AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0814320


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0814320 MtrunA17_Chr5g0432431 94.815 135 7 0 1 135 1 135 3.79e-92 262
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0814320 AT2G30330.1 59.649 114 46 0 22 135 37 150 1.09e-46 148
Msa0814320 AT2G30330.2 48.039 102 52 1 22 123 37 137 9.69e-29 102

Find 24 sgRNAs with CRISPR-Local

Find 125 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTAGCCTTGTATCTTTATTC+TGG 0.213211 5_3:-46339706 Msa0814320:three_prime_UTR
TTTGATGATGAATGTGAATT+AGG 0.250869 5_3:+46341929 None:intergenic
TATTTATTAGTGATTAGTTT+TGG 0.348003 5_3:-46339555 Msa0814320:three_prime_UTR
TGTAGCACTGGTTGGTGATT+TGG 0.356599 5_3:-46339636 Msa0814320:three_prime_UTR
TACGTATATTTGACAAATCA+TGG 0.369629 5_3:-46339611 Msa0814320:three_prime_UTR
TTGAACTTAGATACTCTGTT+TGG 0.389138 5_3:-46342035 Msa0814320:five_prime_UTR
AAATTGGAGACTTTGAGAAT+TGG 0.397575 5_3:-46339948 Msa0814320:CDS
AAGAAAAGCAGAGCGCGTTT+CGG 0.423070 5_3:-46341857 Msa0814320:CDS
TTCACCAAGAGTGATCTTGC+AGG 0.449401 5_3:-46339873 Msa0814320:exon
TGAGAATTGGATGAAGATCA+TGG 0.464193 5_3:-46339935 Msa0814320:CDS
GGCTTCTAATGATGTAGCAC+TGG 0.472814 5_3:-46339648 Msa0814320:three_prime_UTR
TTCGAGATTTGTGAAACAAA+CGG 0.473259 5_3:-46341740 Msa0814320:CDS
TTGTTTCTCAACAAAATAAG+TGG 0.494592 5_3:-46339741 Msa0814320:three_prime_UTR
TTCTCTTAACACTGCTCTCA+AGG 0.509830 5_3:-46341695 Msa0814320:intron
AATACAAAGAAACAAGTGAA+TGG 0.531661 5_3:-46342010 Msa0814320:exon
GCAACCTGCAAGATCACTCT+TGG 0.532927 5_3:+46339869 None:intergenic
ACACGCAGAATCAAAGGGAT+TGG 0.536514 5_3:-46341968 Msa0814320:CDS
TAACACACACGCAGAATCAA+AGG 0.552685 5_3:-46341974 Msa0814320:CDS
CTGTTAGTAGAAGCAGTGAA+TGG 0.564549 5_3:-46341832 Msa0814320:CDS
TCTAATGATGTAGCACTGGT+TGG 0.573738 5_3:-46339644 Msa0814320:three_prime_UTR
AACACACACGCAGAATCAAA+GGG 0.575682 5_3:-46341973 Msa0814320:CDS
TTGTGAAACAAACGGATCAG+TGG 0.597090 5_3:-46341732 Msa0814320:CDS
ACATCCAGAATAAAGATACA+AGG 0.617763 5_3:+46339702 None:intergenic
TTAGTAGAAGCAGTGAATGG+CGG 0.707209 5_3:-46341829 Msa0814320:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTTAGTTAATAATGATA+AGG - chr5_3:46340127-46340146 Msa0814320:intron 10.0%
!!! TGTAAAATTTTATTAGATTA+AGG - chr5_3:46341825-46341844 Msa0814320:CDS 10.0%
!! AATAGAAAAATTAATGGAAA+GGG + chr5_3:46341783-46341802 None:intergenic 15.0%
!!! ATAAAATTTTACATGATGTT+GGG + chr5_3:46341818-46341837 None:intergenic 15.0%
!!! AATAAAATTTTACATGATGT+TGG + chr5_3:46341819-46341838 None:intergenic 15.0%
!!! TTTTAAATGATGAATATGAT+TGG - chr5_3:46341921-46341940 Msa0814320:CDS 15.0%
!!! TATTTATTAGTGATTAGTTT+TGG - chr5_3:46342035-46342054 Msa0814320:five_prime_UTR 15.0%
!!! AAATGTCACAAAAACAATTT+TGG - chr5_3:46340605-46340624 Msa0814320:intron 20.0%
!! AATATGATTCCACAATATAA+AGG + chr5_3:46340829-46340848 None:intergenic 20.0%
!!! CATCATAACCAAAATTATTT+TGG + chr5_3:46340995-46341014 None:intergenic 20.0%
!!! CAAAATAATTTTGGTTATGA+TGG - chr5_3:46340993-46341012 Msa0814320:intron 20.0%
!! TTTGTAAATGTTTATTCTTG+TGG - chr5_3:46341051-46341070 Msa0814320:intron 20.0%
!!! AAACTTTTTTTTTAACTCGT+AGG - chr5_3:46341619-46341638 Msa0814320:intron 20.0%
!! GAATAGAAAAATTAATGGAA+AGG + chr5_3:46341784-46341803 None:intergenic 20.0%
!!! TCCATTAATTTTTCTATTCT+AGG - chr5_3:46341785-46341804 Msa0814320:CDS 20.0%
! AATACAAAGAAACAAGTGAA+TGG - chr5_3:46339580-46339599 Msa0814320:three_prime_UTR 25.0%
!!! TTTGATGATGAATGTGAATT+AGG + chr5_3:46339664-46339683 None:intergenic 25.0%
!! ATTGATAAGTTAGCTTATAG+CGG - chr5_3:46340010-46340029 Msa0814320:intron 25.0%
! GAAGTTAGATACTAAATTGA+CGG - chr5_3:46340390-46340409 Msa0814320:intron 25.0%
!! TAGTTTATGGACTAAATTGA+TGG - chr5_3:46340452-46340471 Msa0814320:intron 25.0%
!!! TGGTAGTGGATTATTAAATT+GGG + chr5_3:46340678-46340697 None:intergenic 25.0%
!!! TTGGTAGTGGATTATTAAAT+TGG + chr5_3:46340679-46340698 None:intergenic 25.0%
! TTTAATAATCCACTACCAAT+TGG - chr5_3:46340680-46340699 Msa0814320:intron 25.0%
!! TTCCTTCTCCAAAATAATTT+TGG - chr5_3:46340984-46341003 Msa0814320:intron 25.0%
!!! AACCAAAATTATTTTGGAGA+AGG + chr5_3:46340989-46341008 None:intergenic 25.0%
! TCTTCTCTTCAAATATTCAT+TGG - chr5_3:46341157-46341176 Msa0814320:intron 25.0%
! CTTCTCTTCAAATATTCATT+GGG - chr5_3:46341158-46341177 Msa0814320:intron 25.0%
! TTAAGGTTGTTAAAGATTCA+AGG - chr5_3:46341280-46341299 Msa0814320:intron 25.0%
! TTTGAAAGAACACTGATAAA+TGG - chr5_3:46341384-46341403 Msa0814320:intron 25.0%
! ATATGAGCAAGAATAAAGAT+GGG - chr5_3:46341454-46341473 Msa0814320:intron 25.0%
!!! TTTTTTAACTCGTAGGAAAT+TGG - chr5_3:46341626-46341645 Msa0814320:intron 25.0%
! GCCTAGAATAGAAAAATTAA+TGG + chr5_3:46341789-46341808 None:intergenic 25.0%
!! TTGTTTCTCAACAAAATAAG+TGG - chr5_3:46341849-46341868 Msa0814320:CDS 25.0%
! TACGTATATTTGACAAATCA+TGG - chr5_3:46341979-46341998 Msa0814320:CDS 25.0%
TTGAACTTAGATACTCTGTT+TGG - chr5_3:46339555-46339574 Msa0814320:three_prime_UTR 30.0%
TTCGAGATTTGTGAAACAAA+CGG - chr5_3:46339850-46339869 Msa0814320:three_prime_UTR 30.0%
CTGATTGAATTTGTAGTGTT+TGG - chr5_3:46340072-46340091 Msa0814320:intron 30.0%
TGACGGAATTCATATACTTT+AGG - chr5_3:46340407-46340426 Msa0814320:intron 30.0%
GACGGAATTCATATACTTTA+GGG - chr5_3:46340408-46340427 Msa0814320:intron 30.0%
GAAGAGAGAGTAATAGTTTA+TGG - chr5_3:46340439-46340458 Msa0814320:intron 30.0%
TTCCAAAAATAAATTCCCCA+AGG - chr5_3:46340479-46340498 Msa0814320:intron 30.0%
TTCCACAATATAAAGGAAAG+TGG + chr5_3:46340822-46340841 None:intergenic 30.0%
ACATAACATACTTCCATTCA+GGG + chr5_3:46340914-46340933 None:intergenic 30.0%
ATTCACCAATAACCCAAAAA+TGG + chr5_3:46341027-46341046 None:intergenic 30.0%
!! TTGTGGTTTGTTCCAAATTA+TGG - chr5_3:46341068-46341087 Msa0814320:intron 30.0%
CTTTATTGTGCACCATAATT+TGG + chr5_3:46341083-46341102 None:intergenic 30.0%
CATTAACATGAACATGTACA+AGG + chr5_3:46341257-46341276 None:intergenic 30.0%
TGTTCATGTTAATGTGCTTA+AGG - chr5_3:46341263-46341282 Msa0814320:intron 30.0%
TGAAATATGCATCAATCTTG+TGG - chr5_3:46341324-46341343 Msa0814320:intron 30.0%
CATATGAGCAAGAATAAAGA+TGG - chr5_3:46341453-46341472 Msa0814320:intron 30.0%
TATGAGCAAGAATAAAGATG+GGG - chr5_3:46341455-46341474 Msa0814320:intron 30.0%
! AAATTGGAGACTTTGAGAAT+TGG - chr5_3:46341642-46341661 Msa0814320:intron 30.0%
ACATCCAGAATAAAGATACA+AGG + chr5_3:46341891-46341910 None:intergenic 30.0%
!!! TGCATCTTTCTTCGCTTTTT+CGG + chr5_3:46339711-46339730 None:intergenic 35.0%
!! TATAGCGGATGAACTTATAG+AGG - chr5_3:46340025-46340044 Msa0814320:intron 35.0%
AGCTCATTTGAAAGTCTGTT+TGG + chr5_3:46340282-46340301 None:intergenic 35.0%
!! CTCCTTGGGGAATTTATTTT+TGG + chr5_3:46340484-46340503 None:intergenic 35.0%
CAAAAATAAATTCCCCAAGG+AGG - chr5_3:46340482-46340501 Msa0814320:intron 35.0%
ACCAAAGGCAATCATATTTG+AGG + chr5_3:46340533-46340552 None:intergenic 35.0%
CAAATATGATTGCCTTTGGT+AGG - chr5_3:46340533-46340552 Msa0814320:intron 35.0%
CACATATATACTCCTACCAA+AGG + chr5_3:46340548-46340567 None:intergenic 35.0%
GTGAATTTCATCTAGAGAGA+TGG - chr5_3:46340565-46340584 Msa0814320:intron 35.0%
TTTCAGAATGCTCAGATTGT+TGG - chr5_3:46340635-46340654 Msa0814320:intron 35.0%
TATAGTGTTCCAATTGGTAG+TGG + chr5_3:46340692-46340711 None:intergenic 35.0%
CATCAGTATAGTGTTCCAAT+TGG + chr5_3:46340698-46340717 None:intergenic 35.0%
TGATGTTGATCTGACATAAG+AGG - chr5_3:46340713-46340732 Msa0814320:intron 35.0%
!!! ATAAGAGGCGTTTTCTTATG+TGG - chr5_3:46340728-46340747 Msa0814320:intron 35.0%
!!! TAAGAGGCGTTTTCTTATGT+GGG - chr5_3:46340729-46340748 Msa0814320:intron 35.0%
!! TCCATCTTTTTGGCATCTAT+GGG - chr5_3:46340767-46340786 Msa0814320:intron 35.0%
AAGGTTTGTGATCATGATCT+TGG + chr5_3:46340882-46340901 None:intergenic 35.0%
GACATAACATACTTCCATTC+AGG + chr5_3:46340915-46340934 None:intergenic 35.0%
TTGGAGAAGGAATCTAACTA+TGG + chr5_3:46340976-46340995 None:intergenic 35.0%
!!! ATGGTTGTCATGCCATTTTT+GGG - chr5_3:46341012-46341031 Msa0814320:intron 35.0%
!!! TCATGCCATTTTTGGGTTAT+TGG - chr5_3:46341019-46341038 Msa0814320:intron 35.0%
!! CCTTCTTTCTTGAGTTGATT+GGG - chr5_3:46341117-46341136 Msa0814320:intron 35.0%
TCAAGGATAATGCAAGAGTT+TGG - chr5_3:46341297-46341316 Msa0814320:intron 35.0%
TAATCTGTATTAGTCACGTC+AGG - chr5_3:46341531-46341550 Msa0814320:intron 35.0%
TGAGAATTGGATGAAGATCA+TGG - chr5_3:46341655-46341674 Msa0814320:intron 35.0%
!! GTAGCCTTGTATCTTTATTC+TGG - chr5_3:46341884-46341903 Msa0814320:CDS 35.0%
TAACACACACGCAGAATCAA+AGG - chr5_3:46339616-46339635 Msa0814320:three_prime_UTR 40.0%
AACACACACGCAGAATCAAA+GGG - chr5_3:46339617-46339636 Msa0814320:three_prime_UTR 40.0%
!!! CTTCGCTTTTTCGGTTTGAT+TGG + chr5_3:46339702-46339721 None:intergenic 40.0%
CTGTTAGTAGAAGCAGTGAA+TGG - chr5_3:46339758-46339777 Msa0814320:three_prime_UTR 40.0%
TTAGTAGAAGCAGTGAATGG+CGG - chr5_3:46339761-46339780 Msa0814320:three_prime_UTR 40.0%
TTGTGAAACAAACGGATCAG+TGG - chr5_3:46339858-46339877 Msa0814320:three_prime_UTR 40.0%
TTCTCTTAACACTGCTCTCA+AGG - chr5_3:46339895-46339914 Msa0814320:CDS 40.0%
ACTTCATCACGAGCTTATAG+CGG + chr5_3:46340184-46340203 None:intergenic 40.0%
! TTCTACTGCAGTTGCTTTGT+TGG - chr5_3:46340507-46340526 Msa0814320:intron 40.0%
GCCTCAAATATGATTGCCTT+TGG - chr5_3:46340529-46340548 Msa0814320:intron 40.0%
!!! AAGAGGCGTTTTCTTATGTG+GGG - chr5_3:46340730-46340749 Msa0814320:intron 40.0%
CAAAAAGATGGAGAGTCATG+TGG + chr5_3:46340759-46340778 None:intergenic 40.0%
! CACATGACTCTCCATCTTTT+TGG - chr5_3:46340757-46340776 Msa0814320:intron 40.0%
!! CTCCATCTTTTTGGCATCTA+TGG - chr5_3:46340766-46340785 Msa0814320:intron 40.0%
! GGCCACTTTCCTTTATATTG+TGG - chr5_3:46340817-46340836 Msa0814320:intron 40.0%
!! CCATTCAGGGCTTTAGAAAA+AGG + chr5_3:46340901-46340920 None:intergenic 40.0%
!!! CCTTTTTCTAAAGCCCTGAA+TGG - chr5_3:46340898-46340917 Msa0814320:intron 40.0%
!!! GATGGTTGTCATGCCATTTT+TGG - chr5_3:46341011-46341030 Msa0814320:intron 40.0%
!! GCCTTCTTTCTTGAGTTGAT+TGG - chr5_3:46341116-46341135 Msa0814320:intron 40.0%
CCCAATCAACTCAAGAAAGA+AGG + chr5_3:46341120-46341139 None:intergenic 40.0%
GGCACACTTACACTGATAAA+TGG - chr5_3:46341345-46341364 Msa0814320:intron 40.0%
TGCTCATATGATTGTGCACA+AGG + chr5_3:46341443-46341462 None:intergenic 40.0%
GCAAGAATAAAGATGGGGAT+AGG - chr5_3:46341460-46341479 Msa0814320:intron 40.0%
!! TCTAATGATGTAGCACTGGT+TGG - chr5_3:46341946-46341965 Msa0814320:CDS 40.0%
ACACGCAGAATCAAAGGGAT+TGG - chr5_3:46339622-46339641 Msa0814320:three_prime_UTR 45.0%
AAGAAAAGCAGAGCGCGTTT+CGG - chr5_3:46339733-46339752 Msa0814320:three_prime_UTR 45.0%
TGCAGTAGAAAACCTCCTTG+GGG + chr5_3:46340497-46340516 None:intergenic 45.0%
CTGCAGTAGAAAACCTCCTT+GGG + chr5_3:46340498-46340517 None:intergenic 45.0%
ACTGCAGTAGAAAACCTCCT+TGG + chr5_3:46340499-46340518 None:intergenic 45.0%
!!! AGAGGCGTTTTCTTATGTGG+GGG - chr5_3:46340731-46340750 Msa0814320:intron 45.0%
GCCCATAGATGCCAAAAAGA+TGG + chr5_3:46340771-46340790 None:intergenic 45.0%
TGATCTTGGCTGCAACATCA+TGG + chr5_3:46340868-46340887 None:intergenic 45.0%
TTCACCAAGAGTGATCTTGC+AGG - chr5_3:46341717-46341736 Msa0814320:CDS 45.0%
GGCTTCTAATGATGTAGCAC+TGG - chr5_3:46341942-46341961 Msa0814320:CDS 45.0%
!! TGTAGCACTGGTTGGTGATT+TGG - chr5_3:46341954-46341973 Msa0814320:CDS 45.0%
GCGTCTACAACTGGACGTTT+GGG - chr5_3:46340351-46340370 Msa0814320:intron 50.0%
CATCTAGAGAGATGGTTGCG+TGG - chr5_3:46340573-46340592 Msa0814320:intron 50.0%
! AGACCGTGTTGCTACTATCG+CGG - chr5_3:46340796-46340815 Msa0814320:intron 50.0%
GCAACCTGCAAGATCACTCT+TGG + chr5_3:46341724-46341743 None:intergenic 50.0%
TAGCCCTTCGCGTCTACAAC+TGG - chr5_3:46340342-46340361 Msa0814320:intron 55.0%
CGTCCAGTTGTAGACGCGAA+GGG + chr5_3:46340348-46340367 None:intergenic 55.0%
ACGTCCAGTTGTAGACGCGA+AGG + chr5_3:46340349-46340368 None:intergenic 55.0%
CGCGTCTACAACTGGACGTT+TGG - chr5_3:46340350-46340369 Msa0814320:intron 55.0%
! GACGTTTGGGAGCGTGAACT+GGG - chr5_3:46340364-46340383 Msa0814320:intron 55.0%
TGGCCGCGATAGTAGCAACA+CGG + chr5_3:46340802-46340821 None:intergenic 55.0%
! GGACGTTTGGGAGCGTGAAC+TGG - chr5_3:46340363-46340382 Msa0814320:intron 60.0%
Chromosome Type Strat End Strand Name
chr5_3 gene 46339554 46342058 46339554 ID=Msa0814320;Name=Msa0814320
chr5_3 mRNA 46339554 46342058 46339554 ID=Msa0814320-mRNA-1;Parent=Msa0814320;Name=Msa0814320-mRNA-1;_AED=0.01;_eAED=0.01;_QI=45|1|1|1|1|1|2|328|135
chr5_3 exon 46339554 46339971 46339554 ID=Msa0814320-mRNA-1:exon:14074;Parent=Msa0814320-mRNA-1
chr5_3 exon 46341696 46342058 46341696 ID=Msa0814320-mRNA-1:exon:14073;Parent=Msa0814320-mRNA-1
chr5_3 five_prime_UTR 46342014 46342058 46342014 ID=Msa0814320-mRNA-1:five_prime_utr;Parent=Msa0814320-mRNA-1
chr5_3 CDS 46341696 46342013 46341696 ID=Msa0814320-mRNA-1:cds;Parent=Msa0814320-mRNA-1
chr5_3 CDS 46339882 46339971 46339882 ID=Msa0814320-mRNA-1:cds;Parent=Msa0814320-mRNA-1
chr5_3 three_prime_UTR 46339554 46339881 46339554 ID=Msa0814320-mRNA-1:three_prime_utr;Parent=Msa0814320-mRNA-1
Gene Sequence

>Msa0814320

ATGGAAGAACGCGATGTTAACACACACGCAGAATCAAAGGGATTGGAAGATTCATTACAAAACCTAATTCACATTCATCATCAAAAATCTCTCATTCTCACCAATCAAACCGAAAAAGCGAAGAAAGATGCAATAAGAAAAGCAGAGCGCGTTTCGGATCTGTTAGTAGAAGCAGTGAATGGCGGTGTTCAAGATTCGTTTATTTATCAGAAGAGAATTGAGCTTGAAATTCGTGCTCTTGCTGTAACTATTTCGAGATTTGTGAAACAAACGGATCAGTGGCTTAATGCTACTCATTCTCTTAACACTGCTCTCAAGGAAATTGGAGACTTTGAGAATTGGATGAAGATCATGGAATACGATTTTAAAAGTATTAATGCAGCTATACAAAACATTCACCAAGAGTGA

Protein sequence

>Msa0814320

MEERDVNTHAESKGLEDSLQNLIHIHHQKSLILTNQTEKAKKDAIRKAERVSDLLVEAVNGGVQDSFIYQKRIELEIRALAVTISRFVKQTDQWLNATHSLNTALKEIGDFENWMKIMEYDFKSINAAIQNIHQE*