AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0587190


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0587190 MtrunA17_Chr4g0003391 96.063 127 5 0 1 127 1 127 1.07e-77 225
Msa0587190 MtrunA17_Chr2g0333051 52.555 137 48 5 1 123 1 134 4.27e-35 117
Msa0587190 MtrunA17_Chr4g0063791 40.411 146 59 6 5 126 35 176 4.91e-17 72.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0587190 AT1G52565.1 43.571 140 52 5 1 127 4 129 3.42e-18 75.1
Msa0587190 AT3G15760.1 40.580 138 60 6 1 123 1 131 4.83e-15 67.0

Find 31 sgRNAs with CRISPR-Local

Find 99 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACAATATTTGAAGTCCTAA+TGG 0.333607 4_2:-8667971 Msa0587190:three_prime_UTR
GTCATTGATCATCTTAGTTA+TGG 0.371239 4_2:-8668160 Msa0587190:exon
AGAGATAGAGTTCAAAGAAT+GGG 0.376812 4_2:-8668188 Msa0587190:CDS
TACAAAGCAACTCTATTTGC+TGG 0.381833 4_2:+8668224 None:intergenic
TAGAACAAGAAGAAATTAGA+TGG 0.398648 4_2:-8668076 Msa0587190:three_prime_UTR
TTTCTGAATTGGGTGTTTCA+TGG 0.405044 4_2:+8668708 None:intergenic
CTCTTAAAATTGCCAAGAGT+TGG 0.419774 4_2:+8667835 None:intergenic
GCTTGTAGAGGAAAAGAAGA+AGG 0.443148 4_2:-8668381 Msa0587190:intron
TATAAACAAGATCGTAGAAT+AGG 0.444103 4_2:+8668680 None:intergenic
AAAAGGTTGTGAATTTATGA+TGG 0.447654 4_2:-8667942 Msa0587190:three_prime_UTR
AAGAGATAGAGTTCAAAGAA+TGG 0.465347 4_2:-8668189 Msa0587190:CDS
GGTGTTTCATGGAATTGAAA+TGG 0.466904 4_2:+8668719 None:intergenic
AATAGAGTTGCTTTGTACAA+TGG 0.493962 4_2:-8668218 Msa0587190:CDS
GCTTGACTATGTCCAACTCT+TGG 0.517400 4_2:-8667847 Msa0587190:three_prime_UTR
GTGAATTTATGATGGAAGGG+TGG 0.540534 4_2:-8667934 Msa0587190:three_prime_UTR
TGAATTTATGATGGAAGGGT+GGG 0.559563 4_2:-8667933 Msa0587190:three_prime_UTR
CTACGATCTTGTTTATACAC+AGG 0.560268 4_2:-8668674 Msa0587190:intron
GGTTGTGAATTTATGATGGA+AGG 0.562242 4_2:-8667938 Msa0587190:three_prime_UTR
AGTTGAAACAACCATGGCTG+TGG 0.569166 4_2:+8668784 None:intergenic
GAGATAGAGTTCAAAGAATG+GGG 0.570523 4_2:-8668187 Msa0587190:CDS
GTGAGATTGAAGTCATGTTG+TGG 0.573467 4_2:+8668822 None:intergenic
AAGGGTGGGTATTCTTGTGA+AGG 0.586206 4_2:-8667919 Msa0587190:three_prime_UTR
TAGTTATGGAAGTTAGAACA+TGG 0.600995 4_2:-8668146 Msa0587190:three_prime_UTR
GTTGTGAATTTATGATGGAA+GGG 0.606258 4_2:-8667937 Msa0587190:three_prime_UTR
TTAGAACATGGTATAGAACA+TGG 0.610591 4_2:-8668104 Msa0587190:three_prime_UTR
AGTTATGGAAGTTAGAACAT+GGG 0.637332 4_2:-8668145 Msa0587190:three_prime_UTR
TAGAACATGGTATAGAACAT+GGG 0.653391 4_2:-8668103 Msa0587190:three_prime_UTR
AACAGTAGTTGAAACAACCA+TGG 0.660669 4_2:+8668778 None:intergenic
AACATGACTTCAATCTCACA+AGG 0.670440 4_2:-8668818 Msa0587190:CDS
AAACAGAGTAAAGAAAACAG+AGG 0.672838 4_2:+8668849 None:intergenic
AAAGATCTAATGTATTCTTG+TGG 0.676296 4_2:-8667882 Msa0587190:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTATTTTATTTTTAGGT+GGG - chr4_2:8668703-8668722 Msa0587190:CDS 10.0%
!!! ATTTTATTTTATTTTTAGGT+GGG - chr4_2:8668703-8668722 Msa0587190:CDS 10.0%
!!! GATTTTATTTTATTTTTAGG+TGG - chr4_2:8668702-8668721 Msa0587190:CDS 15.0%
!!! GATTTTATTTTATTTTTAGG+TGG - chr4_2:8668702-8668721 Msa0587190:CDS 15.0%
!!! TTTTTCAGATACTATTCTAT+AGG - chr4_2:8668116-8668135 Msa0587190:three_prime_UTR 20.0%
!! ATGTTTCATACAAAATATTC+AGG + chr4_2:8668274-8668293 None:intergenic 20.0%
!! AAAGAATTTAGAGAAAAACA+GGG - chr4_2:8668398-8668417 Msa0587190:intron 20.0%
!!! TTTTTCAGATACTATTCTAT+AGG - chr4_2:8668116-8668135 Msa0587190:three_prime_UTR 20.0%
!! ATGTTTCATACAAAATATTC+AGG + chr4_2:8668274-8668293 None:intergenic 20.0%
!! AAAGAATTTAGAGAAAAACA+GGG - chr4_2:8668398-8668417 Msa0587190:intron 20.0%
!!! ATAGGTTTGTTTTCTGAATT+GGG + chr4_2:8668011-8668030 None:intergenic 25.0%
!!! AATAGGTTTGTTTTCTGAAT+TGG + chr4_2:8668012-8668031 None:intergenic 25.0%
! TATAAACAAGATCGTAGAAT+AGG + chr4_2:8668029-8668048 None:intergenic 25.0%
!! GAAATTTTCAGAAAATGTGA+TGG - chr4_2:8668373-8668392 Msa0587190:CDS 25.0%
! GAAAGAATTTAGAGAAAAAC+AGG - chr4_2:8668397-8668416 Msa0587190:intron 25.0%
! AAGAATTTAGAGAAAAACAG+GGG - chr4_2:8668399-8668418 Msa0587190:intron 25.0%
!!! TTTTAAGAGAAGTTAGAACA+TGG - chr4_2:8668590-8668609 Msa0587190:intron 25.0%
! TAGAACAAGAAGAAATTAGA+TGG - chr4_2:8668630-8668649 Msa0587190:intron 25.0%
!! AACAATATTTGAAGTCCTAA+TGG - chr4_2:8668735-8668754 Msa0587190:CDS 25.0%
! AAAAGGTTGTGAATTTATGA+TGG - chr4_2:8668764-8668783 Msa0587190:CDS 25.0%
! AAAGATCTAATGTATTCTTG+TGG - chr4_2:8668824-8668843 Msa0587190:exon 25.0%
!!! ATAGGTTTGTTTTCTGAATT+GGG + chr4_2:8668011-8668030 None:intergenic 25.0%
!!! AATAGGTTTGTTTTCTGAAT+TGG + chr4_2:8668012-8668031 None:intergenic 25.0%
! TATAAACAAGATCGTAGAAT+AGG + chr4_2:8668029-8668048 None:intergenic 25.0%
!! GAAATTTTCAGAAAATGTGA+TGG - chr4_2:8668373-8668392 Msa0587190:CDS 25.0%
! GAAAGAATTTAGAGAAAAAC+AGG - chr4_2:8668397-8668416 Msa0587190:intron 25.0%
! AAGAATTTAGAGAAAAACAG+GGG - chr4_2:8668399-8668418 Msa0587190:intron 25.0%
!!! TTTTAAGAGAAGTTAGAACA+TGG - chr4_2:8668590-8668609 Msa0587190:intron 25.0%
! TAGAACAAGAAGAAATTAGA+TGG - chr4_2:8668630-8668649 Msa0587190:intron 25.0%
!! AACAATATTTGAAGTCCTAA+TGG - chr4_2:8668735-8668754 Msa0587190:CDS 25.0%
! AAAAGGTTGTGAATTTATGA+TGG - chr4_2:8668764-8668783 Msa0587190:CDS 25.0%
! AAAGATCTAATGTATTCTTG+TGG - chr4_2:8668824-8668843 Msa0587190:exon 25.0%
AAACAGAGTAAAGAAAACAG+AGG + chr4_2:8667860-8667879 None:intergenic 30.0%
!!! GTTTTTGTTTTTGCTTGTAG+AGG - chr4_2:8668313-8668332 Msa0587190:CDS 30.0%
! AATAGAGTTGCTTTGTACAA+TGG - chr4_2:8668488-8668507 Msa0587190:intron 30.0%
AAGAGATAGAGTTCAAAGAA+TGG - chr4_2:8668517-8668536 Msa0587190:intron 30.0%
AGAGATAGAGTTCAAAGAAT+GGG - chr4_2:8668518-8668537 Msa0587190:intron 30.0%
GTCATTGATCATCTTAGTTA+TGG - chr4_2:8668546-8668565 Msa0587190:intron 30.0%
TAGTTATGGAAGTTAGAACA+TGG - chr4_2:8668560-8668579 Msa0587190:intron 30.0%
AGTTATGGAAGTTAGAACAT+GGG - chr4_2:8668561-8668580 Msa0587190:intron 30.0%
TTAGAACATGGTATAGAACA+TGG - chr4_2:8668602-8668621 Msa0587190:intron 30.0%
TAGAACATGGTATAGAACAT+GGG - chr4_2:8668603-8668622 Msa0587190:intron 30.0%
! AGTCCTAATGGATCAAAAAA+AGG - chr4_2:8668747-8668766 Msa0587190:CDS 30.0%
!!! CAACCTTTTTTTGATCCATT+AGG + chr4_2:8668753-8668772 None:intergenic 30.0%
! GTTGTGAATTTATGATGGAA+GGG - chr4_2:8668769-8668788 Msa0587190:CDS 30.0%
AAACAGAGTAAAGAAAACAG+AGG + chr4_2:8667860-8667879 None:intergenic 30.0%
!!! GTTTTTGTTTTTGCTTGTAG+AGG - chr4_2:8668313-8668332 Msa0587190:CDS 30.0%
! AATAGAGTTGCTTTGTACAA+TGG - chr4_2:8668488-8668507 Msa0587190:intron 30.0%
AAGAGATAGAGTTCAAAGAA+TGG - chr4_2:8668517-8668536 Msa0587190:intron 30.0%
AGAGATAGAGTTCAAAGAAT+GGG - chr4_2:8668518-8668537 Msa0587190:intron 30.0%
GTCATTGATCATCTTAGTTA+TGG - chr4_2:8668546-8668565 Msa0587190:intron 30.0%
TAGTTATGGAAGTTAGAACA+TGG - chr4_2:8668560-8668579 Msa0587190:intron 30.0%
AGTTATGGAAGTTAGAACAT+GGG - chr4_2:8668561-8668580 Msa0587190:intron 30.0%
TTAGAACATGGTATAGAACA+TGG - chr4_2:8668602-8668621 Msa0587190:intron 30.0%
TAGAACATGGTATAGAACAT+GGG - chr4_2:8668603-8668622 Msa0587190:intron 30.0%
! AGTCCTAATGGATCAAAAAA+AGG - chr4_2:8668747-8668766 Msa0587190:CDS 30.0%
!!! CAACCTTTTTTTGATCCATT+AGG + chr4_2:8668753-8668772 None:intergenic 30.0%
! GTTGTGAATTTATGATGGAA+GGG - chr4_2:8668769-8668788 Msa0587190:CDS 30.0%
AACATGACTTCAATCTCACA+AGG - chr4_2:8667888-8667907 Msa0587190:three_prime_UTR 35.0%
AACAGTAGTTGAAACAACCA+TGG + chr4_2:8667931-8667950 None:intergenic 35.0%
GGTGTTTCATGGAATTGAAA+TGG + chr4_2:8667990-8668009 None:intergenic 35.0%
TTTCTGAATTGGGTGTTTCA+TGG + chr4_2:8668001-8668020 None:intergenic 35.0%
! CTACGATCTTGTTTATACAC+AGG - chr4_2:8668032-8668051 Msa0587190:three_prime_UTR 35.0%
TACAAAGCAACTCTATTTGC+TGG + chr4_2:8668485-8668504 None:intergenic 35.0%
GAGATAGAGTTCAAAGAATG+GGG - chr4_2:8668519-8668538 Msa0587190:intron 35.0%
!!! TTATTTTTAGGTGGGTGTGT+TGG - chr4_2:8668711-8668730 Msa0587190:CDS 35.0%
! GGTTGTGAATTTATGATGGA+AGG - chr4_2:8668768-8668787 Msa0587190:CDS 35.0%
! TGAATTTATGATGGAAGGGT+GGG - chr4_2:8668773-8668792 Msa0587190:CDS 35.0%
CTCTTAAAATTGCCAAGAGT+TGG + chr4_2:8668874-8668893 None:intergenic 35.0%
AACATGACTTCAATCTCACA+AGG - chr4_2:8667888-8667907 Msa0587190:three_prime_UTR 35.0%
AACAGTAGTTGAAACAACCA+TGG + chr4_2:8667931-8667950 None:intergenic 35.0%
GGTGTTTCATGGAATTGAAA+TGG + chr4_2:8667990-8668009 None:intergenic 35.0%
TTTCTGAATTGGGTGTTTCA+TGG + chr4_2:8668001-8668020 None:intergenic 35.0%
! CTACGATCTTGTTTATACAC+AGG - chr4_2:8668032-8668051 Msa0587190:three_prime_UTR 35.0%
TACAAAGCAACTCTATTTGC+TGG + chr4_2:8668485-8668504 None:intergenic 35.0%
GAGATAGAGTTCAAAGAATG+GGG - chr4_2:8668519-8668538 Msa0587190:intron 35.0%
!!! TTATTTTTAGGTGGGTGTGT+TGG - chr4_2:8668711-8668730 Msa0587190:CDS 35.0%
! GGTTGTGAATTTATGATGGA+AGG - chr4_2:8668768-8668787 Msa0587190:CDS 35.0%
! TGAATTTATGATGGAAGGGT+GGG - chr4_2:8668773-8668792 Msa0587190:CDS 35.0%
CTCTTAAAATTGCCAAGAGT+TGG + chr4_2:8668874-8668893 None:intergenic 35.0%
GTGAGATTGAAGTCATGTTG+TGG + chr4_2:8667887-8667906 None:intergenic 40.0%
!!! TCTTGTTTTAACCACAGCCA+TGG - chr4_2:8667911-8667930 Msa0587190:three_prime_UTR 40.0%
GCTTGTAGAGGAAAAGAAGA+AGG - chr4_2:8668325-8668344 Msa0587190:CDS 40.0%
! GTGAATTTATGATGGAAGGG+TGG - chr4_2:8668772-8668791 Msa0587190:CDS 40.0%
AACAACGTTGTCTTGTGTTG+TGG + chr4_2:8667820-8667839 None:intergenic 40.0%
GTGAGATTGAAGTCATGTTG+TGG + chr4_2:8667887-8667906 None:intergenic 40.0%
!!! TCTTGTTTTAACCACAGCCA+TGG - chr4_2:8667911-8667930 Msa0587190:three_prime_UTR 40.0%
GCTTGTAGAGGAAAAGAAGA+AGG - chr4_2:8668325-8668344 Msa0587190:CDS 40.0%
! GTGAATTTATGATGGAAGGG+TGG - chr4_2:8668772-8668791 Msa0587190:CDS 40.0%
AGTTGAAACAACCATGGCTG+TGG + chr4_2:8667925-8667944 None:intergenic 45.0%
!! GCTGGCATTGCTTTTGTTTC+TGG + chr4_2:8668467-8668486 None:intergenic 45.0%
AAGGGTGGGTATTCTTGTGA+AGG - chr4_2:8668787-8668806 Msa0587190:CDS 45.0%
GCTTGACTATGTCCAACTCT+TGG - chr4_2:8668859-8668878 Msa0587190:five_prime_UTR 45.0%
AGTTGAAACAACCATGGCTG+TGG + chr4_2:8667925-8667944 None:intergenic 45.0%
!! GCTGGCATTGCTTTTGTTTC+TGG + chr4_2:8668467-8668486 None:intergenic 45.0%
AAGGGTGGGTATTCTTGTGA+AGG - chr4_2:8668787-8668806 Msa0587190:CDS 45.0%
GCTTGACTATGTCCAACTCT+TGG - chr4_2:8668859-8668878 Msa0587190:five_prime_UTR 45.0%
!!! TTAGATTTTATTTTATTTTT+AGG - chr4_2:8668699-8668718 Msa0587190:CDS 5.0%
!!! TTAGATTTTATTTTATTTTT+AGG - chr4_2:8668699-8668718 Msa0587190:CDS 5.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 8667818 8668910 8667818 ID=Msa0587190;Name=Msa0587190
chr4_2 mRNA 8667818 8668910 8667818 ID=Msa0587190-mRNA-1;Parent=Msa0587190;Name=Msa0587190-mRNA-1;_AED=0.05;_eAED=0.05;_QI=73|1|1|1|1|1|2|357|127
chr4_2 exon 8667818 8668395 8667818 ID=Msa0587190-mRNA-1:exon:2371;Parent=Msa0587190-mRNA-1
chr4_2 exon 8668675 8668910 8668675 ID=Msa0587190-mRNA-1:exon:2370;Parent=Msa0587190-mRNA-1
chr4_2 five_prime_UTR 8668838 8668910 8668838 ID=Msa0587190-mRNA-1:five_prime_utr;Parent=Msa0587190-mRNA-1
chr4_2 CDS 8668675 8668837 8668675 ID=Msa0587190-mRNA-1:cds;Parent=Msa0587190-mRNA-1
chr4_2 CDS 8668175 8668395 8668175 ID=Msa0587190-mRNA-1:cds;Parent=Msa0587190-mRNA-1
chr4_2 three_prime_UTR 8667818 8668174 8667818 ID=Msa0587190-mRNA-1:three_prime_utr;Parent=Msa0587190-mRNA-1
Gene Sequence

>Msa0587190

ATGACTTCAATCTCACAAGGTCTTGTTTTAACCACAGCCATGGTTGTTTCAACTACTGTTCTTTATCTTACTTTCTGTAAACAAAAAAACTCATCACCATTTCAATTCCATGAAACACCCAATTCAGAAAACAAACCTATTCTACGATCTTGTTTATACACAGAGGAAAAGAAGAAGGAAAAATTAAGAAAGAAGAAGAAAGTGAAATTTTCAGAAAATGTGATGGTGAAAGAATTTAGAGAAAAACAGGGGAAGAAAAACAGAGTATCAATTAATGAATGCAGAAATGAAATTCCAGAAACAAAAGCAATGCCAGCAAATAGAGTTGCTTTGTACAATGGAATTTTAAGAGATAGAGTTCAAAGAATGGGGTGTTGTCATTGA

Protein sequence

>Msa0587190

MTSISQGLVLTTAMVVSTTVLYLTFCKQKNSSPFQFHETPNSENKPILRSCLYTEEKKKEKLRKKKKVKFSENVMVKEFREKQGKKNRVSINECRNEIPETKAMPANRVALYNGILRDRVQRMGCCH*