AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0952340

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0952340 MtrunA17_Chr6g0469571 95.161 124 6 0 1 124 1 124 1.36e-75 219
Msa0952340 MtrunA17_Chr6g0469551 93.548 124 8 0 1 124 1 124 4.97e-75 218
Msa0952340 MtrunA17_Chr6g0469591 93.548 124 8 0 1 124 1 124 7.07e-74 215
Msa0952340 MtrunA17_Chr6g0469681 60.465 129 44 3 1 124 1 127 1.76e-38 126
Msa0952340 MtrunA17_Chr7g0233231 56.481 108 45 1 1 108 1 106 4.95e-38 124
Msa0952340 MtrunA17_Chr1g0202541 56.296 135 47 2 1 123 1 135 6.01e-37 122
Msa0952340 MtrunA17_Chr7g0233211 56.075 107 45 1 1 107 1 105 6.12e-37 121
Msa0952340 MtrunA17_Chr7g0233251 56.140 114 45 2 1 111 1 112 2.62e-36 120
Msa0952340 MtrunA17_Chr6g0469651 56.716 134 47 2 1 124 1 133 3.26e-36 120
Msa0952340 MtrunA17_Chr7g0233191 56.075 107 45 1 1 107 1 105 4.43e-36 119
Msa0952340 MtrunA17_Chr7g0233201 56.075 107 45 1 1 107 1 105 9.84e-36 118
Msa0952340 MtrunA17_Chr6g0469541 58.879 107 42 2 1 107 1 105 1.63e-35 118
Msa0952340 MtrunA17_Chr1g0202561 51.449 138 52 2 1 123 1 138 3.34e-35 118
Msa0952340 MtrunA17_Chr7g0233181 55.660 106 45 1 1 106 1 104 8.01e-35 116
Msa0952340 MtrunA17_Chr6g0469671 77.143 70 16 0 1 70 1 70 5.95e-34 114
Msa0952340 MtrunA17_Chr1g0202501 50.000 134 53 3 1 124 1 130 1.72e-33 113
Msa0952340 MtrunA17_Chr1g0202581 56.296 135 43 4 1 123 1 131 2.01e-33 113
Msa0952340 MtrunA17_Chr8g0387471 49.618 131 55 3 1 124 1 127 3.81e-33 112
Msa0952340 MtrunA17_Chr1g0204291 52.593 135 48 4 1 123 1 131 2.69e-32 110
Msa0952340 MtrunA17_Chr7g0248671 61.765 68 26 0 1 68 1 68 8.50e-24 90.1
Msa0952340 MtrunA17_Chr8g0348361 66.176 68 23 0 1 68 1 68 8.39e-15 66.2
Msa0952340 MtrunA17_Chr3g0120541 43.210 81 42 4 3 79 5 85 1.08e-13 62.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0952340 AT1G01490.1 66.197 71 23 1 1 70 1 71 7.51e-25 93.2
Msa0952340 AT1G01490.2 66.197 71 23 1 1 70 1 71 7.51e-25 93.2
Msa0952340 AT1G01490.4 65.714 70 23 1 2 70 29 98 2.74e-24 92.4
Msa0952340 AT5G52740.1 57.143 70 28 1 1 70 1 68 5.53e-19 76.6
Msa0952340 AT5G52760.1 41.346 104 51 3 5 105 7 103 8.66e-16 68.6
Msa0952340 AT5G52750.1 45.455 66 36 0 2 67 4 69 5.54e-13 61.6
Msa0952340 AT1G63950.2 31.200 125 76 3 1 124 1 116 6.85e-11 55.8

Find 27 sgRNAs with CRISPR-Local

Find 112 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAGACTGTCTCAGGCCTTTC+TGG 0.185291 6_3:+46535272 Msa0952340:CDS
ACAGGATCTTGTTCCATTCT+TGG 0.237400 6_3:-46536107 None:intergenic
GACAAGAAATTAACCTTAAC+TGG 0.272704 6_3:+46535885 Msa0952340:CDS
TAAAAGAAGAGCTAGGGTAT+TGG 0.399065 6_3:-46535048 None:intergenic
TAAAATTTAAAAGAAGAGCT+AGG 0.408169 6_3:-46535055 None:intergenic
ATATTCCTCTGTTCCAAGAA+TGG 0.412440 6_3:+46536094 Msa0952340:CDS
TGGATCTGTGTCTCCAGTTA+AGG 0.422934 6_3:-46535898 None:intergenic
AAAAGCTTTATTGAAAATGA+TGG 0.441720 6_3:+46535106 Msa0952340:exon
GTTACAGAAACTAGTATTGA+AGG 0.451235 6_3:+46535211 Msa0952340:intron
AGTTTGCTTACTACATGTAC+TGG 0.452527 6_3:-46535918 None:intergenic
TAGTAAGCAAACTAAGGAAA+TGG 0.458647 6_3:+46535928 Msa0952340:CDS
ATGCTGAAATAGTTTCTGTT+GGG 0.476513 6_3:+46535955 Msa0952340:CDS
AAAATTTAAAAGAAGAGCTA+GGG 0.497403 6_3:-46535054 None:intergenic
AAAGCTATGAAGACTGTCTC+AGG 0.497682 6_3:+46535263 Msa0952340:CDS
CATGCTGAAATAGTTTCTGT+TGG 0.500770 6_3:+46535954 Msa0952340:CDS
TACATGTAGTAAGCAAACTA+AGG 0.515410 6_3:+46535922 Msa0952340:CDS
TAGCATATGACACATCCAAC+AGG 0.524107 6_3:-46536125 None:intergenic
ACAATGAGCTTGTAACATGT+TGG 0.535420 6_3:+46536237 Msa0952340:three_prime_UTR
GAGGAATATTGAATATATTG+TGG 0.535752 6_3:-46536080 None:intergenic
TTGTTCCATTCTTGGAACAG+AGG 0.577364 6_3:-46536099 None:intergenic
TGTTCAATTGTGCAAACAGA+GGG 0.585753 6_3:+46536287 Msa0952340:three_prime_UTR
ACAAGTTGACATTACCAGAA+AGG 0.591138 6_3:-46535286 None:intergenic
CATGTAGTAATAATGAGGAT+AGG 0.591628 6_3:-46536051 None:intergenic
AGAATGGAACAAGATCCTGT+TGG 0.646061 6_3:+46536110 Msa0952340:CDS
TGTTGCATGTAGTAATAATG+AGG 0.650568 6_3:-46536056 None:intergenic
ACAGAAACTAGTATTGAAGG+TGG 0.658613 6_3:+46535214 Msa0952340:intron
GTGTTCAATTGTGCAAACAG+AGG 0.663444 6_3:+46536286 Msa0952340:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTGAAATAATTAAGTAT+TGG + chr6_3:46535610-46535629 Msa0952340:intron 10.0%
!!! AATTTTAGCAAAAAAAATAA+AGG - chr6_3:46535814-46535833 None:intergenic 10.0%
!!! TATTTTATATATTATTTGCA+GGG + chr6_3:46535835-46535854 Msa0952340:intron 10.0%
!!! TGTATTTTCATATTATTTAT+TGG + chr6_3:46536171-46536190 Msa0952340:three_prime_UTR 10.0%
!!! TTTTTGAAATAATTAAGTAT+TGG + chr6_3:46535610-46535629 Msa0952340:intron 10.0%
!!! AATTTTAGCAAAAAAAATAA+AGG - chr6_3:46535814-46535833 None:intergenic 10.0%
!!! TATTTTATATATTATTTGCA+GGG + chr6_3:46535835-46535854 Msa0952340:intron 10.0%
!!! TGTATTTTCATATTATTTAT+TGG + chr6_3:46536171-46536190 Msa0952340:three_prime_UTR 10.0%
!!! AAAAAATTGATAGTAAAAGA+GGG - chr6_3:46535155-46535174 None:intergenic 15.0%
!! TGGAAACATTTAATATATTA+AGG + chr6_3:46535715-46535734 Msa0952340:intron 15.0%
!!! GTATTTTATATATTATTTGC+AGG + chr6_3:46535834-46535853 Msa0952340:intron 15.0%
!!! ATTTTATATATTATTTGCAG+GGG + chr6_3:46535836-46535855 Msa0952340:intron 15.0%
!!! AAAAAATTGATAGTAAAAGA+GGG - chr6_3:46535155-46535174 None:intergenic 15.0%
!! TGGAAACATTTAATATATTA+AGG + chr6_3:46535715-46535734 Msa0952340:intron 15.0%
!!! GTATTTTATATATTATTTGC+AGG + chr6_3:46535834-46535853 Msa0952340:intron 15.0%
!!! ATTTTATATATTATTTGCAG+GGG + chr6_3:46535836-46535855 Msa0952340:intron 15.0%
!! AAAATTTAAAAGAAGAGCTA+GGG - chr6_3:46535057-46535076 None:intergenic 20.0%
!! TAAAATTTAAAAGAAGAGCT+AGG - chr6_3:46535058-46535077 None:intergenic 20.0%
!!! TTTCAATAAAGCTTTTTGAT+AGG - chr6_3:46535102-46535121 None:intergenic 20.0%
!!! AAAAGCTTTATTGAAAATGA+TGG + chr6_3:46535106-46535125 Msa0952340:exon 20.0%
!!! GAAAAAATTGATAGTAAAAG+AGG - chr6_3:46535156-46535175 None:intergenic 20.0%
!!! ATGATATTCAAATTCTTTTG+AGG - chr6_3:46535500-46535519 None:intergenic 20.0%
!!! CATGATTTATATATTTTGAG+TGG + chr6_3:46536204-46536223 Msa0952340:three_prime_UTR 20.0%
!! AAAATTTAAAAGAAGAGCTA+GGG - chr6_3:46535057-46535076 None:intergenic 20.0%
!! TAAAATTTAAAAGAAGAGCT+AGG - chr6_3:46535058-46535077 None:intergenic 20.0%
!!! TTTCAATAAAGCTTTTTGAT+AGG - chr6_3:46535102-46535121 None:intergenic 20.0%
!!! AAAAGCTTTATTGAAAATGA+TGG + chr6_3:46535106-46535125 Msa0952340:exon 20.0%
!!! GAAAAAATTGATAGTAAAAG+AGG - chr6_3:46535156-46535175 None:intergenic 20.0%
!!! ATGATATTCAAATTCTTTTG+AGG - chr6_3:46535500-46535519 None:intergenic 20.0%
!!! CATGATTTATATATTTTGAG+TGG + chr6_3:46536204-46536223 Msa0952340:three_prime_UTR 20.0%
!! ACTTGTCTAGTTTCAATATT+TGG + chr6_3:46535303-46535322 Msa0952340:intron 25.0%
!! TCTAGTTTCAATATTTGGTT+TGG + chr6_3:46535308-46535327 Msa0952340:intron 25.0%
!! GATAATTGTCTTTTACTTTG+AGG + chr6_3:46535632-46535651 Msa0952340:intron 25.0%
! GAAATTAAGCTCATAATTGT+CGG + chr6_3:46535662-46535681 Msa0952340:intron 25.0%
! ATTTAATATATTAAGGCACG+TGG + chr6_3:46535722-46535741 Msa0952340:intron 25.0%
! GAGGAATATTGAATATATTG+TGG - chr6_3:46536083-46536102 None:intergenic 25.0%
! AACATGTTGGAAAAATGAAA+AGG + chr6_3:46536250-46536269 Msa0952340:three_prime_UTR 25.0%
!! ACTTGTCTAGTTTCAATATT+TGG + chr6_3:46535303-46535322 Msa0952340:intron 25.0%
!! TCTAGTTTCAATATTTGGTT+TGG + chr6_3:46535308-46535327 Msa0952340:intron 25.0%
!! GATAATTGTCTTTTACTTTG+AGG + chr6_3:46535632-46535651 Msa0952340:intron 25.0%
! GAAATTAAGCTCATAATTGT+CGG + chr6_3:46535662-46535681 Msa0952340:intron 25.0%
! ATTTAATATATTAAGGCACG+TGG + chr6_3:46535722-46535741 Msa0952340:intron 25.0%
! GAGGAATATTGAATATATTG+TGG - chr6_3:46536083-46536102 None:intergenic 25.0%
! AACATGTTGGAAAAATGAAA+AGG + chr6_3:46536250-46536269 Msa0952340:three_prime_UTR 25.0%
AGTAAAAGAGGGAATTCAAA+AGG - chr6_3:46535144-46535163 None:intergenic 30.0%
! GTTACAGAAACTAGTATTGA+AGG + chr6_3:46535211-46535230 Msa0952340:intron 30.0%
!! TTCGTTTTTCACTGTTTATG+AGG + chr6_3:46535453-46535472 Msa0952340:intron 30.0%
!!! CAAATTCTTTTGAGGTTACT+AGG - chr6_3:46535492-46535511 None:intergenic 30.0%
GACAAGAAATTAACCTTAAC+TGG + chr6_3:46535885-46535904 Msa0952340:CDS 30.0%
TACATGTAGTAAGCAAACTA+AGG + chr6_3:46535922-46535941 Msa0952340:CDS 30.0%
TAGTAAGCAAACTAAGGAAA+TGG + chr6_3:46535928-46535947 Msa0952340:CDS 30.0%
ATGCTGAAATAGTTTCTGTT+GGG + chr6_3:46535955-46535974 Msa0952340:CDS 30.0%
! TTCTTCTTTTCATCTTTTGC+AGG - chr6_3:46535981-46536000 None:intergenic 30.0%
CATGTAGTAATAATGAGGAT+AGG - chr6_3:46536054-46536073 None:intergenic 30.0%
TGTTGCATGTAGTAATAATG+AGG - chr6_3:46536059-46536078 None:intergenic 30.0%
AGTAAAAGAGGGAATTCAAA+AGG - chr6_3:46535144-46535163 None:intergenic 30.0%
! GTTACAGAAACTAGTATTGA+AGG + chr6_3:46535211-46535230 Msa0952340:intron 30.0%
!! TTCGTTTTTCACTGTTTATG+AGG + chr6_3:46535453-46535472 Msa0952340:intron 30.0%
!!! CAAATTCTTTTGAGGTTACT+AGG - chr6_3:46535492-46535511 None:intergenic 30.0%
GACAAGAAATTAACCTTAAC+TGG + chr6_3:46535885-46535904 Msa0952340:CDS 30.0%
TACATGTAGTAAGCAAACTA+AGG + chr6_3:46535922-46535941 Msa0952340:CDS 30.0%
TAGTAAGCAAACTAAGGAAA+TGG + chr6_3:46535928-46535947 Msa0952340:CDS 30.0%
ATGCTGAAATAGTTTCTGTT+GGG + chr6_3:46535955-46535974 Msa0952340:CDS 30.0%
! TTCTTCTTTTCATCTTTTGC+AGG - chr6_3:46535981-46536000 None:intergenic 30.0%
CATGTAGTAATAATGAGGAT+AGG - chr6_3:46536054-46536073 None:intergenic 30.0%
TGTTGCATGTAGTAATAATG+AGG - chr6_3:46536059-46536078 None:intergenic 30.0%
TAAAAGAAGAGCTAGGGTAT+TGG - chr6_3:46535051-46535070 None:intergenic 35.0%
! ACAGAAACTAGTATTGAAGG+TGG + chr6_3:46535214-46535233 Msa0952340:intron 35.0%
! AGTCTTCATAGCTTTTTGCT+TGG - chr6_3:46535258-46535277 None:intergenic 35.0%
! ACAAGTTGACATTACCAGAA+AGG - chr6_3:46535289-46535308 None:intergenic 35.0%
! GTTTTTCACTGTTTATGAGG+TGG + chr6_3:46535456-46535475 Msa0952340:intron 35.0%
AGTGTAACTCAAGTGGTAAA+AGG + chr6_3:46535689-46535708 Msa0952340:intron 35.0%
! AGTTTGCTTACTACATGTAC+TGG - chr6_3:46535921-46535940 None:intergenic 35.0%
CATGCTGAAATAGTTTCTGT+TGG + chr6_3:46535954-46535973 Msa0952340:CDS 35.0%
ATATTCCTCTGTTCCAAGAA+TGG + chr6_3:46536094-46536113 Msa0952340:CDS 35.0%
ACAATGAGCTTGTAACATGT+TGG + chr6_3:46536237-46536256 Msa0952340:three_prime_UTR 35.0%
TGTTCAATTGTGCAAACAGA+GGG + chr6_3:46536287-46536306 Msa0952340:three_prime_UTR 35.0%
TAAAAGAAGAGCTAGGGTAT+TGG - chr6_3:46535051-46535070 None:intergenic 35.0%
! ACAGAAACTAGTATTGAAGG+TGG + chr6_3:46535214-46535233 Msa0952340:intron 35.0%
! AGTCTTCATAGCTTTTTGCT+TGG - chr6_3:46535258-46535277 None:intergenic 35.0%
! ACAAGTTGACATTACCAGAA+AGG - chr6_3:46535289-46535308 None:intergenic 35.0%
! GTTTTTCACTGTTTATGAGG+TGG + chr6_3:46535456-46535475 Msa0952340:intron 35.0%
AGTGTAACTCAAGTGGTAAA+AGG + chr6_3:46535689-46535708 Msa0952340:intron 35.0%
! AGTTTGCTTACTACATGTAC+TGG - chr6_3:46535921-46535940 None:intergenic 35.0%
CATGCTGAAATAGTTTCTGT+TGG + chr6_3:46535954-46535973 Msa0952340:CDS 35.0%
ATATTCCTCTGTTCCAAGAA+TGG + chr6_3:46536094-46536113 Msa0952340:CDS 35.0%
ACAATGAGCTTGTAACATGT+TGG + chr6_3:46536237-46536256 Msa0952340:three_prime_UTR 35.0%
TGTTCAATTGTGCAAACAGA+GGG + chr6_3:46536287-46536306 Msa0952340:three_prime_UTR 35.0%
AAAGCTATGAAGACTGTCTC+AGG + chr6_3:46535263-46535282 Msa0952340:CDS 40.0%
ACTCAAGTGGTAAAAGGTTG+TGG + chr6_3:46535695-46535714 Msa0952340:intron 40.0%
TTGTTCCATTCTTGGAACAG+AGG - chr6_3:46536102-46536121 None:intergenic 40.0%
ACAGGATCTTGTTCCATTCT+TGG - chr6_3:46536110-46536129 None:intergenic 40.0%
AGAATGGAACAAGATCCTGT+TGG + chr6_3:46536110-46536129 Msa0952340:CDS 40.0%
TAGCATATGACACATCCAAC+AGG - chr6_3:46536128-46536147 None:intergenic 40.0%
GTGTTCAATTGTGCAAACAG+AGG + chr6_3:46536286-46536305 Msa0952340:three_prime_UTR 40.0%
AAAGCTATGAAGACTGTCTC+AGG + chr6_3:46535263-46535282 Msa0952340:CDS 40.0%
ACTCAAGTGGTAAAAGGTTG+TGG + chr6_3:46535695-46535714 Msa0952340:intron 40.0%
TTGTTCCATTCTTGGAACAG+AGG - chr6_3:46536102-46536121 None:intergenic 40.0%
ACAGGATCTTGTTCCATTCT+TGG - chr6_3:46536110-46536129 None:intergenic 40.0%
AGAATGGAACAAGATCCTGT+TGG + chr6_3:46536110-46536129 Msa0952340:CDS 40.0%
TAGCATATGACACATCCAAC+AGG - chr6_3:46536128-46536147 None:intergenic 40.0%
GTGTTCAATTGTGCAAACAG+AGG + chr6_3:46536286-46536305 Msa0952340:three_prime_UTR 40.0%
CGGCATAAGTGTAACTCAAG+TGG + chr6_3:46535682-46535701 Msa0952340:intron 45.0%
TGGATCTGTGTCTCCAGTTA+AGG - chr6_3:46535901-46535920 None:intergenic 45.0%
CGGCATAAGTGTAACTCAAG+TGG + chr6_3:46535682-46535701 Msa0952340:intron 45.0%
TGGATCTGTGTCTCCAGTTA+AGG - chr6_3:46535901-46535920 None:intergenic 45.0%
!! TATACATAATTTATTTAATA+TGG + chr6_3:46535355-46535374 Msa0952340:intron 5.0%
!!! TATTTATTTTAATTGAAAAA+TGG - chr6_3:46535549-46535568 None:intergenic 5.0%
!! TATACATAATTTATTTAATA+TGG + chr6_3:46535355-46535374 Msa0952340:intron 5.0%
!!! TATTTATTTTAATTGAAAAA+TGG - chr6_3:46535549-46535568 None:intergenic 5.0%
AAGACTGTCTCAGGCCTTTC+TGG + chr6_3:46535272-46535291 Msa0952340:CDS 50.0%
AAGACTGTCTCAGGCCTTTC+TGG + chr6_3:46535272-46535291 Msa0952340:CDS 50.0%
Chromosome Type Strat End Strand Name
chr6_3 gene 46534992 46536334 46534992 ID=Msa0952340;Name=Msa0952340
chr6_3 mRNA 46534992 46536334 46534992 ID=Msa0952340-mRNA-1;Parent=Msa0952340;Name=Msa0952340-mRNA-1;_AED=0.11;_eAED=0.11;_QI=130|1|1|1|1|1|3|186|124
chr6_3 exon 46534992 46535127 46534992 ID=Msa0952340-mRNA-1:exon:10289;Parent=Msa0952340-mRNA-1
chr6_3 exon 46535218 46535293 46535218 ID=Msa0952340-mRNA-1:exon:10290;Parent=Msa0952340-mRNA-1
chr6_3 exon 46535856 46536334 46535856 ID=Msa0952340-mRNA-1:exon:10291;Parent=Msa0952340-mRNA-1
chr6_3 five_prime_UTR 46534992 46535121 46534992 ID=Msa0952340-mRNA-1:five_prime_utr;Parent=Msa0952340-mRNA-1
chr6_3 CDS 46535122 46535127 46535122 ID=Msa0952340-mRNA-1:cds;Parent=Msa0952340-mRNA-1
chr6_3 CDS 46535218 46535293 46535218 ID=Msa0952340-mRNA-1:cds;Parent=Msa0952340-mRNA-1
chr6_3 CDS 46535856 46536148 46535856 ID=Msa0952340-mRNA-1:cds;Parent=Msa0952340-mRNA-1
chr6_3 three_prime_UTR 46536149 46536334 46536149 ID=Msa0952340-mRNA-1:three_prime_utr;Parent=Msa0952340-mRNA-1
Gene Sequence

>Msa0952340

ATGATGAAACTAGTATTGAAGGTGGATTTACATGATGACAGAACCAAGCAAAAAGCTATGAAGACTGTCTCAGGCCTTTCTGGGGTAGAGTCAGTTTCTGTAGACATGAAAGACAAGAAATTAACCTTAACTGGAGACACAGATCCAGTACATGTAGTAAGCAAACTAAGGAAATGGTGTCATGCTGAAATAGTTTCTGTTGGGCCTGCAAAAGATGAAAAGAAGAAAGAAGAATCTAAGACTGATGTGAAGAAGAATCAAATTCAATTACTTGAAGCCTATCCTCATTATTACTACATGCAACAACCACAATATATTCAATATTCCTCTGTTCCAAGAATGGAACAAGATCCTGTTGGATGTGTCATATGCTAA
Protein sequence

>Msa0952340

MMKLVLKVDLHDDRTKQKAMKTVSGLSGVESVSVDMKDKKLTLTGDTDPVHVVSKLRKWCHAEIVSVGPAKDEKKKEESKTDVKKNQIQLLEAYPHYYYMQQPQYIQYSSVPRMEQDPVGCVIC*