AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene05172

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene05172.t1 MTR_4g051538 80.000 240 38 4 1 236 1 234 1.72e-127 360
MS.gene05172.t1 MTR_3g104630 47.482 139 48 5 106 228 16 145 2.81e-29 107
MS.gene05172.t1 MTR_3g052920 30.000 170 109 3 5 164 5 174 8.75e-17 77.0
MS.gene05172.t1 MTR_1g106070 34.559 136 79 3 1 126 1 136 2.55e-16 74.7
MS.gene05172.t1 MTR_8g043650 34.307 137 80 3 1 127 1 137 2.75e-16 75.5
MS.gene05172.t1 MTR_1g105910 35.338 133 76 3 5 127 5 137 5.27e-16 74.7
MS.gene05172.t1 MTR_1g012570 31.325 166 100 3 5 156 5 170 7.91e-16 74.3
MS.gene05172.t1 MTR_1g108510 31.579 133 81 2 5 127 5 137 1.54e-15 73.6
MS.gene05172.t1 MTR_3g052870 42.308 78 45 0 5 82 5 82 1.81e-15 73.2
MS.gene05172.t1 MTR_3g080940 42.683 82 47 0 1 82 1 82 2.00e-15 72.8
MS.gene05172.t1 MTR_1g077360 40.244 82 49 0 1 82 1 82 2.11e-15 73.2
MS.gene05172.t1 MTR_1g108580 43.056 72 41 0 1 72 1 72 2.35e-15 72.8
MS.gene05172.t1 MTR_1g105920 42.308 78 45 0 5 82 5 82 2.46e-15 73.2
MS.gene05172.t1 MTR_2g085250 40.260 77 46 0 1 77 1 77 3.43e-15 72.8
MS.gene05172.t1 MTR_2g085280 40.260 77 46 0 1 77 1 77 3.83e-15 72.4
MS.gene05172.t1 MTR_2g030740 42.308 78 45 0 5 82 5 82 4.11e-15 72.4
MS.gene05172.t1 MTR_5g053390 27.317 205 107 6 5 191 5 185 4.15e-15 72.4
MS.gene05172.t1 MTR_3g030770 31.387 137 84 2 1 127 1 137 4.19e-15 72.4
MS.gene05172.t1 MTR_5g055100 27.228 202 113 6 1 187 1 183 5.57e-15 72.0
MS.gene05172.t1 MTR_4g094632 35.294 102 62 1 9 106 2 103 1.66e-14 69.3
MS.gene05172.t1 MTR_8g086290 28.125 160 108 2 4 158 7 164 4.22e-14 68.6
MS.gene05172.t1 MTR_5g045560 40.260 77 46 0 1 77 1 77 5.62e-14 69.3
MS.gene05172.t1 MTR_0121s0100 36.364 77 49 0 1 77 1 77 7.49e-14 66.6
MS.gene05172.t1 MTR_2g093190 37.805 82 51 0 1 82 1 82 1.26e-13 68.2
MS.gene05172.t1 MTR_4g094638 38.571 70 43 0 9 78 2 71 1.38e-13 67.0
MS.gene05172.t1 MTR_1g075600 37.179 78 49 0 5 82 5 82 1.58e-13 68.2
MS.gene05172.t1 MTR_2g105290 25.625 160 112 2 4 158 7 164 2.47e-13 66.2
MS.gene05172.t1 MTR_3g030780 38.889 72 44 0 1 72 1 72 4.84e-13 64.7
MS.gene05172.t1 MTR_0121s0080 28.205 117 71 1 5 121 5 108 1.39e-12 65.5
MS.gene05172.t1 MTR_8g079502 33.735 83 47 1 9 83 2 84 2.38e-11 61.2
MS.gene05172.t1 MTR_1g047550 33.333 72 48 0 9 80 2 73 6.09e-11 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene05172.t1 AT4G36590 33.136 169 92 5 5 156 3 167 2.83e-17 78.6
MS.gene05172.t1 AT2G34440 31.646 158 99 5 9 159 2 157 1.94e-16 74.7
MS.gene05172.t1 AT1G29962 43.750 80 44 1 1 80 1 79 3.94e-16 74.3
MS.gene05172.t1 AT5G60440 42.308 78 44 1 5 82 3 79 2.10e-14 71.2
MS.gene05172.t1 AT2G24840 40.000 80 48 0 7 86 61 140 3.18e-14 70.5
MS.gene05172.t1 AT1G28460 28.649 185 108 5 1 167 1 179 8.09e-14 67.8
MS.gene05172.t1 AT1G01530 33.645 107 67 1 5 107 3 109 6.60e-13 66.6
MS.gene05172.t1 AT3G04100 35.714 84 51 1 5 88 10 90 4.73e-12 63.5
MS.gene05172.t1 AT1G28450 38.750 80 48 1 1 80 1 79 1.61e-11 61.6
MS.gene05172.t1 AT3G66656 40.000 65 39 0 9 73 2 66 1.63e-11 61.6
MS.gene05172.t1 AT1G65360 39.683 63 38 0 5 67 3 65 9.23e-11 60.1

Find 34 sgRNAs with CRISPR-Local

Find 64 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTGAGTTAACAACACTTTC+AGG 0.202264 6.4:+51790955 MS.gene05172:CDS
TTGAAGATGTTGGAAAGTTC+TGG 0.270990 6.4:+51791186 MS.gene05172:CDS
ACACAAGGAGTCAACCTTAT+TGG 0.323352 6.4:+51791870 MS.gene05172:CDS
ATCATTTCCTCTTCTATTGA+AGG 0.331143 6.4:-51791081 None:intergenic
AACAGCAAAGATCATGAAAT+TGG 0.350136 6.4:+51791527 MS.gene05172:CDS
ATCCTCCGCTTGCACCAATA+AGG 0.357163 6.4:-51791884 None:intergenic
ATTCTCATGCTTTCTCCAAC+AGG 0.390835 6.4:+51790991 MS.gene05172:CDS
TGTTGGAAAGTTCTGGATAT+TGG 0.391346 6.4:+51791193 MS.gene05172:CDS
TTTCTTTCACTTGATCATAC+TGG 0.398154 6.4:-51791245 None:intergenic
TTTATTTGTGACAGCAACTA+AGG 0.402905 6.4:-51791277 None:intergenic
TTTGTTATAGATTCAGAAGA+TGG 0.410640 6.4:-51791036 None:intergenic
TTTCCTCTTGATGACCTCTT+CGG 0.442032 6.4:-51790844 None:intergenic
GCATTTACAACGAGAAAGTC+TGG 0.455029 6.4:+51790916 MS.gene05172:CDS
CTGAGTTAACAACACTTTCA+GGG 0.482866 6.4:+51790956 MS.gene05172:CDS
TGATCCAAAAGGTAAAGGTA+TGG 0.511773 6.4:+51791821 MS.gene05172:intron
CCTCTTGATGACCTCTTCGG+TGG 0.545503 6.4:-51790841 None:intergenic
TGAAAATCCTTCAATAGAAG+AGG 0.547647 6.4:+51791074 MS.gene05172:CDS
GACTCCATTCAGTTCCTCGA+TGG 0.554069 6.4:-51791474 None:intergenic
TCTACCATCGAGGAACTGAA+TGG 0.572587 6.4:+51791470 MS.gene05172:CDS
TGGATATTGGTCAATTCAAG+AGG 0.585196 6.4:+51791206 MS.gene05172:CDS
GTCAACCTTATTGGTGCAAG+CGG 0.586884 6.4:+51791879 MS.gene05172:CDS
AACCTTATTGGTGCAAGCGG+AGG 0.596051 6.4:+51791882 MS.gene05172:CDS
TGAGTTAACAACACTTTCAG+GGG 0.607847 6.4:+51790957 MS.gene05172:CDS
GAGTAAGAATGCCACCGAAG+AGG 0.632968 6.4:+51790830 None:intergenic
TTTGGATGAAAAGCATGCTG+CGG 0.652054 6.4:+51791146 MS.gene05172:CDS
TGTAGTAATTTCTACCATCG+AGG 0.654680 6.4:+51791460 MS.gene05172:intron
CCACCGAAGAGGTCATCAAG+AGG 0.664394 6.4:+51790841 MS.gene05172:CDS
TGAAAGTGTTGTTAACTCAG+AGG 0.669188 6.4:-51790953 None:intergenic
GGAGGAGATCTTAACCCTCG+TGG 0.672202 6.4:+51791324 MS.gene05172:CDS
GCAAGCGGAGGATATGAAAG+TGG 0.676676 6.4:+51791894 MS.gene05172:CDS
TCTCGTGATATAGAAACACA+AGG 0.706006 6.4:+51791855 MS.gene05172:CDS
AAGCATGAGAATATCAACTG+AGG 0.718686 6.4:-51790980 None:intergenic
AAGATGTACACATACCACGA+GGG 0.757349 6.4:-51791338 None:intergenic
AAAGTCTGGAATTTACAACA+AGG 0.757794 6.4:+51790930 MS.gene05172:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTAAAATAATTAGACAAAA+AGG - chr6.4:51791421-51791440 None:intergenic 10.0%
!! AAAAACAAAAAATTAAACAC+AGG - chr6.4:51791573-51791592 None:intergenic 15.0%
!! ATAAATAAAGTCTTGAAAAA+TGG + chr6.4:51791303-51791322 MS.gene05172:CDS 15.0%
!!! CTAATTATTTTAAATGAATC+TGG + chr6.4:51791427-51791446 MS.gene05172:intron 15.0%
!! AAAAAATTAAACACAGGAAT+GGG - chr6.4:51791567-51791586 None:intergenic 20.0%
!! AATATTAAATGGTAAAAGCT+GGG - chr6.4:51791667-51791686 None:intergenic 20.0%
!! ACCATTTAATATTCACTTAT+GGG + chr6.4:51791674-51791693 MS.gene05172:intron 20.0%
!! TACCATTTAATATTCACTTA+TGG + chr6.4:51791673-51791692 MS.gene05172:intron 20.0%
!! TCTTCTTAATTTCTATTACT+AGG + chr6.4:51791714-51791733 MS.gene05172:intron 20.0%
!!! TCATTTTGCTGTATAATATT+CGG - chr6.4:51791111-51791130 None:intergenic 20.0%
!!! TGAAAAAAATGATGATCTTT+TGG + chr6.4:51791128-51791147 MS.gene05172:CDS 20.0%
! AAAAAGATTGAATCCATGAA+AGG - chr6.4:51791802-51791821 None:intergenic 25.0%
! AATAAAGTCTTGAAAAATGG+AGG + chr6.4:51791306-51791325 MS.gene05172:CDS 25.0%
! ACGTAAAAATTTGAAGATGT+TGG + chr6.4:51791176-51791195 MS.gene05172:CDS 25.0%
! CAAAAAATTAAACACAGGAA+TGG - chr6.4:51791568-51791587 None:intergenic 25.0%
! GAATATTAAATGGTAAAAGC+TGG - chr6.4:51791668-51791687 None:intergenic 25.0%
! TCCCATAAGTGAATATTAAA+TGG - chr6.4:51791678-51791697 None:intergenic 25.0%
!! TTCAATCTTTTTGATCCAAA+AGG + chr6.4:51791810-51791829 MS.gene05172:intron 25.0%
!! TTTGTTATAGATTCAGAAGA+TGG - chr6.4:51791039-51791058 None:intergenic 25.0%
!! TTTTGCTTGAAATATTCTAG+CGG + chr6.4:51791589-51791608 MS.gene05172:intron 25.0%
AACAGCAAAGATCATGAAAT+TGG + chr6.4:51791527-51791546 MS.gene05172:CDS 30.0%
ATCAAGAGGAAAACAAAAAG+TGG + chr6.4:51790855-51790874 MS.gene05172:CDS 30.0%
ATCATTTCCTCTTCTATTGA+AGG - chr6.4:51791084-51791103 None:intergenic 30.0%
TATGTATTGTCTTCCTTTCA+TGG + chr6.4:51791786-51791805 MS.gene05172:intron 30.0%
TGAAAATCCTTCAATAGAAG+AGG + chr6.4:51791074-51791093 MS.gene05172:CDS 30.0%
TTTATTTGTGACAGCAACTA+AGG - chr6.4:51791280-51791299 None:intergenic 30.0%
TTTCTTTCACTTGATCATAC+TGG - chr6.4:51791248-51791267 None:intergenic 30.0%
! AAAGTCTGGAATTTACAACA+AGG + chr6.4:51790930-51790949 MS.gene05172:CDS 30.0%
! ACAGGAAAACCATTTTGTTA+TGG + chr6.4:51791009-51791028 MS.gene05172:CDS 30.0%
! CTTTTTGATCCAAAAGGTAA+AGG + chr6.4:51791816-51791835 MS.gene05172:intron 30.0%
! GATGGTTTTCCATAACAAAA+TGG - chr6.4:51791021-51791040 None:intergenic 30.0%
! TAACAAAATGGTTTTCCTGT+TGG - chr6.4:51791009-51791028 None:intergenic 30.0%
!! AAATCCTGCATATGTTTTTG+AGG + chr6.4:51791502-51791521 MS.gene05172:CDS 30.0%
AAGCATGAGAATATCAACTG+AGG - chr6.4:51790983-51791002 None:intergenic 35.0%
CTGAGTTAACAACACTTTCA+GGG + chr6.4:51790956-51790975 MS.gene05172:CDS 35.0%
TCTCGTGATATAGAAACACA+AGG + chr6.4:51791855-51791874 MS.gene05172:CDS 35.0%
TCTGAGTTAACAACACTTTC+AGG + chr6.4:51790955-51790974 MS.gene05172:CDS 35.0%
TGAGTTAACAACACTTTCAG+GGG + chr6.4:51790957-51790976 MS.gene05172:CDS 35.0%
TGATCCAAAAGGTAAAGGTA+TGG + chr6.4:51791821-51791840 MS.gene05172:intron 35.0%
TGGATATTGGTCAATTCAAG+AGG + chr6.4:51791206-51791225 MS.gene05172:CDS 35.0%
TGTAGTAATTTCTACCATCG+AGG + chr6.4:51791460-51791479 MS.gene05172:intron 35.0%
TTGAAGATGTTGGAAAGTTC+TGG + chr6.4:51791186-51791205 MS.gene05172:CDS 35.0%
TTGTCCTCAAAAACATATGC+AGG - chr6.4:51791509-51791528 None:intergenic 35.0%
! TTTTAGACCAGAGATGCTAT+TGG + chr6.4:51791631-51791650 MS.gene05172:intron 35.0%
!! TGAAAGTGTTGTTAACTCAG+AGG - chr6.4:51790956-51790975 None:intergenic 35.0%
!! TGTTGGAAAGTTCTGGATAT+TGG + chr6.4:51791193-51791212 MS.gene05172:CDS 35.0%
AAGATGTACACATACCACGA+GGG - chr6.4:51791341-51791360 None:intergenic 40.0%
ACACAAGGAGTCAACCTTAT+TGG + chr6.4:51791870-51791889 MS.gene05172:CDS 40.0%
ATTCTCATGCTTTCTCCAAC+AGG + chr6.4:51790991-51791010 MS.gene05172:CDS 40.0%
CGATTAACCAATAGCATCTC+TGG - chr6.4:51791641-51791660 None:intergenic 40.0%
GCATTTACAACGAGAAAGTC+TGG + chr6.4:51790916-51790935 MS.gene05172:CDS 40.0%
! GCAACCATACCTTTACCTTT+TGG - chr6.4:51791828-51791847 None:intergenic 40.0%
! TTTCCTCTTGATGACCTCTT+CGG - chr6.4:51790847-51790866 None:intergenic 40.0%
! TTTGGATGAAAAGCATGCTG+CGG + chr6.4:51791146-51791165 MS.gene05172:CDS 40.0%
GAAGATGTACACATACCACG+AGG - chr6.4:51791342-51791361 None:intergenic 45.0%
GTCAACCTTATTGGTGCAAG+CGG + chr6.4:51791879-51791898 MS.gene05172:CDS 45.0%
TCTACCATCGAGGAACTGAA+TGG + chr6.4:51791470-51791489 MS.gene05172:CDS 45.0%
AACCTTATTGGTGCAAGCGG+AGG + chr6.4:51791882-51791901 MS.gene05172:CDS 50.0%
ATCCTCCGCTTGCACCAATA+AGG - chr6.4:51791887-51791906 None:intergenic 50.0%
GACTCCATTCAGTTCCTCGA+TGG - chr6.4:51791477-51791496 None:intergenic 50.0%
GCAAGCGGAGGATATGAAAG+TGG + chr6.4:51791894-51791913 MS.gene05172:CDS 50.0%
CCACCGAAGAGGTCATCAAG+AGG + chr6.4:51790841-51790860 MS.gene05172:CDS 55.0%
GGAGGAGATCTTAACCCTCG+TGG + chr6.4:51791324-51791343 MS.gene05172:CDS 55.0%
! CCTCTTGATGACCTCTTCGG+TGG - chr6.4:51790844-51790863 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr6.4 gene 51790838 51791944 51790838 ID=MS.gene05172
chr6.4 mRNA 51790838 51791944 51790838 ID=MS.gene05172.t1;Parent=MS.gene05172
chr6.4 exon 51790838 51791345 51790838 ID=MS.gene05172.t1.exon1;Parent=MS.gene05172.t1
chr6.4 CDS 51790838 51791345 51790838 ID=cds.MS.gene05172.t1;Parent=MS.gene05172.t1
chr6.4 exon 51791465 51791554 51791465 ID=MS.gene05172.t1.exon2;Parent=MS.gene05172.t1
chr6.4 CDS 51791465 51791554 51791465 ID=cds.MS.gene05172.t1;Parent=MS.gene05172.t1
chr6.4 exon 51791832 51791944 51791832 ID=MS.gene05172.t1.exon3;Parent=MS.gene05172.t1
chr6.4 CDS 51791832 51791944 51791832 ID=cds.MS.gene05172.t1;Parent=MS.gene05172.t1
Gene Sequence

>MS.gene05172

ATGCCACCGAAGAGGTCATCAAGAGGAAAACAAAAAGTGGAGCTAAAAAAAATTGAGAGTAAGAATGATCTCTTTGTTGCATTTACAACGAGAAAGTCTGGAATTTACAACAAGGCCTCTGAGTTAACAACACTTTCAGGGGCCTCAGTTGATATTCTCATGCTTTCTCCAACAGGAAAACCATTTTGTTATGGAAAACCATCTTCTGAATCTATAACAAAAACTAGTTTGAATGATGAAAATCCTTCAATAGAAGAGGAAATGATGAAACCGAATATTATACAGCAAAATGAAAAAAATGATGATCTTTTGGATGAAAAGCATGCTGCGGAAGCACAACGTAAAAATTTGAAGATGTTGGAAAGTTCTGGATATTGGTCAATTCAAGAGGAAGATGATAAAAGCTGCCAGTATGATCAAGTGAAAGAAATTGACAAATCCTTAGTTGCTGTCACAAATAAATTGATAAATAAAGTCTTGAAAAATGGAGGAGATCTTAACCCTCGTGGTATGTGTACATCTTCTAATTAACTATGTGTTATATTTGATCTATTAATGACGTCAAATGATTTCATGTCATCCTTTTTGTCTAATTATTTTAAATGAATCTGGTTATAATTTTTGTAGTAATTTCTACCATCGAGGAACTGAATGGAGTCAAAACAAATCCTGCATATGTTTTTGAGGACAACAGCAAAGATCATGAAATTGGTGCAAGTAAGAATTCCCATTCCTGTGTTTAATTTTTTGTTTTTGCTTGAAATATTCTAGCGGTGACACTCACACATTAAACTTTTAGACCAGAGATGCTATTGGTTAATCGTGTCCCAGCTTTTACCATTTAATATTCACTTATGGGAAAATCTCAATTACTTTTCTTCTTAATTTCTATTACTAGGCATGCAAGCATTTACTTATAATATTTCATGCGACAAATCTAACATATGTTATGTATTGTCTTCCTTTCATGGATTCAATCTTTTTGATCCAAAAGGTAAAGGTATGGTTGCTAATGCTTCTCGTGATATAGAAACACAAGGAGTCAACCTTATTGGTGCAAGCGGAGGATATGAAAGTGGTGTTGATCATGCTTCTCGAGATATATGA
Protein sequence

>MS.gene05172.t1

MPPKRSSRGKQKVELKKIESKNDLFVAFTTRKSGIYNKASELTTLSGASVDILMLSPTGKPFCYGKPSSESITKTSLNDENPSIEEEMMKPNIIQQNEKNDDLLDEKHAAEAQRKNLKMLESSGYWSIQEEDDKSCQYDQVKEIDKSLVAVTNKLINKVLKNGGDLNPRVISTIEELNGVKTNPAYVFEDNSKDHEIGASKGMVANASRDIETQGVNLIGASGGYESGVDHASRDI