AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1227690


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1227690 MtrunA17_Chr8g0334441 100.000 64 0 0 1 64 1 64 1.31e-43 134
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1227690 AT3G08610.1 75.000 64 16 0 1 64 1 64 2.50e-33 108

Find 47 sgRNAs with CRISPR-Local

Find 126 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GACATAAATCTTGGTATTTA+TGG 0.074576 8_2:-3034661 Msa1227690:three_prime_UTR
TAGGGTACCTGTTTGTTAAT+TGG 0.273208 8_2:+3036085 None:intergenic
CAGGGATTCATTTAAAATAA+AGG 0.278340 8_2:+3034594 None:intergenic
ACATAAATCTTGGTATTTAT+GGG 0.302254 8_2:-3034660 Msa1227690:three_prime_UTR
TGCTGGAATGCTTTGTGTTA+TGG 0.308874 8_2:-3036322 Msa1227690:CDS
AGCTAGGCTGGGCTTATATA+TGG 0.316757 8_2:-3036478 None:intergenic
GCTGGAATGCTTTGTGTTAT+GGG 0.333642 8_2:-3036321 Msa1227690:CDS
TTACCTTTGGGAATAATTGC+TGG 0.341296 8_2:-3036339 Msa1227690:CDS
GTTGGAAGCTATGTTACCTT+TGG 0.352532 8_2:-3036352 Msa1227690:CDS
AATCGATAATTTATGTAAGT+TGG 0.365119 8_2:-3034523 Msa1227690:three_prime_UTR
AAGAAAGAAAGAAAGAAAGA+AGG 0.384033 8_2:-3036407 Msa1227690:five_prime_UTR
AAGGCAAGGATTGGGATTAC+AGG 0.384711 8_2:+3034613 None:intergenic
TTTAAAATAAAGGCAAGGAT+TGG 0.393599 8_2:+3034604 None:intergenic
TTGTGCTTTGACATAAATCT+TGG 0.394534 8_2:-3034670 Msa1227690:three_prime_UTR
TTGGAAGCTATGTTACCTTT+GGG 0.406774 8_2:-3036351 Msa1227690:CDS
AGAAAGAAAGAAAGAAAGAA+GGG 0.406986 8_2:-3036406 Msa1227690:five_prime_UTR
CTCTGCTTCCATGGAACAGC+TGG 0.418718 8_2:+3034867 None:intergenic
ATCGATAATTTATGTAAGTT+GGG 0.419344 8_2:-3034522 Msa1227690:three_prime_UTR
TTAAAATAAAGGCAAGGATT+GGG 0.421257 8_2:+3034605 None:intergenic
TCTTCTTCCAATTAACAAAC+AGG 0.422157 8_2:-3036092 Msa1227690:intron
CTTCTTGTCCCTACGTTCCA+TGG 0.446698 8_2:+3036130 None:intergenic
TGCTTAGTGAAGGTGTGGAC+AGG 0.462427 8_2:+3034575 None:intergenic
AAATCATTGCCGATGTGCTT+AGG 0.473520 8_2:+3036164 None:intergenic
AGTGAGTCTTGAAGAAGGAG+AGG 0.485634 8_2:-3036448 Msa1227690:five_prime_UTR
AGCACATCGGCAATGATTTG+TGG 0.486432 8_2:-3036160 Msa1227690:CDS
AGAGATGGCGTTGCATTGGT+TGG 0.487344 8_2:-3036370 Msa1227690:exon
AAGTGAGTGAGTCTTGAAGA+AGG 0.499853 8_2:-3036453 Msa1227690:five_prime_UTR
GCACATCGGCAATGATTTGT+GGG 0.508503 8_2:-3036159 Msa1227690:CDS
AGAGAGAGATGGCGTTGCAT+TGG 0.509492 8_2:-3036374 Msa1227690:exon
AGCAATCTACTCTGCTTCCA+TGG 0.524941 8_2:+3034858 None:intergenic
CGGCAATGATTTGTGGGACG+TGG 0.531999 8_2:-3036153 Msa1227690:CDS
GTTGCTCTCCAGCTGTTCCA+TGG 0.544090 8_2:-3034875 Msa1227690:three_prime_UTR
TATGTATATTATAACGCTTA+CGG 0.553100 8_2:+3034797 None:intergenic
TGATTTGTGGGACGTGGCCA+TGG 0.553811 8_2:-3036147 Msa1227690:CDS
ATTCATTTAAAATAAAGGCA+AGG 0.569026 8_2:+3034599 None:intergenic
GGACGTGGCCATGGAACGTA+GGG 0.570234 8_2:-3036138 Msa1227690:CDS
GGAATTGAAGAAGAGAGAGA+TGG 0.582978 8_2:-3036385 Msa1227690:exon
ACATAAATTATCGATTGCCA+TGG 0.587402 8_2:+3034530 None:intergenic
ATTCCAGCAATTATTCCCAA+AGG 0.601922 8_2:+3036336 None:intergenic
GCTTAGTGAAGGTGTGGACA+GGG 0.615579 8_2:+3034576 None:intergenic
AGCACAAAATTGTACAAGAG+AGG 0.616768 8_2:-3034556 Msa1227690:three_prime_UTR
TGTGGTTAGCCTAAGCACAT+CGG 0.628887 8_2:-3036173 Msa1227690:intron
ATTTCATACAAGAAAACACA+TGG 0.631983 8_2:+3034823 None:intergenic
CTCGTCCGTGAGCAGCTCTG+TGG 0.632697 8_2:+3036280 None:intergenic
TACATCCACAGAGCTGCTCA+CGG 0.640107 8_2:-3036285 Msa1227690:CDS
GGGACGTGGCCATGGAACGT+AGG 0.664354 8_2:-3036139 Msa1227690:CDS
TTGTACAAGAGAGGACACCA+TGG 0.707418 8_2:-3034547 Msa1227690:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATTAAAATTGAATTGAAT+TGG - chr8_2:3034784-3034803 Msa1227690:three_prime_UTR 10.0%
!!! TTTTATTTTAAGATAAAGCA+TGG - chr8_2:3035213-3035232 Msa1227690:intron 15.0%
!!! TTTATTTTAAGATAAAGCAT+GGG - chr8_2:3035214-3035233 Msa1227690:intron 15.0%
!! TCAAAATCTTAAAAACTATT+TGG - chr8_2:3035508-3035527 Msa1227690:intron 15.0%
!!! TAAAACTTAATTTTCCTATC+AGG - chr8_2:3035069-3035088 Msa1227690:intron 20.0%
!! TTCTCATATAAATGCAAATA+AGG + chr8_2:3035294-3035313 None:intergenic 20.0%
!! ATATAATTTCTTGCCATTAT+CGG - chr8_2:3035657-3035676 Msa1227690:intron 20.0%
!!! TTTCTTTTTTCTCTCAATAA+AGG + chr8_2:3035879-3035898 None:intergenic 20.0%
!! TACATAAAGAAAATCAAATC+TGG + chr8_2:3035998-3036017 None:intergenic 20.0%
!! CTTTATGTATGAAATTATCA+AGG - chr8_2:3036009-3036028 Msa1227690:intron 20.0%
!! ATTTATATGTTTCCAAATGT+AGG - chr8_2:3036050-3036069 Msa1227690:intron 20.0%
!! TATGTATATTATAACGCTTA+CGG + chr8_2:3036195-3036214 None:intergenic 20.0%
!! ACATAAATCTTGGTATTTAT+GGG - chr8_2:3036329-3036348 Msa1227690:CDS 20.0%
!!! ATTCATTTAAAATAAAGGCA+AGG + chr8_2:3036393-3036412 None:intergenic 20.0%
!! AATCGATAATTTATGTAAGT+TGG - chr8_2:3036466-3036485 Msa1227690:five_prime_UTR 20.0%
! AAGAAAGAAAGAAAGAAAGA+AGG - chr8_2:3034578-3034597 Msa1227690:three_prime_UTR 25.0%
! AGAAAGAAAGAAAGAAAGAA+GGG - chr8_2:3034575-3034594 Msa1227690:three_prime_UTR 25.0%
!!! TTGAATTGGATCTATTTTTG+TGG - chr8_2:3034798-3034817 Msa1227690:three_prime_UTR 25.0%
! AAAGAAAGAAAGAAAGAAAG+GGG + chr8_2:3034577-3034596 None:intergenic 25.0%
! GAAAGAAAGAAAGAAAGAAA+GGG + chr8_2:3034576-3034595 None:intergenic 25.0%
! AGAAAGAAAGAAAGAAAGAA+AGG + chr8_2:3034575-3034594 None:intergenic 25.0%
!! AATCAGATCCATTGATAATA+GGG + chr8_2:3034967-3034986 None:intergenic 25.0%
! TTTAAGTATTCTATCCTGAT+AGG + chr8_2:3035086-3035105 None:intergenic 25.0%
! ATTCTCGTATGCTAATTTAT+TGG - chr8_2:3035110-3035129 Msa1227690:intron 25.0%
!!! TATGCTAATTTATTGGTTTG+TGG - chr8_2:3035117-3035136 Msa1227690:intron 25.0%
! AAATTATAGTGAAGTTAGAG+AGG - chr8_2:3035240-3035259 Msa1227690:intron 25.0%
! AATTATAGTGAAGTTAGAGA+GGG - chr8_2:3035241-3035260 Msa1227690:intron 25.0%
! AGAAATTACCTTCATTATGT+TGG + chr8_2:3035567-3035586 None:intergenic 25.0%
! ATTTCATACAAGAAAACACA+TGG + chr8_2:3036169-3036188 None:intergenic 25.0%
!!! TGTTTTCTTTTAGTTGAACA+TGG - chr8_2:3036228-3036247 Msa1227690:intron 25.0%
! GACATAAATCTTGGTATTTA+TGG - chr8_2:3036328-3036347 Msa1227690:CDS 25.0%
! TTAAAATAAAGGCAAGGATT+GGG + chr8_2:3036387-3036406 None:intergenic 25.0%
!! TTTAAAATAAAGGCAAGGAT+TGG + chr8_2:3036388-3036407 None:intergenic 25.0%
!! CAGGGATTCATTTAAAATAA+AGG + chr8_2:3036398-3036417 None:intergenic 25.0%
TCTTCTTCCAATTAACAAAC+AGG - chr8_2:3034897-3034916 Msa1227690:three_prime_UTR 30.0%
CTTTCTTTCCCTATTATCAA+TGG - chr8_2:3034956-3034975 Msa1227690:intron 30.0%
! CAATCAGATCCATTGATAAT+AGG + chr8_2:3034968-3034987 None:intergenic 30.0%
GTTAAAATCCGTTATAGAGT+TGG + chr8_2:3034991-3035010 None:intergenic 30.0%
! TAGAGATGCAATTGCAATTT+TGG - chr8_2:3035044-3035063 Msa1227690:intron 30.0%
! AAGTGTTAAGCTTAAGTTGT+TGG - chr8_2:3035147-3035166 Msa1227690:intron 30.0%
! AGTGTTAAGCTTAAGTTGTT+GGG - chr8_2:3035148-3035167 Msa1227690:intron 30.0%
TTCCAAAATGTTTAGGCATA+GGG - chr8_2:3035268-3035287 Msa1227690:intron 30.0%
TGTAAGTGAGTGACTTAAAT+AGG + chr8_2:3035357-3035376 None:intergenic 30.0%
AATCTCAGCACAAAAACAAA+TGG + chr8_2:3035419-3035438 None:intergenic 30.0%
TTACACATCCAACATAATGA+AGG - chr8_2:3035556-3035575 Msa1227690:intron 30.0%
TGCAATATCTGCAATGATTT+GGG - chr8_2:3035597-3035616 Msa1227690:intron 30.0%
CTATATGATAGATCCGATAA+TGG + chr8_2:3035673-3035692 None:intergenic 30.0%
TTATCGGATCTATCATATAG+TGG - chr8_2:3035673-3035692 Msa1227690:intron 30.0%
TGGTCTTTAACAACTTCTTT+AGG - chr8_2:3035693-3035712 Msa1227690:intron 30.0%
GTTGGATATTCTGAATCATA+GGG - chr8_2:3035746-3035765 Msa1227690:intron 30.0%
ATATTCTGAATCATAGGGAT+TGG - chr8_2:3035751-3035770 Msa1227690:intron 30.0%
!! TCTCCTTGATAATCTTCTTT+TGG - chr8_2:3035783-3035802 Msa1227690:intron 30.0%
TGACCAAAAGAAGATTATCA+AGG + chr8_2:3035789-3035808 None:intergenic 30.0%
CAGATAAAACAACCTACATT+TGG + chr8_2:3036065-3036084 None:intergenic 30.0%
TTGTGCTTTGACATAAATCT+TGG - chr8_2:3036319-3036338 Msa1227690:CDS 30.0%
! TACAATTTTGTGCTTAGTGA+AGG + chr8_2:3036427-3036446 None:intergenic 30.0%
! ACATAAATTATCGATTGCCA+TGG + chr8_2:3036462-3036481 None:intergenic 30.0%
TTGGAAGCTATGTTACCTTT+GGG - chr8_2:3034638-3034657 Msa1227690:three_prime_UTR 35.0%
! TTACCTTTGGGAATAATTGC+TGG - chr8_2:3034650-3034669 Msa1227690:three_prime_UTR 35.0%
ATTCCAGCAATTATTCCCAA+AGG + chr8_2:3034656-3034675 None:intergenic 35.0%
! TAGGGTACCTGTTTGTTAAT+TGG + chr8_2:3034907-3034926 None:intergenic 35.0%
GAAAGAAAGAAAGGGGATTA+GGG + chr8_2:3034925-3034944 None:intergenic 35.0%
AGAAAGAAAGAAAGGGGATT+AGG + chr8_2:3034926-3034945 None:intergenic 35.0%
TCTGATTGCCAACTCTATAA+CGG - chr8_2:3034980-3034999 Msa1227690:intron 35.0%
CTAAGCTTAACACACAGTAA+TGG + chr8_2:3035027-3035046 None:intergenic 35.0%
!! GCTAATTTATTGGTTTGTGG+AGG - chr8_2:3035120-3035139 Msa1227690:intron 35.0%
CTTCCAAAATGTTTAGGCAT+AGG - chr8_2:3035267-3035286 Msa1227690:intron 35.0%
!!! GTGGTTTGTCATTTTTGCAA+TGG + chr8_2:3035335-3035354 None:intergenic 35.0%
AAGTGAGTGACTTAAATAGG+TGG + chr8_2:3035354-3035373 None:intergenic 35.0%
!! GATCCTTTGAGCTTTAAGTA+TGG - chr8_2:3035380-3035399 Msa1227690:intron 35.0%
TGTCCATACTTAAAGCTCAA+AGG + chr8_2:3035386-3035405 None:intergenic 35.0%
GTGCAATATCTGCAATGATT+TGG - chr8_2:3035596-3035615 Msa1227690:intron 35.0%
GCAATATCTGCAATGATTTG+GGG - chr8_2:3035598-3035617 Msa1227690:intron 35.0%
!! CAACTTCTTTAGGATGCTAA+TGG - chr8_2:3035703-3035722 Msa1227690:intron 35.0%
GATGCTAATGGTTATTCAGA+GGG - chr8_2:3035715-3035734 Msa1227690:intron 35.0%
CGTTGGATATTCTGAATCAT+AGG - chr8_2:3035745-3035764 Msa1227690:intron 35.0%
! GATAATCTTCTTTTGGTCAG+TGG - chr8_2:3035790-3035809 Msa1227690:intron 35.0%
! TTTTGGTCAGTGGTTTCATT+AGG - chr8_2:3035800-3035819 Msa1227690:intron 35.0%
!! TTGCAATTTTGACGACTACA+AGG - chr8_2:3035903-3035922 Msa1227690:intron 35.0%
ACGACTACAAGGACAATATT+AGG - chr8_2:3035914-3035933 Msa1227690:intron 35.0%
AGCACAAAATTGTACAAGAG+AGG - chr8_2:3036433-3036452 Msa1227690:five_prime_UTR 35.0%
AAGTGAGTGAGTCTTGAAGA+AGG - chr8_2:3034536-3034555 Msa1227690:three_prime_UTR 40.0%
GGAATTGAAGAAGAGAGAGA+TGG - chr8_2:3034604-3034623 Msa1227690:three_prime_UTR 40.0%
GTTGGAAGCTATGTTACCTT+TGG - chr8_2:3034637-3034656 Msa1227690:three_prime_UTR 40.0%
TGCTGGAATGCTTTGTGTTA+TGG - chr8_2:3034667-3034686 Msa1227690:three_prime_UTR 40.0%
GCTGGAATGCTTTGTGTTAT+GGG - chr8_2:3034668-3034687 Msa1227690:three_prime_UTR 40.0%
AAATCATTGCCGATGTGCTT+AGG + chr8_2:3034828-3034847 None:intergenic 40.0%
! GTTAAGCTTAAGTTGTTGGG+TGG - chr8_2:3035151-3035170 Msa1227690:intron 40.0%
GGGAGACTTCCAAAATGTTT+AGG - chr8_2:3035261-3035280 Msa1227690:intron 40.0%
AATGTATAGACCACCTAACC+TGG - chr8_2:3035470-3035489 Msa1227690:intron 40.0%
ATGTATAGACCACCTAACCT+GGG - chr8_2:3035471-3035490 Msa1227690:intron 40.0%
GGATGCTAATGGTTATTCAG+AGG - chr8_2:3035714-3035733 Msa1227690:intron 40.0%
! ATTCAGAGGGTTTTCTTCGT+TGG - chr8_2:3035728-3035747 Msa1227690:intron 40.0%
GTGGTTTCATTAGGAGGATT+AGG - chr8_2:3035809-3035828 Msa1227690:intron 40.0%
! TTTTGTGCTTAGTGAAGGTG+TGG + chr8_2:3036422-3036441 None:intergenic 40.0%
AGTGAGTCTTGAAGAAGGAG+AGG - chr8_2:3034541-3034560 Msa1227690:three_prime_UTR 45.0%
!! TGTGGTTAGCCTAAGCACAT+CGG - chr8_2:3034816-3034835 Msa1227690:three_prime_UTR 45.0%
AGCACATCGGCAATGATTTG+TGG - chr8_2:3034829-3034848 Msa1227690:three_prime_UTR 45.0%
! GCACATCGGCAATGATTTGT+GGG - chr8_2:3034830-3034849 Msa1227690:three_prime_UTR 45.0%
CAGTAATGGCAACGAGAGTA+TGG + chr8_2:3035013-3035032 None:intergenic 45.0%
! GGCCCTATGCCTAAACATTT+TGG + chr8_2:3035273-3035292 None:intergenic 45.0%
! CTGCAATGATTTGGGGTCTA+TGG - chr8_2:3035605-3035624 Msa1227690:intron 45.0%
! TCTGAATCATAGGGATTGGC+AGG - chr8_2:3035755-3035774 Msa1227690:intron 45.0%
TGGTCAGTGGTTTCATTAGG+AGG - chr8_2:3035803-3035822 Msa1227690:intron 45.0%
! TGTTTTATCTGCGTGCGTGA+AGG - chr8_2:3036074-3036093 Msa1227690:intron 45.0%
! GTTTTATCTGCGTGCGTGAA+GGG - chr8_2:3036075-3036094 Msa1227690:intron 45.0%
AGCAATCTACTCTGCTTCCA+TGG + chr8_2:3036134-3036153 None:intergenic 45.0%
AAGGCAAGGATTGGGATTAC+AGG + chr8_2:3036379-3036398 None:intergenic 45.0%
TTGTACAAGAGAGGACACCA+TGG - chr8_2:3036442-3036461 Msa1227690:five_prime_UTR 45.0%
AGAGAGAGATGGCGTTGCAT+TGG - chr8_2:3034615-3034634 Msa1227690:three_prime_UTR 50.0%
! AGAGATGGCGTTGCATTGGT+TGG - chr8_2:3034619-3034638 Msa1227690:three_prime_UTR 50.0%
TACATCCACAGAGCTGCTCA+CGG - chr8_2:3034704-3034723 Msa1227690:three_prime_UTR 50.0%
CTTCTTGTCCCTACGTTCCA+TGG + chr8_2:3034862-3034881 None:intergenic 50.0%
TATAGACCACCTAACCTGGG+AGG - chr8_2:3035474-3035493 Msa1227690:intron 50.0%
TAGTTAGAGCCTCCCAGGTT+AGG + chr8_2:3035486-3035505 None:intergenic 50.0%
TGAGATAGTTAGAGCCTCCC+AGG + chr8_2:3035491-3035510 None:intergenic 50.0%
! GCTTAGTGAAGGTGTGGACA+GGG + chr8_2:3036416-3036435 None:intergenic 50.0%
! TGCTTAGTGAAGGTGTGGAC+AGG + chr8_2:3036417-3036436 None:intergenic 50.0%
! CGGCAATGATTTGTGGGACG+TGG - chr8_2:3034836-3034855 Msa1227690:three_prime_UTR 55.0%
! TGATTTGTGGGACGTGGCCA+TGG - chr8_2:3034842-3034861 Msa1227690:three_prime_UTR 55.0%
TTAGAGCCTCCCAGGTTAGG+TGG + chr8_2:3035483-3035502 None:intergenic 55.0%
GTTGCTCTCCAGCTGTTCCA+TGG - chr8_2:3036114-3036133 Msa1227690:CDS 55.0%
CTCTGCTTCCATGGAACAGC+TGG + chr8_2:3036125-3036144 None:intergenic 55.0%
GGACGTGGCCATGGAACGTA+GGG - chr8_2:3034851-3034870 Msa1227690:three_prime_UTR 60.0%
CTCGTCCGTGAGCAGCTCTG+TGG + chr8_2:3034712-3034731 None:intergenic 65.0%
GGGACGTGGCCATGGAACGT+AGG - chr8_2:3034850-3034869 Msa1227690:three_prime_UTR 65.0%
Chromosome Type Strat End Strand Name
chr8_2 gene 3034522 3036489 3034522 ID=Msa1227690;Name=Msa1227690
chr8_2 mRNA 3034522 3036489 3034522 ID=Msa1227690-mRNA-1;Parent=Msa1227690;Name=Msa1227690-mRNA-1;_AED=0.00;_eAED=0.00;_QI=101|1|1|1|0.5|0.33|3|425|64
chr8_2 exon 3034522 3034939 3034522 ID=Msa1227690-mRNA-1:exon:849;Parent=Msa1227690-mRNA-1
chr8_2 exon 3036093 3036186 3036093 ID=Msa1227690-mRNA-1:exon:848;Parent=Msa1227690-mRNA-1
chr8_2 exon 3036281 3036489 3036281 ID=Msa1227690-mRNA-1:exon:847;Parent=Msa1227690-mRNA-1
chr8_2 five_prime_UTR 3036389 3036489 3036389 ID=Msa1227690-mRNA-1:five_prime_utr;Parent=Msa1227690-mRNA-1
chr8_2 CDS 3036281 3036388 3036281 ID=Msa1227690-mRNA-1:cds;Parent=Msa1227690-mRNA-1
chr8_2 CDS 3036100 3036186 3036100 ID=Msa1227690-mRNA-1:cds;Parent=Msa1227690-mRNA-1
chr8_2 three_prime_UTR 3036093 3036099 3036093 ID=Msa1227690-mRNA-1:three_prime_utr;Parent=Msa1227690-mRNA-1
chr8_2 three_prime_UTR 3034522 3034939 3034522 ID=Msa1227690-mRNA-1:three_prime_utr;Parent=Msa1227690-mRNA-1
Gene Sequence

>Msa1227690

ATGGCGTTGCATTGGTTGGAAGCTATGTTACCTTTGGGAATAATTGCTGGAATGCTTTGTGTTATGGGTAACGCTCAGTATTACATCCACAGAGCTGCTCACGGACGACCTAAGCACATCGGCAATGATTTGTGGGACGTGGCCATGGAACGTAGGGACAAGAAGCTCGTCGATCAAGCTTCTTCTTCCAATTAA

Protein sequence

>Msa1227690

MALHWLEAMLPLGIIAGMLCVMGNAQYYIHRAAHGRPKHIGNDLWDVAMERRDKKLVDQASSSN*