AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1303870


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1303870 MtrunA17_Chr4g0070271 93.171 205 10 2 1 204 1 202 2.94e-129 362
Msa1303870 MtrunA17_Chr2g0301131 44.828 261 76 11 1 204 1 250 1.53e-49 161
Msa1303870 MtrunA17_Chr4g0070241 79.688 64 13 0 70 133 1 64 2.88e-29 104
Msa1303870 MtrunA17_Chr5g0399881 36.478 159 71 5 76 204 5 163 1.83e-21 87.0
Msa1303870 MtrunA17_Chr5g0399861 32.515 163 71 4 76 204 5 162 4.07e-21 85.9
Msa1303870 MtrunA17_Chr5g0399851 36.364 132 60 2 94 201 11 142 2.98e-20 83.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1303870 AT1G19180.1 36.328 256 106 10 1 203 1 252 1.14e-35 126
Msa1303870 AT1G19180.3 36.328 256 106 10 1 203 1 252 1.14e-35 126
Msa1303870 AT1G74950.1 35.745 235 84 10 7 180 1 229 2.15e-27 104
Msa1303870 AT1G74950.2 35.683 227 79 10 7 172 1 221 5.94e-24 95.1
Msa1303870 AT1G19180.2 39.098 133 52 5 99 203 55 186 1.19e-18 80.1
Msa1303870 AT1G17380.1 29.353 201 108 5 13 180 7 206 6.92e-14 68.9

Find 49 sgRNAs with CRISPR-Local

Find 98 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCGACTTCATCGGACATTTC+TGG 0.184990 8_3:-67174335 Msa1303870:CDS
ATTGTCAATTGTGCAGTTTC+TGG 0.207124 8_3:+67173713 None:intergenic
CCTTCTTCTCCTTGAGGTAT+TGG 0.218986 8_3:+67174243 None:intergenic
GGTTGTTGAGGGATCATATT+AGG 0.246891 8_3:+67173590 None:intergenic
CAACAACCTCCCTCACTAAT+TGG 0.267401 8_3:-67173575 Msa1303870:intron
TAGATCTATCATACAGTCTT+AGG 0.298138 8_3:+67172753 None:intergenic
AGCTTCACTTCGTCGATTCA+TGG 0.304214 8_3:-67173394 Msa1303870:CDS
TCAGGAAAGGTTCTTTGATA+TGG 0.341074 8_3:+67172946 None:intergenic
TTTATTTACCATTTGTTTCA+GGG 0.363709 8_3:+67174183 None:intergenic
CGACTTTATCAGTTTGTTGC+CGG 0.376712 8_3:+67174307 None:intergenic
AGCTCCTCAACTTTCTCAGC+AGG 0.410410 8_3:+67173653 None:intergenic
TCCGCTCCATGGCTTGTGTT+AGG 0.414480 8_3:-67172898 Msa1303870:CDS
TTACAGAGTTATTAATCCTA+TGG 0.427315 8_3:-67173744 Msa1303870:intron
TCATGGAGAAGAGGAAAGAT+AGG 0.451183 8_3:-67173377 Msa1303870:intron
GTTTCTGGCTCTTTAACCAT+AGG 0.475200 8_3:+67173728 None:intergenic
CCAATACCTCAAGGAGAAGA+AGG 0.480824 8_3:-67174243 Msa1303870:CDS
CAATCTACAGGGTCATCACC+TGG 0.484929 8_3:-67173963 Msa1303870:intron
TTAGTGAGGGAGGTTGTTGA+GGG 0.495882 8_3:+67173579 None:intergenic
TTATTTACCATTTGTTTCAG+GGG 0.508177 8_3:+67174184 None:intergenic
ACGAACAGAAAGTGGGTTGA+AGG 0.513252 8_3:+67174371 None:intergenic
GATACCAATGTCGACTTCAT+CGG 0.515126 8_3:-67174345 Msa1303870:exon
ATTAGTGAGGGAGGTTGTTG+AGG 0.517348 8_3:+67173578 None:intergenic
GCATGCACCCCTGAAACAAA+TGG 0.517892 8_3:-67174191 Msa1303870:intron
TAATGGACAAGTTATTGTGT+TGG 0.534161 8_3:-67173684 Msa1303870:CDS
GAGAAGAAGGGTAGTTTCGA+AGG 0.535740 8_3:-67174230 Msa1303870:CDS
CAGGGGTGCATGCGTTGTGA+AGG 0.536647 8_3:+67174201 None:intergenic
CCTGGTTCATCTTCTCACTC+TGG 0.547944 8_3:-67173945 Msa1303870:CDS
CCAGAGTGAGAAGATGAACC+AGG 0.548191 8_3:+67173945 None:intergenic
AGCATGCTGACTCCGCTCCA+TGG 0.562298 8_3:-67172909 Msa1303870:CDS
TAACTTAGTTCTATTAGCTG+AGG 0.565990 8_3:-67172732 Msa1303870:three_prime_UTR
GTATCTACACGAACAGAAAG+TGG 0.569348 8_3:+67174363 None:intergenic
TGCATGCGTTGTGAAGGTTA+AGG 0.575616 8_3:+67174207 None:intergenic
AAATCAATTACCAATTAGTG+AGG 0.584879 8_3:+67173565 None:intergenic
GGTTCTTTGATATGGTGAGT+AGG 0.584950 8_3:+67172954 None:intergenic
TTCTGGAGCAGAGTCAGGAA+AGG 0.587295 8_3:+67172933 None:intergenic
GTTTGTGGGAAATAAATCCA+TGG 0.589977 8_3:+67173917 None:intergenic
TTAGCACCTAACACAAGCCA+TGG 0.596993 8_3:+67172892 None:intergenic
AACTACCCTTCTTCTCCTTG+AGG 0.603992 8_3:+67174237 None:intergenic
TTCTCACTCTGGAATAACCA+TGG 0.605298 8_3:-67173934 Msa1303870:CDS
CAATTACCAATTAGTGAGGG+AGG 0.610131 8_3:+67173569 None:intergenic
CAATACCTCAAGGAGAAGAA+GGG 0.616382 8_3:-67174242 Msa1303870:CDS
TTCGTCGATTCATGGAGAAG+AGG 0.618289 8_3:-67173386 Msa1303870:CDS
ACCTAACACAAGCCATGGAG+CGG 0.623220 8_3:+67172897 None:intergenic
TCTATTGAGCCAATACCTCA+AGG 0.624878 8_3:-67174252 Msa1303870:CDS
AATCAATTACCAATTAGTGA+GGG 0.634671 8_3:+67173566 None:intergenic
ATGTCCGATGAAGTCGACAT+TGG 0.636880 8_3:+67174341 None:intergenic
TTACAAGTTTGAGAAAACGT+AGG 0.650898 8_3:+67174275 None:intergenic
CAACAAACTGATAAAGTCGT+CGG 0.655555 8_3:-67174303 Msa1303870:CDS
TATCTACACGAACAGAAAGT+GGG 0.660823 8_3:+67174364 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTATTTTTAATTTAACTGA+TGG - chr8_3:67173649-67173668 Msa1303870:CDS 10.0%
!!! TCTCATAATAAATCTTTTTT+CGG - chr8_3:67173859-67173878 Msa1303870:intron 15.0%
!! TTTATTTACCATTTGTTTCA+GGG + chr8_3:67172925-67172944 None:intergenic 20.0%
!!! TTTTATTTACCATTTGTTTC+AGG + chr8_3:67172926-67172945 None:intergenic 20.0%
!!! TTTTTCTTTTTTCAATCTAC+AGG - chr8_3:67173130-67173149 Msa1303870:intron 20.0%
!!! TTTTCTTTTTTCAATCTACA+GGG - chr8_3:67173131-67173150 Msa1303870:intron 20.0%
!!! CAATTGACAATGTTTTATAA+TGG - chr8_3:67173404-67173423 Msa1303870:CDS 20.0%
!!! ATAATAAATCTTTTTTCGGT+TGG - chr8_3:67173863-67173882 Msa1303870:intron 20.0%
!! GAATGACAAAAATTAATTAC+AGG + chr8_3:67174423-67174442 None:intergenic 20.0%
! TTATTTACCATTTGTTTCAG+GGG + chr8_3:67172924-67172943 None:intergenic 25.0%
!! AATTCAGTTCCTATAGTTTT+GGG - chr8_3:67172962-67172981 Msa1303870:CDS 25.0%
! TAGTCTTTGTTAAATGAACT+TGG - chr8_3:67173017-67173036 Msa1303870:intron 25.0%
! AAATGAACTTGGTCAAAAAA+TGG - chr8_3:67173028-67173047 Msa1303870:intron 25.0%
!!! TTCCCTTATTTTTCTCTATT+CGG - chr8_3:67173082-67173101 Msa1303870:intron 25.0%
! AACCGAATAGAGAAAAATAA+GGG + chr8_3:67173087-67173106 None:intergenic 25.0%
! TAACCGAATAGAGAAAAATA+AGG + chr8_3:67173088-67173107 None:intergenic 25.0%
! AGAAAAAATCCATAGTTGTA+AGG + chr8_3:67173228-67173247 None:intergenic 25.0%
! TTACAGAGTTATTAATCCTA+TGG - chr8_3:67173361-67173380 Msa1303870:intron 25.0%
! AATCAATTACCAATTAGTGA+GGG + chr8_3:67173542-67173561 None:intergenic 25.0%
! AAATCAATTACCAATTAGTG+AGG + chr8_3:67173543-67173562 None:intergenic 25.0%
!! TTGTGATTTGAAACAAATAC+AGG - chr8_3:67173588-67173607 Msa1303870:CDS 25.0%
!! CAAATACAGGAAATTGTTTT+TGG - chr8_3:67173601-67173620 Msa1303870:CDS 25.0%
!!! ATTTAATTTGTTTGAGAGAG+AGG + chr8_3:67173758-67173777 None:intergenic 25.0%
! AATCCAAAATCCAAATTAGT+TGG + chr8_3:67173891-67173910 None:intergenic 25.0%
!!! TTGAACATTTTTTGAGCTTT+TGG - chr8_3:67173909-67173928 Msa1303870:CDS 25.0%
! CTTGATAAGTAAATAACAAG+AGG + chr8_3:67174055-67174074 None:intergenic 25.0%
TTACAAGTTTGAGAAAACGT+AGG + chr8_3:67172833-67172852 None:intergenic 30.0%
! CAATTCAGTTCCTATAGTTT+TGG - chr8_3:67172961-67172980 Msa1303870:CDS 30.0%
!! ATTCAGTTCCTATAGTTTTG+GGG - chr8_3:67172963-67172982 Msa1303870:CDS 30.0%
ATTCTAAACCCCAAAACTAT+AGG + chr8_3:67172974-67172993 None:intergenic 30.0%
TTTCTCTATTCGGTTACAAT+TGG - chr8_3:67173092-67173111 Msa1303870:intron 30.0%
TTCTCTATTCGGTTACAATT+GGG - chr8_3:67173093-67173112 Msa1303870:intron 30.0%
! TCCATAGTTGTAAGGTTTTT+CGG + chr8_3:67173220-67173239 None:intergenic 30.0%
!!! CTATGGATTTTTTCTTTCCA+AGG - chr8_3:67173233-67173252 Msa1303870:intron 30.0%
AATTGCAATGACTCAAACAA+TGG + chr8_3:67173310-67173329 None:intergenic 30.0%
! TAATGGACAAGTTATTGTGT+TGG - chr8_3:67173421-67173440 Msa1303870:intron 30.0%
!!! AGGAAATTGTTTTTGGTATC+AGG - chr8_3:67173608-67173627 Msa1303870:CDS 30.0%
!!! GGAAATTGTTTTTGGTATCA+GGG - chr8_3:67173609-67173628 Msa1303870:CDS 30.0%
! GTACCAACTAATTTGGATTT+TGG - chr8_3:67173885-67173904 Msa1303870:CDS 30.0%
TAGATCTATCATACAGTCTT+AGG + chr8_3:67174355-67174374 None:intergenic 30.0%
!! TAACTTAGTTCTATTAGCTG+AGG - chr8_3:67174373-67174392 Msa1303870:five_prime_UTR 30.0%
TATCTACACGAACAGAAAGT+GGG + chr8_3:67172744-67172763 None:intergenic 35.0%
CAACAAACTGATAAAGTCGT+CGG - chr8_3:67172802-67172821 Msa1303870:three_prime_UTR 35.0%
GTTTGTGGGAAATAAATCCA+TGG + chr8_3:67173191-67173210 None:intergenic 35.0%
ACCGAAAAACCTTACAACTA+TGG - chr8_3:67173216-67173235 Msa1303870:intron 35.0%
! AAAAGCACAAAAACTCACCT+TGG + chr8_3:67173253-67173272 None:intergenic 35.0%
ATTGTCAATTGTGCAGTTTC+TGG + chr8_3:67173395-67173414 None:intergenic 35.0%
!! AGTGAAGCTTTTCTAGCAAT+TGG + chr8_3:67173700-67173719 None:intergenic 35.0%
ATGCATGCATAGCATAAATC+TGG - chr8_3:67173934-67173953 Msa1303870:CDS 35.0%
ATTTCCAGTCACACAAAGAA+AGG + chr8_3:67173960-67173979 None:intergenic 35.0%
TCAGGAAAGGTTCTTTGATA+TGG + chr8_3:67174162-67174181 None:intergenic 35.0%
GTATCTACACGAACAGAAAG+TGG + chr8_3:67172745-67172764 None:intergenic 40.0%
!! GATACCAATGTCGACTTCAT+CGG - chr8_3:67172760-67172779 Msa1303870:three_prime_UTR 40.0%
!!! TCGGACATTTCTGGTTTTTC+CGG - chr8_3:67172779-67172798 Msa1303870:three_prime_UTR 40.0%
!! CGACTTTATCAGTTTGTTGC+CGG + chr8_3:67172801-67172820 None:intergenic 40.0%
TCTATTGAGCCAATACCTCA+AGG - chr8_3:67172853-67172872 Msa1303870:three_prime_UTR 40.0%
CAATACCTCAAGGAGAAGAA+GGG - chr8_3:67172863-67172882 Msa1303870:exon 40.0%
!! TTCTCACTCTGGAATAACCA+TGG - chr8_3:67173171-67173190 Msa1303870:intron 40.0%
!!! TTTTTCGGTGTCACGTTTGT+GGG + chr8_3:67173205-67173224 None:intergenic 40.0%
!! GTTTCTGGCTCTTTAACCAT+AGG + chr8_3:67173380-67173399 None:intergenic 40.0%
! TTTTCCTGCTGAGAAAGTTG+AGG - chr8_3:67173448-67173467 Msa1303870:intron 40.0%
GGTTGTTGAGGGATCATATT+AGG + chr8_3:67173518-67173537 None:intergenic 40.0%
CAATTACCAATTAGTGAGGG+AGG + chr8_3:67173539-67173558 None:intergenic 40.0%
TCATGGAGAAGAGGAAAGAT+AGG - chr8_3:67173728-67173747 Msa1303870:CDS 40.0%
! TCGGTTGGTACCAACTAATT+TGG - chr8_3:67173878-67173897 Msa1303870:CDS 40.0%
AGGCAAAGCAATTTGCACAA+TGG + chr8_3:67174035-67174054 None:intergenic 40.0%
GGTTCTTTGATATGGTGAGT+AGG + chr8_3:67174154-67174173 None:intergenic 40.0%
!! ACGAACAGAAAGTGGGTTGA+AGG + chr8_3:67172737-67172756 None:intergenic 45.0%
ATGTCCGATGAAGTCGACAT+TGG + chr8_3:67172767-67172786 None:intergenic 45.0%
TCGACTTCATCGGACATTTC+TGG - chr8_3:67172770-67172789 Msa1303870:three_prime_UTR 45.0%
CCTTCTTCTCCTTGAGGTAT+TGG + chr8_3:67172865-67172884 None:intergenic 45.0%
CCAATACCTCAAGGAGAAGA+AGG - chr8_3:67172862-67172881 Msa1303870:three_prime_UTR 45.0%
AACTACCCTTCTTCTCCTTG+AGG + chr8_3:67172871-67172890 None:intergenic 45.0%
GAGAAGAAGGGTAGTTTCGA+AGG - chr8_3:67172875-67172894 Msa1303870:exon 45.0%
TGCATGCGTTGTGAAGGTTA+AGG + chr8_3:67172901-67172920 None:intergenic 45.0%
!!! GTTTTTCGGTGTCACGTTTG+TGG + chr8_3:67173206-67173225 None:intergenic 45.0%
TTAGTGAGGGAGGTTGTTGA+GGG + chr8_3:67173529-67173548 None:intergenic 45.0%
ATTAGTGAGGGAGGTTGTTG+AGG + chr8_3:67173530-67173549 None:intergenic 45.0%
CAACAACCTCCCTCACTAAT+TGG - chr8_3:67173530-67173549 Msa1303870:intron 45.0%
!! AGCTTCACTTCGTCGATTCA+TGG - chr8_3:67173711-67173730 Msa1303870:CDS 45.0%
!! TTCGTCGATTCATGGAGAAG+AGG - chr8_3:67173719-67173738 Msa1303870:CDS 45.0%
TTAGCACCTAACACAAGCCA+TGG + chr8_3:67174216-67174235 None:intergenic 45.0%
!! AATAACAATATTATTAAATT+AGG + chr8_3:67174103-67174122 None:intergenic 5.0%
!! TAAAAATAATAAACAAAAAA+AGG + chr8_3:67174292-67174311 None:intergenic 5.0%
!!! TTTATTATTTTTATTTTGAT+CGG - chr8_3:67174299-67174318 Msa1303870:CDS 5.0%
GCATGCACCCCTGAAACAAA+TGG - chr8_3:67172914-67172933 Msa1303870:CDS 50.0%
CAATCTACAGGGTCATCACC+TGG - chr8_3:67173142-67173161 Msa1303870:intron 50.0%
CCAGAGTGAGAAGATGAACC+AGG + chr8_3:67173163-67173182 None:intergenic 50.0%
CCTGGTTCATCTTCTCACTC+TGG - chr8_3:67173160-67173179 Msa1303870:intron 50.0%
AGCTCCTCAACTTTCTCAGC+AGG + chr8_3:67173455-67173474 None:intergenic 50.0%
! CTGGCCTTTCTTTGTGTGAC+TGG - chr8_3:67173953-67173972 Msa1303870:CDS 50.0%
!! TTCTGGAGCAGAGTCAGGAA+AGG + chr8_3:67174175-67174194 None:intergenic 50.0%
!!! TGCTTTTCTGGAGCAGAGTC+AGG + chr8_3:67174180-67174199 None:intergenic 50.0%
ACCTAACACAAGCCATGGAG+CGG + chr8_3:67174211-67174230 None:intergenic 50.0%
! GCGGAGTCAGCATGCTTTTC+TGG + chr8_3:67174192-67174211 None:intergenic 55.0%
! TCCGCTCCATGGCTTGTGTT+AGG - chr8_3:67174207-67174226 Msa1303870:CDS 55.0%
! CAGGGGTGCATGCGTTGTGA+AGG + chr8_3:67172907-67172926 None:intergenic 60.0%
!! AGCATGCTGACTCCGCTCCA+TGG - chr8_3:67174196-67174215 Msa1303870:CDS 60.0%
Chromosome Type Strat End Strand Name
chr8_3 gene 67172675 67174452 67172675 ID=Msa1303870;Name=Msa1303870
chr8_3 mRNA 67172675 67174452 67172675 ID=Msa1303870-mRNA-1;Parent=Msa1303870;Name=Msa1303870-mRNA-1;_AED=0.23;_eAED=0.23;_QI=92|1|1|1|1|1|5|207|205
chr8_3 exon 67172675 67172984 67172675 ID=Msa1303870-mRNA-1:exon:20530;Parent=Msa1303870-mRNA-1
chr8_3 exon 67173378 67173435 67173378 ID=Msa1303870-mRNA-1:exon:20529;Parent=Msa1303870-mRNA-1
chr8_3 exon 67173576 67173760 67173576 ID=Msa1303870-mRNA-1:exon:20528;Parent=Msa1303870-mRNA-1
chr8_3 exon 67173873 67173975 67173873 ID=Msa1303870-mRNA-1:exon:20527;Parent=Msa1303870-mRNA-1
chr8_3 exon 67174192 67174452 67174192 ID=Msa1303870-mRNA-1:exon:20526;Parent=Msa1303870-mRNA-1
chr8_3 five_prime_UTR 67174361 67174452 67174361 ID=Msa1303870-mRNA-1:five_prime_utr;Parent=Msa1303870-mRNA-1
chr8_3 CDS 67174192 67174360 67174192 ID=Msa1303870-mRNA-1:cds;Parent=Msa1303870-mRNA-1
chr8_3 CDS 67173873 67173975 67173873 ID=Msa1303870-mRNA-1:cds;Parent=Msa1303870-mRNA-1
chr8_3 CDS 67173576 67173760 67173576 ID=Msa1303870-mRNA-1:cds;Parent=Msa1303870-mRNA-1
chr8_3 CDS 67173378 67173435 67173378 ID=Msa1303870-mRNA-1:cds;Parent=Msa1303870-mRNA-1
chr8_3 CDS 67172882 67172984 67172882 ID=Msa1303870-mRNA-1:cds;Parent=Msa1303870-mRNA-1
chr8_3 three_prime_UTR 67172675 67172881 67172675 ID=Msa1303870-mRNA-1:three_prime_utr;Parent=Msa1303870-mRNA-1
Gene Sequence

>Msa1303870

ATGTCGACTTCATCGGACATTTCTGGTTTTTCCGGCAACAAACTGATAAAGTCGTCGGAGAAACCTACGTTTTCTCAAACTTGTAATCTATTGAGCCAATACCTCAAGGAGAAGAAGGGTAGTTTCGAAGGCCTTAACCTTCACAACGCATGCACCCCTGAAACAAATGGGTCATCACCTGGTTCATCTTCTCACTCTGGAATAACCATGGATTTATTTCCCACAAACGTGACACCGAAAAACCTTACAACTATGGATTTTTTCTTTCCAAGAGTTATTAATCCTATGGTTAAAGAGCCAGAAACTGCACAATTGACAATGTTTTATAATGGACAAGTTATTGTGTTGGATGATTTTCCTGCTGAGAAAGTTGAGGAGCTGAAATCATTTGCTAGAACTCAGACTCAGCATTCAGATGTTCCTAATATGATCCCTCAACAACCTCCCTCACTAATTGATATGCCAATTGCTAGAAAAGCTTCACTTCGTCGATTCATGGAGAAGAGGAAAGATAGAGTTTCTGCCTACTCACCATATCAAAGAACCTTTCCTGACTCTGCTCCAGAAAAGCATGCTGACTCCGCTCCATGGCTTGTGTTAGGTGCTAAATCAATGTAA

Protein sequence

>Msa1303870

MSTSSDISGFSGNKLIKSSEKPTFSQTCNLLSQYLKEKKGSFEGLNLHNACTPETNGSSPGSSSHSGITMDLFPTNVTPKNLTTMDFFFPRVINPMVKEPETAQLTMFYNGQVIVLDDFPAEKVEELKSFARTQTQHSDVPNMIPQQPPSLIDMPIARKASLRRFMEKRKDRVSAYSPYQRTFPDSAPEKHADSAPWLVLGAKSM*