AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0841730


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0841730 MtrunA17_Chr5g0441261 94.231 104 6 0 1 104 1 104 4.26e-67 196
Msa0841730 MtrunA17_Chr3g0093771 62.000 100 35 1 1 100 25 121 1.61e-38 125
Msa0841730 MtrunA17_Chr8g0354141 50.476 105 50 2 1 104 38 141 1.70e-31 110
Msa0841730 MtrunA17_Chr3g0097041 46.000 100 51 1 4 103 62 158 2.65e-21 82.8
Msa0841730 MtrunA17_Chr4g0076001 37.647 85 52 1 5 89 29 112 1.18e-14 64.3
Msa0841730 MtrunA17_Chr7g0255521 50.980 51 25 0 11 61 39 89 5.93e-11 54.7
Msa0841730 MtrunA17_Chr3g0096881 45.902 61 33 0 20 80 78 138 8.66e-11 56.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0841730 AT3G12490.1 54.808 104 44 1 1 104 1 101 2.40e-35 118
Msa0841730 AT3G12490.2 54.808 104 44 1 1 104 34 134 2.65e-34 118
Msa0841730 AT2G40880.1 51.163 86 42 0 4 89 35 120 2.06e-27 97.4
Msa0841730 AT5G05110.1 51.064 94 45 1 4 96 45 138 8.52e-27 99.0
Msa0841730 AT5G12140.1 47.126 87 46 0 4 90 10 96 3.26e-25 91.3
Msa0841730 AT4G16500.2 44.444 72 39 1 22 92 46 117 1.06e-13 62.4
Msa0841730 AT4G16500.1 44.444 72 39 1 22 92 46 117 1.06e-13 62.4

Find 23 sgRNAs with CRISPR-Local

Find 118 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAGAAGGAGCATCGTAATTT+TGG 0.195527 5_4:-18326871 None:intergenic
AAAGATAGAAATTAAATTAA+TGG 0.234510 5_4:+18325437 Msa0841730:exon
GCAAAGAAGCAAGTGGTTTC+TGG 0.255766 5_4:+18326728 Msa0841730:CDS
CCATAGCTTCTCTAAAATCT+TGG 0.357443 5_4:-18326810 None:intergenic
GAAGCTATGGTTGAACTTCA+AGG 0.441137 5_4:+18326823 Msa0841730:CDS
TCAAGAACACAATATCAAAC+AGG 0.464934 5_4:+18325536 Msa0841730:CDS
CTCTAAAGTGATGTCGTACA+AGG 0.516796 5_4:-18326753 None:intergenic
GTTGAACTTCAAGGAGGTGC+AGG 0.521993 5_4:+18326832 Msa0841730:CDS
ATTAAATTAATGGCGACTCT+AGG 0.533183 5_4:+18325447 Msa0841730:exon
AATGGATGGTGGGAAGCAAA+AGG 0.558878 5_4:+18326778 Msa0841730:CDS
CTTTAGAGACAATGGATGGT+GGG 0.567845 5_4:+18326768 Msa0841730:CDS
CGACATCACTTTAGAGACAA+TGG 0.568752 5_4:+18326760 Msa0841730:CDS
CTTGAACAGCAAAGATAGCA+AGG 0.570675 5_4:-18325518 None:intergenic
ATGCAGTTCTAGAGTTTGTG+AGG 0.589311 5_4:+18326696 Msa0841730:CDS
TCTAGGTGGTAGCACTGAGG+TGG 0.608936 5_4:+18325464 Msa0841730:CDS
ACTTTAGAGACAATGGATGG+TGG 0.617779 5_4:+18326767 Msa0841730:CDS
GTTAAATGCAAAGAAGCAAG+TGG 0.625710 5_4:+18326721 Msa0841730:CDS
AACTAAGTGCTAGATACAGA+AGG 0.629142 5_4:-18326887 None:intergenic
TGCAGTTCTAGAGTTTGTGA+GGG 0.629223 5_4:+18326697 Msa0841730:CDS
AAATTAATGGCGACTCTAGG+TGG 0.639281 5_4:+18325450 Msa0841730:exon
ATCACTTTAGAGACAATGGA+TGG 0.646105 5_4:+18326764 Msa0841730:CDS
GACTCTAGGTGGTAGCACTG+AGG 0.714011 5_4:+18325461 Msa0841730:CDS
GCTATGGTTGAACTTCAAGG+AGG 0.769675 5_4:+18326826 Msa0841730:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATATATATATATATATAT+AGG + chr5_4:18326148-18326167 Msa0841730:intron 0.0%
!! ATATATATATATATATATAT+AGG + chr5_4:18326148-18326167 Msa0841730:intron 0.0%
!! AAAGATAGAAATTAAATTAA+TGG + chr5_4:18325437-18325456 Msa0841730:exon 10.0%
!! ATAAATGAACATTAAATAAA+TGG + chr5_4:18325910-18325929 Msa0841730:intron 10.0%
!! AACTTATTCATAATTTATTA+GGG - chr5_4:18326114-18326133 None:intergenic 10.0%
!! TAACTTATTCATAATTTATT+AGG - chr5_4:18326115-18326134 None:intergenic 10.0%
!! TTAATCTAACTAAAATTAAT+TGG + chr5_4:18326616-18326635 Msa0841730:intron 10.0%
!! AAAGATAGAAATTAAATTAA+TGG + chr5_4:18325437-18325456 Msa0841730:exon 10.0%
!! ATAAATGAACATTAAATAAA+TGG + chr5_4:18325910-18325929 Msa0841730:intron 10.0%
!! AACTTATTCATAATTTATTA+GGG - chr5_4:18326114-18326133 None:intergenic 10.0%
!! TAACTTATTCATAATTTATT+AGG - chr5_4:18326115-18326134 None:intergenic 10.0%
!! TTAATCTAACTAAAATTAAT+TGG + chr5_4:18326616-18326635 Msa0841730:intron 10.0%
!!! TTCTATACTATATTTTACAA+AGG - chr5_4:18325635-18325654 None:intergenic 15.0%
!! ACTTATTCATAATTTATTAG+GGG - chr5_4:18326113-18326132 None:intergenic 15.0%
!! ATGAATAAGTTATTAACATT+TGG + chr5_4:18326123-18326142 Msa0841730:intron 15.0%
!! TAATCATTAATATAACGATT+TGG - chr5_4:18326284-18326303 None:intergenic 15.0%
!!! TTCTATACTATATTTTACAA+AGG - chr5_4:18325635-18325654 None:intergenic 15.0%
!! ACTTATTCATAATTTATTAG+GGG - chr5_4:18326113-18326132 None:intergenic 15.0%
!! ATGAATAAGTTATTAACATT+TGG + chr5_4:18326123-18326142 Msa0841730:intron 15.0%
!! TAATCATTAATATAACGATT+TGG - chr5_4:18326284-18326303 None:intergenic 15.0%
!! TTAATGTTTATCTCTTTACA+CGG - chr5_4:18325824-18325843 None:intergenic 20.0%
!! TGAGATTCACTTATTAAAAA+GGG + chr5_4:18325854-18325873 Msa0841730:intron 20.0%
!! ATATATATAGGCAAATTCTA+TGG + chr5_4:18326228-18326247 Msa0841730:intron 20.0%
!! ACTCAAATGCATATATATTA+TGG + chr5_4:18326470-18326489 Msa0841730:intron 20.0%
!! TTAATGTTTATCTCTTTACA+CGG - chr5_4:18325824-18325843 None:intergenic 20.0%
!! TGAGATTCACTTATTAAAAA+GGG + chr5_4:18325854-18325873 Msa0841730:intron 20.0%
!! ATATATATAGGCAAATTCTA+TGG + chr5_4:18326228-18326247 Msa0841730:intron 20.0%
!! ACTCAAATGCATATATATTA+TGG + chr5_4:18326470-18326489 Msa0841730:intron 20.0%
!! CTATATTTTACAAAGGAAAC+TGG - chr5_4:18325628-18325647 None:intergenic 25.0%
!!! GTTTTTTTTTTCCTTTGTAC+CGG + chr5_4:18325692-18325711 Msa0841730:intron 25.0%
!!! TTTTTTTTTTCCTTTGTACC+GGG + chr5_4:18325693-18325712 Msa0841730:intron 25.0%
!!! TTCAAAAGTACTAAGAGTTT+CGG - chr5_4:18325748-18325767 None:intergenic 25.0%
! GTGAGATTCACTTATTAAAA+AGG + chr5_4:18325853-18325872 Msa0841730:intron 25.0%
!! TATCATTGTATTAGTCTAGA+AGG + chr5_4:18326005-18326024 Msa0841730:intron 25.0%
!! CTATATTTTACAAAGGAAAC+TGG - chr5_4:18325628-18325647 None:intergenic 25.0%
!!! GTTTTTTTTTTCCTTTGTAC+CGG + chr5_4:18325692-18325711 Msa0841730:intron 25.0%
!!! TTTTTTTTTTCCTTTGTACC+GGG + chr5_4:18325693-18325712 Msa0841730:intron 25.0%
!!! TTCAAAAGTACTAAGAGTTT+CGG - chr5_4:18325748-18325767 None:intergenic 25.0%
! GTGAGATTCACTTATTAAAA+AGG + chr5_4:18325853-18325872 Msa0841730:intron 25.0%
!! TATCATTGTATTAGTCTAGA+AGG + chr5_4:18326005-18326024 Msa0841730:intron 25.0%
ATTAAATTAATGGCGACTCT+AGG + chr5_4:18325447-18325466 Msa0841730:exon 30.0%
TCAAGAACACAATATCAAAC+AGG + chr5_4:18325536-18325555 Msa0841730:CDS 30.0%
AGGACAGAACAAAATTGAAA+TGG - chr5_4:18325571-18325590 None:intergenic 30.0%
TTATCAAGCAAACAAAACAC+AGG - chr5_4:18325591-18325610 None:intergenic 30.0%
!! AATATAACGATTTGGTGTAC+CGG - chr5_4:18326276-18326295 None:intergenic 30.0%
!! TTTTATTTCGTCGAAGCTTT+TGG - chr5_4:18326375-18326394 None:intergenic 30.0%
ATTAAATTAATGGCGACTCT+AGG + chr5_4:18325447-18325466 Msa0841730:exon 30.0%
TCAAGAACACAATATCAAAC+AGG + chr5_4:18325536-18325555 Msa0841730:CDS 30.0%
AGGACAGAACAAAATTGAAA+TGG - chr5_4:18325571-18325590 None:intergenic 30.0%
TTATCAAGCAAACAAAACAC+AGG - chr5_4:18325591-18325610 None:intergenic 30.0%
!! AATATAACGATTTGGTGTAC+CGG - chr5_4:18326276-18326295 None:intergenic 30.0%
!! TTTTATTTCGTCGAAGCTTT+TGG - chr5_4:18326375-18326394 None:intergenic 30.0%
AAATCGATCATGAAATGACC+CGG - chr5_4:18325714-18325733 None:intergenic 35.0%
ACCCAAAAATTTGAGTGTAC+CGG + chr5_4:18326254-18326273 Msa0841730:intron 35.0%
! ACCGGTACACTCAAATTTTT+GGG - chr5_4:18326258-18326277 None:intergenic 35.0%
! TACCGGTACACTCAAATTTT+TGG - chr5_4:18326259-18326278 None:intergenic 35.0%
GTTAAATGCAAAGAAGCAAG+TGG + chr5_4:18326721-18326740 Msa0841730:CDS 35.0%
! ATCACTTTAGAGACAATGGA+TGG + chr5_4:18326764-18326783 Msa0841730:CDS 35.0%
!! CCATAGCTTCTCTAAAATCT+TGG - chr5_4:18326813-18326832 None:intergenic 35.0%
!! CCAAGATTTTAGAGAAGCTA+TGG + chr5_4:18326810-18326829 Msa0841730:CDS 35.0%
AAATCGATCATGAAATGACC+CGG - chr5_4:18325714-18325733 None:intergenic 35.0%
ACCCAAAAATTTGAGTGTAC+CGG + chr5_4:18326254-18326273 Msa0841730:intron 35.0%
! ACCGGTACACTCAAATTTTT+GGG - chr5_4:18326258-18326277 None:intergenic 35.0%
! TACCGGTACACTCAAATTTT+TGG - chr5_4:18326259-18326278 None:intergenic 35.0%
GTTAAATGCAAAGAAGCAAG+TGG + chr5_4:18326721-18326740 Msa0841730:CDS 35.0%
! ATCACTTTAGAGACAATGGA+TGG + chr5_4:18326764-18326783 Msa0841730:CDS 35.0%
!! CCATAGCTTCTCTAAAATCT+TGG - chr5_4:18326813-18326832 None:intergenic 35.0%
!! CCAAGATTTTAGAGAAGCTA+TGG + chr5_4:18326810-18326829 Msa0841730:CDS 35.0%
AAATTAATGGCGACTCTAGG+TGG + chr5_4:18325450-18325469 Msa0841730:exon 40.0%
CTTGAACAGCAAAGATAGCA+AGG - chr5_4:18325521-18325540 None:intergenic 40.0%
!! AAGGAGTATCCAACTGGTTT+GGG + chr5_4:18326024-18326043 Msa0841730:intron 40.0%
GTGAAGGAGTTATATGCAGT+AGG + chr5_4:18326056-18326075 Msa0841730:intron 40.0%
CGTGACATAATAATGAGACG+TGG + chr5_4:18326557-18326576 Msa0841730:intron 40.0%
TTCTGCGCATTTAAGCATCA+AGG - chr5_4:18326677-18326696 None:intergenic 40.0%
!! ATGCAGTTCTAGAGTTTGTG+AGG + chr5_4:18326696-18326715 Msa0841730:CDS 40.0%
!! TGCAGTTCTAGAGTTTGTGA+GGG + chr5_4:18326697-18326716 Msa0841730:CDS 40.0%
!! CTCTAAAGTGATGTCGTACA+AGG - chr5_4:18326756-18326775 None:intergenic 40.0%
! CGACATCACTTTAGAGACAA+TGG + chr5_4:18326760-18326779 Msa0841730:CDS 40.0%
! ACTTTAGAGACAATGGATGG+TGG + chr5_4:18326767-18326786 Msa0841730:CDS 40.0%
! CTTTAGAGACAATGGATGGT+GGG + chr5_4:18326768-18326787 Msa0841730:CDS 40.0%
GAAGCTATGGTTGAACTTCA+AGG + chr5_4:18326823-18326842 Msa0841730:CDS 40.0%
!!! CAGAAGGAGCATCGTAATTT+TGG - chr5_4:18326874-18326893 None:intergenic 40.0%
AAATTAATGGCGACTCTAGG+TGG + chr5_4:18325450-18325469 Msa0841730:exon 40.0%
CTTGAACAGCAAAGATAGCA+AGG - chr5_4:18325521-18325540 None:intergenic 40.0%
!! AAGGAGTATCCAACTGGTTT+GGG + chr5_4:18326024-18326043 Msa0841730:intron 40.0%
GTGAAGGAGTTATATGCAGT+AGG + chr5_4:18326056-18326075 Msa0841730:intron 40.0%
CGTGACATAATAATGAGACG+TGG + chr5_4:18326557-18326576 Msa0841730:intron 40.0%
TTCTGCGCATTTAAGCATCA+AGG - chr5_4:18326677-18326696 None:intergenic 40.0%
!! ATGCAGTTCTAGAGTTTGTG+AGG + chr5_4:18326696-18326715 Msa0841730:CDS 40.0%
!! TGCAGTTCTAGAGTTTGTGA+GGG + chr5_4:18326697-18326716 Msa0841730:CDS 40.0%
!! CTCTAAAGTGATGTCGTACA+AGG - chr5_4:18326756-18326775 None:intergenic 40.0%
! CGACATCACTTTAGAGACAA+TGG + chr5_4:18326760-18326779 Msa0841730:CDS 40.0%
! ACTTTAGAGACAATGGATGG+TGG + chr5_4:18326767-18326786 Msa0841730:CDS 40.0%
! CTTTAGAGACAATGGATGGT+GGG + chr5_4:18326768-18326787 Msa0841730:CDS 40.0%
GAAGCTATGGTTGAACTTCA+AGG + chr5_4:18326823-18326842 Msa0841730:CDS 40.0%
!!! CAGAAGGAGCATCGTAATTT+TGG - chr5_4:18326874-18326893 None:intergenic 40.0%
CATGAAATGACCCGGTACAA+AGG - chr5_4:18325706-18325725 None:intergenic 45.0%
!! GTCTAGAAGGAGTATCCAAC+TGG + chr5_4:18326018-18326037 Msa0841730:intron 45.0%
!! GAAGGAGTATCCAACTGGTT+TGG + chr5_4:18326023-18326042 Msa0841730:intron 45.0%
GCAAAGAAGCAAGTGGTTTC+TGG + chr5_4:18326728-18326747 Msa0841730:CDS 45.0%
!! AATGGATGGTGGGAAGCAAA+AGG + chr5_4:18326778-18326797 Msa0841730:CDS 45.0%
GCTATGGTTGAACTTCAAGG+AGG + chr5_4:18326826-18326845 Msa0841730:CDS 45.0%
CATGAAATGACCCGGTACAA+AGG - chr5_4:18325706-18325725 None:intergenic 45.0%
!! GTCTAGAAGGAGTATCCAAC+TGG + chr5_4:18326018-18326037 Msa0841730:intron 45.0%
!! GAAGGAGTATCCAACTGGTT+TGG + chr5_4:18326023-18326042 Msa0841730:intron 45.0%
GCAAAGAAGCAAGTGGTTTC+TGG + chr5_4:18326728-18326747 Msa0841730:CDS 45.0%
!! AATGGATGGTGGGAAGCAAA+AGG + chr5_4:18326778-18326797 Msa0841730:CDS 45.0%
GCTATGGTTGAACTTCAAGG+AGG + chr5_4:18326826-18326845 Msa0841730:CDS 45.0%
GTGTTACAGCCCAAACCAGT+TGG - chr5_4:18326036-18326055 None:intergenic 50.0%
GTTTGGGCTGTAACACGTGA+AGG + chr5_4:18326040-18326059 Msa0841730:intron 50.0%
! GTTGAACTTCAAGGAGGTGC+AGG + chr5_4:18326832-18326851 Msa0841730:CDS 50.0%
GTGTTACAGCCCAAACCAGT+TGG - chr5_4:18326036-18326055 None:intergenic 50.0%
GTTTGGGCTGTAACACGTGA+AGG + chr5_4:18326040-18326059 Msa0841730:intron 50.0%
! GTTGAACTTCAAGGAGGTGC+AGG + chr5_4:18326832-18326851 Msa0841730:CDS 50.0%
GACTCTAGGTGGTAGCACTG+AGG + chr5_4:18325461-18325480 Msa0841730:CDS 55.0%
! TCTAGGTGGTAGCACTGAGG+TGG + chr5_4:18325464-18325483 Msa0841730:CDS 55.0%
GACTCTAGGTGGTAGCACTG+AGG + chr5_4:18325461-18325480 Msa0841730:CDS 55.0%
! TCTAGGTGGTAGCACTGAGG+TGG + chr5_4:18325464-18325483 Msa0841730:CDS 55.0%
Chromosome Type Strat End Strand Name
chr5_4 gene 18325436 18326907 18325436 ID=Msa0841730;Name=Msa0841730
chr5_4 mRNA 18325436 18326907 18325436 ID=Msa0841730-mRNA-1;Parent=Msa0841730;Name=Msa0841730-mRNA-1;_AED=0.07;_eAED=0.07;_QI=20|1|0.5|1|1|1|2|0|104
chr5_4 exon 18325436 18325557 18325436 ID=Msa0841730-mRNA-1:exon:7649;Parent=Msa0841730-mRNA-1
chr5_4 exon 18326695 18326907 18326695 ID=Msa0841730-mRNA-1:exon:7650;Parent=Msa0841730-mRNA-1
chr5_4 five_prime_UTR 18325436 18325455 18325436 ID=Msa0841730-mRNA-1:five_prime_utr;Parent=Msa0841730-mRNA-1
chr5_4 CDS 18325456 18325557 18325456 ID=Msa0841730-mRNA-1:cds;Parent=Msa0841730-mRNA-1
chr5_4 CDS 18326695 18326907 18326695 ID=Msa0841730-mRNA-1:cds;Parent=Msa0841730-mRNA-1
Gene Sequence

>Msa0841730

ATGGCGACTCTAGGTGGTAGCACTGAGGTGGAATATACACAAAACAGTGTTGAGATAGATAACCTTGCTATCTTTGCTGTTCAAGAACACAATATCAAACAGAATGCAGTTCTAGAGTTTGTGAGGGTGTTAAATGCAAAGAAGCAAGTGGTTTCTGGCACCTTGTACGACATCACTTTAGAGACAATGGATGGTGGGAAGCAAAAGGTGTATGAAGCCAAGATTTTAGAGAAGCTATGGTTGAACTTCAAGGAGGTGCAGGAATTCAATCTCATTAGCCAAAATTACGATGCTCCTTCTGTATCTAGCACTTAG

Protein sequence

>Msa0841730

MATLGGSTEVEYTQNSVEIDNLAIFAVQEHNIKQNAVLEFVRVLNAKKQVVSGTLYDITLETMDGGKQKVYEAKILEKLWLNFKEVQEFNLISQNYDAPSVSST*