AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene50039

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene50039.t1 MTR_8g028150 87.288 118 13 1 44 161 229 344 3.65e-64 202
MS.gene50039.t1 MTR_7g116890 68.067 119 31 2 48 161 229 345 2.42e-44 151
MS.gene50039.t1 MTR_8g070820 41.912 136 55 4 48 161 238 371 9.40e-20 85.1
MS.gene50039.t1 MTR_8g077950 60.526 76 27 2 87 161 249 322 7.45e-19 82.0
MS.gene50039.t1 MTR_8g077950 60.526 76 27 2 87 161 251 324 8.22e-19 82.0
MS.gene50039.t1 MTR_8g077950 60.526 76 27 2 87 161 191 264 1.16e-18 80.9
MS.gene50039.t1 MTR_5g028850 60.274 73 27 1 89 161 302 372 2.95e-18 80.9
MS.gene50039.t1 MTR_5g028850 60.274 73 27 1 89 161 300 370 3.81e-18 80.5
MS.gene50039.t1 MTR_8g070820 44.915 118 51 4 48 161 238 345 1.12e-17 79.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene50039.t1 AT2G46270 59.813 107 33 3 54 160 226 322 6.03e-30 112
MS.gene50039.t1 AT2G46270 59.813 107 33 3 54 160 226 322 6.03e-30 112
MS.gene50039.t1 AT2G46270 75.362 69 15 1 92 160 233 299 5.13e-24 96.3
MS.gene50039.t1 AT2G46270 75.362 69 15 1 92 160 233 299 5.13e-24 96.3
MS.gene50039.t1 AT4G01120 51.000 100 36 4 61 160 226 312 4.92e-20 85.5
MS.gene50039.t1 AT2G35530 51.546 97 34 3 73 161 278 369 1.02e-19 85.1
MS.gene50039.t1 AT1G32150 57.333 75 28 2 89 161 287 359 1.81e-17 78.6
MS.gene50039.t1 AT4G36730 54.167 72 31 1 90 161 215 284 4.09e-15 71.6
MS.gene50039.t1 AT4G36730 54.167 72 31 1 90 161 217 286 4.23e-15 71.6

Find 37 sgRNAs with CRISPR-Local

Find 81 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCATTGACTGCCGAGAATT+TGG 0.257432 2.3:-3498504 MS.gene50039:CDS
GTTGGACCTCTACTTTCTTC+AGG 0.305646 2.3:-3499307 MS.gene50039:CDS
TTTGGAAGCGGCAGTCTCTT+TGG 0.337449 2.3:+3499370 None:intergenic
GCAACCAGTGCTGCAGAAAA+TGG 0.342628 2.3:-3499329 MS.gene50039:CDS
CGAGAATTTGGTGCTGAAAT+CGG 0.374258 2.3:-3498492 MS.gene50039:CDS
TGTGGAACACTGGTGGAAAT+AGG 0.380405 2.3:+3499250 None:intergenic
CGATTTCAGCACCAAATTCT+CGG 0.384484 2.3:+3498493 None:intergenic
ACAGGCTGAGGCTGAAGAAT+TGG 0.391234 2.3:-3498540 MS.gene50039:intron
GCCTCCTGAAGCTTGGATGC+AGG 0.426706 2.3:-3499212 MS.gene50039:intron
CATTGGTCTGTTTATAACAT+TGG 0.447505 2.3:+3499762 None:intergenic
GAAATCGGAAATGAATGAAT+TGG 0.472002 2.3:-3498477 MS.gene50039:CDS
TTCAGGTATGACCACATCAC+TGG 0.473232 2.3:-3499290 MS.gene50039:CDS
AGTGGTTGTTGGTGTTCCAT+TGG 0.474613 2.3:+3499745 None:intergenic
GAAGATCCAGGCTTAGGCTT+AGG 0.474677 2.3:-3498997 MS.gene50039:CDS
AGTACCTGCATCCAAGCTTC+AGG 0.494330 2.3:+3499208 None:intergenic
ACCAGTGTTCCACAGCCTTG+TGG 0.495543 2.3:-3499241 MS.gene50039:CDS
TTTATCATACCAGTGGTTGT+TGG 0.502643 2.3:+3499734 None:intergenic
CTGCTAGAAGATCCAGGCTT+AGG 0.520262 2.3:-3499003 MS.gene50039:CDS
GGCAAAACTCCACAAGGCTG+TGG 0.541143 2.3:+3499232 None:intergenic
TTGCTTCCTAAGCCTAAGCC+TGG 0.544129 2.3:+3498991 None:intergenic
GTGAATCTGCTAGAAGATCC+AGG 0.554001 2.3:-3499009 MS.gene50039:CDS
TCCACAAGGCTGTGGAACAC+TGG 0.554932 2.3:+3499240 None:intergenic
CCAGTGCTGCAGAAAATGGT+TGG 0.563429 2.3:-3499325 MS.gene50039:CDS
GTGAGCTGAAACGTGAGAGG+AGG 0.579172 2.3:-3499045 MS.gene50039:CDS
AATGGAACACCAACAACCAC+TGG 0.585041 2.3:-3499743 MS.gene50039:intron
TTACTTGAACAGATGGAGAA+GGG 0.588445 2.3:-3499421 MS.gene50039:intron
ATTACTTGAACAGATGGAGA+AGG 0.590419 2.3:-3499422 MS.gene50039:intron
TGACCACATCACTGGAACTG+AGG 0.592621 2.3:-3499282 MS.gene50039:CDS
ACAAGGCTGTGGAACACTGG+TGG 0.593279 2.3:+3499243 None:intergenic
GTTCCTCAGTTCCAGTGATG+TGG 0.596954 2.3:+3499279 None:intergenic
ACACTGGTGGAAATAGGCGA+AGG 0.605436 2.3:+3499256 None:intergenic
AGAGTGAGCTGAAACGTGAG+AGG 0.623183 2.3:-3499048 MS.gene50039:CDS
CAATGTTATAAACAGACCAA+TGG 0.632904 2.3:-3499761 MS.gene50039:CDS
ACCTGCATCCAAGCTTCAGG+AGG 0.636392 2.3:+3499211 None:intergenic
TCAGGAGGCAAAACTCCACA+AGG 0.658647 2.3:+3499226 None:intergenic
CACTGGTGGAAATAGGCGAA+GGG 0.662789 2.3:+3499257 None:intergenic
GTCATACCTGAAGAAAGTAG+AGG 0.696910 2.3:+3499301 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTAATTACATTCAATTTTTT+TGG - chr2.3:3498692-3498711 MS.gene50039:intron 10.0%
!! AAAGAAAATGTTATCACAAA+AGG - chr2.3:3499597-3499616 MS.gene50039:intron 20.0%
!! ATAAACAATACTAGTTATTC+TGG - chr2.3:3498477-3498496 MS.gene50039:CDS 20.0%
!! TAATCAGAAATTTAAAAGCA+TGG + chr2.3:3498630-3498649 None:intergenic 20.0%
!! TGAAAACAACTTATAGAATA+TGG - chr2.3:3499438-3499457 MS.gene50039:intron 20.0%
!!! TCAATTTTTTTGGTTTCATA+AGG - chr2.3:3498702-3498721 MS.gene50039:intron 20.0%
!! GTGATAACATTTTCTTTCAA+GGG + chr2.3:3499594-3499613 None:intergenic 25.0%
!! TGTGATAACATTTTCTTTCA+AGG + chr2.3:3499595-3499614 None:intergenic 25.0%
!! TTAAGTTGTTTATCCAAACA+CGG - chr2.3:3499547-3499566 MS.gene50039:intron 25.0%
!!! TATTTGTCACGTGTTTTTAT+GGG - chr2.3:3499276-3499295 MS.gene50039:CDS 25.0%
!!! TTATTTGTCACGTGTTTTTA+TGG - chr2.3:3499275-3499294 MS.gene50039:CDS 25.0%
AATAAGCTGAAAAGAGCTTA+TGG + chr2.3:3499393-3499412 None:intergenic 30.0%
ACTGACACTAAAGTAATTCT+TGG - chr2.3:3499104-3499123 MS.gene50039:intron 30.0%
AGTATTGTTTATCATACCAG+TGG + chr2.3:3498469-3498488 None:intergenic 30.0%
ATGTAATTAACTCTCAAACG+AGG + chr2.3:3498682-3498701 None:intergenic 30.0%
CAATGTTATAAACAGACCAA+TGG - chr2.3:3498432-3498451 MS.gene50039:CDS 30.0%
CCAATTGTTAATGCATGATA+AGG - chr2.3:3498596-3498615 MS.gene50039:intron 30.0%
CCTTATCATGCATTAACAAT+TGG + chr2.3:3498599-3498618 None:intergenic 30.0%
CTGGATTACAAATATACTTC+TGG - chr2.3:3498496-3498515 MS.gene50039:CDS 30.0%
GAAATCGGAAATGAATGAAT+TGG - chr2.3:3499716-3499735 MS.gene50039:intron 30.0%
GTACTAATTACTTGAACAGA+TGG - chr2.3:3498765-3498784 MS.gene50039:intron 30.0%
TAAACACATATGAGACTGTT+CGG - chr2.3:3499337-3499356 MS.gene50039:CDS 30.0%
TTTAGTGTCAGTAAAAGACA+AGG + chr2.3:3499096-3499115 None:intergenic 30.0%
! CATTGGTCTGTTTATAACAT+TGG + chr2.3:3498434-3498453 None:intergenic 30.0%
!! TTTTATGGGTTTGTTTGGAT+TGG - chr2.3:3499290-3499309 MS.gene50039:CDS 30.0%
AAACTATCCTGAAGAGCTTA+TGG + chr2.3:3499417-3499436 None:intergenic 35.0%
ATTACTTGAACAGATGGAGA+AGG - chr2.3:3498771-3498790 MS.gene50039:intron 35.0%
CTTATTTCCATAAGCTCTTC+AGG - chr2.3:3499407-3499426 MS.gene50039:CDS 35.0%
GAATCATTTGATACCAAGAC+TGG - chr2.3:3498654-3498673 MS.gene50039:intron 35.0%
TCAATGAATTGTTGACACCA+CGG + chr2.3:3498550-3498569 None:intergenic 35.0%
TTACTTGAACAGATGGAGAA+GGG - chr2.3:3498772-3498791 MS.gene50039:intron 35.0%
TTTATCATACCAGTGGTTGT+TGG + chr2.3:3498462-3498481 None:intergenic 35.0%
!! CGTGTTTTTATGGGTTTGTT+TGG - chr2.3:3499285-3499304 MS.gene50039:CDS 35.0%
CGATTTCAGCACCAAATTCT+CGG + chr2.3:3499703-3499722 None:intergenic 40.0%
CGTTCTTATCTCCTCTATAC+AGG - chr2.3:3499635-3499654 MS.gene50039:intron 40.0%
GTCATACCTGAAGAAAGTAG+AGG + chr2.3:3498895-3498914 None:intergenic 40.0%
TTCAGCTCACTCTCATTCTA+AGG + chr2.3:3499138-3499157 None:intergenic 40.0%
! GATAACTGACACCGTCTTTT+TGG + chr2.3:3498844-3498863 None:intergenic 40.0%
!! CGAGAATTTGGTGCTGAAAT+CGG - chr2.3:3499701-3499720 MS.gene50039:intron 40.0%
AATGGAACACCAACAACCAC+TGG - chr2.3:3498450-3498469 MS.gene50039:CDS 45.0%
GAGCATATAGAACCAGCGTA+TGG - chr2.3:3499362-3499381 MS.gene50039:CDS 45.0%
GGCTACATGTACATGCATCA+GGG + chr2.3:3499573-3499592 None:intergenic 45.0%
GTCATGAATGACTGTAACCG+TGG - chr2.3:3498530-3498549 MS.gene50039:CDS 45.0%
GTGAATCTGCTAGAAGATCC+AGG - chr2.3:3499184-3499203 MS.gene50039:intron 45.0%
GTTGGACCTCTACTTTCTTC+AGG - chr2.3:3498886-3498905 MS.gene50039:intron 45.0%
TATAGAACCAGCGTATGGCA+TGG - chr2.3:3499367-3499386 MS.gene50039:CDS 45.0%
TATCTCCTCTATACAGGCTG+AGG - chr2.3:3499641-3499660 MS.gene50039:intron 45.0%
TGTGGAACACTGGTGGAAAT+AGG + chr2.3:3498946-3498965 None:intergenic 45.0%
TTCAGGTATGACCACATCAC+TGG - chr2.3:3498903-3498922 MS.gene50039:intron 45.0%
! AGTGGTTGTTGGTGTTCCAT+TGG + chr2.3:3498451-3498470 None:intergenic 45.0%
!! TGACACCGTCTTTTTGGAAG+CGG + chr2.3:3498838-3498857 None:intergenic 45.0%
!! TGCATTGACTGCCGAGAATT+TGG - chr2.3:3499689-3499708 MS.gene50039:intron 45.0%
ACACTGGTGGAAATAGGCGA+AGG + chr2.3:3498940-3498959 None:intergenic 50.0%
ACAGGCTGAGGCTGAAGAAT+TGG - chr2.3:3499653-3499672 MS.gene50039:intron 50.0%
AGAGTGAGCTGAAACGTGAG+AGG - chr2.3:3499145-3499164 MS.gene50039:intron 50.0%
AGTACCTGCATCCAAGCTTC+AGG + chr2.3:3498988-3499007 None:intergenic 50.0%
CACTGGTGGAAATAGGCGAA+GGG + chr2.3:3498939-3498958 None:intergenic 50.0%
CCAGTGCTGCAGAAAATGGT+TGG - chr2.3:3498868-3498887 MS.gene50039:intron 50.0%
CTGCTAGAAGATCCAGGCTT+AGG - chr2.3:3499190-3499209 MS.gene50039:intron 50.0%
GAAGATCCAGGCTTAGGCTT+AGG - chr2.3:3499196-3499215 MS.gene50039:intron 50.0%
GCAACCAGTGCTGCAGAAAA+TGG - chr2.3:3498864-3498883 MS.gene50039:intron 50.0%
GGGCTACATGTACATGCATC+AGG + chr2.3:3499574-3499593 None:intergenic 50.0%
GTTCCTCAGTTCCAGTGATG+TGG + chr2.3:3498917-3498936 None:intergenic 50.0%
TCAGGAGGCAAAACTCCACA+AGG + chr2.3:3498970-3498989 None:intergenic 50.0%
TGACCACATCACTGGAACTG+AGG - chr2.3:3498911-3498930 MS.gene50039:intron 50.0%
TTCAGCCTCAGCCTGTATAG+AGG + chr2.3:3499649-3499668 None:intergenic 50.0%
TTGCTTCCTAAGCCTAAGCC+TGG + chr2.3:3499205-3499224 None:intergenic 50.0%
TTTGGAAGCGGCAGTCTCTT+TGG + chr2.3:3498826-3498845 None:intergenic 50.0%
! CCAACCATTTTCTGCAGCAC+TGG + chr2.3:3498871-3498890 None:intergenic 50.0%
! GACTGCCGCTTCCAAAAAGA+CGG - chr2.3:3498830-3498849 MS.gene50039:intron 50.0%
! GAGTTTTGCCTCCTGAAGCT+TGG - chr2.3:3498974-3498993 MS.gene50039:intron 50.0%
ACAAGGCTGTGGAACACTGG+TGG + chr2.3:3498953-3498972 None:intergenic 55.0%
ACATGCATCAGGGCCGTGTT+TGG + chr2.3:3499563-3499582 None:intergenic 55.0%
ACCAGTGTTCCACAGCCTTG+TGG - chr2.3:3498952-3498971 MS.gene50039:intron 55.0%
ACCTGCATCCAAGCTTCAGG+AGG + chr2.3:3498985-3499004 None:intergenic 55.0%
CTTATGGCCATGCCATACGC+TGG + chr2.3:3499377-3499396 None:intergenic 55.0%
GGCAAAACTCCACAAGGCTG+TGG + chr2.3:3498964-3498983 None:intergenic 55.0%
GTGAGCTGAAACGTGAGAGG+AGG - chr2.3:3499148-3499167 MS.gene50039:intron 55.0%
TCCACAAGGCTGTGGAACAC+TGG + chr2.3:3498956-3498975 None:intergenic 55.0%
! CTCAAACGAGGTGCCAGTCT+TGG + chr2.3:3498670-3498689 None:intergenic 55.0%
GCCTCCTGAAGCTTGGATGC+AGG - chr2.3:3498981-3499000 MS.gene50039:intron 60.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 3498418 3499797 3498418 ID=MS.gene50039
chr2.3 mRNA 3498418 3499797 3498418 ID=MS.gene50039.t1;Parent=MS.gene50039
chr2.3 exon 3499744 3499797 3499744 ID=MS.gene50039.t1.exon1;Parent=MS.gene50039.t1
chr2.3 CDS 3499744 3499797 3499744 ID=cds.MS.gene50039.t1;Parent=MS.gene50039.t1
chr2.3 exon 3499213 3499431 3499213 ID=MS.gene50039.t1.exon2;Parent=MS.gene50039.t1
chr2.3 CDS 3499213 3499431 3499213 ID=cds.MS.gene50039.t1;Parent=MS.gene50039.t1
chr2.3 exon 3498991 3499074 3498991 ID=MS.gene50039.t1.exon3;Parent=MS.gene50039.t1
chr2.3 CDS 3498991 3499074 3498991 ID=cds.MS.gene50039.t1;Parent=MS.gene50039.t1
chr2.3 exon 3498418 3498558 3498418 ID=MS.gene50039.t1.exon4;Parent=MS.gene50039.t1
chr2.3 CDS 3498418 3498558 3498418 ID=cds.MS.gene50039.t1;Parent=MS.gene50039.t1
Gene Sequence

>MS.gene50039

ATGAAAATGTTTGCCAATGTTATAAACAGACCAATGGAACACCAACAACCACTGGTATGATAAACAATACTAGTTATTCTGGATTACAAATATACTTCTGGTGTCATGTCATGTCATGAATGACTGTAACCGTGGTGTCAACAATTCATTGAGTATGATCTTGATAAATAAATACTATCCAATTGTTAATGCATGATAAGGTGAAGTTACCATGCTTTTAAATTTCTGATTAATTTGAATCATTTGATACCAAGACTGGCACCTCGTTTGAGAGTTAATTACATTCAATTTTTTTGGTTTCATAAGGATGCATTTATCGATAAAACGTTATCTACTAGTAACTTAATGTACTAATTACTTGAACAGATGGAGAAGGGAAAACTGAGATGCAAGATAATCAAGTTTCCAAAGAGACTGCCGCTTCCAAAAAGACGGTGTCAGTTATCGCAACCAGTGCTGCAGAAAATGGTTGGACCTCTACTTTCTTCAGGTATGACCACATCACTGGAACTGAGGAACCCTTCGCCTATTTCCACCAGTGTTCCACAGCCTTGTGGAGTTTTGCCTCCTGAAGCTTGGATGCAGGTACTGTAAGATTTTAGTTCTACTAATGTTTCATTTCTCACATCTAGTACATTAGAGATTCTTTTGAATCACACAACAATAATGCAGCATCCTTGTCTTTTACTGACACTAAAGTAATTCTTGGTCTGAATTCCTTAGAATGAGAGTGAGCTGAAACGTGAGAGGAGGAAACAATCAAATCGTGAATCTGCTAGAAGATCCAGGCTTAGGCTTAGGAAGCAAGTATGATTTGATGCAAATTTGCAATTTTTGTTTCACGTGTTCGTGTTTTTTTATTTGTCACGTGTTTTTATGGGTTTGTTTGGATTGGCTAATTTGAGCTTATCAACTAACATAAACACATATGAGACTGTTCGGAAGAGCATATAGAACCAGCGTATGGCATGGCCATAAGCTCTTTTCAGCTTATTTCCATAAGCTCTTCAGGATAGTTTATGAAAACAACTTATAGAATATGGAAACAATTTGACTTTAATTTATCTTTTGCTATAGTAGTTTATACATAAACACTTATATGATGAACATTTATGCTACAAGCACTCAGTTAAGTTGTTTATCCAAACACGGCCCTGATGCATGTACATGTAGCCCTTGAAAGAAAATGTTATCACAAAAGGAAAGTTCATGACAAACGTTCTTATCTCCTCTATACAGGCTGAGGCTGAAGAATTGGCACGAAGAGTCGATGCATTGACTGCCGAGAATTTGGTGCTGAAATCGGAAATGAATGAATTGGCTGAAAATTCTGAGAAGCTGAAGATTGAAAATGCTACATTAAAGATAATGCACACATAA
Protein sequence

>MS.gene50039.t1

MKMFANVINRPMEHQQPLMEKGKLRCKIIKFPKRLPLPKRRCQLSQPVLQKMVGPLLSSGMTTSLELRNPSPISTSVPQPCGVLPPEAWMQNESELKRERRKQSNRESARRSRLRLRKQAEAEELARRVDALTAENLVLKSEMNELAENSEKLKIENATLKIMHT