AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0578090


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0578090 MtrunA17_Chr4g0002781 78.641 206 17 3 1 181 1 204 2.14e-96 283
Msa0578090 MtrunA17_Chr4g0002801 67.500 200 28 5 1 181 1 182 2.82e-72 221
Msa0578090 MtrunA17_Chr2g0333621 40.741 189 83 5 1 181 1 168 3.47e-29 109
Msa0578090 MtrunA17_Chr2g0333641 42.105 190 78 7 1 181 1 167 5.29e-28 106
Msa0578090 MtrunA17_Chr8g0368371 37.037 162 74 6 25 182 6 143 1.38e-19 80.5
Msa0578090 MtrunA17_Chr7g0249811 33.173 208 99 9 1 181 1 195 4.28e-19 82.8
Msa0578090 MtrunA17_Chr8g0336681 48.913 92 44 2 91 181 97 186 7.19e-15 71.2
Msa0578090 MtrunA17_Chr8g0336671 69.767 43 13 0 140 182 24 66 1.42e-13 63.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 35 sgRNAs with CRISPR-Local

Find 88 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCAACAACATCAAAACTTTC+TGG 0.157589 4_1:+82538819 None:intergenic
TGGAGGTAGTATAATTTATT+AGG 0.168388 4_1:+82538395 None:intergenic
CTTGTGTTAATTTGAGTTCT+AGG 0.232838 4_1:-82538617 Msa0578090:CDS
CCTCCATTGGATCAATGTTT+TGG 0.240607 4_1:+82539218 None:intergenic
CTGGCTTGAGCAAGGTAAAT+TGG 0.282324 4_1:-82538425 Msa0578090:CDS
GCACTTTCAGCTACTATTCC+TGG 0.324686 4_1:-82538444 Msa0578090:CDS
AAAGACAAAATGTATGTCTT+TGG 0.328953 4_1:+82538675 None:intergenic
GGAGGTAGTATAATTTATTA+GGG 0.346108 4_1:+82538396 None:intergenic
ATATAGAGTGTAAATGACTA+TGG 0.383180 4_1:+82539144 None:intergenic
AATCATCATCGTCAGTGTTA+AGG 0.430939 4_1:+82538868 None:intergenic
TTTCCCAATGACTCCTCCAT+TGG 0.449389 4_1:+82539035 None:intergenic
TTTCCAATGGAGGAGTCATT+GGG 0.455919 4_1:-82539038 Msa0578090:exon
CAATTTACCTTGCTCAAGCC+AGG 0.465848 4_1:+82538426 None:intergenic
CAATGATATTACTCCTCCAT+TGG 0.466815 4_1:+82539205 None:intergenic
ACTAATTATTTAATATGAGA+TGG 0.467564 4_1:+82538375 None:intergenic
CTCAAATTAACACAAGGTTC+TGG 0.471060 4_1:+82538624 None:intergenic
ACAGTGTATTGATCATATAA+TGG 0.475067 4_1:-82538508 Msa0578090:CDS
TATTAAATAATTAGTTTCAT+CGG 0.475091 4_1:-82538367 Msa0578090:three_prime_UTR
TGTTCTTGTTCTTGTTCTTG+TGG 0.483186 4_1:+82538744 None:intergenic
AATGTTAGATGTGAAATTGA+TGG 0.491247 4_1:+82539179 None:intergenic
ATATAATGGCAGAGAGAAAA+CGG 0.495978 4_1:-82538494 Msa0578090:CDS
AAAACTAATCAACAAATCAA+TGG 0.499326 4_1:-82538555 Msa0578090:CDS
ACACAAGGTTCTGGTGTAGC+TGG 0.499575 4_1:+82538633 None:intergenic
CAAATCAATGGAGCTAAGAA+AGG 0.524101 4_1:-82538543 Msa0578090:CDS
ATTCCAAAACATTGATCCAA+TGG 0.536922 4_1:-82539221 None:intergenic
ATGTTAGATGTGAAATTGAT+GGG 0.540365 4_1:+82539180 None:intergenic
TACTATTCCTGGCTTGAGCA+AGG 0.585542 4_1:-82538433 Msa0578090:CDS
TATAGAGTGTAAATGACTAT+GGG 0.585936 4_1:+82539145 None:intergenic
AATTATTTAATATGAGATGG+AGG 0.603927 4_1:+82538378 None:intergenic
CTAGAACTCAAATTAACACA+AGG 0.614675 4_1:+82538618 None:intergenic
GTGTTGTAGGAATTGGATTG+CGG 0.620465 4_1:-82538921 Msa0578090:intron
CCAAAACATTGATCCAATGG+AGG 0.635641 4_1:-82539218 Msa0578090:five_prime_UTR
CAAGAACAAGAACAACAACA+TGG 0.670092 4_1:-82538735 Msa0578090:CDS
TGTTAGATGTGAAATTGATG+GGG 0.703761 4_1:+82539181 None:intergenic
TTTGGAGAAGAACCTTTACG+AGG 0.704448 4_1:+82538693 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTAAATAATTAGTTTCAT+CGG - chr4_1:82539202-82539221 Msa0578090:five_prime_UTR 10.0%
!!! TATTAAATAATTAGTTTCAT+CGG - chr4_1:82539202-82539221 Msa0578090:five_prime_UTR 10.0%
!! ACTAATTATTTAATATGAGA+TGG + chr4_1:82539197-82539216 None:intergenic 15.0%
!! ACTAATTATTTAATATGAGA+TGG + chr4_1:82539197-82539216 None:intergenic 15.0%
!!! TATATAATTTTGTGTGTTGT+AGG - chr4_1:82538635-82538654 Msa0578090:CDS 20.0%
!! AAAACTAATCAACAAATCAA+TGG - chr4_1:82539014-82539033 Msa0578090:intron 20.0%
!! AATTATTTAATATGAGATGG+AGG + chr4_1:82539194-82539213 None:intergenic 20.0%
!!! TATATAATTTTGTGTGTTGT+AGG - chr4_1:82538635-82538654 Msa0578090:CDS 20.0%
!! AAAACTAATCAACAAATCAA+TGG - chr4_1:82539014-82539033 Msa0578090:intron 20.0%
!! AATTATTTAATATGAGATGG+AGG + chr4_1:82539194-82539213 None:intergenic 20.0%
! ATGTTAGATGTGAAATTGAT+GGG + chr4_1:82538392-82538411 None:intergenic 25.0%
! AATGTTAGATGTGAAATTGA+TGG + chr4_1:82538393-82538412 None:intergenic 25.0%
! TATAGAGTGTAAATGACTAT+GGG + chr4_1:82538427-82538446 None:intergenic 25.0%
! ATATAGAGTGTAAATGACTA+TGG + chr4_1:82538428-82538447 None:intergenic 25.0%
!!! ATGTTTTTTATTTGCACAAG+AGG + chr4_1:82538467-82538486 None:intergenic 25.0%
!! ACATGGTTTGAAATCAAAAA+AGG - chr4_1:82538851-82538870 Msa0578090:CDS 25.0%
! AAAGACAAAATGTATGTCTT+TGG + chr4_1:82538897-82538916 None:intergenic 25.0%
!! ACAGTGTATTGATCATATAA+TGG - chr4_1:82539061-82539080 Msa0578090:five_prime_UTR 25.0%
! GGAGGTAGTATAATTTATTA+GGG + chr4_1:82539176-82539195 None:intergenic 25.0%
! TGGAGGTAGTATAATTTATT+AGG + chr4_1:82539177-82539196 None:intergenic 25.0%
! ATGTTAGATGTGAAATTGAT+GGG + chr4_1:82538392-82538411 None:intergenic 25.0%
! AATGTTAGATGTGAAATTGA+TGG + chr4_1:82538393-82538412 None:intergenic 25.0%
! TATAGAGTGTAAATGACTAT+GGG + chr4_1:82538427-82538446 None:intergenic 25.0%
! ATATAGAGTGTAAATGACTA+TGG + chr4_1:82538428-82538447 None:intergenic 25.0%
!!! ATGTTTTTTATTTGCACAAG+AGG + chr4_1:82538467-82538486 None:intergenic 25.0%
!! ACATGGTTTGAAATCAAAAA+AGG - chr4_1:82538851-82538870 Msa0578090:CDS 25.0%
! AAAGACAAAATGTATGTCTT+TGG + chr4_1:82538897-82538916 None:intergenic 25.0%
!! ACAGTGTATTGATCATATAA+TGG - chr4_1:82539061-82539080 Msa0578090:five_prime_UTR 25.0%
! GGAGGTAGTATAATTTATTA+GGG + chr4_1:82539176-82539195 None:intergenic 25.0%
! TGGAGGTAGTATAATTTATT+AGG + chr4_1:82539177-82539196 None:intergenic 25.0%
TGTTAGATGTGAAATTGATG+GGG + chr4_1:82538391-82538410 None:intergenic 30.0%
! AGCTCAATTCAATTTTCCAA+TGG - chr4_1:82538518-82538537 Msa0578090:CDS 30.0%
! TCAATTCAATTTTCCAATGG+AGG - chr4_1:82538521-82538540 Msa0578090:CDS 30.0%
! ATTTTGTGTGTTGTAGGAAT+TGG - chr4_1:82538641-82538660 Msa0578090:CDS 30.0%
!!! TTTTGATGTTGTTGGTAACA+TGG - chr4_1:82538758-82538777 Msa0578090:CDS 30.0%
CTAGAACTCAAATTAACACA+AGG + chr4_1:82538954-82538973 None:intergenic 30.0%
! CTTGTGTTAATTTGAGTTCT+AGG - chr4_1:82538952-82538971 Msa0578090:intron 30.0%
ATATAATGGCAGAGAGAAAA+CGG - chr4_1:82539075-82539094 Msa0578090:five_prime_UTR 30.0%
TGTTAGATGTGAAATTGATG+GGG + chr4_1:82538391-82538410 None:intergenic 30.0%
! AGCTCAATTCAATTTTCCAA+TGG - chr4_1:82538518-82538537 Msa0578090:CDS 30.0%
! TCAATTCAATTTTCCAATGG+AGG - chr4_1:82538521-82538540 Msa0578090:CDS 30.0%
! ATTTTGTGTGTTGTAGGAAT+TGG - chr4_1:82538641-82538660 Msa0578090:CDS 30.0%
!!! TTTTGATGTTGTTGGTAACA+TGG - chr4_1:82538758-82538777 Msa0578090:CDS 30.0%
CTAGAACTCAAATTAACACA+AGG + chr4_1:82538954-82538973 None:intergenic 30.0%
! CTTGTGTTAATTTGAGTTCT+AGG - chr4_1:82538952-82538971 Msa0578090:intron 30.0%
ATATAATGGCAGAGAGAAAA+CGG - chr4_1:82539075-82539094 Msa0578090:five_prime_UTR 30.0%
CAATGATATTACTCCTCCAT+TGG + chr4_1:82538367-82538386 None:intergenic 35.0%
! GGGAAATTTTCATCTTGACA+TGG - chr4_1:82538551-82538570 Msa0578090:CDS 35.0%
AATCATCATCGTCAGTGTTA+AGG + chr4_1:82538704-82538723 None:intergenic 35.0%
CCAACAACATCAAAACTTTC+TGG + chr4_1:82538753-82538772 None:intergenic 35.0%
!! CCAGAAAGTTTTGATGTTGT+TGG - chr4_1:82538750-82538769 Msa0578090:CDS 35.0%
TGTTCTTGTTCTTGTTCTTG+TGG + chr4_1:82538828-82538847 None:intergenic 35.0%
CAAGAACAAGAACAACAACA+TGG - chr4_1:82538834-82538853 Msa0578090:CDS 35.0%
TCAAAAAAGGTTCCTCGTAA+AGG - chr4_1:82538864-82538883 Msa0578090:CDS 35.0%
CTCAAATTAACACAAGGTTC+TGG + chr4_1:82538948-82538967 None:intergenic 35.0%
!!! CAGCTTTTTGAGTACTTTCA+CGG + chr4_1:82538989-82539008 None:intergenic 35.0%
CAAATCAATGGAGCTAAGAA+AGG - chr4_1:82539026-82539045 Msa0578090:CDS 35.0%
CAATGATATTACTCCTCCAT+TGG + chr4_1:82538367-82538386 None:intergenic 35.0%
! GGGAAATTTTCATCTTGACA+TGG - chr4_1:82538551-82538570 Msa0578090:CDS 35.0%
AATCATCATCGTCAGTGTTA+AGG + chr4_1:82538704-82538723 None:intergenic 35.0%
CCAACAACATCAAAACTTTC+TGG + chr4_1:82538753-82538772 None:intergenic 35.0%
!! CCAGAAAGTTTTGATGTTGT+TGG - chr4_1:82538750-82538769 Msa0578090:CDS 35.0%
TGTTCTTGTTCTTGTTCTTG+TGG + chr4_1:82538828-82538847 None:intergenic 35.0%
CAAGAACAAGAACAACAACA+TGG - chr4_1:82538834-82538853 Msa0578090:CDS 35.0%
TCAAAAAAGGTTCCTCGTAA+AGG - chr4_1:82538864-82538883 Msa0578090:CDS 35.0%
CTCAAATTAACACAAGGTTC+TGG + chr4_1:82538948-82538967 None:intergenic 35.0%
!!! CAGCTTTTTGAGTACTTTCA+CGG + chr4_1:82538989-82539008 None:intergenic 35.0%
CAAATCAATGGAGCTAAGAA+AGG - chr4_1:82539026-82539045 Msa0578090:CDS 35.0%
! TTTTCCAATGGAGGAGTCAT+TGG - chr4_1:82538530-82538549 Msa0578090:CDS 40.0%
TTTCCAATGGAGGAGTCATT+GGG - chr4_1:82538531-82538550 Msa0578090:CDS 40.0%
GTGTTGTAGGAATTGGATTG+CGG - chr4_1:82538648-82538667 Msa0578090:CDS 40.0%
TTTGGAGAAGAACCTTTACG+AGG + chr4_1:82538879-82538898 None:intergenic 40.0%
! TTTTCCAATGGAGGAGTCAT+TGG - chr4_1:82538530-82538549 Msa0578090:CDS 40.0%
TTTCCAATGGAGGAGTCATT+GGG - chr4_1:82538531-82538550 Msa0578090:CDS 40.0%
GTGTTGTAGGAATTGGATTG+CGG - chr4_1:82538648-82538667 Msa0578090:CDS 40.0%
TTTGGAGAAGAACCTTTACG+AGG + chr4_1:82538879-82538898 None:intergenic 40.0%
TTTCCCAATGACTCCTCCAT+TGG + chr4_1:82538537-82538556 None:intergenic 45.0%
GCACTTTCAGCTACTATTCC+TGG - chr4_1:82539125-82539144 Msa0578090:five_prime_UTR 45.0%
! TACTATTCCTGGCTTGAGCA+AGG - chr4_1:82539136-82539155 Msa0578090:five_prime_UTR 45.0%
CAATTTACCTTGCTCAAGCC+AGG + chr4_1:82539146-82539165 None:intergenic 45.0%
! CTGGCTTGAGCAAGGTAAAT+TGG - chr4_1:82539144-82539163 Msa0578090:five_prime_UTR 45.0%
TTTCCCAATGACTCCTCCAT+TGG + chr4_1:82538537-82538556 None:intergenic 45.0%
GCACTTTCAGCTACTATTCC+TGG - chr4_1:82539125-82539144 Msa0578090:five_prime_UTR 45.0%
! TACTATTCCTGGCTTGAGCA+AGG - chr4_1:82539136-82539155 Msa0578090:five_prime_UTR 45.0%
CAATTTACCTTGCTCAAGCC+AGG + chr4_1:82539146-82539165 None:intergenic 45.0%
! CTGGCTTGAGCAAGGTAAAT+TGG - chr4_1:82539144-82539163 Msa0578090:five_prime_UTR 45.0%
! ACACAAGGTTCTGGTGTAGC+TGG + chr4_1:82538939-82538958 None:intergenic 50.0%
! ACACAAGGTTCTGGTGTAGC+TGG + chr4_1:82538939-82538958 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 82538353 82539238 82538353 ID=Msa0578090;Name=Msa0578090
chr4_1 mRNA 82538353 82539238 82538353 ID=Msa0578090-mRNA-1;Parent=Msa0578090;Name=Msa0578090-mRNA-1;_AED=0.05;_eAED=0.05;_QI=184|1|1|1|1|1|2|69|182
chr4_1 exon 82538353 82538934 82538353 ID=Msa0578090-mRNA-1:exon:29930;Parent=Msa0578090-mRNA-1
chr4_1 exon 82539019 82539238 82539019 ID=Msa0578090-mRNA-1:exon:29929;Parent=Msa0578090-mRNA-1
chr4_1 five_prime_UTR 82539055 82539238 82539055 ID=Msa0578090-mRNA-1:five_prime_utr;Parent=Msa0578090-mRNA-1
chr4_1 CDS 82539019 82539054 82539019 ID=Msa0578090-mRNA-1:cds;Parent=Msa0578090-mRNA-1
chr4_1 CDS 82538422 82538934 82538422 ID=Msa0578090-mRNA-1:cds;Parent=Msa0578090-mRNA-1
chr4_1 three_prime_UTR 82538353 82538421 82538353 ID=Msa0578090-mRNA-1:three_prime_utr;Parent=Msa0578090-mRNA-1
Gene Sequence

>Msa0578090

ATGGAGGAGTCATTGGGAAATTTTCATCTTGACATGGAATTGGATTGCGGTGATGATTATTTCATAGATGATTGTAACAACCTTAACACTGACGATGATGATTTTCTTAGAGAGATTTTGTTACAAACACCAGAAAGTTTTGATGTTGTTGGTAACATGGTTAAAAGTAACAGTTCAAACTCAATTGTGTCTCAACAACATCAACCACAAGAACAAGAACAAGAACAACAACATGGTTTGAAATCAAAAAAGGTTCCTCGTAAAGGTTCTTCTCCAAAGACATACATTTTGTCTTTTGACAATTCAACTATGATACCAGCTACACCAGAACCTTGTGTTAATTTGAGTTCTAGGAATAAACGTAGCCGTGAAAGTACTCAAAAAGCTGAAGTGAAAACTAATCAACAAATCAATGGAGCTAAGAAAGGTAGAAGCAGTTCACAGTGTATTGATCATATAATGGCAGAGAGAAAACGGAGACAAGAATTGTCTGAGAAATTCATTGCACTTTCAGCTACTATTCCTGGCTTGAGCAAGGTAAATTGGTAA

Protein sequence

>Msa0578090

MEESLGNFHLDMELDCGDDYFIDDCNNLNTDDDDFLREILLQTPESFDVVGNMVKSNSSNSIVSQQHQPQEQEQEQQHGLKSKKVPRKGSSPKTYILSFDNSTMIPATPEPCVNLSSRNKRSRESTQKAEVKTNQQINGAKKGRSSSQCIDHIMAERKRRQELSEKFIALSATIPGLSKVNW*