AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene021295

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene021295.t1 MTR_4g080787 46.531 245 126 2 30 273 223 463 1.71e-53 181
MS.gene021295.t1 MTR_7g023330 46.586 249 122 6 30 273 153 395 1.14e-52 176
MS.gene021295.t1 MTR_4g080590 44.770 239 128 4 34 271 214 449 8.55e-49 167
MS.gene021295.t1 MTR_4g080773 44.490 245 134 2 30 273 223 466 3.15e-48 167
MS.gene021295.t1 MTR_4g080773 44.490 245 134 2 30 273 223 466 4.68e-48 167
MS.gene021295.t1 MTR_4g080807 44.770 239 128 3 30 267 88 323 2.69e-47 163
MS.gene021295.t1 MTR_4g130200 49.505 202 100 2 73 273 191 391 3.33e-47 162
MS.gene021295.t1 MTR_3g048290 42.353 255 129 5 30 273 217 464 2.10e-40 146
MS.gene021295.t1 MTR_7g023310 40.385 260 124 7 30 274 214 457 2.08e-39 143
MS.gene021295.t1 MTR_5g039950 36.187 257 156 4 20 273 168 419 2.02e-35 131
MS.gene021295.t1 MTR_2g094750 43.871 155 82 3 31 180 303 457 4.96e-22 95.5
MS.gene021295.t1 MTR_7g039630 41.212 165 72 5 30 180 183 336 2.00e-21 92.4
MS.gene021295.t1 MTR_2g094450 38.690 168 85 5 31 195 48 200 1.11e-19 85.1
MS.gene021295.t1 MTR_4g080590 41.611 149 83 4 33 180 213 358 1.29e-19 87.8
MS.gene021295.t1 MTR_5g039970 50.000 108 52 1 30 135 211 318 3.47e-19 85.9
MS.gene021295.t1 MTR_4g081030 36.527 167 85 3 27 180 195 353 2.15e-14 72.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene021295.t1 AT4G14096 26.538 260 158 10 35 274 204 450 4.99e-11 63.2
MS.gene021295.t1 AT4G14096 26.538 260 158 10 35 274 204 450 4.99e-11 63.2

Find 37 sgRNAs with CRISPR-Local

Find 83 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACAATAATAAATTCTGCTTT+TGG 0.232716 6.1:+47012335 None:intergenic
TTGACACAACTTCATATTTC+GGG 0.245721 6.1:-47011963 MS.gene021295:CDS
TTTGACACAACTTCATATTT+CGG 0.272729 6.1:-47011964 MS.gene021295:CDS
GATGCATATGTGGATCATTA+TGG 0.300142 6.1:-47012293 MS.gene021295:CDS
AAAGTAAGGGCTTCCAGTTT+AGG 0.317966 6.1:+47011891 None:intergenic
GTTCTTACCACATCTTTGAT+AGG 0.338656 6.1:+47013010 None:intergenic
GGGACAAGCTGCTTGGTGTT+TGG 0.347656 6.1:-47011559 MS.gene021295:CDS
CTCGTGCATCTTAAAGATAA+AGG 0.370959 6.1:+47012362 None:intergenic
TCTCGAGAAGACTCCTAAAC+TGG 0.386564 6.1:-47011904 MS.gene021295:CDS
ATCCACATATGCATCAACTA+TGG 0.393239 6.1:+47012301 None:intergenic
TTAGGGATTTCGATACGTAT+TGG 0.412349 6.1:-47011762 MS.gene021295:intron
AGCTGCTTGGTGTTTGGAGC+CGG 0.419168 6.1:-47011553 MS.gene021295:CDS
CAATGCTTGAAAGTTGAAAC+CGG 0.458627 6.1:+47011534 None:intergenic
TTACGGTCACGATTGATGTT+GGG 0.461347 6.1:-47012388 MS.gene021295:CDS
TTTACGGTCACGATTGATGT+TGG 0.473147 6.1:-47012389 MS.gene021295:CDS
ATGCATATGTGGATCATTAT+GGG 0.490003 6.1:-47012292 MS.gene021295:CDS
TATGAAGTTGTGTCAAATTG+TGG 0.493741 6.1:+47011970 None:intergenic
TTCTTACCACATCTTTGATA+GGG 0.495142 6.1:+47013011 None:intergenic
CGGTTTCAACTTTCAAGCAT+TGG 0.496239 6.1:-47011533 MS.gene021295:CDS
AATGGTCAACTTTCTTAATG+TGG 0.502182 6.1:+47012448 None:intergenic
CTCCATAGTTGATGCATATG+TGG 0.506734 6.1:-47012303 MS.gene021295:CDS
AGATGAAGATGAAATCCAAT+TGG 0.511956 6.1:-47011657 MS.gene021295:CDS
TTGACCATTGATCTTGACTC+TGG 0.521176 6.1:-47012434 MS.gene021295:CDS
ATGCATCAACTATGGAGGTC+GGG 0.521863 6.1:+47012309 None:intergenic
AAAGATGATTTGAAACAGCA+AGG 0.543207 6.1:+47011710 None:intergenic
TAGTGTCTTTATGTTGCAAG+CGG 0.550733 6.1:-47012017 MS.gene021295:CDS
TGTGTCAAATTGTGGAATGA+AGG 0.552447 6.1:+47011978 None:intergenic
TACGATTAGCGACGTACCTG+TGG 0.555928 6.1:-47013062 MS.gene021295:CDS
ACAACCAGAGTCAAGATCAA+TGG 0.560521 6.1:+47012430 None:intergenic
GTTGATCGGGACAAGCTGCT+TGG 0.581922 6.1:-47011566 MS.gene021295:CDS
ACGTATTGGATGTTGAAGAC+TGG 0.587647 6.1:-47011748 MS.gene021295:CDS
TATGCATCAACTATGGAGGT+CGG 0.587779 6.1:+47012308 None:intergenic
AATAACGAAGTATACTCTTG+AGG 0.607707 6.1:-47012186 MS.gene021295:intron
TGACACAACTTCATATTTCG+GGG 0.629948 6.1:-47011962 MS.gene021295:CDS
ATATAAAGAAGAACATCCAC+AGG 0.631353 6.1:+47013046 None:intergenic
CACATATGCATCAACTATGG+AGG 0.645315 6.1:+47012304 None:intergenic
TAATACATAGTCAGTCAGAG+TGG 0.684256 6.1:+47011935 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GTTTTTTATAAATAATGTCA+CGG - chr6.1:47012957-47012976 MS.gene021295:intron 15.0%
!!! TGATAATGACAATAATTTTA+CGG - chr6.1:47012182-47012201 MS.gene021295:intron 15.0%
!!! TTTTGATTTTACAATTCATT+GGG - chr6.1:47011648-47011667 MS.gene021295:CDS 15.0%
!!! TTTTTGATTTTACAATTCAT+TGG - chr6.1:47011647-47011666 MS.gene021295:CDS 15.0%
!! ATATACCTTAGAAAAAGTAA+GGG + chr6.1:47012712-47012731 None:intergenic 20.0%
!! TTATAAAAAACTCAACCAAT+TGG + chr6.1:47012948-47012967 None:intergenic 20.0%
!!! AACTGATTTTTCATTTTCAA+AGG + chr6.1:47012028-47012047 None:intergenic 20.0%
!!! AATTTTTCGAGTAGAATATT+TGG + chr6.1:47012996-47013015 None:intergenic 20.0%
!!! ACAATAATAAATTCTGCTTT+TGG + chr6.1:47012255-47012274 None:intergenic 20.0%
! ATCACTCTTTATATTCATGA+TGG - chr6.1:47011958-47011977 MS.gene021295:CDS 25.0%
! CGAAAAATTTATCAGTTGAT+CGG - chr6.1:47013007-47013026 MS.gene021295:intron 25.0%
! CTTCCATATTATCAAAAAAG+TGG - chr6.1:47011599-47011618 MS.gene021295:CDS 25.0%
! GAAAAATTTATCAGTTGATC+GGG - chr6.1:47013008-47013027 MS.gene021295:intron 25.0%
! GATATACCTTAGAAAAAGTA+AGG + chr6.1:47012713-47012732 None:intergenic 25.0%
! TTAGTATCTACAAATTCAAC+AGG + chr6.1:47012479-47012498 None:intergenic 25.0%
! TTTGACACAACTTCATATTT+CGG - chr6.1:47012623-47012642 MS.gene021295:intron 25.0%
!! TCCTTGGTTAATTGTTATTA+GGG - chr6.1:47012087-47012106 MS.gene021295:intron 25.0%
!! TTTAGCATTTCAGATTTTGA+CGG - chr6.1:47012907-47012926 MS.gene021295:intron 25.0%
!! TTTTTATATTGCCTAAGATC+AGG - chr6.1:47012453-47012472 MS.gene021295:CDS 25.0%
!!! TCTCCACTTTTTTGATAATA+TGG + chr6.1:47011605-47011624 None:intergenic 25.0%
AATAACGAAGTATACTCTTG+AGG - chr6.1:47012401-47012420 MS.gene021295:CDS 30.0%
AATGGTCAACTTTCTTAATG+TGG + chr6.1:47012142-47012161 None:intergenic 30.0%
ACAAATCTCATTCTGTTGAA+AGG - chr6.1:47011749-47011768 MS.gene021295:CDS 30.0%
AGATGAAGATGAAATCCAAT+TGG - chr6.1:47012930-47012949 MS.gene021295:intron 30.0%
AGCATTTATATCATCTGCTA+AGG + chr6.1:47011872-47011891 None:intergenic 30.0%
ATATAAAGAAGAACATCCAC+AGG + chr6.1:47011544-47011563 None:intergenic 30.0%
ATGCAGCTTATTAAATGACT+TGG + chr6.1:47011926-47011945 None:intergenic 30.0%
ATGCATATGTGGATCATTAT+GGG - chr6.1:47012295-47012314 MS.gene021295:CDS 30.0%
TATGAAGTTGTGTCAAATTG+TGG + chr6.1:47012620-47012639 None:intergenic 30.0%
TTCTTACCACATCTTTGATA+GGG + chr6.1:47011579-47011598 None:intergenic 30.0%
TTGACACAACTTCATATTTC+GGG - chr6.1:47012624-47012643 MS.gene021295:intron 30.0%
! AAAGATGATTTGAAACAGCA+AGG + chr6.1:47012880-47012899 None:intergenic 30.0%
! AGGCTTTGTATTTCAATAGA+TGG - chr6.1:47011769-47011788 MS.gene021295:intron 30.0%
! CCTTGGTTAATTGTTATTAG+GGG - chr6.1:47012088-47012107 MS.gene021295:intron 30.0%
! GTCCTTGGTTAATTGTTATT+AGG - chr6.1:47012086-47012105 MS.gene021295:intron 30.0%
!! AAATAATGTCACGGTTTTAG+AGG - chr6.1:47012966-47012985 MS.gene021295:intron 30.0%
AATCGGTAAACAAGTCAAGA+TGG + chr6.1:47012800-47012819 None:intergenic 35.0%
ACTTGGAAGCTAAGAAAGTA+TGG + chr6.1:47011909-47011928 None:intergenic 35.0%
ATCCACATATGCATCAACTA+TGG + chr6.1:47012289-47012308 None:intergenic 35.0%
CAAAAAAGTGGAGATTTCTG+TGG - chr6.1:47011611-47011630 MS.gene021295:CDS 35.0%
CAATGCTTGAAAGTTGAAAC+CGG + chr6.1:47013056-47013075 None:intergenic 35.0%
CCCCTAATAACAATTAACCA+AGG + chr6.1:47012091-47012110 None:intergenic 35.0%
CTCGTGCATCTTAAAGATAA+AGG + chr6.1:47012228-47012247 None:intergenic 35.0%
GATGCATATGTGGATCATTA+TGG - chr6.1:47012294-47012313 MS.gene021295:CDS 35.0%
GCAACATAAAGACACTAGTA+AGG + chr6.1:47012567-47012586 None:intergenic 35.0%
GTTCTTACCACATCTTTGAT+AGG + chr6.1:47011580-47011599 None:intergenic 35.0%
TAATACATAGTCAGTCAGAG+TGG + chr6.1:47012655-47012674 None:intergenic 35.0%
TAGTGTCTTTATGTTGCAAG+CGG - chr6.1:47012570-47012589 MS.gene021295:intron 35.0%
TGACACAACTTCATATTTCG+GGG - chr6.1:47012625-47012644 MS.gene021295:intron 35.0%
TGTGTCAAATTGTGGAATGA+AGG + chr6.1:47012612-47012631 None:intergenic 35.0%
TTAGGGATTTCGATACGTAT+TGG - chr6.1:47012825-47012844 MS.gene021295:intron 35.0%
! AGATCTCCTCTTTGATCTTT+TGG - chr6.1:47011714-47011733 MS.gene021295:CDS 35.0%
! CAGTTCAACAACTTTTCTCT+GGG - chr6.1:47012043-47012062 MS.gene021295:intron 35.0%
! CTGCAGAATTTGGATTTTTG+TGG + chr6.1:47011696-47011715 None:intergenic 35.0%
! CTTGGAAGCTAAGAAAGTAT+GGG + chr6.1:47011908-47011927 None:intergenic 35.0%
! TCAGTTCAACAACTTTTCTC+TGG - chr6.1:47012042-47012061 MS.gene021295:intron 35.0%
! TTGGAAGCTAAGAAAGTATG+GGG + chr6.1:47011907-47011926 None:intergenic 35.0%
! TTTTCTCCCTATCAAAGATG+TGG - chr6.1:47011570-47011589 MS.gene021295:CDS 35.0%
!! TGTTTACCGATTCTGGTTTA+GGG - chr6.1:47012808-47012827 MS.gene021295:intron 35.0%
!! TTGTTTACCGATTCTGGTTT+AGG - chr6.1:47012807-47012826 MS.gene021295:intron 35.0%
AAAGTAAGGGCTTCCAGTTT+AGG + chr6.1:47012699-47012718 None:intergenic 40.0%
AAGAGGAGATCTGCAGAATT+TGG + chr6.1:47011706-47011725 None:intergenic 40.0%
AATTCAACAGGCCTGATCTT+AGG + chr6.1:47012467-47012486 None:intergenic 40.0%
ACAACCAGAGTCAAGATCAA+TGG + chr6.1:47012160-47012179 None:intergenic 40.0%
ACGTATTGGATGTTGAAGAC+TGG - chr6.1:47012839-47012858 MS.gene021295:intron 40.0%
CACATATGCATCAACTATGG+AGG + chr6.1:47012286-47012305 None:intergenic 40.0%
CGAAATCCCTAAACCAGAAT+CGG + chr6.1:47012817-47012836 None:intergenic 40.0%
CGGTTTCAACTTTCAAGCAT+TGG - chr6.1:47013054-47013073 MS.gene021295:CDS 40.0%
GTCTGTCCAAAAGATCAAAG+AGG + chr6.1:47011723-47011742 None:intergenic 40.0%
TATGCATCAACTATGGAGGT+CGG + chr6.1:47012282-47012301 None:intergenic 40.0%
TGTACTTCAAGAGTTGTCCT+TGG - chr6.1:47012071-47012090 MS.gene021295:intron 40.0%
TTACGGTCACGATTGATGTT+GGG - chr6.1:47012199-47012218 MS.gene021295:CDS 40.0%
TTGACCATTGATCTTGACTC+TGG - chr6.1:47012153-47012172 MS.gene021295:intron 40.0%
TTTACGGTCACGATTGATGT+TGG - chr6.1:47012198-47012217 MS.gene021295:CDS 40.0%
! CTCCATAGTTGATGCATATG+TGG - chr6.1:47012284-47012303 MS.gene021295:CDS 40.0%
!! CTTGACTTGTTTACCGATTC+TGG - chr6.1:47012801-47012820 MS.gene021295:intron 40.0%
!!! GGAAGCCCTTACTTTTTCTA+AGG - chr6.1:47012704-47012723 MS.gene021295:intron 40.0%
ATGCATCAACTATGGAGGTC+GGG + chr6.1:47012281-47012300 None:intergenic 45.0%
TCTCGAGAAGACTCCTAAAC+TGG - chr6.1:47012683-47012702 MS.gene021295:intron 45.0%
TACGATTAGCGACGTACCTG+TGG - chr6.1:47011525-47011544 MS.gene021295:CDS 50.0%
GTTGATCGGGACAAGCTGCT+TGG - chr6.1:47013021-47013040 MS.gene021295:CDS 55.0%
!! AGCTGCTTGGTGTTTGGAGC+CGG - chr6.1:47013034-47013053 MS.gene021295:CDS 55.0%
!! GGGACAAGCTGCTTGGTGTT+TGG - chr6.1:47013028-47013047 MS.gene021295:CDS 55.0%


Chromosome Type Strat End Strand Name
chr6.1 gene 47011508 47013101 47011508 ID=MS.gene021295
chr6.1 mRNA 47011508 47013101 47011508 ID=MS.gene021295.t1;Parent=MS.gene021295
chr6.1 exon 47013018 47013101 47013018 ID=MS.gene021295.t1.exon1;Parent=MS.gene021295.t1
chr6.1 CDS 47013018 47013101 47013018 ID=cds.MS.gene021295.t1;Parent=MS.gene021295.t1
chr6.1 exon 47012187 47012501 47012187 ID=MS.gene021295.t1.exon2;Parent=MS.gene021295.t1
chr6.1 CDS 47012187 47012501 47012187 ID=cds.MS.gene021295.t1;Parent=MS.gene021295.t1
chr6.1 exon 47011884 47012036 47011884 ID=MS.gene021295.t1.exon3;Parent=MS.gene021295.t1
chr6.1 CDS 47011884 47012036 47011884 ID=cds.MS.gene021295.t1;Parent=MS.gene021295.t1
chr6.1 exon 47011508 47011780 47011508 ID=MS.gene021295.t1.exon4;Parent=MS.gene021295.t1
chr6.1 CDS 47011508 47011780 47011508 ID=cds.MS.gene021295.t1;Parent=MS.gene021295.t1
Gene Sequence

>MS.gene021295

ATGGGTGTTATGAAAGATACGATTAGCGACGTACCTGTGGATGTTCTTCTTTATATCATGTCTTTTCTCCCTATCAAAGATGTGGTAAGAACTTCCATATTATCAAAAAAGTGGAGATTTCTGTGGACTCAGTTATCTGTTTTTGATTTTACAATTCATTGGGATGAGTCAGAGTTAAAGTCAGACCACAAAAATCCAAATTCTGCAGATCTCCTCTTTGATCTTTTGGACAGACTACTTAACAAATCTCATTCTGTTGAAAGGCTTTGTATTTCAATAGATGGAACTAGTGTTGATCAAGTTAAAGTTACTTCTTTTATATCTTCTGTTTTGAAGCACAAAGTCAACGATTTTAGTTTATCCTTAGCAGATGATATAAATGCTAGTTTTGTGTTGCCCCATACTTTCTTAGCTTCCAAGTCATTTAATAAGCTGCATTTAGATCTTAATATCACTCTTTATATTCATGATGGTATTTGTTTCTCTAGCTTGTATACATTAATACTTTCGAATGTTACCTTTGAAAATGAAAAATCAGTTCAACAACTTTTCTCTGGGTGCATTGTACTTCAAGAGTTGTCCTTGGTTAATTGTTATTAGGGGAACATAAAGCAGATCAATGTTTCAATTTCCACATTAAGAAAGTTGACCATTGATCTTGACTCTGGTTGTCATGATAATGACAATAATTTTACGGTCACGATTGATGTTGGGAATCCTTTATCTTTAAGATGCACGAGTAATCCAAAAGCAGAATTTATTATTGTTAACCCGACCTCCATAGTTGATGCATATGTGGATCATTATGGGTATGATTGTGCAAAAGATATGATTGATTTCACTATAAGTACATTTGATCTTTTGAGTATGCTTTGTAGTGTCAAATCTCTCAAAATAACGAAGTATACTCTTGAGGTATGTTTATTTTCTTATCATCTTTATTTATTTTTATATTGCCTAAGATCAGGCCTGTTGAATTTGTAGATACTAATTACGCATTGCTGATATTCGTTTCATATTCTATGTTTATCACAATAATGAATTACATTTTGTTTGCCTTACTAGTGTCTTTATGTTGCAAGCGGTTCTCTCGATCTTCTTCCTTCATTCCACAATTTGACACAACTTCATATTTCGGGGAATTCCACTCTGACTGACTATGTATTAATGAATATTCTCGAGAAGACTCCTAAACTGGAAGCCCTTACTTTTTCTAAGGTATATCTTATAATATGTTTCAGTGTCTGAGTCTGTCATGTTTCATTGCAAGCAATTACAGAAATATTATTCCATCTTGACTTGTTTACCGATTCTGGTTTAGGGATTTCGATACGTATTGGATGTTGAAGACTGGATGTCGAGTTCAGTGCCTTGCTGTTTCAAATCATCTTTCAAATTATTTAGCATTTCAGATTTTGACGGAGATGAAGATGAAATCCAATTGGTTGAGTTTTTTATAAATAATGTCACGGTTTTAGAGGAGATCCAAATATTCTACTCGAAAAATTTATCAGTTGATCGGGACAAGCTGCTTGGTGTTTGGAGCCGGTTTCAACTTTCAAGCATTGGAAGTTGTGTCATTAAGTTTCTGTAA
Protein sequence

>MS.gene021295.t1

MGVMKDTISDVPVDVLLYIMSFLPIKDVGNIKQINVSISTLRKLTIDLDSGCHDNDNNFTVTIDVGNPLSLRCTSNPKAEFIIVNPTSIVDAYVDHYGYDCAKDMIDFTISTFDLLSMLCSVKSLKITKYTLECLYVASGSLDLLPSFHNLTQLHISGNSTLTDYVLMNILEKTPKLEALTFSKGFRYVLDVEDWMSSSVPCCFKSSFKLFSISDFDGDEDEIQLVEFFINNVTVLEEIQIFYSKNLSVDRDKLLGVWSRFQLSSIGSCVIKFL