AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0053800

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0053800 MtrunA17_Chr1g0150981 93.827 81 5 0 1 81 1 81 5.01e-50 154
Msa0053800 MtrunA17_Chr1g0151011 92.593 81 6 0 1 81 1 81 1.56e-48 150
Msa0053800 MtrunA17_Chr3g0136311 60.241 83 32 1 1 82 1 83 9.48e-22 82.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 24 sgRNAs with CRISPR-Local

Find 150 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACCAATTAGTGTTACTTTA+TGG 0.143171 1_2:+8284160 Msa0053800:CDS
AACAAGAAATAAATCATTAA+TGG 0.260027 1_2:+8285700 Msa0053800:three_prime_UTR
TTTACCCTCCTATTTGCTTC+AGG 0.281136 1_2:-8284027 None:intergenic
AACCATAAAGTAACACTAAT+TGG 0.291426 1_2:-8284162 None:intergenic
TCAGAAGTTACATTCGTAAA+TGG 0.336516 1_2:+8285629 Msa0053800:exon
ACTTCCGGTAGTTATGTATA+CGG 0.370187 1_2:-8285593 None:intergenic
TGCTAGAACTACTAAGCTTA+TGG 0.394299 1_2:-8284079 None:intergenic
GAATGGAACCTGAAGCAAAT+AGG 0.404269 1_2:+8284019 None:intergenic
GAAAGAGAGAATCTGCTGAT+AGG 0.428557 1_2:-8285762 None:intergenic
AAGTTGCGTTCCGGTGCTCT+TGG 0.448354 1_2:+8285667 Msa0053800:three_prime_UTR
TTAATGGCAAATTAAAAGAA+TGG 0.448926 1_2:+8285716 Msa0053800:three_prime_UTR
AATACTCAGAAGTTGCGTTC+CGG 0.456712 1_2:+8285658 Msa0053800:three_prime_UTR
GAGTATCTGAAAGCAACTTC+CGG 0.463106 1_2:-8285608 None:intergenic
TGGCAAATTAAAAGAATGGT+TGG 0.485759 1_2:+8285720 Msa0053800:three_prime_UTR
GATCTGTTATCTATGTATAG+AGG 0.518663 1_2:-8284111 None:intergenic
TAACAGATCAGAGAGTGAGT+TGG 0.526376 1_2:+8284125 Msa0053800:CDS
CAAATTAAAAGAATGGTTGG+TGG 0.568561 1_2:+8285723 Msa0053800:three_prime_UTR
CTTCCGGTAGTTATGTATAC+GGG 0.576015 1_2:-8285592 None:intergenic
TTTATAACTTCCAAGAGCAC+CGG 0.585739 1_2:-8285677 None:intergenic
TGGAACCTGAAGCAAATAGG+AGG 0.590316 1_2:+8284022 Msa0053800:CDS
TGAAGCAGAAGAACTGAGGA+TGG 0.595626 1_2:-8285800 None:intergenic
ATACCCGTATACATAACTAC+CGG 0.634495 1_2:+8285589 Msa0053800:CDS
GGAACCTGAAGCAAATAGGA+GGG 0.643854 1_2:+8284023 Msa0053800:CDS
AAGCTTAGTAGTTCTAGCAG+TGG 0.645576 1_2:+8284083 Msa0053800:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATTTAAACTTAATTTAAAG+TGG - chr1_2:8285087-8285106 None:intergenic 10.0%
!! TAAATTAAGTTTAAATATGA+AGG + chr1_2:8285090-8285109 Msa0053800:intron 10.0%
!! TATTTAAACTTAATTTAAAG+TGG - chr1_2:8285087-8285106 None:intergenic 10.0%
!! TAAATTAAGTTTAAATATGA+AGG + chr1_2:8285090-8285109 Msa0053800:intron 10.0%
!!! TAATAAACTTCATATTTTCA+TGG + chr1_2:8284594-8284613 Msa0053800:intron 15.0%
!!! GTAATACATTAAACTAATTT+TGG - chr1_2:8284675-8284694 None:intergenic 15.0%
!! ATATCAAAAGAATGATTAAA+AGG - chr1_2:8284738-8284757 None:intergenic 15.0%
!! CTTCCATTAAAAAATATTTA+AGG + chr1_2:8285509-8285528 Msa0053800:intron 15.0%
!! CATAAACAACATATAATAAA+CGG - chr1_2:8285536-8285555 None:intergenic 15.0%
!!! TTATTATATGTTGTTTATGT+AGG + chr1_2:8285537-8285556 Msa0053800:intron 15.0%
!! AACAAGAAATAAATCATTAA+TGG + chr1_2:8285700-8285719 Msa0053800:three_prime_UTR 15.0%
!!! TAATAAACTTCATATTTTCA+TGG + chr1_2:8284594-8284613 Msa0053800:intron 15.0%
!!! GTAATACATTAAACTAATTT+TGG - chr1_2:8284675-8284694 None:intergenic 15.0%
!! ATATCAAAAGAATGATTAAA+AGG - chr1_2:8284738-8284757 None:intergenic 15.0%
!! CTTCCATTAAAAAATATTTA+AGG + chr1_2:8285509-8285528 Msa0053800:intron 15.0%
!! CATAAACAACATATAATAAA+CGG - chr1_2:8285536-8285555 None:intergenic 15.0%
!!! TTATTATATGTTGTTTATGT+AGG + chr1_2:8285537-8285556 Msa0053800:intron 15.0%
!! AACAAGAAATAAATCATTAA+TGG + chr1_2:8285700-8285719 Msa0053800:three_prime_UTR 15.0%
!!! ACGTGTAATTTTTTTAATTC+TGG - chr1_2:8284893-8284912 None:intergenic 20.0%
!!! TAATTTCTTTTAGCCAAATT+TGG - chr1_2:8285031-8285050 None:intergenic 20.0%
!! ACAAAATCAATAAGCAAATT+TGG + chr1_2:8285142-8285161 Msa0053800:intron 20.0%
!! CAAAATCAATAAGCAAATTT+GGG + chr1_2:8285143-8285162 Msa0053800:intron 20.0%
!! CCATAAACTAGAAAAATATA+CGG + chr1_2:8285212-8285231 Msa0053800:intron 20.0%
!! TTCTATTTGAAAGTAATTGA+GGG - chr1_2:8285466-8285485 None:intergenic 20.0%
!! TTTCTATTTGAAAGTAATTG+AGG - chr1_2:8285467-8285486 None:intergenic 20.0%
!!! GGTCCTTAAATATTTTTTAA+TGG - chr1_2:8285515-8285534 None:intergenic 20.0%
!! TTAATGGCAAATTAAAAGAA+TGG + chr1_2:8285716-8285735 Msa0053800:three_prime_UTR 20.0%
!!! ACGTGTAATTTTTTTAATTC+TGG - chr1_2:8284893-8284912 None:intergenic 20.0%
!!! TAATTTCTTTTAGCCAAATT+TGG - chr1_2:8285031-8285050 None:intergenic 20.0%
!! ACAAAATCAATAAGCAAATT+TGG + chr1_2:8285142-8285161 Msa0053800:intron 20.0%
!! CAAAATCAATAAGCAAATTT+GGG + chr1_2:8285143-8285162 Msa0053800:intron 20.0%
!! CCATAAACTAGAAAAATATA+CGG + chr1_2:8285212-8285231 Msa0053800:intron 20.0%
!! TTCTATTTGAAAGTAATTGA+GGG - chr1_2:8285466-8285485 None:intergenic 20.0%
!! TTTCTATTTGAAAGTAATTG+AGG - chr1_2:8285467-8285486 None:intergenic 20.0%
!!! GGTCCTTAAATATTTTTTAA+TGG - chr1_2:8285515-8285534 None:intergenic 20.0%
!! TTAATGGCAAATTAAAAGAA+TGG + chr1_2:8285716-8285735 Msa0053800:three_prime_UTR 20.0%
!!! AACCAATTAGTGTTACTTTA+TGG + chr1_2:8284160-8284179 Msa0053800:CDS 25.0%
! AACCATAAAGTAACACTAAT+TGG - chr1_2:8284165-8284184 None:intergenic 25.0%
! TGACATTACATTTGTAAACA+AGG + chr1_2:8284777-8284796 Msa0053800:intron 25.0%
!!! CAAGTATTTTCTTTTGTTGT+AGG - chr1_2:8284835-8284854 None:intergenic 25.0%
! CTACAACAAAAGAAAATACT+TGG + chr1_2:8284833-8284852 Msa0053800:intron 25.0%
!!! TTTGGTTTTGAATAAAGACT+TGG - chr1_2:8284964-8284983 None:intergenic 25.0%
!! TTAATTTAAAGTGGATGCAT+TGG - chr1_2:8285078-8285097 None:intergenic 25.0%
!!! CCGTATATTTTTCTAGTTTA+TGG - chr1_2:8285215-8285234 None:intergenic 25.0%
! AAAAATATACGGCCAATAAA+TGG + chr1_2:8285223-8285242 Msa0053800:intron 25.0%
!! TTTTAAATTCTGTGATGTCT+GGG - chr1_2:8285568-8285587 None:intergenic 25.0%
!! TTTTTAAATTCTGTGATGTC+TGG - chr1_2:8285569-8285588 None:intergenic 25.0%
!!! AACCAATTAGTGTTACTTTA+TGG + chr1_2:8284160-8284179 Msa0053800:CDS 25.0%
! AACCATAAAGTAACACTAAT+TGG - chr1_2:8284165-8284184 None:intergenic 25.0%
! TGACATTACATTTGTAAACA+AGG + chr1_2:8284777-8284796 Msa0053800:intron 25.0%
!!! CAAGTATTTTCTTTTGTTGT+AGG - chr1_2:8284835-8284854 None:intergenic 25.0%
! CTACAACAAAAGAAAATACT+TGG + chr1_2:8284833-8284852 Msa0053800:intron 25.0%
!!! TTTGGTTTTGAATAAAGACT+TGG - chr1_2:8284964-8284983 None:intergenic 25.0%
!! TTAATTTAAAGTGGATGCAT+TGG - chr1_2:8285078-8285097 None:intergenic 25.0%
!!! CCGTATATTTTTCTAGTTTA+TGG - chr1_2:8285215-8285234 None:intergenic 25.0%
! AAAAATATACGGCCAATAAA+TGG + chr1_2:8285223-8285242 Msa0053800:intron 25.0%
!! TTTTAAATTCTGTGATGTCT+GGG - chr1_2:8285568-8285587 None:intergenic 25.0%
!! TTTTTAAATTCTGTGATGTC+TGG - chr1_2:8285569-8285588 None:intergenic 25.0%
GATCTGTTATCTATGTATAG+AGG - chr1_2:8284114-8284133 None:intergenic 30.0%
!!! CATAGCTTTATCAGCTTTTT+TGG + chr1_2:8284215-8284234 Msa0053800:CDS 30.0%
CACAAGTGTACAAAATATAG+AGG - chr1_2:8284458-8284477 None:intergenic 30.0%
TGTAAACAAGGTAAACACTA+AGG + chr1_2:8284789-8284808 Msa0053800:intron 30.0%
!! TTCTAGTTTATGGCCTAAAT+GGG - chr1_2:8285205-8285224 None:intergenic 30.0%
!! TTTCTAGTTTATGGCCTAAA+TGG - chr1_2:8285206-8285225 None:intergenic 30.0%
TCAGAAGTTACATTCGTAAA+TGG + chr1_2:8285629-8285648 Msa0053800:exon 30.0%
TGGCAAATTAAAAGAATGGT+TGG + chr1_2:8285720-8285739 Msa0053800:three_prime_UTR 30.0%
CAAATTAAAAGAATGGTTGG+TGG + chr1_2:8285723-8285742 Msa0053800:three_prime_UTR 30.0%
GATCTGTTATCTATGTATAG+AGG - chr1_2:8284114-8284133 None:intergenic 30.0%
!!! CATAGCTTTATCAGCTTTTT+TGG + chr1_2:8284215-8284234 Msa0053800:CDS 30.0%
CACAAGTGTACAAAATATAG+AGG - chr1_2:8284458-8284477 None:intergenic 30.0%
TGTAAACAAGGTAAACACTA+AGG + chr1_2:8284789-8284808 Msa0053800:intron 30.0%
!! TTCTAGTTTATGGCCTAAAT+GGG - chr1_2:8285205-8285224 None:intergenic 30.0%
!! TTTCTAGTTTATGGCCTAAA+TGG - chr1_2:8285206-8285225 None:intergenic 30.0%
TCAGAAGTTACATTCGTAAA+TGG + chr1_2:8285629-8285648 Msa0053800:exon 30.0%
TGGCAAATTAAAAGAATGGT+TGG + chr1_2:8285720-8285739 Msa0053800:three_prime_UTR 30.0%
CAAATTAAAAGAATGGTTGG+TGG + chr1_2:8285723-8285742 Msa0053800:three_prime_UTR 30.0%
TGCTAGAACTACTAAGCTTA+TGG - chr1_2:8284082-8284101 None:intergenic 35.0%
!!! ACCTATGCTGCTTTTTGTAT+TGG + chr1_2:8284185-8284204 Msa0053800:CDS 35.0%
ACCAATACAAAAAGCAGCAT+AGG - chr1_2:8284189-8284208 None:intergenic 35.0%
TCACAAGGTTTGATCGTAAT+TGG + chr1_2:8284247-8284266 Msa0053800:intron 35.0%
CGTAATTGGATTCATAGAGT+TGG + chr1_2:8284261-8284280 Msa0053800:intron 35.0%
AATTGGATTCATAGAGTTGG+TGG + chr1_2:8284264-8284283 Msa0053800:intron 35.0%
!! ATTTTCTTTTGTTGTAGGCG+TGG - chr1_2:8284830-8284849 None:intergenic 35.0%
! TGCTACTACTTTCTGAGTTT+TGG - chr1_2:8284982-8285001 None:intergenic 35.0%
ACTGCAGAAAGAACCAAATT+TGG + chr1_2:8285015-8285034 Msa0053800:intron 35.0%
! ATTTTGCTAGACTGCAACTT+CGG + chr1_2:8285118-8285137 Msa0053800:intron 35.0%
GGGAGAGAAACAATTGTTTA+GGG - chr1_2:8285185-8285204 None:intergenic 35.0%
TGGGAGAGAAACAATTGTTT+AGG - chr1_2:8285186-8285205 None:intergenic 35.0%
! CAATTGTTTCTCTCCCATTT+AGG + chr1_2:8285189-8285208 Msa0053800:intron 35.0%
ATACCCGTATACATAACTAC+CGG + chr1_2:8285589-8285608 Msa0053800:CDS 35.0%
ACTTCCGGTAGTTATGTATA+CGG - chr1_2:8285596-8285615 None:intergenic 35.0%
! TTTATAACTTCCAAGAGCAC+CGG - chr1_2:8285680-8285699 None:intergenic 35.0%
TGCTAGAACTACTAAGCTTA+TGG - chr1_2:8284082-8284101 None:intergenic 35.0%
!!! ACCTATGCTGCTTTTTGTAT+TGG + chr1_2:8284185-8284204 Msa0053800:CDS 35.0%
ACCAATACAAAAAGCAGCAT+AGG - chr1_2:8284189-8284208 None:intergenic 35.0%
TCACAAGGTTTGATCGTAAT+TGG + chr1_2:8284247-8284266 Msa0053800:intron 35.0%
CGTAATTGGATTCATAGAGT+TGG + chr1_2:8284261-8284280 Msa0053800:intron 35.0%
AATTGGATTCATAGAGTTGG+TGG + chr1_2:8284264-8284283 Msa0053800:intron 35.0%
!! ATTTTCTTTTGTTGTAGGCG+TGG - chr1_2:8284830-8284849 None:intergenic 35.0%
! TGCTACTACTTTCTGAGTTT+TGG - chr1_2:8284982-8285001 None:intergenic 35.0%
ACTGCAGAAAGAACCAAATT+TGG + chr1_2:8285015-8285034 Msa0053800:intron 35.0%
! ATTTTGCTAGACTGCAACTT+CGG + chr1_2:8285118-8285137 Msa0053800:intron 35.0%
GGGAGAGAAACAATTGTTTA+GGG - chr1_2:8285185-8285204 None:intergenic 35.0%
TGGGAGAGAAACAATTGTTT+AGG - chr1_2:8285186-8285205 None:intergenic 35.0%
! CAATTGTTTCTCTCCCATTT+AGG + chr1_2:8285189-8285208 Msa0053800:intron 35.0%
ATACCCGTATACATAACTAC+CGG + chr1_2:8285589-8285608 Msa0053800:CDS 35.0%
ACTTCCGGTAGTTATGTATA+CGG - chr1_2:8285596-8285615 None:intergenic 35.0%
! TTTATAACTTCCAAGAGCAC+CGG - chr1_2:8285680-8285699 None:intergenic 35.0%
TTTACCCTCCTATTTGCTTC+AGG - chr1_2:8284030-8284049 None:intergenic 40.0%
!! AAGCTTAGTAGTTCTAGCAG+TGG + chr1_2:8284083-8284102 Msa0053800:CDS 40.0%
TAACAGATCAGAGAGTGAGT+TGG + chr1_2:8284125-8284144 Msa0053800:CDS 40.0%
! TTTTGGACAAGAGCTTCACA+AGG + chr1_2:8284232-8284251 Msa0053800:CDS 40.0%
! TTTTGCTAGACTGCAACTTC+GGG + chr1_2:8285119-8285138 Msa0053800:intron 40.0%
CCACGAACTTGACCATTTAT+TGG - chr1_2:8285238-8285257 None:intergenic 40.0%
CCAATAAATGGTCAAGTTCG+TGG + chr1_2:8285235-8285254 Msa0053800:intron 40.0%
CTTCCGGTAGTTATGTATAC+GGG - chr1_2:8285595-8285614 None:intergenic 40.0%
GAGTATCTGAAAGCAACTTC+CGG - chr1_2:8285611-8285630 None:intergenic 40.0%
AATACTCAGAAGTTGCGTTC+CGG + chr1_2:8285658-8285677 Msa0053800:three_prime_UTR 40.0%
GAAAGAGAGAATCTGCTGAT+AGG - chr1_2:8285765-8285784 None:intergenic 40.0%
TTTACCCTCCTATTTGCTTC+AGG - chr1_2:8284030-8284049 None:intergenic 40.0%
!! AAGCTTAGTAGTTCTAGCAG+TGG + chr1_2:8284083-8284102 Msa0053800:CDS 40.0%
TAACAGATCAGAGAGTGAGT+TGG + chr1_2:8284125-8284144 Msa0053800:CDS 40.0%
! TTTTGGACAAGAGCTTCACA+AGG + chr1_2:8284232-8284251 Msa0053800:CDS 40.0%
! TTTTGCTAGACTGCAACTTC+GGG + chr1_2:8285119-8285138 Msa0053800:intron 40.0%
CCACGAACTTGACCATTTAT+TGG - chr1_2:8285238-8285257 None:intergenic 40.0%
CCAATAAATGGTCAAGTTCG+TGG + chr1_2:8285235-8285254 Msa0053800:intron 40.0%
CTTCCGGTAGTTATGTATAC+GGG - chr1_2:8285595-8285614 None:intergenic 40.0%
GAGTATCTGAAAGCAACTTC+CGG - chr1_2:8285611-8285630 None:intergenic 40.0%
AATACTCAGAAGTTGCGTTC+CGG + chr1_2:8285658-8285677 Msa0053800:three_prime_UTR 40.0%
GAAAGAGAGAATCTGCTGAT+AGG - chr1_2:8285765-8285784 None:intergenic 40.0%
TGGAACCTGAAGCAAATAGG+AGG + chr1_2:8284022-8284041 Msa0053800:CDS 45.0%
GGAACCTGAAGCAAATAGGA+GGG + chr1_2:8284023-8284042 Msa0053800:CDS 45.0%
!! CATAGAGTTGGTGGTTCTTC+TGG + chr1_2:8284273-8284292 Msa0053800:intron 45.0%
! TGCTGATAGGTTTTCGCTGA+GGG - chr1_2:8285752-8285771 None:intergenic 45.0%
TGGAACCTGAAGCAAATAGG+AGG + chr1_2:8284022-8284041 Msa0053800:CDS 45.0%
GGAACCTGAAGCAAATAGGA+GGG + chr1_2:8284023-8284042 Msa0053800:CDS 45.0%
!! CATAGAGTTGGTGGTTCTTC+TGG + chr1_2:8284273-8284292 Msa0053800:intron 45.0%
! TGCTGATAGGTTTTCGCTGA+GGG - chr1_2:8285752-8285771 None:intergenic 45.0%
!!! AAATTTATTTATTTTACTAT+TGG - chr1_2:8285364-8285383 None:intergenic 5.0%
!!! AAATTTATTTATTTTACTAT+TGG - chr1_2:8285364-8285383 None:intergenic 5.0%
!! AGAGTTGGTGGTTCTTCTGG+TGG + chr1_2:8284276-8284295 Msa0053800:intron 50.0%
CTTGAGCATGCATGCATGCA+AGG - chr1_2:8284368-8284387 None:intergenic 50.0%
CTTGCATGCATGCATGCTCA+AGG + chr1_2:8284366-8284385 Msa0053800:intron 50.0%
! CTGCTGATAGGTTTTCGCTG+AGG - chr1_2:8285753-8285772 None:intergenic 50.0%
!! AGAGTTGGTGGTTCTTCTGG+TGG + chr1_2:8284276-8284295 Msa0053800:intron 50.0%
CTTGAGCATGCATGCATGCA+AGG - chr1_2:8284368-8284387 None:intergenic 50.0%
CTTGCATGCATGCATGCTCA+AGG + chr1_2:8284366-8284385 Msa0053800:intron 50.0%
! CTGCTGATAGGTTTTCGCTG+AGG - chr1_2:8285753-8285772 None:intergenic 50.0%
AAGTTGCGTTCCGGTGCTCT+TGG + chr1_2:8285667-8285686 Msa0053800:three_prime_UTR 55.0%
AAGTTGCGTTCCGGTGCTCT+TGG + chr1_2:8285667-8285686 Msa0053800:three_prime_UTR 55.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 8284021 8285809 8284021 ID=Msa0053800;Name=Msa0053800
chr1_2 mRNA 8284021 8285809 8284021 ID=Msa0053800-mRNA-1;Parent=Msa0053800;Name=Msa0053800-mRNA-1;_AED=0.11;_eAED=0.11;_QI=0|0|0.5|1|0|0|2|162|109
chr1_2 exon 8284021 8284261 8284021 ID=Msa0053800-mRNA-1:exon:2939;Parent=Msa0053800-mRNA-1
chr1_2 exon 8285559 8285809 8285559 ID=Msa0053800-mRNA-1:exon:2940;Parent=Msa0053800-mRNA-1
chr1_2 CDS 8284021 8284261 8284021 ID=Msa0053800-mRNA-1:cds;Parent=Msa0053800-mRNA-1
chr1_2 CDS 8285559 8285647 8285559 ID=Msa0053800-mRNA-1:cds;Parent=Msa0053800-mRNA-1
chr1_2 three_prime_UTR 8285648 8285809 8285648 ID=Msa0053800-mRNA-1:three_prime_utr;Parent=Msa0053800-mRNA-1
Gene Sequence

>Msa0053800

ATGGAACCTGAAGCAAATAGGAGGGTAAACAAATTTTCATCTTATGAGAGAGTAGCAGCCATAAGCTTAGTAGTTCTAGCAGTGGCTTCTCCTCTATACATAGATAACAGATCAGAGAGTGAGTTGGAAGATGATGAACAACCAATTAGTGTTACTTTATGGTTACCTATGCTGCTTTTTGTATTGGTTTTAGTCATAGCTTTATCAGCTTTTTTGGACAAGAGCTTCACAAGGTTTGATCGTTACTCCCAGACATCACAGAATTTAAAAAATACCCGTATACATAACTACCGGAAGTTGCTTTCAGATACTCAGAAGTTACATTCGTAA
Protein sequence

>Msa0053800

MEPEANRRVNKFSSYERVAAISLVVLAVASPLYIDNRSESELEDDEQPISVTLWLPMLLFVLVLVIALSAFLDKSFTRFDRYSQTSQNLKNTRIHNYRKLLSDTQKLHS*