AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene32498

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene32498.t1 MTR_4g072090 81.132 53 10 0 1 53 348 400 8.48e-23 90.1
MS.gene32498.t1 MTR_4g072090 81.132 53 10 0 1 53 348 400 1.48e-22 89.4
MS.gene32498.t1 MTR_0405s0060 70.000 60 13 1 1 60 112 166 2.15e-19 78.6
MS.gene32498.t1 MTR_1g023690 77.778 45 10 0 1 45 375 419 7.90e-17 73.2
MS.gene32498.t1 MTR_2g099050 64.151 53 19 0 1 53 209 261 1.37e-16 72.4
MS.gene32498.t1 MTR_6g034945 66.038 53 18 0 1 53 139 191 1.96e-16 71.6
MS.gene32498.t1 MTR_5g075390 64.151 53 19 0 1 53 147 199 2.19e-15 68.9
MS.gene32498.t1 MTR_3g467120 64.151 53 19 0 1 53 165 217 2.79e-15 68.6
MS.gene32498.t1 MTR_3g094020 56.604 53 23 0 1 53 96 148 1.79e-13 63.5
MS.gene32498.t1 MTR_2g090900 62.791 43 16 0 11 53 189 231 1.55e-11 58.2
MS.gene32498.t1 MTR_2g090900 62.791 43 16 0 11 53 189 231 1.76e-11 58.2
MS.gene32498.t1 MTR_4g079500 58.696 46 19 0 11 56 192 237 8.09e-11 56.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene32498.t1 AT4G38900 71.698 53 15 0 1 53 382 434 1.09e-19 81.3
MS.gene32498.t1 AT4G38900 71.698 53 15 0 1 53 382 434 1.09e-19 81.3
MS.gene32498.t1 AT2G21230 71.154 52 15 0 2 53 359 410 3.01e-18 77.4
MS.gene32498.t1 AT2G21230 71.154 52 15 0 2 53 359 410 5.16e-18 76.6
MS.gene32498.t1 AT2G21230 71.154 52 15 0 2 53 359 410 5.25e-18 76.6
MS.gene32498.t1 AT2G21230 71.154 52 15 0 2 53 359 410 5.25e-18 76.6
MS.gene32498.t1 AT4G38900 64.407 59 15 1 1 53 382 440 2.03e-17 75.1
MS.gene32498.t1 AT1G43700 60.377 53 21 0 1 53 182 234 2.12e-15 68.9
MS.gene32498.t1 AT2G40620 64.151 53 19 0 1 53 136 188 2.66e-15 68.9
MS.gene32498.t1 AT1G06850 62.264 53 20 0 1 53 136 188 2.69e-15 67.8
MS.gene32498.t1 AT1G06070 65.306 49 17 0 5 53 202 250 2.81e-15 68.9
MS.gene32498.t1 AT2G31370 62.264 53 20 0 1 53 189 241 8.30e-15 67.4
MS.gene32498.t1 AT2G31370 62.264 53 20 0 1 53 189 241 8.30e-15 67.4
MS.gene32498.t1 AT2G31370 62.264 53 20 0 1 53 189 241 8.30e-15 67.4
MS.gene32498.t1 AT2G31370 62.264 53 20 0 1 53 189 241 8.30e-15 67.4
MS.gene32498.t1 AT2G31370 62.264 53 20 0 1 53 189 241 8.30e-15 67.4
MS.gene32498.t1 AT2G31370 62.264 53 20 0 1 53 189 241 8.30e-15 67.4
MS.gene32498.t1 AT2G31370 62.264 53 20 0 1 53 189 241 8.76e-15 67.4
MS.gene32498.t1 AT1G06850 62.264 53 20 0 1 53 136 188 1.67e-14 66.6
MS.gene32498.t1 AT2G42380 73.171 41 11 0 13 53 186 226 2.29e-14 65.1
MS.gene32498.t1 AT2G42380 73.171 41 11 0 13 53 186 226 2.29e-14 65.1
MS.gene32498.t1 AT3G58120 65.854 41 14 0 13 53 202 242 4.11e-12 59.7
MS.gene32498.t1 AT2G42380 65.854 41 14 0 13 53 186 226 7.19e-12 58.9
MS.gene32498.t1 AT3G58120 65.854 41 14 0 13 53 202 242 9.84e-12 58.5
MS.gene32498.t1 AT2G42380 65.854 41 14 0 13 53 186 226 1.50e-11 58.2

Find 14 sgRNAs with CRISPR-Local

Find 73 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCGAAGCCACTACACTTTC+TGG 0.193760 5.1:-62948113 MS.gene32498:CDS
TGGACAACTTACTTTGTTGC+AGG 0.307186 5.1:-62948093 MS.gene32498:intron
GCGCAAGATGCAATACATTT+CGG 0.444328 5.1:-62948160 MS.gene32498:CDS
GCTCAAAGGAGTACAAAATC+TGG 0.448935 5.1:+62947010 None:intergenic
CAACACCTCTTAGCCCGCTT+CGG 0.460625 5.1:+62948304 None:intergenic
GAAAGTTGCCGAGATTGTTA+TGG 0.488140 5.1:-62948332 MS.gene32498:CDS
CGGATCAGCCATAACAATCT+CGG 0.532249 5.1:+62948324 None:intergenic
CTGATCCGAAGCGGGCTAAG+AGG 0.536785 5.1:-62948309 MS.gene32498:intron
TGTTATGGCTGATCCGAAGC+GGG 0.561676 5.1:-62948317 MS.gene32498:CDS
CATTTCGGAGCTAGAACACA+AGG 0.586933 5.1:-62948145 MS.gene32498:CDS
GTATTGCATCTTGCGCACAT+TGG 0.617188 5.1:+62948167 None:intergenic
ATGACAGGCTGCAATTGCAT+CGG 0.638131 5.1:-62947043 MS.gene32498:intron
TTGTTATGGCTGATCCGAAG+CGG 0.656660 5.1:-62948318 MS.gene32498:CDS
AAGTTGTCCAGAAAGTGTAG+TGG 0.688059 5.1:+62948106 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTATTTCATAAAAAGAA+TGG - chr5.1:62948077-62948096 MS.gene32498:intron 10.0%
!! AAAATAAATAAGCAATATGA+AGG + chr5.1:62948241-62948260 None:intergenic 15.0%
!! AAATAAATAAGCAATATGAA+GGG + chr5.1:62948240-62948259 None:intergenic 15.0%
!!! AGATATTTGTTAATAGAAAT+GGG + chr5.1:62947445-62947464 None:intergenic 15.0%
!!! GTTTTGGATATTTTTTTTTT+TGG - chr5.1:62947782-62947801 MS.gene32498:intron 15.0%
!!! TAGATATTTGTTAATAGAAA+TGG + chr5.1:62947446-62947465 None:intergenic 15.0%
!!! TTTTAGTATATTTTTTCGTT+TGG - chr5.1:62947916-62947935 MS.gene32498:intron 15.0%
!! AAAATTAAGCTAAAATGAGA+AGG - chr5.1:62947682-62947701 MS.gene32498:intron 20.0%
!! AAATTAAGCTAAAATGAGAA+GGG - chr5.1:62947683-62947702 MS.gene32498:intron 20.0%
!! AATAGTATAGATGTCTATAA+AGG + chr5.1:62947626-62947645 None:intergenic 20.0%
!! AGATTAAACAATTATTGTCA+TGG + chr5.1:62947830-62947849 None:intergenic 20.0%
!! ATAGACATCTATACTATTAT+TGG - chr5.1:62947628-62947647 MS.gene32498:intron 20.0%
!! GAGATAAATTACATAAACAA+TGG + chr5.1:62947720-62947739 None:intergenic 20.0%
!! TAGACATCTATACTATTATT+GGG - chr5.1:62947629-62947648 MS.gene32498:intron 20.0%
!! TTTAGTTAGTAATGTCAATA+TGG - chr5.1:62947093-62947112 MS.gene32498:intron 20.0%
!!! ATATTTTTTTGGGTTATTTC+AGG - chr5.1:62947134-62947153 MS.gene32498:intron 20.0%
!!! ATTGTTTCTTATATCTGAAA+TGG - chr5.1:62947507-62947526 MS.gene32498:intron 20.0%
!!! ATTTGACTTGGATATTTTTT+TGG - chr5.1:62947123-62947142 MS.gene32498:intron 20.0%
!!! GATATTTTTTTTTTTGGTGA+AGG - chr5.1:62947788-62947807 MS.gene32498:intron 20.0%
!!! TTTGACTTGGATATTTTTTT+GGG - chr5.1:62947124-62947143 MS.gene32498:intron 20.0%
! AAGAGATTAATAACTTTAGC+TGG + chr5.1:62947991-62948010 None:intergenic 25.0%
! AATTAAGCTAAAATGAGAAG+GGG - chr5.1:62947684-62947703 MS.gene32498:intron 25.0%
! ACAATGTCAAATTGATGTAT+AGG + chr5.1:62947660-62947679 None:intergenic 25.0%
! ATCTCATGTTAAGAACTAAA+CGG + chr5.1:62947583-62947602 None:intergenic 25.0%
! TAAACCATCAACAATATGAA+GGG + chr5.1:62948280-62948299 None:intergenic 25.0%
! TCTTATTGAACATTTAGTGA+AGG - chr5.1:62947410-62947429 MS.gene32498:intron 25.0%
! TGTAAAACTACTCAAATCAT+AGG + chr5.1:62947383-62947402 None:intergenic 25.0%
! TTCAAATAATCCTCAAAACA+TGG + chr5.1:62947315-62947334 None:intergenic 25.0%
! TTCATTGAACATTGCAAATT+TGG + chr5.1:62947356-62947375 None:intergenic 25.0%
!! TACAAATGAATCAGATTTTG+AGG - chr5.1:62948108-62948127 MS.gene32498:CDS 25.0%
!! TTATATCTGAAATGGACAAA+AGG - chr5.1:62947515-62947534 MS.gene32498:intron 25.0%
!! TTTTTACAATAGGTTGTCAA+TGG + chr5.1:62947963-62947982 None:intergenic 25.0%
!!! AAATATGCTAAAAGCATTCA+TGG + chr5.1:62947473-62947492 None:intergenic 25.0%
!!! AGTTTAGTTTTTAACACAGA+AGG - chr5.1:62947548-62947567 MS.gene32498:intron 25.0%
!!! ATATTTTTTCGTTTGGAGTT+TGG - chr5.1:62947923-62947942 MS.gene32498:intron 25.0%
AAAGACACTACTTGTGAAAA+TGG + chr5.1:62948024-62948043 None:intergenic 30.0%
CTAAACCATCAACAATATGA+AGG + chr5.1:62948281-62948300 None:intergenic 30.0%
CTTCATTATCTCCATATCAA+AGG + chr5.1:62948161-62948180 None:intergenic 30.0%
GTTAGTAATGTCAATATGGA+TGG - chr5.1:62947097-62947116 MS.gene32498:intron 30.0%
! TATGGATGGTTAATTTGACT+TGG - chr5.1:62947111-62947130 MS.gene32498:intron 30.0%
!! ATTTCAGGATTTTGAGAAAC+AGG - chr5.1:62947149-62947168 MS.gene32498:intron 30.0%
!!! TATAGTGCTGATACAAGTTT+TGG - chr5.1:62947766-62947785 MS.gene32498:intron 30.0%
ATTATTGTCATGGCAAAGTG+AGG + chr5.1:62947820-62947839 None:intergenic 35.0%
CTTTCCCTTCATATTGTTGA+TGG - chr5.1:62948273-62948292 MS.gene32498:intron 35.0%
GTCTTCATGTTCCTTTGATA+TGG - chr5.1:62948147-62948166 MS.gene32498:CDS 35.0%
TTAGCAAACACATGTATGAC+AGG - chr5.1:62948297-62948316 MS.gene32498:intron 35.0%
! GTTTGTGAAACCATGTTTTG+AGG - chr5.1:62947302-62947321 MS.gene32498:intron 35.0%
!! GATTTTGAGAAACAGGCAAT+CGG - chr5.1:62947156-62947175 MS.gene32498:intron 35.0%
AAAGGAACATGAAGACAGAG+AGG + chr5.1:62948143-62948162 None:intergenic 40.0%
ACAACTTACTTTGTTGCAGG+TGG - chr5.1:62947265-62947284 MS.gene32498:intron 40.0%
ATATGAAGGGAAAAATCCCG+TGG + chr5.1:62948227-62948246 None:intergenic 40.0%
ATTGCAAATTTGGCAGCTCT+TGG + chr5.1:62947346-62947365 None:intergenic 40.0%
CAACTTACTTTGTTGCAGGT+GGG - chr5.1:62947266-62947285 MS.gene32498:intron 40.0%
GAAAGTTGCCGAGATTGTTA+TGG - chr5.1:62947023-62947042 MS.gene32498:CDS 40.0%
GACACTACTTGTGAAAATGG+TGG + chr5.1:62948021-62948040 None:intergenic 40.0%
GCGCAAGATGCAATACATTT+CGG - chr5.1:62947195-62947214 MS.gene32498:intron 40.0%
TGCTGCTCTATTATCTACCA+CGG - chr5.1:62948207-62948226 MS.gene32498:intron 40.0%
TGGACAACTTACTTTGTTGC+AGG - chr5.1:62947262-62947281 MS.gene32498:intron 40.0%
! AAGTTGTCCAGAAAGTGTAG+TGG + chr5.1:62947252-62947271 None:intergenic 40.0%
! CTCTATCAACTGTCGTTTCA+TGG - chr5.1:62947737-62947756 MS.gene32498:intron 40.0%
!!! GCTGGAGCTGTTTTTACAAT+AGG + chr5.1:62947973-62947992 None:intergenic 40.0%
ATGACAGGCTGCAATTGCAT+CGG - chr5.1:62948312-62948331 MS.gene32498:CDS 45.0%
CATTTCGGAGCTAGAACACA+AGG - chr5.1:62947210-62947229 MS.gene32498:intron 45.0%
CGGATCAGCCATAACAATCT+CGG + chr5.1:62947034-62947053 None:intergenic 45.0%
GCTGCTCTATTATCTACCAC+GGG - chr5.1:62948208-62948227 MS.gene32498:intron 45.0%
GTATTGCATCTTGCGCACAT+TGG + chr5.1:62947191-62947210 None:intergenic 45.0%
TTGTTATGGCTGATCCGAAG+CGG - chr5.1:62947037-62947056 MS.gene32498:CDS 45.0%
CAAATTTGGCAGCTCTTGGC+AGG + chr5.1:62947342-62947361 None:intergenic 50.0%
GGAACATGAAGACAGAGAGG+AGG + chr5.1:62948140-62948159 None:intergenic 50.0%
TGCGAAGCCACTACACTTTC+TGG - chr5.1:62947242-62947261 MS.gene32498:intron 50.0%
TGTTATGGCTGATCCGAAGC+GGG - chr5.1:62947038-62947057 MS.gene32498:CDS 50.0%
CAACACCTCTTAGCCCGCTT+CGG + chr5.1:62947054-62947073 None:intergenic 55.0%
!! CTGATCCGAAGCGGGCTAAG+AGG - chr5.1:62947046-62947065 MS.gene32498:intron 60.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 62947012 62948365 62947012 ID=MS.gene32498
chr5.1 mRNA 62947012 62948365 62947012 ID=MS.gene32498.t1;Parent=MS.gene32498
chr5.1 exon 62948310 62948365 62948310 ID=MS.gene32498.t1.exon1;Parent=MS.gene32498.t1
chr5.1 CDS 62948310 62948365 62948310 ID=cds.MS.gene32498.t1;Parent=MS.gene32498.t1
chr5.1 exon 62948094 62948221 62948094 ID=MS.gene32498.t1.exon2;Parent=MS.gene32498.t1
chr5.1 CDS 62948094 62948221 62948094 ID=cds.MS.gene32498.t1;Parent=MS.gene32498.t1
chr5.1 exon 62947012 62947058 62947012 ID=MS.gene32498.t1.exon3;Parent=MS.gene32498.t1
chr5.1 CDS 62947012 62947058 62947012 ID=cds.MS.gene32498.t1;Parent=MS.gene32498.t1
Gene Sequence

>MS.gene32498

ATGGCTAATGAGAAAGTTGCCGAGATTGTTATGGCTGATCCGAAGCGGGCTAAGAGGTGTTGTAATTAACTTATTCAACGTTTTAGTTAGTAATGTCAATATGGATGGTTAATTTGACTTGGATATTTTTTTGGGTTATTTCAGGATTTTGAGAAACAGGCAATCGGCTGCGCGTTCCAATGTGCGCAAGATGCAATACATTTCGGAGCTAGAACACAAGGTTCAGACTCTGCGAAGCCACTACACTTTCTGGACAACTTACTTTGTTGCAGGTGGGAACATTTATTTATGTTTGTGAAACCATGTTTTGAGGATTATTTGAATAAGCCTGCCAAGAGCTGCCAAATTTGCAATGTTCAATGAAATTGCCTATGATTTGAGTAGTTTTACATAATTTTTCTTATTGAACATTTAGTGAAGGCATCTTTATCCCATTTCTATTAACAAATATCTACTAACCATGAATGCTTTTAGCATATTTTGTTAAATTTGAAAATTGTTTCTTATATCTGAAATGGACAAAAGGTAGCTACATCAGTTTAGTTTTTAACACAGAAGGTAGCTATATCCGTTTAGTTCTTAACATGAGATTTCATTGTTCTAATTTATATCCTTTATAGACATCTATACTATTATTGGGTCTATCCTATACATCAATTTGACATTGTCGAAAATTAAGCTAAAATGAGAAGGGGTTGATGTAATCCATTGTTTATGTAATTTATCTCTATCAACTGTCGTTTCATGGCAAGAATATAGTGCTGATACAAGTTTTGGATATTTTTTTTTTTGGTGAAGGTATTCACCTCACTTTGCCATGACAATAATTGTTTAATCTATTAGTTGTAATAAATATTTAGAAATGTTTGTTGTTATCAATAAATTAACATACTCATGATCATTTTTTTAGTATATTTTTTCGTTTGGAGTTTGGTGTTTATTTATAGTCCATTGACAACCTATTGTAAAAACAGCTCCAGCTAAAGTTATTAATCTCTTTTTTTTTCCACCATTTTCACAAGTAGTGTCTTTGACTAAATTTCATTAATTTTAGCATGTAGTAAATTTTTATTTCATAAAAAGAATGGATTCATTTTACAAATGAATCAGATTTTGAGGTTATATCCTCCTCTCTGTCTTCATGTTCCTTTGATATGGAGATAATGAAGAATATGATCTATTTAAAGTACGTACGTGCTGCTCTATTATCTACCACGGGATTTTTCCCTTCATATTGCTTATTTATTTTCTATAGCAAGTTCTTTCCCTTCATATTGTTGATGGTTTAGCAAACACATGTATGACAGGCTGCAATTGCATCGGTATTATGACGCCAGATTTTGTACTCCTTTGA
Protein sequence

>MS.gene32498.t1

MANEKVAEIVMADPKRAKRILRNRQSAARSNVRKMQYISELEHKVQTLRSHYTFWTTYFVAGCNCIGIMTPDFVLL