AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0312840


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0312840 MtrunA17_Chr2g0282341 87.826 115 14 0 84 198 3 117 9.90e-70 209
Msa0312840 MtrunA17_Chr2g0324511 41.250 160 89 2 50 204 12 171 4.11e-35 122
Msa0312840 MtrunA17_Chr4g0040201 44.375 160 73 6 47 196 7 160 6.94e-32 114
Msa0312840 MtrunA17_Chr2g0324521 40.179 112 67 0 85 196 5 116 9.07e-26 96.7
Msa0312840 MtrunA17_Chr2g0324571 36.842 114 70 1 85 196 5 118 7.86e-24 91.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0312840 AT4G20970.1 42.236 161 82 4 47 196 7 167 6.92e-36 125

Find 42 sgRNAs with CRISPR-Local

Find 102 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACATGATCCGTTCATATTAA+AGG 0.193611 2_4:+8037702 None:intergenic
TTAGAGGTTGTTCTAATAAC+TGG 0.223327 2_4:-8037872 Msa0312840:CDS
AAAATTAAGATACAACAAAT+TGG 0.306857 2_4:-8037902 Msa0312840:CDS
TTTCTATTCATATTCACATT+TGG 0.306963 2_4:+8037950 None:intergenic
TTCCTTAACTTGTGTTCTTA+AGG 0.308434 2_4:+8037670 None:intergenic
ACAAATTGGTTTAGTCTTAG+AGG 0.319445 2_4:-8037888 Msa0312840:CDS
TCTGCCTCATCAAACTTCTA+AGG 0.344529 2_4:-8038297 Msa0312840:intron
CTGTCAACTCTTGATGAACT+AGG 0.359161 2_4:+8038383 None:intergenic
TATTGTCAATGCAAGTTATA+AGG 0.360092 2_4:-8037789 Msa0312840:CDS
AATGGTAGGGCCACTATGTT+TGG 0.381490 2_4:+8038575 None:intergenic
TTGAGTATCTCCTGTTATTG+AGG 0.401617 2_4:-8038429 Msa0312840:intron
TGCCTTAAGAACACAAGTTA+AGG 0.402786 2_4:-8037672 Msa0312840:three_prime_UTR
GCATCTAATCAAATTATATA+TGG 0.405535 2_4:-8038525 Msa0312840:intron
ACTGTTCCAACCTCAATAAC+AGG 0.406192 2_4:+8038419 None:intergenic
GGTTGTTCTAATAACTGGAT+TGG 0.435753 2_4:-8037867 Msa0312840:CDS
TTTCCATTCAATACATTGCC+AGG 0.438842 2_4:-8037750 Msa0312840:CDS
GTATCTCCTGTTATTGAGGT+TGG 0.448324 2_4:-8038425 Msa0312840:CDS
CTTCGTGTTCTTCATGAAGA+AGG 0.454763 2_4:-8037818 Msa0312840:CDS
TTACCTGGCAATGTATTGAA+TGG 0.496250 2_4:+8037747 None:intergenic
TTAATTTCCTTTAATATGAA+CGG 0.510962 2_4:-8037709 Msa0312840:exon
TTTGTGATTATTAGAATGGT+AGG 0.520845 2_4:+8038561 None:intergenic
ACAAATGTGGCCAAACATAG+TGG 0.522894 2_4:-8038585 Msa0312840:CDS
ACCATCCTTCTGTTGCTGCA+TGG 0.532610 2_4:-8038618 None:intergenic
GAAAAGAAGAACTTTCTACT+AGG 0.532951 2_4:-8037983 Msa0312840:CDS
TGTCAACTCTTGATGAACTA+GGG 0.540967 2_4:+8038384 None:intergenic
TTGTGATTATTAGAATGGTA+GGG 0.550106 2_4:+8038562 None:intergenic
GATCAACTTGGAGAAAATGA+AGG 0.550998 2_4:-8038005 Msa0312840:CDS
CTAGTTCATCAAGAGTTGAC+AGG 0.559038 2_4:-8038382 Msa0312840:CDS
GTAACAATTTATGATTTACC+TGG 0.575321 2_4:+8037732 None:intergenic
ACTTTCTACTAGGAATTCAA+AGG 0.595040 2_4:-8037973 Msa0312840:CDS
AAAGAAATTACAGATCAACT+TGG 0.602314 2_4:-8038017 Msa0312840:CDS
TATTGAGGTTGGAACAGTGA+TGG 0.604127 2_4:-8038414 Msa0312840:CDS
TTCTAATAATCACAAAACAT+TGG 0.614322 2_4:-8038554 Msa0312840:CDS
GAGACCTTAGAAGTTTGATG+AGG 0.624740 2_4:+8038293 None:intergenic
ATGAATAGAAACAAGAACAT+GGG 0.625623 2_4:-8037938 Msa0312840:CDS
TATGAATAGAAACAAGAACA+TGG 0.630359 2_4:-8037939 Msa0312840:CDS
TCTGATGCAGGCGATTTCAG+CGG 0.655278 2_4:-8038071 Msa0312840:intron
GCAGAAATGAGTTGAGCTTG+TGG 0.677546 2_4:+8038315 None:intergenic
CTTCTTCATGAAGAACACGA+AGG 0.679799 2_4:+8037819 None:intergenic
TGGTGTGCTACGCACAAATG+TGG 0.685764 2_4:-8038598 Msa0312840:CDS
GAAATGAGTTGAGCTTGTGG+CGG 0.691957 2_4:+8038318 None:intergenic
TTCAGCGGCAGATCAGCTCG+AGG 0.698732 2_4:-8038056 Msa0312840:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTGTTGTATCTTAATTTT+TGG + chr2_4:8038232-8038251 None:intergenic 15.0%
!! AAAATTAAGATACAACAAAT+TGG - chr2_4:8038232-8038251 Msa0312840:intron 15.0%
!! TTAATTTCCTTTAATATGAA+CGG - chr2_4:8038425-8038444 Msa0312840:CDS 15.0%
!!! ATTAACTTTTGTCTTAATTA+AGG - chr2_4:8038593-8038612 Msa0312840:CDS 15.0%
!!! ATTTGTTGTATCTTAATTTT+TGG + chr2_4:8038232-8038251 None:intergenic 15.0%
!! AAAATTAAGATACAACAAAT+TGG - chr2_4:8038232-8038251 Msa0312840:intron 15.0%
!! TTAATTTCCTTTAATATGAA+CGG - chr2_4:8038425-8038444 Msa0312840:CDS 15.0%
!!! ATTAACTTTTGTCTTAATTA+AGG - chr2_4:8038593-8038612 Msa0312840:CDS 15.0%
!!! ATGTTTTGTGATTATTAGAA+TGG + chr2_4:8037580-8037599 None:intergenic 20.0%
!! TTCTAATAATCACAAAACAT+TGG - chr2_4:8037580-8037599 Msa0312840:three_prime_UTR 20.0%
!! GCATCTAATCAAATTATATA+TGG - chr2_4:8037609-8037628 Msa0312840:three_prime_UTR 20.0%
!! TCGCTTATAAGTTATAATAT+TGG + chr2_4:8037676-8037695 None:intergenic 20.0%
!! GAAAAAAATAGAATTAGTGA+CGG - chr2_4:8037925-8037944 Msa0312840:CDS 20.0%
!! ATGTTAGTATTGTTAGTATT+TGG - chr2_4:8038024-8038043 Msa0312840:CDS 20.0%
!!! TAATTTAATTTATCTGATGC+AGG - chr2_4:8038051-8038070 Msa0312840:CDS 20.0%
!! TTTCTATTCATATTCACATT+TGG + chr2_4:8038187-8038206 None:intergenic 20.0%
!!! ATGTTTTGTGATTATTAGAA+TGG + chr2_4:8037580-8037599 None:intergenic 20.0%
!! TTCTAATAATCACAAAACAT+TGG - chr2_4:8037580-8037599 Msa0312840:three_prime_UTR 20.0%
!! GCATCTAATCAAATTATATA+TGG - chr2_4:8037609-8037628 Msa0312840:three_prime_UTR 20.0%
!! TCGCTTATAAGTTATAATAT+TGG + chr2_4:8037676-8037695 None:intergenic 20.0%
!! GAAAAAAATAGAATTAGTGA+CGG - chr2_4:8037925-8037944 Msa0312840:CDS 20.0%
!! ATGTTAGTATTGTTAGTATT+TGG - chr2_4:8038024-8038043 Msa0312840:CDS 20.0%
!!! TAATTTAATTTATCTGATGC+AGG - chr2_4:8038051-8038070 Msa0312840:CDS 20.0%
!! TTTCTATTCATATTCACATT+TGG + chr2_4:8038187-8038206 None:intergenic 20.0%
! TTGTGATTATTAGAATGGTA+GGG + chr2_4:8037575-8037594 None:intergenic 25.0%
! TTTGTGATTATTAGAATGGT+AGG + chr2_4:8037576-8037595 None:intergenic 25.0%
!! ATTTCTTCTTTTGCTTTCAA+TGG + chr2_4:8037782-8037801 None:intergenic 25.0%
! AAAGAAATTACAGATCAACT+TGG - chr2_4:8038117-8038136 Msa0312840:intron 25.0%
! TATGAATAGAAACAAGAACA+TGG - chr2_4:8038195-8038214 Msa0312840:intron 25.0%
! ATGAATAGAAACAAGAACAT+GGG - chr2_4:8038196-8038215 Msa0312840:intron 25.0%
! TATTGTCAATGCAAGTTATA+AGG - chr2_4:8038345-8038364 Msa0312840:CDS 25.0%
! GTAACAATTTATGATTTACC+TGG + chr2_4:8038405-8038424 None:intergenic 25.0%
! TTGTGATTATTAGAATGGTA+GGG + chr2_4:8037575-8037594 None:intergenic 25.0%
! TTTGTGATTATTAGAATGGT+AGG + chr2_4:8037576-8037595 None:intergenic 25.0%
!! ATTTCTTCTTTTGCTTTCAA+TGG + chr2_4:8037782-8037801 None:intergenic 25.0%
! AAAGAAATTACAGATCAACT+TGG - chr2_4:8038117-8038136 Msa0312840:intron 25.0%
! TATGAATAGAAACAAGAACA+TGG - chr2_4:8038195-8038214 Msa0312840:intron 25.0%
! ATGAATAGAAACAAGAACAT+GGG - chr2_4:8038196-8038215 Msa0312840:intron 25.0%
! TATTGTCAATGCAAGTTATA+AGG - chr2_4:8038345-8038364 Msa0312840:CDS 25.0%
! GTAACAATTTATGATTTACC+TGG + chr2_4:8038405-8038424 None:intergenic 25.0%
!!! GTCACTATGTTTTAAAACGA+CGG - chr2_4:8038001-8038020 Msa0312840:CDS 30.0%
GAAAAGAAGAACTTTCTACT+AGG - chr2_4:8038151-8038170 Msa0312840:intron 30.0%
ACTTTCTACTAGGAATTCAA+AGG - chr2_4:8038161-8038180 Msa0312840:intron 30.0%
!! ACAAATTGGTTTAGTCTTAG+AGG - chr2_4:8038246-8038265 Msa0312840:intron 30.0%
TTAGAGGTTGTTCTAATAAC+TGG - chr2_4:8038262-8038281 Msa0312840:intron 30.0%
ACATGATCCGTTCATATTAA+AGG + chr2_4:8038435-8038454 None:intergenic 30.0%
!! TTCCTTAACTTGTGTTCTTA+AGG + chr2_4:8038467-8038486 None:intergenic 30.0%
!!! GTCACTATGTTTTAAAACGA+CGG - chr2_4:8038001-8038020 Msa0312840:CDS 30.0%
GAAAAGAAGAACTTTCTACT+AGG - chr2_4:8038151-8038170 Msa0312840:intron 30.0%
ACTTTCTACTAGGAATTCAA+AGG - chr2_4:8038161-8038180 Msa0312840:intron 30.0%
!! ACAAATTGGTTTAGTCTTAG+AGG - chr2_4:8038246-8038265 Msa0312840:intron 30.0%
TTAGAGGTTGTTCTAATAAC+TGG - chr2_4:8038262-8038281 Msa0312840:intron 30.0%
ACATGATCCGTTCATATTAA+AGG + chr2_4:8038435-8038454 None:intergenic 30.0%
!! TTCCTTAACTTGTGTTCTTA+AGG + chr2_4:8038467-8038486 None:intergenic 30.0%
TTGAGTATCTCCTGTTATTG+AGG - chr2_4:8037705-8037724 Msa0312840:exon 35.0%
TGTCAACTCTTGATGAACTA+GGG + chr2_4:8037753-8037772 None:intergenic 35.0%
CTAAGAGAAGAAGAGAGTAA+AGG + chr2_4:8037876-8037895 None:intergenic 35.0%
GATCAACTTGGAGAAAATGA+AGG - chr2_4:8038129-8038148 Msa0312840:intron 35.0%
GGTTGTTCTAATAACTGGAT+TGG - chr2_4:8038267-8038286 Msa0312840:intron 35.0%
TTTCCATTCAATACATTGCC+AGG - chr2_4:8038384-8038403 Msa0312840:CDS 35.0%
TTACCTGGCAATGTATTGAA+TGG + chr2_4:8038390-8038409 None:intergenic 35.0%
TGCCTTAAGAACACAAGTTA+AGG - chr2_4:8038462-8038481 Msa0312840:intron 35.0%
TTGAGTATCTCCTGTTATTG+AGG - chr2_4:8037705-8037724 Msa0312840:exon 35.0%
TGTCAACTCTTGATGAACTA+GGG + chr2_4:8037753-8037772 None:intergenic 35.0%
CTAAGAGAAGAAGAGAGTAA+AGG + chr2_4:8037876-8037895 None:intergenic 35.0%
GATCAACTTGGAGAAAATGA+AGG - chr2_4:8038129-8038148 Msa0312840:intron 35.0%
GGTTGTTCTAATAACTGGAT+TGG - chr2_4:8038267-8038286 Msa0312840:intron 35.0%
TTTCCATTCAATACATTGCC+AGG - chr2_4:8038384-8038403 Msa0312840:CDS 35.0%
TTACCTGGCAATGTATTGAA+TGG + chr2_4:8038390-8038409 None:intergenic 35.0%
TGCCTTAAGAACACAAGTTA+AGG - chr2_4:8038462-8038481 Msa0312840:intron 35.0%
ACAAATGTGGCCAAACATAG+TGG - chr2_4:8037549-8037568 Msa0312840:three_prime_UTR 40.0%
GTATCTCCTGTTATTGAGGT+TGG - chr2_4:8037709-8037728 Msa0312840:exon 40.0%
ACTGTTCCAACCTCAATAAC+AGG + chr2_4:8037718-8037737 None:intergenic 40.0%
TATTGAGGTTGGAACAGTGA+TGG - chr2_4:8037720-8037739 Msa0312840:CDS 40.0%
CTGTCAACTCTTGATGAACT+AGG + chr2_4:8037754-8037773 None:intergenic 40.0%
CTAGTTCATCAAGAGTTGAC+AGG - chr2_4:8037752-8037771 Msa0312840:CDS 40.0%
TCTGCCTCATCAAACTTCTA+AGG - chr2_4:8037837-8037856 Msa0312840:CDS 40.0%
GAGACCTTAGAAGTTTGATG+AGG + chr2_4:8037844-8037863 None:intergenic 40.0%
CTTCTTCATGAAGAACACGA+AGG + chr2_4:8038318-8038337 None:intergenic 40.0%
CTTCGTGTTCTTCATGAAGA+AGG - chr2_4:8038316-8038335 Msa0312840:CDS 40.0%
ACAAATGTGGCCAAACATAG+TGG - chr2_4:8037549-8037568 Msa0312840:three_prime_UTR 40.0%
GTATCTCCTGTTATTGAGGT+TGG - chr2_4:8037709-8037728 Msa0312840:exon 40.0%
ACTGTTCCAACCTCAATAAC+AGG + chr2_4:8037718-8037737 None:intergenic 40.0%
TATTGAGGTTGGAACAGTGA+TGG - chr2_4:8037720-8037739 Msa0312840:CDS 40.0%
CTGTCAACTCTTGATGAACT+AGG + chr2_4:8037754-8037773 None:intergenic 40.0%
CTAGTTCATCAAGAGTTGAC+AGG - chr2_4:8037752-8037771 Msa0312840:CDS 40.0%
TCTGCCTCATCAAACTTCTA+AGG - chr2_4:8037837-8037856 Msa0312840:CDS 40.0%
GAGACCTTAGAAGTTTGATG+AGG + chr2_4:8037844-8037863 None:intergenic 40.0%
CTTCTTCATGAAGAACACGA+AGG + chr2_4:8038318-8038337 None:intergenic 40.0%
CTTCGTGTTCTTCATGAAGA+AGG - chr2_4:8038316-8038335 Msa0312840:CDS 40.0%
AATGGTAGGGCCACTATGTT+TGG + chr2_4:8037562-8037581 None:intergenic 45.0%
! GAAATGAGTTGAGCTTGTGG+CGG + chr2_4:8037819-8037838 None:intergenic 45.0%
! GCAGAAATGAGTTGAGCTTG+TGG + chr2_4:8037822-8037841 None:intergenic 45.0%
AATGGTAGGGCCACTATGTT+TGG + chr2_4:8037562-8037581 None:intergenic 45.0%
! GAAATGAGTTGAGCTTGTGG+CGG + chr2_4:8037819-8037838 None:intergenic 45.0%
! GCAGAAATGAGTTGAGCTTG+TGG + chr2_4:8037822-8037841 None:intergenic 45.0%
TGGTGTGCTACGCACAAATG+TGG - chr2_4:8037536-8037555 Msa0312840:three_prime_UTR 50.0%
TCTGATGCAGGCGATTTCAG+CGG - chr2_4:8038063-8038082 Msa0312840:CDS 50.0%
TGGTGTGCTACGCACAAATG+TGG - chr2_4:8037536-8037555 Msa0312840:three_prime_UTR 50.0%
TCTGATGCAGGCGATTTCAG+CGG - chr2_4:8038063-8038082 Msa0312840:CDS 50.0%
TTCAGCGGCAGATCAGCTCG+AGG - chr2_4:8038078-8038097 Msa0312840:intron 60.0%
TTCAGCGGCAGATCAGCTCG+AGG - chr2_4:8038078-8038097 Msa0312840:intron 60.0%
Chromosome Type Strat End Strand Name
chr2_4 gene 8037528 8038628 8037528 ID=Msa0312840;Name=Msa0312840
chr2_4 mRNA 8037528 8038628 8037528 ID=Msa0312840-mRNA-1;Parent=Msa0312840;Name=Msa0312840-mRNA-1;_AED=0.09;_eAED=0.09;_QI=0|0.5|0.33|0.66|0.5|0.33|3|190|205
chr2_4 exon 8037528 8038083 8037528 ID=Msa0312840-mRNA-1:exon:3131;Parent=Msa0312840-mRNA-1
chr2_4 exon 8038298 8038446 8038298 ID=Msa0312840-mRNA-1:exon:3130;Parent=Msa0312840-mRNA-1
chr2_4 exon 8038526 8038628 8038526 ID=Msa0312840-mRNA-1:exon:3129;Parent=Msa0312840-mRNA-1
chr2_4 CDS 8038526 8038628 8038526 ID=Msa0312840-mRNA-1:cds;Parent=Msa0312840-mRNA-1
chr2_4 CDS 8038298 8038446 8038298 ID=Msa0312840-mRNA-1:cds;Parent=Msa0312840-mRNA-1
chr2_4 CDS 8037718 8038083 8037718 ID=Msa0312840-mRNA-1:cds;Parent=Msa0312840-mRNA-1
chr2_4 three_prime_UTR 8037528 8037717 8037528 ID=Msa0312840-mRNA-1:three_prime_utr;Parent=Msa0312840-mRNA-1
Gene Sequence

>Msa0312840

TTGCTGCATGGTGTGCTACGCACAAATGTGGCCAAACATAGTGGCCCTACCATTCTAATAATCACAAAACATTGGTCAGTAGCATCTAATCAAATTATATATGTATCTCCTGTTATTGAGGTTGGAACAGTGATGGAGAATAACCCTAGTTCATCAAGAGTTGACAGGAAATCCATTGAAAGCAAAAGAAGAAATCAAATGAAAGCTCTCCGCCACAAGCTCAACTCATTTCTGCCTCATCAAACTTCTAAGGCGATTTCAGCGGCAGATCAGCTCGAGGAAGCAACAAACTACATAAAGAAATTACAGATCAACTTGGAGAAAATGAAGGAAAAGAAGAACTTTCTACTAGGAATTCAAAGGCCAAATGTGAATATGAATAGAAACAAGAACATGGGATTAAAGACTCCAAAAATTAAGATACAACAAATTGGTTTAGTCTTAGAGGTTGTTCTAATAACTGGATTGGATTCTCAGTTTTTGTTCAATGAAATCCTTCGTGTTCTTCATGAAGAAGGAGTTGATATTGTCAATGCAAGTTATAAGGTCAATGAAGATTCAGTTTTCCATTCAATACATTGCCAGGTAAATCATAAATTGTTACTTAATTTCCTTTAA

Protein sequence

>Msa0312840

LLHGVLRTNVAKHSGPTILIITKHWSVASNQIIYVSPVIEVGTVMENNPSSSRVDRKSIESKRRNQMKALRHKLNSFLPHQTSKAISAADQLEEATNYIKKLQINLEKMKEKKNFLLGIQRPNVNMNRNKNMGLKTPKIKIQQIGLVLEVVLITGLDSQFLFNEILRVLHEEGVDIVNASYKVNEDSVFHSIHCQVNHKLLLNFL*