AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0714600


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0714600 MtrunA17_Chr5g0401881 97.619 84 2 0 1 84 141 224 1.96e-53 165
Msa0714600 MtrunA17_Chr4g0044531 69.512 82 25 0 1 82 138 219 5.36e-39 128
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0714600 AT4G34120.1 72.289 83 23 0 1 83 155 237 4.14e-41 134
Msa0714600 AT4G36910.1 72.619 84 23 0 1 84 153 236 2.25e-40 132

Find 31 sgRNAs with CRISPR-Local

Find 101 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGAATTAGAAGTAAAATTT+TGG 0.185158 5_1:+7220973 Msa0714600:three_prime_UTR
AATCCTATCATGCTTTCTTT+TGG 0.275870 5_1:-7220877 None:intergenic
GAAATCAAACAACAAATCTT+TGG 0.298554 5_1:-7220912 None:intergenic
TCCGAATGTTCACATTGATA+AGG 0.418921 5_1:+7221056 Msa0714600:three_prime_UTR
CAGCCAAAAGAAAGCATGAT+AGG 0.423036 5_1:+7220874 Msa0714600:exon
TCCTTATCAATGTGAACATT+CGG 0.451797 5_1:-7221057 None:intergenic
ATTGATGACCACTGCTCCTA+TGG 0.465013 5_1:+7220429 Msa0714600:CDS
CTACCCTCAGCATCTACAAC+TGG 0.468514 5_1:-7220701 None:intergenic
TGTAGATGCTGAGGGTAGAT+TGG 0.480195 5_1:+7220706 Msa0714600:CDS
TAATCATGTTCCACGGGCTA+AGG 0.497927 5_1:+7221122 Msa0714600:three_prime_UTR
CCTAGCAGCATCCTCAAGAT+TGG 0.497947 5_1:-7220467 None:intergenic
GATTGCTGAGTAAGACCAAC+GGG 0.500361 5_1:+7220392 Msa0714600:CDS
GTTGTATTAATCATGTTCCA+CGG 0.528897 5_1:+7221115 Msa0714600:three_prime_UTR
TTGTATTAATCATGTTCCAC+GGG 0.546451 5_1:+7221116 Msa0714600:three_prime_UTR
GTGGTCTCGCGAACAACCAT+AGG 0.552213 5_1:-7220445 None:intergenic
AGCAGCATCCTCAAGATTGG+TGG 0.555993 5_1:-7220464 None:intergenic
AAGACCAACGGGAAGGTGAT+CGG 0.559075 5_1:+7220403 Msa0714600:CDS
TCGCGAGACCACCAATCTTG+AGG 0.577555 5_1:+7220456 Msa0714600:CDS
TTCACCGATCACCTTCCCGT+TGG 0.578952 5_1:-7220407 None:intergenic
CCTTCCAGTTGTAGATGCTG+AGG 0.595431 5_1:+7220697 Msa0714600:CDS
CCAATCTTGAGGATGCTGCT+AGG 0.597922 5_1:+7220467 Msa0714600:CDS
CACATTGATAAGGACCACCT+TGG 0.607291 5_1:+7221066 Msa0714600:three_prime_UTR
CTTGAATTATCCTTAGCCCG+TGG 0.622195 5_1:-7221132 None:intergenic
CTTCCAGTTGTAGATGCTGA+GGG 0.623183 5_1:+7220698 Msa0714600:CDS
CCTCAGCATCTACAACTGGA+AGG 0.651284 5_1:-7220697 None:intergenic
GCGAACAACCATAGGAGCAG+TGG 0.657026 5_1:-7220437 None:intergenic
GCTGAGTAAGACCAACGGGA+AGG 0.657142 5_1:+7220396 Msa0714600:CDS
AAGGTTGGGATTATCACTAG+AGG 0.659792 5_1:+7220815 Msa0714600:intron
TTTCAACATCATTATCACCA+AGG 0.662460 5_1:-7221083 None:intergenic
AGATTGCTGAGTAAGACCAA+CGG 0.671463 5_1:+7220391 Msa0714600:CDS
CAACATCATTATCACCAAGG+TGG 0.699176 5_1:-7221080 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTGTTTTCACTATTTAATTA+AGG + chr5_1:7220547-7220566 Msa0714600:intron 15.0%
!!! TTGAATTAGAAGTAAAATTT+TGG + chr5_1:7220973-7220992 Msa0714600:three_prime_UTR 15.0%
!!! TTGTTTTCACTATTTAATTA+AGG + chr5_1:7220547-7220566 Msa0714600:intron 15.0%
!!! TTGAATTAGAAGTAAAATTT+TGG + chr5_1:7220973-7220992 Msa0714600:three_prime_UTR 15.0%
!! TGATGAAAAATATTCAACAA+AGG - chr5_1:7220649-7220668 None:intergenic 20.0%
!! TGATGAAAAATATTCAACAA+AGG - chr5_1:7220649-7220668 None:intergenic 20.0%
! ACAAACATGAAAACAATGAA+AGG - chr5_1:7220767-7220786 None:intergenic 25.0%
!! CATTGTTTTCATGTTTGTAA+AGG + chr5_1:7220769-7220788 Msa0714600:intron 25.0%
!!! TGTTTTTATGTGATACATGA+AGG + chr5_1:7220796-7220815 Msa0714600:intron 25.0%
! GAAATCAAACAACAAATCTT+TGG - chr5_1:7220915-7220934 None:intergenic 25.0%
!!! TAGAAGTAAAATTTTGGCTT+AGG + chr5_1:7220979-7220998 Msa0714600:three_prime_UTR 25.0%
! ACAAACATGAAAACAATGAA+AGG - chr5_1:7220767-7220786 None:intergenic 25.0%
!! CATTGTTTTCATGTTTGTAA+AGG + chr5_1:7220769-7220788 Msa0714600:intron 25.0%
!!! TGTTTTTATGTGATACATGA+AGG + chr5_1:7220796-7220815 Msa0714600:intron 25.0%
! GAAATCAAACAACAAATCTT+TGG - chr5_1:7220915-7220934 None:intergenic 25.0%
!!! TAGAAGTAAAATTTTGGCTT+AGG + chr5_1:7220979-7220998 Msa0714600:three_prime_UTR 25.0%
ATGACACGCATAAAATTCAA+CGG - chr5_1:7220593-7220612 None:intergenic 30.0%
! ATTTTTCATCAGATTGTTGC+TGG + chr5_1:7220658-7220677 Msa0714600:intron 30.0%
TTTATGTGATACATGAAGGT+TGG + chr5_1:7220800-7220819 Msa0714600:intron 30.0%
TTATGTGATACATGAAGGTT+GGG + chr5_1:7220801-7220820 Msa0714600:intron 30.0%
! AATCCTATCATGCTTTCTTT+TGG - chr5_1:7220880-7220899 None:intergenic 30.0%
TCCTTATCAATGTGAACATT+CGG - chr5_1:7221060-7221079 None:intergenic 30.0%
TTTCAACATCATTATCACCA+AGG - chr5_1:7221086-7221105 None:intergenic 30.0%
GTTGTATTAATCATGTTCCA+CGG + chr5_1:7221115-7221134 Msa0714600:three_prime_UTR 30.0%
TTGTATTAATCATGTTCCAC+GGG + chr5_1:7221116-7221135 Msa0714600:three_prime_UTR 30.0%
ATGACACGCATAAAATTCAA+CGG - chr5_1:7220593-7220612 None:intergenic 30.0%
! ATTTTTCATCAGATTGTTGC+TGG + chr5_1:7220658-7220677 Msa0714600:intron 30.0%
TTTATGTGATACATGAAGGT+TGG + chr5_1:7220800-7220819 Msa0714600:intron 30.0%
TTATGTGATACATGAAGGTT+GGG + chr5_1:7220801-7220820 Msa0714600:intron 30.0%
! AATCCTATCATGCTTTCTTT+TGG - chr5_1:7220880-7220899 None:intergenic 30.0%
TCCTTATCAATGTGAACATT+CGG - chr5_1:7221060-7221079 None:intergenic 30.0%
TTTCAACATCATTATCACCA+AGG - chr5_1:7221086-7221105 None:intergenic 30.0%
GTTGTATTAATCATGTTCCA+CGG + chr5_1:7221115-7221134 Msa0714600:three_prime_UTR 30.0%
TTGTATTAATCATGTTCCAC+GGG + chr5_1:7221116-7221135 Msa0714600:three_prime_UTR 30.0%
TTCAAAATGAACAGACACCA+AGG - chr5_1:7220508-7220527 None:intergenic 35.0%
GCATAAAATTCAACGGTTTG+AGG - chr5_1:7220586-7220605 None:intergenic 35.0%
CCAAAGATAACAGAAGAAAG+GGG - chr5_1:7220739-7220758 None:intergenic 35.0%
CCCAAAGATAACAGAAGAAA+GGG - chr5_1:7220740-7220759 None:intergenic 35.0%
CCCTTTCTTCTGTTATCTTT+GGG + chr5_1:7220737-7220756 Msa0714600:intron 35.0%
ACCCAAAGATAACAGAAGAA+AGG - chr5_1:7220741-7220760 None:intergenic 35.0%
TCCGAATGTTCACATTGATA+AGG + chr5_1:7221056-7221075 Msa0714600:three_prime_UTR 35.0%
AACTTCATTGAAAGTCTGCA+TGG - chr5_1:7220368-7220387 None:intergenic 35.0%
TTCAAAATGAACAGACACCA+AGG - chr5_1:7220508-7220527 None:intergenic 35.0%
GCATAAAATTCAACGGTTTG+AGG - chr5_1:7220586-7220605 None:intergenic 35.0%
CCAAAGATAACAGAAGAAAG+GGG - chr5_1:7220739-7220758 None:intergenic 35.0%
CCCAAAGATAACAGAAGAAA+GGG - chr5_1:7220740-7220759 None:intergenic 35.0%
CCCTTTCTTCTGTTATCTTT+GGG + chr5_1:7220737-7220756 Msa0714600:intron 35.0%
ACCCAAAGATAACAGAAGAA+AGG - chr5_1:7220741-7220760 None:intergenic 35.0%
TCCGAATGTTCACATTGATA+AGG + chr5_1:7221056-7221075 Msa0714600:three_prime_UTR 35.0%
AGATTGCTGAGTAAGACCAA+CGG + chr5_1:7220391-7220410 Msa0714600:CDS 40.0%
! GGTTCTTCTATCCTTTTCCT+TGG + chr5_1:7220488-7220507 Msa0714600:intron 40.0%
ATGAACAGACACCAAGGAAA+AGG - chr5_1:7220502-7220521 None:intergenic 40.0%
CCCCTTTCTTCTGTTATCTT+TGG + chr5_1:7220736-7220755 Msa0714600:intron 40.0%
AAGGTTGGGATTATCACTAG+AGG + chr5_1:7220815-7220834 Msa0714600:intron 40.0%
! CAGCCAAAAGAAAGCATGAT+AGG + chr5_1:7220874-7220893 Msa0714600:exon 40.0%
CAACATCATTATCACCAAGG+TGG - chr5_1:7221083-7221102 None:intergenic 40.0%
AGATTGCTGAGTAAGACCAA+CGG + chr5_1:7220391-7220410 Msa0714600:CDS 40.0%
! GGTTCTTCTATCCTTTTCCT+TGG + chr5_1:7220488-7220507 Msa0714600:intron 40.0%
ATGAACAGACACCAAGGAAA+AGG - chr5_1:7220502-7220521 None:intergenic 40.0%
CCCCTTTCTTCTGTTATCTT+TGG + chr5_1:7220736-7220755 Msa0714600:intron 40.0%
AAGGTTGGGATTATCACTAG+AGG + chr5_1:7220815-7220834 Msa0714600:intron 40.0%
! CAGCCAAAAGAAAGCATGAT+AGG + chr5_1:7220874-7220893 Msa0714600:exon 40.0%
CAACATCATTATCACCAAGG+TGG - chr5_1:7221083-7221102 None:intergenic 40.0%
GATTGCTGAGTAAGACCAAC+GGG + chr5_1:7220392-7220411 Msa0714600:CDS 45.0%
! ATTGATGACCACTGCTCCTA+TGG + chr5_1:7220429-7220448 Msa0714600:CDS 45.0%
CTTCCAGTTGTAGATGCTGA+GGG + chr5_1:7220698-7220717 Msa0714600:CDS 45.0%
TGTAGATGCTGAGGGTAGAT+TGG + chr5_1:7220706-7220725 Msa0714600:CDS 45.0%
CACATTGATAAGGACCACCT+TGG + chr5_1:7221066-7221085 Msa0714600:three_prime_UTR 45.0%
! TAATCATGTTCCACGGGCTA+AGG + chr5_1:7221122-7221141 Msa0714600:three_prime_UTR 45.0%
CTTGAATTATCCTTAGCCCG+TGG - chr5_1:7221135-7221154 None:intergenic 45.0%
GATTGCTGAGTAAGACCAAC+GGG + chr5_1:7220392-7220411 Msa0714600:CDS 45.0%
! ATTGATGACCACTGCTCCTA+TGG + chr5_1:7220429-7220448 Msa0714600:CDS 45.0%
CTTCCAGTTGTAGATGCTGA+GGG + chr5_1:7220698-7220717 Msa0714600:CDS 45.0%
TGTAGATGCTGAGGGTAGAT+TGG + chr5_1:7220706-7220725 Msa0714600:CDS 45.0%
CACATTGATAAGGACCACCT+TGG + chr5_1:7221066-7221085 Msa0714600:three_prime_UTR 45.0%
! TAATCATGTTCCACGGGCTA+AGG + chr5_1:7221122-7221141 Msa0714600:three_prime_UTR 45.0%
CTTGAATTATCCTTAGCCCG+TGG - chr5_1:7221135-7221154 None:intergenic 45.0%
AAGACCAACGGGAAGGTGAT+CGG + chr5_1:7220403-7220422 Msa0714600:CDS 50.0%
AGCAGCATCCTCAAGATTGG+TGG - chr5_1:7220467-7220486 None:intergenic 50.0%
CCTAGCAGCATCCTCAAGAT+TGG - chr5_1:7220470-7220489 None:intergenic 50.0%
CCAATCTTGAGGATGCTGCT+AGG + chr5_1:7220467-7220486 Msa0714600:CDS 50.0%
CCTCAGCATCTACAACTGGA+AGG - chr5_1:7220700-7220719 None:intergenic 50.0%
CCTTCCAGTTGTAGATGCTG+AGG + chr5_1:7220697-7220716 Msa0714600:CDS 50.0%
CTACCCTCAGCATCTACAAC+TGG - chr5_1:7220704-7220723 None:intergenic 50.0%
AAGACCAACGGGAAGGTGAT+CGG + chr5_1:7220403-7220422 Msa0714600:CDS 50.0%
AGCAGCATCCTCAAGATTGG+TGG - chr5_1:7220467-7220486 None:intergenic 50.0%
CCTAGCAGCATCCTCAAGAT+TGG - chr5_1:7220470-7220489 None:intergenic 50.0%
CCAATCTTGAGGATGCTGCT+AGG + chr5_1:7220467-7220486 Msa0714600:CDS 50.0%
CCTCAGCATCTACAACTGGA+AGG - chr5_1:7220700-7220719 None:intergenic 50.0%
CCTTCCAGTTGTAGATGCTG+AGG + chr5_1:7220697-7220716 Msa0714600:CDS 50.0%
CTACCCTCAGCATCTACAAC+TGG - chr5_1:7220704-7220723 None:intergenic 50.0%
GCTGAGTAAGACCAACGGGA+AGG + chr5_1:7220396-7220415 Msa0714600:CDS 55.0%
TTCACCGATCACCTTCCCGT+TGG - chr5_1:7220410-7220429 None:intergenic 55.0%
GCGAACAACCATAGGAGCAG+TGG - chr5_1:7220440-7220459 None:intergenic 55.0%
GTGGTCTCGCGAACAACCAT+AGG - chr5_1:7220448-7220467 None:intergenic 55.0%
TCGCGAGACCACCAATCTTG+AGG + chr5_1:7220456-7220475 Msa0714600:CDS 55.0%
GCTGAGTAAGACCAACGGGA+AGG + chr5_1:7220396-7220415 Msa0714600:CDS 55.0%
TTCACCGATCACCTTCCCGT+TGG - chr5_1:7220410-7220429 None:intergenic 55.0%
GCGAACAACCATAGGAGCAG+TGG - chr5_1:7220440-7220459 None:intergenic 55.0%
GTGGTCTCGCGAACAACCAT+AGG - chr5_1:7220448-7220467 None:intergenic 55.0%
TCGCGAGACCACCAATCTTG+AGG + chr5_1:7220456-7220475 Msa0714600:CDS 55.0%
Chromosome Type Strat End Strand Name
chr5_1 gene 7220367 7221183 7220367 ID=Msa0714600;Name=Msa0714600
chr5_1 mRNA 7220367 7221183 7220367 ID=Msa0714600-mRNA-1;Parent=Msa0714600;Name=Msa0714600-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|1|0.66|1|1|1|3|291|84
chr5_1 exon 7220367 7220488 7220367 ID=Msa0714600-mRNA-1:exon:3030;Parent=Msa0714600-mRNA-1
chr5_1 exon 7220670 7220727 7220670 ID=Msa0714600-mRNA-1:exon:3031;Parent=Msa0714600-mRNA-1
chr5_1 exon 7220818 7221183 7220818 ID=Msa0714600-mRNA-1:exon:3032;Parent=Msa0714600-mRNA-1
chr5_1 CDS 7220367 7220488 7220367 ID=Msa0714600-mRNA-1:cds;Parent=Msa0714600-mRNA-1
chr5_1 CDS 7220670 7220727 7220670 ID=Msa0714600-mRNA-1:cds;Parent=Msa0714600-mRNA-1
chr5_1 CDS 7220818 7220892 7220818 ID=Msa0714600-mRNA-1:cds;Parent=Msa0714600-mRNA-1
chr5_1 three_prime_UTR 7220893 7221183 7220893 ID=Msa0714600-mRNA-1:three_prime_utr;Parent=Msa0714600-mRNA-1
Gene Sequence

>Msa0714600

ATGCAGACTTTCAATGAAGTTCAGAGATTGCTGAGTAAGACCAACGGGAAGGTGATCGGTGAATTGATGACCACTGCTCCTATGGTTGTTCGCGAGACCACCAATCTTGAGGATGCTGCTAGATTGTTGCTGGAAACAAAATTTCGACGCCTTCCAGTTGTAGATGCTGAGGGTAGATTGGTTGGGATTATCACTAGAGGAAATGTTGTAAGAGCTGCGCTTCAAATGAAACGAGACAGCCAAAAGAAAGCATGA

Protein sequence

>Msa0714600

MQTFNEVQRLLSKTNGKVIGELMTTAPMVVRETTNLEDAARLLLETKFRRLPVVDAEGRLVGIITRGNVVRAALQMKRDSQKKA*