AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene055525

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene055525.t1 MTR_3g098790 94.118 136 8 0 1 136 177 312 5.47e-93 272
MS.gene055525.t1 MTR_7g050580 69.231 143 44 0 1 143 168 310 1.20e-67 207
MS.gene055525.t1 MTR_7g050710 68.116 138 42 1 1 136 183 320 1.30e-62 195
MS.gene055525.t1 MTR_7g050560 62.676 142 52 1 2 143 170 310 6.79e-61 190
MS.gene055525.t1 MTR_7g050590 65.441 136 46 1 2 136 158 293 5.38e-60 187
MS.gene055525.t1 MTR_7g050720 60.000 125 46 4 5 125 193 317 1.53e-42 143
MS.gene055525.t1 MTR_1g035460 42.342 111 53 3 13 123 188 287 1.95e-20 86.3
MS.gene055525.t1 MTR_4g068320 37.795 127 71 3 14 140 285 403 2.40e-20 86.3
MS.gene055525.t1 MTR_1g034240 33.793 145 86 3 2 142 277 415 1.36e-19 84.0
MS.gene055525.t1 MTR_1g108780 38.333 120 61 4 5 123 183 290 2.52e-18 80.5
MS.gene055525.t1 MTR_8g103940 43.860 114 51 4 11 123 230 331 9.77e-18 79.0
MS.gene055525.t1 MTR_5g044670 33.607 122 75 3 10 131 196 311 1.89e-14 68.9
MS.gene055525.t1 MTR_1g035490 35.537 121 71 4 5 123 81 196 1.94e-13 66.2
MS.gene055525.t1 MTR_1g034210 30.328 122 79 2 2 123 243 358 9.71e-13 64.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene055525.t1 AT1G49480 32.787 122 69 4 8 123 107 221 3.14e-13 64.7
MS.gene055525.t1 AT1G49480 32.787 122 69 4 8 123 107 221 3.14e-13 64.7
MS.gene055525.t1 AT1G49480 32.787 122 69 4 8 123 107 221 3.14e-13 64.7
MS.gene055525.t1 AT3G18990 30.400 125 80 3 2 126 222 339 6.65e-13 65.1
MS.gene055525.t1 AT3G18990 30.328 122 78 3 2 123 222 336 1.48e-12 63.9

Find 24 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTTCCAAGTTCATATATTC+AGG 0.253552 3.2:+82232029 MS.gene055525:CDS
ATTGAGTAGCTTCTTTCATT+TGG 0.267478 3.2:-82232179 None:intergenic
TGCAACTTACCAGAAGAAAA+TGG 0.347556 3.2:-82231412 None:intergenic
ATCCTGATTCGGTACTTTGC+AGG 0.347997 3.2:-82231890 None:intergenic
TTGAGTAGCTTCTTTCATTT+GGG 0.352726 3.2:-82232178 None:intergenic
AAGTGTCAAATGGCAGAGTT+TGG 0.384047 3.2:+82231867 MS.gene055525:CDS
TTATCAGCATCAACAATCAT+TGG 0.392502 3.2:-82231305 None:intergenic
GGCCTGCAAAGTACCGAATC+AGG 0.422243 3.2:+82231888 MS.gene055525:CDS
TCCATCCTTTGTTGTTGTCA+TGG 0.427556 3.2:+82231370 MS.gene055525:CDS
CCATCCTTTGTTGTTGTCAT+GGG 0.446533 3.2:+82231371 MS.gene055525:CDS
GAAGACAATAACTTGAAAGT+TGG 0.499244 3.2:+82231965 MS.gene055525:CDS
TCTCCCTGAATATATGAACT+TGG 0.502600 3.2:-82232033 None:intergenic
CTGTGTGGGACATCCTGATT+CGG 0.531424 3.2:-82231901 None:intergenic
CAGACTATACCGTCTATGTT+CGG 0.532014 3.2:+82231797 MS.gene055525:intron
TTTCCAAGTTCATATATTCA+GGG 0.536079 3.2:+82232030 MS.gene055525:CDS
CCCATGACAACAACAAAGGA+TGG 0.571041 3.2:-82231371 None:intergenic
CTAAGATTTGAACTCTCAAG+TGG 0.579522 3.2:+82231926 MS.gene055525:CDS
GATTTGAACTCTCAAGTGGA+TGG 0.585291 3.2:+82231930 MS.gene055525:CDS
TTCAAATCTTAGTCCTGTGT+GGG 0.598172 3.2:-82231915 None:intergenic
TTTAATTTGAATAAGAAGCG+AGG 0.603085 3.2:+82231830 MS.gene055525:CDS
GTTCAAATCTTAGTCCTGTG+TGG 0.647989 3.2:-82231916 None:intergenic
TGTCTCTTACCGAACATAGA+CGG 0.669663 3.2:-82231806 None:intergenic
CGAATCAGGATGTCCCACAC+AGG 0.680142 3.2:+82231902 MS.gene055525:CDS
TGCACCCATGACAACAACAA+AGG 0.693553 3.2:-82231375 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CATATCAAAGTAAGATTAAT+TGG + chr3.2:82232083-82232102 MS.gene055525:intron 20.0%
!! CTCCATTAAGAAATATATAT+TGG + chr3.2:82231500-82231519 MS.gene055525:intron 20.0%
!! GACCAATATATATTTCTTAA+TGG - chr3.2:82231505-82231524 None:intergenic 20.0%
! GTAAGTTGCAAAGATAAATT+TGG + chr3.2:82231425-82231444 MS.gene055525:intron 25.0%
! TTTCCAAGTTCATATATTCA+GGG + chr3.2:82232030-82232049 MS.gene055525:CDS 25.0%
! TTTCTTAATGGAGAAAGATT+TGG - chr3.2:82231493-82231512 None:intergenic 25.0%
!!! ATTCATTTTCAAGTGTCAAA+TGG + chr3.2:82231857-82231876 MS.gene055525:CDS 25.0%
!!! TTTAATTTGAATAAGAAGCG+AGG + chr3.2:82231830-82231849 MS.gene055525:CDS 25.0%
ATTGAGTAGCTTCTTTCATT+TGG - chr3.2:82232182-82232201 None:intergenic 30.0%
CTTTCCAAGTTCATATATTC+AGG + chr3.2:82232029-82232048 MS.gene055525:CDS 30.0%
GAAGACAATAACTTGAAAGT+TGG + chr3.2:82231965-82231984 MS.gene055525:CDS 30.0%
TTGAGTAGCTTCTTTCATTT+GGG - chr3.2:82232181-82232200 None:intergenic 30.0%
! GATTTGGTTATTGATGTTGT+TGG - chr3.2:82231477-82231496 None:intergenic 30.0%
CTAAGATTTGAACTCTCAAG+TGG + chr3.2:82231926-82231945 MS.gene055525:CDS 35.0%
TCTCCCTGAATATATGAACT+TGG - chr3.2:82232036-82232055 None:intergenic 35.0%
TGCAACTTACCAGAAGAAAA+TGG - chr3.2:82231415-82231434 None:intergenic 35.0%
TGGGAAAATTCTGCATAAAG+TGG - chr3.2:82232162-82232181 None:intergenic 35.0%
TTCAAATCTTAGTCCTGTGT+GGG - chr3.2:82231918-82231937 None:intergenic 35.0%
! CATTTGCCTTTTCTTTTGCT+TGG + chr3.2:82231774-82231793 MS.gene055525:intron 35.0%
AAGTGTCAAATGGCAGAGTT+TGG + chr3.2:82231867-82231886 MS.gene055525:CDS 40.0%
AGTCTGCCAAGCAAAAGAAA+AGG - chr3.2:82231783-82231802 None:intergenic 40.0%
CAGACTATACCGTCTATGTT+CGG + chr3.2:82231797-82231816 MS.gene055525:intron 40.0%
GATTTGAACTCTCAAGTGGA+TGG + chr3.2:82231930-82231949 MS.gene055525:CDS 40.0%
GTTCAAATCTTAGTCCTGTG+TGG - chr3.2:82231919-82231938 None:intergenic 40.0%
TGTCTCTTACCGAACATAGA+CGG - chr3.2:82231809-82231828 None:intergenic 40.0%
!! CCATCCTTTGTTGTTGTCAT+GGG + chr3.2:82231371-82231390 MS.gene055525:CDS 40.0%
!! TCCATCCTTTGTTGTTGTCA+TGG + chr3.2:82231370-82231389 MS.gene055525:CDS 40.0%
CCCATGACAACAACAAAGGA+TGG - chr3.2:82231374-82231393 None:intergenic 45.0%
TGCACCCATGACAACAACAA+AGG - chr3.2:82231378-82231397 None:intergenic 45.0%
! CGTTGAGCACCATTTTCTTC+TGG + chr3.2:82231403-82231422 MS.gene055525:CDS 45.0%
!! ATCCTGATTCGGTACTTTGC+AGG - chr3.2:82231893-82231912 None:intergenic 45.0%
CTGTGTGGGACATCCTGATT+CGG - chr3.2:82231904-82231923 None:intergenic 50.0%
CGAATCAGGATGTCCCACAC+AGG + chr3.2:82231902-82231921 MS.gene055525:CDS 55.0%
!! GGCCTGCAAAGTACCGAATC+AGG + chr3.2:82231888-82231907 MS.gene055525:CDS 55.0%


Chromosome Type Strat End Strand Name
chr3.2 gene 82231308 82232203 82231308 ID=MS.gene055525
chr3.2 mRNA 82231308 82232203 82231308 ID=MS.gene055525.t1;Parent=MS.gene055525
chr3.2 exon 82231308 82231424 82231308 ID=MS.gene055525.t1.exon1;Parent=MS.gene055525.t1
chr3.2 CDS 82231308 82231424 82231308 ID=cds.MS.gene055525.t1;Parent=MS.gene055525.t1
chr3.2 exon 82231800 82232091 82231800 ID=MS.gene055525.t1.exon2;Parent=MS.gene055525.t1
chr3.2 CDS 82231800 82232091 82231800 ID=cds.MS.gene055525.t1;Parent=MS.gene055525.t1
chr3.2 exon 82232172 82232203 82232172 ID=MS.gene055525.t1.exon3;Parent=MS.gene055525.t1
chr3.2 CDS 82232172 82232203 82232172 ID=cds.MS.gene055525.t1;Parent=MS.gene055525.t1
Gene Sequence

>MS.gene055525

ATGATTGTTGATGCTGATAAAGTTACAACACTTGAAAGAGCAAAATCTTTCAAAACATGTAATCCATCCTTTGTTGTTGTCATGGGTGCATCATACGTTGAGCACCATTTTCTTCTGGTAAGTTGCAAAGATAAATTTGGCTCTTAAAGCATAATTAAGTTGACAGCCAACAACATCAATAACCAAATCTTTCTCCATTAAGAAATATATATTGGTCATTTAAGAATAATTTAAAGAGTATGTATACAATAACATGTCAGTGTTTTACAAAGTTATTCAATCAGATGTCACAACATAGATGTTTATTGAAATAGTATAAGAAATAATGTAACTAAATGACATCTTCATAAAATATGATTAGAAAACTATGTAAAAAATGTATACTGTTCAGTGTCAATACACAGTCATTAAACTCATTTACATAACTGCACTTTTCAACAAGAAGTTTTTGTATTTTATTCTTTAACATTTGCCTTTTCTTTTGCTTGGCAGACTATACCGTCTATGTTCGGTAAGAGACACTTTAATTTGAATAAGAAGCGAGGAGATATTCATTTTCAAGTGTCAAATGGCAGAGTTTGGCCTGCAAAGTACCGAATCAGGATGTCCCACACAGGACTAAGATTTGAACTCTCAAGTGGATGGAAGACATTCGCAGAAGACAATAACTTGAAAGTTGGTGATGCTTGCAACTTTGAGCTCATTCTTAGTACTAATATGACTTTCCAAGTTCATATATTCAGGGAGACAGATAAAGACAACGCAGATTGTTTAACATATCAAAGTAAGATTAATTGGTGTTTAATTTTCTTTTCAATTCTTTTTCTCTTATGACAAATAAATTTATTCTTCCACTTTATGCAGAATTTTCCCAAATGAAAGAAGCTACTCAATGA
Protein sequence

>MS.gene055525.t1

MIVDADKVTTLERAKSFKTCNPSFVVVMGASYVEHHFLLTIPSMFGKRHFNLNKKRGDIHFQVSNGRVWPAKYRIRMSHTGLRFELSSGWKTFAEDNNLKVGDACNFELILSTNMTFQVHIFRETDKDNADCLTYQKFSQMKEATQ