AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0521520


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0521520 MtrunA17_Chr3g0139391 93.529 170 5 1 1 164 1 170 4.53e-118 330
Msa0521520 MtrunA17_Chr1g0147401 75.301 166 33 3 1 158 1 166 1.51e-85 248
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0521520 AT4G32690.1 69.591 171 39 2 1 158 1 171 6.42e-81 237

Find 37 sgRNAs with CRISPR-Local

Find 112 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAAAACCAGTACGAATTCT+TGG 0.289012 3_4:-74393636 Msa0521520:CDS
ATAGAACCTGTTGTAGAAAT+TGG 0.299176 3_4:+74393805 None:intergenic
AAAGTTAATCAACATTATCT+TGG 0.353946 3_4:+74393030 None:intergenic
GCTTCATGTGTCACAGGAAA+TGG 0.391868 3_4:+74393118 None:intergenic
GAGGAGGACCTCCCATTCTC+TGG 0.415467 3_4:+74393612 None:intergenic
TGCTTTGTCTTTATCAGACT+TGG 0.418611 3_4:+74393661 None:intergenic
CGAATTCTTGGTCCAGAGAA+TGG 0.418706 3_4:-74393624 Msa0521520:CDS
TTTCCACCAATTTCTACAAC+AGG 0.420675 3_4:-74393811 Msa0521520:intron
CTTCCAGCTGCATCCTTGCA+AGG 0.423236 3_4:+74392863 None:intergenic
AAACAAGTTGGTGTCATCAA+TGG 0.436122 3_4:+74393865 None:intergenic
AAAGGTTAATGAAAGTTTGA+AGG 0.487596 3_4:+74393831 None:intergenic
ACTTCATATGCAACAAGCAT+TGG 0.490000 3_4:-74393080 Msa0521520:CDS
TTCCAGCTGCATCCTTGCAA+GGG 0.503260 3_4:+74392864 None:intergenic
GAATTCTTGGTCCAGAGAAT+GGG 0.505694 3_4:-74393623 Msa0521520:CDS
CACCCTTGCAAGGATGCAGC+TGG 0.514180 3_4:-74392866 Msa0521520:CDS
TCTGGACCAAGAATTCGTAC+TGG 0.524772 3_4:+74393630 None:intergenic
TGTTGTAGAAATTGGTGGAA+AGG 0.527682 3_4:+74393813 None:intergenic
CTGCATCCTTGCAAGGGTGA+AGG 0.528329 3_4:+74392870 None:intergenic
TGCAAGAGAAGGCTTCTGAA+TGG 0.530466 3_4:-74393916 Msa0521520:CDS
TCGGCAGCTTCATGTGTCAC+AGG 0.536702 3_4:+74393112 None:intergenic
GAACCTGTTGTAGAAATTGG+TGG 0.539038 3_4:+74393808 None:intergenic
GATGACGATGAGGAGTGGTT+TGG 0.563976 3_4:-74393695 Msa0521520:CDS
CGATGTCTAGTAATTAGAGC+AGG 0.568423 3_4:+74393142 None:intergenic
CACATGAAGCTGCCGAGAGG+TGG 0.582503 3_4:-74393105 Msa0521520:CDS
CCTCTGTATTCTCAGAGAAG+AGG 0.592545 3_4:-74393593 Msa0521520:intron
TCAAAGCCTTCACCCTTGCA+AGG 0.595706 3_4:-74392876 Msa0521520:CDS
ACCAACTTGTTTCAAAAGCT+AGG 0.598000 3_4:-74393854 Msa0521520:CDS
CTTGCAAGGATGCAGCTGGA+AGG 0.604226 3_4:-74392862 Msa0521520:CDS
GATGCAGAATCTGCAAGAGA+AGG 0.605698 3_4:-74393927 Msa0521520:CDS
TTCTTGGTCCAGAGAATGGG+AGG 0.632605 3_4:-74393620 Msa0521520:CDS
CATATGAAGTAACCACCTCT+CGG 0.635321 3_4:+74393093 None:intergenic
TAGAGTGTATGATGACGATG+AGG 0.661998 3_4:-74393705 Msa0521520:CDS
GAGAAGGCTTCTGAATGGAG+TGG 0.664521 3_4:-74393911 Msa0521520:CDS
TGTATGATGACGATGAGGAG+TGG 0.684110 3_4:-74393700 Msa0521520:CDS
CCTCTTCTCTGAGAATACAG+AGG 0.698670 3_4:+74393593 None:intergenic
CTTCTCTGAGAATACAGAGG+AGG 0.701310 3_4:+74393596 None:intergenic
TGACACATGAAGCTGCCGAG+AGG 0.786257 3_4:-74393108 Msa0521520:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CTTTTAGATTTTTAACTTTT+CGG - chr3_4:74393282-74393301 Msa0521520:intron 15.0%
!! AGTCAATAATATTCTTTATT+TGG - chr3_4:74393485-74393504 Msa0521520:intron 15.0%
!!! GTCAATAATATTCTTTATTT+GGG - chr3_4:74393486-74393505 Msa0521520:intron 15.0%
!!! TCAATAATATTCTTTATTTG+GGG - chr3_4:74393487-74393506 Msa0521520:intron 15.0%
!!! TTTGAAACCTATATATATTT+AGG - chr3_4:74393577-74393596 Msa0521520:intron 15.0%
!! TATATGACCTAAATATATAT+AGG + chr3_4:74393587-74393606 None:intergenic 15.0%
!!! CTTTTAGATTTTTAACTTTT+CGG - chr3_4:74393282-74393301 Msa0521520:intron 15.0%
!! AGTCAATAATATTCTTTATT+TGG - chr3_4:74393485-74393504 Msa0521520:intron 15.0%
!!! GTCAATAATATTCTTTATTT+GGG - chr3_4:74393486-74393505 Msa0521520:intron 15.0%
!!! TCAATAATATTCTTTATTTG+GGG - chr3_4:74393487-74393506 Msa0521520:intron 15.0%
!!! TTTGAAACCTATATATATTT+AGG - chr3_4:74393577-74393596 Msa0521520:intron 15.0%
!! TATATGACCTAAATATATAT+AGG + chr3_4:74393587-74393606 None:intergenic 15.0%
!! ATATATCTCTAATAAATGTG+TGG - chr3_4:74393604-74393623 Msa0521520:CDS 20.0%
!! AAAGTTAATCAACATTATCT+TGG + chr3_4:74393781-74393800 None:intergenic 20.0%
!! ATATATCTCTAATAAATGTG+TGG - chr3_4:74393604-74393623 Msa0521520:CDS 20.0%
!! AAAGTTAATCAACATTATCT+TGG + chr3_4:74393781-74393800 None:intergenic 20.0%
! AAAGGTTAATGAAAGTTTGA+AGG + chr3_4:74392980-74392999 None:intergenic 25.0%
! ACTAAGTTCATGACAATTAA+TGG - chr3_4:74393069-74393088 Msa0521520:CDS 25.0%
!! TAATATTCTTTATTTGGGGA+TGG - chr3_4:74393491-74393510 Msa0521520:intron 25.0%
! ATATATAGGTTTCAAAGCTT+AGG + chr3_4:74393573-74393592 None:intergenic 25.0%
!!! AACCTGTGTTTTTACTTTTT+AGG - chr3_4:74393868-74393887 Msa0521520:CDS 25.0%
! AAAGGTTAATGAAAGTTTGA+AGG + chr3_4:74392980-74392999 None:intergenic 25.0%
! ACTAAGTTCATGACAATTAA+TGG - chr3_4:74393069-74393088 Msa0521520:CDS 25.0%
!! TAATATTCTTTATTTGGGGA+TGG - chr3_4:74393491-74393510 Msa0521520:intron 25.0%
! ATATATAGGTTTCAAAGCTT+AGG + chr3_4:74393573-74393592 None:intergenic 25.0%
!!! AACCTGTGTTTTTACTTTTT+AGG - chr3_4:74393868-74393887 Msa0521520:CDS 25.0%
ATAGAACCTGTTGTAGAAAT+TGG + chr3_4:74393006-74393025 None:intergenic 30.0%
GTCATGAACTTAGTAAAGAA+AGG + chr3_4:74393063-74393082 None:intergenic 30.0%
TGCCTAAAAAGTAAAAACAC+AGG + chr3_4:74393873-74393892 None:intergenic 30.0%
! TTGATTCTTCTTTTCAACTC+CGG + chr3_4:74393916-74393935 None:intergenic 30.0%
ATAGAACCTGTTGTAGAAAT+TGG + chr3_4:74393006-74393025 None:intergenic 30.0%
GTCATGAACTTAGTAAAGAA+AGG + chr3_4:74393063-74393082 None:intergenic 30.0%
TGCCTAAAAAGTAAAAACAC+AGG + chr3_4:74393873-74393892 None:intergenic 30.0%
! TTGATTCTTCTTTTCAACTC+CGG + chr3_4:74393916-74393935 None:intergenic 30.0%
!! AAACAAGTTGGTGTCATCAA+TGG + chr3_4:74392946-74392965 None:intergenic 35.0%
! ACCAACTTGTTTCAAAAGCT+AGG - chr3_4:74392954-74392973 Msa0521520:intron 35.0%
TGTTGTAGAAATTGGTGGAA+AGG + chr3_4:74392998-74393017 None:intergenic 35.0%
TTTCCACCAATTTCTACAAC+AGG - chr3_4:74392997-74393016 Msa0521520:intron 35.0%
TGCTTTGTCTTTATCAGACT+TGG + chr3_4:74393150-74393169 None:intergenic 35.0%
TCAAAACCAGTACGAATTCT+TGG - chr3_4:74393172-74393191 Msa0521520:intron 35.0%
ATGTCCTGTAATGTGAAGTA+CGG + chr3_4:74393646-74393665 None:intergenic 35.0%
ACTTCATATGCAACAAGCAT+TGG - chr3_4:74393728-74393747 Msa0521520:intron 35.0%
! ACTGCATATTTTCTTGTTGC+CGG - chr3_4:74393894-74393913 Msa0521520:CDS 35.0%
!! AAACAAGTTGGTGTCATCAA+TGG + chr3_4:74392946-74392965 None:intergenic 35.0%
! ACCAACTTGTTTCAAAAGCT+AGG - chr3_4:74392954-74392973 Msa0521520:intron 35.0%
TGTTGTAGAAATTGGTGGAA+AGG + chr3_4:74392998-74393017 None:intergenic 35.0%
TTTCCACCAATTTCTACAAC+AGG - chr3_4:74392997-74393016 Msa0521520:intron 35.0%
TGCTTTGTCTTTATCAGACT+TGG + chr3_4:74393150-74393169 None:intergenic 35.0%
TCAAAACCAGTACGAATTCT+TGG - chr3_4:74393172-74393191 Msa0521520:intron 35.0%
ATGTCCTGTAATGTGAAGTA+CGG + chr3_4:74393646-74393665 None:intergenic 35.0%
ACTTCATATGCAACAAGCAT+TGG - chr3_4:74393728-74393747 Msa0521520:intron 35.0%
! ACTGCATATTTTCTTGTTGC+CGG - chr3_4:74393894-74393913 Msa0521520:CDS 35.0%
!!! GCCTAGCTTTTGAAACAAGT+TGG + chr3_4:74392958-74392977 None:intergenic 40.0%
GAACCTGTTGTAGAAATTGG+TGG + chr3_4:74393003-74393022 None:intergenic 40.0%
! TAGAGTGTATGATGACGATG+AGG - chr3_4:74393103-74393122 Msa0521520:CDS 40.0%
GAATTCTTGGTCCAGAGAAT+GGG - chr3_4:74393185-74393204 Msa0521520:intron 40.0%
GGGATGGTTAGTAAAATGAC+AGG - chr3_4:74393507-74393526 Msa0521520:intron 40.0%
CGATGTCTAGTAATTAGAGC+AGG + chr3_4:74393669-74393688 None:intergenic 40.0%
CATATGAAGTAACCACCTCT+CGG + chr3_4:74393718-74393737 None:intergenic 40.0%
!!! GCCTAGCTTTTGAAACAAGT+TGG + chr3_4:74392958-74392977 None:intergenic 40.0%
GAACCTGTTGTAGAAATTGG+TGG + chr3_4:74393003-74393022 None:intergenic 40.0%
! TAGAGTGTATGATGACGATG+AGG - chr3_4:74393103-74393122 Msa0521520:CDS 40.0%
GAATTCTTGGTCCAGAGAAT+GGG - chr3_4:74393185-74393204 Msa0521520:intron 40.0%
GGGATGGTTAGTAAAATGAC+AGG - chr3_4:74393507-74393526 Msa0521520:intron 40.0%
CGATGTCTAGTAATTAGAGC+AGG + chr3_4:74393669-74393688 None:intergenic 40.0%
CATATGAAGTAACCACCTCT+CGG + chr3_4:74393718-74393737 None:intergenic 40.0%
GATGCAGAATCTGCAAGAGA+AGG - chr3_4:74392881-74392900 Msa0521520:CDS 45.0%
TGCAAGAGAAGGCTTCTGAA+TGG - chr3_4:74392892-74392911 Msa0521520:CDS 45.0%
! TGTATGATGACGATGAGGAG+TGG - chr3_4:74393108-74393127 Msa0521520:CDS 45.0%
TCTGGACCAAGAATTCGTAC+TGG + chr3_4:74393181-74393200 None:intergenic 45.0%
CGAATTCTTGGTCCAGAGAA+TGG - chr3_4:74393184-74393203 Msa0521520:intron 45.0%
! CTTCTCTGAGAATACAGAGG+AGG + chr3_4:74393215-74393234 None:intergenic 45.0%
! CCTCTTCTCTGAGAATACAG+AGG + chr3_4:74393218-74393237 None:intergenic 45.0%
CCTCTGTATTCTCAGAGAAG+AGG - chr3_4:74393215-74393234 Msa0521520:intron 45.0%
GCTACCGTACTTCACATTAC+AGG - chr3_4:74393639-74393658 Msa0521520:CDS 45.0%
GCTTCATGTGTCACAGGAAA+TGG + chr3_4:74393693-74393712 None:intergenic 45.0%
GATGCAGAATCTGCAAGAGA+AGG - chr3_4:74392881-74392900 Msa0521520:CDS 45.0%
TGCAAGAGAAGGCTTCTGAA+TGG - chr3_4:74392892-74392911 Msa0521520:CDS 45.0%
! TGTATGATGACGATGAGGAG+TGG - chr3_4:74393108-74393127 Msa0521520:CDS 45.0%
TCTGGACCAAGAATTCGTAC+TGG + chr3_4:74393181-74393200 None:intergenic 45.0%
CGAATTCTTGGTCCAGAGAA+TGG - chr3_4:74393184-74393203 Msa0521520:intron 45.0%
! CTTCTCTGAGAATACAGAGG+AGG + chr3_4:74393215-74393234 None:intergenic 45.0%
! CCTCTTCTCTGAGAATACAG+AGG + chr3_4:74393218-74393237 None:intergenic 45.0%
CCTCTGTATTCTCAGAGAAG+AGG - chr3_4:74393215-74393234 Msa0521520:intron 45.0%
GCTACCGTACTTCACATTAC+AGG - chr3_4:74393639-74393658 Msa0521520:CDS 45.0%
GCTTCATGTGTCACAGGAAA+TGG + chr3_4:74393693-74393712 None:intergenic 45.0%
GAGAAGGCTTCTGAATGGAG+TGG - chr3_4:74392897-74392916 Msa0521520:CDS 50.0%
GATGACGATGAGGAGTGGTT+TGG - chr3_4:74393113-74393132 Msa0521520:CDS 50.0%
TTCTTGGTCCAGAGAATGGG+AGG - chr3_4:74393188-74393207 Msa0521520:intron 50.0%
TCAAAGCCTTCACCCTTGCA+AGG - chr3_4:74393932-74393951 Msa0521520:exon 50.0%
TTCCAGCTGCATCCTTGCAA+GGG + chr3_4:74393947-74393966 None:intergenic 50.0%
GAGAAGGCTTCTGAATGGAG+TGG - chr3_4:74392897-74392916 Msa0521520:CDS 50.0%
GATGACGATGAGGAGTGGTT+TGG - chr3_4:74393113-74393132 Msa0521520:CDS 50.0%
TTCTTGGTCCAGAGAATGGG+AGG - chr3_4:74393188-74393207 Msa0521520:intron 50.0%
TCAAAGCCTTCACCCTTGCA+AGG - chr3_4:74393932-74393951 Msa0521520:exon 50.0%
TTCCAGCTGCATCCTTGCAA+GGG + chr3_4:74393947-74393966 None:intergenic 50.0%
TCGGCAGCTTCATGTGTCAC+AGG + chr3_4:74393699-74393718 None:intergenic 55.0%
TGACACATGAAGCTGCCGAG+AGG - chr3_4:74393700-74393719 Msa0521520:CDS 55.0%
CTGCATCCTTGCAAGGGTGA+AGG + chr3_4:74393941-74393960 None:intergenic 55.0%
CTTCCAGCTGCATCCTTGCA+AGG + chr3_4:74393948-74393967 None:intergenic 55.0%
CTTGCAAGGATGCAGCTGGA+AGG - chr3_4:74393946-74393965 Msa0521520:exon 55.0%
TCGGCAGCTTCATGTGTCAC+AGG + chr3_4:74393699-74393718 None:intergenic 55.0%
TGACACATGAAGCTGCCGAG+AGG - chr3_4:74393700-74393719 Msa0521520:CDS 55.0%
CTGCATCCTTGCAAGGGTGA+AGG + chr3_4:74393941-74393960 None:intergenic 55.0%
CTTCCAGCTGCATCCTTGCA+AGG + chr3_4:74393948-74393967 None:intergenic 55.0%
CTTGCAAGGATGCAGCTGGA+AGG - chr3_4:74393946-74393965 Msa0521520:exon 55.0%
GAGGAGGACCTCCCATTCTC+TGG + chr3_4:74393199-74393218 None:intergenic 60.0%
CACATGAAGCTGCCGAGAGG+TGG - chr3_4:74393703-74393722 Msa0521520:CDS 60.0%
CACCCTTGCAAGGATGCAGC+TGG - chr3_4:74393942-74393961 Msa0521520:exon 60.0%
GAGGAGGACCTCCCATTCTC+TGG + chr3_4:74393199-74393218 None:intergenic 60.0%
CACATGAAGCTGCCGAGAGG+TGG - chr3_4:74393703-74393722 Msa0521520:CDS 60.0%
CACCCTTGCAAGGATGCAGC+TGG - chr3_4:74393942-74393961 Msa0521520:exon 60.0%
Chromosome Type Strat End Strand Name
chr3_4 gene 74392841 74393989 74392841 ID=Msa0521520;Name=Msa0521520
chr3_4 mRNA 74392841 74393989 74392841 ID=Msa0521520-mRNA-1;Parent=Msa0521520;Name=Msa0521520-mRNA-1;_AED=0.43;_eAED=0.43;_QI=41|0.33|0.25|1|1|1|4|0|164
chr3_4 exon 74392841 74392940 74392841 ID=Msa0521520-mRNA-1:exon:21064;Parent=Msa0521520-mRNA-1
chr3_4 exon 74393043 74393169 74393043 ID=Msa0521520-mRNA-1:exon:21063;Parent=Msa0521520-mRNA-1
chr3_4 exon 74393594 74393724 74393594 ID=Msa0521520-mRNA-1:exon:21062;Parent=Msa0521520-mRNA-1
chr3_4 exon 74393812 74393989 74393812 ID=Msa0521520-mRNA-1:exon:21061;Parent=Msa0521520-mRNA-1
chr3_4 five_prime_UTR 74393949 74393989 74393949 ID=Msa0521520-mRNA-1:five_prime_utr;Parent=Msa0521520-mRNA-1
chr3_4 CDS 74393812 74393948 74393812 ID=Msa0521520-mRNA-1:cds;Parent=Msa0521520-mRNA-1
chr3_4 CDS 74393594 74393724 74393594 ID=Msa0521520-mRNA-1:cds;Parent=Msa0521520-mRNA-1
chr3_4 CDS 74393043 74393169 74393043 ID=Msa0521520-mRNA-1:cds;Parent=Msa0521520-mRNA-1
chr3_4 CDS 74392841 74392940 74392841 ID=Msa0521520-mRNA-1:cds;Parent=Msa0521520-mRNA-1
Gene Sequence

>Msa0521520

ATGCAGAATCTGCAAGAGAAGGCTTCTGAATGGAGTGGTGTTGAGACAAATCATGCTTTTGCCATTGATGACACCAACTTGTTTCAAAAGCTAGGCCTTCAAACTTTCATTAACCTTTCCACCAATTTCTACAACAGAGTGTATGATGACGATGAGGAGTGGTTTGGTTCAATATTTGCCAAGTCTGATAAAGACAAAGCAATTCAAAACCAGTACGAATTCTTGGTCCAGAGAATGGGAGGTCCTCCTCTGTATTCTCAGAGAAGAGGACATCCTGCTCTAATTACTAGACATCGACCATTTCCTGTGACACATGAAGCTGCCGAGAGGTGGTTACTTCATATGCAACAAGCATTGGACAATATTTCAGATATAGATCATGATTCCAAGATAATGCACACTGCATATTTTCTTGTTGCCGGAGTTGAAAAGAAGAATCAAAGCCTTCACCCTTGCAAGGATGCAGCTGGAAGGCATCCATGTAAAAACTTTTAA

Protein sequence

>Msa0521520

MQNLQEKASEWSGVETNHAFAIDDTNLFQKLGLQTFINLSTNFYNRVYDDDEEWFGSIFAKSDKDKAIQNQYEFLVQRMGGPPLYSQRRGHPALITRHRPFPVTHEAAERWLLHMQQALDNISDIDHDSKIMHTAYFLVAGVEKKNQSLHPCKDAAGRHPCKNF*