AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0979490


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0979490 MtrunA17_Chr6g0459201 98.305 118 2 0 2 119 653 770 1.70e-76 240
Msa0979490 MtrunA17_Chr7g0226051 76.636 107 25 0 9 115 658 764 3.40e-53 177
Msa0979490 MtrunA17_Chr3g0116231 62.105 95 36 0 15 109 658 752 9.85e-34 123
Msa0979490 MtrunA17_Chr7g0253951 42.718 103 56 2 19 118 655 757 5.39e-20 84.0
Msa0979490 MtrunA17_Chr8g0355271 44.211 95 50 2 18 109 723 817 2.95e-17 76.3
Msa0979490 MtrunA17_Chr6g0460961 35.185 108 68 1 13 118 661 768 6.12e-16 72.4
Msa0979490 MtrunA17_Chr5g0416141 35.417 96 57 1 19 109 11 106 6.82e-16 68.2
Msa0979490 MtrunA17_Chr8g0362301 40.000 95 53 1 19 109 614 708 2.00e-15 70.9
Msa0979490 MtrunA17_Chr7g0274261 33.654 104 65 3 19 118 712 815 5.26e-11 58.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0979490 AT5G14210.2 68.644 118 36 1 2 119 687 803 8.46e-48 163
Msa0979490 AT5G14210.1 68.644 118 36 1 2 119 656 772 1.26e-47 162
Msa0979490 AT5G63410.1 50.459 109 54 0 8 116 571 679 2.34e-33 122
Msa0979490 AT3G03770.2 44.144 111 57 3 4 109 645 755 2.31e-21 88.2
Msa0979490 AT3G03770.3 44.144 111 57 3 4 109 645 755 2.31e-21 88.2
Msa0979490 AT3G03770.1 44.144 111 57 3 4 109 645 755 2.31e-21 88.2
Msa0979490 AT1G14390.1 34.737 95 58 1 19 109 618 712 6.20e-12 61.2
Msa0979490 AT5G61350.1 36.792 106 62 4 19 119 713 818 8.74e-12 60.8
Msa0979490 AT2G02780.1 33.333 117 61 4 5 109 612 723 2.24e-11 59.7
Msa0979490 AT5G14210.3 63.043 46 16 1 2 47 656 700 4.38e-11 58.9

Find 17 sgRNAs with CRISPR-Local

Find 114 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATAATGATGTTTACAATTT+TGG 0.095230 6_4:-16753198 Msa0979490:CDS
TCATTATCCATCTTTGTCTT+TGG 0.227925 6_4:+16753213 None:intergenic
GAGCAAGTTGTTAACACTAT+TGG 0.267996 6_4:+16752554 None:intergenic
TCACCTTTGTCACGTGTAAT+GGG 0.349873 6_4:+16753147 None:intergenic
TTCACCTTTGTCACGTGTAA+TGG 0.380537 6_4:+16753146 None:intergenic
TGTGAACCAAAGGCATCATT+TGG 0.400283 6_4:-16752608 Msa0979490:intron
TAGGTGCATAGAAAGAAATC+AGG 0.422471 6_4:-16752368 Msa0979490:three_prime_UTR
AGATTAAGATTTAACATCAT+AGG 0.426749 6_4:-16752387 Msa0979490:exon
ATATTGTTGGAATCACTTGT+TGG 0.440120 6_4:-16753171 Msa0979490:CDS
AGAGTCTTGAGATATACATT+TGG 0.468063 6_4:+16752496 None:intergenic
GTGAGAAGAAATCAAAATCA+TGG 0.495146 6_4:-16753738 Msa0979490:intron
GCATCATTTGGAAGTCAAGA+TGG 0.509749 6_4:-16752596 Msa0979490:CDS
CATAAAACATCTTCAAAAGA+AGG 0.510715 6_4:+16752464 None:intergenic
TTGTAGTCCAAAGACAAAGA+TGG 0.514643 6_4:-16753220 Msa0979490:intron
AGATGGAAGAAGAAAGATTG+TGG 0.565623 6_4:-16752579 Msa0979490:CDS
AGGTGCATAGAAAGAAATCA+GGG 0.608128 6_4:-16752367 Msa0979490:three_prime_UTR
GGACCCATTACACGTGACAA+AGG 0.646311 6_4:-16753150 Msa0979490:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATGATACTATAATAACTTT+TGG - chr6_4:16752506-16752525 Msa0979490:CDS 15.0%
!!! ATGATACTATAATAACTTTT+GGG - chr6_4:16752507-16752526 Msa0979490:CDS 15.0%
!! TTTCTTTAAATTATTATCAG+TGG + chr6_4:16752652-16752671 None:intergenic 15.0%
!!! AACATTTTTCATTAATGAAA+AGG - chr6_4:16753097-16753116 Msa0979490:intron 15.0%
!!! ACTATTTAAAAAGATGTTTT+AGG + chr6_4:16753219-16753238 None:intergenic 15.0%
!!! TATGATACTATAATAACTTT+TGG - chr6_4:16752506-16752525 Msa0979490:CDS 15.0%
!!! ATGATACTATAATAACTTTT+GGG - chr6_4:16752507-16752526 Msa0979490:CDS 15.0%
!! TTTCTTTAAATTATTATCAG+TGG + chr6_4:16752652-16752671 None:intergenic 15.0%
!!! AACATTTTTCATTAATGAAA+AGG - chr6_4:16753097-16753116 Msa0979490:intron 15.0%
!!! ACTATTTAAAAAGATGTTTT+AGG + chr6_4:16753219-16753238 None:intergenic 15.0%
!! TAAATGATCAAAATCATAGT+AGG + chr6_4:16752424-16752443 None:intergenic 20.0%
!!! GATAATGATGTTTACAATTT+TGG - chr6_4:16753023-16753042 Msa0979490:intron 20.0%
!! AAAATATGTAGTGTAATTTG+AGG + chr6_4:16753351-16753370 None:intergenic 20.0%
!! AGTTCTTAAATGAATTCTTA+GGG + chr6_4:16753525-16753544 None:intergenic 20.0%
!! AAGTTCTTAAATGAATTCTT+AGG + chr6_4:16753526-16753545 None:intergenic 20.0%
!! AGATTAAGATTTAACATCAT+AGG - chr6_4:16753834-16753853 Msa0979490:intron 20.0%
!! TAAATGATCAAAATCATAGT+AGG + chr6_4:16752424-16752443 None:intergenic 20.0%
!!! GATAATGATGTTTACAATTT+TGG - chr6_4:16753023-16753042 Msa0979490:intron 20.0%
!! AAAATATGTAGTGTAATTTG+AGG + chr6_4:16753351-16753370 None:intergenic 20.0%
!! AGTTCTTAAATGAATTCTTA+GGG + chr6_4:16753525-16753544 None:intergenic 20.0%
!! AAGTTCTTAAATGAATTCTT+AGG + chr6_4:16753526-16753545 None:intergenic 20.0%
!! AGATTAAGATTTAACATCAT+AGG - chr6_4:16753834-16753853 Msa0979490:intron 20.0%
! TAATGATAAAACAGCTACAT+TGG + chr6_4:16752401-16752420 None:intergenic 25.0%
!! CAATTTTGGATTCATATTGT+TGG - chr6_4:16753037-16753056 Msa0979490:intron 25.0%
!! ATTAGACTTGTCTAAAACAT+TGG + chr6_4:16753310-16753329 None:intergenic 25.0%
! TCTAATTAACAACTCAAAGT+GGG - chr6_4:16753324-16753343 Msa0979490:intron 25.0%
! CATAAAACATCTTCAAAAGA+AGG + chr6_4:16753760-16753779 None:intergenic 25.0%
!!! CTTCTTTTGAAGATGTTTTA+TGG - chr6_4:16753758-16753777 Msa0979490:intron 25.0%
! TAATGATAAAACAGCTACAT+TGG + chr6_4:16752401-16752420 None:intergenic 25.0%
!! CAATTTTGGATTCATATTGT+TGG - chr6_4:16753037-16753056 Msa0979490:intron 25.0%
!! ATTAGACTTGTCTAAAACAT+TGG + chr6_4:16753310-16753329 None:intergenic 25.0%
! TCTAATTAACAACTCAAAGT+GGG - chr6_4:16753324-16753343 Msa0979490:intron 25.0%
! CATAAAACATCTTCAAAAGA+AGG + chr6_4:16753760-16753779 None:intergenic 25.0%
!!! CTTCTTTTGAAGATGTTTTA+TGG - chr6_4:16753758-16753777 Msa0979490:intron 25.0%
TTCGATATCTTCTTTGATGA+TGG + chr6_4:16752354-16752373 None:intergenic 30.0%
GTGAGAAGAAATCAAAATCA+TGG - chr6_4:16752483-16752502 Msa0979490:CDS 30.0%
! GAAAGCATGAAGGATTAAAA+AGG + chr6_4:16752562-16752581 None:intergenic 30.0%
! TCAATTTTCACCCTTTACTA+TGG - chr6_4:16752912-16752931 Msa0979490:intron 30.0%
GAACTTCAAACCATAGTAAA+GGG + chr6_4:16752925-16752944 None:intergenic 30.0%
TGAACTTCAAACCATAGTAA+AGG + chr6_4:16752926-16752945 None:intergenic 30.0%
TCATTATCCATCTTTGTCTT+TGG + chr6_4:16753011-16753030 None:intergenic 30.0%
ATATTGTTGGAATCACTTGT+TGG - chr6_4:16753050-16753069 Msa0979490:intron 30.0%
GTCTAATTAACAACTCAAAG+TGG - chr6_4:16753323-16753342 Msa0979490:intron 30.0%
AGAGTCTTGAGATATACATT+TGG + chr6_4:16753728-16753747 None:intergenic 30.0%
TTCGATATCTTCTTTGATGA+TGG + chr6_4:16752354-16752373 None:intergenic 30.0%
GTGAGAAGAAATCAAAATCA+TGG - chr6_4:16752483-16752502 Msa0979490:CDS 30.0%
! GAAAGCATGAAGGATTAAAA+AGG + chr6_4:16752562-16752581 None:intergenic 30.0%
! TCAATTTTCACCCTTTACTA+TGG - chr6_4:16752912-16752931 Msa0979490:intron 30.0%
GAACTTCAAACCATAGTAAA+GGG + chr6_4:16752925-16752944 None:intergenic 30.0%
TGAACTTCAAACCATAGTAA+AGG + chr6_4:16752926-16752945 None:intergenic 30.0%
TCATTATCCATCTTTGTCTT+TGG + chr6_4:16753011-16753030 None:intergenic 30.0%
ATATTGTTGGAATCACTTGT+TGG - chr6_4:16753050-16753069 Msa0979490:intron 30.0%
GTCTAATTAACAACTCAAAG+TGG - chr6_4:16753323-16753342 Msa0979490:intron 30.0%
AGAGTCTTGAGATATACATT+TGG + chr6_4:16753728-16753747 None:intergenic 30.0%
TATTGAACACTGACACATGT+CGG - chr6_4:16752715-16752734 Msa0979490:intron 35.0%
! ACGCCTTATATCTAAAGTGT+CGG - chr6_4:16752775-16752794 Msa0979490:intron 35.0%
! ATAGCATTGAAAACCAAGCA+TGG + chr6_4:16752872-16752891 None:intergenic 35.0%
TTGTAGTCCAAAGACAAAGA+TGG - chr6_4:16753001-16753020 Msa0979490:intron 35.0%
AACATGTTGTTGTGAACCAA+AGG - chr6_4:16753603-16753622 Msa0979490:intron 35.0%
AGATGGAAGAAGAAAGATTG+TGG - chr6_4:16753642-16753661 Msa0979490:intron 35.0%
GAGCAAGTTGTTAACACTAT+TGG + chr6_4:16753670-16753689 None:intergenic 35.0%
TAGGTGCATAGAAAGAAATC+AGG - chr6_4:16753853-16753872 Msa0979490:intron 35.0%
AGGTGCATAGAAAGAAATCA+GGG - chr6_4:16753854-16753873 Msa0979490:intron 35.0%
TATTGAACACTGACACATGT+CGG - chr6_4:16752715-16752734 Msa0979490:intron 35.0%
! ACGCCTTATATCTAAAGTGT+CGG - chr6_4:16752775-16752794 Msa0979490:intron 35.0%
! ATAGCATTGAAAACCAAGCA+TGG + chr6_4:16752872-16752891 None:intergenic 35.0%
TTGTAGTCCAAAGACAAAGA+TGG - chr6_4:16753001-16753020 Msa0979490:intron 35.0%
AACATGTTGTTGTGAACCAA+AGG - chr6_4:16753603-16753622 Msa0979490:intron 35.0%
AGATGGAAGAAGAAAGATTG+TGG - chr6_4:16753642-16753661 Msa0979490:intron 35.0%
GAGCAAGTTGTTAACACTAT+TGG + chr6_4:16753670-16753689 None:intergenic 35.0%
TAGGTGCATAGAAAGAAATC+AGG - chr6_4:16753853-16753872 Msa0979490:intron 35.0%
AGGTGCATAGAAAGAAATCA+GGG - chr6_4:16753854-16753873 Msa0979490:intron 35.0%
! GGTAGAGATTGAAAGCATGA+AGG + chr6_4:16752572-16752591 None:intergenic 40.0%
CGTTTGTGTTTGTGCTTCAT+AGG + chr6_4:16752593-16752612 None:intergenic 40.0%
CTTTAGATATAAGGCGTGTC+TGG + chr6_4:16752772-16752791 None:intergenic 40.0%
! GCACCGACACTTTAGATATA+AGG + chr6_4:16752781-16752800 None:intergenic 40.0%
AAAACCAAGCATGGTTGTGT+TGG + chr6_4:16752863-16752882 None:intergenic 40.0%
TCACCTTTGTCACGTGTAAT+GGG + chr6_4:16753077-16753096 None:intergenic 40.0%
TTCACCTTTGTCACGTGTAA+TGG + chr6_4:16753078-16753097 None:intergenic 40.0%
!! TGTGAACCAAAGGCATCATT+TGG - chr6_4:16753613-16753632 Msa0979490:intron 40.0%
TGACTTCCAAATGATGCCTT+TGG + chr6_4:16753622-16753641 None:intergenic 40.0%
GCATCATTTGGAAGTCAAGA+TGG - chr6_4:16753625-16753644 Msa0979490:intron 40.0%
! TTTTTGATCTGCATCTGCTG+TGG + chr6_4:16753812-16753831 None:intergenic 40.0%
! GGTAGAGATTGAAAGCATGA+AGG + chr6_4:16752572-16752591 None:intergenic 40.0%
CGTTTGTGTTTGTGCTTCAT+AGG + chr6_4:16752593-16752612 None:intergenic 40.0%
CTTTAGATATAAGGCGTGTC+TGG + chr6_4:16752772-16752791 None:intergenic 40.0%
! GCACCGACACTTTAGATATA+AGG + chr6_4:16752781-16752800 None:intergenic 40.0%
AAAACCAAGCATGGTTGTGT+TGG + chr6_4:16752863-16752882 None:intergenic 40.0%
TCACCTTTGTCACGTGTAAT+GGG + chr6_4:16753077-16753096 None:intergenic 40.0%
TTCACCTTTGTCACGTGTAA+TGG + chr6_4:16753078-16753097 None:intergenic 40.0%
!! TGTGAACCAAAGGCATCATT+TGG - chr6_4:16753613-16753632 Msa0979490:intron 40.0%
TGACTTCCAAATGATGCCTT+TGG + chr6_4:16753622-16753641 None:intergenic 40.0%
GCATCATTTGGAAGTCAAGA+TGG - chr6_4:16753625-16753644 Msa0979490:intron 40.0%
! TTTTTGATCTGCATCTGCTG+TGG + chr6_4:16753812-16753831 None:intergenic 40.0%
TGAAGCACAAACACAAACGC+CGG - chr6_4:16752594-16752613 Msa0979490:CDS 45.0%
! GACACTATTGAAAGCGTGTC+TGG + chr6_4:16752744-16752763 None:intergenic 45.0%
ATCACCAACACAACCATGCT+TGG - chr6_4:16752856-16752875 Msa0979490:intron 45.0%
TGAAGCACAAACACAAACGC+CGG - chr6_4:16752594-16752613 Msa0979490:CDS 45.0%
! GACACTATTGAAAGCGTGTC+TGG + chr6_4:16752744-16752763 None:intergenic 45.0%
ATCACCAACACAACCATGCT+TGG - chr6_4:16752856-16752875 Msa0979490:intron 45.0%
!!! TAAAAATAATTAATTTGTTA+AGG + chr6_4:16752976-16752995 None:intergenic 5.0%
!!! TTTTATTTAATTTTCAAAAT+AGG - chr6_4:16753393-16753412 Msa0979490:intron 5.0%
!!! TAAAAATAATTAATTTGTTA+AGG + chr6_4:16752976-16752995 None:intergenic 5.0%
!!! TTTTATTTAATTTTCAAAAT+AGG - chr6_4:16753393-16753412 Msa0979490:intron 5.0%
GACCACATGTGTCAGTGTCA+TGG - chr6_4:16752689-16752708 Msa0979490:intron 50.0%
CACCATGACACTGACACATG+TGG + chr6_4:16752694-16752713 None:intergenic 50.0%
CACATGTGTCAGTGTCATGG+TGG - chr6_4:16752692-16752711 Msa0979490:intron 50.0%
GGACCCATTACACGTGACAA+AGG - chr6_4:16753071-16753090 Msa0979490:intron 50.0%
GACCACATGTGTCAGTGTCA+TGG - chr6_4:16752689-16752708 Msa0979490:intron 50.0%
CACCATGACACTGACACATG+TGG + chr6_4:16752694-16752713 None:intergenic 50.0%
CACATGTGTCAGTGTCATGG+TGG - chr6_4:16752692-16752711 Msa0979490:intron 50.0%
GGACCCATTACACGTGACAA+AGG - chr6_4:16753071-16753090 Msa0979490:intron 50.0%
GTCAGTGTCAGTGTCGTGTC+CGG + chr6_4:16752616-16752635 None:intergenic 55.0%
GTCAGTGTCAGTGTCGTGTC+CGG + chr6_4:16752616-16752635 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr6_4 gene 16752342 16753901 16752342 ID=Msa0979490;Name=Msa0979490
chr6_4 mRNA 16752342 16753901 16752342 ID=Msa0979490-mRNA-1;Parent=Msa0979490;Name=Msa0979490-mRNA-1;_AED=0.05;_eAED=0.05;_QI=0|0.33|0.25|0.5|0.33|0.5|4|61|119
chr6_4 exon 16752342 16752618 16752342 ID=Msa0979490-mRNA-1:exon:5287;Parent=Msa0979490-mRNA-1
chr6_4 exon 16753125 16753236 16753125 ID=Msa0979490-mRNA-1:exon:5286;Parent=Msa0979490-mRNA-1
chr6_4 exon 16753739 16753767 16753739 ID=Msa0979490-mRNA-1:exon:5285;Parent=Msa0979490-mRNA-1
chr6_4 exon 16753899 16753901 16753899 ID=Msa0979490-mRNA-1:exon:5284;Parent=Msa0979490-mRNA-1
chr6_4 CDS 16753899 16753901 16753899 ID=Msa0979490-mRNA-1:cds;Parent=Msa0979490-mRNA-1
chr6_4 CDS 16753739 16753767 16753739 ID=Msa0979490-mRNA-1:cds;Parent=Msa0979490-mRNA-1
chr6_4 CDS 16753125 16753236 16753125 ID=Msa0979490-mRNA-1:cds;Parent=Msa0979490-mRNA-1
chr6_4 CDS 16752403 16752618 16752403 ID=Msa0979490-mRNA-1:cds;Parent=Msa0979490-mRNA-1
chr6_4 three_prime_UTR 16752342 16752402 16752342 ID=Msa0979490-mRNA-1:three_prime_utr;Parent=Msa0979490-mRNA-1
Gene Sequence

>Msa0979490

ATGACAAAGAGTGAGAAGAAATCAAAATCATGTCCAAAGACAAAGATGGATAATGATGTTTACAATTTTGGATTCATATTGTTGGAATCACTTGTTGGACCCATTACACGTGACAAAGGTGAAACATTTTTCATTAATGAAAAGGCATCATTTGGAAGTCAAGATGGAAGAAGAAAGATTGTGGATCCAATAGTGTTAACAACTTGCTCTCAAAAATCATTATCAATTGCAATATCTATAACAACCAAATGTATATCTCAAGACTCTTCATCTCGTCCTTCTTTTGAAGATGTTTTATGGAACTTACAATATGCAGCTCAAGTTCAAGCCACAGCAGATGCAGATCAAAAATCAGATTAA

Protein sequence

>Msa0979490

MTKSEKKSKSCPKTKMDNDVYNFGFILLESLVGPITRDKGETFFINEKASFGSQDGRRKIVDPIVLTTCSQKSLSIAISITTKCISQDSSSRPSFEDVLWNLQYAAQVQATADADQKSD*