AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene56696


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene56696.t1 MTR_5g081705 100.000 112 0 0 1 112 26 137 1.99e-79 229
MS.gene56696.t1 MTR_0699s0020 94.643 112 6 0 1 112 1 112 3.79e-77 223
MS.gene56696.t1 MTR_0699s0010 93.750 112 7 0 1 112 1 112 1.49e-76 221
MS.gene56696.t1 MTR_5g081705 100.000 99 0 0 1 99 26 124 3.59e-69 203
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene56696.t1 AT1G74270 88.393 112 13 0 1 112 1 112 9.66e-73 212
MS.gene56696.t1 AT1G07070 87.500 112 14 0 1 112 1 112 9.87e-73 212
MS.gene56696.t1 AT3G55750 89.189 111 12 0 2 112 1 111 6.67e-72 209
MS.gene56696.t1 AT1G41880 88.288 111 13 0 2 112 1 111 9.58e-72 209
MS.gene56696.t1 AT1G41880 88.288 111 13 0 2 112 1 111 9.58e-72 209

Find 45 sgRNAs with CRISPR-Local

Find 86 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAAAGAATTACCATTGATTT+TGG 0.162742 5.1:-63881386 None:intergenic
ACACCAATCAAAATGGTTAA+AGG 0.309838 5.1:+63880348 None:intergenic
TATGTCAGGGGTACAGTTCT+TGG 0.323600 5.1:+63880537 MS.gene56696:CDS
GAAGCCACTATCGCTGCATT+TGG 0.347443 5.1:+63881297 MS.gene56696:CDS
ATTTGTTTGTGCAGGGAGCC+AGG 0.348132 5.1:+63881479 MS.gene56696:intron
TTGTAATCAGGCTTTATGTC+AGG 0.353861 5.1:+63880523 MS.gene56696:intron
AAGCCACTATCGCTGCATTT+GGG 0.371781 5.1:+63881298 MS.gene56696:CDS
ATGTATCCAAGCAATATATA+AGG 0.407008 5.1:+63881514 MS.gene56696:CDS
AAATTACCTTATATATTGCT+TGG 0.412163 5.1:-63881520 None:intergenic
ATCTGAACAAGAGAGGTGTT+TGG 0.416693 5.1:-63881188 None:intergenic
GACGACAAGGAGAACGTATC+AGG 0.417479 5.1:+63880370 MS.gene56696:CDS
GAGGAGGTTGCATGGTATGC+TGG 0.417733 5.1:+63881230 MS.gene56696:CDS
GCATTTGGGGCAAGGTTACC+AGG 0.451709 5.1:+63881312 MS.gene56696:CDS
TCTGAACAAGAGAGGTGTTT+GGG 0.453404 5.1:-63881187 None:intergenic
TGCCCCAAATGCAGCGATAG+TGG 0.453767 5.1:-63881301 None:intergenic
GTTTGGGTATTGATTTACCT+TGG 0.466066 5.1:-63881171 None:intergenic
ATGGTATGCTGGGAAGAAAT+TGG 0.469927 5.1:+63881241 MS.gene56696:CDS
GCTTCCATCCTTCTTCACCT+TGG 0.472167 5.1:-63881279 None:intergenic
CTATCGCTGCATTTGGGGCA+AGG 0.487554 5.1:+63881304 MS.gene56696:CDS
ACCTCTCTTGTTCAGATCGA+GGG 0.499812 5.1:+63881194 MS.gene56696:CDS
ATACCATGCAACCTCCTCCT+TGG 0.519241 5.1:-63881225 None:intergenic
GCCACTGTTACCATGAGGCC+TGG 0.523824 5.1:-63881330 None:intergenic
AGGAGGTTGCATGGTATGCT+GGG 0.527652 5.1:+63881231 MS.gene56696:CDS
TGTAATCAGGCTTTATGTCA+GGG 0.533103 5.1:+63880524 MS.gene56696:intron
TTTGTTTGTGCAGGGAGCCA+GGG 0.534698 5.1:+63881480 MS.gene56696:intron
TTACAAGGCCAAGGTGAAGA+AGG 0.537680 5.1:+63881271 MS.gene56696:CDS
TAACCTACCACCAAAATCAA+TGG 0.539094 5.1:+63881376 MS.gene56696:CDS
GGCATACATTTACAAGGCCA+AGG 0.547418 5.1:+63881262 MS.gene56696:CDS
GAAATTGGCATACATTTACA+AGG 0.562532 5.1:+63881256 MS.gene56696:CDS
GGCAAGGTTACCAGGCCTCA+TGG 0.565570 5.1:+63881320 MS.gene56696:CDS
GTAATGTTGTTATAGGTCCA+AGG 0.573819 5.1:+63881154 MS.gene56696:intron
ATACATAAATACTCTAACCC+TGG 0.583670 5.1:-63881497 None:intergenic
AAGGCCAAGGTGAAGAAGGA+TGG 0.591334 5.1:+63881275 MS.gene56696:CDS
CACCTCTCTTGTTCAGATCG+AGG 0.592183 5.1:+63881193 MS.gene56696:CDS
GTAATCAGGCTTTATGTCAG+GGG 0.604013 5.1:+63880525 MS.gene56696:intron
ACACCAAGGAGGAGGTTGCA+TGG 0.606757 5.1:+63881222 MS.gene56696:CDS
AGCCACTATCGCTGCATTTG+GGG 0.617770 5.1:+63881299 MS.gene56696:CDS
GGTTAGACTTGAACTTTGCG+CGG 0.621246 5.1:-63881358 None:intergenic
CCTCTCTTGTTCAGATCGAG+GGG 0.637714 5.1:+63881195 MS.gene56696:CDS
GTACAGTTCTTGGATACAAG+AGG 0.641528 5.1:+63880547 MS.gene56696:CDS
CCCCTCGATCTGAACAAGAG+AGG 0.655801 5.1:-63881195 None:intergenic
ACCAGGCCTCATGGTAACAG+TGG 0.661908 5.1:+63881329 MS.gene56696:CDS
AAAATGGTTAAAGGACGACA+AGG 0.679088 5.1:+63880357 None:intergenic
CTCTCTTGTTCAGATCGAGG+GGG 0.711001 5.1:+63881196 MS.gene56696:CDS
ACAATGCCACTGTTACCATG+AGG 0.746625 5.1:-63881335 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAATTAAATCTAATTTGTTT+GGG + chr5.1:63880663-63880682 MS.gene56696:intron 10.0%
!!! AATGTTGTTATTTTGATTTT+GGG + chr5.1:63880499-63880518 MS.gene56696:intron 15.0%
!!! AATTCTTTAAGACATTTAAA+TGG + chr5.1:63881400-63881419 MS.gene56696:intron 15.0%
!!! CTAATTAAATCTAATTTGTT+TGG + chr5.1:63880662-63880681 MS.gene56696:intron 15.0%
!!! TAATGTTGTTATTTTGATTT+TGG + chr5.1:63880498-63880517 MS.gene56696:intron 15.0%
!! TAGATGAACAATTATATACT+TGG - chr5.1:63881075-63881094 None:intergenic 20.0%
!!! AACTAAATGATTACTGATTT+GGG + chr5.1:63880999-63881018 MS.gene56696:intron 20.0%
!!! ATTTTTTATTGAGGATACAT+TGG - chr5.1:63880912-63880931 None:intergenic 20.0%
!!! TAAAGAATTACCATTGATTT+TGG - chr5.1:63881389-63881408 None:intergenic 20.0%
!!! TTGGGTATTATTTTTTATTG+AGG - chr5.1:63880921-63880940 None:intergenic 20.0%
!!! TTTGGGTATTATTTTTTGTA+TGG + chr5.1:63881016-63881035 MS.gene56696:intron 20.0%
!!! TTTTTTATTGAGGATACATT+GGG - chr5.1:63880911-63880930 None:intergenic 20.0%
! ACAAACACAAATTAAAAGCT+GGG - chr5.1:63880834-63880853 None:intergenic 25.0%
! GATTATTTGTGCTAAGAAAT+TGG + chr5.1:63881132-63881151 MS.gene56696:intron 25.0%
! TTAAGAACCAATACTCAATT+TGG + chr5.1:63880865-63880884 MS.gene56696:intron 25.0%
!! GAACTAAATGATTACTGATT+TGG + chr5.1:63880998-63881017 MS.gene56696:intron 25.0%
!!! ATGTTTAATGTTGTTTTAGC+TGG + chr5.1:63880750-63880769 MS.gene56696:intron 25.0%
!!! GAAATTGGTAATGTTGTTAT+AGG + chr5.1:63881147-63881166 MS.gene56696:intron 25.0%
!!! TTTATGGTTTCTGAAAGTTT+TGG + chr5.1:63881451-63881470 MS.gene56696:intron 25.0%
!!! TTTGATTTTGATGTTGATCT+GGG + chr5.1:63881101-63881120 MS.gene56696:intron 25.0%
!!! TTTTGATTTTGATGTTGATC+TGG + chr5.1:63881100-63881119 MS.gene56696:intron 25.0%
ATACATAAATACTCTAACCC+TGG - chr5.1:63881500-63881519 None:intergenic 30.0%
CACAAACACAAATTAAAAGC+TGG - chr5.1:63880835-63880854 None:intergenic 30.0%
GAAATTGGCATACATTTACA+AGG + chr5.1:63881256-63881275 MS.gene56696:CDS 30.0%
GCTGTATTTGATGTATTCTT+GGG + chr5.1:63880606-63880625 MS.gene56696:intron 30.0%
GTTAAACGAAATAGATCGAA+GGG - chr5.1:63880408-63880427 None:intergenic 30.0%
TGCTGTATTTGATGTATTCT+TGG + chr5.1:63880605-63880624 MS.gene56696:intron 30.0%
TGTTAAACGAAATAGATCGA+AGG - chr5.1:63880409-63880428 None:intergenic 30.0%
TTCAGAAACCATAAAACAGT+TGG - chr5.1:63881446-63881465 None:intergenic 30.0%
! TCTTTTCACCAACTGTTTTA+TGG + chr5.1:63881435-63881454 MS.gene56696:intron 30.0%
!!! AGAATTACCATTGATTTTGG+TGG - chr5.1:63881386-63881405 None:intergenic 30.0%
!!! TTGATTTTGGGTTTGTAATC+AGG + chr5.1:63880511-63880530 MS.gene56696:intron 30.0%
GTAATGTTGTTATAGGTCCA+AGG + chr5.1:63881154-63881173 MS.gene56696:intron 35.0%
TAACCTACCACCAAAATCAA+TGG + chr5.1:63881376-63881395 MS.gene56696:CDS 35.0%
TGAAGGACCAAATTGAGTAT+TGG - chr5.1:63880875-63880894 None:intergenic 35.0%
TTGGTCCTTCACAATATTTG+CGG + chr5.1:63880884-63880903 MS.gene56696:intron 35.0%
! TGTAATCAGGCTTTATGTCA+GGG + chr5.1:63880524-63880543 MS.gene56696:intron 35.0%
! TTGTAATCAGGCTTTATGTC+AGG + chr5.1:63880523-63880542 MS.gene56696:intron 35.0%
!! GTTTGGGTATTGATTTACCT+TGG - chr5.1:63881174-63881193 None:intergenic 35.0%
!!! TTACCATTGATTTTGGTGGT+AGG - chr5.1:63881382-63881401 None:intergenic 35.0%
ATGGTATGCTGGGAAGAAAT+TGG + chr5.1:63881241-63881260 MS.gene56696:CDS 40.0%
GTACAGTTCTTGGATACAAG+AGG + chr5.1:63880547-63880566 MS.gene56696:CDS 40.0%
TCTAGACTCATCATCACAAG+CGG - chr5.1:63880980-63880999 None:intergenic 40.0%
TGGTCCTTCACAATATTTGC+GGG + chr5.1:63880885-63880904 MS.gene56696:intron 40.0%
! GTAATCAGGCTTTATGTCAG+GGG + chr5.1:63880525-63880544 MS.gene56696:intron 40.0%
!! ATCTGAACAAGAGAGGTGTT+TGG - chr5.1:63881191-63881210 None:intergenic 40.0%
!! GATAATGCTGGGACTAGTTT+GGG - chr5.1:63880939-63880958 None:intergenic 40.0%
!! GGTGTTGATTTGTTTGTGCA+GGG + chr5.1:63881472-63881491 MS.gene56696:intron 40.0%
!! TCTGAACAAGAGAGGTGTTT+GGG - chr5.1:63881190-63881209 None:intergenic 40.0%
!! TGATAATGCTGGGACTAGTT+TGG - chr5.1:63880940-63880959 None:intergenic 40.0%
!! TGGTGTTGATTTGTTTGTGC+AGG + chr5.1:63881471-63881490 MS.gene56696:intron 40.0%
AAGCCACTATCGCTGCATTT+GGG + chr5.1:63881298-63881317 MS.gene56696:CDS 45.0%
ACAATGCCACTGTTACCATG+AGG - chr5.1:63881338-63881357 None:intergenic 45.0%
ACCTCTCTTGTTCAGATCGA+GGG + chr5.1:63881194-63881213 MS.gene56696:CDS 45.0%
GGCATACATTTACAAGGCCA+AGG + chr5.1:63881262-63881281 MS.gene56696:CDS 45.0%
GGTTAGACTTGAACTTTGCG+CGG - chr5.1:63881361-63881380 None:intergenic 45.0%
TCCCAGCATTATCACAGTAC+AGG + chr5.1:63880946-63880965 MS.gene56696:intron 45.0%
TTACAAGGCCAAGGTGAAGA+AGG + chr5.1:63881271-63881290 MS.gene56696:CDS 45.0%
! GCCTGTACTGTGATAATGCT+GGG - chr5.1:63880950-63880969 None:intergenic 45.0%
! TATGTCAGGGGTACAGTTCT+TGG + chr5.1:63880537-63880556 MS.gene56696:CDS 45.0%
! TGCCTGTACTGTGATAATGC+TGG - chr5.1:63880951-63880970 None:intergenic 45.0%
AAGGCCAAGGTGAAGAAGGA+TGG + chr5.1:63881275-63881294 MS.gene56696:CDS 50.0%
AGCCACTATCGCTGCATTTG+GGG + chr5.1:63881299-63881318 MS.gene56696:CDS 50.0%
AGGAGGTTGCATGGTATGCT+GGG + chr5.1:63881231-63881250 MS.gene56696:CDS 50.0%
ATACCATGCAACCTCCTCCT+TGG - chr5.1:63881228-63881247 None:intergenic 50.0%
ATTTGTTTGTGCAGGGAGCC+AGG + chr5.1:63881479-63881498 MS.gene56696:intron 50.0%
CACCTCTCTTGTTCAGATCG+AGG + chr5.1:63881193-63881212 MS.gene56696:CDS 50.0%
CCTCTCTTGTTCAGATCGAG+GGG + chr5.1:63881195-63881214 MS.gene56696:CDS 50.0%
CTCTCTTGTTCAGATCGAGG+GGG + chr5.1:63881196-63881215 MS.gene56696:CDS 50.0%
GAAGCCACTATCGCTGCATT+TGG + chr5.1:63881297-63881316 MS.gene56696:CDS 50.0%
GACGACAAGGAGAACGTATC+AGG + chr5.1:63880370-63880389 MS.gene56696:CDS 50.0%
GCTTCCATCCTTCTTCACCT+TGG - chr5.1:63881282-63881301 None:intergenic 50.0%
TGGGCCCGCAAATATTGTGA+AGG - chr5.1:63880892-63880911 None:intergenic 50.0%
TTTGTTTGTGCAGGGAGCCA+GGG + chr5.1:63881480-63881499 MS.gene56696:intron 50.0%
ACACCAAGGAGGAGGTTGCA+TGG + chr5.1:63881222-63881241 MS.gene56696:CDS 55.0%
ACCAGGCCTCATGGTAACAG+TGG + chr5.1:63881329-63881348 MS.gene56696:CDS 55.0%
CCCCTCGATCTGAACAAGAG+AGG - chr5.1:63881198-63881217 None:intergenic 55.0%
GAGGAGGTTGCATGGTATGC+TGG + chr5.1:63881230-63881249 MS.gene56696:CDS 55.0%
GATCGAGGGGGTAAACACCA+AGG + chr5.1:63881208-63881227 MS.gene56696:CDS 55.0%
TGCCCCAAATGCAGCGATAG+TGG - chr5.1:63881304-63881323 None:intergenic 55.0%
! CTATCGCTGCATTTGGGGCA+AGG + chr5.1:63881304-63881323 MS.gene56696:CDS 55.0%
! GCATTTGGGGCAAGGTTACC+AGG + chr5.1:63881312-63881331 MS.gene56696:CDS 55.0%
CGAGGGGGTAAACACCAAGG+AGG + chr5.1:63881211-63881230 MS.gene56696:CDS 60.0%
GCCACTGTTACCATGAGGCC+TGG - chr5.1:63881333-63881352 None:intergenic 60.0%
GGCAAGGTTACCAGGCCTCA+TGG + chr5.1:63881320-63881339 MS.gene56696:CDS 60.0%
GGGGGTAAACACCAAGGAGG+AGG + chr5.1:63881214-63881233 MS.gene56696:CDS 60.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 63880360 63881534 63880360 ID=MS.gene56696
chr5.1 mRNA 63880360 63881534 63880360 ID=MS.gene56696.t1;Parent=MS.gene56696
chr5.1 exon 63880360 63880391 63880360 ID=MS.gene56696.t1.exon1;Parent=MS.gene56696.t1
chr5.1 CDS 63880360 63880391 63880360 ID=cds.MS.gene56696.t1;Parent=MS.gene56696.t1
chr5.1 exon 63880533 63880568 63880533 ID=MS.gene56696.t1.exon2;Parent=MS.gene56696.t1
chr5.1 CDS 63880533 63880568 63880533 ID=cds.MS.gene56696.t1;Parent=MS.gene56696.t1
chr5.1 exon 63881169 63881397 63881169 ID=MS.gene56696.t1.exon3;Parent=MS.gene56696.t1
chr5.1 CDS 63881169 63881397 63881169 ID=cds.MS.gene56696.t1;Parent=MS.gene56696.t1
chr5.1 exon 63881493 63881534 63881493 ID=MS.gene56696.t1.exon4;Parent=MS.gene56696.t1
chr5.1 CDS 63881493 63881534 63881493 ID=cds.MS.gene56696.t1;Parent=MS.gene56696.t1
Gene Sequence

>MS.gene56696

ATGGTTAAAGGACGACAAGGAGAACGTATCAGGTTTCTCTTCTTACCCTTCGATCTATTTCGTTTAACACGAATTTGAGCTAGTTTTCATGATTAAAATCGTAGTTTGTATAGTTAATCATATTTAATGAGTATTTACTAATGTTGTTATTTTGATTTTGGGTTTGTAATCAGGCTTTATGTCAGGGGTACAGTTCTTGGATACAAGAGGTAAATGTTTTTCTTCTCGATTTATTTTTCAGTTTTTGCTGTATTTGATGTATTCTTGGGTTTTCTTAAGTTAATGAAATCTAATATCTTAAGCTAATTAAATCTAATTTGTTTGGGTTTGTAATTATATAGAAATATGTAATGTATGATTTGTTTAGCTGAGCTTTATTTGTGCTAAGAAATGTTTAATGTTGTTTTAGCTGGATATGTTGTTCTTTGAATTTTGTAGTTTATGTTAGTTTTTAAAGTTTTCTGAAGTAAACCCAGCTTTTAATTTGTGTTTGTGATTGATAAATTTAAGAACCAATACTCAATTTGGTCCTTCACAATATTTGCGGGCCCAATGTATCCTCAATAAAAAATAATACCCAAACTAGTCCCAGCATTATCACAGTACAGGCAATCAATCCGCTTGTGATGATGAGTCTAGAACTAAATGATTACTGATTTGGGTATTATTTTTTGTATGGAGCTAGATTAAGCAGTCGCAAAATTACGAGAGACCAAGTATATAATTGTTCATCTACTAGTTTTTGATTTTGATGTTGATCTGGGTTGCTCGTGATTATTTGTGCTAAGAAATTGGTAATGTTGTTATAGGTCCAAGGTAAATCAATACCCAAACACCTCTCTTGTTCAGATCGAGGGGGTAAACACCAAGGAGGAGGTTGCATGGTATGCTGGGAAGAAATTGGCATACATTTACAAGGCCAAGGTGAAGAAGGATGGAAGCCACTATCGCTGCATTTGGGGCAAGGTTACCAGGCCTCATGGTAACAGTGGCATTGTCCGCGCAAAGTTCAAGTCTAACCTACCACCAAAATCAATGGTAATTCTTTAAGACATTTAAATGGTTTTTTTCTTTTTCTTTTCACCAACTGTTTTATGGTTTCTGAAAGTTTTGGTGTTGATTTGTTTGTGCAGGGAGCCAGGGTTAGAGTATTTATGTATCCAAGCAATATATAA

Protein sequence

>MS.gene56696.t1

MVKGRQGERIRLYVRGTVLGYKRSKVNQYPNTSLVQIEGVNTKEEVAWYAGKKLAYIYKAKVKKDGSHYRCIWGKVTRPHGNSGIVRAKFKSNLPPKSMGARVRVFMYPSNI