AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene036215

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene036215.t1 MTR_1g072110 93.750 240 12 2 1 240 1 237 7.90e-137 384
MS.gene036215.t1 MTR_7g095150 51.037 241 59 10 6 238 12 201 8.56e-60 187
MS.gene036215.t1 MTR_1g103640 47.101 138 50 3 102 237 63 179 1.14e-34 124
MS.gene036215.t1 MTR_2g102140 38.636 132 69 3 118 237 142 273 1.51e-17 80.5
MS.gene036215.t1 MTR_7g105780 40.157 127 52 5 111 237 97 199 1.84e-17 79.7
MS.gene036215.t1 MTR_4g012060 50.649 77 35 2 159 234 175 249 9.39e-16 75.1
MS.gene036215.t1 MTR_1g111640 51.429 70 29 2 166 235 135 199 7.39e-15 72.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene036215.t1 AT1G05420 37.220 223 87 7 49 239 19 220 1.02e-27 105
MS.gene036215.t1 AT1G05420 37.220 223 87 7 49 239 35 236 1.53e-27 105
MS.gene036215.t1 AT2G32100 37.423 163 72 5 95 239 88 238 7.51e-24 96.3
MS.gene036215.t1 AT4G14860 57.143 77 31 1 165 239 96 172 3.80e-22 90.1
MS.gene036215.t1 AT1G79960 45.946 74 40 0 164 237 187 260 3.16e-17 79.3
MS.gene036215.t1 AT5G04820 32.895 152 89 4 86 237 74 212 2.49e-15 73.6
MS.gene036215.t1 AT2G36050 33.600 125 55 2 113 237 77 173 8.46e-13 66.6
MS.gene036215.t1 AT3G52540 31.200 125 58 3 113 237 104 200 1.53e-11 63.2

Find 58 sgRNAs with CRISPR-Local

Find 62 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAACACGCACAAGTTCATTT+TGG 0.210500 1.3:+51912404 MS.gene036215:CDS
TCACTGATAGTTGTAGAAAT+TGG 0.240910 1.3:-51911826 None:intergenic
ATGAACTTGTGCGTGTTCTT+TGG 0.335283 1.3:-51912399 None:intergenic
CTTCTCACGCTCAATACTAT+TGG 0.339069 1.3:-51912187 None:intergenic
AAATCTGCTGGCTCAGGTTC+GGG 0.339475 1.3:-51912045 None:intergenic
TTCCTCAGATTTCTTGTGCT+TGG 0.343096 1.3:-51911748 None:intergenic
CTACTCGCCTGATCCTTATA+TGG 0.343274 1.3:+51912266 MS.gene036215:CDS
TAAAGTGTGGTCTGAGGTTA+AGG 0.350644 1.3:-51911962 None:intergenic
GATCTTCTAAAATCCATATA+AGG 0.364006 1.3:-51912279 None:intergenic
ATTAATGAGTTGGAGCTTCC+GGG 0.367960 1.3:-51912108 None:intergenic
TGATGGATGTGAAATCAAAT+TGG 0.370791 1.3:+51912334 MS.gene036215:CDS
TGAACTTGTGCGTGTTCTTT+GGG 0.379007 1.3:-51912398 None:intergenic
AATTAATGAGTTGGAGCTTC+CGG 0.382882 1.3:-51912109 None:intergenic
GAAATCTGCTGGCTCAGGTT+CGG 0.383556 1.3:-51912046 None:intergenic
AAGGCTGCTGCGAAATCTGC+TGG 0.394882 1.3:-51912057 None:intergenic
TGTATATTCAATTAATGAGT+TGG 0.404911 1.3:-51912118 None:intergenic
GTTGTAGAAATTGGACTTGT+GGG 0.416852 1.3:-51911817 None:intergenic
CGCTTCTTCTTCTCCTCCCC+CGG 0.417257 1.3:+51912090 MS.gene036215:CDS
GAAACAGGAGAAAGAGAAAG+AGG 0.423520 1.3:+51912209 MS.gene036215:CDS
TATTGAGCGTGAGAAGAAAC+AGG 0.440175 1.3:+51912194 MS.gene036215:CDS
AATTCTTGATCATAATTGAC+GGG 0.444957 1.3:-51911918 None:intergenic
GCTGCGAAATCTGCTGGCTC+AGG 0.454177 1.3:-51912051 None:intergenic
CTAAAATCCATATAAGGATC+AGG 0.457441 1.3:-51912273 None:intergenic
ATACTATTGGACTTATCCAT+TGG 0.483511 1.3:-51912174 None:intergenic
GGAGGCGCGACCCGAGTTGA+TGG 0.488669 1.3:+51912317 MS.gene036215:CDS
AGATTGCATTCAGCATTCTT+CGG 0.492875 1.3:+51912146 MS.gene036215:CDS
GAAGAAGCGTTGAGAGGCGA+AGG 0.509416 1.3:-51912076 None:intergenic
CTATTGGACTTATCCATTGG+TGG 0.513854 1.3:-51912171 None:intergenic
AGAGGTTGATGTAGTGAAGG+TGG 0.515313 1.3:-51912004 None:intergenic
TTCAACTTCGAGTTCAAAAG+AGG 0.515870 1.3:-51912022 None:intergenic
GCATTCTTCGGTACCACCAA+TGG 0.516823 1.3:+51912158 MS.gene036215:CDS
TGTTCTTTGGGTTGAGAGCA+AGG 0.520513 1.3:-51912386 None:intergenic
AAATTCTTGATCATAATTGA+CGG 0.524121 1.3:-51911919 None:intergenic
GATGCAGATGTAGATGAAGA+AGG 0.533865 1.3:-51911892 None:intergenic
TGATTTCACATCCATCAACT+CGG 0.562865 1.3:-51912328 None:intergenic
GATTTCACATCCATCAACTC+GGG 0.568855 1.3:-51912327 None:intergenic
CATATAAGGATCAGGCGAGT+AGG 0.570056 1.3:-51912265 None:intergenic
GTGTGGTCTGAGGTTAAGGA+AGG 0.576057 1.3:-51911958 None:intergenic
TAGAAGATCGATGCAAGAGA+TGG 0.580424 1.3:+51912293 MS.gene036215:CDS
AAAAGAGGTTGATGTAGTGA+AGG 0.582071 1.3:-51912007 None:intergenic
AAGATCGATGCAAGAGATGG+TGG 0.583074 1.3:+51912296 MS.gene036215:CDS
TAAGGATCAGGCGAGTAGGT+TGG 0.588332 1.3:-51912261 None:intergenic
ACAGGAGAAAGAGAAAGAGG+AGG 0.589206 1.3:+51912212 MS.gene036215:CDS
TTAATGAGTTGGAGCTTCCG+GGG 0.589321 1.3:-51912107 None:intergenic
AGTTGTAGAAATTGGACTTG+TGG 0.600672 1.3:-51911818 None:intergenic
ATCGATGCAAGAGATGGTGG+AGG 0.602628 1.3:+51912299 MS.gene036215:CDS
ACCATGACTAGAATGACATG+AGG 0.606821 1.3:-51912452 None:intergenic
GGAGAAGAAGAAGCGTTGAG+AGG 0.620274 1.3:-51912082 None:intergenic
TAATGAGTTGGAGCTTCCGG+GGG 0.644702 1.3:-51912106 None:intergenic
GTAGAAATTGGACTTGTGGG+TGG 0.648560 1.3:-51911814 None:intergenic
AGAGCATAAAGTGTGGTCTG+AGG 0.656840 1.3:-51911968 None:intergenic
ATTCTTGATCATAATTGACG+GGG 0.668719 1.3:-51911917 None:intergenic
GTGAAGAAGAGCATAAAGTG+TGG 0.669604 1.3:-51911975 None:intergenic
CCATGACTAGAATGACATGA+GGG 0.681003 1.3:-51912451 None:intergenic
TGTGGTCTGAGGTTAAGGAA+GGG 0.682154 1.3:-51911957 None:intergenic
TTGATGATGATGTTGATGTG+AGG 0.685082 1.3:-51911857 None:intergenic
TGCCAAGCACAAGAAATCTG+AGG 0.689018 1.3:+51911746 MS.gene036215:CDS
AGAATGACATGAGGGTAACG+AGG 0.703021 1.3:-51912443 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATTCTTGATCATAATTGA+CGG - chr1.3:51911922-51911941 None:intergenic 20.0%
!! TGTATATTCAATTAATGAGT+TGG - chr1.3:51912121-51912140 None:intergenic 20.0%
! AATTCTTGATCATAATTGAC+GGG - chr1.3:51911921-51911940 None:intergenic 25.0%
! AATTTGAAAAACATAGGTTG+AGG - chr1.3:51911774-51911793 None:intergenic 25.0%
! GAGTTGAATTTGAAAAACAT+AGG - chr1.3:51911780-51911799 None:intergenic 25.0%
!!! GATCTTCTAAAATCCATATA+AGG - chr1.3:51912282-51912301 None:intergenic 25.0%
ATACTATTGGACTTATCCAT+TGG - chr1.3:51912177-51912196 None:intergenic 30.0%
ATTCTTGATCATAATTGACG+GGG - chr1.3:51911920-51911939 None:intergenic 30.0%
CTAAAATCCATATAAGGATC+AGG - chr1.3:51912276-51912295 None:intergenic 30.0%
TCACTGATAGTTGTAGAAAT+TGG - chr1.3:51911829-51911848 None:intergenic 30.0%
! TGATGGATGTGAAATCAAAT+TGG + chr1.3:51912334-51912353 MS.gene036215:CDS 30.0%
AGATTGCATTCAGCATTCTT+CGG + chr1.3:51912146-51912165 MS.gene036215:CDS 35.0%
AGTTGTAGAAATTGGACTTG+TGG - chr1.3:51911821-51911840 None:intergenic 35.0%
GTTGTAGAAATTGGACTTGT+GGG - chr1.3:51911820-51911839 None:intergenic 35.0%
TGATTTCACATCCATCAACT+CGG - chr1.3:51912331-51912350 None:intergenic 35.0%
! AACACGCACAAGTTCATTTT+GGG + chr1.3:51912405-51912424 MS.gene036215:CDS 35.0%
! AATTAATGAGTTGGAGCTTC+CGG - chr1.3:51912112-51912131 None:intergenic 35.0%
! TTCAACTTCGAGTTCAAAAG+AGG - chr1.3:51912025-51912044 None:intergenic 35.0%
!! AAAAGAGGTTGATGTAGTGA+AGG - chr1.3:51912010-51912029 None:intergenic 35.0%
!! TTGATGATGATGTTGATGTG+AGG - chr1.3:51911860-51911879 None:intergenic 35.0%
!!! AAAGAGGAGGTTTTGTTCAA+CGG + chr1.3:51912225-51912244 MS.gene036215:CDS 35.0%
ATGAACTTGTGCGTGTTCTT+TGG - chr1.3:51912402-51912421 None:intergenic 40.0%
CTATTGGACTTATCCATTGG+TGG - chr1.3:51912174-51912193 None:intergenic 40.0%
CTTCTCACGCTCAATACTAT+TGG - chr1.3:51912190-51912209 None:intergenic 40.0%
GAAACAGGAGAAAGAGAAAG+AGG + chr1.3:51912209-51912228 MS.gene036215:CDS 40.0%
GATGCAGATGTAGATGAAGA+AGG - chr1.3:51911895-51911914 None:intergenic 40.0%
GATTTCACATCCATCAACTC+GGG - chr1.3:51912330-51912349 None:intergenic 40.0%
TAGAAGATCGATGCAAGAGA+TGG + chr1.3:51912293-51912312 MS.gene036215:CDS 40.0%
TATTGAGCGTGAGAAGAAAC+AGG + chr1.3:51912194-51912213 MS.gene036215:CDS 40.0%
TGAACTTGTGCGTGTTCTTT+GGG - chr1.3:51912401-51912420 None:intergenic 40.0%
TTCCTCAGATTTCTTGTGCT+TGG - chr1.3:51911751-51911770 None:intergenic 40.0%
! ATTAATGAGTTGGAGCTTCC+GGG - chr1.3:51912111-51912130 None:intergenic 40.0%
! GAACACGCACAAGTTCATTT+TGG + chr1.3:51912404-51912423 MS.gene036215:CDS 40.0%
! GTGAAGAAGAGCATAAAGTG+TGG - chr1.3:51911978-51911997 None:intergenic 40.0%
! TAAAGTGTGGTCTGAGGTTA+AGG - chr1.3:51911965-51911984 None:intergenic 40.0%
AAGATCGATGCAAGAGATGG+TGG + chr1.3:51912296-51912315 MS.gene036215:CDS 45.0%
ACAGGAGAAAGAGAAAGAGG+AGG + chr1.3:51912212-51912231 MS.gene036215:CDS 45.0%
AGAATGACATGAGGGTAACG+AGG - chr1.3:51912446-51912465 None:intergenic 45.0%
AGAGCATAAAGTGTGGTCTG+AGG - chr1.3:51911971-51911990 None:intergenic 45.0%
CATATAAGGATCAGGCGAGT+AGG - chr1.3:51912268-51912287 None:intergenic 45.0%
CTACTCGCCTGATCCTTATA+TGG + chr1.3:51912266-51912285 MS.gene036215:CDS 45.0%
GTAGAAATTGGACTTGTGGG+TGG - chr1.3:51911817-51911836 None:intergenic 45.0%
TGCCAAGCACAAGAAATCTG+AGG + chr1.3:51911746-51911765 MS.gene036215:CDS 45.0%
! TGTGGTCTGAGGTTAAGGAA+GGG - chr1.3:51911960-51911979 None:intergenic 45.0%
! TTAATGAGTTGGAGCTTCCG+GGG - chr1.3:51912110-51912129 None:intergenic 45.0%
!! AGAGGTTGATGTAGTGAAGG+TGG - chr1.3:51912007-51912026 None:intergenic 45.0%
!! TGTTCTTTGGGTTGAGAGCA+AGG - chr1.3:51912389-51912408 None:intergenic 45.0%
!!! GGTTTTGTTCAACGGAAGTG+TGG + chr1.3:51912233-51912252 MS.gene036215:CDS 45.0%
GCATTCTTCGGTACCACCAA+TGG + chr1.3:51912158-51912177 MS.gene036215:CDS 50.0%
TAAGGATCAGGCGAGTAGGT+TGG - chr1.3:51912264-51912283 None:intergenic 50.0%
! ATCGATGCAAGAGATGGTGG+AGG + chr1.3:51912299-51912318 MS.gene036215:CDS 50.0%
! GTGTGGTCTGAGGTTAAGGA+AGG - chr1.3:51911961-51911980 None:intergenic 50.0%
! TAATGAGTTGGAGCTTCCGG+GGG - chr1.3:51912109-51912128 None:intergenic 50.0%
!! AAATCTGCTGGCTCAGGTTC+GGG - chr1.3:51912048-51912067 None:intergenic 50.0%
!! GAAATCTGCTGGCTCAGGTT+CGG - chr1.3:51912049-51912068 None:intergenic 50.0%
!! GGAGAAGAAGAAGCGTTGAG+AGG - chr1.3:51912085-51912104 None:intergenic 50.0%
AAGGCTGCTGCGAAATCTGC+TGG - chr1.3:51912060-51912079 None:intergenic 55.0%
!! GAAGAAGCGTTGAGAGGCGA+AGG - chr1.3:51912079-51912098 None:intergenic 55.0%
CGCTTCTTCTTCTCCTCCCC+CGG + chr1.3:51912090-51912109 MS.gene036215:CDS 60.0%
!! GCTGCGAAATCTGCTGGCTC+AGG - chr1.3:51912054-51912073 None:intergenic 60.0%
! TGAGTTGGAGCTTCCGGGGG+AGG - chr1.3:51912106-51912125 None:intergenic 65.0%
! GGAGGCGCGACCCGAGTTGA+TGG + chr1.3:51912317-51912336 MS.gene036215:CDS 70.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 51911745 51912467 51911745 ID=MS.gene036215
chr1.3 mRNA 51911745 51912467 51911745 ID=MS.gene036215.t1;Parent=MS.gene036215
chr1.3 exon 51911745 51912467 51911745 ID=MS.gene036215.t1.exon1;Parent=MS.gene036215.t1
chr1.3 CDS 51911745 51912467 51911745 ID=cds.MS.gene036215.t1;Parent=MS.gene036215.t1
Gene Sequence

>MS.gene036215

ATGCCAAGCACAAGAAATCTGAGGAACCTCAACCTATGTTTTTCAAATTCAACTCTTGAATCAAAAACTCCACCCACAAGTCCAATTTCTACAACTATCAGTGAAGCAGCTTCCTCACATCAACATCATCATCAAATTCATCACAAACCTTCTTCATCTACATCTGCATCTTCCCCGTCAATTATGATCAAGAATTTCAACTCTCTCTATGACCCTTCCTTAACCTCAGACCACACTTTATGCTCTTCTTCACTCTCTACCACCTTCACTACATCAACCTCTTTTGAACTCGAAGTTGAACCCGAACCTGAGCCAGCAGATTTCGCAGCAGCCTTCGCCTCTCAACGCTTCTTCTTCTCCTCCCCCGGAAGCTCCAACTCATTAATTGAATATACAAACACAGATTGCATTCAGCATTCTTCGGTACCACCAATGGATAAGTCCAATAGTATTGAGCGTGAGAAGAAACAGGAGAAAGAGAAAGAGGAGGTTTTGTTCAACGGAAGTGTGGCAGTACCAACCTACTCGCCTGATCCTTATATGGATTTTAGAAGATCGATGCAAGAGATGGTGGAGGCGCGACCCGAGTTGATGGATGTGAAATCAAATTGGAACATCTTGCATGAGTTGCTTCTTTGTTACCTTGCTCTCAACCCAAAGAACACGCACAAGTTCATTTTGGGTGCTTTCGCTGATCTCCTCGTTACCCTCATGTCATTCTAG
Protein sequence

>MS.gene036215.t1

MPSTRNLRNLNLCFSNSTLESKTPPTSPISTTISEAASSHQHHHQIHHKPSSSTSASSPSIMIKNFNSLYDPSLTSDHTLCSSSLSTTFTTSTSFELEVEPEPEPADFAAAFASQRFFFSSPGSSNSLIEYTNTDCIQHSSVPPMDKSNSIEREKKQEKEKEEVLFNGSVAVPTYSPDPYMDFRRSMQEMVEARPELMDVKSNWNILHELLLCYLALNPKNTHKFILGAFADLLVTLMSF