AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene055797

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene055797.t1 MTR_2g090440 84.793 217 23 3 1 207 1 217 6.39e-128 359
MS.gene055797.t1 MTR_2g090480 81.279 219 29 2 1 207 1 219 5.33e-124 349
MS.gene055797.t1 MTR_2g090425 80.693 202 26 2 1 189 1 202 7.78e-110 318
MS.gene055797.t1 MTR_2g090500 87.135 171 16 2 43 207 60 230 4.81e-101 292
MS.gene055797.t1 MTR_4g078350 67.021 188 57 3 9 191 14 201 2.75e-84 248
MS.gene055797.t1 MTR_2g013920 44.944 178 83 5 1 170 1 171 2.78e-43 143
MS.gene055797.t1 MTR_2g090515 74.545 55 11 1 1 52 1 55 1.88e-19 79.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene055797.t1 AT4G20970 40.107 187 92 6 3 172 5 188 2.58e-34 120
MS.gene055797.t1 AT1G10585 28.994 169 114 3 8 174 13 177 2.31e-14 68.6
MS.gene055797.t1 AT5G51780 29.586 169 105 3 11 166 3 170 7.27e-12 62.0
MS.gene055797.t1 AT5G51780 29.586 169 105 3 11 166 26 193 1.02e-11 62.0
MS.gene055797.t1 AT1G10586 26.061 165 116 3 9 171 14 174 5.41e-11 59.3

Find 39 sgRNAs with CRISPR-Local

Find 90 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCACAAACTTTGTTACAATT+TGG 0.173105 2.1:+10456880 MS.gene055797:CDS
TATCTCTTCAAATTCTTCTT+TGG 0.234992 2.1:+10456138 MS.gene055797:CDS
CAATTGTGGGATCTTGAAAT+TGG 0.247122 2.1:+10456973 MS.gene055797:CDS
ATGCTTCTTAATTAAGGATT+TGG 0.266624 2.1:-10457042 None:intergenic
AACAAGAAAGAAAGTTTAAA+AGG 0.273993 2.1:+10455983 MS.gene055797:CDS
AGAGAAGAAAGAAAGTTTAA+TGG 0.275748 2.1:+10455958 MS.gene055797:CDS
GAGAGTTAAGTTTGGAATAG+AGG 0.305206 2.1:-10455226 None:intergenic
GAGAAGAAAGAAAGTTTAAT+GGG 0.355968 2.1:+10455959 MS.gene055797:CDS
CCAACTTTAGATTTGTCTCT+AGG 0.356186 2.1:-10455931 None:intergenic
AGGAAGAAGAGAGTTAAGTT+TGG 0.360183 2.1:-10455234 None:intergenic
CCAAATTGTAACAAAGTTTG+TGG 0.389197 2.1:-10456880 None:intergenic
AACATCCTTTCTTTCGACTT+TGG 0.397896 2.1:-10455174 None:intergenic
TCTTCAAATTCTTCTTTGGC+TGG 0.403407 2.1:+10456142 MS.gene055797:CDS
TTGAAATTGGAAGTGAGAGT+TGG 0.404544 2.1:+10456986 MS.gene055797:CDS
TAATTTCACAGAAAATAAAA+TGG 0.425918 2.1:-10456084 None:intergenic
ATAGCCTCATCTACTTGATC+AGG 0.429867 2.1:-10455893 None:intergenic
TGAAATTGGAAGTGAGAGTT+GGG 0.469657 2.1:+10456987 MS.gene055797:CDS
TCTTCATACCGTGCATGCTC+AGG 0.472764 2.1:+10456174 MS.gene055797:CDS
AAAATAGAGATTCATGAAAT+GGG 0.475198 2.1:+10456022 MS.gene055797:CDS
TCTTGTTGATTATGTTCCAT+TGG 0.483862 2.1:-10455143 None:intergenic
TTCAACCAAAGTCGAAAGAA+AGG 0.492351 2.1:+10455169 MS.gene055797:CDS
CCTAGAGACAAATCTAAAGT+TGG 0.498284 2.1:+10455931 MS.gene055797:CDS
ATTTCAAGATCCCACAATTG+AGG 0.509351 2.1:-10456970 None:intergenic
TTAAGGATTTGGTAAACTCA+TGG 0.514490 2.1:-10457031 None:intergenic
TCATCTACTTGATCAGGTAA+TGG 0.522136 2.1:-10455887 None:intergenic
TACAAGTGATTGTAACATGT+GGG 0.544345 2.1:+10456053 MS.gene055797:CDS
GGAAACACAGCCTCAATTGT+GGG 0.559018 2.1:+10456960 MS.gene055797:CDS
TGGAAACACAGCCTCAATTG+TGG 0.568137 2.1:+10456959 MS.gene055797:CDS
ATGACCTTCGAATTATAGCT+AGG 0.581881 2.1:-10455254 None:intergenic
TCTTCCTAGCTATAATTCGA+AGG 0.587922 2.1:+10455250 MS.gene055797:CDS
TATATATACCTGAGCATGCA+CGG 0.590008 2.1:-10456182 None:intergenic
GAGCAATCAAAATAAGTGAG+AGG 0.593941 2.1:+10456902 MS.gene055797:CDS
CTACAAGTGATTGTAACATG+TGG 0.615945 2.1:+10456052 MS.gene055797:CDS
AGGTTGAAAGAGTTTGTGAA+CGG 0.618184 2.1:+10456922 MS.gene055797:CDS
TGTTACAATCACTTGTAGAG+TGG 0.628540 2.1:-10456047 None:intergenic
ATTACCTGATCAAGTAGATG+AGG 0.636526 2.1:+10455889 MS.gene055797:CDS
GAACGGATCTGTGAGCGATG+TGG 0.701045 2.1:+10456939 MS.gene055797:CDS
ACAAGTGATTGTAACATGTG+GGG 0.739715 2.1:+10456054 MS.gene055797:CDS
ACTGCATGAAGAGAACGTCG+AGG 0.768331 2.1:+10456114 MS.gene055797:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGAAAAATGTATAAATAAAT+AGG + chr2.1:10455660-10455679 MS.gene055797:intron 10.0%
!!! TTTTTTTTTGTAATAAGTTT+TGG - chr2.1:10456612-10456631 None:intergenic 10.0%
!! AAAGTAGAATATATTGTATT+GGG + chr2.1:10455683-10455702 MS.gene055797:intron 15.0%
!! AATTAGAGTTATATTGTATT+GGG + chr2.1:10455724-10455743 MS.gene055797:intron 15.0%
!! TAATTAGAGTTATATTGTAT+TGG + chr2.1:10455723-10455742 MS.gene055797:intron 15.0%
!! TAATTTCACAGAAAATAAAA+TGG - chr2.1:10456087-10456106 None:intergenic 15.0%
!! TTATTAAATAATGCTACATT+AGG - chr2.1:10455584-10455603 None:intergenic 15.0%
!!! AAAATTTTTTCTTTGACTTT+TGG - chr2.1:10456491-10456510 None:intergenic 15.0%
!!! AATTTAGAGCTTATTTTTTA+GGG - chr2.1:10456566-10456585 None:intergenic 15.0%
!!! ATTTATTTTTCTAATTTTGG+CGG - chr2.1:10455429-10455448 None:intergenic 15.0%
!!! CAGCTTTAATAATAATATAA+GGG - chr2.1:10456265-10456284 None:intergenic 15.0%
!!! TGTTATTTTTAATTTAATGC+AGG + chr2.1:10455853-10455872 MS.gene055797:intron 15.0%
!!! TTCTGATTTGATTATTAATT+TGG + chr2.1:10456848-10456867 MS.gene055797:intron 15.0%
!! AAAAATAGAGATTCATGAAA+TGG + chr2.1:10456021-10456040 MS.gene055797:CDS 20.0%
!! AAAATAGAGATTCATGAAAT+GGG + chr2.1:10456022-10456041 MS.gene055797:CDS 20.0%
!! AACAAGAAAGAAAGTTTAAA+AGG + chr2.1:10455983-10456002 MS.gene055797:CDS 20.0%
!! CGAAAAGTTTGAATATTTAT+AGG + chr2.1:10456522-10456541 MS.gene055797:intron 20.0%
!! GAAAGTAGAATATATTGTAT+TGG + chr2.1:10455682-10455701 MS.gene055797:intron 20.0%
!! TAAAAAGATAAGGTTGAATA+TGG - chr2.1:10456342-10456361 None:intergenic 20.0%
!! TTTAACGCTATAAAAAGATA+AGG - chr2.1:10456352-10456371 None:intergenic 20.0%
!!! ATTTCATGAATCTCTATTTT+TGG - chr2.1:10456022-10456041 None:intergenic 20.0%
!!! CAATTTAGAGCTTATTTTTT+AGG - chr2.1:10456567-10456586 None:intergenic 20.0%
!!! GACACTTTTTTTTAGAAAAT+GGG + chr2.1:10455793-10455812 MS.gene055797:intron 20.0%
!!! GCAGCTTTAATAATAATATA+AGG - chr2.1:10456266-10456285 None:intergenic 20.0%
!!! TAACATAGATTATTTTGTGA+AGG + chr2.1:10455484-10455503 MS.gene055797:intron 20.0%
!!! TGAAATGACTCAATTATTTT+GGG + chr2.1:10455771-10455790 MS.gene055797:intron 20.0%
!!! TGATGATGTAAAACTTTTAA+GGG + chr2.1:10456464-10456483 MS.gene055797:intron 20.0%
!!! TTATTATTCAAATGCACTTT+TGG - chr2.1:10456715-10456734 None:intergenic 20.0%
!!! TTGAAATGACTCAATTATTT+TGG + chr2.1:10455770-10455789 MS.gene055797:intron 20.0%
!!! TTTTATAGCGTTAAAAGATA+GGG + chr2.1:10456357-10456376 MS.gene055797:intron 20.0%
!!! TTTTTATAGCGTTAAAAGAT+AGG + chr2.1:10456356-10456375 MS.gene055797:intron 20.0%
! ACGGATGAAGTATATTAATT+TGG + chr2.1:10455830-10455849 MS.gene055797:intron 25.0%
! ACTAGACTTGAATACATATT+TGG + chr2.1:10456313-10456332 MS.gene055797:intron 25.0%
! AGAGAAGAAAGAAAGTTTAA+TGG + chr2.1:10455958-10455977 MS.gene055797:CDS 25.0%
! GAGAAGAAAGAAAGTTTAAT+GGG + chr2.1:10455959-10455978 MS.gene055797:CDS 25.0%
! TATCTCTTCAAATTCTTCTT+TGG + chr2.1:10456138-10456157 MS.gene055797:CDS 25.0%
!! CTCTTAACAATATTTTGCAA+AGG + chr2.1:10456763-10456782 MS.gene055797:intron 25.0%
!!! GGACACTTTTTTTTAGAAAA+TGG + chr2.1:10455792-10455811 MS.gene055797:intron 25.0%
!!! GTGATGATGTAAAACTTTTA+AGG + chr2.1:10456463-10456482 MS.gene055797:intron 25.0%
!!! TAAATTTTTTTTCGCACGTT+TGG - chr2.1:10456690-10456709 None:intergenic 25.0%
!!! TCAAGTCTAGTTTTAAACTA+CGG - chr2.1:10456304-10456323 None:intergenic 25.0%
!!! TGTTAGATAGTTTAGTCTTA+TGG - chr2.1:10455469-10455488 None:intergenic 25.0%
ATTAAAGCTGCAATTGCAAT+TGG + chr2.1:10456275-10456294 MS.gene055797:intron 30.0%
CAAACTGAGTCAGATAAAAT+GGG - chr2.1:10455623-10455642 None:intergenic 30.0%
CCAAATTGTAACAAAGTTTG+TGG - chr2.1:10456883-10456902 None:intergenic 30.0%
CCACAAACTTTGTTACAATT+TGG + chr2.1:10456880-10456899 MS.gene055797:CDS 30.0%
GAAAGACTAAATCATGTTTC+TGG + chr2.1:10456652-10456671 MS.gene055797:intron 30.0%
GAAAGGATGTTGAGAAAAAT+AGG + chr2.1:10455186-10455205 MS.gene055797:CDS 30.0%
GATGTAAATAATGCAACATG+TGG + chr2.1:10455361-10455380 MS.gene055797:intron 30.0%
TACAAGTGATTGTAACATGT+GGG + chr2.1:10456053-10456072 MS.gene055797:CDS 30.0%
! TTAAGGATTTGGTAAACTCA+TGG - chr2.1:10457034-10457053 None:intergenic 30.0%
!! GTTTAGTCTTATGGTATGTT+AGG - chr2.1:10455460-10455479 None:intergenic 30.0%
!! TAAGCTCTAAATTGAGTTGT+AGG + chr2.1:10456573-10456592 MS.gene055797:intron 30.0%
AACATCCTTTCTTTCGACTT+TGG - chr2.1:10455177-10455196 None:intergenic 35.0%
ACAAGTGATTGTAACATGTG+GGG + chr2.1:10456054-10456073 MS.gene055797:CDS 35.0%
AGAAAATGGGTCAGATATTC+CGG + chr2.1:10455806-10455825 MS.gene055797:intron 35.0%
AGGAAGAAGAGAGTTAAGTT+TGG - chr2.1:10455237-10455256 None:intergenic 35.0%
AGGTTGAAAGAGTTTGTGAA+CGG + chr2.1:10456922-10456941 MS.gene055797:CDS 35.0%
ATGACCTTCGAATTATAGCT+AGG - chr2.1:10455257-10455276 None:intergenic 35.0%
ATTACCTGATCAAGTAGATG+AGG + chr2.1:10455889-10455908 MS.gene055797:CDS 35.0%
ATTTCAAGATCCCACAATTG+AGG - chr2.1:10456973-10456992 None:intergenic 35.0%
CAATTGTGGGATCTTGAAAT+TGG + chr2.1:10456973-10456992 MS.gene055797:CDS 35.0%
CCAAACTGAGTCAGATAAAA+TGG - chr2.1:10455624-10455643 None:intergenic 35.0%
CCAACTTTAGATTTGTCTCT+AGG - chr2.1:10455934-10455953 None:intergenic 35.0%
CTACAAGTGATTGTAACATG+TGG + chr2.1:10456052-10456071 MS.gene055797:CDS 35.0%
GAGCAATCAAAATAAGTGAG+AGG + chr2.1:10456902-10456921 MS.gene055797:CDS 35.0%
TATATATACCTGAGCATGCA+CGG - chr2.1:10456185-10456204 None:intergenic 35.0%
TCATCTACTTGATCAGGTAA+TGG - chr2.1:10455890-10455909 None:intergenic 35.0%
TCTTCAAATTCTTCTTTGGC+TGG + chr2.1:10456142-10456161 MS.gene055797:CDS 35.0%
TCTTCCTAGCTATAATTCGA+AGG + chr2.1:10455250-10455269 MS.gene055797:CDS 35.0%
TGAAATTGGAAGTGAGAGTT+GGG + chr2.1:10456987-10457006 MS.gene055797:CDS 35.0%
TGTTACAATCACTTGTAGAG+TGG - chr2.1:10456050-10456069 None:intergenic 35.0%
TTAATATACTTCATCCGTCC+CGG - chr2.1:10455828-10455847 None:intergenic 35.0%
TTCAACCAAAGTCGAAAGAA+AGG + chr2.1:10455169-10455188 MS.gene055797:CDS 35.0%
TTGAAATTGGAAGTGAGAGT+TGG + chr2.1:10456986-10457005 MS.gene055797:CDS 35.0%
! CCATTTTATCTGACTCAGTT+TGG + chr2.1:10455621-10455640 MS.gene055797:intron 35.0%
! CCTAGAGACAAATCTAAAGT+TGG + chr2.1:10455931-10455950 MS.gene055797:CDS 35.0%
! GAGAGTTAAGTTTGGAATAG+AGG - chr2.1:10455229-10455248 None:intergenic 35.0%
ATAGCCTCATCTACTTGATC+AGG - chr2.1:10455896-10455915 None:intergenic 40.0%
CTGAGTCAGATAAAATGGGA+CGG - chr2.1:10455619-10455638 None:intergenic 40.0%
GAAAATGGGTCAGATATTCC+GGG + chr2.1:10455807-10455826 MS.gene055797:intron 40.0%
AGTCAGATAAAATGGGACGG+AGG - chr2.1:10455616-10455635 None:intergenic 45.0%
GGAAACACAGCCTCAATTGT+GGG + chr2.1:10456960-10456979 MS.gene055797:CDS 45.0%
GTCAGATAAAATGGGACGGA+GGG - chr2.1:10455615-10455634 None:intergenic 45.0%
TGGAAACACAGCCTCAATTG+TGG + chr2.1:10456959-10456978 MS.gene055797:CDS 45.0%
!!! TAAATTTATTTTTCTAATTT+TGG - chr2.1:10455432-10455451 None:intergenic 5.0%
ACTGCATGAAGAGAACGTCG+AGG + chr2.1:10456114-10456133 MS.gene055797:CDS 50.0%
ATGGGTCAGATATTCCGGGA+CGG + chr2.1:10455811-10455830 MS.gene055797:intron 50.0%
TCTTCATACCGTGCATGCTC+AGG + chr2.1:10456174-10456193 MS.gene055797:CDS 50.0%
GAACGGATCTGTGAGCGATG+TGG + chr2.1:10456939-10456958 MS.gene055797:CDS 55.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 10455146 10457053 10455146 ID=MS.gene055797
chr2.1 mRNA 10455146 10457053 10455146 ID=MS.gene055797.t1;Parent=MS.gene055797
chr2.1 exon 10455146 10455271 10455146 ID=MS.gene055797.t1.exon1;Parent=MS.gene055797.t1
chr2.1 CDS 10455146 10455271 10455146 ID=cds.MS.gene055797.t1;Parent=MS.gene055797.t1
chr2.1 exon 10455875 10456195 10455875 ID=MS.gene055797.t1.exon2;Parent=MS.gene055797.t1
chr2.1 CDS 10455875 10456195 10455875 ID=cds.MS.gene055797.t1;Parent=MS.gene055797.t1
chr2.1 exon 10456877 10457053 10456877 ID=MS.gene055797.t1.exon3;Parent=MS.gene055797.t1
chr2.1 CDS 10456877 10457053 10456877 ID=cds.MS.gene055797.t1;Parent=MS.gene055797.t1
Gene Sequence

>MS.gene055797

ATGGAACATAATCAACAAGAATGTTCAACCAAAGTCGAAAGAAAGGATGTTGAGAAAAATAGGAGAAATCAGATGAAGATCCTCTATTCCAAACTTAACTCTCTTCTTCCTAGCTATAATTCGAAGGTCATCTCTTCTATTTTCATCACGTATATATGTATATATTCATTTGAGAAAGTCTACATTGTTTTTATTATTTTATTTTTTATTGTTATGATGTAAATAATGCAACATGTGGTAGTGTATGTAGAAATAACTTTTTTTAAGAAGAGAAACTAATCCGCCAAAATTAGAAAAATAAATTTATTATACCTAACATACCATAAGACTAAACTATCTAACATAGATTATTTTGTGAAGGTTTTTTTTTAAGACTAAACTATCTAACATATGAAAACATTCATCATACTTGTGAAATTTCACGAAGAAAACATTCCTAATGTAGCATTATTTAATAATACATACTCCCTCCGTCCCATTTTATCTGACTCAGTTTGGTTTTTCACACAGATTAAGAAAAATGTATAAATAAATAGGAAAGTAGAATATATTGTATTGGGAATGATGAAAATAGTATTAATTAGAGTTATATTGTATTGGGAATGATGAAAGTTGTATTGAAAATTGAAATGACTCAATTATTTTGGGACACTTTTTTTTAGAAAATGGGTCAGATATTCCGGGACGGATGAAGTATATTAATTTGGTGTTATTTTTAATTTAATGCAGGAATTAACGTTACCATTACCTGATCAAGTAGATGAGGCTATAAACTACATAAAGAGCCTAGAGACAAATCTAAAGTTGGCAAAAGAGAAGAAAGAAAGTTTAATGGGAAACAAGAAAGAAAGTTTAAAAGGAAGCATAAAGTTACCAAAAATAGAGATTCATGAAATGGGAACCACTCTACAAGTGATTGTAACATGTGGGGTTGATGACCATTTTATTTTCTGTGAAATTATGAGAATACTGCATGAAGAGAACGTCGAGGTTATCTCTTCAAATTCTTCTTTGGCTGGTGATTCACTTCTTCATACCGTGCATGCTCAGGTATATATATACATAAACACATTTGCATGTTTAACTGCATTATGATGTTACTGCAACTTGCAAAGACCCTTATATTATTATTAAAGCTGCAATTGCAATTGGAGACCGTAGTTTAAAACTAGACTTGAATACATATTTGGTTACCATATTCAACCTTATCTTTTTATAGCGTTAAAAGATAGGGTTAAATACGTTTCATTTAATTTGTTCTGTTATAAAAAATTAAACTTTTAAATGATAACGTTGACTTAACAACAATGATCAAATGTGATGATGTAAAACTTTTAAGGGACCAAAAGTCAAAGAAAAAATTTTAAGTACTAAAACGAAAAGTTTGAATATTTATAGGAACTCAAAATATATTTAACCCTAAAAAATAAGCTCTAAATTGAGTTGTAGGAAGAAAAAAAATTCCAAAACTTATTACAAAAAAAAAAAAAAAGAAACTAAGAAATAGAAAGACTAAATCATGTTTCTGGTATACTAAGAGACCAAACGTGCGAAAAAAAATTTAAACCAAAAGTGCATTTGAATAATAAAACAATGATTGTATGCATATATTCTTTACTCTTAACAATATTTTGCAAAGGAATCAATTAAGCTCTTCAACATTAAGAAACTTAATGATGAATGATTTGTTTTCTGATTTGTTTTCTGATTTGATTATTAATTTGGATGCAGATTCCACAAACTTTGTTACAATTTGGAGCAATCAAAATAAGTGAGAGGTTGAAAGAGTTTGTGAACGGATCTGTGAGCGATGTGGAAACACAGCCTCAATTGTGGGATCTTGAAATTGGAAGTGAGAGTTGGGAGCTTCTACATTCTGTAGTAACCATGAGTTTACCAAATCCTTAA
Protein sequence

>MS.gene055797.t1

MEHNQQECSTKVERKDVEKNRRNQMKILYSKLNSLLPSYNSKELTLPLPDQVDEAINYIKSLETNLKLAKEKKESLMGNKKESLKGSIKLPKIEIHEMGTTLQVIVTCGVDDHFIFCEIMRILHEENVEVISSNSSLAGDSLLHTVHAQIPQTLLQFGAIKISERLKEFVNGSVSDVETQPQLWDLEIGSESWELLHSVVTMSLPNP