AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene002226

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene002226.t1 MTR_2g009390 98.214 112 2 0 1 112 1 112 1.41e-78 226
MS.gene002226.t1 MTR_8g080980 45.455 110 54 4 2 110 38 142 4.55e-20 84.3
MS.gene002226.t1 MTR_8g080980 36.937 111 64 3 3 110 272 379 9.12e-15 68.9
MS.gene002226.t1 MTR_5g080300 40.000 110 63 3 2 110 12 119 1.36e-19 79.3
MS.gene002226.t1 MTR_8g038785 42.857 105 49 3 11 111 180 277 7.46e-19 80.9
MS.gene002226.t1 MTR_7g053470 45.263 95 47 3 16 110 49 138 2.32e-17 76.6
MS.gene002226.t1 MTR_8g012340 46.316 95 46 3 16 110 55 144 3.10e-17 76.3
MS.gene002226.t1 MTR_4g094785 36.364 110 56 4 11 110 133 238 9.33e-12 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene002226.t1 AT5G64350 85.714 112 16 0 1 112 1 112 2.11e-70 206
MS.gene002226.t1 AT3G55520 35.780 109 69 1 2 110 12 119 1.35e-17 74.3
MS.gene002226.t1 AT3G55520 35.780 109 69 1 2 110 12 119 1.35e-17 74.3
MS.gene002226.t1 AT3G55520 35.780 109 69 1 2 110 12 119 1.35e-17 74.3
MS.gene002226.t1 AT5G48570 40.000 110 60 4 2 110 47 151 7.88e-16 72.0
MS.gene002226.t1 AT5G48570 35.135 111 68 3 3 110 282 391 5.25e-11 58.5
MS.gene002226.t1 AT3G25230 40.367 109 59 4 2 109 39 142 3.90e-15 70.1
MS.gene002226.t1 AT3G25230 40.367 109 59 4 2 109 39 142 4.92e-15 69.7
MS.gene002226.t1 AT4G25340 41.176 102 53 4 12 112 382 477 2.85e-14 67.8
MS.gene002226.t1 AT5G05420 40.196 102 53 4 12 112 49 143 7.94e-13 60.8
MS.gene002226.t1 AT5G45680 40.367 109 51 4 11 109 101 205 1.02e-12 62.0

Find 31 sgRNAs with CRISPR-Local

Find 77 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGCTAGTGGCTTTCCTGCTT+GGG 0.208113 2.3:+73518490 MS.gene002226:CDS
GTGACCTTTCTCAGAAATTC+TGG 0.269473 2.3:+73517359 MS.gene002226:CDS
TGCTCTCCTGATTATGCTTA+TGG 0.301017 2.3:+73518467 MS.gene002226:CDS
TCGGAGAAGTTGCTCGTCTT+CGG 0.329775 2.3:+73517882 MS.gene002226:CDS
AATACAACCCAACTCTGTTT+TGG 0.332199 2.3:+73518514 MS.gene002226:CDS
GCGCTAGTGGCTTTCCTGCT+TGG 0.337892 2.3:+73518489 MS.gene002226:CDS
CGGAGAAGTTGCTCGTCTTC+GGG 0.345948 2.3:+73517883 MS.gene002226:CDS
AATCCATTCACTTTCAAAAT+CGG 0.376739 2.3:+73517489 MS.gene002226:CDS
GAGAGAGTGCTCACCGTATC+CGG 0.441515 2.3:-73517179 None:intergenic
TTTGGCTTAGGACCGTTTCC+AGG 0.443287 2.3:-73517127 None:intergenic
CTAGCGCCATAAGCATAATC+AGG 0.449393 2.3:-73518473 None:intergenic
TCAAACTCCAAAACAGAGTT+GGG 0.461799 2.3:-73518521 None:intergenic
CTCAAACTCCAAAACAGAGT+TGG 0.473985 2.3:-73518522 None:intergenic
GGTGTCATTGGCATGCAAAT+CGG 0.478078 2.3:+73517863 MS.gene002226:CDS
AAAGTGAATGGATTCTGGCC+AGG 0.495829 2.3:-73517480 None:intergenic
AACGGTCCTAAGCCAAATCC+TGG 0.510092 2.3:+73517133 MS.gene002226:CDS
CAAATCGTTCGACCTGGAAA+CGG 0.515678 2.3:+73517115 MS.gene002226:CDS
ACCTCCAGAATTTCTGAGAA+AGG 0.516160 2.3:-73517363 None:intergenic
ACTGTCCACTGCACCGGATA+CGG 0.518197 2.3:+73517166 MS.gene002226:CDS
TTCACTTTCAAAATCGGCAA+AGG 0.528436 2.3:+73517495 MS.gene002226:CDS
GGATGGGATGAAGGTGTCAT+TGG 0.529844 2.3:+73517851 MS.gene002226:intron
TATTACAGTACAAAAGATCC+TGG 0.543772 2.3:+73517462 MS.gene002226:intron
GATTATGCTTATGGCGCTAG+TGG 0.545830 2.3:+73518476 MS.gene002226:CDS
AACGTCACTGTCCACTGCAC+CGG 0.551030 2.3:+73517160 MS.gene002226:CDS
TTGTGTGTAGGATGGGATGA+AGG 0.556041 2.3:+73517842 MS.gene002226:intron
TTGGGTTGTATTCCCCAAGC+AGG 0.558631 2.3:-73518503 None:intergenic
GCTAGTGGCTTTCCTGCTTG+GGG 0.575669 2.3:+73518491 MS.gene002226:CDS
ACCTTTCTCAGAAATTCTGG+AGG 0.582702 2.3:+73517362 MS.gene002226:CDS
GGCAAAGGTTCTGTCATCAA+AGG 0.586910 2.3:+73517510 MS.gene002226:CDS
GCTCACCGTATCCGGTGCAG+TGG 0.596990 2.3:-73517171 None:intergenic
GAGAAGCAAATCGTTCGACC+TGG 0.621651 2.3:+73517109 MS.gene002226:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTTAATTCAAATTATAAG+GGG - chr2.3:73517252-73517271 None:intergenic 10.0%
!! ACAATATTAAAAACAAAAAA+TGG - chr2.3:73517420-73517439 None:intergenic 10.0%
!! CTAATTTAATTCAAATTATA+AGG - chr2.3:73517254-73517273 None:intergenic 10.0%
!! ATATAAGCTAAAATAGTTTA+TGG - chr2.3:73518050-73518069 None:intergenic 15.0%
!! TAAAATGAAAGATAAGAAAT+GGG - chr2.3:73517225-73517244 None:intergenic 15.0%
!! TTAAAATGAAAGATAAGAAA+TGG - chr2.3:73517226-73517245 None:intergenic 15.0%
!! AAAATGAAAGATAAGAAATG+GGG - chr2.3:73517224-73517243 None:intergenic 20.0%
!!! ATATGTGATAAACTATTTTC+AGG - chr2.3:73518013-73518032 None:intergenic 20.0%
!!! TACTACTTTTACTTTATTTC+TGG + chr2.3:73517737-73517756 MS.gene002226:intron 20.0%
! AAACAAAAAATGGAATGACA+AGG - chr2.3:73517410-73517429 None:intergenic 25.0%
! AACAAAAAATGGAATGACAA+GGG - chr2.3:73517409-73517428 None:intergenic 25.0%
! AATCCATTCACTTTCAAAAT+CGG + chr2.3:73517489-73517508 MS.gene002226:CDS 25.0%
! ATGCACAGTTCAATTAATTA+AGG - chr2.3:73518199-73518218 None:intergenic 25.0%
! CAACATATTAATGTCATGTT+TGG - chr2.3:73518222-73518241 None:intergenic 25.0%
! GTTGATACTTTGTTAAATAG+TGG + chr2.3:73518398-73518417 MS.gene002226:intron 25.0%
! TGCACAGTTCAATTAATTAA+GGG - chr2.3:73518198-73518217 None:intergenic 25.0%
!!! AAATGGGGTTTTTAGTTTTA+GGG - chr2.3:73517209-73517228 None:intergenic 25.0%
TATTACAGTACAAAAGATCC+TGG + chr2.3:73517462-73517481 MS.gene002226:intron 30.0%
TGAGTAAAAACAAACAGCAA+AGG - chr2.3:73518250-73518269 None:intergenic 30.0%
TTACACACTTGTGAAACTTT+AGG - chr2.3:73517647-73517666 None:intergenic 30.0%
! GTGTAGAGTTTTTACACTAT+CGG + chr2.3:73517555-73517574 MS.gene002226:intron 30.0%
! TTTTTACTCACACACATACA+AGG + chr2.3:73518260-73518279 MS.gene002226:intron 30.0%
!! TTATAACTTGTTGCCACTTT+GGG + chr2.3:73517934-73517953 MS.gene002226:intron 30.0%
!! TTTATAACTTGTTGCCACTT+TGG + chr2.3:73517933-73517952 MS.gene002226:intron 30.0%
!! TTTTGAAAGTGAATGGATTC+TGG - chr2.3:73517488-73517507 None:intergenic 30.0%
!!! GAAATGGGGTTTTTAGTTTT+AGG - chr2.3:73517210-73517229 None:intergenic 30.0%
CAATGTACATTCAGATGTGT+TGG + chr2.3:73517783-73517802 MS.gene002226:intron 35.0%
CAATTCAATAAAGCCCAAAG+TGG - chr2.3:73517950-73517969 None:intergenic 35.0%
TATCAACAAGGTCAATGACA+GGG - chr2.3:73518438-73518457 None:intergenic 35.0%
TCAAACTCCAAAACAGAGTT+GGG - chr2.3:73518524-73518543 None:intergenic 35.0%
TTATCAACAAGGTCAATGAC+AGG - chr2.3:73518439-73518458 None:intergenic 35.0%
TTCACTTTCAAAATCGGCAA+AGG + chr2.3:73517495-73517514 MS.gene002226:CDS 35.0%
! AATACAACCCAACTCTGTTT+TGG + chr2.3:73518514-73518533 MS.gene002226:CDS 35.0%
! TGATGATGATCAGGCAAAAA+CGG + chr2.3:73517337-73517356 MS.gene002226:intron 35.0%
!! CACTTTGGGCTTTATTGAAT+TGG + chr2.3:73517948-73517967 MS.gene002226:intron 35.0%
!! CTTGTGAAACTTTAGGACTT+AGG - chr2.3:73517640-73517659 None:intergenic 35.0%
!! TGATTGTGTTGATGATGATC+AGG + chr2.3:73517328-73517347 MS.gene002226:intron 35.0%
!!! TGTTTTGGAGTTTGAGATTG+AGG + chr2.3:73518529-73518548 MS.gene002226:CDS 35.0%
!!! TTGCCGATTTTGAAAGTGAA+TGG - chr2.3:73517495-73517514 None:intergenic 35.0%
ACCTTTCTCAGAAATTCTGG+AGG + chr2.3:73517362-73517381 MS.gene002226:CDS 40.0%
ACTATCTGTTGTGTGTAGGA+TGG + chr2.3:73517834-73517853 MS.gene002226:intron 40.0%
ATACACGCAACTCGATTAAG+TGG - chr2.3:73518293-73518312 None:intergenic 40.0%
CTATCTGTTGTGTGTAGGAT+GGG + chr2.3:73517835-73517854 MS.gene002226:intron 40.0%
CTCAAACTCCAAAACAGAGT+TGG - chr2.3:73518525-73518544 None:intergenic 40.0%
GCACTGCAAGATTATCAACA+AGG - chr2.3:73518450-73518469 None:intergenic 40.0%
GTGACCTTTCTCAGAAATTC+TGG + chr2.3:73517359-73517378 MS.gene002226:CDS 40.0%
TCCAACTATCTGTTGTGTGT+AGG + chr2.3:73517830-73517849 MS.gene002226:intron 40.0%
TCCTACACACAACAGATAGT+TGG - chr2.3:73517834-73517853 None:intergenic 40.0%
TGCTCTCCTGATTATGCTTA+TGG + chr2.3:73518467-73518486 MS.gene002226:CDS 40.0%
! ACCTCCAGAATTTCTGAGAA+AGG - chr2.3:73517366-73517385 None:intergenic 40.0%
! TTCTCAGAAATTCTGGAGGT+TGG + chr2.3:73517366-73517385 MS.gene002226:intron 40.0%
!! GAAACTTTAGGACTTAGGAG+TGG - chr2.3:73517635-73517654 None:intergenic 40.0%
!! TTTTGACCAGGATTTGGCTT+AGG - chr2.3:73517142-73517161 None:intergenic 40.0%
CAAATCGTTCGACCTGGAAA+CGG + chr2.3:73517115-73517134 MS.gene002226:CDS 45.0%
CTAGCGCCATAAGCATAATC+AGG - chr2.3:73518476-73518495 None:intergenic 45.0%
GATTATGCTTATGGCGCTAG+TGG + chr2.3:73518476-73518495 MS.gene002226:CDS 45.0%
GGCAAAGGTTCTGTCATCAA+AGG + chr2.3:73517510-73517529 MS.gene002226:CDS 45.0%
TTGTGTGTAGGATGGGATGA+AGG + chr2.3:73517842-73517861 MS.gene002226:intron 45.0%
! AAAGTGAATGGATTCTGGCC+AGG - chr2.3:73517483-73517502 None:intergenic 45.0%
!! GGTGTCATTGGCATGCAAAT+CGG + chr2.3:73517863-73517882 MS.gene002226:CDS 45.0%
!! GTGACGTTTTGACCAGGATT+TGG - chr2.3:73517148-73517167 None:intergenic 45.0%
!! TAATTTAATTCAAATTATAA+GGG - chr2.3:73517253-73517272 None:intergenic 5.0%
AACGGTCCTAAGCCAAATCC+TGG + chr2.3:73517133-73517152 MS.gene002226:CDS 50.0%
GAGAAGCAAATCGTTCGACC+TGG + chr2.3:73517109-73517128 MS.gene002226:CDS 50.0%
TCGGAGAAGTTGCTCGTCTT+CGG + chr2.3:73517882-73517901 MS.gene002226:CDS 50.0%
! TTGGGTTGTATTCCCCAAGC+AGG - chr2.3:73518506-73518525 None:intergenic 50.0%
! TTTGGCTTAGGACCGTTTCC+AGG - chr2.3:73517130-73517149 None:intergenic 50.0%
!! GGATGGGATGAAGGTGTCAT+TGG + chr2.3:73517851-73517870 MS.gene002226:intron 50.0%
!! TGGACAGTGACGTTTTGACC+AGG - chr2.3:73517154-73517173 None:intergenic 50.0%
AACGTCACTGTCCACTGCAC+CGG + chr2.3:73517160-73517179 MS.gene002226:CDS 55.0%
ACTGTCCACTGCACCGGATA+CGG + chr2.3:73517166-73517185 MS.gene002226:CDS 55.0%
CGCTAGTGGCTTTCCTGCTT+GGG + chr2.3:73518490-73518509 MS.gene002226:CDS 55.0%
CGGAGAAGTTGCTCGTCTTC+GGG + chr2.3:73517883-73517902 MS.gene002226:CDS 55.0%
GCTAGTGGCTTTCCTGCTTG+GGG + chr2.3:73518491-73518510 MS.gene002226:CDS 55.0%
!! GAGAGAGTGCTCACCGTATC+CGG - chr2.3:73517182-73517201 None:intergenic 55.0%
GCGCTAGTGGCTTTCCTGCT+TGG + chr2.3:73518489-73518508 MS.gene002226:CDS 60.0%
GCTCACCGTATCCGGTGCAG+TGG - chr2.3:73517174-73517193 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 73517100 73518568 73517100 ID=MS.gene002226
chr2.3 mRNA 73517100 73518568 73517100 ID=MS.gene002226.t1;Parent=MS.gene002226
chr2.3 exon 73517100 73517187 73517100 ID=MS.gene002226.t1.exon1;Parent=MS.gene002226.t1
chr2.3 CDS 73517100 73517187 73517100 ID=cds.MS.gene002226.t1;Parent=MS.gene002226.t1
chr2.3 exon 73517350 73517383 73517350 ID=MS.gene002226.t1.exon2;Parent=MS.gene002226.t1
chr2.3 CDS 73517350 73517383 73517350 ID=cds.MS.gene002226.t1;Parent=MS.gene002226.t1
chr2.3 exon 73517470 73517531 73517470 ID=MS.gene002226.t1.exon3;Parent=MS.gene002226.t1
chr2.3 CDS 73517470 73517531 73517470 ID=cds.MS.gene002226.t1;Parent=MS.gene002226.t1
chr2.3 exon 73517852 73517904 73517852 ID=MS.gene002226.t1.exon4;Parent=MS.gene002226.t1
chr2.3 CDS 73517852 73517904 73517852 ID=cds.MS.gene002226.t1;Parent=MS.gene002226.t1
chr2.3 exon 73518467 73518568 73518467 ID=MS.gene002226.t1.exon5;Parent=MS.gene002226.t1
chr2.3 CDS 73518467 73518568 73518467 ID=cds.MS.gene002226.t1;Parent=MS.gene002226.t1
Gene Sequence

>MS.gene002226

ATGGGAGTTGAGAAGCAAATCGTTCGACCTGGAAACGGTCCTAAGCCAAATCCTGGTCAAAACGTCACTGTCCACTGCACCGGATACGGTGAGCACTCTCTCTAAACCCTAAAACTAAAAACCCCATTTCTTATCTTTCATTTTAATTACCCCTTATAATTTGAATTAAATTAGATCTACTCGTTCTTTGTTTGTCTTTGATTCATTGATTCATTCGCTAATTGTTTTTGATTGTGTTGATGATGATCAGGCAAAAACGGTGACCTTTCTCAGAAATTCTGGAGGTTGGTTAATTTACTTACTTTACCCTTGTCATTCCATTTTTTGTTTTTAATATTGTGTTCATTTCATTTCATTTACTTTATTACAGTACAAAAGATCCTGGCCAGAATCCATTCACTTTCAAAATCGGCAAAGGTTCTGTCATCAAAGGTACTATTATAACATTACTGTCAGTGTAGAGTTTTTACACTATCGGTTAATCATATTCATAACTGTCTTGATAATCAGAAACATTTGACTTTTATCACAACCACTCCTAAGTCCTAAAGTTTCACAAGTGTGTAAAATTGTTTACACTAACGATGCATGATAATTAAAATTGTACATTATCATGATAACTAATTAGTGTTAATTTTACTACTTTTACTTTATTTCTGGCTTCATTACACATAAAAATGCTGCAATGTACATTCAGATGTGTTGGCAACTCATTCACTATATGATTTATTCCAACTATCTGTTGTGTGTAGGATGGGATGAAGGTGTCATTGGCATGCAAATCGGAGAAGTTGCTCGTCTTCGGGTATAATATCTATTCTCTGCTCTTACTTTTTATAACTTGTTGCCACTTTGGGCTTTATTGAATTGGATACTAAGATAAACATTTGTGATACTGTTAGAGAGAGTTCCTGAAAATAGTTTATCACATATTCACATTCATATGTCCATAAACTATTTTAGCTTATATGAAAACAATTTGACTTTTTATGAAAACAGCTTATAGCTTATACGAAAATAATGACTTTATTTTATACTTTATTATAGAAATAGCTTATACGTAAGCATTTCTATGATAAGTGTTTATAGTATAAGCCCTTAATTAATTGAACTGTGCATCCAAACATGACATTAATATGTTGAATTTCCTTTGCTGTTTGTTTTTACTCACACACATACAAGGTGAAAATCCACTTAATCGAGTTGCGTGTATTAAATTTTATCAACTTAATTGTTAAATCAAACGTTCTTATTATTGAGCATGTCTAGTTTATAAATTTTTGCAATTTTATAAGCGAGTTGATACTTTGTTAAATAGTGGTCAGTTTGAGTTATCCCTGTCATTGACCTTGTTGATAATCTTGCAGTGCTCTCCTGATTATGCTTATGGCGCTAGTGGCTTTCCTGCTTGGGGAATACAACCCAACTCTGTTTTGGAGTTTGAGATTGAGGTCTTGAGTGCAGAATGA
Protein sequence

>MS.gene002226.t1

MGVEKQIVRPGNGPKPNPGQNVTVHCTGYGKNGDLSQKFWSTKDPGQNPFTFKIGKGSVIKGWDEGVIGMQIGEVARLRCSPDYAYGASGFPAWGIQPNSVLEFEIEVLSAE