AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1336190

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1336190 MtrunA17_Chr3g0121191 84.277 159 19 2 3 157 5 161 2.40e-70 212
Msa1336190 MtrunA17_Chr8g0391691 48.101 79 31 1 89 157 36 114 3.99e-12 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 37 sgRNAs with CRISPR-Local

Find 99 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCATATGATATGACAATAAT+TGG 0.191098 tig0000805:+9940 Msa1336190:five_prime_UTR
TGCTATACTTAATTTATTAT+CGG 0.307266 tig0000805:+9909 Msa1336190:five_prime_UTR
CTGCTACGGAGAAACAAAAT+TGG 0.349996 tig0000805:+10333 Msa1336190:CDS
CAATGTCAACACATTGGAAT+TGG 0.350732 tig0000805:+10362 Msa1336190:CDS
AGAGGAAATGGAAAACTTAA+AGG 0.354653 tig0000805:+10560 Msa1336190:CDS
CTATGAATCTGAAGAGGAAA+TGG 0.373890 tig0000805:+10548 Msa1336190:CDS
AAAGATGACAACAACAATAA+TGG 0.375899 tig0000805:-10304 Msa1336200:CDS
GCTATACTTAATTTATTATC+GGG 0.378300 tig0000805:+9910 Msa1336190:five_prime_UTR
CGGATTATCTGAGTTGGAAT+TGG 0.386893 tig0000805:-10008 None:intergenic
ATAGATGGTGTATTGTTGTT+TGG 0.388629 tig0000805:-10271 None:intergenic
TCAGATCTGAGATCGATAAC+TGG 0.401362 tig0000805:+10441 Msa1336190:CDS
CAATTCCAACTCAGATAATC+CGG 0.409288 tig0000805:+10009 Msa1336190:CDS
ATAACTGGAAAGTTGGATAT+AGG 0.436939 tig0000805:+10456 Msa1336190:CDS
CACGTAGAGTATTGTTTAGT+AGG 0.438826 tig0000805:-9888 None:intergenic
GATGACGTTGATGGCATTGA+TGG 0.458924 tig0000805:+10480 Msa1336190:CDS
CAAAGGATCACAAGCAATGA+AGG 0.462782 tig0000805:+10153 Msa1336190:intron
AGGATCTGAAAAGAAATTCC+AGG 0.462891 tig0000805:-9868 None:intergenic
ACTCAGATAATCCGGCTTCA+AGG 0.465470 tig0000805:+10017 Msa1336190:CDS
TGCTAACAAAACAGCTAAAA+CGG 0.468639 tig0000805:-10217 None:intergenic
GAGATCGATAACTGGAAAGT+TGG 0.474110 tig0000805:+10449 Msa1336190:CDS
TCATCTTTCTTAATCTGCTA+CGG 0.479201 tig0000805:+10319 Msa1336190:CDS
AATGGAGGAGATGAAATAGA+TGG 0.486385 tig0000805:-10286 None:intergenic
CGAGGTTCTGACCTTGAAGC+CGG 0.497573 tig0000805:-10028 None:intergenic
GATATAGGAGATGACGTTGA+TGG 0.498114 tig0000805:+10471 Msa1336190:CDS
GCACTGAATTACACAGAAGC+TGG 0.501469 tig0000805:+10237 Msa1336190:CDS
GTGTATGACATTGATGGTGA+TGG 0.505283 tig0000805:+10593 Msa1336190:CDS
TGAAGCCGGATTATCTGAGT+TGG 0.528924 tig0000805:-10014 None:intergenic
CAACACATTGGAATTGGAGA+TGG 0.533055 tig0000805:+10368 Msa1336190:CDS
TATTCTTAAAGTCATTCTGA+TGG 0.549569 tig0000805:+9982 Msa1336190:exon
CTATACTTAATTTATTATCG+GGG 0.574628 tig0000805:+9911 Msa1336190:five_prime_UTR
AACAAACTATGAATCTGAAG+AGG 0.586456 tig0000805:+10542 Msa1336190:CDS
CAATGTCAATGTCAACACAT+TGG 0.601927 tig0000805:+10356 Msa1336190:CDS
TTCAAGAAATTGGACACAGA+TGG 0.611437 tig0000805:+10399 Msa1336190:CDS
TGAAGGAAAGTTGAAAGACA+TGG 0.629688 tig0000805:+10170 Msa1336190:CDS
GATGACAACAACAATAATGG+AGG 0.629703 tig0000805:-10301 Msa1336200:CDS
AAATTGGACACAGATGGTGA+TGG 0.649231 tig0000805:+10405 Msa1336190:CDS
GACGTTGATGGCATTGATGG+AGG 0.660924 tig0000805:+10483 Msa1336190:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGCTATACTTAATTTATTAT+CGG + tig0000805:9909-9928 Msa1336190:five_prime_UTR 15.0%
!!! AATCATTTTGTATAAGATTT+TGG - tig0000805:10196-10215 None:intergenic 15.0%
!! TGCTATACTTAATTTATTAT+CGG + tig0000805:9909-9928 Msa1336190:five_prime_UTR 15.0%
!!! AATCATTTTGTATAAGATTT+TGG - tig0000805:10196-10215 None:intergenic 15.0%
!! GCTATACTTAATTTATTATC+GGG + tig0000805:9910-9929 Msa1336190:five_prime_UTR 20.0%
!! CTATACTTAATTTATTATCG+GGG + tig0000805:9911-9930 Msa1336190:five_prime_UTR 20.0%
!! TCATATGATATGACAATAAT+TGG + tig0000805:9940-9959 Msa1336190:five_prime_UTR 20.0%
!! GCTATACTTAATTTATTATC+GGG + tig0000805:9910-9929 Msa1336190:five_prime_UTR 20.0%
!! CTATACTTAATTTATTATCG+GGG + tig0000805:9911-9930 Msa1336190:five_prime_UTR 20.0%
!! TCATATGATATGACAATAAT+TGG + tig0000805:9940-9959 Msa1336190:five_prime_UTR 20.0%
!!! TTTTTTTATGTGAGAGAATC+TGG - tig0000805:9803-9822 None:intergenic 25.0%
! TATTCTTAAAGTCATTCTGA+TGG + tig0000805:9982-10001 Msa1336190:exon 25.0%
!!! TTTTTTTTGTTTTCCCTCAA+AGG + tig0000805:10136-10155 Msa1336190:intron 25.0%
! AAAGATGACAACAACAATAA+TGG - tig0000805:10307-10326 Msa1336200:CDS 25.0%
!!! TTTTTTTATGTGAGAGAATC+TGG - tig0000805:9803-9822 None:intergenic 25.0%
! TATTCTTAAAGTCATTCTGA+TGG + tig0000805:9982-10001 Msa1336190:exon 25.0%
!!! TTTTTTTTGTTTTCCCTCAA+AGG + tig0000805:10136-10155 Msa1336190:intron 25.0%
! AAAGATGACAACAACAATAA+TGG - tig0000805:10307-10326 Msa1336200:CDS 25.0%
! TTTCTTTTCTCTTTTTCTCC+TGG + tig0000805:9850-9869 Msa1336190:five_prime_UTR 30.0%
TTTGAACTTGAAAGGTGAAA+TGG - tig0000805:10084-10103 None:intergenic 30.0%
!! CTAACTTGTTTGAACTTGAA+AGG - tig0000805:10092-10111 None:intergenic 30.0%
TGCTAACAAAACAGCTAAAA+CGG - tig0000805:10220-10239 None:intergenic 30.0%
! ATAGATGGTGTATTGTTGTT+TGG - tig0000805:10274-10293 None:intergenic 30.0%
TCATCTTTCTTAATCTGCTA+CGG + tig0000805:10319-10338 Msa1336190:CDS 30.0%
GGAAAAACTCTTCAAGAAAT+TGG + tig0000805:10389-10408 Msa1336190:CDS 30.0%
ATAACTGGAAAGTTGGATAT+AGG + tig0000805:10456-10475 Msa1336190:CDS 30.0%
AACAAACTATGAATCTGAAG+AGG + tig0000805:10542-10561 Msa1336190:CDS 30.0%
AGAGGAAATGGAAAACTTAA+AGG + tig0000805:10560-10579 Msa1336190:CDS 30.0%
! TTTTCTGTGTATGACATTGA+TGG + tig0000805:10587-10606 Msa1336190:CDS 30.0%
! TTTCTTTTCTCTTTTTCTCC+TGG + tig0000805:9850-9869 Msa1336190:five_prime_UTR 30.0%
TTTGAACTTGAAAGGTGAAA+TGG - tig0000805:10084-10103 None:intergenic 30.0%
!! CTAACTTGTTTGAACTTGAA+AGG - tig0000805:10092-10111 None:intergenic 30.0%
TGCTAACAAAACAGCTAAAA+CGG - tig0000805:10220-10239 None:intergenic 30.0%
! ATAGATGGTGTATTGTTGTT+TGG - tig0000805:10274-10293 None:intergenic 30.0%
TCATCTTTCTTAATCTGCTA+CGG + tig0000805:10319-10338 Msa1336190:CDS 30.0%
GGAAAAACTCTTCAAGAAAT+TGG + tig0000805:10389-10408 Msa1336190:CDS 30.0%
ATAACTGGAAAGTTGGATAT+AGG + tig0000805:10456-10475 Msa1336190:CDS 30.0%
AACAAACTATGAATCTGAAG+AGG + tig0000805:10542-10561 Msa1336190:CDS 30.0%
AGAGGAAATGGAAAACTTAA+AGG + tig0000805:10560-10579 Msa1336190:CDS 30.0%
! TTTTCTGTGTATGACATTGA+TGG + tig0000805:10587-10606 Msa1336190:CDS 30.0%
AGGATCTGAAAAGAAATTCC+AGG - tig0000805:9871-9890 None:intergenic 35.0%
!! CACGTAGAGTATTGTTTAGT+AGG - tig0000805:9891-9910 None:intergenic 35.0%
CAATTCCAACTCAGATAATC+CGG + tig0000805:10009-10028 Msa1336190:CDS 35.0%
TGAAGGAAAGTTGAAAGACA+TGG + tig0000805:10170-10189 Msa1336190:CDS 35.0%
AATGGAGGAGATGAAATAGA+TGG - tig0000805:10289-10308 None:intergenic 35.0%
GATGACAACAACAATAATGG+AGG - tig0000805:10304-10323 Msa1336200:CDS 35.0%
CAATGTCAATGTCAACACAT+TGG + tig0000805:10356-10375 Msa1336190:CDS 35.0%
CAATGTCAACACATTGGAAT+TGG + tig0000805:10362-10381 Msa1336190:CDS 35.0%
TTCAAGAAATTGGACACAGA+TGG + tig0000805:10399-10418 Msa1336190:CDS 35.0%
CTATGAATCTGAAGAGGAAA+TGG + tig0000805:10548-10567 Msa1336190:CDS 35.0%
! AAGCGTATTAAGCTCTTTTG+CGG - tig0000805:10627-10646 Msa1336200:intron 35.0%
AGAGCTTAATACGCTTATGA+CGG + tig0000805:10631-10650 Msa1336190:CDS 35.0%
AGGATCTGAAAAGAAATTCC+AGG - tig0000805:9871-9890 None:intergenic 35.0%
!! CACGTAGAGTATTGTTTAGT+AGG - tig0000805:9891-9910 None:intergenic 35.0%
CAATTCCAACTCAGATAATC+CGG + tig0000805:10009-10028 Msa1336190:CDS 35.0%
TGAAGGAAAGTTGAAAGACA+TGG + tig0000805:10170-10189 Msa1336190:CDS 35.0%
AATGGAGGAGATGAAATAGA+TGG - tig0000805:10289-10308 None:intergenic 35.0%
GATGACAACAACAATAATGG+AGG - tig0000805:10304-10323 Msa1336200:CDS 35.0%
CAATGTCAATGTCAACACAT+TGG + tig0000805:10356-10375 Msa1336190:CDS 35.0%
CAATGTCAACACATTGGAAT+TGG + tig0000805:10362-10381 Msa1336190:CDS 35.0%
TTCAAGAAATTGGACACAGA+TGG + tig0000805:10399-10418 Msa1336190:CDS 35.0%
CTATGAATCTGAAGAGGAAA+TGG + tig0000805:10548-10567 Msa1336190:CDS 35.0%
! AAGCGTATTAAGCTCTTTTG+CGG - tig0000805:10627-10646 Msa1336200:intron 35.0%
! CGGATTATCTGAGTTGGAAT+TGG - tig0000805:10011-10030 None:intergenic 40.0%
CAATTCATAGTAGTGAAGCG+AGG - tig0000805:10049-10068 None:intergenic 40.0%
CATTGCTTGTGATCCTTTGA+GGG - tig0000805:10152-10171 None:intergenic 40.0%
TCATTGCTTGTGATCCTTTG+AGG - tig0000805:10153-10172 None:intergenic 40.0%
CAAAGGATCACAAGCAATGA+AGG + tig0000805:10153-10172 Msa1336190:intron 40.0%
CTGCTACGGAGAAACAAAAT+TGG + tig0000805:10333-10352 Msa1336190:CDS 40.0%
CAACACATTGGAATTGGAGA+TGG + tig0000805:10368-10387 Msa1336190:CDS 40.0%
AAATTGGACACAGATGGTGA+TGG + tig0000805:10405-10424 Msa1336190:CDS 40.0%
! TCAGATCTGAGATCGATAAC+TGG + tig0000805:10441-10460 Msa1336190:CDS 40.0%
GAGATCGATAACTGGAAAGT+TGG + tig0000805:10449-10468 Msa1336190:CDS 40.0%
GATATAGGAGATGACGTTGA+TGG + tig0000805:10471-10490 Msa1336190:CDS 40.0%
!! GTGTATGACATTGATGGTGA+TGG + tig0000805:10593-10612 Msa1336190:CDS 40.0%
! CGGATTATCTGAGTTGGAAT+TGG - tig0000805:10011-10030 None:intergenic 40.0%
CAATTCATAGTAGTGAAGCG+AGG - tig0000805:10049-10068 None:intergenic 40.0%
CATTGCTTGTGATCCTTTGA+GGG - tig0000805:10152-10171 None:intergenic 40.0%
TCATTGCTTGTGATCCTTTG+AGG - tig0000805:10153-10172 None:intergenic 40.0%
CAAAGGATCACAAGCAATGA+AGG + tig0000805:10153-10172 Msa1336190:intron 40.0%
CTGCTACGGAGAAACAAAAT+TGG + tig0000805:10333-10352 Msa1336190:CDS 40.0%
CAACACATTGGAATTGGAGA+TGG + tig0000805:10368-10387 Msa1336190:CDS 40.0%
AAATTGGACACAGATGGTGA+TGG + tig0000805:10405-10424 Msa1336190:CDS 40.0%
! TCAGATCTGAGATCGATAAC+TGG + tig0000805:10441-10460 Msa1336190:CDS 40.0%
GAGATCGATAACTGGAAAGT+TGG + tig0000805:10449-10468 Msa1336190:CDS 40.0%
GATATAGGAGATGACGTTGA+TGG + tig0000805:10471-10490 Msa1336190:CDS 40.0%
!! GTGTATGACATTGATGGTGA+TGG + tig0000805:10593-10612 Msa1336190:CDS 40.0%
TGAAGCCGGATTATCTGAGT+TGG - tig0000805:10017-10036 None:intergenic 45.0%
ACTCAGATAATCCGGCTTCA+AGG + tig0000805:10017-10036 Msa1336190:CDS 45.0%
GCACTGAATTACACAGAAGC+TGG + tig0000805:10237-10256 Msa1336190:CDS 45.0%
!! GATGACGTTGATGGCATTGA+TGG + tig0000805:10480-10499 Msa1336190:CDS 45.0%
TGAAGCCGGATTATCTGAGT+TGG - tig0000805:10017-10036 None:intergenic 45.0%
ACTCAGATAATCCGGCTTCA+AGG + tig0000805:10017-10036 Msa1336190:CDS 45.0%
GCACTGAATTACACAGAAGC+TGG + tig0000805:10237-10256 Msa1336190:CDS 45.0%
!! GATGACGTTGATGGCATTGA+TGG + tig0000805:10480-10499 Msa1336190:CDS 45.0%
!! GACGTTGATGGCATTGATGG+AGG + tig0000805:10483-10502 Msa1336190:CDS 50.0%
!! GACGTTGATGGCATTGATGG+AGG + tig0000805:10483-10502 Msa1336190:CDS 50.0%
! CGAGGTTCTGACCTTGAAGC+CGG - tig0000805:10031-10050 None:intergenic 55.0%
! CGAGGTTCTGACCTTGAAGC+CGG - tig0000805:10031-10050 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
tig0000805 gene 9795 10650 9795 ID=Msa1336190;Name=Msa1336190
tig0000805 mRNA 9795 10650 9795 ID=Msa1336190-mRNA-1;Parent=Msa1336190;Name=Msa1336190-mRNA-1;_AED=0.03;_eAED=0.03;_QI=206|1|0.5|1|1|1|2|0|176
tig0000805 exon 9795 10038 9795 ID=Msa1336190-mRNA-1:exon:615;Parent=Msa1336190-mRNA-1
tig0000805 exon 10158 10650 10158 ID=Msa1336190-mRNA-1:exon:616;Parent=Msa1336190-mRNA-1
tig0000805 five_prime_UTR 9795 10000 9795 ID=Msa1336190-mRNA-1:five_prime_utr;Parent=Msa1336190-mRNA-1
tig0000805 CDS 10001 10038 10001 ID=Msa1336190-mRNA-1:cds;Parent=Msa1336190-mRNA-1
tig0000805 CDS 10158 10650 10158 ID=Msa1336190-mRNA-1:cds;Parent=Msa1336190-mRNA-1
Gene Sequence

>Msa1336190

ATGGTTTCCAATTCCAACTCAGATAATCCGGCTTCAAGGATCACAAGCAATGAAGGAAAGTTGAAAGACATGGCCAAAATCTTATACAAAATGATTGCCGTTTTAGCTGTTTTGTTAGCACTGAATTACACAGAAGCTGGAAACAAATTTTCCAAACAACAATACACCATCTATTTCATCTCCTCCATTATTGTTGTTGTCATCTTTCTTAATCTGCTACGGAGAAACAAAATTGGCAATGTCAATGTCAACACATTGGAATTGGAGATGGAAAAACTCTTCAAGAAATTGGACACAGATGGTGATGGAAAGATATCGATCTCAGATCTGAGATCGATAACTGGAAAGTTGGATATAGGAGATGACGTTGATGGCATTGATGGAGGATCTATCACGCTTCAAGAGTTTATTGAGCTAAGCACAACAAACTATGAATCTGAAGAGGAAATGGAAAACTTAAAGGCACGTTTTCTGTGTATGACATTGATGGTGATGGTTTCATTACCGCAAAAGAGCTTAATACGCTTATGA
Protein sequence

>Msa1336190

MVSNSNSDNPASRITSNEGKLKDMAKILYKMIAVLAVLLALNYTEAGNKFSKQQYTIYFISSIIVVVIFLNLLRRNKIGNVNVNTLELEMEKLFKKLDTDGDGKISISDLRSITGKLDIGDDVDGIDGGSITLQEFIELSTTNYESEEEMENLKARFLCMTLMVMVSLPQKSLIRL*