AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene060403


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060403.t1 MTR_2g036690 98.522 203 3 0 1 203 40 242 4.60e-144 401
MS.gene060403.t1 MTR_2g036690 97.872 141 3 0 1 141 40 180 1.74e-97 281
MS.gene060403.t1 MTR_2g005900 71.951 164 46 0 39 202 60 223 2.74e-78 234
MS.gene060403.t1 MTR_2g005900 40.217 92 50 2 113 200 53 143 3.25e-11 60.8
MS.gene060403.t1 MTR_7g109850 38.650 163 94 4 32 191 49 208 2.46e-25 98.2
MS.gene060403.t1 MTR_8g038785 44.318 88 49 0 31 118 48 135 3.14e-16 76.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060403.t1 AT4G25910 70.588 204 57 2 1 203 35 236 3.08e-95 277
MS.gene060403.t1 AT5G49940 70.787 178 48 1 25 202 62 235 2.26e-81 242
MS.gene060403.t1 AT5G49940 65.812 117 36 1 25 141 62 174 2.69e-44 146
MS.gene060403.t1 AT5G49940 47.297 74 34 2 133 202 85 157 6.35e-12 62.0
MS.gene060403.t1 AT4G01940 36.649 191 115 5 2 191 38 223 4.80e-26 100

Find 37 sgRNAs with CRISPR-Local

Find 69 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAGAACCTGCTTTGTTTCT+TGG 0.155090 2.1:-53602259 None:intergenic
TGTTCAACCTCCAAGATTTC+TGG 0.161640 2.1:-53602950 None:intergenic
GAAATTAGACCATATCTTAT+TGG 0.195631 2.1:+53603382 MS.gene060403:CDS
AGAGAATGTAGAGAAAGTTT+TGG 0.294107 2.1:+53602766 MS.gene060403:CDS
AGACCATATCTTATTGGAAC+TGG 0.334639 2.1:+53603388 MS.gene060403:CDS
CGATAAGATTCCAGAAATCT+TGG 0.378676 2.1:+53602940 MS.gene060403:CDS
ATGATTACATTGTTAAAGTT+CGG 0.389938 2.1:+53603440 MS.gene060403:CDS
CACACGCTCCTTGTAGTTTG+AGG 0.390945 2.1:-53602862 None:intergenic
CGGCTAAGTGGACCGGCAGC+AGG 0.440486 2.1:+53603460 MS.gene060403:CDS
AGCTGCACAGCAGCAATAGA+AGG 0.442231 2.1:-53603532 None:intergenic
TGAAGTAAGGCCTGGTTTGA+TGG 0.459751 2.1:+53602790 MS.gene060403:CDS
CTCAACCATGACATTGAAGA+TGG 0.471530 2.1:+53602898 MS.gene060403:CDS
ATTGTTAAAGTTCGGCTAAG+TGG 0.495444 2.1:+53603448 MS.gene060403:CDS
TCCTTGAAGAATCTTATAGC+AGG 0.507331 2.1:+53602145 None:intergenic
GACCATATCTTATTGGAACT+GGG 0.523059 2.1:+53603389 MS.gene060403:CDS
CATTCTCTTCTGTCAGTGGC+AGG 0.536464 2.1:-53602751 None:intergenic
TCTACATTCTCTTCTGTCAG+TGG 0.539215 2.1:-53602755 None:intergenic
GATCCCCATCTTCAATGTCA+TGG 0.540108 2.1:-53602903 None:intergenic
TAAAGTTCGGCTAAGTGGAC+CGG 0.546274 2.1:+53603453 MS.gene060403:CDS
CCTCCATCAGCCATCAAACC+AGG 0.556402 2.1:-53602800 None:intergenic
GTTGTTATCCTCAAACTACA+AGG 0.559144 2.1:+53602854 MS.gene060403:CDS
GTGGCATTGCATGAGATAGA+TGG 0.565280 2.1:+53602827 MS.gene060403:CDS
TTCAATGTCATGGTTGAGCT+AGG 0.567639 2.1:-53602893 None:intergenic
TCAACCATGACATTGAAGAT+GGG 0.574515 2.1:+53602899 MS.gene060403:CDS
CAGATACTAGATACTGAGAC+TGG 0.580123 2.1:+53602971 MS.gene060403:CDS
TAAGATTCCAGAAATCTTGG+AGG 0.581548 2.1:+53602943 MS.gene060403:CDS
CTGGTTTGATGGCTGATGGA+GGG 0.590897 2.1:+53602801 MS.gene060403:CDS
CCTGGTTTGATGGCTGATGG+AGG 0.592266 2.1:+53602800 MS.gene060403:CDS
GTCAGTGGCAGGACACATCT+CGG 0.597217 2.1:-53602740 None:intergenic
ACCATATCTTATTGGAACTG+GGG 0.604069 2.1:+53603390 MS.gene060403:CDS
CCATATCTTATTGGAACTGG+GGG 0.604476 2.1:+53603391 MS.gene060403:CDS
GATGGCTGATGGAGGGAATG+TGG 0.613469 2.1:+53602808 MS.gene060403:CDS
AGGCCTGGTTTGATGGCTGA+TGG 0.614038 2.1:+53602797 MS.gene060403:CDS
CGTGCTCCAAGAAACAAAGC+AGG 0.615747 2.1:+53602253 MS.gene060403:CDS
CAACCATGACATTGAAGATG+GGG 0.616574 2.1:+53602900 MS.gene060403:CDS
ACTGTCATAACTCCTGCTGC+CGG 0.622897 2.1:-53603472 None:intergenic
CTCAAACTACAAGGAGCGTG+TGG 0.626569 2.1:+53602863 MS.gene060403:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAATCATGAATTCATATTA+AGG - chr2.1:53602440-53602459 None:intergenic 15.0%
!!! ATAAAATTATTCATTTTTCC+AGG + chr2.1:53603351-53603370 MS.gene060403:intron 15.0%
!!! ATTAATATTAAGCAAGTTTT+CGG + chr2.1:53602217-53602236 MS.gene060403:CDS 15.0%
!!! GTTAAATTTTAATCAATTCT+TGG + chr2.1:53602322-53602341 MS.gene060403:intron 15.0%
!! ATGATTACATTGTTAAAGTT+CGG + chr2.1:53603440-53603459 MS.gene060403:CDS 20.0%
!! GTGATATACAAATGAAATTA+TGG - chr2.1:53603066-53603085 None:intergenic 20.0%
!!! AATCAATTCTTGGATTTTAT+TGG + chr2.1:53602332-53602351 MS.gene060403:intron 20.0%
!!! TTAATATTAAGCAAGTTTTC+GGG + chr2.1:53602218-53602237 MS.gene060403:CDS 20.0%
! AATTTCTCTACAAACATGTA+AGG - chr2.1:53603235-53603254 None:intergenic 25.0%
! GAAATTAGACCATATCTTAT+TGG + chr2.1:53603382-53603401 MS.gene060403:CDS 25.0%
AATGCAAGAAATGATGCATA+AGG - chr2.1:53603042-53603061 None:intergenic 30.0%
ACTAAGTTGTTTATCCAAAC+AGG + chr2.1:53603175-53603194 MS.gene060403:intron 30.0%
! ACGCTATTCTTGAGATTTTA+TGG - chr2.1:53603120-53603139 None:intergenic 30.0%
! AGAGAATGTAGAGAAAGTTT+TGG + chr2.1:53602766-53602785 MS.gene060403:CDS 30.0%
! ATGTCGAAAGTGTATGTAAT+TGG + chr2.1:53603014-53603033 MS.gene060403:intron 30.0%
! CGCTATTCTTGAGATTTTAT+GGG - chr2.1:53603119-53603138 None:intergenic 30.0%
! TACACTTTCGACATTTTCTT+CGG - chr2.1:53603008-53603027 None:intergenic 30.0%
!!! AGAAAGTTTTGGATGAAGTA+AGG + chr2.1:53602777-53602796 MS.gene060403:CDS 30.0%
!!! CATTGCAATGTTTTTTTTGC+AGG + chr2.1:53602704-53602723 MS.gene060403:intron 30.0%
ACCATATCTTATTGGAACTG+GGG + chr2.1:53603390-53603409 MS.gene060403:CDS 35.0%
AGACCATATCTTATTGGAAC+TGG + chr2.1:53603388-53603407 MS.gene060403:CDS 35.0%
AGTTAAGCACTTACCTTATC+AGG - chr2.1:53603158-53603177 None:intergenic 35.0%
ATTGTTAAAGTTCGGCTAAG+TGG + chr2.1:53603448-53603467 MS.gene060403:CDS 35.0%
CGATAAGATTCCAGAAATCT+TGG + chr2.1:53602940-53602959 MS.gene060403:CDS 35.0%
GAAAACAGTTTGACCTGATA+AGG + chr2.1:53603142-53603161 MS.gene060403:intron 35.0%
GACCATATCTTATTGGAACT+GGG + chr2.1:53603389-53603408 MS.gene060403:CDS 35.0%
GTTGTTATCCTCAAACTACA+AGG + chr2.1:53602854-53602873 MS.gene060403:CDS 35.0%
TAAGATTCCAGAAATCTTGG+AGG + chr2.1:53602943-53602962 MS.gene060403:CDS 35.0%
TCAACCATGACATTGAAGAT+GGG + chr2.1:53602899-53602918 MS.gene060403:CDS 35.0%
TTGTGAACTTAGATCCTGTT+TGG - chr2.1:53603192-53603211 None:intergenic 35.0%
! AATGAGTGTTGTGTCTCTAT+TGG - chr2.1:53602486-53602505 None:intergenic 35.0%
! ATCTAATCAAGTAGCTTGCA+AGG + chr2.1:53602650-53602669 MS.gene060403:intron 35.0%
! GTCTAATTTCTGAAAGAACC+TGG - chr2.1:53603372-53603391 None:intergenic 35.0%
! TCTAATCAAGTAGCTTGCAA+GGG + chr2.1:53602651-53602670 MS.gene060403:intron 35.0%
!! AATGAGAGTTGTTTTCTCAG+AGG + chr2.1:53602187-53602206 MS.gene060403:CDS 35.0%
AACATGTGTCAGTGTCATGT+TGG + chr2.1:53602553-53602572 MS.gene060403:intron 40.0%
CAACCATGACATTGAAGATG+GGG + chr2.1:53602900-53602919 MS.gene060403:CDS 40.0%
CACAACACTCATTGACATGT+AGG + chr2.1:53602493-53602512 MS.gene060403:intron 40.0%
CAGATACTAGATACTGAGAC+TGG + chr2.1:53602971-53602990 MS.gene060403:CDS 40.0%
CCATATCTTATTGGAACTGG+GGG + chr2.1:53603391-53603410 MS.gene060403:CDS 40.0%
CTCAACCATGACATTGAAGA+TGG + chr2.1:53602898-53602917 MS.gene060403:CDS 40.0%
TCTACATTCTCTTCTGTCAG+TGG - chr2.1:53602758-53602777 None:intergenic 40.0%
TGTTCAACCTCCAAGATTTC+TGG - chr2.1:53602953-53602972 None:intergenic 40.0%
TTCAATGTCATGGTTGAGCT+AGG - chr2.1:53602896-53602915 None:intergenic 40.0%
!! GAAGAACCTGCTTTGTTTCT+TGG - chr2.1:53602262-53602281 None:intergenic 40.0%
CCAAACACGTCGTCAATCTA+AGG + chr2.1:53602602-53602621 MS.gene060403:intron 45.0%
CCCCCAGTTCCAATAAGATA+TGG - chr2.1:53603394-53603413 None:intergenic 45.0%
CCTTAGATTGACGACGTGTT+TGG - chr2.1:53602605-53602624 None:intergenic 45.0%
GATCCCCATCTTCAATGTCA+TGG - chr2.1:53602906-53602925 None:intergenic 45.0%
GTGGCATTGCATGAGATAGA+TGG + chr2.1:53602827-53602846 MS.gene060403:CDS 45.0%
TAAAGTTCGGCTAAGTGGAC+CGG + chr2.1:53603453-53603472 MS.gene060403:CDS 45.0%
TATCTTATTGGAACTGGGGG+AGG + chr2.1:53603394-53603413 MS.gene060403:CDS 45.0%
! TGAAGTAAGGCCTGGTTTGA+TGG + chr2.1:53602790-53602809 MS.gene060403:CDS 45.0%
! TTGGTGTCTGACATGTGTCA+GGG - chr2.1:53602586-53602605 None:intergenic 45.0%
!! GTTTTGGATGAAGTAAGGCC+TGG + chr2.1:53602782-53602801 MS.gene060403:CDS 45.0%
!! TTTGGTGTCTGACATGTGTC+AGG - chr2.1:53602587-53602606 None:intergenic 45.0%
ACTGTCATAACTCCTGCTGC+CGG - chr2.1:53603475-53603494 None:intergenic 50.0%
AGCTGCACAGCAGCAATAGA+AGG - chr2.1:53603535-53603554 None:intergenic 50.0%
CACACGCTCCTTGTAGTTTG+AGG - chr2.1:53602865-53602884 None:intergenic 50.0%
CATTCTCTTCTGTCAGTGGC+AGG - chr2.1:53602754-53602773 None:intergenic 50.0%
CGTGCTCCAAGAAACAAAGC+AGG + chr2.1:53602253-53602272 MS.gene060403:CDS 50.0%
! CTCAAACTACAAGGAGCGTG+TGG + chr2.1:53602863-53602882 MS.gene060403:CDS 50.0%
! CTGGTTTGATGGCTGATGGA+GGG + chr2.1:53602801-53602820 MS.gene060403:CDS 50.0%
CCTCCATCAGCCATCAAACC+AGG - chr2.1:53602803-53602822 None:intergenic 55.0%
GATGGCTGATGGAGGGAATG+TGG + chr2.1:53602808-53602827 MS.gene060403:CDS 55.0%
GTCAGTGGCAGGACACATCT+CGG - chr2.1:53602743-53602762 None:intergenic 55.0%
! AGGCCTGGTTTGATGGCTGA+TGG + chr2.1:53602797-53602816 MS.gene060403:CDS 55.0%
! CCTGGTTTGATGGCTGATGG+AGG + chr2.1:53602800-53602819 MS.gene060403:CDS 55.0%
CGGCTAAGTGGACCGGCAGC+AGG + chr2.1:53603460-53603479 MS.gene060403:CDS 70.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 53602154 53603564 53602154 ID=MS.gene060403
chr2.1 mRNA 53602154 53603564 53602154 ID=MS.gene060403.t1;Parent=MS.gene060403
chr2.1 exon 53602154 53602274 53602154 ID=MS.gene060403.t1.exon1;Parent=MS.gene060403.t1
chr2.1 CDS 53602154 53602274 53602154 ID=cds.MS.gene060403.t1;Parent=MS.gene060403.t1
chr2.1 exon 53602726 53603024 53602726 ID=MS.gene060403.t1.exon2;Parent=MS.gene060403.t1
chr2.1 CDS 53602726 53603024 53602726 ID=cds.MS.gene060403.t1;Parent=MS.gene060403.t1
chr2.1 exon 53603373 53603564 53603373 ID=MS.gene060403.t1.exon3;Parent=MS.gene060403.t1
chr2.1 CDS 53603373 53603564 53603373 ID=cds.MS.gene060403.t1;Parent=MS.gene060403.t1
Gene Sequence

>MS.gene060403

AATCTTATAGCAGGTAATAGAAGATTTTCATCAAATGAGAGTTGTTTTCTCAGAGGTCATCAAATTAATATTAAGCAAGTTTTCGGGCTAATCTCTCGTCGTGCTCCAAGAAACAAAGCAGGTTCTTCTAGAGTTTCATCAATTTGAATATACTTGTATTCATTATTTGTTAAATTTTAATCAATTCTTGGATTTTATTGGATGAAAGTTAGTACTAGTAGTTTAGTATAATACATTTCAATTGTTTAGCACTAAGATAATTGAAAGTGTGACTGATTTTGTTCCTTAATATGAATTCATGATTTTAACAAATTGCAATCTATGAAGCACCAATAGAGACACAACACTCATTGACATGTAGGTTTAGTAATAATTTAAAAAATACAAGTGATTAAACGTAACATGTGTCAGTGTCATGTTGGTGTCAGACCCTGACACATGTCAGACACCAAACACGTCGTCAATCTAAGGTGACAGTGCTACATAGATTGCAATCATCTAATCAAGTAGCTTGCAAGGGATGTGAGAAAATAGTTGAATCTAGCATTCACATTGCAATGTTTTTTTTGCAGGACTTTTTGTTTCTCCGAGATGTGTCCTGCCACTGACAGAAGAGAATGTAGAGAAAGTTTTGGATGAAGTAAGGCCTGGTTTGATGGCTGATGGAGGGAATGTGGCATTGCATGAGATAGATGGTCTTGTTGTTATCCTCAAACTACAAGGAGCGTGTGGATCATGTCCTAGCTCAACCATGACATTGAAGATGGGGATCGAAACTCGTCTTCGCGATAAGATTCCAGAAATCTTGGAGGTTGAACAGATACTAGATACTGAGACTGGTCTTGAGCTAACCGAAGAAAATGTCGAAAGTGTATGTAATTGGAACCTTATGCATCATTTCTTGCATTGCCATAATTTCATTTGTATATCACTTACTTCGTAAAAAAACATAAAAGCTTCTTCCCATAAAATCTCAAGAATAGCGTGTGAAAACAGTTTGACCTGATAAGGTAAGTGCTTAACTAAGTTGTTTATCCAAACAGGATCTAAGTTCACAAATATTCTCATATTTATAGTGCCTTACATGTTTGTAGAGAAATTATCTATAAGAAAACATTGACATGTATCTATATAAGCTGAATAATTATGTTGCTAGTGACAACTTCTTGTTGCTTTAATGTAAAGATTGCGAATCATATAAAATTATTCATTTTTCCAGGTTCTTTCAGAAATTAGACCATATCTTATTGGAACTGGGGGAGGAACATTAGAGCTTGTTGAAATTAATGATTACATTGTTAAAGTTCGGCTAAGTGGACCGGCAGCAGGAGTTATGACAGTTCGTGTTGCGTTAACGCAGAAGCTGAGAGACAAGATACCTTCTATTGCTGCTGTGCAGCTAATAGAATGA

Protein sequence

>MS.gene060403.t1

NLIAGNRRFSSNESCFLRGHQINIKQVFGLISRRAPRNKAGLFVSPRCVLPLTEENVEKVLDEVRPGLMADGGNVALHEIDGLVVILKLQGACGSCPSSTMTLKMGIETRLRDKIPEILEVEQILDTETGLELTEENVESVLSEIRPYLIGTGGGTLELVEINDYIVKVRLSGPAAGVMTVRVALTQKLRDKIPSIAAVQLIE