AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene20892

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene20892.t1 MTR_1g086340 86.395 147 20 0 2 148 4 150 3.30e-88 257
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene20892.t1 AT4G01883 54.630 108 49 0 56 163 59 166 2.00e-37 127
MS.gene20892.t1 AT4G01883 61.702 94 33 1 56 149 59 149 2.05e-37 128
MS.gene20892.t1 AT4G01883 61.702 94 33 1 56 149 59 149 2.28e-37 127
MS.gene20892.t1 AT1G02475 59.794 97 39 0 67 163 68 164 2.92e-36 125
MS.gene20892.t1 AT1G02470 58.108 74 31 0 67 140 69 142 1.15e-26 100
MS.gene20892.t1 AT1G02470 58.108 74 31 0 67 140 69 142 1.53e-26 100

Find 44 sgRNAs with CRISPR-Local

Find 101 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACCTTAACAGTGGAAATAA+AGG 0.283136 1.3:-61146290 None:intergenic
GAAATAAAGGGCATCCATTC+CGG 0.313746 1.3:-61146277 None:intergenic
GCCCTTTATTTCCACTGTTA+AGG 0.341799 1.3:+61146288 MS.gene20892:CDS
GTCAGAATATTGAGTTCTCT+TGG 0.369456 1.3:+61146800 MS.gene20892:CDS
GAAGCTTCTAGAAGTAAAAT+TGG 0.382494 1.3:-61145237 None:intergenic
GAAAATCCATTGGCGATCTC+TGG 0.391451 1.3:+61146946 MS.gene20892:CDS
TTCCCCTGTCATGGAGTGGC+AGG 0.393458 1.3:+61145355 MS.gene20892:CDS
CTCTGGATGGTCTTCCCAAC+AGG 0.395898 1.3:+61146963 MS.gene20892:CDS
TGCGACAGGTCAGGTTTGTC+TGG 0.396361 1.3:-61146751 None:intergenic
AAATAAAGGGCATCCATTCC+GGG 0.416616 1.3:-61146276 None:intergenic
TCCTTGAAGTATAAGGCATT+TGG 0.430828 1.3:+61146778 MS.gene20892:CDS
ACCAAATGCCTTATACTTCA+AGG 0.433774 1.3:-61146779 None:intergenic
TTCCGAATGCAGGGTTAAGA+TGG 0.435808 1.3:+61146198 MS.gene20892:intron
AAGGACCATTGCGACAGGTC+AGG 0.449994 1.3:-61146760 None:intergenic
GCAATGGTCCTTGAAGTATA+AGG 0.452028 1.3:+61146771 MS.gene20892:CDS
TTGGAAGAGAGTGAAGTTGA+GGG 0.452562 1.3:-61145260 None:intergenic
CAATCCTGCCACTCCATGAC+AGG 0.454346 1.3:-61145359 None:intergenic
GCCCTTGTCAGTTACCTGTT+GGG 0.457466 1.3:-61146977 None:intergenic
TGCCCTTGTCAGTTACCTGT+TGG 0.475529 1.3:-61146978 None:intergenic
CAATCATATGCTACAGAGAT+CGG 0.479919 1.3:-61146232 None:intergenic
ACCTTAACAGTGGAAATAAA+GGG 0.493335 1.3:-61146289 None:intergenic
ATTGGAAGAGAGTGAAGTTG+AGG 0.504072 1.3:-61145261 None:intergenic
CTAGCATTGCGATTCAAAGA+TGG 0.510418 1.3:-61145200 None:intergenic
TTCTGATCGTGAAGCCATCC+CGG 0.524092 1.3:+61146258 MS.gene20892:CDS
AATCATATGCTACAGAGATC+GGG 0.541146 1.3:-61146231 None:intergenic
CGAATGCAGGGTTAAGATGG+AGG 0.555585 1.3:+61146201 MS.gene20892:intron
ATCCATTGGCGATCTCTGGA+TGG 0.567929 1.3:+61146950 MS.gene20892:CDS
CTCCAAATCAGAAAATCCAT+TGG 0.568507 1.3:+61146936 MS.gene20892:CDS
ATCGTGAAGCCATCCCGGAA+TGG 0.574790 1.3:+61146263 MS.gene20892:CDS
TGGAAGAGAGTGAAGTTGAG+GGG 0.576892 1.3:-61145259 None:intergenic
GAGTCTGAAGAAGAAGCGAT+TGG 0.577061 1.3:-61145279 None:intergenic
ACTTCAAGGACCATTGCGAC+AGG 0.589808 1.3:-61146765 None:intergenic
GACCATCCAGAGATCGCCAA+TGG 0.590298 1.3:-61146952 None:intergenic
ACAAACCTGACCTGTCGCAA+TGG 0.598815 1.3:+61146755 MS.gene20892:CDS
GCTTCTAGAAGTAAAATTGG+CGG 0.606768 1.3:-61145234 None:intergenic
GCTTAGAAGAAGAAGTGTGA+GGG 0.616908 1.3:-61145301 None:intergenic
AATCCTGCCACTCCATGACA+GGG 0.620352 1.3:-61145358 None:intergenic
TTCCCAACAGGTAACTGACA+AGG 0.625814 1.3:+61146975 MS.gene20892:CDS
CGCTTAGAAGAAGAAGTGTG+AGG 0.627236 1.3:-61145302 None:intergenic
AAAGGGCATCCATTCCGGGA+TGG 0.645388 1.3:-61146272 None:intergenic
CTTGAATCGATGGAAAGTTG+AGG 0.645424 1.3:-61145327 None:intergenic
TCCCAACAGGTAACTGACAA+GGG 0.672306 1.3:+61146976 MS.gene20892:CDS
GAGCAAGCACACCTTAACAG+TGG 0.691318 1.3:-61146299 None:intergenic
ATCCTGCCACTCCATGACAG+GGG 0.702823 1.3:-61145357 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAGAAAAAATAAGCAAAAT+CGG - chr1.3:61145572-61145591 None:intergenic 15.0%
!! AATGTTGTATATTTCTTAAT+TGG + chr1.3:61146095-61146114 MS.gene20892:intron 15.0%
!!! TTATTTTTTTCATTGAAAGT+AGG - chr1.3:61146175-61146194 None:intergenic 15.0%
!! AATATCATAATCACTATTGT+TGG + chr1.3:61146351-61146370 MS.gene20892:intron 20.0%
!! AATTGAAAATCTTTACCTTA+TGG + chr1.3:61146386-61146405 MS.gene20892:intron 20.0%
!! CTCAAATTATTATAAACCAA+TGG - chr1.3:61145729-61145748 None:intergenic 20.0%
!! TATTAGAGGAATATGAAATA+AGG - chr1.3:61145994-61146013 None:intergenic 20.0%
!! TATTTCATATTCCTCTAATA+GGG + chr1.3:61145994-61146013 MS.gene20892:intron 20.0%
!! TTATTTCATATTCCTCTAAT+AGG + chr1.3:61145993-61146012 MS.gene20892:intron 20.0%
!!! CATTGGTTTATAATAATTTG+AGG + chr1.3:61145727-61145746 MS.gene20892:intron 20.0%
!!! GCTTTTCTATTTTATATGTA+TGG + chr1.3:61145410-61145429 MS.gene20892:intron 20.0%
! AAAATAATATTTCCGAATGC+AGG + chr1.3:61146188-61146207 MS.gene20892:intron 25.0%
! AAATAATATTTCCGAATGCA+GGG + chr1.3:61146189-61146208 MS.gene20892:intron 25.0%
! ATATGAAATAAGGCCATATT+TGG - chr1.3:61145984-61146003 None:intergenic 25.0%
! TAGAAAAGCGAAAGAAAAAA+AGG - chr1.3:61145399-61145418 None:intergenic 25.0%
! TATTATAAACCAATGGAAAG+AGG - chr1.3:61145722-61145741 None:intergenic 25.0%
! TTCTTTGTAATATATGCACA+AGG + chr1.3:61145602-61145621 MS.gene20892:intron 25.0%
!! ACTGTTTTCATAATCTATCT+TGG - chr1.3:61145845-61145864 None:intergenic 25.0%
!! TTAAGTTGCTTATCCAAATA+TGG + chr1.3:61145968-61145987 MS.gene20892:intron 25.0%
!!! ATTAGCCTTGTAATTAATCA+GGG - chr1.3:61146334-61146353 None:intergenic 25.0%
!!! TATTAGCCTTGTAATTAATC+AGG - chr1.3:61146335-61146354 None:intergenic 25.0%
!!! TTTGATTTTATGCAAAACGT+TGG + chr1.3:61146709-61146728 MS.gene20892:intron 25.0%
AAAAATTCCATCCCTATTAG+AGG - chr1.3:61146008-61146027 None:intergenic 30.0%
ACCTTAACAGTGGAAATAAA+GGG - chr1.3:61146292-61146311 None:intergenic 30.0%
CTAAAACGAATGGAACAAAA+TGG - chr1.3:61146045-61146064 None:intergenic 30.0%
GAATATCTATGCTAATTGCA+AGG - chr1.3:61145696-61145715 None:intergenic 30.0%
TCTAACCCTGATTAATTACA+AGG + chr1.3:61146326-61146345 MS.gene20892:intron 30.0%
TGTAATTAATCAGGGTTAGA+AGG - chr1.3:61146326-61146345 None:intergenic 30.0%
! ATAAGCAAAATCGGCATTTT+TGG - chr1.3:61145563-61145582 None:intergenic 30.0%
! GAAGCTTCTAGAAGTAAAAT+TGG - chr1.3:61145240-61145259 None:intergenic 30.0%
! TAGATTAAACTGTGTTGATG+AGG + chr1.3:61146455-61146474 MS.gene20892:intron 30.0%
!! GTTTTCACCTTATTTCCATA+AGG + chr1.3:61145816-61145835 MS.gene20892:intron 30.0%
!! TCGTCTAATTCTAAAACGAA+TGG - chr1.3:61146055-61146074 None:intergenic 30.0%
AATCATATGCTACAGAGATC+GGG - chr1.3:61146234-61146253 None:intergenic 35.0%
AATCTATCTTGGAGACCTTA+TGG - chr1.3:61145834-61145853 None:intergenic 35.0%
ACAGTTTAATCTAGTCTGAC+AGG - chr1.3:61146448-61146467 None:intergenic 35.0%
ACCAAATGCCTTATACTTCA+AGG - chr1.3:61146782-61146801 None:intergenic 35.0%
AGTTATCATCACAAGTGCTT+TGG - chr1.3:61145764-61145783 None:intergenic 35.0%
CAATCATATGCTACAGAGAT+CGG - chr1.3:61146235-61146254 None:intergenic 35.0%
CACCTTAACAGTGGAAATAA+AGG - chr1.3:61146293-61146312 None:intergenic 35.0%
CTCCAAATCAGAAAATCCAT+TGG + chr1.3:61146936-61146955 MS.gene20892:CDS 35.0%
GTCAGAATATTGAGTTCTCT+TGG + chr1.3:61146800-61146819 MS.gene20892:CDS 35.0%
TCACATGCTATGATTCCATA+AGG - chr1.3:61146404-61146423 None:intergenic 35.0%
TCATATTCCTCTAATAGGGA+TGG + chr1.3:61145998-61146017 MS.gene20892:intron 35.0%
TGAAAAAGAGCTTATGACGA+CGG - chr1.3:61145174-61145193 None:intergenic 35.0%
TTGGAGACCTTATGGAAATA+AGG - chr1.3:61145826-61145845 None:intergenic 35.0%
! GCTTCTAGAAGTAAAATTGG+CGG - chr1.3:61145237-61145256 None:intergenic 35.0%
! TCCTTGAAGTATAAGGCATT+TGG + chr1.3:61146778-61146797 MS.gene20892:CDS 35.0%
!! AAGAAGCAAAAGTATCAGGT+AGG - chr1.3:61146854-61146873 None:intergenic 35.0%
!! CGAAAAGAAGCAAAAGTATC+AGG - chr1.3:61146858-61146877 None:intergenic 35.0%
!!! ATGGATTTTCTGATTTGGAG+TGG - chr1.3:61146936-61146955 None:intergenic 35.0%
!!! CAGTTTTTAGCACTTCTGTT+TGG + chr1.3:61146121-61146140 MS.gene20892:intron 35.0%
!!! TGGATTTTCTGATTTGGAGT+GGG - chr1.3:61146935-61146954 None:intergenic 35.0%
ATATTCGTGCCTCTTTCCAT+TGG + chr1.3:61145710-61145729 MS.gene20892:intron 40.0%
ATTGGAAGAGAGTGAAGTTG+AGG - chr1.3:61145264-61145283 None:intergenic 40.0%
CTAGCATTGCGATTCAAAGA+TGG - chr1.3:61145203-61145222 None:intergenic 40.0%
CTTGAATCGATGGAAAGTTG+AGG - chr1.3:61145330-61145349 None:intergenic 40.0%
GCAATGGTCCTTGAAGTATA+AGG + chr1.3:61146771-61146790 MS.gene20892:CDS 40.0%
GTCTGGCAATATCTGCAAAA+TGG - chr1.3:61146737-61146756 None:intergenic 40.0%
TCATTGAAAGTAGGAAGCTG+TGG - chr1.3:61146166-61146185 None:intergenic 40.0%
TCTGACAGGAAAAGAGTCAA+AGG - chr1.3:61146434-61146453 None:intergenic 40.0%
TTGGAAGAGAGTGAAGTTGA+GGG - chr1.3:61145263-61145282 None:intergenic 40.0%
! GCCCTTTATTTCCACTGTTA+AGG + chr1.3:61146288-61146307 MS.gene20892:CDS 40.0%
! GCTTAGAAGAAGAAGTGTGA+GGG - chr1.3:61145304-61145323 None:intergenic 40.0%
!! AAATAAAGGGCATCCATTCC+GGG - chr1.3:61146279-61146298 None:intergenic 40.0%
!! CGCCAATGGATTTTCTGATT+TGG - chr1.3:61146941-61146960 None:intergenic 40.0%
!! GAAATAAAGGGCATCCATTC+CGG - chr1.3:61146280-61146299 None:intergenic 40.0%
ATCACAAGTGCTTTGGTGAG+TGG - chr1.3:61145757-61145776 None:intergenic 45.0%
CTCCATCTTAACCCTGCATT+CGG - chr1.3:61146203-61146222 None:intergenic 45.0%
GAAAATCCATTGGCGATCTC+TGG + chr1.3:61146946-61146965 MS.gene20892:CDS 45.0%
GAAAGTAGGAAGCTGTGGTT+GGG - chr1.3:61146161-61146180 None:intergenic 45.0%
GAGTCTGAAGAAGAAGCGAT+TGG - chr1.3:61145282-61145301 None:intergenic 45.0%
GGGAAAAACGCTTGAATCGA+TGG - chr1.3:61145340-61145359 None:intergenic 45.0%
TCCCAACAGGTAACTGACAA+GGG + chr1.3:61146976-61146995 MS.gene20892:CDS 45.0%
TGAAAGTAGGAAGCTGTGGT+TGG - chr1.3:61146162-61146181 None:intergenic 45.0%
TGGAAGAGAGTGAAGTTGAG+GGG - chr1.3:61145262-61145281 None:intergenic 45.0%
TTCCCAACAGGTAACTGACA+AGG + chr1.3:61146975-61146994 MS.gene20892:CDS 45.0%
TTCCGAATGCAGGGTTAAGA+TGG + chr1.3:61146198-61146217 MS.gene20892:intron 45.0%
! CGCTTAGAAGAAGAAGTGTG+AGG - chr1.3:61145305-61145324 None:intergenic 45.0%
!! TTGGCTTGCTCGTAATATGC+AGG + chr1.3:61146819-61146838 MS.gene20892:intron 45.0%
AATCCTGCCACTCCATGACA+GGG - chr1.3:61145361-61145380 None:intergenic 50.0%
ACAAACCTGACCTGTCGCAA+TGG + chr1.3:61146755-61146774 MS.gene20892:CDS 50.0%
ACTTCAAGGACCATTGCGAC+AGG - chr1.3:61146768-61146787 None:intergenic 50.0%
ATCCATTGGCGATCTCTGGA+TGG + chr1.3:61146950-61146969 MS.gene20892:CDS 50.0%
CGAATGCAGGGTTAAGATGG+AGG + chr1.3:61146201-61146220 MS.gene20892:intron 50.0%
GAGCAAGCACACCTTAACAG+TGG - chr1.3:61146302-61146321 None:intergenic 50.0%
GCCCTTGTCAGTTACCTGTT+GGG - chr1.3:61146980-61146999 None:intergenic 50.0%
TGCCCTTGTCAGTTACCTGT+TGG - chr1.3:61146981-61147000 None:intergenic 50.0%
TTCTGATCGTGAAGCCATCC+CGG + chr1.3:61146258-61146277 MS.gene20892:CDS 50.0%
! CAAGCGTTTTTCCCCTGTCA+TGG + chr1.3:61145346-61145365 MS.gene20892:CDS 50.0%
! GTTTTTCCCCTGTCATGGAG+TGG + chr1.3:61145351-61145370 MS.gene20892:CDS 50.0%
!! ATTTGGAGTGGGCTGCAAGA+AGG - chr1.3:61146924-61146943 None:intergenic 50.0%
AAGGACCATTGCGACAGGTC+AGG - chr1.3:61146763-61146782 None:intergenic 55.0%
ATCCTGCCACTCCATGACAG+GGG - chr1.3:61145360-61145379 None:intergenic 55.0%
ATCGTGAAGCCATCCCGGAA+TGG + chr1.3:61146263-61146282 MS.gene20892:CDS 55.0%
CAATCCTGCCACTCCATGAC+AGG - chr1.3:61145362-61145381 None:intergenic 55.0%
CTCTGGATGGTCTTCCCAAC+AGG + chr1.3:61146963-61146982 MS.gene20892:CDS 55.0%
GACCATCCAGAGATCGCCAA+TGG - chr1.3:61146955-61146974 None:intergenic 55.0%
TGCGACAGGTCAGGTTTGTC+TGG - chr1.3:61146754-61146773 None:intergenic 55.0%
!! AAAGGGCATCCATTCCGGGA+TGG - chr1.3:61146275-61146294 None:intergenic 55.0%
TTCCCCTGTCATGGAGTGGC+AGG + chr1.3:61145355-61145374 MS.gene20892:CDS 60.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 61145149 61147008 61145149 ID=MS.gene20892
chr1.3 mRNA 61145149 61147008 61145149 ID=MS.gene20892.t1;Parent=MS.gene20892
chr1.3 exon 61145149 61145384 61145149 ID=MS.gene20892.t1.exon1;Parent=MS.gene20892.t1
chr1.3 CDS 61145149 61145384 61145149 ID=cds.MS.gene20892.t1;Parent=MS.gene20892.t1
chr1.3 exon 61146210 61146309 61146210 ID=MS.gene20892.t1.exon2;Parent=MS.gene20892.t1
chr1.3 CDS 61146210 61146309 61146210 ID=cds.MS.gene20892.t1;Parent=MS.gene20892.t1
chr1.3 exon 61146745 61146829 61146745 ID=MS.gene20892.t1.exon3;Parent=MS.gene20892.t1
chr1.3 CDS 61146745 61146829 61146745 ID=cds.MS.gene20892.t1;Parent=MS.gene20892.t1
chr1.3 exon 61146932 61147008 61146932 ID=MS.gene20892.t1.exon4;Parent=MS.gene20892.t1
chr1.3 CDS 61146932 61147008 61146932 ID=cds.MS.gene20892.t1;Parent=MS.gene20892.t1
Gene Sequence

>MS.gene20892

ATGTCTTCAACTGCAACTTCAACCGTCGTCATAAGCTCTTTTTCAACAATTCCATCTTTGAATCGCAATGCTAGAATCACATTTGCCGCCAATTTTACTTCTAGAAGCTTCCCCTCAACTTCACTCTCTTCCAATCGCTTCTTCTTCAGACTCCCTCACACTTCTTCTTCTAAGCGATCCTCAACTTTCCATCGATTCAAGCGTTTTTCCCCTGTCATGGAGTGGCAGGATTGCACGTAACTACTTTCCTTTTTTTCTTTCGCTTTTCTATTTTATATGTATGGCTAAATTGAAATTTAAAACTGTTGATGATAAGCATCAGTTTAGCTCAGTTTTGTAATTTTGATTGATATAATATTTACTGAATCAAAAAATTTGAGTGTGAATTTGATAGTTTCTATTATTCATCAACCAAAAATGCCGATTTTGCTTATTTTTTCTTTCTTTCTTTCTTTCTTTGTAATATATGCACAAGGATATAGTTTTTACATGTAACTCGTTAATTGTCATGTAGTATACTCTCTTTTCATATTTACTGTACATTCCTTGCAATTAGCATAGATATTCGTGCCTCTTTCCATTGGTTTATAATAATTTGAGGTTATCCACTCACCAAAGCACTTGTGATGATAACTTATGAAAACAACTTATGACATGTTCATAAGCTGTTTTCACCTTATTTCCATAAGGTCTCCAAGATAGATTATGAAAACAGTGTAAAGCTTTTAAGAAATTTGTTTGACTTTATTTTATCTTGTCTTGACAATATCTTATAATAAACAGTTATATATGATAAGCGTTTATGCTTTAAGCTGCAAATTAAGTTGCTTATCCAAATATGGCCTTATTTCATATTCCTCTAATAGGGATGGAATTTTTGTTTTGTGATTTTGCCATTTTGTTCCATTCGTTTTAGAATTAGACGACAATCTTCTCTCATGTCATTAATGTTGTATATTTCTTAATTGGTGTCAGTTTTTAGCACTTCTGTTTGGTTTCATCAAGCTGACCCAACCACAGCTTCCTACTTTCAATGAAAAAAATAATATTTCCGAATGCAGGGTTAAGATGGAGGTTGATGTCCCGATCTCTGTAGCATATGATTGTTATTCTGATCGTGAAGCCATCCCGGAATGGATGCCCTTTATTTCCACTGTTAAGGTGTGCTTGCTCTCCTTCTAACCCTGATTAATTACAAGGCTAATATCATAATCACTATTGTTGGTTTTTAAGAAAGAATTGAAAATCTTTACCTTATGGAATCATAGCATGTGAAATGCAACCTTTGACTCTTTTCCTGTCAGACTAGATTAAACTGTGTTGATGAGGATATTTCACTTCAAATTAGACAATATTGAATTGTGCATGATATTTTTTATAACATGAAGAATCATGAAAAATATAGCTTCTGCTTGTTTCTCTTTGCTAAATCATATATTTAGCTTGTTCGTTTGAAGTTTATGATCTTTATCTTTCGAATTTTAGCTGCTTTCAACTGTTTAAATTATCATAAACATGCATTCTTCGTACAAATATCATAAAATGTAATCAGTAATAAATTTTGATTTTATGCAAAACGTTGGATCCATTTTGCAGATATTGCCAGACAAACCTGACCTGTCGCAATGGTCCTTGAAGTATAAGGCATTTGGTCAGAATATTGAGTTCTCTTGGCTTGCTCGTAATATGCAGGAAAAGATTGCCTACCTGATACTTTTGCTTCTTTTCGAAAATGCTCTTTACAATTAGTATTTTGTATTCATGTTTTATTGCCTTCTTGCAGCCCACTCCAAATCAGAAAATCCATTGGCGATCTCTGGATGGTCTTCCCAACAGGTAACTGACAAGGGCATTTTCTGA
Protein sequence

>MS.gene20892.t1

MSSTATSTVVISSFSTIPSLNRNARITFAANFTSRSFPSTSLSSNRFFFRLPHTSSSKRSSTFHRFKRFSPVMEWQDCTVKMEVDVPISVAYDCYSDREAIPEWMPFISTVKILPDKPDLSQWSLKYKAFGQNIEFSWLAPHSKSENPLAISGWSSQQVTDKGIF