AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene27227

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene27227.t1 MTR_8g073345 100.000 109 0 0 1 109 1 109 5.23e-76 221
MS.gene27227.t1 MTR_8g073345 100.000 109 0 0 1 109 1 109 1.16e-75 220
MS.gene27227.t1 MTR_5g024180 68.182 110 34 1 1 110 1 109 4.40e-48 150
MS.gene27227.t1 MTR_3g115580 64.286 112 34 3 3 108 5 116 8.27e-38 125
MS.gene27227.t1 MTR_7g082820 62.651 83 30 1 28 110 4 85 6.80e-29 102
MS.gene27227.t1 MTR_7g068280 63.158 76 28 0 33 108 47 122 1.55e-28 102
MS.gene27227.t1 MTR_4g094622 49.351 77 39 0 33 109 60 136 8.61e-23 87.0
MS.gene27227.t1 MTR_1g115220 51.351 74 36 0 33 106 98 171 2.11e-22 87.4
MS.gene27227.t1 MTR_5g024180 59.091 66 24 1 44 106 3 68 8.53e-20 77.8
MS.gene27227.t1 MTR_1g022345 44.000 75 41 1 33 107 554 627 1.80e-12 62.8
MS.gene27227.t1 MTR_8g099305 44.737 76 39 1 33 108 262 334 2.32e-12 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene27227.t1 AT1G20696 68.539 89 28 0 25 113 23 111 8.30e-37 122
MS.gene27227.t1 AT1G20696 70.930 86 25 0 25 110 23 108 1.54e-36 121
MS.gene27227.t1 AT1G20693 67.391 92 26 1 18 109 23 110 6.41e-36 120
MS.gene27227.t1 AT1G20693 67.391 92 26 1 18 109 23 110 6.46e-36 120
MS.gene27227.t1 AT1G20693 67.391 92 26 1 18 109 23 110 6.65e-36 120
MS.gene27227.t1 AT1G20696 70.588 85 25 0 25 109 23 107 2.41e-35 118
MS.gene27227.t1 AT2G17560 57.143 105 41 1 5 109 7 107 7.34e-35 117
MS.gene27227.t1 AT2G17560 57.143 105 41 1 5 109 7 107 7.34e-35 117
MS.gene27227.t1 AT2G17560 56.075 107 43 1 5 111 7 109 8.50e-35 117
MS.gene27227.t1 AT4G35570 46.789 109 53 1 3 111 5 108 1.17e-32 111
MS.gene27227.t1 AT4G35570 46.789 109 53 1 3 111 5 108 1.17e-32 111
MS.gene27227.t1 AT3G51880 62.353 85 32 0 25 109 41 125 1.15e-30 107
MS.gene27227.t1 AT3G51880 62.353 85 32 0 25 109 41 125 1.49e-30 107
MS.gene27227.t1 AT3G51880 62.353 85 32 0 25 109 41 125 1.49e-30 107
MS.gene27227.t1 AT3G51880 62.353 85 32 0 25 109 41 125 1.49e-30 107
MS.gene27227.t1 AT3G51880 62.353 85 32 0 25 109 41 125 1.53e-30 107
MS.gene27227.t1 AT1G20696 61.538 65 25 0 45 109 1 65 8.05e-21 80.5
MS.gene27227.t1 AT1G20696 61.538 65 25 0 45 109 1 65 1.03e-20 80.1
MS.gene27227.t1 AT2G34450 45.205 73 40 0 37 109 63 135 6.64e-20 79.7
MS.gene27227.t1 AT2G34450 45.205 73 40 0 37 109 63 135 6.64e-20 79.7
MS.gene27227.t1 AT2G34450 45.205 73 40 0 37 109 63 135 6.64e-20 79.7
MS.gene27227.t1 AT2G34450 44.595 74 40 1 37 109 63 136 2.03e-18 75.9
MS.gene27227.t1 AT5G23420 50.000 72 33 2 28 98 106 175 3.87e-15 68.9
MS.gene27227.t1 AT4G23800 42.308 78 40 2 33 108 369 443 2.43e-11 59.3
MS.gene27227.t1 AT4G23800 45.205 73 37 1 33 105 251 320 4.99e-11 58.5
MS.gene27227.t1 AT4G23800 42.308 78 40 2 33 108 375 449 2.46e-11 59.3
MS.gene27227.t1 AT4G23800 45.205 73 37 1 33 105 251 320 5.20e-11 58.5
MS.gene27227.t1 AT4G11080 45.205 73 37 1 33 105 242 311 6.29e-11 58.2

Find 25 sgRNAs with CRISPR-Local

Find 41 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGAGGCCTCTTTGGCTTGTT+AGG 0.248195 8.3:+29035612 None:intergenic
AAAGCACTTGGAGGCCTCTT+TGG 0.273715 8.3:+29035603 None:intergenic
CTTATACTGTTCTCTAAAAT+CGG 0.321982 8.3:+29035467 None:intergenic
ATTCACCAGTTTCTTGTTGT+AGG 0.325921 8.3:+29035054 None:intergenic
GCGGCAACGGATTTGTTGTT+AGG 0.341320 8.3:+29035435 None:intergenic
TTACCGGTTATCAGCGGGTT+TGG 0.344714 8.3:+29035826 None:intergenic
TTGGAATCAGCTTTAACTTT+CGG 0.360829 8.3:+29035845 None:intergenic
AGCTTGAAGCGCAAAGGTGC+TGG 0.381485 8.3:-29035672 MS.gene27227:CDS
TTCTTTCTTCTTCAATGCCC+TGG 0.433917 8.3:+29035099 None:intergenic
TTCAATGCCCTGGCAGCATA+AGG 0.435858 8.3:+29035109 None:intergenic
ATTCCAAACCCGCTGATAAC+CGG 0.438213 8.3:-29035829 MS.gene27227:intron
ACAAGCCTACAACAAGAAAC+TGG 0.447828 8.3:-29035059 MS.gene27227:CDS
AAGCGCAAAGGTGCTGGAGC+TGG 0.461656 8.3:-29035666 MS.gene27227:CDS
ACAAGGCACCTTATGCTGCC+AGG 0.470959 8.3:-29035117 MS.gene27227:CDS
GCGATTTACCGGTTATCAGC+GGG 0.487221 8.3:+29035821 None:intergenic
GAGATTTCTTACAGCGGCAA+CGG 0.506191 8.3:+29035422 None:intergenic
GAAAAGCTTGCGGTGAAGCA+TGG 0.538505 8.3:-29035288 MS.gene27227:CDS
AAAACGAAGAAAGCACTTGG+AGG 0.557236 8.3:+29035594 None:intergenic
ATCAGCTTTAACTTTCGGCA+TGG 0.563633 8.3:+29035850 None:intergenic
CAAGGCACCTTATGCTGCCA+GGG 0.575091 8.3:-29035116 MS.gene27227:CDS
ATGAAAACGAAGAAAGCACT+TGG 0.589018 8.3:+29035591 None:intergenic
AATTAGGTCGGAAAAGCTTG+CGG 0.608945 8.3:-29035298 MS.gene27227:intron
AAGATCCTAACAAGCCAAAG+AGG 0.610559 8.3:-29035617 MS.gene27227:CDS
GCAAAGGTGCTGGAGCTGGA+AGG 0.622916 8.3:-29035662 MS.gene27227:CDS
AGCGATTTACCGGTTATCAG+CGG 0.628276 8.3:+29035820 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAAAAAATATTAAAAAAAT+TGG + chr8.3:29035117-29035136 None:intergenic 0.0%
!!! TTTTTATTTATTTTATTTTT+TGG - chr8.3:29035502-29035521 MS.gene27227:intron 0.0%
!!! TAATTTTTCGAAATTTAATT+AGG - chr8.3:29035573-29035592 MS.gene27227:intron 10.0%
!!! TTAATTTTAATTGATGATTT+AGG - chr8.3:29035396-29035415 MS.gene27227:intron 10.0%
!! AATATTAAAAAAATTGGAGA+AGG + chr8.3:29035111-29035130 None:intergenic 15.0%
!!! ATTTTTTGGATCATAATTTG+TGG - chr8.3:29035516-29035535 MS.gene27227:intron 20.0%
!!! TTTTCGAAATTTAATTAGGT+CGG - chr8.3:29035577-29035596 MS.gene27227:intron 20.0%
!! AATTTGTGGATTTTTACTGT+CGG - chr8.3:29035530-29035549 MS.gene27227:intron 25.0%
!!! CTGATTTGTTCGTTTTTTAA+CGG - chr8.3:29035369-29035388 MS.gene27227:intron 25.0%
!!! CTTATACTGTTCTCTAAAAT+CGG + chr8.3:29035423-29035442 None:intergenic 25.0%
CAACCAAAACAGATTCAAAT+CGG + chr8.3:29035336-29035355 None:intergenic 30.0%
! TTGGAATCAGCTTTAACTTT+CGG + chr8.3:29035045-29035064 None:intergenic 30.0%
!! TTTCCGATTTGAATCTGTTT+TGG - chr8.3:29035330-29035349 MS.gene27227:intron 30.0%
!!! GTACTGTGATTTTGTTTTTC+AGG - chr8.3:29035747-29035766 MS.gene27227:intron 30.0%
!!! TGATTTTGTTTTTCAGGACA+AGG - chr8.3:29035753-29035772 MS.gene27227:intron 30.0%
GTAAACGAGATTTCTTACAG+CGG + chr8.3:29035474-29035493 None:intergenic 35.0%
TTGGAGAAGGAAAAATCGAA+CGG + chr8.3:29035098-29035117 None:intergenic 35.0%
! ATTCACCAGTTTCTTGTTGT+AGG + chr8.3:29035836-29035855 None:intergenic 35.0%
!! ATGAAAACGAAGAAAGCACT+TGG + chr8.3:29035299-29035318 None:intergenic 35.0%
AAGATCCTAACAAGCCAAAG+AGG - chr8.3:29035270-29035289 MS.gene27227:CDS 40.0%
AATTAGGTCGGAAAAGCTTG+CGG - chr8.3:29035589-29035608 MS.gene27227:intron 40.0%
ACAAGCCTACAACAAGAAAC+TGG - chr8.3:29035828-29035847 MS.gene27227:intron 40.0%
TTCTTTCTTCTTCAATGCCC+TGG + chr8.3:29035791-29035810 None:intergenic 40.0%
!! AAAACGAAGAAAGCACTTGG+AGG + chr8.3:29035296-29035315 None:intergenic 40.0%
!!! GATTTTAGCTTGAAGCGCAA+AGG - chr8.3:29035209-29035228 MS.gene27227:intron 40.0%
AACGGAGAGAAGCGATTTAC+CGG + chr8.3:29035080-29035099 None:intergenic 45.0%
ATTCCAAACCCGCTGATAAC+CGG - chr8.3:29035058-29035077 MS.gene27227:CDS 45.0%
GAGATTTCTTACAGCGGCAA+CGG + chr8.3:29035468-29035487 None:intergenic 45.0%
! AGCGATTTACCGGTTATCAG+CGG + chr8.3:29035070-29035089 None:intergenic 45.0%
GAAAAGCTTGCGGTGAAGCA+TGG - chr8.3:29035599-29035618 MS.gene27227:CDS 50.0%
TTCAATGCCCTGGCAGCATA+AGG + chr8.3:29035781-29035800 None:intergenic 50.0%
! AAAGCACTTGGAGGCCTCTT+TGG + chr8.3:29035287-29035306 None:intergenic 50.0%
! GCGATTTACCGGTTATCAGC+GGG + chr8.3:29035069-29035088 None:intergenic 50.0%
! TTACCGGTTATCAGCGGGTT+TGG + chr8.3:29035064-29035083 None:intergenic 50.0%
!! GCGGCAACGGATTTGTTGTT+AGG + chr8.3:29035455-29035474 None:intergenic 50.0%
! ACAAGGCACCTTATGCTGCC+AGG - chr8.3:29035770-29035789 MS.gene27227:intron 55.0%
! AGCTTGAAGCGCAAAGGTGC+TGG - chr8.3:29035215-29035234 MS.gene27227:intron 55.0%
! CAAGGCACCTTATGCTGCCA+GGG - chr8.3:29035771-29035790 MS.gene27227:intron 55.0%
!! GGAGGCCTCTTTGGCTTGTT+AGG + chr8.3:29035278-29035297 None:intergenic 55.0%
!! AAGCGCAAAGGTGCTGGAGC+TGG - chr8.3:29035221-29035240 MS.gene27227:intron 60.0%
!! GCAAAGGTGCTGGAGCTGGA+AGG - chr8.3:29035225-29035244 MS.gene27227:intron 60.0%


Chromosome Type Strat End Strand Name
chr8.3 gene 29035039 29035870 29035039 ID=MS.gene27227
chr8.3 mRNA 29035039 29035870 29035039 ID=MS.gene27227.t1;Parent=MS.gene27227
chr8.3 exon 29035830 29035870 29035830 ID=MS.gene27227.t1.exon1;Parent=MS.gene27227.t1
chr8.3 CDS 29035830 29035870 29035830 ID=cds.MS.gene27227.t1;Parent=MS.gene27227.t1
chr8.3 exon 29035591 29035692 29035591 ID=MS.gene27227.t1.exon2;Parent=MS.gene27227.t1
chr8.3 CDS 29035591 29035692 29035591 ID=cds.MS.gene27227.t1;Parent=MS.gene27227.t1
chr8.3 exon 29035434 29035491 29035434 ID=MS.gene27227.t1.exon3;Parent=MS.gene27227.t1
chr8.3 CDS 29035434 29035491 29035434 ID=cds.MS.gene27227.t1;Parent=MS.gene27227.t1
chr8.3 exon 29035270 29035314 29035270 ID=MS.gene27227.t1.exon4;Parent=MS.gene27227.t1
chr8.3 CDS 29035270 29035314 29035270 ID=cds.MS.gene27227.t1;Parent=MS.gene27227.t1
chr8.3 exon 29035039 29035140 29035039 ID=MS.gene27227.t1.exon5;Parent=MS.gene27227.t1
chr8.3 CDS 29035039 29035140 29035039 ID=cds.MS.gene27227.t1;Parent=MS.gene27227.t1
Gene Sequence

>MS.gene27227

ATGCCGAAAGTTAAAGCTGATTCCAAACCCGCTGATAACCGGTAAATCGCTTCTCTCCGTTCGATTTTTCCTTCTCCAATTTTTTTAATATTTTTTTAGATCTGATTAGTTCGATCTAGTTTTTGTTGATTTTTTGCTATTTTTGTTGATTTTTCGATTTCTTTTTTGTTGATTTTAGCTTGAAGCGCAAAGGTGCTGGAGCTGGAAGGAAACAGACGAAGAAAGCAGCGAAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCATGTATAATTTTTTTTCCGATTTGAATCTGTTTTGGTTGTGAATTTTTGTTTCTGATTTGTTCGTTTTTTAACGGTTTTTTAATTTTAATTGATGATTTAGGTCCGATTTTAGAGAACAGTATAAGAAAGATCATCCTAACAACAAATCCGTTGCCGCTGTAAGAAATCTCGTTTACTTTTCGATTTTTTATTTATTTTATTTTTTGGATCATAATTTGTGGATTTTTACTGTCGGAAAATTATTATTATTTTAATTAATTTTTCGAAATTTAATTAGGTCGGAAAAGCTTGCGGTGAAGCATGGAAATCGATGTCTGAAGAAGTGAGTTATTTTATGCTTGATTTTTTATTTTTAACTTTCATTTTTATTATGTGATTTAATTAATTTAATTAATCAATTATATATAGTTTTTTTTTTTAATTTAGTTTGTACTGTGATTTTGTTTTTCAGGACAAGGCACCTTATGCTGCCAGGGCATTGAAGAAGAAAGAAGAGTATGAAGTTGCTACACAAGCCTACAACAAGAAACTGGTGAATATTCATTCATATTAG
Protein sequence

>MS.gene27227.t1

MPKVKADSKPADNRLKRKGAGAGRKQTKKAAKDPNKPKRPPSAFFVFMSDFREQYKKDHPNNKSVAAVGKACGEAWKSMSEEDKAPYAARALKKKEEYEVATQAYNKKLVNIHSY