTTGTTTTGAAAA+AGG - chr3_3:83676168-83676187 Msa0478860:intron 15.0%
!!! CTGAATTGTTTTTGAATTTA+TGG + chr3_3:83674322-83674341 None:intergenic 20.0%
!! ATGGTTCAAATATATTAAAC+TGG + chr3_3:83674369-83674388 None:intergenic 20.0%
!!! GAAAGTGTACTAAAAAAATA+TGG + chr3_3:83674388-83674407 None:intergenic 20.0%
!! AACAACTTATTTACGTAAAA+CGG - chr3_3:83674631-83674650 Msa0478860:intron 20.0%
!! AACAACTTATTTACGTAAAA+CGG - chr3_3:83674631-83674650 Msa0478860:intron 20.0%
!! TTACACAAAAAAAGCTTATT+AGG - chr3_3:83674943-83674962 Msa0478860:intron 20.0%
!! TTACACAAAAAAAGCTTATT+AGG + chr3_3:83674943-83674962 None:intergenic 20.0%
!! AACAACTTATTTACGTAAAA+CGG + chr3_3:83674631-83674650 None:intergenic 20.0%
!! AACAACTTATTTACGTAAAA+CGG + chr3_3:83674631-83674650 None:intergenic 20.0%
!!! ATAAGTTATTTTGAAAAAGG+AGG - chr3_3:83675402-83675421 Msa0478860:intron 20.0%
!! ATTACGTAAAACAACTTATT+AGG + chr3_3:83676152-83676171 None:intergenic 20.0%
!!! GATTTTAGTCATTGTTTATT+AGG + chr3_3:83676198-83676217 None:intergenic 20.0%
!! AATAAACAATGACTAAAATC+CGG - chr3_3:83676198-83676217 Msa0478860:intron 20.0%
!!! TAAACCAGTTTTTTTTAAAG+TGG - chr3_3:83676369-83676388 Msa0478860:intron 20.0%
!!! AAAACCACTTTAAAAAAAAC+TGG + chr3_3:83676376-83676395 None:intergenic 20.0%
! ATTCTTTACTATTTGATGCA+AGG + chr3_3:83673979-83673998 None:intergenic 25.0%
! AAATATAACAGAGACAATGA+AGG - chr3_3:83674100-83674119 Msa0478860:intron 25.0%
!!! TTAAATGGTGCAGTTTTTTT+TGG + chr3_3:83674282-83674301 None:intergenic 25.0%
! AAAAAACTGCACCATTTAAA+TGG - chr3_3:83674283-83674302 Msa0478860:intron 25.0%
! CAGTTCATAAACCATTTAAA+TGG + chr3_3:83674297-83674316 None:intergenic 25.0%
!! ATTCAGTTCAAGTTTAAAAC+CGG - chr3_3:83674336-83674355 Msa0478860:intron 25.0%
! TTTACGCAAAATAGCTTATT+AGG - chr3_3:83674700-83674719 Msa0478860:intron 25.0%
! TTTACGCAAAATAGCTTATT+AGG - chr3_3:83674700-83674719 Msa0478860:intron 25.0%
! TTTATGCAAAACGACTTATT+CGG - chr3_3:83674880-83674899 Msa0478860:intron 25.0%
! TTTACGCAAAATAGCTTATT+AGG + chr3_3:83674700-83674719 None:intergenic 25.0%
! AACAGCTTATTTACGTAAAA+CGG + chr3_3:83675135-83675154 None:intergenic 25.0%
! TTTATGCAAAACGACTTATT+AGG + chr3_3:83674880-83674899 None:intergenic 25.0%
! TTTACGCAAAATAGCTTATT+AGG + chr3_3:83674700-83674719 None:intergenic 25.0%
! AACAGCTTATTTACGTAAAA+CGG + chr3_3:83675135-83675154 None:intergenic 25.0%
! TTTATGCAAAACGACTTATT+CGG + chr3_3:83674880-83674899 None:intergenic 25.0%
! TTTACGCAAAATAGCTTATT+AGG + chr3_3:83674700-83674719 None:intergenic 25.0%
! TTTACGCAAAATAGCTTATT+AGG + chr3_3:83674700-83674719 None:intergenic 25.0%
! TTTACACAAAACAGCTTATT+AGG + chr3_3:83674579-83674598 None:intergenic 25.0%
!! CTGATTCGAAATAAATAAAC+CGG - chr3_3:83676286-83676305 Msa0478860:intron 25.0%
TAATTCCAACATTTGTGTTC+TGG - chr3_3:83673894-83673913 Msa0478860:CDS 30.0%
AATTCCAACATTTGTGTTCT+GGG - chr3_3:83673895-83673914 Msa0478860:CDS 30.0%
TTTACTATTTGATGCAAGGT+CGG + chr3_3:83673975-83673994 None:intergenic 30.0%
!! TGTATCAATTTTGGTGAACA+AGG + chr3_3:83674021-83674040 None:intergenic 30.0%
TGTTATATTTCCTGCAAAGT+AGG + chr3_3:83674090-83674109 None:intergenic 30.0%
ATGAAGGTAAGAAGAATGAT+CGG - chr3_3:83674116-83674135 Msa0478860:intron 30.0%
ATCCATAAACTGAACTAAAC+TGG - chr3_3:83674255-83674274 Msa0478860:intron 30.0%
TTTACGTAAAACGGCTTATT+AGG - chr3_3:83674640-83674659 Msa0478860:intron 30.0%
TTTACGTAAAACGGCTTATT+AGG - chr3_3:83674640-83674659 Msa0478860:intron 30.0%
TTTACGTAAAACGGCTTATT+AGG + chr3_3:83674640-83674659 None:intergenic 30.0%
TTTACGTAAAACGGCTTATT+AGG + chr3_3:83674640-83674659 None:intergenic 30.0%
TTTACGTAAAACGGCTTATT+AGG + chr3_3:83674640-83674659 None:intergenic 30.0%
AAACCAGTTCAAGAATAATC+TGG - chr3_3:83676226-83676245 Msa0478860:intron 30.0%
! GAATAATCTGGTTCAAAAAC+TGG - chr3_3:83676238-83676257 Msa0478860:intron 30.0%
! ACTGGTTTAAAACTGTAAAC+CGG - chr3_3:83676256-83676275 Msa0478860:intron 30.0%
CTGAATTGTATCCATTAATG+TGG - chr3_3:83676401-83676420 Msa0478860:intron 30.0%
TGGCAATGGTAATAATGATA+CGG + chr3_3:83676481-83676500 None:intergenic 30.0%
! GTGTTGGTGTGATTATTGTA+AGG + chr3_3:83673925-83673944 None:intergenic 35.0%
AGTAGGACACAGAGATTAAT+TGG + chr3_3:83674073-83674092 None:intergenic 35.0%
TGAAGGTAAGAAGAATGATC+GGG - chr3_3:83674117-83674136 Msa0478860:intron 35.0%
! GTCCAGTTTAGTTCAGTTTA+TGG + chr3_3:83674260-83674279 None:intergenic 35.0%
! GTTCAAGTTTAAAACCGGTT+CGG - chr3_3:83674341-83674360 Msa0478860:intron 35.0%
! ATATTAAACTGGTTCCGAAC+CGG + chr3_3:83674358-83674377 None:intergenic 35.0%
TTTACGTAAAACGGCTTAGT+AGG + chr3_3:83675126-83675145 None:intergenic 35.0%
!!! TCTTGAACTGGTTTTCAAAC+CGG + chr3_3:83676220-83676239 None:intergenic 35.0%
GAACCAGATTATTCTTGAAC+TGG + chr3_3:83676232-83676251 None:intergenic 35.0%
ATTTCGAATCAGTTTCGAAC+CGG + chr3_3:83676278-83676297 None:intergenic 35.0%
! TTTTCAAACCAGTTCCAGTT+CGG + chr3_3:83676348-83676367 None:intergenic 35.0%
TTGGAACTGAACCACATTAA+TGG + chr3_3:83676415-83676434 None:intergenic 35.0%
!! TTCATGGTTCTAAACTGCAT+TGG + chr3_3:83676434-83676453 None:intergenic 35.0%
TGATTATGATGCGATTGTGA+TGG + chr3_3:83676507-83676526 None:intergenic 35.0%
!! TTGTACTTTGGAAGCATCAT+CGG + chr3_3:83676562-83676581 None:intergenic 35.0%
!! TTTGACTTGGACTTGTACTT+TGG + chr3_3:83676574-83676593 None:intergenic 35.0%
AAAGCCCAGAACACAAATGT+TGG + chr3_3:83673902-83673921 None:intergenic 40.0%
TCGGACAAGAGAATTAGTGT+TGG + chr3_3:83673941-83673960 None:intergenic 40.0%
!! AAGGTCGGCTTTTGAATTCT+CGG + chr3_3:83673960-83673979 None:intergenic 40.0%
! ACCGGTTCAAAACTGTAAAC+CGG - chr3_3:83676304-83676323 Msa0478860:CDS 40.0%
!!! ACCGGTTTACAGTTTTGAAC+CGG + chr3_3:83676308-83676327 None:intergenic 40.0%
! GTTTAAAACCGGTTCAGAAC+CGG + chr3_3:83676326-83676345 None:intergenic 40.0%
! GTTCCAGTTCGGTTTAAAAC+CGG + chr3_3:83676337-83676356 None:intergenic 40.0%
!! GTTTTAAACCGAACTGGAAC+TGG - chr3_3:83676337-83676356 Msa0478860:CDS 40.0%
AATAATGATACGGTTGCAGC+TGG + chr3_3:83676471-83676490 None:intergenic 40.0%
ATCTCTGTGTCCTACTTTGC+AGG - chr3_3:83674077-83674096 Msa0478860:intron 45.0%
!!! CACATTTTTTGCACACCCCT+AGG + chr3_3:83674221-83674240 None:intergenic 45.0%
! CTAGGGGTGTGCAAAAAATG+TGG - chr3_3:83674219-83674238 Msa0478860:intron 45.0%
!! ACTGTAAACCGGTTCTGAAC+CGG - chr3_3:83676315-83676334 Msa0478860:CDS 45.0%
!!! GAACCGGTTTTAAACCGAAC+TGG - chr3_3:83676331-83676350 Msa0478860:CDS 45.0%
! GATTGTGATGGAGTTGGCAA+TGG + chr3_3:83676495-83676514 None:intergenic 45.0%
! TGATGCGATTGTGATGGAGT+TGG + chr3_3:83676501-83676520 None:intergenic 45.0%
!! TACTTTGGAAGCATCATCGG+TGG + chr3_3:83676559-83676578 None:intergenic 45.0%
!!! AAACAATTTAAAATTTTATT+AGG - chr3_3:83674458-83674477 Msa0478860:intron 5.0%
!! TCTACAACCACTGACTTGGC+AGG + chr3_3:83674179-83674198 None:intergenic 50.0%
! CTGCTCTACAACCACTGACT+TGG + chr3_3:83674183-83674202 None:intergenic 50.0%
CAAGTCAGTGGTTGTAGAGC+AGG - chr3_3:83674181-83674200 Msa0478860:intron 50.0%
!! ACAACCACTGACTTGGCAGG+TGG + chr3_3:83674176-83674195 None:intergenic 55.0%
TTTGCACACCCCTAGGTGCT+GGG + chr3_3:83674214-83674233 None:intergenic 55.0%
! TTTTGCACACCCCTAGGTGC+TGG + chr3_3:83674215-83674234 None:intergenic 55.0%
!! ACCACTGACTTGGCAGGTGG+CGG + chr3_3:83674173-83674192 None:intergenic 60.0%
AGGAACTTGCCCCAGCACCT+AGG - chr3_3:83674201-83674220 Msa0478860:intron 60.0%
GGAACTTGCCCCAGCACCTA+GGG - chr3_3:83674202-83674221 Msa0478860:intron 60.0%
GAACTTGCCCCAGCACCTAG+GGG - chr3_3:83674203-83674222 Msa0478860:intron 60.0%
! TTGCACACCCCTAGGTGCTG+GGG + chr3_3:83674213-83674232 None:intergenic 60.0%
!! GGTGCTGGTAGGGGTGTTCA+TGG + chr3_3:83676450-83676469 None:intergenic 60.0%
!! GTTGCAGCTGGTGCTGGTAG+GGG + chr3_3:83676459-83676478 None:intergenic 60.0%
!! GGTTGCAGCTGGTGCTGGTA+GGG + chr3_3:83676460-83676479 None:intergenic 60.0%
GATACGGTTGCAGCTGGTGC+TGG + chr3_3:83676465-83676484 None:intergenic 60.0%
ACCGCCACCTGCCAAGTCAG+TGG - chr3_3:83674169-83674188 Msa0478860:intron 65.0%
!! CGGTTGCAGCTGGTGCTGGT+AGG + chr3_3:83676461-83676480 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr3_3 gene 83673872 83676605 83673872 ID=Msa0478860;Name=Msa0478860
chr3_3 mRNA 83673872 83676605 83673872 ID=Msa0478860-mRNA-1;Parent=Msa0478860;Name=Msa0478860-mRNA-1;_AED=0.21;_eAED=0.21;_QI=0|0|0|1|0|0|3|0|87
chr3_3 exon 83676488 83676605 83676488 ID=Msa0478860-mRNA-1:exon:23609;Parent=Msa0478860-mRNA-1
chr3_3 exon 83676294 83676378 83676294 ID=Msa0478860-mRNA-1:exon:23608;Parent=Msa0478860-mRNA-1
chr3_3 exon 83673872 83673932 83673872 ID=Msa0478860-mRNA-1:exon:23607;Parent=Msa0478860-mRNA-1
chr3_3 CDS 83676488 83676605 83676488 ID=Msa0478860-mRNA-1:cds;Parent=Msa0478860-mRNA-1
chr3_3 CDS 83676294 83676378 83676294 ID=Msa0478860-mRNA-1:cds;Parent=Msa0478860-mRNA-1
chr3_3 CDS 83673872 83673932 83673872 ID=Msa0478860-mRNA-1:cds;Parent=Msa0478860-mRNA-1
Gene Sequence

>Msa0478860

ATGATGATGAGAGAAAGAACTCTAATTCCAACATTTGTGTTCTGGGCTTTCCTTACAATAATCACACCAACACTAATTCTCTTGTCCGAGAATTCAAAAGCCGACCTTGCATCAAATAGAAATATAACAGAGACAATGAAGGTAAGAAGAATGATCGGGCACACACAGAGTAACATCATAAGAACAGCACCGCCACCTGCCAACAATCACAATACCACCGATGATGCTTCCAAAGTACAAGTCCAAGTCAAACAAGATACATGA

Protein sequence

>Msa0478860

MMMRERTLIPTFVFWAFLTIITPTLILLSENSKADLASNRNITETMKVRRMIGHTQSNIIRTAPPPANNHNTTDDASKVQVQVKQDT*