AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0242140

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 44 sgRNAs with CRISPR-Local

Find 104 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAATACACTGTCTAACTTCT+AGG 0.168588 2_2:-18134033 Msa0242140:five_prime_UTR
TTGAAGTTCCTATCTGGATA+TGG 0.251500 2_2:-18133701 Msa0242140:five_prime_UTR
AATCGTGATGTTTCACTCTA+AGG 0.341127 2_2:+18133535 None:intergenic
AGGAATTTGTCGAAAGTATC+AGG 0.344052 2_2:+18133555 None:intergenic
CGATTATTCTACGAGTTTAG+TGG 0.386306 2_2:-18133856 Msa0242140:five_prime_UTR
TCCGAACATCACATTTGGTA+TGG 0.417548 2_2:+18133449 None:intergenic
ATCTACTTCCACCAAGGTAC+TGG 0.428620 2_2:+18133815 None:intergenic
CCGAACATCACATTTGGTAT+GGG 0.451435 2_2:+18133450 None:intergenic
ATTATTGCTTTCCAGTACCT+TGG 0.461507 2_2:-18133826 Msa0242140:five_prime_UTR
TGCCGCACTCATGGAATGAT+AGG 0.462626 2_2:+18133744 None:intergenic
TTGTGCTGCCAATGGTATTG+AGG 0.463000 2_2:-18133409 Msa0242140:CDS
TGATAGGGTGGATAATCAAC+TGG 0.472004 2_2:+18133760 None:intergenic
CCAAATGTGATGTTCGGAAA+AGG 0.475440 2_2:-18133444 Msa0242140:CDS
CCCATACCAAATGTGATGTT+CGG 0.477035 2_2:-18133450 Msa0242140:CDS
GAGCAATGACACTTGCTAGA+TGG 0.483539 2_2:-18133957 Msa0242140:five_prime_UTR
TCGTCGATCCATATCCAGAT+AGG 0.486078 2_2:+18133693 None:intergenic
GGCCGTTGTTGACAGATGGT+TGG 0.487397 2_2:-18133890 Msa0242140:five_prime_UTR
ACACGATGCTGCCGCACTCA+TGG 0.487735 2_2:+18133735 None:intergenic
GTCATGCGTTTATCAACGCT+TGG 0.494559 2_2:+18133326 None:intergenic
TGTGCTGCCAATGGTATTGA+GGG 0.501205 2_2:-18133408 Msa0242140:CDS
TCTACGAGTTTAGTGGAAGT+AGG 0.509601 2_2:-18133849 Msa0242140:five_prime_UTR
AAAATATTTCTACGAGCTAC+CGG 0.521929 2_2:-18133979 Msa0242140:five_prime_UTR
ACATGAATGATATTGTCATA+AGG 0.526037 2_2:+18133495 None:intergenic
AGTCGGCCGTTGTTGACAGA+TGG 0.531450 2_2:-18133894 Msa0242140:five_prime_UTR
ATATTAAATCCAACGAAAAG+AGG 0.531474 2_2:+18134102 None:intergenic
ATCCAGATAGGAACTTCAAA+AGG 0.531873 2_2:+18133705 None:intergenic
ATTGCTTTCCAGTACCTTGG+TGG 0.549152 2_2:-18133823 Msa0242140:five_prime_UTR
CGAACATCACATTTGGTATG+GGG 0.552019 2_2:+18133451 None:intergenic
TCTAGCAAGTGTCATTGCTC+CGG 0.553561 2_2:+18133960 None:intergenic
TTTCAAGTGCAAGTGCGTCA+TGG 0.567746 2_2:-18133370 Msa0242140:CDS
CTGTCTAACTTCTAGGATGT+CGG 0.570416 2_2:-18134026 Msa0242140:five_prime_UTR
GTCTCCGCCCTCAATACCAT+TGG 0.581950 2_2:+18133401 None:intergenic
CACGATTACGTCATGTTGTG+CGG 0.590860 2_2:-18133519 Msa0242140:exon
TGACACTTGCTAGATGGTGA+TGG 0.594754 2_2:-18133951 Msa0242140:five_prime_UTR
ATGTGATGTTCGGAAAAGGT+TGG 0.606400 2_2:-18133440 Msa0242140:CDS
TGTTCAACAAATCAGTTAGT+CGG 0.609582 2_2:-18133911 Msa0242140:five_prime_UTR
GACACTTGCTAGATGGTGAT+GGG 0.615365 2_2:-18133950 Msa0242140:five_prime_UTR
GCCGCACTCATGGAATGATA+GGG 0.629158 2_2:+18133745 None:intergenic
ACCCTATCATTCCATGAGTG+CGG 0.640367 2_2:-18133746 Msa0242140:five_prime_UTR
GCACTCATGGAATGATAGGG+TGG 0.649652 2_2:+18133748 None:intergenic
CTCCAACCATCTGTCAACAA+CGG 0.679074 2_2:+18133888 None:intergenic
TTTGAAATCTACTTCCACCA+AGG 0.681040 2_2:+18133809 None:intergenic
TGGATCGACGAAATCACCGA+AGG 0.700849 2_2:-18133681 Msa0242140:intron
GCTGCCAATGGTATTGAGGG+CGG 0.739556 2_2:-18133405 Msa0242140:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTTATATATGCTATAATAA+AGG - chr2_2:18133841-18133860 Msa0242140:five_prime_UTR 10.0%
!!! CAATTTTTTTTTCTTTTTTT+AGG - chr2_2:18133882-18133901 Msa0242140:five_prime_UTR 10.0%
!! ATTTATATATGCTATAATAA+AGG - chr2_2:18133841-18133860 Msa0242140:five_prime_UTR 10.0%
!!! CAATTTTTTTTTCTTTTTTT+AGG - chr2_2:18133882-18133901 Msa0242140:five_prime_UTR 10.0%
!! TAGACAGTGTATTAAAAAAA+AGG + chr2_2:18133426-18133445 None:intergenic 20.0%
!! AAAAAACAATAAACAACCTT+CGG + chr2_2:18133803-18133822 None:intergenic 20.0%
!! TAGACAGTGTATTAAAAAAA+AGG + chr2_2:18133426-18133445 None:intergenic 20.0%
!! AAAAAACAATAAACAACCTT+CGG + chr2_2:18133803-18133822 None:intergenic 20.0%
!! AAATTAAATCCTCTTTTCGT+TGG - chr2_2:18133354-18133373 Msa0242140:CDS 25.0%
! ATATTAAATCCAACGAAAAG+AGG + chr2_2:18133366-18133385 None:intergenic 25.0%
!! AAATATTTTGCAACGAAGAA+TGG + chr2_2:18133475-18133494 None:intergenic 25.0%
! ACATGAATGATATTGTCATA+AGG + chr2_2:18133973-18133992 None:intergenic 25.0%
!! AAATTAAATCCTCTTTTCGT+TGG - chr2_2:18133354-18133373 Msa0242140:CDS 25.0%
! ATATTAAATCCAACGAAAAG+AGG + chr2_2:18133366-18133385 None:intergenic 25.0%
!! AAATATTTTGCAACGAAGAA+TGG + chr2_2:18133475-18133494 None:intergenic 25.0%
! ACATGAATGATATTGTCATA+AGG + chr2_2:18133973-18133992 None:intergenic 25.0%
TAATACACTGTCTAACTTCT+AGG - chr2_2:18133432-18133451 Msa0242140:CDS 30.0%
! AAAATATTTCTACGAGCTAC+CGG - chr2_2:18133486-18133505 Msa0242140:CDS 30.0%
TGTTCAACAAATCAGTTAGT+CGG - chr2_2:18133554-18133573 Msa0242140:five_prime_UTR 30.0%
TAATACACTGTCTAACTTCT+AGG - chr2_2:18133432-18133451 Msa0242140:CDS 30.0%
! AAAATATTTCTACGAGCTAC+CGG - chr2_2:18133486-18133505 Msa0242140:CDS 30.0%
TGTTCAACAAATCAGTTAGT+CGG - chr2_2:18133554-18133573 Msa0242140:five_prime_UTR 30.0%
CGATTATTCTACGAGTTTAG+TGG - chr2_2:18133609-18133628 Msa0242140:intron 35.0%
ATTATTGCTTTCCAGTACCT+TGG - chr2_2:18133639-18133658 Msa0242140:intron 35.0%
! TTTGAAATCTACTTCCACCA+AGG + chr2_2:18133659-18133678 None:intergenic 35.0%
!!! TACCTTTTGAAGTTCCTATC+TGG - chr2_2:18133758-18133777 Msa0242140:five_prime_UTR 35.0%
ATCCAGATAGGAACTTCAAA+AGG + chr2_2:18133763-18133782 None:intergenic 35.0%
TTGAAGTTCCTATCTGGATA+TGG - chr2_2:18133764-18133783 Msa0242140:five_prime_UTR 35.0%
!! AGGAATTTGTCGAAAGTATC+AGG + chr2_2:18133913-18133932 None:intergenic 35.0%
AATCGTGATGTTTCACTCTA+AGG + chr2_2:18133933-18133952 None:intergenic 35.0%
CGATTATTCTACGAGTTTAG+TGG - chr2_2:18133609-18133628 Msa0242140:intron 35.0%
ATTATTGCTTTCCAGTACCT+TGG - chr2_2:18133639-18133658 Msa0242140:intron 35.0%
! TTTGAAATCTACTTCCACCA+AGG + chr2_2:18133659-18133678 None:intergenic 35.0%
!!! TACCTTTTGAAGTTCCTATC+TGG - chr2_2:18133758-18133777 Msa0242140:five_prime_UTR 35.0%
ATCCAGATAGGAACTTCAAA+AGG + chr2_2:18133763-18133782 None:intergenic 35.0%
TTGAAGTTCCTATCTGGATA+TGG - chr2_2:18133764-18133783 Msa0242140:five_prime_UTR 35.0%
!! AGGAATTTGTCGAAAGTATC+AGG + chr2_2:18133913-18133932 None:intergenic 35.0%
AATCGTGATGTTTCACTCTA+AGG + chr2_2:18133933-18133952 None:intergenic 35.0%
!! CTGTCTAACTTCTAGGATGT+CGG - chr2_2:18133439-18133458 Msa0242140:CDS 40.0%
TCTACGAGTTTAGTGGAAGT+AGG - chr2_2:18133616-18133635 Msa0242140:intron 40.0%
TGATAGGGTGGATAATCAAC+TGG + chr2_2:18133708-18133727 None:intergenic 40.0%
CGAACATCACATTTGGTATG+GGG + chr2_2:18134017-18134036 None:intergenic 40.0%
CCGAACATCACATTTGGTAT+GGG + chr2_2:18134018-18134037 None:intergenic 40.0%
CCCATACCAAATGTGATGTT+CGG - chr2_2:18134015-18134034 Msa0242140:five_prime_UTR 40.0%
TCCGAACATCACATTTGGTA+TGG + chr2_2:18134019-18134038 None:intergenic 40.0%
! CCTTTTCCGAACATCACATT+TGG + chr2_2:18134024-18134043 None:intergenic 40.0%
CCAAATGTGATGTTCGGAAA+AGG - chr2_2:18134021-18134040 Msa0242140:five_prime_UTR 40.0%
ATGTGATGTTCGGAAAAGGT+TGG - chr2_2:18134025-18134044 Msa0242140:five_prime_UTR 40.0%
!! CTGTCTAACTTCTAGGATGT+CGG - chr2_2:18133439-18133458 Msa0242140:CDS 40.0%
TCTACGAGTTTAGTGGAAGT+AGG - chr2_2:18133616-18133635 Msa0242140:intron 40.0%
TGATAGGGTGGATAATCAAC+TGG + chr2_2:18133708-18133727 None:intergenic 40.0%
CGAACATCACATTTGGTATG+GGG + chr2_2:18134017-18134036 None:intergenic 40.0%
CCGAACATCACATTTGGTAT+GGG + chr2_2:18134018-18134037 None:intergenic 40.0%
CCCATACCAAATGTGATGTT+CGG - chr2_2:18134015-18134034 Msa0242140:five_prime_UTR 40.0%
TCCGAACATCACATTTGGTA+TGG + chr2_2:18134019-18134038 None:intergenic 40.0%
! CCTTTTCCGAACATCACATT+TGG + chr2_2:18134024-18134043 None:intergenic 40.0%
CCAAATGTGATGTTCGGAAA+AGG - chr2_2:18134021-18134040 Msa0242140:five_prime_UTR 40.0%
ATGTGATGTTCGGAAAAGGT+TGG - chr2_2:18134025-18134044 Msa0242140:five_prime_UTR 40.0%
! TCTAGCAAGTGTCATTGCTC+CGG + chr2_2:18133508-18133527 None:intergenic 45.0%
! GAGCAATGACACTTGCTAGA+TGG - chr2_2:18133508-18133527 Msa0242140:CDS 45.0%
! TGACACTTGCTAGATGGTGA+TGG - chr2_2:18133514-18133533 Msa0242140:exon 45.0%
! GACACTTGCTAGATGGTGAT+GGG - chr2_2:18133515-18133534 Msa0242140:exon 45.0%
CTCCAACCATCTGTCAACAA+CGG + chr2_2:18133580-18133599 None:intergenic 45.0%
ATTGCTTTCCAGTACCTTGG+TGG - chr2_2:18133642-18133661 Msa0242140:intron 45.0%
ATCTACTTCCACCAAGGTAC+TGG + chr2_2:18133653-18133672 None:intergenic 45.0%
ACCCTATCATTCCATGAGTG+CGG - chr2_2:18133719-18133738 Msa0242140:five_prime_UTR 45.0%
TCGTCGATCCATATCCAGAT+AGG + chr2_2:18133775-18133794 None:intergenic 45.0%
CACGATTACGTCATGTTGTG+CGG - chr2_2:18133946-18133965 Msa0242140:five_prime_UTR 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG - chr2_2:18134048-18134067 Msa0242140:five_prime_UTR 45.0%
TTGTGCTGCCAATGGTATTG+AGG - chr2_2:18134056-18134075 Msa0242140:five_prime_UTR 45.0%
! TGTGCTGCCAATGGTATTGA+GGG - chr2_2:18134057-18134076 Msa0242140:five_prime_UTR 45.0%
! TTTCAAGTGCAAGTGCGTCA+TGG - chr2_2:18134095-18134114 Msa0242140:five_prime_UTR 45.0%
! TCTAGCAAGTGTCATTGCTC+CGG + chr2_2:18133508-18133527 None:intergenic 45.0%
! GAGCAATGACACTTGCTAGA+TGG - chr2_2:18133508-18133527 Msa0242140:CDS 45.0%
! TGACACTTGCTAGATGGTGA+TGG - chr2_2:18133514-18133533 Msa0242140:exon 45.0%
! GACACTTGCTAGATGGTGAT+GGG - chr2_2:18133515-18133534 Msa0242140:exon 45.0%
CTCCAACCATCTGTCAACAA+CGG + chr2_2:18133580-18133599 None:intergenic 45.0%
ATTGCTTTCCAGTACCTTGG+TGG - chr2_2:18133642-18133661 Msa0242140:intron 45.0%
ATCTACTTCCACCAAGGTAC+TGG + chr2_2:18133653-18133672 None:intergenic 45.0%
ACCCTATCATTCCATGAGTG+CGG - chr2_2:18133719-18133738 Msa0242140:five_prime_UTR 45.0%
TCGTCGATCCATATCCAGAT+AGG + chr2_2:18133775-18133794 None:intergenic 45.0%
CACGATTACGTCATGTTGTG+CGG - chr2_2:18133946-18133965 Msa0242140:five_prime_UTR 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG - chr2_2:18134048-18134067 Msa0242140:five_prime_UTR 45.0%
TTGTGCTGCCAATGGTATTG+AGG - chr2_2:18134056-18134075 Msa0242140:five_prime_UTR 45.0%
! TGTGCTGCCAATGGTATTGA+GGG - chr2_2:18134057-18134076 Msa0242140:five_prime_UTR 45.0%
! TTTCAAGTGCAAGTGCGTCA+TGG - chr2_2:18134095-18134114 Msa0242140:five_prime_UTR 45.0%
GCACTCATGGAATGATAGGG+TGG + chr2_2:18133720-18133739 None:intergenic 50.0%
GCCGCACTCATGGAATGATA+GGG + chr2_2:18133723-18133742 None:intergenic 50.0%
TGCCGCACTCATGGAATGAT+AGG + chr2_2:18133724-18133743 None:intergenic 50.0%
TGGATCGACGAAATCACCGA+AGG - chr2_2:18133784-18133803 Msa0242140:five_prime_UTR 50.0%
GCACTCATGGAATGATAGGG+TGG + chr2_2:18133720-18133739 None:intergenic 50.0%
GCCGCACTCATGGAATGATA+GGG + chr2_2:18133723-18133742 None:intergenic 50.0%
TGCCGCACTCATGGAATGAT+AGG + chr2_2:18133724-18133743 None:intergenic 50.0%
TGGATCGACGAAATCACCGA+AGG - chr2_2:18133784-18133803 Msa0242140:five_prime_UTR 50.0%
AGTCGGCCGTTGTTGACAGA+TGG - chr2_2:18133571-18133590 Msa0242140:intron 55.0%
GGCCGTTGTTGACAGATGGT+TGG - chr2_2:18133575-18133594 Msa0242140:intron 55.0%
! GCTGCCAATGGTATTGAGGG+CGG - chr2_2:18134060-18134079 Msa0242140:five_prime_UTR 55.0%
GTCTCCGCCCTCAATACCAT+TGG + chr2_2:18134067-18134086 None:intergenic 55.0%
AGTCGGCCGTTGTTGACAGA+TGG - chr2_2:18133571-18133590 Msa0242140:intron 55.0%
GGCCGTTGTTGACAGATGGT+TGG - chr2_2:18133575-18133594 Msa0242140:intron 55.0%
! GCTGCCAATGGTATTGAGGG+CGG - chr2_2:18134060-18134079 Msa0242140:five_prime_UTR 55.0%
GTCTCCGCCCTCAATACCAT+TGG + chr2_2:18134067-18134086 None:intergenic 55.0%
ACACGATGCTGCCGCACTCA+TGG + chr2_2:18133733-18133752 None:intergenic 60.0%
ACACGATGCTGCCGCACTCA+TGG + chr2_2:18133733-18133752 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 18133338 18134149 18133338 ID=Msa0242140;Name=Msa0242140
chr2_2 mRNA 18133338 18134149 18133338 ID=Msa0242140-mRNA-1;Parent=Msa0242140;Name=Msa0242140-mRNA-1;_AED=0.10;_eAED=0.10;_QI=522|1|0.5|1|1|1|2|0|63
chr2_2 exon 18133338 18133583 18133338 ID=Msa0242140-mRNA-1:exon:7434;Parent=Msa0242140-mRNA-1
chr2_2 exon 18133682 18134149 18133682 ID=Msa0242140-mRNA-1:exon:7433;Parent=Msa0242140-mRNA-1
chr2_2 five_prime_UTR 18133682 18134149 18133682 ID=Msa0242140-mRNA-1:five_prime_utr;Parent=Msa0242140-mRNA-1
chr2_2 five_prime_UTR 18133530 18133583 18133530 ID=Msa0242140-mRNA-1:five_prime_utr;Parent=Msa0242140-mRNA-1
chr2_2 CDS 18133338 18133529 18133338 ID=Msa0242140-mRNA-1:cds;Parent=Msa0242140-mRNA-1
Gene Sequence

>Msa0242140

ATGTTGTGCGGACCTTATGACAATATCATTCATGTGAGACTCAAATATACAGACGACCCCATACCAAATGTGATGTTCGGAAAAGGTTGGACGAGTTTTTGTGCTGCCAATGGTATTGAGGGCGGAGACGTGTTGATTTTCAAGTGCAAGTGCGTCATGGACAAAAAATATGTTATCGTATCCAAGCGTTGA
Protein sequence

>Msa0242140

MLCGPYDNIIHVRLKYTDDPIPNVMFGKGWTSFCAANGIEGGDVLIFKCKCVMDKKYVIVSKR*