AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene69341

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene69341.t1 MTR_6g081160 34.615 286 107 8 27 253 8 272 1.43e-32 120
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene69341.t1 AT3G19580 40.206 97 39 4 45 137 106 187 1.35e-13 69.3
MS.gene69341.t1 AT3G19580 40.206 97 39 4 45 137 106 187 1.35e-13 69.3
MS.gene69341.t1 AT1G49900 39.130 92 38 2 46 137 194 267 1.14e-11 64.7
MS.gene69341.t1 AT5G67450 39.175 97 48 2 45 137 97 186 3.29e-11 62.0

Find 36 sgRNAs with CRISPR-Local

Find 44 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTAATTTCTCTTTACCAAAA+TGG 0.235457 3.3:-93938519 MS.gene69341:CDS
AAGCATGAGGTTATTATTAC+AGG 0.279433 3.3:-93938937 MS.gene69341:CDS
TCTAACTTTATCTTCTTAAG+AGG 0.301299 3.3:+93938838 None:intergenic
TCCGACTCTTCATAAGTATT+CGG 0.323788 3.3:+93938790 None:intergenic
CCTCTTGTCAGACTCTTCAT+AGG 0.349643 3.3:+93939005 None:intergenic
CATAAAGAAGATCAAGCTTA+TGG 0.366706 3.3:-93938541 MS.gene69341:CDS
TTACGAATAACATGATTTGC+TGG 0.441171 3.3:+93938604 None:intergenic
GAATGAGCCATATGCTATTG+AGG 0.477019 3.3:-93938305 MS.gene69341:CDS
AGAAGAGGTAGAAAGTGTAT+TGG 0.483023 3.3:-93938484 MS.gene69341:CDS
GCTTAGTCCTCAATAGCATA+TGG 0.486464 3.3:+93938298 None:intergenic
TTGGTGAGTCATCATCAAAT+TGG 0.494071 3.3:-93938405 MS.gene69341:CDS
CTAACTTTATCTTCTTAAGA+GGG 0.512429 3.3:+93938839 None:intergenic
TGAGATCTCCGGTGAGGAAG+GGG 0.514342 3.3:+93938813 None:intergenic
ACTGATGATCAGCTAAAGAA+AGG 0.524124 3.3:-93938346 MS.gene69341:CDS
GTGAGATCTCCGGTGAGGAA+GGG 0.530993 3.3:+93938812 None:intergenic
TAAGTATTCGGTGAGATCTC+CGG 0.541580 3.3:+93938802 None:intergenic
TTTAGCAGCGGACAAGCACT+TGG 0.544373 3.3:-93938880 MS.gene69341:CDS
CTTATGAAGAGTCGGAAAAG+AGG 0.546986 3.3:-93938783 MS.gene69341:CDS
GAAAAGCATTGGGTGGTCAC+CGG 0.556634 3.3:-93938660 MS.gene69341:CDS
TCTTCTTTATGATGTTCAGT+AGG 0.559242 3.3:+93938553 None:intergenic
GGTGAGATCTCCGGTGAGGA+AGG 0.559786 3.3:+93938811 None:intergenic
GTTAGAAACCCCTTCCTCAC+CGG 0.572034 3.3:-93938821 MS.gene69341:CDS
ACCGAATACTTATGAAGAGT+CGG 0.572679 3.3:-93938791 MS.gene69341:CDS
TCTTAATAGAGTGAGATCTC+CGG 0.581386 3.3:+93938641 None:intergenic
GAGTCATCATCAAATTGGAA+TGG 0.587360 3.3:-93938400 MS.gene69341:CDS
TGGCAAAAGAAAGATAGAAG+AGG 0.598017 3.3:-93938499 MS.gene69341:CDS
AGCAGCGGACAAGCACTTGG+TGG 0.609210 3.3:-93938877 MS.gene69341:CDS
TCTTGTTCACTATCAAGTGA+CGG 0.609728 3.3:-93938970 MS.gene69341:CDS
TGGAATGGCAAGAATGAGCT+TGG 0.611635 3.3:-93938385 MS.gene69341:CDS
CCTATGAAGAGTCTGACAAG+AGG 0.641227 3.3:-93939005 MS.gene69341:CDS
CGAAGATGATGTCAAGCATG+AGG 0.647694 3.3:-93938728 MS.gene69341:CDS
CGGAGATGATGCAAAGCATG+AGG 0.655546 3.3:-93938950 MS.gene69341:CDS
GTGTATTGGTAGTGTTGAAG+CGG 0.655661 3.3:-93938470 MS.gene69341:CDS
AAAAGTACTTATCTGAACGA+AGG 0.659168 3.3:+93938431 None:intergenic
AATGGCAAGAATGAGCTTGG+TGG 0.663111 3.3:-93938382 MS.gene69341:CDS
ATTCGGTGAGATCTCCGGTG+AGG 0.731513 3.3:+93938807 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGCAGAAAAACTTTTAAAAA+TGG - chr3.3:93938657-93938676 MS.gene69341:CDS 20.0%
!!! TTTAAAAATGGAAAAGCATT+GGG - chr3.3:93938669-93938688 MS.gene69341:CDS 20.0%
!!! TTTTAAAAATGGAAAAGCAT+TGG - chr3.3:93938668-93938687 MS.gene69341:CDS 20.0%
! CTAACTTTATCTTCTTAAGA+GGG + chr3.3:93938503-93938522 None:intergenic 25.0%
! GTAATTTCTCTTTACCAAAA+TGG - chr3.3:93938820-93938839 MS.gene69341:CDS 25.0%
! TCTAACTTTATCTTCTTAAG+AGG + chr3.3:93938504-93938523 None:intergenic 25.0%
AAGCATGAGGTTATTATTAC+AGG - chr3.3:93938402-93938421 MS.gene69341:CDS 30.0%
CATAAAGAAGATCAAGCTTA+TGG - chr3.3:93938798-93938817 MS.gene69341:CDS 30.0%
TCTTCTTTATGATGTTCAGT+AGG + chr3.3:93938789-93938808 None:intergenic 30.0%
TGTGAAAAAGAATTTAGCAG+CGG - chr3.3:93938447-93938466 MS.gene69341:CDS 30.0%
! GTTTTCTCATAATCATGCTT+AGG + chr3.3:93938315-93938334 None:intergenic 30.0%
! TCAGATAAGTACTTTTGTGT+TGG - chr3.3:93938915-93938934 MS.gene69341:CDS 30.0%
! TTACGAATAACATGATTTGC+TGG + chr3.3:93938738-93938757 None:intergenic 30.0%
! TTTTTCTGCAAATATTGCAC+TGG + chr3.3:93938647-93938666 None:intergenic 30.0%
!! AAAAGTACTTATCTGAACGA+AGG + chr3.3:93938911-93938930 None:intergenic 30.0%
!! CTATCTTTCTTTTGCCATTT+TGG + chr3.3:93938837-93938856 None:intergenic 30.0%
ACCGAATACTTATGAAGAGT+CGG - chr3.3:93938548-93938567 MS.gene69341:CDS 35.0%
ACTGATGATCAGCTAAAGAA+AGG - chr3.3:93938993-93939012 MS.gene69341:CDS 35.0%
GAGTCATCATCAAATTGGAA+TGG - chr3.3:93938939-93938958 MS.gene69341:CDS 35.0%
TCCGACTCTTCATAAGTATT+CGG + chr3.3:93938552-93938571 None:intergenic 35.0%
TCTTAATAGAGTGAGATCTC+CGG + chr3.3:93938701-93938720 None:intergenic 35.0%
TCTTGTTCACTATCAAGTGA+CGG - chr3.3:93938369-93938388 MS.gene69341:CDS 35.0%
TGGCAAAAGAAAGATAGAAG+AGG - chr3.3:93938840-93938859 MS.gene69341:CDS 35.0%
TTGGTGAGTCATCATCAAAT+TGG - chr3.3:93938934-93938953 MS.gene69341:CDS 35.0%
! AGAAGAGGTAGAAAGTGTAT+TGG - chr3.3:93938855-93938874 MS.gene69341:CDS 35.0%
!! AAAAATGGAAAAGCATTGGG+TGG - chr3.3:93938672-93938691 MS.gene69341:CDS 35.0%
CTTATGAAGAGTCGGAAAAG+AGG - chr3.3:93938556-93938575 MS.gene69341:CDS 40.0%
GAATGAGCCATATGCTATTG+AGG - chr3.3:93939034-93939053 MS.gene69341:CDS 40.0%
! TAAGTATTCGGTGAGATCTC+CGG + chr3.3:93938540-93938559 None:intergenic 40.0%
!! GTGTATTGGTAGTGTTGAAG+CGG - chr3.3:93938869-93938888 MS.gene69341:CDS 40.0%
AATGGCAAGAATGAGCTTGG+TGG - chr3.3:93938957-93938976 MS.gene69341:CDS 45.0%
CCTATGAAGAGTCTGACAAG+AGG - chr3.3:93938334-93938353 MS.gene69341:CDS 45.0%
CCTCTTGTCAGACTCTTCAT+AGG + chr3.3:93938337-93938356 None:intergenic 45.0%
CGAAGATGATGTCAAGCATG+AGG - chr3.3:93938611-93938630 MS.gene69341:CDS 45.0%
TGGAATGGCAAGAATGAGCT+TGG - chr3.3:93938954-93938973 MS.gene69341:CDS 45.0%
CGGAGATGATGCAAAGCATG+AGG - chr3.3:93938389-93938408 MS.gene69341:CDS 50.0%
GTTAGAAACCCCTTCCTCAC+CGG - chr3.3:93938518-93938537 MS.gene69341:CDS 50.0%
TTTAGCAGCGGACAAGCACT+TGG - chr3.3:93938459-93938478 MS.gene69341:CDS 50.0%
!! GAAAAGCATTGGGTGGTCAC+CGG - chr3.3:93938679-93938698 MS.gene69341:CDS 50.0%
GTGAGATCTCCGGTGAGGAA+GGG + chr3.3:93938530-93938549 None:intergenic 55.0%
TGAGATCTCCGGTGAGGAAG+GGG + chr3.3:93938529-93938548 None:intergenic 55.0%
! ATTCGGTGAGATCTCCGGTG+AGG + chr3.3:93938535-93938554 None:intergenic 55.0%
AGCAGCGGACAAGCACTTGG+TGG - chr3.3:93938462-93938481 MS.gene69341:CDS 60.0%
GGTGAGATCTCCGGTGAGGA+AGG + chr3.3:93938531-93938550 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 93938300 93939061 93938300 ID=MS.gene69341
chr3.3 mRNA 93938300 93939061 93938300 ID=MS.gene69341.t1;Parent=MS.gene69341
chr3.3 exon 93938300 93939061 93938300 ID=MS.gene69341.t1.exon1;Parent=MS.gene69341.t1
chr3.3 CDS 93938300 93939061 93938300 ID=cds.MS.gene69341.t1;Parent=MS.gene69341.t1
Gene Sequence

>MS.gene69341

ATGGCTAAAGTTCCTAAGCATGATTATGAGAAAACCTATGAAGAGTCTGACAAGAGGATTAAAAAGTCTTCTTGTTCACTATCAAGTGACGGAGATGATGCAAAGCATGAGGTTATTATTACAGGATCTACGCACAAGTGCAATATTTGTGAAAAAGAATTTAGCAGCGGACAAGCACTTGGTGGTCACAAGAGATCTCACCCTCTTAAGAAGATAAAGTTAGAAACCCCTTCCTCACCGGAGATCTCACCGAATACTTATGAAGAGTCGGAAAAGAGGATGAAAAAGTCTTCATTTTCGCTATCAAGTGACGAAGATGATGTCAAGCATGAGGTTTCTCAGCACCAGTGCAATATTTGCAGAAAAACTTTTAAAAATGGAAAAGCATTGGGTGGTCACCGGAGATCTCACTCTATTAAGAAGAAACTTAATCATCCAGCAAATCATGTTATTCGTAAGTCTTCTTCGTCTTGCAATTATAAATCTCCTACTGAACATCATAAAGAAGATCAAGCTTATGGTAATTTCTCTTTACCAAAATGGCAAAAGAAAGATAGAAGAGGTAGAAAGTGTATTGGTAGTGTTGAAGCGGCTGAAAATCTTTTGCTCCTTCGTTCAGATAAGTACTTTTGTGTTGGTGAGTCATCATCAAATTGGAATGGCAAGAATGAGCTTGGTGGTGATAGAAACAGTACTGATGATCAGCTAAAGAAAGGAAAATGTTTATTTGATTTGAATGAGCCATATGCTATTGAGGACTAA
Protein sequence

>MS.gene69341.t1

MAKVPKHDYEKTYEESDKRIKKSSCSLSSDGDDAKHEVIITGSTHKCNICEKEFSSGQALGGHKRSHPLKKIKLETPSSPEISPNTYEESEKRMKKSSFSLSSDEDDVKHEVSQHQCNICRKTFKNGKALGGHRRSHSIKKKLNHPANHVIRKSSSSCNYKSPTEHHKEDQAYGNFSLPKWQKKDRRGRKCIGSVEAAENLLLLRSDKYFCVGESSSNWNGKNELGGDRNSTDDQLKKGKCLFDLNEPYAIED