AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0823760


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0823760 MtrunA17_Chr5g0444521 89.344 122 10 1 1 122 1 119 2.83e-75 218
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 47 sgRNAs with CRISPR-Local

Find 112 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTCTTCAGTAAGTTCATTA+AGG 0.284385 5_3:-62505875 Msa0823760:CDS
CCCTTAAGCAATCGTTGTTC+TGG 0.294188 5_3:+62505445 None:intergenic
CTTCTGCATCATCAACCTTC+TGG 0.304356 5_3:+62505538 None:intergenic
CCAGAACAACGATTGCTTAA+GGG 0.353383 5_3:-62505445 Msa0823760:three_prime_UTR
CGCAGCAGCAACATTATCTA+AGG 0.361910 5_3:-62505962 Msa0823760:CDS
GCAGCAACAACAATGATATC+TGG 0.364461 5_3:+62505840 None:intergenic
GCACAACACAAAACTACTTT+GGG 0.366214 5_3:-62505934 Msa0823760:CDS
TGTTCACTTGGGATAATGTT+TGG 0.377532 5_3:+62506109 None:intergenic
TCCAGAACAACGATTGCTTA+AGG 0.377860 5_3:-62505446 Msa0823760:three_prime_UTR
GTTCACTTGGGATAATGTTT+GGG 0.382397 5_3:+62506110 None:intergenic
TCTTCAACAAGATATAGTTT+TGG 0.385269 5_3:+62506079 None:intergenic
ATGGATCGGCGGGTTGTGGC+AGG 0.389363 5_3:+62505811 None:intergenic
AAATACTTGCTTATAAAATC+TGG 0.401289 5_3:+62505585 None:intergenic
AGTTGTAAATTTATAATGTA+AGG 0.402084 5_3:-62506163 None:intergenic
GAAGCAATGAAGAGGGGAGG+TGG 0.407582 5_3:+62506006 None:intergenic
CTATGTGGCATGGTCTTGCT+TGG 0.417895 5_3:+62505906 None:intergenic
TTTGGTTCACTGTGTTCACT+TGG 0.441499 5_3:+62506097 None:intergenic
AGCACAACACAAAACTACTT+TGG 0.452055 5_3:-62505935 Msa0823760:CDS
CAATGATATCTGGAATTGCC+TGG 0.462076 5_3:+62505850 None:intergenic
TGAAGTATACTGATATAAGC+AGG 0.464588 5_3:+62505625 None:intergenic
CTTACTCGGAGAAAAGTAGA+TGG 0.479013 5_3:+62505792 None:intergenic
GTAGATGGATCGGCGGGTTG+TGG 0.490348 5_3:+62505807 None:intergenic
AAGCAATCGTTGTTCTGGAA+TGG 0.491369 5_3:+62505450 None:intergenic
GAAAAGAACCGAACCTTACT+CGG 0.537160 5_3:+62505778 None:intergenic
CTTAGATAATGTTGCTGCTG+CGG 0.540896 5_3:+62505963 None:intergenic
TTGGGATAATGTTTGGGAGG+AGG 0.545339 5_3:+62506116 None:intergenic
TTGGTTCACTGTGTTCACTT+GGG 0.550658 5_3:+62506098 None:intergenic
TTTAGATTTGATAAACTAGA+GGG 0.553590 5_3:-62505564 Msa0823760:CDS
CACTTGGGATAATGTTTGGG+AGG 0.556445 5_3:+62506113 None:intergenic
TGCATGAGAAGCAATGAAGA+GGG 0.563172 5_3:+62505999 None:intergenic
TGGATCGGCGGGTTGTGGCA+GGG 0.568272 5_3:+62505812 None:intergenic
AATGATATCTGGAATTGCCT+GGG 0.588413 5_3:+62505851 None:intergenic
GAAGAAAAGTGCTTACTATG+TGG 0.588606 5_3:+62505891 None:intergenic
AGAAAAGTAGATGGATCGGC+GGG 0.589351 5_3:+62505801 None:intergenic
GCAGCAACATTATCTAAGGA+TGG 0.606428 5_3:-62505958 Msa0823760:CDS
AGTAAGTTCATTAAGGACCC+AGG 0.609846 5_3:-62505868 Msa0823760:CDS
TCGGAGAAAAGTAGATGGAT+CGG 0.611697 5_3:+62505797 None:intergenic
TAAACTAGAGGGAGACCAGA+AGG 0.616294 5_3:-62505553 Msa0823760:CDS
TTAGTTAAACTAGTTATGCG+TGG 0.617347 5_3:+62506048 None:intergenic
AAAGTGCTTACTATGTGGCA+TGG 0.619717 5_3:+62505896 None:intergenic
GAAGTATACTGATATAAGCA+GGG 0.632422 5_3:+62505626 None:intergenic
GGGGAGGTGGAGACAAGTCA+TGG 0.642574 5_3:+62506019 None:intergenic
ATGCATGAGAAGCAATGAAG+AGG 0.647708 5_3:+62505998 None:intergenic
TGAGAAGCAATGAAGAGGGG+AGG 0.663602 5_3:+62506003 None:intergenic
GAGAAAAGTAGATGGATCGG+CGG 0.667923 5_3:+62505800 None:intergenic
GCATGAGAAGCAATGAAGAG+GGG 0.705476 5_3:+62506000 None:intergenic
CACAACACAAAACTACTTTG+GGG 0.712340 5_3:-62505933 Msa0823760:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGTATTTATTTTTTTACACT+AGG - chr5_3:62505777-62505796 Msa0823760:intron 15.0%
!!! AGTATTTATTTTTTTACACT+AGG - chr5_3:62505777-62505796 Msa0823760:intron 15.0%
!! AAATACTTGCTTATAAAATC+TGG + chr5_3:62505911-62505930 None:intergenic 20.0%
!!! TTTTAGATTTGATAAACTAG+AGG - chr5_3:62505928-62505947 Msa0823760:CDS 20.0%
!! TTTAGATTTGATAAACTAGA+GGG - chr5_3:62505929-62505948 Msa0823760:CDS 20.0%
!!! ATTGTTTTAGTGTATGAATT+TGG - chr5_3:62506079-62506098 Msa0823760:five_prime_UTR 20.0%
!! AAATACTTGCTTATAAAATC+TGG + chr5_3:62505911-62505930 None:intergenic 20.0%
!!! TTTTAGATTTGATAAACTAG+AGG - chr5_3:62505928-62505947 Msa0823760:CDS 20.0%
!! TTTAGATTTGATAAACTAGA+GGG - chr5_3:62505929-62505948 Msa0823760:CDS 20.0%
!!! ATTGTTTTAGTGTATGAATT+TGG - chr5_3:62506079-62506098 Msa0823760:five_prime_UTR 20.0%
!! TCTTCAACAAGATATAGTTT+TGG + chr5_3:62505417-62505436 None:intergenic 25.0%
! TTTCTTCAGTAAGTTCATTA+AGG - chr5_3:62505618-62505637 Msa0823760:CDS 25.0%
! GTTCATTATGTCATATTTCA+TGG - chr5_3:62505746-62505765 Msa0823760:intron 25.0%
!!! TACTTTTTTTCTTCACATCA+GGG + chr5_3:62505997-62506016 None:intergenic 25.0%
!!! ATACTTTTTTTCTTCACATC+AGG + chr5_3:62505998-62506017 None:intergenic 25.0%
!!! CATCTGTATTGTTTTAAACA+TGG - chr5_3:62506139-62506158 Msa0823760:five_prime_UTR 25.0%
!! TCTTCAACAAGATATAGTTT+TGG + chr5_3:62505417-62505436 None:intergenic 25.0%
! TTTCTTCAGTAAGTTCATTA+AGG - chr5_3:62505618-62505637 Msa0823760:CDS 25.0%
! GTTCATTATGTCATATTTCA+TGG - chr5_3:62505746-62505765 Msa0823760:intron 25.0%
!!! TACTTTTTTTCTTCACATCA+GGG + chr5_3:62505997-62506016 None:intergenic 25.0%
!!! ATACTTTTTTTCTTCACATC+AGG + chr5_3:62505998-62506017 None:intergenic 25.0%
!!! CATCTGTATTGTTTTAAACA+TGG - chr5_3:62506139-62506158 Msa0823760:five_prime_UTR 25.0%
TTAGTTAAACTAGTTATGCG+TGG + chr5_3:62505448-62505467 None:intergenic 30.0%
GAAGTATACTGATATAAGCA+GGG + chr5_3:62505870-62505889 None:intergenic 30.0%
TGAAGTATACTGATATAAGC+AGG + chr5_3:62505871-62505890 None:intergenic 30.0%
TTAGTTAAACTAGTTATGCG+TGG + chr5_3:62505448-62505467 None:intergenic 30.0%
GAAGTATACTGATATAAGCA+GGG + chr5_3:62505870-62505889 None:intergenic 30.0%
TGAAGTATACTGATATAAGC+AGG + chr5_3:62505871-62505890 None:intergenic 30.0%
GTTCACTTGGGATAATGTTT+GGG + chr5_3:62505386-62505405 None:intergenic 35.0%
TGTTCACTTGGGATAATGTT+TGG + chr5_3:62505387-62505406 None:intergenic 35.0%
AGCACAACACAAAACTACTT+TGG - chr5_3:62505558-62505577 Msa0823760:CDS 35.0%
GCACAACACAAAACTACTTT+GGG - chr5_3:62505559-62505578 Msa0823760:CDS 35.0%
CACAACACAAAACTACTTTG+GGG - chr5_3:62505560-62505579 Msa0823760:CDS 35.0%
!! GAAGAAAAGTGCTTACTATG+TGG + chr5_3:62505605-62505624 None:intergenic 35.0%
! AATGATATCTGGAATTGCCT+GGG + chr5_3:62505645-62505664 None:intergenic 35.0%
ACAAGCTGCAAACTTAAACA+AGG - chr5_3:62505807-62505826 Msa0823760:CDS 35.0%
GTTCACTTGGGATAATGTTT+GGG + chr5_3:62505386-62505405 None:intergenic 35.0%
TGTTCACTTGGGATAATGTT+TGG + chr5_3:62505387-62505406 None:intergenic 35.0%
AGCACAACACAAAACTACTT+TGG - chr5_3:62505558-62505577 Msa0823760:CDS 35.0%
GCACAACACAAAACTACTTT+GGG - chr5_3:62505559-62505578 Msa0823760:CDS 35.0%
CACAACACAAAACTACTTTG+GGG - chr5_3:62505560-62505579 Msa0823760:CDS 35.0%
!! GAAGAAAAGTGCTTACTATG+TGG + chr5_3:62505605-62505624 None:intergenic 35.0%
! AATGATATCTGGAATTGCCT+GGG + chr5_3:62505645-62505664 None:intergenic 35.0%
ACAAGCTGCAAACTTAAACA+AGG - chr5_3:62505807-62505826 Msa0823760:CDS 35.0%
TTGGTTCACTGTGTTCACTT+GGG + chr5_3:62505398-62505417 None:intergenic 40.0%
! TTTGGTTCACTGTGTTCACT+TGG + chr5_3:62505399-62505418 None:intergenic 40.0%
TGCATGAGAAGCAATGAAGA+GGG + chr5_3:62505497-62505516 None:intergenic 40.0%
ATGCATGAGAAGCAATGAAG+AGG + chr5_3:62505498-62505517 None:intergenic 40.0%
CTTAGATAATGTTGCTGCTG+CGG + chr5_3:62505533-62505552 None:intergenic 40.0%
GCAGCAACATTATCTAAGGA+TGG - chr5_3:62505535-62505554 Msa0823760:CDS 40.0%
! AAAGTGCTTACTATGTGGCA+TGG + chr5_3:62505600-62505619 None:intergenic 40.0%
AGTAAGTTCATTAAGGACCC+AGG - chr5_3:62505625-62505644 Msa0823760:CDS 40.0%
! CAATGATATCTGGAATTGCC+TGG + chr5_3:62505646-62505665 None:intergenic 40.0%
GCAGCAACAACAATGATATC+TGG + chr5_3:62505656-62505675 None:intergenic 40.0%
TCGGAGAAAAGTAGATGGAT+CGG + chr5_3:62505699-62505718 None:intergenic 40.0%
CTTACTCGGAGAAAAGTAGA+TGG + chr5_3:62505704-62505723 None:intergenic 40.0%
!! CATCTACTTTTCTCCGAGTA+AGG - chr5_3:62505702-62505721 Msa0823760:intron 40.0%
! ACTTTTCTCCGAGTAAGGTT+CGG - chr5_3:62505707-62505726 Msa0823760:intron 40.0%
GAAAAGAACCGAACCTTACT+CGG + chr5_3:62505718-62505737 None:intergenic 40.0%
!! AAGCAATCGTTGTTCTGGAA+TGG + chr5_3:62506046-62506065 None:intergenic 40.0%
TCCAGAACAACGATTGCTTA+AGG - chr5_3:62506047-62506066 Msa0823760:five_prime_UTR 40.0%
CCAGAACAACGATTGCTTAA+GGG - chr5_3:62506048-62506067 Msa0823760:five_prime_UTR 40.0%
TTGGTTCACTGTGTTCACTT+GGG + chr5_3:62505398-62505417 None:intergenic 40.0%
! TTTGGTTCACTGTGTTCACT+TGG + chr5_3:62505399-62505418 None:intergenic 40.0%
TGCATGAGAAGCAATGAAGA+GGG + chr5_3:62505497-62505516 None:intergenic 40.0%
ATGCATGAGAAGCAATGAAG+AGG + chr5_3:62505498-62505517 None:intergenic 40.0%
CTTAGATAATGTTGCTGCTG+CGG + chr5_3:62505533-62505552 None:intergenic 40.0%
GCAGCAACATTATCTAAGGA+TGG - chr5_3:62505535-62505554 Msa0823760:CDS 40.0%
! AAAGTGCTTACTATGTGGCA+TGG + chr5_3:62505600-62505619 None:intergenic 40.0%
AGTAAGTTCATTAAGGACCC+AGG - chr5_3:62505625-62505644 Msa0823760:CDS 40.0%
! CAATGATATCTGGAATTGCC+TGG + chr5_3:62505646-62505665 None:intergenic 40.0%
GCAGCAACAACAATGATATC+TGG + chr5_3:62505656-62505675 None:intergenic 40.0%
TCGGAGAAAAGTAGATGGAT+CGG + chr5_3:62505699-62505718 None:intergenic 40.0%
CTTACTCGGAGAAAAGTAGA+TGG + chr5_3:62505704-62505723 None:intergenic 40.0%
!! CATCTACTTTTCTCCGAGTA+AGG - chr5_3:62505702-62505721 Msa0823760:intron 40.0%
! ACTTTTCTCCGAGTAAGGTT+CGG - chr5_3:62505707-62505726 Msa0823760:intron 40.0%
GAAAAGAACCGAACCTTACT+CGG + chr5_3:62505718-62505737 None:intergenic 40.0%
!! AAGCAATCGTTGTTCTGGAA+TGG + chr5_3:62506046-62506065 None:intergenic 40.0%
TCCAGAACAACGATTGCTTA+AGG - chr5_3:62506047-62506066 Msa0823760:five_prime_UTR 40.0%
CCAGAACAACGATTGCTTAA+GGG - chr5_3:62506048-62506067 Msa0823760:five_prime_UTR 40.0%
TTGGGATAATGTTTGGGAGG+AGG + chr5_3:62505380-62505399 None:intergenic 45.0%
CACTTGGGATAATGTTTGGG+AGG + chr5_3:62505383-62505402 None:intergenic 45.0%
GCATGAGAAGCAATGAAGAG+GGG + chr5_3:62505496-62505515 None:intergenic 45.0%
CGCAGCAGCAACATTATCTA+AGG - chr5_3:62505531-62505550 Msa0823760:CDS 45.0%
AGAAAAGTAGATGGATCGGC+GGG + chr5_3:62505695-62505714 None:intergenic 45.0%
GAGAAAAGTAGATGGATCGG+CGG + chr5_3:62505696-62505715 None:intergenic 45.0%
TAAACTAGAGGGAGACCAGA+AGG - chr5_3:62505940-62505959 Msa0823760:CDS 45.0%
CTTCTGCATCATCAACCTTC+TGG + chr5_3:62505958-62505977 None:intergenic 45.0%
CCCTTAAGCAATCGTTGTTC+TGG + chr5_3:62506051-62506070 None:intergenic 45.0%
TTGGGATAATGTTTGGGAGG+AGG + chr5_3:62505380-62505399 None:intergenic 45.0%
CACTTGGGATAATGTTTGGG+AGG + chr5_3:62505383-62505402 None:intergenic 45.0%
GCATGAGAAGCAATGAAGAG+GGG + chr5_3:62505496-62505515 None:intergenic 45.0%
CGCAGCAGCAACATTATCTA+AGG - chr5_3:62505531-62505550 Msa0823760:CDS 45.0%
AGAAAAGTAGATGGATCGGC+GGG + chr5_3:62505695-62505714 None:intergenic 45.0%
GAGAAAAGTAGATGGATCGG+CGG + chr5_3:62505696-62505715 None:intergenic 45.0%
TAAACTAGAGGGAGACCAGA+AGG - chr5_3:62505940-62505959 Msa0823760:CDS 45.0%
CTTCTGCATCATCAACCTTC+TGG + chr5_3:62505958-62505977 None:intergenic 45.0%
CCCTTAAGCAATCGTTGTTC+TGG + chr5_3:62506051-62506070 None:intergenic 45.0%
TGAGAAGCAATGAAGAGGGG+AGG + chr5_3:62505493-62505512 None:intergenic 50.0%
! CTATGTGGCATGGTCTTGCT+TGG + chr5_3:62505590-62505609 None:intergenic 50.0%
TGAGAAGCAATGAAGAGGGG+AGG + chr5_3:62505493-62505512 None:intergenic 50.0%
! CTATGTGGCATGGTCTTGCT+TGG + chr5_3:62505590-62505609 None:intergenic 50.0%
GAAGCAATGAAGAGGGGAGG+TGG + chr5_3:62505490-62505509 None:intergenic 55.0%
GAAGCAATGAAGAGGGGAGG+TGG + chr5_3:62505490-62505509 None:intergenic 55.0%
GGGGAGGTGGAGACAAGTCA+TGG + chr5_3:62505477-62505496 None:intergenic 60.0%
!! GTAGATGGATCGGCGGGTTG+TGG + chr5_3:62505689-62505708 None:intergenic 60.0%
GGGGAGGTGGAGACAAGTCA+TGG + chr5_3:62505477-62505496 None:intergenic 60.0%
!! GTAGATGGATCGGCGGGTTG+TGG + chr5_3:62505689-62505708 None:intergenic 60.0%
!! TGGATCGGCGGGTTGTGGCA+GGG + chr5_3:62505684-62505703 None:intergenic 65.0%
!! ATGGATCGGCGGGTTGTGGC+AGG + chr5_3:62505685-62505704 None:intergenic 65.0%
!! TGGATCGGCGGGTTGTGGCA+GGG + chr5_3:62505684-62505703 None:intergenic 65.0%
!! ATGGATCGGCGGGTTGTGGC+AGG + chr5_3:62505685-62505704 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr5_3 gene 62505334 62506181 62505334 ID=Msa0823760;Name=Msa0823760
chr5_3 mRNA 62505334 62506181 62505334 ID=Msa0823760-mRNA-1;Parent=Msa0823760;Name=Msa0823760-mRNA-1;_AED=0.08;_eAED=0.08;_QI=142|1|1|1|1|1|2|196|122
chr5_3 exon 62505334 62505650 62505334 ID=Msa0823760-mRNA-1:exon:19438;Parent=Msa0823760-mRNA-1
chr5_3 exon 62505792 62506181 62505792 ID=Msa0823760-mRNA-1:exon:19437;Parent=Msa0823760-mRNA-1
chr5_3 five_prime_UTR 62506040 62506181 62506040 ID=Msa0823760-mRNA-1:five_prime_utr;Parent=Msa0823760-mRNA-1
chr5_3 CDS 62505792 62506039 62505792 ID=Msa0823760-mRNA-1:cds;Parent=Msa0823760-mRNA-1
chr5_3 CDS 62505530 62505650 62505530 ID=Msa0823760-mRNA-1:cds;Parent=Msa0823760-mRNA-1
chr5_3 three_prime_UTR 62505334 62505529 62505334 ID=Msa0823760-mRNA-1:three_prime_utr;Parent=Msa0823760-mRNA-1
Gene Sequence

>Msa0823760

ATGACTTGTCTCCACCTCCCCTCTTCATTGCTTCTCATGCATACAAAACTCAAACCGCAGCAGCAACATTATCTAAGGATGGAGCACAACACAAAACTACTTTGGGGAGAACCAAGCAAGACCATGCCACATAGTAAGCACTTTTCTTCAGTAAGTTCATTAAGGACCCAGGCAATTCCAGATATCATTGTTGTTGCTGCTACTTCCCTGCCACAACCCGCCGATCCATCTACTTTTCTCCGAGTAAGTGCCCTGCTTATATCAGTATACTTCATAGCAAATTTCGTCGTGCCAGATTTTATAAGCAAGTATTTTAGATTTGATAAACTAGAGGGAGACCAGAAGGTTGATGATGCAGAAGATAAATAG

Protein sequence

>Msa0823760

MTCLHLPSSLLLMHTKLKPQQQHYLRMEHNTKLLWGEPSKTMPHSKHFSSVSSLRTQAIPDIIVVAATSLPQPADPSTFLRVSALLISVYFIANFVVPDFISKYFRFDKLEGDQKVDDAEDK*