AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0914260

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0914260 MtrunA17_Chr6g0469571 96.774 124 4 0 1 124 1 124 1.23e-85 245
Msa0914260 MtrunA17_Chr6g0469551 95.161 124 6 0 1 124 1 124 1.45e-75 219
Msa0914260 MtrunA17_Chr6g0469591 95.161 124 6 0 1 124 1 124 1.81e-74 217
Msa0914260 MtrunA17_Chr6g0469681 60.465 129 44 3 1 124 1 127 2.97e-38 125
Msa0914260 MtrunA17_Chr7g0233231 56.481 108 45 1 1 108 1 106 1.12e-37 123
Msa0914260 MtrunA17_Chr1g0202541 56.296 135 47 2 1 123 1 135 7.16e-37 122
Msa0914260 MtrunA17_Chr7g0233211 56.075 107 45 1 1 107 1 105 1.30e-36 120
Msa0914260 MtrunA17_Chr6g0469651 56.716 134 47 2 1 124 1 133 3.12e-36 120
Msa0914260 MtrunA17_Chr7g0233251 56.140 114 45 2 1 111 1 112 4.89e-36 119
Msa0914260 MtrunA17_Chr7g0233191 56.075 107 45 1 1 107 1 105 1.09e-35 118
Msa0914260 MtrunA17_Chr6g0469541 58.879 107 42 2 1 107 1 105 2.33e-35 117
Msa0914260 MtrunA17_Chr7g0233201 56.075 107 45 1 1 107 1 105 2.52e-35 117
Msa0914260 MtrunA17_Chr1g0202561 51.449 138 52 2 1 123 1 138 3.68e-35 118
Msa0914260 MtrunA17_Chr7g0233181 54.717 106 46 1 1 106 1 104 1.65e-34 115
Msa0914260 MtrunA17_Chr6g0469671 77.143 70 16 0 1 70 1 70 6.71e-34 114
Msa0914260 MtrunA17_Chr1g0202581 55.556 135 44 3 1 123 1 131 1.12e-33 114
Msa0914260 MtrunA17_Chr8g0387471 49.618 131 55 3 1 124 1 127 2.99e-33 112
Msa0914260 MtrunA17_Chr1g0202501 50.000 134 53 3 1 124 1 130 3.85e-33 112
Msa0914260 MtrunA17_Chr1g0204291 52.593 135 48 4 1 123 1 131 4.07e-32 110
Msa0914260 MtrunA17_Chr7g0248671 61.765 68 26 0 1 68 1 68 7.80e-24 90.1
Msa0914260 MtrunA17_Chr8g0348361 66.176 68 23 0 1 68 1 68 7.46e-15 66.6
Msa0914260 MtrunA17_Chr3g0120541 43.210 81 42 4 3 79 5 85 1.02e-13 62.8
Msa0914260 MtrunA17_Chr5g0404641 30.719 153 74 4 3 123 4 156 5.85e-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
Msa0914260 AT1G01490.1 66.197 71 23 1 1 70 1 71 6.82e-25 93.6
Msa0914260 AT1G01490.2 66.197 71 23 1 1 70 1 71 6.82e-25 93.6
Msa0914260 AT1G01490.4 65.714 70 23 1 2 70 29 98 2.49e-24 92.8
Msa0914260 AT5G52740.1 57.143 70 28 1 1 70 1 68 5.84e-19 76.6
Msa0914260 AT5G52760.1 43.269 104 49 4 5 105 7 103 3.54e-16 69.7
Msa0914260 AT5G52750.1 45.455 66 36 0 2 67 4 69 5.20e-13 62.0

Find 27 sgRNAs with CRISPR-Local

Find 114 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAGACTGTCTCAGGCCTTTC+TGG 0.185291 6_2:+27709803 Msa0914260:CDS
GACAAGAAATTAACCTTAAC+TGG 0.272704 6_2:+27710457 Msa0914260:CDS
TAAAAGAAGAACTAGGGTAT+TGG 0.382666 6_2:-27709579 None:intergenic
ATTTGATTCTTCTTCACATC+AGG 0.383077 6_2:-27710586 None:intergenic
ATATTCCTCTGTTTCAAGAA+TGG 0.394512 6_2:+27710666 Msa0914260:CDS
TGGATCTGTGTCTCCAGTTA+AGG 0.422934 6_2:-27710470 None:intergenic
AAAAGCTTTATTGAAAATGA+TGG 0.441720 6_2:+27709637 Msa0914260:exon
GTTACAGAAACTAGTATTGA+AGG 0.451235 6_2:+27709742 Msa0914260:intron
AGTTTGCTTACTACATGTAC+TGG 0.452527 6_2:-27710490 None:intergenic
TAAAATTTAAAAGAAGAACT+AGG 0.458445 6_2:-27709586 None:intergenic
TAGTAAGCAAACTAAGGAAA+TGG 0.458647 6_2:+27710500 Msa0914260:CDS
AAAATTTAAAAGAAGAACTA+GGG 0.473038 6_2:-27709585 None:intergenic
ATGCTGAAATAGTTTCTGTT+GGG 0.476513 6_2:+27710527 Msa0914260:CDS
AAAGCTATGAAGACTGTCTC+AGG 0.497682 6_2:+27709794 Msa0914260:CDS
CATGCTGAAATAGTTTCTGT+TGG 0.500770 6_2:+27710526 Msa0914260:CDS
TACATGTAGTAAGCAAACTA+AGG 0.515410 6_2:+27710494 Msa0914260:CDS
TAGCATATGACACATCCAAC+AGG 0.524107 6_2:-27710697 None:intergenic
ACAATGAGCTTGTAACATGT+TGG 0.535420 6_2:+27710811 Msa0914260:three_prime_UTR
GAGGAATATTGAATATATTG+TGG 0.535752 6_2:-27710652 None:intergenic
TTGTTCCATTCTTGAAACAG+AGG 0.577364 6_2:-27710671 None:intergenic
TGTTCAATTGTGCAAACAGA+GGG 0.585753 6_2:+27710861 Msa0914260:three_prime_UTR
ACAAGTTGACATTACCAGAA+AGG 0.591138 6_2:-27709817 None:intergenic
CATGTAGTAATAATGAGGAT+AGG 0.591628 6_2:-27710623 None:intergenic
AGAATGGAACAAGATCCTGT+TGG 0.628668 6_2:+27710682 Msa0914260:CDS
TGTTGCATGTAGTAATAATG+AGG 0.650568 6_2:-27710628 None:intergenic
ACAGAAACTAGTATTGAAGG+TGG 0.658613 6_2:+27709745 Msa0914260:intron
GTGTTCAATTGTGCAAACAG+AGG 0.663444 6_2:+27710860 Msa0914260:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CTTTTTTTTTTTTACAAATT+GGG - chr6_2:27710121-27710140 None:intergenic 10.0%
!!! ACTTTTTTTTTTTTACAAAT+TGG - chr6_2:27710122-27710141 None:intergenic 10.0%
!!! TTTTTGAAATAATTAAGTAT+TGG + chr6_2:27710143-27710162 Msa0914260:intron 10.0%
!!! AATTTTAGCAAAAAAATTAA+AGG - chr6_2:27710386-27710405 None:intergenic 10.0%
!!! TATTTTATATATTATTTGCA+GGG + chr6_2:27710407-27710426 Msa0914260:intron 10.0%
!!! TGTATTTTCATATTATTTAT+TGG + chr6_2:27710743-27710762 Msa0914260:three_prime_UTR 10.0%
!!! CTTTTTTTTTTTTACAAATT+GGG - chr6_2:27710121-27710140 None:intergenic 10.0%
!!! ACTTTTTTTTTTTTACAAAT+TGG - chr6_2:27710122-27710141 None:intergenic 10.0%
!!! TTTTTGAAATAATTAAGTAT+TGG + chr6_2:27710143-27710162 Msa0914260:intron 10.0%
!!! AATTTTAGCAAAAAAATTAA+AGG - chr6_2:27710386-27710405 None:intergenic 10.0%
!!! TATTTTATATATTATTTGCA+GGG + chr6_2:27710407-27710426 Msa0914260:intron 10.0%
!!! TGTATTTTCATATTATTTAT+TGG + chr6_2:27710743-27710762 Msa0914260:three_prime_UTR 10.0%
!! AAAATTTAAAAGAAGAACTA+GGG - chr6_2:27709588-27709607 None:intergenic 15.0%
!! TAAAATTTAAAAGAAGAACT+AGG - chr6_2:27709589-27709608 None:intergenic 15.0%
!!! AAAAAATTGATAGTAAAAGA+GGG - chr6_2:27709686-27709705 None:intergenic 15.0%
!!! ATGATATTTAAATTCTTTTG+AGG - chr6_2:27710031-27710050 None:intergenic 15.0%
!!! GTATTTTATATATTATTTGC+AGG + chr6_2:27710406-27710425 Msa0914260:intron 15.0%
!!! ATTTTATATATTATTTGCAG+GGG + chr6_2:27710408-27710427 Msa0914260:intron 15.0%
!!! TGATTTATATATTTTTTGAG+TGG + chr6_2:27710778-27710797 Msa0914260:three_prime_UTR 15.0%
!! AAAATTTAAAAGAAGAACTA+GGG - chr6_2:27709588-27709607 None:intergenic 15.0%
!! TAAAATTTAAAAGAAGAACT+AGG - chr6_2:27709589-27709608 None:intergenic 15.0%
!!! AAAAAATTGATAGTAAAAGA+GGG - chr6_2:27709686-27709705 None:intergenic 15.0%
!!! ATGATATTTAAATTCTTTTG+AGG - chr6_2:27710031-27710050 None:intergenic 15.0%
!!! GTATTTTATATATTATTTGC+AGG + chr6_2:27710406-27710425 Msa0914260:intron 15.0%
!!! ATTTTATATATTATTTGCAG+GGG + chr6_2:27710408-27710427 Msa0914260:intron 15.0%
!!! TGATTTATATATTTTTTGAG+TGG + chr6_2:27710778-27710797 Msa0914260:three_prime_UTR 15.0%
!!! TTTCAATAAAGCTTTTTGAT+AGG - chr6_2:27709633-27709652 None:intergenic 20.0%
!!! AAAAGCTTTATTGAAAATGA+TGG + chr6_2:27709637-27709656 Msa0914260:exon 20.0%
!!! GAAAAAATTGATAGTAAAAG+AGG - chr6_2:27709687-27709706 None:intergenic 20.0%
!! GAAATTAAACTCATAATTGT+CGG + chr6_2:27710195-27710214 Msa0914260:intron 20.0%
!!! TTTCAATAAAGCTTTTTGAT+AGG - chr6_2:27709633-27709652 None:intergenic 20.0%
!!! AAAAGCTTTATTGAAAATGA+TGG + chr6_2:27709637-27709656 Msa0914260:exon 20.0%
!!! GAAAAAATTGATAGTAAAAG+AGG - chr6_2:27709687-27709706 None:intergenic 20.0%
!! GAAATTAAACTCATAATTGT+CGG + chr6_2:27710195-27710214 Msa0914260:intron 20.0%
!! ACTTGTCTAGTTTCAATATT+TGG + chr6_2:27709834-27709853 Msa0914260:intron 25.0%
!! TCTAGTTTCAATATTTGGTT+TGG + chr6_2:27709839-27709858 Msa0914260:intron 25.0%
!!! TAAATTCTTTTGAGGTTACT+AGG - chr6_2:27710023-27710042 None:intergenic 25.0%
! CGGAAACATTTAATATATCA+AGG + chr6_2:27710248-27710267 Msa0914260:intron 25.0%
! GAGGAATATTGAATATATTG+TGG - chr6_2:27710655-27710674 None:intergenic 25.0%
! AACATGTTGGAAAAATGAAA+AGG + chr6_2:27710824-27710843 Msa0914260:three_prime_UTR 25.0%
!! ACTTGTCTAGTTTCAATATT+TGG + chr6_2:27709834-27709853 Msa0914260:intron 25.0%
!! TCTAGTTTCAATATTTGGTT+TGG + chr6_2:27709839-27709858 Msa0914260:intron 25.0%
!!! TAAATTCTTTTGAGGTTACT+AGG - chr6_2:27710023-27710042 None:intergenic 25.0%
! CGGAAACATTTAATATATCA+AGG + chr6_2:27710248-27710267 Msa0914260:intron 25.0%
! GAGGAATATTGAATATATTG+TGG - chr6_2:27710655-27710674 None:intergenic 25.0%
! AACATGTTGGAAAAATGAAA+AGG + chr6_2:27710824-27710843 Msa0914260:three_prime_UTR 25.0%
TAAAAGAAGAACTAGGGTAT+TGG - chr6_2:27709582-27709601 None:intergenic 30.0%
! GTTACAGAAACTAGTATTGA+AGG + chr6_2:27709742-27709761 Msa0914260:intron 30.0%
!! TTCGTTTTTCACTGTTTATG+AGG + chr6_2:27709984-27710003 Msa0914260:intron 30.0%
!! TTCTTAGTGTGTTTGAGTTT+TGG + chr6_2:27710307-27710326 Msa0914260:intron 30.0%
GACAAGAAATTAACCTTAAC+TGG + chr6_2:27710457-27710476 Msa0914260:CDS 30.0%
TACATGTAGTAAGCAAACTA+AGG + chr6_2:27710494-27710513 Msa0914260:CDS 30.0%
TAGTAAGCAAACTAAGGAAA+TGG + chr6_2:27710500-27710519 Msa0914260:CDS 30.0%
ATGCTGAAATAGTTTCTGTT+GGG + chr6_2:27710527-27710546 Msa0914260:CDS 30.0%
! TTCTTCTTTTCATCTTTTGC+AGG - chr6_2:27710553-27710572 None:intergenic 30.0%
ATTTGATTCTTCTTCACATC+AGG - chr6_2:27710589-27710608 None:intergenic 30.0%
CATGTAGTAATAATGAGGAT+AGG - chr6_2:27710626-27710645 None:intergenic 30.0%
TGTTGCATGTAGTAATAATG+AGG - chr6_2:27710631-27710650 None:intergenic 30.0%
ATATTCCTCTGTTTCAAGAA+TGG + chr6_2:27710666-27710685 Msa0914260:CDS 30.0%
TAAAAGAAGAACTAGGGTAT+TGG - chr6_2:27709582-27709601 None:intergenic 30.0%
! GTTACAGAAACTAGTATTGA+AGG + chr6_2:27709742-27709761 Msa0914260:intron 30.0%
!! TTCGTTTTTCACTGTTTATG+AGG + chr6_2:27709984-27710003 Msa0914260:intron 30.0%
!! TTCTTAGTGTGTTTGAGTTT+TGG + chr6_2:27710307-27710326 Msa0914260:intron 30.0%
GACAAGAAATTAACCTTAAC+TGG + chr6_2:27710457-27710476 Msa0914260:CDS 30.0%
TACATGTAGTAAGCAAACTA+AGG + chr6_2:27710494-27710513 Msa0914260:CDS 30.0%
TAGTAAGCAAACTAAGGAAA+TGG + chr6_2:27710500-27710519 Msa0914260:CDS 30.0%
ATGCTGAAATAGTTTCTGTT+GGG + chr6_2:27710527-27710546 Msa0914260:CDS 30.0%
! TTCTTCTTTTCATCTTTTGC+AGG - chr6_2:27710553-27710572 None:intergenic 30.0%
ATTTGATTCTTCTTCACATC+AGG - chr6_2:27710589-27710608 None:intergenic 30.0%
CATGTAGTAATAATGAGGAT+AGG - chr6_2:27710626-27710645 None:intergenic 30.0%
TGTTGCATGTAGTAATAATG+AGG - chr6_2:27710631-27710650 None:intergenic 30.0%
ATATTCCTCTGTTTCAAGAA+TGG + chr6_2:27710666-27710685 Msa0914260:CDS 30.0%
AGTAAAAGAGGGAATTCACA+AGG - chr6_2:27709675-27709694 None:intergenic 35.0%
! ACAGAAACTAGTATTGAAGG+TGG + chr6_2:27709745-27709764 Msa0914260:intron 35.0%
! AGTCTTCATAGCTTTTTGCT+TGG - chr6_2:27709789-27709808 None:intergenic 35.0%
! ACAAGTTGACATTACCAGAA+AGG - chr6_2:27709820-27709839 None:intergenic 35.0%
! GTTTTTCACTGTTTATGAGG+TGG + chr6_2:27709987-27710006 Msa0914260:intron 35.0%
ACTCAAGTGGTAAAAGATTG+CGG + chr6_2:27710228-27710247 Msa0914260:intron 35.0%
! AGTTTGCTTACTACATGTAC+TGG - chr6_2:27710493-27710512 None:intergenic 35.0%
CATGCTGAAATAGTTTCTGT+TGG + chr6_2:27710526-27710545 Msa0914260:CDS 35.0%
TTGTTCCATTCTTGAAACAG+AGG - chr6_2:27710674-27710693 None:intergenic 35.0%
ACAATGAGCTTGTAACATGT+TGG + chr6_2:27710811-27710830 Msa0914260:three_prime_UTR 35.0%
TGTTCAATTGTGCAAACAGA+GGG + chr6_2:27710861-27710880 Msa0914260:three_prime_UTR 35.0%
AGTAAAAGAGGGAATTCACA+AGG - chr6_2:27709675-27709694 None:intergenic 35.0%
! ACAGAAACTAGTATTGAAGG+TGG + chr6_2:27709745-27709764 Msa0914260:intron 35.0%
! AGTCTTCATAGCTTTTTGCT+TGG - chr6_2:27709789-27709808 None:intergenic 35.0%
! ACAAGTTGACATTACCAGAA+AGG - chr6_2:27709820-27709839 None:intergenic 35.0%
! GTTTTTCACTGTTTATGAGG+TGG + chr6_2:27709987-27710006 Msa0914260:intron 35.0%
ACTCAAGTGGTAAAAGATTG+CGG + chr6_2:27710228-27710247 Msa0914260:intron 35.0%
! AGTTTGCTTACTACATGTAC+TGG - chr6_2:27710493-27710512 None:intergenic 35.0%
CATGCTGAAATAGTTTCTGT+TGG + chr6_2:27710526-27710545 Msa0914260:CDS 35.0%
TTGTTCCATTCTTGAAACAG+AGG - chr6_2:27710674-27710693 None:intergenic 35.0%
ACAATGAGCTTGTAACATGT+TGG + chr6_2:27710811-27710830 Msa0914260:three_prime_UTR 35.0%
TGTTCAATTGTGCAAACAGA+GGG + chr6_2:27710861-27710880 Msa0914260:three_prime_UTR 35.0%
AAAGCTATGAAGACTGTCTC+AGG + chr6_2:27709794-27709813 Msa0914260:CDS 40.0%
AATATATCAAGGCGCGTGTT+TGG + chr6_2:27710259-27710278 Msa0914260:intron 40.0%
ATATATCAAGGCGCGTGTTT+GGG + chr6_2:27710260-27710279 Msa0914260:intron 40.0%
AGAATGGAACAAGATCCTGT+TGG + chr6_2:27710682-27710701 Msa0914260:CDS 40.0%
TAGCATATGACACATCCAAC+AGG - chr6_2:27710700-27710719 None:intergenic 40.0%
GTGTTCAATTGTGCAAACAG+AGG + chr6_2:27710860-27710879 Msa0914260:three_prime_UTR 40.0%
AAAGCTATGAAGACTGTCTC+AGG + chr6_2:27709794-27709813 Msa0914260:CDS 40.0%
AATATATCAAGGCGCGTGTT+TGG + chr6_2:27710259-27710278 Msa0914260:intron 40.0%
ATATATCAAGGCGCGTGTTT+GGG + chr6_2:27710260-27710279 Msa0914260:intron 40.0%
AGAATGGAACAAGATCCTGT+TGG + chr6_2:27710682-27710701 Msa0914260:CDS 40.0%
TAGCATATGACACATCCAAC+AGG - chr6_2:27710700-27710719 None:intergenic 40.0%
GTGTTCAATTGTGCAAACAG+AGG + chr6_2:27710860-27710879 Msa0914260:three_prime_UTR 40.0%
CGGCATAAGTGTAACTCAAG+TGG + chr6_2:27710215-27710234 Msa0914260:intron 45.0%
TGGATCTGTGTCTCCAGTTA+AGG - chr6_2:27710473-27710492 None:intergenic 45.0%
CGGCATAAGTGTAACTCAAG+TGG + chr6_2:27710215-27710234 Msa0914260:intron 45.0%
TGGATCTGTGTCTCCAGTTA+AGG - chr6_2:27710473-27710492 None:intergenic 45.0%
!!! TATTTATTTTAATTGAAAAA+TGG - chr6_2:27710080-27710099 None:intergenic 5.0%
!!! TATTTATTTTAATTGAAAAA+TGG - chr6_2:27710080-27710099 None:intergenic 5.0%
AAGACTGTCTCAGGCCTTTC+TGG + chr6_2:27709803-27709822 Msa0914260:CDS 50.0%
AAGACTGTCTCAGGCCTTTC+TGG + chr6_2:27709803-27709822 Msa0914260:CDS 50.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 27709523 27710908 27709523 ID=Msa0914260;Name=Msa0914260
chr6_2 mRNA 27709523 27710908 27709523 ID=Msa0914260-mRNA-1;Parent=Msa0914260;Name=Msa0914260-mRNA-1;_AED=0.11;_eAED=0.11;_QI=130|1|1|1|1|1|3|188|124
chr6_2 exon 27709523 27709658 27709523 ID=Msa0914260-mRNA-1:exon:5138;Parent=Msa0914260-mRNA-1
chr6_2 exon 27709749 27709824 27709749 ID=Msa0914260-mRNA-1:exon:5139;Parent=Msa0914260-mRNA-1
chr6_2 exon 27710428 27710908 27710428 ID=Msa0914260-mRNA-1:exon:5140;Parent=Msa0914260-mRNA-1
chr6_2 five_prime_UTR 27709523 27709652 27709523 ID=Msa0914260-mRNA-1:five_prime_utr;Parent=Msa0914260-mRNA-1
chr6_2 CDS 27709653 27709658 27709653 ID=Msa0914260-mRNA-1:cds;Parent=Msa0914260-mRNA-1
chr6_2 CDS 27709749 27709824 27709749 ID=Msa0914260-mRNA-1:cds;Parent=Msa0914260-mRNA-1
chr6_2 CDS 27710428 27710720 27710428 ID=Msa0914260-mRNA-1:cds;Parent=Msa0914260-mRNA-1
chr6_2 three_prime_UTR 27710721 27710908 27710721 ID=Msa0914260-mRNA-1:three_prime_utr;Parent=Msa0914260-mRNA-1
Gene Sequence

>Msa0914260

ATGATGAAACTAGTATTGAAGGTGGATTTACATGATGACAGAACCAAGCAAAAAGCTATGAAGACTGTCTCAGGCCTTTCTGGGGTAGAGTCAGTATCTGTAGACATGAAAGACAAGAAATTAACCTTAACTGGAGACACAGATCCAGTACATGTAGTAAGCAAACTAAGGAAATGGTGTCATGCTGAAATAGTTTCTGTTGGGCCTGCAAAAGATGAAAAGAAGAAAGAAGAATCTAAGCCTGATGTGAAGAAGAATCAAATTCAATTACTTGAAGCCTATCCTCATTATTACTACATGCAACAACCACAATATATTCAATATTCCTCTGTTTCAAGAATGGAACAAGATCCTGTTGGATGTGTCATATGCTAA
Protein sequence

>Msa0914260

MMKLVLKVDLHDDRTKQKAMKTVSGLSGVESVSVDMKDKKLTLTGDTDPVHVVSKLRKWCHAEIVSVGPAKDEKKKEESKPDVKKNQIQLLEAYPHYYYMQQPQYIQYSSVSRMEQDPVGCVIC*