AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene070814

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 19 sgRNAs with CRISPR-Local

Find 49 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGCCATTAGGTTGCTTTCT+TGG 0.248489 8.4:-44920390 None:intergenic
TCATTGCTTCATTAAGATCT+TGG 0.330442 8.4:-44920092 None:intergenic
TGGTTAACACAGAGCTTTAG+AGG 0.331097 8.4:+44920211 MS.gene070814:intron
GCAATAGAAAGAAGGCTAAA+TGG 0.337305 8.4:+44920252 MS.gene070814:CDS
AGAGGTTCATCAACTTGCTC+AGG 0.406730 8.4:+44920229 MS.gene070814:CDS
TATCCACAATCATTGCCATT+AGG 0.411955 8.4:-44920402 None:intergenic
TCTTGACTTGTATAACGCTT+AGG 0.431501 8.4:+44920656 MS.gene070814:CDS
CTGCTAATATTACTAAGTCT+TGG 0.472781 8.4:+44920457 MS.gene070814:CDS
GTATGATTTGCGAAACCAAT+GGG 0.494818 8.4:+44920623 MS.gene070814:CDS
TAGCCAAGAAAGCAACCTAA+TGG 0.495668 8.4:+44920387 MS.gene070814:intron
TCATCTTCAGTTAATGTCGC+TGG 0.495751 8.4:-44920597 None:intergenic
CAACCTAATGGCAATGATTG+TGG 0.497368 8.4:+44920399 MS.gene070814:CDS
CAAGAAAACAAGTTGCCCAT+TGG 0.504204 8.4:-44920638 None:intergenic
TGCTCAGGGCAATAGAAAGA+AGG 0.548493 8.4:+44920244 MS.gene070814:CDS
GAGGTTCATCAACTTGCTCA+GGG 0.558482 8.4:+44920230 MS.gene070814:CDS
TGTATGATTTGCGAAACCAA+TGG 0.592485 8.4:+44920622 MS.gene070814:CDS
TAATATTACTAAGTCTTGGA+TGG 0.604101 8.4:+44920461 MS.gene070814:CDS
GATCTTGGTGCATTGAACAA+AGG 0.604500 8.4:-44920077 None:intergenic
TATTACTAAGTCTTGGATGG+AGG 0.643493 8.4:+44920464 MS.gene070814:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACTAATCACTATATAAAAA+TGG + chr8.4:44920353-44920372 MS.gene070814:intron 15.0%
!! AATAAGGATATGTTTATATT+TGG - chr8.4:44920530-44920549 None:intergenic 15.0%
!! TATACTTACTTAAATAGATA+TGG - chr8.4:44919934-44919953 None:intergenic 15.0%
!!! CTTTGATGATTTTTTTAATT+TGG + chr8.4:44920191-44920210 MS.gene070814:intron 15.0%
!!! CTTTTTTACTATTATCAATA+TGG + chr8.4:44919691-44919710 MS.gene070814:intron 15.0%
!!! TGTTAATTTTAAATTTGTCT+AGG + chr8.4:44919746-44919765 MS.gene070814:intron 15.0%
!! AACACTTAAATATTGAATTG+TGG - chr8.4:44919730-44919749 None:intergenic 20.0%
! ACGTAGAAGAACAATTATTA+AGG - chr8.4:44920000-44920019 None:intergenic 25.0%
! GTTAATAATTATTTGTCCCA+AGG + chr8.4:44920038-44920057 MS.gene070814:intron 25.0%
! TAATATTACTAAGTCTTGGA+TGG + chr8.4:44920461-44920480 MS.gene070814:CDS 25.0%
! TAGTACTAAAACTAAAGTTC+AGG + chr8.4:44919858-44919877 MS.gene070814:intron 25.0%
! TATATTAACCTACACATTGT+AGG + chr8.4:44920563-44920582 MS.gene070814:intron 25.0%
!!! GTTATACATTTTAGTGTTGT+AGG - chr8.4:44920172-44920191 None:intergenic 25.0%
!!! GTTTTAGTACTATGATCTTT+TGG - chr8.4:44919850-44919869 None:intergenic 25.0%
AATCTACACCATACTTACTT+TGG - chr8.4:44920285-44920304 None:intergenic 30.0%
ACAACTAAACTATTGTCCTT+GGG - chr8.4:44920057-44920076 None:intergenic 30.0%
ATCTACACCATACTTACTTT+GGG - chr8.4:44920284-44920303 None:intergenic 30.0%
ATTGAATACCTACAATGTGT+AGG - chr8.4:44920574-44920593 None:intergenic 30.0%
CTGCTAATATTACTAAGTCT+TGG + chr8.4:44920457-44920476 MS.gene070814:CDS 30.0%
GATTAAAATCCAAGCATACT+GGG - chr8.4:44919828-44919847 None:intergenic 30.0%
TCATTGCTTCATTAAGATCT+TGG - chr8.4:44920095-44920114 None:intergenic 30.0%
!! AGAAATAGATCGAAAGTGTT+TGG + chr8.4:44919793-44919812 MS.gene070814:intron 30.0%
!! GAAATAGATCGAAAGTGTTT+GGG + chr8.4:44919794-44919813 MS.gene070814:intron 30.0%
CTTTCTTGGCTACAAATGAA+TGG - chr8.4:44920379-44920398 None:intergenic 35.0%
GACAACTAAACTATTGTCCT+TGG - chr8.4:44920058-44920077 None:intergenic 35.0%
GCAATAGAAAGAAGGCTAAA+TGG + chr8.4:44920252-44920271 MS.gene070814:CDS 35.0%
GGATTAAAATCCAAGCATAC+TGG - chr8.4:44919829-44919848 None:intergenic 35.0%
TATCCACAATCATTGCCATT+AGG - chr8.4:44920405-44920424 None:intergenic 35.0%
TATTACTAAGTCTTGGATGG+AGG + chr8.4:44920464-44920483 MS.gene070814:CDS 35.0%
! GTATGATTTGCGAAACCAAT+GGG + chr8.4:44920623-44920642 MS.gene070814:CDS 35.0%
! TGTATGATTTGCGAAACCAA+TGG + chr8.4:44920622-44920641 MS.gene070814:CDS 35.0%
!! TCTTGACTTGTATAACGCTT+AGG + chr8.4:44920656-44920675 MS.gene070814:CDS 35.0%
!!! ATCGAAAGTGTTTGGGATTT+TGG + chr8.4:44919801-44919820 MS.gene070814:intron 35.0%
CAACCTAATGGCAATGATTG+TGG + chr8.4:44920399-44920418 MS.gene070814:CDS 40.0%
CAAGAAAACAAGTTGCCCAT+TGG - chr8.4:44920641-44920660 None:intergenic 40.0%
GTTTCGTCCCAAAGTAAGTA+TGG + chr8.4:44920274-44920293 MS.gene070814:intron 40.0%
TAGCCAAGAAAGCAACCTAA+TGG + chr8.4:44920387-44920406 MS.gene070814:intron 40.0%
TCATCTTCAGTTAATGTCGC+TGG - chr8.4:44920600-44920619 None:intergenic 40.0%
TTCAGGAACACATGCAAACT+AGG + chr8.4:44919875-44919894 MS.gene070814:intron 40.0%
! GATCTTGGTGCATTGAACAA+AGG - chr8.4:44920080-44920099 None:intergenic 40.0%
! TGGTTAACACAGAGCTTTAG+AGG + chr8.4:44920211-44920230 MS.gene070814:intron 40.0%
! TTGCCATTAGGTTGCTTTCT+TGG - chr8.4:44920393-44920412 None:intergenic 40.0%
TGCTCAGGGCAATAGAAAGA+AGG + chr8.4:44920244-44920263 MS.gene070814:CDS 45.0%
TTGTTCTTCTACGTGTGCAG+AGG + chr8.4:44920006-44920025 MS.gene070814:intron 45.0%
! AGAGGTTCATCAACTTGCTC+AGG + chr8.4:44920229-44920248 MS.gene070814:CDS 45.0%
! GAGGTTCATCAACTTGCTCA+GGG + chr8.4:44920230-44920249 MS.gene070814:CDS 45.0%
! GATTTTGGACCCAGTATGCT+TGG + chr8.4:44919816-44919835 MS.gene070814:intron 45.0%
!! ATAAGTAATTAATATTAATA+AGG - chr8.4:44920546-44920565 None:intergenic 5.0%
TCTACGTGTGCAGAGGACAC+TGG + chr8.4:44920013-44920032 MS.gene070814:intron 55.0%


Chromosome Type Strat End Strand Name
chr8.4 gene 44919646 44920677 44919646 ID=MS.gene070814
chr8.4 mRNA 44919646 44920677 44919646 ID=MS.gene070814.t1;Parent=MS.gene070814
chr8.4 exon 44919646 44919677 44919646 ID=MS.gene070814.t1.exon1;Parent=MS.gene070814.t1
chr8.4 CDS 44919646 44919677 44919646 ID=cds.MS.gene070814.t1;Parent=MS.gene070814.t1
chr8.4 exon 44920073 44920130 44920073 ID=MS.gene070814.t1.exon2;Parent=MS.gene070814.t1
chr8.4 CDS 44920073 44920130 44920073 ID=cds.MS.gene070814.t1;Parent=MS.gene070814.t1
chr8.4 exon 44920223 44920286 44920223 ID=MS.gene070814.t1.exon3;Parent=MS.gene070814.t1
chr8.4 CDS 44920223 44920286 44920223 ID=cds.MS.gene070814.t1;Parent=MS.gene070814.t1
chr8.4 exon 44920390 44920485 44920390 ID=MS.gene070814.t1.exon4;Parent=MS.gene070814.t1
chr8.4 CDS 44920390 44920485 44920390 ID=cds.MS.gene070814.t1;Parent=MS.gene070814.t1
chr8.4 exon 44920585 44920677 44920585 ID=MS.gene070814.t1.exon5;Parent=MS.gene070814.t1
chr8.4 CDS 44920585 44920677 44920585 ID=cds.MS.gene070814.t1;Parent=MS.gene070814.t1
Gene Sequence

>MS.gene070814

GCTTGACTTTCTATTCTACAACTTTGATGCACGTAAGTACATTTTCTTTTTTACTATTATCAATATGGATTAGTAGTATATCCACAATTCAATATTTAAGTGTTAATTTTAAATTTGTCTAGGTGTATGCATAGTCTCTGTATCTCAAGAAATAGATCGAAAGTGTTTGGGATTTTGGACCCAGTATGCTTGGATTTTAATCCAAAAGATCATAGTACTAAAACTAAAGTTCAGGAACACATGCAAACTAGGTTGCGTGATTTGAACAAAGTGTGTTACTTAGCACCATATCTATTTAAGTAAGTATATATTTAAATTAATATTTTTCTTATTTATCTTTGATAGCTTAAACCTTAATAATTGTTCTTCTACGTGTGCAGAGGACACTGGCAGTTAATAATTATTTGTCCCAAGGACAATAGTTTAGTTGTCCTTTGTTCAATGCACCAAGATCTTAATGAAGCAATGATTAAGATTGTTTCAAAGTAAGTGTATATTTTACGTTGTATTTGATATATTACTTCCTACAACACTAAAATGTATAACTTTGATGATTTTTTTAATTTGGTTAACACAGAGCTTTAGAGGTTCATCAACTTGCTCAGGGCAATAGAAAGAAGGCTAAATGGTTTCGTCCCAAAGTAAGTATGGTGTAGATTCTGTCATTTTTTTACGTTAACAAATGAAATTTGTTTTTTTTTTATATGAACTAATCACTATATAAAAATGGCCATTCATTTGTAGCCAAGAAAGCAACCTAATGGCAATGATTGTGGATACTATGTGATGAAGAATATGCTAGATATCATCTCTGCTAATATTACTAAGTCTTGGATGGAGGTATTTTAATTTATGATAACATGTTTATACTATATGTATTACCAAATATAAACATATCCTTATTAATATTAATTACTTATATTAACCTACACATTGTAGGTATTCAATGATCCAGCGACATTAACTGAAGATGACTTGTATGATTTGCGAAACCAATGGGCAACTTGTTTTCTTGACTTGTATAACGCTTAG
Protein sequence

>MS.gene070814.t1

AULSILQLUCTCPLFNAPRSUUSNDUDCFKSFRGSSTCSGQUKEGUMVSSQTKKATUWQULWILCDEEYARYHLCUYYUVLDGGIQUSSDINURULVUFAKPMGNLFSULVURL