AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0615580


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0615580 MtrunA17_Chr4g0052211 100.000 86 0 0 1 86 1 86 3.17e-59 177
Msa0615580 MtrunA17_Chr2g0286111 98.837 86 1 0 1 86 1 86 1.85e-58 176
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0615580 AT3G11510.1 89.286 84 9 0 3 86 2 85 2.83e-51 157
Msa0615580 AT3G52580.1 88.095 84 10 0 3 86 2 85 8.75e-51 156
Msa0615580 AT2G36160.1 86.905 84 11 0 3 86 2 85 6.64e-50 154

Find 17 sgRNAs with CRISPR-Local

Find 130 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAGTCACTGTTTCTTCCTT+TGG 0.286906 4_2:+65052446 None:intergenic
CACGATGAAGGTATCGTTAA+AGG 0.289627 4_2:+65052367 None:intergenic
GAAACACTTGTCCGTATTAC+TGG 0.323177 4_2:-65052229 Msa0615580:intron
CAGCATGTAACTGATTTGTC+TGG 0.432105 4_2:-65052256 Msa0615580:CDS
AAATGCAATTACCTTGCATC+TGG 0.446928 4_2:+65051116 None:intergenic
CTATCTTTCAGGTGGAATGA+AGG 0.447568 4_2:-65051202 Msa0615580:intron
TGTTCACCATCTTTAACAGC+TGG 0.478914 4_2:+65052419 None:intergenic
AAACACACTTACCAGTAATA+CGG 0.508460 4_2:+65052218 None:intergenic
GCAGCAAGCATAGCAGCATA+TGG 0.514159 4_2:+65051153 None:intergenic
TGCAATTACCTTGCATCTGG+TGG 0.525795 4_2:+65051119 None:intergenic
AAGGAAGAAACAGTGACTCT+TGG 0.536189 4_2:-65052443 Msa0615580:CDS
GGTAAATAGACTCACGATGA+AGG 0.542298 4_2:+65052355 None:intergenic
ATTGTAGTCGTCGAAGAGAA+AGG 0.542368 4_2:-65052477 Msa0615580:intron
CTTGGTCCAGCTGTTAAAGA+TGG 0.556489 4_2:-65052425 Msa0615580:CDS
GAGAAAGGTTAGAGAGCCAA+AGG 0.564924 4_2:-65052462 Msa0615580:CDS
AGATGTCGCCACCAGATGCA+AGG 0.617051 4_2:-65051127 None:intergenic
AGCATGTAACTGATTTGTCT+GGG 0.620131 4_2:-65052255 Msa0615580:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAATAAGTCAATCAAAAT+GGG + chr4_2:65051865-65051884 None:intergenic 15.0%
!! AAAAAATAAGTCAATCAAAA+TGG + chr4_2:65051866-65051885 None:intergenic 15.0%
!! AAAAATAAGTCAATCAAAAT+GGG + chr4_2:65051865-65051884 None:intergenic 15.0%
!! AAAAAATAAGTCAATCAAAA+TGG + chr4_2:65051866-65051885 None:intergenic 15.0%
!! TTATTACAGATCAATGTTTA+TGG + chr4_2:65051145-65051164 None:intergenic 20.0%
!! GAAAAACATTTCAATTTCAA+AGG + chr4_2:65051235-65051254 None:intergenic 20.0%
!! ACTTATCATGATTAGATATA+TGG - chr4_2:65051839-65051858 Msa0615580:intron 20.0%
!! AACACCAAATAAAAAACATT+TGG - chr4_2:65052315-65052334 Msa0615580:intron 20.0%
!! ACACCAAATAAAAAACATTT+GGG - chr4_2:65052316-65052335 Msa0615580:intron 20.0%
!! ACCCATAATGAAAAATATTT+GGG + chr4_2:65052458-65052477 None:intergenic 20.0%
!! AACCCATAATGAAAAATATT+TGG + chr4_2:65052459-65052478 None:intergenic 20.0%
!! TTATTACAGATCAATGTTTA+TGG + chr4_2:65051145-65051164 None:intergenic 20.0%
!! GAAAAACATTTCAATTTCAA+AGG + chr4_2:65051235-65051254 None:intergenic 20.0%
!! ACTTATCATGATTAGATATA+TGG - chr4_2:65051839-65051858 Msa0615580:intron 20.0%
!! AACACCAAATAAAAAACATT+TGG - chr4_2:65052315-65052334 Msa0615580:intron 20.0%
!! ACACCAAATAAAAAACATTT+GGG - chr4_2:65052316-65052335 Msa0615580:intron 20.0%
!! ACCCATAATGAAAAATATTT+GGG + chr4_2:65052458-65052477 None:intergenic 20.0%
!! AACCCATAATGAAAAATATT+TGG + chr4_2:65052459-65052478 None:intergenic 20.0%
! ATTTCACTACAAACACTTTA+TGG - chr4_2:65051164-65051183 Msa0615580:CDS 25.0%
! AAAAAACACACAAAACAATC+TGG + chr4_2:65051459-65051478 None:intergenic 25.0%
!! TATGTTTGATATGTGTTTTG+TGG - chr4_2:65051708-65051727 Msa0615580:intron 25.0%
! AAAAATAAGCTAATCCTAAC+AGG - chr4_2:65051988-65052007 Msa0615580:intron 25.0%
! TAGCTTATATGAAAACACTT+GGG + chr4_2:65052050-65052069 None:intergenic 25.0%
! ATAGCTTATATGAAAACACT+TGG + chr4_2:65052051-65052070 None:intergenic 25.0%
! AAAATTGTAAATGGCAAGAA+GGG + chr4_2:65052251-65052270 None:intergenic 25.0%
! TTGCTCCATTTATATTATCA+GGG + chr4_2:65052280-65052299 None:intergenic 25.0%
! ATTGCTCCATTTATATTATC+AGG + chr4_2:65052281-65052300 None:intergenic 25.0%
!! TGCCCAAATATTTTTCATTA+TGG - chr4_2:65052453-65052472 Msa0615580:CDS 25.0%
!! GCCCAAATATTTTTCATTAT+GGG - chr4_2:65052454-65052473 Msa0615580:CDS 25.0%
! TGTCTAATTTACTATCTTTC+AGG - chr4_2:65052557-65052576 Msa0615580:intron 25.0%
! ATTTCACTACAAACACTTTA+TGG - chr4_2:65051164-65051183 Msa0615580:CDS 25.0%
! AAAAAACACACAAAACAATC+TGG + chr4_2:65051459-65051478 None:intergenic 25.0%
!! TATGTTTGATATGTGTTTTG+TGG - chr4_2:65051708-65051727 Msa0615580:intron 25.0%
! AAAAATAAGCTAATCCTAAC+AGG - chr4_2:65051988-65052007 Msa0615580:intron 25.0%
! TAGCTTATATGAAAACACTT+GGG + chr4_2:65052050-65052069 None:intergenic 25.0%
! ATAGCTTATATGAAAACACT+TGG + chr4_2:65052051-65052070 None:intergenic 25.0%
! AAAATTGTAAATGGCAAGAA+GGG + chr4_2:65052251-65052270 None:intergenic 25.0%
! TTGCTCCATTTATATTATCA+GGG + chr4_2:65052280-65052299 None:intergenic 25.0%
! ATTGCTCCATTTATATTATC+AGG + chr4_2:65052281-65052300 None:intergenic 25.0%
!! TGCCCAAATATTTTTCATTA+TGG - chr4_2:65052453-65052472 Msa0615580:CDS 25.0%
!! GCCCAAATATTTTTCATTAT+GGG - chr4_2:65052454-65052473 Msa0615580:CDS 25.0%
! TGTCTAATTTACTATCTTTC+AGG - chr4_2:65052557-65052576 Msa0615580:intron 25.0%
!!! TGTTTTTCTCTAAGATCTGA+TGG - chr4_2:65051247-65051266 Msa0615580:intron 30.0%
! AAAGATGGTGAACAAGTTTT+TGG - chr4_2:65051360-65051379 Msa0615580:intron 30.0%
TGGAATGAATGATAAAACGA+AGG + chr4_2:65051439-65051458 None:intergenic 30.0%
AAACACACTTACCAGTAATA+CGG + chr4_2:65051555-65051574 None:intergenic 30.0%
AATGCCAAAAGTGAAGATTT+GGG - chr4_2:65051782-65051801 Msa0615580:intron 30.0%
AAGTTGGAAATAACCAAACA+GGG + chr4_2:65051808-65051827 None:intergenic 30.0%
! TAAGTTGGAAATAACCAAAC+AGG + chr4_2:65051809-65051828 None:intergenic 30.0%
ACATTATGCAAAACAGCTTA+CGG + chr4_2:65051966-65051985 None:intergenic 30.0%
AAATAGCTTATGAACCTGTT+AGG + chr4_2:65052005-65052024 None:intergenic 30.0%
!! ATTTTCCAAAATAGCTTGTG+AGG + chr4_2:65052081-65052100 None:intergenic 30.0%
!!! ACACTTGTTTTAGAGAACTT+AGG + chr4_2:65052187-65052206 None:intergenic 30.0%
CAAAATTGTAAATGGCAAGA+AGG + chr4_2:65052252-65052271 None:intergenic 30.0%
CTCTACCCTGATAATATAAA+TGG - chr4_2:65052272-65052291 Msa0615580:intron 30.0%
AAATGGAGCAATTCTTCTAT+TGG - chr4_2:65052289-65052308 Msa0615580:intron 30.0%
!!! GTGCCCAAATGTTTTTTATT+TGG + chr4_2:65052322-65052341 None:intergenic 30.0%
ATAAATGAGCGATTCTACTA+TGG + chr4_2:65052486-65052505 None:intergenic 30.0%
CTAATTTACTATCTTTCAGG+TGG - chr4_2:65052560-65052579 Msa0615580:intron 30.0%
!!! TGTTTTTCTCTAAGATCTGA+TGG - chr4_2:65051247-65051266 Msa0615580:intron 30.0%
! AAAGATGGTGAACAAGTTTT+TGG - chr4_2:65051360-65051379 Msa0615580:intron 30.0%
TGGAATGAATGATAAAACGA+AGG + chr4_2:65051439-65051458 None:intergenic 30.0%
AAACACACTTACCAGTAATA+CGG + chr4_2:65051555-65051574 None:intergenic 30.0%
AATGCCAAAAGTGAAGATTT+GGG - chr4_2:65051782-65051801 Msa0615580:intron 30.0%
AAGTTGGAAATAACCAAACA+GGG + chr4_2:65051808-65051827 None:intergenic 30.0%
! TAAGTTGGAAATAACCAAAC+AGG + chr4_2:65051809-65051828 None:intergenic 30.0%
ACATTATGCAAAACAGCTTA+CGG + chr4_2:65051966-65051985 None:intergenic 30.0%
AAATAGCTTATGAACCTGTT+AGG + chr4_2:65052005-65052024 None:intergenic 30.0%
!! ATTTTCCAAAATAGCTTGTG+AGG + chr4_2:65052081-65052100 None:intergenic 30.0%
!!! ACACTTGTTTTAGAGAACTT+AGG + chr4_2:65052187-65052206 None:intergenic 30.0%
CAAAATTGTAAATGGCAAGA+AGG + chr4_2:65052252-65052271 None:intergenic 30.0%
CTCTACCCTGATAATATAAA+TGG - chr4_2:65052272-65052291 Msa0615580:intron 30.0%
AAATGGAGCAATTCTTCTAT+TGG - chr4_2:65052289-65052308 Msa0615580:intron 30.0%
!!! GTGCCCAAATGTTTTTTATT+TGG + chr4_2:65052322-65052341 None:intergenic 30.0%
ATAAATGAGCGATTCTACTA+TGG + chr4_2:65052486-65052505 None:intergenic 30.0%
CTAATTTACTATCTTTCAGG+TGG - chr4_2:65052560-65052579 Msa0615580:intron 30.0%
! AGATCTGATGGTTTGTGAAA+TGG - chr4_2:65051259-65051278 Msa0615580:intron 35.0%
!! AGCATGTAACTGATTTGTCT+GGG - chr4_2:65051515-65051534 Msa0615580:intron 35.0%
!! TTTGTGGAACTCTGTTTCTA+TGG - chr4_2:65051724-65051743 Msa0615580:intron 35.0%
CAATGCCAAAAGTGAAGATT+TGG - chr4_2:65051781-65051800 Msa0615580:intron 35.0%
TAAGTGCACACACTATAAGT+TGG + chr4_2:65051824-65051843 None:intergenic 35.0%
GGGTAGAGCAAAATTGTAAA+TGG + chr4_2:65052260-65052279 None:intergenic 35.0%
! AGATCTGATGGTTTGTGAAA+TGG - chr4_2:65051259-65051278 Msa0615580:intron 35.0%
!! AGCATGTAACTGATTTGTCT+GGG - chr4_2:65051515-65051534 Msa0615580:intron 35.0%
!! TTTGTGGAACTCTGTTTCTA+TGG - chr4_2:65051724-65051743 Msa0615580:intron 35.0%
CAATGCCAAAAGTGAAGATT+TGG - chr4_2:65051781-65051800 Msa0615580:intron 35.0%
TAAGTGCACACACTATAAGT+TGG + chr4_2:65051824-65051843 None:intergenic 35.0%
GGGTAGAGCAAAATTGTAAA+TGG + chr4_2:65052260-65052279 None:intergenic 35.0%
! CTGATGGTTTGTGAAATGGT+TGG - chr4_2:65051263-65051282 Msa0615580:intron 40.0%
ATTGTAGTCGTCGAAGAGAA+AGG - chr4_2:65051293-65051312 Msa0615580:intron 40.0%
! AGAGTCACTGTTTCTTCCTT+TGG + chr4_2:65051327-65051346 None:intergenic 40.0%
AAGGAAGAAACAGTGACTCT+TGG - chr4_2:65051327-65051346 Msa0615580:intron 40.0%
TGTTCACCATCTTTAACAGC+TGG + chr4_2:65051354-65051373 None:intergenic 40.0%
!! CACGATGAAGGTATCGTTAA+AGG + chr4_2:65051406-65051425 None:intergenic 40.0%
GGTAAATAGACTCACGATGA+AGG + chr4_2:65051418-65051437 None:intergenic 40.0%
!! CAGCATGTAACTGATTTGTC+TGG - chr4_2:65051514-65051533 Msa0615580:intron 40.0%
GAAACACTTGTCCGTATTAC+TGG - chr4_2:65051541-65051560 Msa0615580:intron 40.0%
! CTATCTTTCAGGTGGAATGA+AGG - chr4_2:65052568-65052587 Msa0615580:intron 40.0%
! CTGATGGTTTGTGAAATGGT+TGG - chr4_2:65051263-65051282 Msa0615580:intron 40.0%
ATTGTAGTCGTCGAAGAGAA+AGG - chr4_2:65051293-65051312 Msa0615580:intron 40.0%
! AGAGTCACTGTTTCTTCCTT+TGG + chr4_2:65051327-65051346 None:intergenic 40.0%
AAGGAAGAAACAGTGACTCT+TGG - chr4_2:65051327-65051346 Msa0615580:intron 40.0%
TGTTCACCATCTTTAACAGC+TGG + chr4_2:65051354-65051373 None:intergenic 40.0%
!! CACGATGAAGGTATCGTTAA+AGG + chr4_2:65051406-65051425 None:intergenic 40.0%
GGTAAATAGACTCACGATGA+AGG + chr4_2:65051418-65051437 None:intergenic 40.0%
!! CAGCATGTAACTGATTTGTC+TGG - chr4_2:65051514-65051533 Msa0615580:intron 40.0%
GAAACACTTGTCCGTATTAC+TGG - chr4_2:65051541-65051560 Msa0615580:intron 40.0%
! CTATCTTTCAGGTGGAATGA+AGG - chr4_2:65052568-65052587 Msa0615580:intron 40.0%
GAGAAAGGTTAGAGAGCCAA+AGG - chr4_2:65051308-65051327 Msa0615580:intron 45.0%
CTTGGTCCAGCTGTTAAAGA+TGG - chr4_2:65051345-65051364 Msa0615580:intron 45.0%
! AGGGCCCAAATCTTCACTTT+TGG + chr4_2:65051789-65051808 None:intergenic 45.0%
! CCAAAATAGCTTGTGAGGAC+AGG + chr4_2:65052076-65052095 None:intergenic 45.0%
! CCTGTCCTCACAAGCTATTT+TGG - chr4_2:65052073-65052092 Msa0615580:intron 45.0%
AATGGCAAGAAGGGTCTGTT+TGG + chr4_2:65052242-65052261 None:intergenic 45.0%
CTTTGTTGCCATTAACCAGC+TGG - chr4_2:65052510-65052529 Msa0615580:intron 45.0%
ACATGCATCCAGCTGGTTAA+TGG + chr4_2:65052521-65052540 None:intergenic 45.0%
GAGAAAGGTTAGAGAGCCAA+AGG - chr4_2:65051308-65051327 Msa0615580:intron 45.0%
CTTGGTCCAGCTGTTAAAGA+TGG - chr4_2:65051345-65051364 Msa0615580:intron 45.0%
! AGGGCCCAAATCTTCACTTT+TGG + chr4_2:65051789-65051808 None:intergenic 45.0%
! CCAAAATAGCTTGTGAGGAC+AGG + chr4_2:65052076-65052095 None:intergenic 45.0%
! CCTGTCCTCACAAGCTATTT+TGG - chr4_2:65052073-65052092 Msa0615580:intron 45.0%
AATGGCAAGAAGGGTCTGTT+TGG + chr4_2:65052242-65052261 None:intergenic 45.0%
CTTTGTTGCCATTAACCAGC+TGG - chr4_2:65052510-65052529 Msa0615580:intron 45.0%
ACATGCATCCAGCTGGTTAA+TGG + chr4_2:65052521-65052540 None:intergenic 45.0%
GTGAAGATTTGGGCCCTGTT+TGG - chr4_2:65051792-65051811 Msa0615580:intron 50.0%
GACTTAGACATGCATCCAGC+TGG + chr4_2:65052528-65052547 None:intergenic 50.0%
GCAGCAAGCATAGCAGCATA+TGG + chr4_2:65052620-65052639 None:intergenic 50.0%
GTGAAGATTTGGGCCCTGTT+TGG - chr4_2:65051792-65051811 Msa0615580:intron 50.0%
GACTTAGACATGCATCCAGC+TGG + chr4_2:65052528-65052547 None:intergenic 50.0%
GCAGCAAGCATAGCAGCATA+TGG + chr4_2:65052620-65052639 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 65051128 65052664 65051128 ID=Msa0615580;Name=Msa0615580
chr4_2 mRNA 65051128 65052664 65051128 ID=Msa0615580-mRNA-1;Parent=Msa0615580;Name=Msa0615580-mRNA-1;_AED=0.17;_eAED=0.17;_QI=0|0|0|0.75|1|1|4|0|86
chr4_2 exon 65052662 65052664 65052662 ID=Msa0615580-mRNA-1:exon:18370;Parent=Msa0615580-mRNA-1
chr4_2 exon 65052370 65052492 65052370 ID=Msa0615580-mRNA-1:exon:18369;Parent=Msa0615580-mRNA-1
chr4_2 exon 65052230 65052275 65052230 ID=Msa0615580-mRNA-1:exon:18368;Parent=Msa0615580-mRNA-1
chr4_2 exon 65051128 65051213 65051128 ID=Msa0615580-mRNA-1:exon:18367;Parent=Msa0615580-mRNA-1
chr4_2 CDS 65052662 65052664 65052662 ID=Msa0615580-mRNA-1:cds;Parent=Msa0615580-mRNA-1
chr4_2 CDS 65052370 65052492 65052370 ID=Msa0615580-mRNA-1:cds;Parent=Msa0615580-mRNA-1
chr4_2 CDS 65052230 65052275 65052230 ID=Msa0615580-mRNA-1:cds;Parent=Msa0615580-mRNA-1
chr4_2 CDS 65051128 65051213 65051128 ID=Msa0615580-mRNA-1:cds;Parent=Msa0615580-mRNA-1
Gene Sequence

>Msa0615580

ATGTCGTCGAAGAGAAAGGTTAGAGAGCCAAAGGAAGAAACAGTGACTCTTGGTCCAGCTGTTAAAGATGGTGAACAAGTTTTTGGTGTTGCTCGTATCTTTGCTTCCTTTAACGATACCTTCATCCATGTAACTGATTTGTCTGGGAGAGAAACACTTGTCCGTATTACTGGTGGAATGAAGGTCAAAGCTGACAGAGATGAGTCATCTCCATATGCTGCTATGCTTGCTGCACAAGATGTCGCCACCAGATGCAAG

Protein sequence

>Msa0615580

MSSKRKVREPKEETVTLGPAVKDGEQVFGVARIFASFNDTFIHVTDLSGRETLVRITGGMKVKADRDESSPYAAMLAAQDVATRCK