AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0530650


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0530650 MtrunA17_Chr4g0003391 96.063 127 5 0 1 127 1 127 1.07e-77 225
Msa0530650 MtrunA17_Chr2g0333051 52.555 137 48 5 1 123 1 134 4.27e-35 117
Msa0530650 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
Msa0530650 AT1G52565.1 43.571 140 52 5 1 127 4 129 3.42e-18 75.1
Msa0530650 AT3G15760.1 40.580 138 60 6 1 123 1 131 4.83e-15 67.0

Find 32 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_1:+4702194 Msa0530650:three_prime_UTR
GTCATTGATCATCTTAGTTA+TGG 0.371239 4_1:+4702005 Msa0530650:exon
AGAGATAGAGTTCAAAGAAT+GGG 0.376812 4_1:+4701977 Msa0530650:CDS
TACAAAGCAACTCTATTTGC+TGG 0.381833 4_1:-4701941 None:intergenic
TAGAACAAGAAGAAATTAGA+TGG 0.398648 4_1:+4702089 Msa0530650:three_prime_UTR
TTTCTGAATTGGGTGTTTCA+TGG 0.405044 4_1:-4701457 None:intergenic
CTCTTAAAATTGCCAAGAGT+TGG 0.419774 4_1:-4702330 None:intergenic
GCTTGTAGAGGAAAAGAAGA+AGG 0.443148 4_1:+4701784 Msa0530650:intron
TATAAACAAGATCGTAGAAT+AGG 0.444103 4_1:-4701485 None:intergenic
AAAAGGTTGTGAATTTATGA+TGG 0.447654 4_1:+4702223 Msa0530650:three_prime_UTR
AAGAGATAGAGTTCAAAGAA+TGG 0.465347 4_1:+4701976 Msa0530650:CDS
GGTGTTTCATGGAATTGAAA+TGG 0.466904 4_1:-4701446 None:intergenic
AATAGAGTTGCTTTGTACAA+TGG 0.493962 4_1:+4701947 Msa0530650:CDS
GCTTGACTATGTCCAACTCT+TGG 0.517400 4_1:+4702318 Msa0530650:three_prime_UTR
GTGAATTTATGATGGAAGGG+TGG 0.540534 4_1:+4702231 Msa0530650:three_prime_UTR
CATGTTGTGGTTTGAAACAG+AGG 0.556760 4_1:-4701330 None:intergenic
TGAATTTATGATGGAAGGGT+GGG 0.559563 4_1:+4702232 Msa0530650:three_prime_UTR
CTACGATCTTGTTTATACAC+AGG 0.560268 4_1:+4701491 Msa0530650:CDS
GGTTGTGAATTTATGATGGA+AGG 0.562242 4_1:+4702227 Msa0530650:three_prime_UTR
AGTTGAAACAACCATGGCTG+TGG 0.569166 4_1:-4701381 None:intergenic
GAGATAGAGTTCAAAGAATG+GGG 0.570523 4_1:+4701978 Msa0530650:CDS
GTGAGATTGAAGTCATGTTG+TGG 0.573467 4_1:-4701343 None:intergenic
AAGGGTGGGTATTCTTGTGA+AGG 0.586206 4_1:+4702246 Msa0530650:three_prime_UTR
TAGTTATGGAAGTTAGAACA+TGG 0.600995 4_1:+4702019 Msa0530650:three_prime_UTR
GTTGTGAATTTATGATGGAA+GGG 0.606258 4_1:+4702228 Msa0530650:three_prime_UTR
TTAGAACATGGTATAGAACA+TGG 0.610591 4_1:+4702061 Msa0530650:three_prime_UTR
AGTTATGGAAGTTAGAACAT+GGG 0.637332 4_1:+4702020 Msa0530650:three_prime_UTR
TAGAACATGGTATAGAACAT+GGG 0.653391 4_1:+4702062 Msa0530650:three_prime_UTR
AACAGTAGTTGAAACAACCA+TGG 0.660669 4_1:-4701387 None:intergenic
AACATGACTTCAATCTCACA+AGG 0.670440 4_1:+4701347 Msa0530650:exon
AAAGATCTAATGTATTCTTG+TGG 0.676296 4_1:+4702283 Msa0530650:three_prime_UTR
AAACAGAGGAAAGAAAACAG+AGG 0.701650 4_1:-4701316 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GATTTTATTTTATTTTTAGA+TGG + chr4_1:4702161-4702180 Msa0530650:three_prime_UTR 10.0%
!!! GATTTTATTTTATTTTTAGA+TGG + chr4_1:4702161-4702180 Msa0530650:three_prime_UTR 10.0%
!!! TTTTTCAGATACTATTCTAT+AGG + chr4_1:4701575-4701594 Msa0530650:intron 20.0%
!! ATGTTTCATACAAAATATTC+AGG - chr4_1:4701733-4701752 None:intergenic 20.0%
!! AAAGAATTTAGAGAAAAACA+GGG + chr4_1:4701857-4701876 Msa0530650:CDS 20.0%
!!! TTTTTCAGATACTATTCTAT+AGG + chr4_1:4701575-4701594 Msa0530650:intron 20.0%
!! ATGTTTCATACAAAATATTC+AGG - chr4_1:4701733-4701752 None:intergenic 20.0%
!! AAAGAATTTAGAGAAAAACA+GGG + chr4_1:4701857-4701876 Msa0530650:CDS 20.0%
!!! ATAGGTTTGTTTTCTGAATT+GGG - chr4_1:4701470-4701489 None:intergenic 25.0%
!!! AATAGGTTTGTTTTCTGAAT+TGG - chr4_1:4701471-4701490 None:intergenic 25.0%
! TATAAACAAGATCGTAGAAT+AGG - chr4_1:4701488-4701507 None:intergenic 25.0%
!! GAAATTTTCAGAAAATGTGA+TGG + chr4_1:4701832-4701851 Msa0530650:CDS 25.0%
! GAAAGAATTTAGAGAAAAAC+AGG + chr4_1:4701856-4701875 Msa0530650:CDS 25.0%
! AAGAATTTAGAGAAAAACAG+GGG + chr4_1:4701858-4701877 Msa0530650:CDS 25.0%
!!! TTTTAAGAGAAGTTAGAACA+TGG + chr4_1:4702049-4702068 Msa0530650:three_prime_UTR 25.0%
! TAGAACAAGAAGAAATTAGA+TGG + chr4_1:4702089-4702108 Msa0530650:three_prime_UTR 25.0%
!! AACAATATTTGAAGTCCTAA+TGG + chr4_1:4702194-4702213 Msa0530650:three_prime_UTR 25.0%
! AAAAGGTTGTGAATTTATGA+TGG + chr4_1:4702223-4702242 Msa0530650:three_prime_UTR 25.0%
! AAAGATCTAATGTATTCTTG+TGG + chr4_1:4702283-4702302 Msa0530650:three_prime_UTR 25.0%
!!! ATAGGTTTGTTTTCTGAATT+GGG - chr4_1:4701470-4701489 None:intergenic 25.0%
!!! AATAGGTTTGTTTTCTGAAT+TGG - chr4_1:4701471-4701490 None:intergenic 25.0%
! TATAAACAAGATCGTAGAAT+AGG - chr4_1:4701488-4701507 None:intergenic 25.0%
!! GAAATTTTCAGAAAATGTGA+TGG + chr4_1:4701832-4701851 Msa0530650:CDS 25.0%
! GAAAGAATTTAGAGAAAAAC+AGG + chr4_1:4701856-4701875 Msa0530650:CDS 25.0%
! AAGAATTTAGAGAAAAACAG+GGG + chr4_1:4701858-4701877 Msa0530650:CDS 25.0%
!!! TTTTAAGAGAAGTTAGAACA+TGG + chr4_1:4702049-4702068 Msa0530650:three_prime_UTR 25.0%
! TAGAACAAGAAGAAATTAGA+TGG + chr4_1:4702089-4702108 Msa0530650:three_prime_UTR 25.0%
!! AACAATATTTGAAGTCCTAA+TGG + chr4_1:4702194-4702213 Msa0530650:three_prime_UTR 25.0%
! AAAAGGTTGTGAATTTATGA+TGG + chr4_1:4702223-4702242 Msa0530650:three_prime_UTR 25.0%
! AAAGATCTAATGTATTCTTG+TGG + chr4_1:4702283-4702302 Msa0530650:three_prime_UTR 25.0%
!!! GTTTTTGTTTTTGCTTGTAG+AGG + chr4_1:4701772-4701791 Msa0530650:intron 30.0%
! AATAGAGTTGCTTTGTACAA+TGG + chr4_1:4701947-4701966 Msa0530650:CDS 30.0%
AAGAGATAGAGTTCAAAGAA+TGG + chr4_1:4701976-4701995 Msa0530650:CDS 30.0%
AGAGATAGAGTTCAAAGAAT+GGG + chr4_1:4701977-4701996 Msa0530650:CDS 30.0%
GTCATTGATCATCTTAGTTA+TGG + chr4_1:4702005-4702024 Msa0530650:exon 30.0%
TAGTTATGGAAGTTAGAACA+TGG + chr4_1:4702019-4702038 Msa0530650:three_prime_UTR 30.0%
AGTTATGGAAGTTAGAACAT+GGG + chr4_1:4702020-4702039 Msa0530650:three_prime_UTR 30.0%
TTAGAACATGGTATAGAACA+TGG + chr4_1:4702061-4702080 Msa0530650:three_prime_UTR 30.0%
TAGAACATGGTATAGAACAT+GGG + chr4_1:4702062-4702081 Msa0530650:three_prime_UTR 30.0%
!!! TTATTTTTAGATGGGTGTGT+TGG + chr4_1:4702170-4702189 Msa0530650:three_prime_UTR 30.0%
! AGTCCTAATGGATCAAAAAA+AGG + chr4_1:4702206-4702225 Msa0530650:three_prime_UTR 30.0%
!!! CAACCTTTTTTTGATCCATT+AGG - chr4_1:4702212-4702231 None:intergenic 30.0%
! GTTGTGAATTTATGATGGAA+GGG + chr4_1:4702228-4702247 Msa0530650:three_prime_UTR 30.0%
!!! GTTTTTGTTTTTGCTTGTAG+AGG + chr4_1:4701772-4701791 Msa0530650:intron 30.0%
! AATAGAGTTGCTTTGTACAA+TGG + chr4_1:4701947-4701966 Msa0530650:CDS 30.0%
AAGAGATAGAGTTCAAAGAA+TGG + chr4_1:4701976-4701995 Msa0530650:CDS 30.0%
AGAGATAGAGTTCAAAGAAT+GGG + chr4_1:4701977-4701996 Msa0530650:CDS 30.0%
GTCATTGATCATCTTAGTTA+TGG + chr4_1:4702005-4702024 Msa0530650:exon 30.0%
TAGTTATGGAAGTTAGAACA+TGG + chr4_1:4702019-4702038 Msa0530650:three_prime_UTR 30.0%
AGTTATGGAAGTTAGAACAT+GGG + chr4_1:4702020-4702039 Msa0530650:three_prime_UTR 30.0%
TTAGAACATGGTATAGAACA+TGG + chr4_1:4702061-4702080 Msa0530650:three_prime_UTR 30.0%
TAGAACATGGTATAGAACAT+GGG + chr4_1:4702062-4702081 Msa0530650:three_prime_UTR 30.0%
!!! TTATTTTTAGATGGGTGTGT+TGG + chr4_1:4702170-4702189 Msa0530650:three_prime_UTR 30.0%
! AGTCCTAATGGATCAAAAAA+AGG + chr4_1:4702206-4702225 Msa0530650:three_prime_UTR 30.0%
!!! CAACCTTTTTTTGATCCATT+AGG - chr4_1:4702212-4702231 None:intergenic 30.0%
! GTTGTGAATTTATGATGGAA+GGG + chr4_1:4702228-4702247 Msa0530650:three_prime_UTR 30.0%
AAACAGAGGAAAGAAAACAG+AGG - chr4_1:4701319-4701338 None:intergenic 35.0%
AACATGACTTCAATCTCACA+AGG + chr4_1:4701347-4701366 Msa0530650:exon 35.0%
AACAGTAGTTGAAACAACCA+TGG - chr4_1:4701390-4701409 None:intergenic 35.0%
GGTGTTTCATGGAATTGAAA+TGG - chr4_1:4701449-4701468 None:intergenic 35.0%
TTTCTGAATTGGGTGTTTCA+TGG - chr4_1:4701460-4701479 None:intergenic 35.0%
! CTACGATCTTGTTTATACAC+AGG + chr4_1:4701491-4701510 Msa0530650:CDS 35.0%
TACAAAGCAACTCTATTTGC+TGG - chr4_1:4701944-4701963 None:intergenic 35.0%
GAGATAGAGTTCAAAGAATG+GGG + chr4_1:4701978-4701997 Msa0530650:CDS 35.0%
! GGTTGTGAATTTATGATGGA+AGG + chr4_1:4702227-4702246 Msa0530650:three_prime_UTR 35.0%
! TGAATTTATGATGGAAGGGT+GGG + chr4_1:4702232-4702251 Msa0530650:three_prime_UTR 35.0%
CTCTTAAAATTGCCAAGAGT+TGG - chr4_1:4702333-4702352 None:intergenic 35.0%
AAACAGAGGAAAGAAAACAG+AGG - chr4_1:4701319-4701338 None:intergenic 35.0%
AACATGACTTCAATCTCACA+AGG + chr4_1:4701347-4701366 Msa0530650:exon 35.0%
AACAGTAGTTGAAACAACCA+TGG - chr4_1:4701390-4701409 None:intergenic 35.0%
GGTGTTTCATGGAATTGAAA+TGG - chr4_1:4701449-4701468 None:intergenic 35.0%
TTTCTGAATTGGGTGTTTCA+TGG - chr4_1:4701460-4701479 None:intergenic 35.0%
! CTACGATCTTGTTTATACAC+AGG + chr4_1:4701491-4701510 Msa0530650:CDS 35.0%
TACAAAGCAACTCTATTTGC+TGG - chr4_1:4701944-4701963 None:intergenic 35.0%
GAGATAGAGTTCAAAGAATG+GGG + chr4_1:4701978-4701997 Msa0530650:CDS 35.0%
! GGTTGTGAATTTATGATGGA+AGG + chr4_1:4702227-4702246 Msa0530650:three_prime_UTR 35.0%
! TGAATTTATGATGGAAGGGT+GGG + chr4_1:4702232-4702251 Msa0530650:three_prime_UTR 35.0%
CTCTTAAAATTGCCAAGAGT+TGG - chr4_1:4702333-4702352 None:intergenic 35.0%
! CATGTTGTGGTTTGAAACAG+AGG - chr4_1:4701333-4701352 None:intergenic 40.0%
GTGAGATTGAAGTCATGTTG+TGG - chr4_1:4701346-4701365 None:intergenic 40.0%
!!! TCTTGTTTTAACCACAGCCA+TGG + chr4_1:4701370-4701389 Msa0530650:CDS 40.0%
GCTTGTAGAGGAAAAGAAGA+AGG + chr4_1:4701784-4701803 Msa0530650:intron 40.0%
! GTGAATTTATGATGGAAGGG+TGG + chr4_1:4702231-4702250 Msa0530650:three_prime_UTR 40.0%
AACAACGTTGTCTTGTGTTG+TGG - chr4_1:4701279-4701298 None:intergenic 40.0%
! CATGTTGTGGTTTGAAACAG+AGG - chr4_1:4701333-4701352 None:intergenic 40.0%
GTGAGATTGAAGTCATGTTG+TGG - chr4_1:4701346-4701365 None:intergenic 40.0%
!!! TCTTGTTTTAACCACAGCCA+TGG + chr4_1:4701370-4701389 Msa0530650:CDS 40.0%
GCTTGTAGAGGAAAAGAAGA+AGG + chr4_1:4701784-4701803 Msa0530650:intron 40.0%
! GTGAATTTATGATGGAAGGG+TGG + chr4_1:4702231-4702250 Msa0530650:three_prime_UTR 40.0%
AGTTGAAACAACCATGGCTG+TGG - chr4_1:4701384-4701403 None:intergenic 45.0%
!! GCTGGCATTGCTTTTGTTTC+TGG - chr4_1:4701926-4701945 None:intergenic 45.0%
AAGGGTGGGTATTCTTGTGA+AGG + chr4_1:4702246-4702265 Msa0530650:three_prime_UTR 45.0%
GCTTGACTATGTCCAACTCT+TGG + chr4_1:4702318-4702337 Msa0530650:three_prime_UTR 45.0%
AGTTGAAACAACCATGGCTG+TGG - chr4_1:4701384-4701403 None:intergenic 45.0%
!! GCTGGCATTGCTTTTGTTTC+TGG - chr4_1:4701926-4701945 None:intergenic 45.0%
AAGGGTGGGTATTCTTGTGA+AGG + chr4_1:4702246-4702265 Msa0530650:three_prime_UTR 45.0%
GCTTGACTATGTCCAACTCT+TGG + chr4_1:4702318-4702337 Msa0530650:three_prime_UTR 45.0%
!!! ATTTTATTTTATTTTTAGAT+GGG + chr4_1:4702162-4702181 Msa0530650:three_prime_UTR 5.0%
!!! ATTTTATTTTATTTTTAGAT+GGG + chr4_1:4702162-4702181 Msa0530650:three_prime_UTR 5.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 4701277 4702369 4701277 ID=Msa0530650;Name=Msa0530650
chr4_1 mRNA 4701277 4702369 4701277 ID=Msa0530650-mRNA-1;Parent=Msa0530650;Name=Msa0530650-mRNA-1;_AED=0.05;_eAED=0.05;_QI=73|1|1|1|1|1|2|357|127
chr4_1 exon 4701277 4701512 4701277 ID=Msa0530650-mRNA-1:exon:1431;Parent=Msa0530650-mRNA-1
chr4_1 exon 4701792 4702369 4701792 ID=Msa0530650-mRNA-1:exon:1432;Parent=Msa0530650-mRNA-1
chr4_1 five_prime_UTR 4701277 4701349 4701277 ID=Msa0530650-mRNA-1:five_prime_utr;Parent=Msa0530650-mRNA-1
chr4_1 CDS 4701350 4701512 4701350 ID=Msa0530650-mRNA-1:cds;Parent=Msa0530650-mRNA-1
chr4_1 CDS 4701792 4702012 4701792 ID=Msa0530650-mRNA-1:cds;Parent=Msa0530650-mRNA-1
chr4_1 three_prime_UTR 4702013 4702369 4702013 ID=Msa0530650-mRNA-1:three_prime_utr;Parent=Msa0530650-mRNA-1
Gene Sequence

>Msa0530650

ATGACTTCAATCTCACAAGGTCTTGTTTTAACCACAGCCATGGTTGTTTCAACTACTGTTCTTTATCTTACTTTCTGTAAACAAAAAAACTCATCACCATTTCAATTCCATGAAACACCCAATTCAGAAAACAAACCTATTCTACGATCTTGTTTATACACAGAGGAAAAGAAGAAGGAAAAATTAAGAAAGAAGAAGAAAGTGAAATTTTCAGAAAATGTGATGGTGAAAGAATTTAGAGAAAAACAGGGGAAGAAAAACAGAGTATCAATTAATGAATGCAGAAATGAAATTCCAGAAACAAAAGCAATGCCAGCAAATAGAGTTGCTTTGTACAATGGAATTTTAAGAGATAGAGTTCAAAGAATGGGGTGTTGTCATTGA

Protein sequence

>Msa0530650

MTSISQGLVLTTAMVVSTTVLYLTFCKQKNSSPFQFHETPNSENKPILRSCLYTEEKKKEKLRKKKKVKFSENVMVKEFREKQGKKNRVSINECRNEIPETKAMPANRVALYNGILRDRVQRMGCCH*