AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0275660


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0275660 MtrunA17_Chr2g0287961 97.391 115 3 0 1 115 1 115 4.19e-80 230
Msa0275660 MtrunA17_Chr4g0074501 70.370 108 30 2 1 106 1 108 2.06e-52 160
Msa0275660 MtrunA17_Chr0c30g0494111 67.164 67 20 2 42 106 1 67 2.92e-26 93.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0275660 AT5G19190.1 43.810 105 48 4 1 98 1 101 6.73e-18 74.3
Msa0275660 AT3G06070.1 42.045 88 46 3 1 83 1 88 5.97e-15 66.6

Find 30 sgRNAs with CRISPR-Local

Find 98 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTTTCTTGTACCTCCTTCT+TGG 0.150935 2_3:-7805035 None:intergenic
CTTCATCTTCATCCATTATT+AGG 0.195790 2_3:-7804578 None:intergenic
CTAGAAACTAAATACACTTT+TGG 0.281635 2_3:+7804458 Msa0275660:five_prime_UTR
TAATTAATTCTTTAGCCTTT+AGG 0.285393 2_3:+7805244 Msa0275660:three_prime_UTR
GGAAATTGCTCTCCTAATAA+TGG 0.320698 2_3:+7804566 Msa0275660:CDS
TTCTTGGTTGTGTTGCTTGT+GGG 0.344306 2_3:-7805019 None:intergenic
TCAACCTGCAAACTCTCTTC+AGG 0.344380 2_3:+7804614 Msa0275660:CDS
AATTAACATGGAGGTTGCTT+TGG 0.348717 2_3:+7804506 Msa0275660:exon
CATGGAGGTTGCTTTGGAAA+TGG 0.372075 2_3:+7804512 Msa0275660:exon
AGGAAAGGGATGTTACATTA+AGG 0.380469 2_3:-7805320 None:intergenic
TGTTTGATAGAATTCTTGTT+AGG 0.386930 2_3:-7805122 None:intergenic
GCCTTTAGGCAATAATTGTA+TGG 0.401046 2_3:+7805258 Msa0275660:three_prime_UTR
ATCACACAGCTTTAACTAGA+AGG 0.419335 2_3:-7805170 None:intergenic
CTTCTTGGTTGTGTTGCTTG+TGG 0.425984 2_3:-7805020 None:intergenic
AGAACCTGAAGAGAGTTTGC+AGG 0.436707 2_3:-7804618 None:intergenic
AGAAGAGAAAGCAAAGGAAC+AGG 0.437484 2_3:+7804987 Msa0275660:CDS
AATTCTATCAAACAGTGAAA+TGG 0.469397 2_3:+7805131 Msa0275660:exon
GCCATACAATTATTGCCTAA+AGG 0.474343 2_3:-7805259 None:intergenic
AAGAAATCAAACTGTGGAGG+AGG 0.531737 2_3:-7804945 None:intergenic
CCAAGAAGGAGGTACAAGAA+AGG 0.544633 2_3:+7805035 Msa0275660:CDS
CACAAGCAACACAACCAAGA+AGG 0.551661 2_3:+7805021 Msa0275660:CDS
TTTGCAGGTTGAGAAGCAAG+TGG 0.620205 2_3:-7804603 None:intergenic
GATGTTACATTAAGGACGGA+GGG 0.630582 2_3:-7805312 None:intergenic
TAGAAGAAATCAAACTGTGG+AGG 0.634181 2_3:-7804948 None:intergenic
AAGGGATGTTACATTAAGGA+CGG 0.646362 2_3:-7805316 None:intergenic
AAGCAACACAACCAAGAAGG+AGG 0.648331 2_3:+7805024 Msa0275660:CDS
GGATGTTACATTAAGGACGG+AGG 0.668039 2_3:-7805313 None:intergenic
TTGATGAGAAGAGAAAGCAA+AGG 0.681166 2_3:+7804981 Msa0275660:CDS
TTATATTTGAATTAACATGG+AGG 0.709748 2_3:+7804497 Msa0275660:exon
TCATAGAAGAAATCAAACTG+TGG 0.762193 2_3:-7804951 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CTTTTATATTTGAATTAACA+TGG + chr2_3:7804494-7804513 Msa0275660:exon 15.0%
!!! CTTTAAAAAAAATTCATGAT+TGG - chr2_3:7804777-7804796 None:intergenic 15.0%
!!! CTTTTATATTTGAATTAACA+TGG + chr2_3:7804494-7804513 Msa0275660:exon 15.0%
!!! CTTTAAAAAAAATTCATGAT+TGG - chr2_3:7804777-7804796 None:intergenic 15.0%
!! TTATATTTGAATTAACATGG+AGG + chr2_3:7804497-7804516 Msa0275660:exon 20.0%
!!! TTTAAAAAAAGTGTCATGAT+TGG - chr2_3:7804732-7804751 None:intergenic 20.0%
!!! TTAAAGAATTTATTTCTGCA+TGG + chr2_3:7804791-7804810 Msa0275660:intron 20.0%
!! CTTAAACTAATTTCATTTGT+AGG + chr2_3:7804902-7804921 Msa0275660:intron 20.0%
!!! TAATTAATTCTTTAGCCTTT+AGG + chr2_3:7805244-7805263 Msa0275660:three_prime_UTR 20.0%
!! TTCTTAAGAAATGTGAAAAA+AGG - chr2_3:7805343-7805362 None:intergenic 20.0%
!! TTATATTTGAATTAACATGG+AGG + chr2_3:7804497-7804516 Msa0275660:exon 20.0%
!!! TTTAAAAAAAGTGTCATGAT+TGG - chr2_3:7804732-7804751 None:intergenic 20.0%
!!! TTAAAGAATTTATTTCTGCA+TGG + chr2_3:7804791-7804810 Msa0275660:intron 20.0%
!! CTTAAACTAATTTCATTTGT+AGG + chr2_3:7804902-7804921 Msa0275660:intron 20.0%
!!! TAATTAATTCTTTAGCCTTT+AGG + chr2_3:7805244-7805263 Msa0275660:three_prime_UTR 20.0%
!! TTCTTAAGAAATGTGAAAAA+AGG - chr2_3:7805343-7805362 None:intergenic 20.0%
!! CTAGAAACTAAATACACTTT+TGG + chr2_3:7804458-7804477 Msa0275660:five_prime_UTR 25.0%
! TGTTTGATAGAATTCTTGTT+AGG - chr2_3:7805125-7805144 None:intergenic 25.0%
! AATTCTATCAAACAGTGAAA+TGG + chr2_3:7805131-7805150 Msa0275660:exon 25.0%
! AGAAATGTGAAAAAAGGAAA+GGG - chr2_3:7805337-7805356 None:intergenic 25.0%
! AAGAAATGTGAAAAAAGGAA+AGG - chr2_3:7805338-7805357 None:intergenic 25.0%
!! CTAGAAACTAAATACACTTT+TGG + chr2_3:7804458-7804477 Msa0275660:five_prime_UTR 25.0%
! TGTTTGATAGAATTCTTGTT+AGG - chr2_3:7805125-7805144 None:intergenic 25.0%
! AATTCTATCAAACAGTGAAA+TGG + chr2_3:7805131-7805150 Msa0275660:exon 25.0%
! AGAAATGTGAAAAAAGGAAA+GGG - chr2_3:7805337-7805356 None:intergenic 25.0%
! AAGAAATGTGAAAAAAGGAA+AGG - chr2_3:7805338-7805357 None:intergenic 25.0%
!!! ATTTTTTGCAAACTTGAGCA+AGG + chr2_3:7804545-7804564 Msa0275660:CDS 30.0%
CTTCATCTTCATCCATTATT+AGG - chr2_3:7804581-7804600 None:intergenic 30.0%
GAGTATAGTATGTAACTATG+AGG - chr2_3:7804678-7804697 None:intergenic 30.0%
AACTTGGAAGAAGGATAAAA+GGG - chr2_3:7804709-7804728 None:intergenic 30.0%
! ATTTTGCATGTAGAGAAGAA+GGG - chr2_3:7804875-7804894 None:intergenic 30.0%
! TATTTTGCATGTAGAGAAGA+AGG - chr2_3:7804876-7804895 None:intergenic 30.0%
TCATAGAAGAAATCAAACTG+TGG - chr2_3:7804954-7804973 None:intergenic 30.0%
!!! ATTTTTTGCAAACTTGAGCA+AGG + chr2_3:7804545-7804564 Msa0275660:CDS 30.0%
CTTCATCTTCATCCATTATT+AGG - chr2_3:7804581-7804600 None:intergenic 30.0%
GAGTATAGTATGTAACTATG+AGG - chr2_3:7804678-7804697 None:intergenic 30.0%
AACTTGGAAGAAGGATAAAA+GGG - chr2_3:7804709-7804728 None:intergenic 30.0%
! ATTTTGCATGTAGAGAAGAA+GGG - chr2_3:7804875-7804894 None:intergenic 30.0%
! TATTTTGCATGTAGAGAAGA+AGG - chr2_3:7804876-7804895 None:intergenic 30.0%
TCATAGAAGAAATCAAACTG+TGG - chr2_3:7804954-7804973 None:intergenic 30.0%
AATTAACATGGAGGTTGCTT+TGG + chr2_3:7804506-7804525 Msa0275660:exon 35.0%
GGAAATTGCTCTCCTAATAA+TGG + chr2_3:7804566-7804585 Msa0275660:CDS 35.0%
GTGCATGTATTTACTTAAGG+AGG - chr2_3:7804656-7804675 None:intergenic 35.0%
GAGGTGCATGTATTTACTTA+AGG - chr2_3:7804659-7804678 None:intergenic 35.0%
GAACTTGGAAGAAGGATAAA+AGG - chr2_3:7804710-7804729 None:intergenic 35.0%
! AAAGTGTCATGATTGGAACT+TGG - chr2_3:7804725-7804744 None:intergenic 35.0%
TAGAAGAAATCAAACTGTGG+AGG - chr2_3:7804951-7804970 None:intergenic 35.0%
TTGATGAGAAGAGAAAGCAA+AGG + chr2_3:7804981-7805000 Msa0275660:CDS 35.0%
! ATCACACAGCTTTAACTAGA+AGG - chr2_3:7805173-7805192 None:intergenic 35.0%
GCCTTTAGGCAATAATTGTA+TGG + chr2_3:7805258-7805277 Msa0275660:three_prime_UTR 35.0%
GCCATACAATTATTGCCTAA+AGG - chr2_3:7805262-7805281 None:intergenic 35.0%
AAGGGATGTTACATTAAGGA+CGG - chr2_3:7805319-7805338 None:intergenic 35.0%
AGGAAAGGGATGTTACATTA+AGG - chr2_3:7805323-7805342 None:intergenic 35.0%
AATTAACATGGAGGTTGCTT+TGG + chr2_3:7804506-7804525 Msa0275660:exon 35.0%
GGAAATTGCTCTCCTAATAA+TGG + chr2_3:7804566-7804585 Msa0275660:CDS 35.0%
GTGCATGTATTTACTTAAGG+AGG - chr2_3:7804656-7804675 None:intergenic 35.0%
GAGGTGCATGTATTTACTTA+AGG - chr2_3:7804659-7804678 None:intergenic 35.0%
GAACTTGGAAGAAGGATAAA+AGG - chr2_3:7804710-7804729 None:intergenic 35.0%
! AAAGTGTCATGATTGGAACT+TGG - chr2_3:7804725-7804744 None:intergenic 35.0%
TAGAAGAAATCAAACTGTGG+AGG - chr2_3:7804951-7804970 None:intergenic 35.0%
TTGATGAGAAGAGAAAGCAA+AGG + chr2_3:7804981-7805000 Msa0275660:CDS 35.0%
! ATCACACAGCTTTAACTAGA+AGG - chr2_3:7805173-7805192 None:intergenic 35.0%
GCCTTTAGGCAATAATTGTA+TGG + chr2_3:7805258-7805277 Msa0275660:three_prime_UTR 35.0%
GCCATACAATTATTGCCTAA+AGG - chr2_3:7805262-7805281 None:intergenic 35.0%
AAGGGATGTTACATTAAGGA+CGG - chr2_3:7805319-7805338 None:intergenic 35.0%
AGGAAAGGGATGTTACATTA+AGG - chr2_3:7805323-7805342 None:intergenic 35.0%
CATGATTGGAACTTGGAAGA+AGG - chr2_3:7804718-7804737 None:intergenic 40.0%
AAGAAATCAAACTGTGGAGG+AGG - chr2_3:7804948-7804967 None:intergenic 40.0%
AGAAGAGAAAGCAAAGGAAC+AGG + chr2_3:7804987-7805006 Msa0275660:CDS 40.0%
!! TTCTTGGTTGTGTTGCTTGT+GGG - chr2_3:7805022-7805041 None:intergenic 40.0%
GATGTTACATTAAGGACGGA+GGG - chr2_3:7805315-7805334 None:intergenic 40.0%
CATGATTGGAACTTGGAAGA+AGG - chr2_3:7804718-7804737 None:intergenic 40.0%
AAGAAATCAAACTGTGGAGG+AGG - chr2_3:7804948-7804967 None:intergenic 40.0%
AGAAGAGAAAGCAAAGGAAC+AGG + chr2_3:7804987-7805006 Msa0275660:CDS 40.0%
!! TTCTTGGTTGTGTTGCTTGT+GGG - chr2_3:7805022-7805041 None:intergenic 40.0%
GATGTTACATTAAGGACGGA+GGG - chr2_3:7805315-7805334 None:intergenic 40.0%
!! CATGGAGGTTGCTTTGGAAA+TGG + chr2_3:7804512-7804531 Msa0275660:exon 45.0%
! TTTGCAGGTTGAGAAGCAAG+TGG - chr2_3:7804606-7804625 None:intergenic 45.0%
TCAACCTGCAAACTCTCTTC+AGG + chr2_3:7804614-7804633 Msa0275660:CDS 45.0%
AGAACCTGAAGAGAGTTTGC+AGG - chr2_3:7804621-7804640 None:intergenic 45.0%
ATTTCTGCATGGCAGTTCAG+TGG + chr2_3:7804802-7804821 Msa0275660:intron 45.0%
!! CTTCTTGGTTGTGTTGCTTG+TGG - chr2_3:7805023-7805042 None:intergenic 45.0%
CACAAGCAACACAACCAAGA+AGG + chr2_3:7805021-7805040 Msa0275660:CDS 45.0%
AAGCAACACAACCAAGAAGG+AGG + chr2_3:7805024-7805043 Msa0275660:CDS 45.0%
CCTTTCTTGTACCTCCTTCT+TGG - chr2_3:7805038-7805057 None:intergenic 45.0%
! CCAAGAAGGAGGTACAAGAA+AGG + chr2_3:7805035-7805054 Msa0275660:CDS 45.0%
GGATGTTACATTAAGGACGG+AGG - chr2_3:7805316-7805335 None:intergenic 45.0%
!! CATGGAGGTTGCTTTGGAAA+TGG + chr2_3:7804512-7804531 Msa0275660:exon 45.0%
! TTTGCAGGTTGAGAAGCAAG+TGG - chr2_3:7804606-7804625 None:intergenic 45.0%
TCAACCTGCAAACTCTCTTC+AGG + chr2_3:7804614-7804633 Msa0275660:CDS 45.0%
AGAACCTGAAGAGAGTTTGC+AGG - chr2_3:7804621-7804640 None:intergenic 45.0%
ATTTCTGCATGGCAGTTCAG+TGG + chr2_3:7804802-7804821 Msa0275660:intron 45.0%
!! CTTCTTGGTTGTGTTGCTTG+TGG - chr2_3:7805023-7805042 None:intergenic 45.0%
CACAAGCAACACAACCAAGA+AGG + chr2_3:7805021-7805040 Msa0275660:CDS 45.0%
AAGCAACACAACCAAGAAGG+AGG + chr2_3:7805024-7805043 Msa0275660:CDS 45.0%
CCTTTCTTGTACCTCCTTCT+TGG - chr2_3:7805038-7805057 None:intergenic 45.0%
! CCAAGAAGGAGGTACAAGAA+AGG + chr2_3:7805035-7805054 Msa0275660:CDS 45.0%
GGATGTTACATTAAGGACGG+AGG - chr2_3:7805316-7805335 None:intergenic 45.0%
Chromosome Type Strat End Strand Name
chr2_3 gene 7804422 7805412 7804422 ID=Msa0275660;Name=Msa0275660
chr2_3 mRNA 7804422 7805412 7804422 ID=Msa0275660-mRNA-1;Parent=Msa0275660;Name=Msa0275660-mRNA-1;_AED=0.05;_eAED=0.05;_QI=91|1|1|1|1|1|2|264|115
chr2_3 exon 7804422 7804635 7804422 ID=Msa0275660-mRNA-1:exon:3539;Parent=Msa0275660-mRNA-1
chr2_3 exon 7804924 7805412 7804924 ID=Msa0275660-mRNA-1:exon:3540;Parent=Msa0275660-mRNA-1
chr2_3 five_prime_UTR 7804422 7804512 7804422 ID=Msa0275660-mRNA-1:five_prime_utr;Parent=Msa0275660-mRNA-1
chr2_3 CDS 7804513 7804635 7804513 ID=Msa0275660-mRNA-1:cds;Parent=Msa0275660-mRNA-1
chr2_3 CDS 7804924 7805148 7804924 ID=Msa0275660-mRNA-1:cds;Parent=Msa0275660-mRNA-1
chr2_3 three_prime_UTR 7805149 7805412 7805149 ID=Msa0275660-mRNA-1:three_prime_utr;Parent=Msa0275660-mRNA-1
Gene Sequence

>Msa0275660

ATGGAGGTTGCTTTGGAAATGGAAGATGATTTATTTTTTGCAAACTTGAGCAAGGAAATTGCTCTCCTAATAATGGATGAAGATGAAGATCCACTTGCTTCTCAACCTGCAAACTCTCTTCAGGATTTCTCTAGAGTAATTCATCCTCCTCCACAGTTTGATTTCTTCTATGAGCAAGCTTTGATGAGAAGAGAAAGCAAAGGAACAGGAGTGTTTATCCCACAAGCAACACAACCAAGAAGGAGGTACAAGAAAGGAAGATCTAATTCATTCTCAAAATATCAAAAGCAGTCTCAAGACACAAGAATGATTTCTCAAGTTCCTAACAAGAATTCTATCAAACAGTGA

Protein sequence

>Msa0275660

MEVALEMEDDLFFANLSKEIALLIMDEDEDPLASQPANSLQDFSRVIHPPPQFDFFYEQALMRRESKGTGVFIPQATQPRRRYKKGRSNSFSKYQKQSQDTRMISQVPNKNSIKQ*