AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene047000

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene047000.t1 MTR_8g107300 83.721 129 6 3 1 125 1 118 2.49e-70 206
MS.gene047000.t1 MTR_2g019190 76.471 136 19 3 1 125 1 134 9.65e-68 200
MS.gene047000.t1 MTR_8g107300 82.979 94 5 1 32 125 1 83 1.01e-48 150
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene047000.t1 AT1G30135 41.912 136 57 7 1 124 3 128 2.13e-21 83.2
MS.gene047000.t1 AT2G34600 39.062 128 72 5 1 124 20 145 1.25e-16 71.2

Find 26 sgRNAs with CRISPR-Local

Find 48 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GACTGATGTCACAGAGTTTC+AGG 0.192920 4.3:+280232 MS.gene047000:CDS
TGCCAGCATTAAGATGGATT+TGG 0.344981 4.3:-280366 None:intergenic
CAGAATCATAGAGAGGAAAA+AGG 0.376693 4.3:-279993 None:intergenic
CATCTTCCCATCATAGAATA+TGG 0.389620 4.3:-280204 None:intergenic
CCTCATCAATTGTATAGCCC+TGG 0.405940 4.3:+280464 MS.gene047000:CDS
GATGGTATGGAGATGCTTCT+TGG 0.408900 4.3:-280547 None:intergenic
GGAAAGCCCAATGCAAAATC+AGG 0.420902 4.3:+280169 MS.gene047000:CDS
TTTATTTGCCAGCATTAAGA+TGG 0.422633 4.3:-280372 None:intergenic
TTCTCTTATCTTACATGTGG+TGG 0.433401 4.3:-280035 None:intergenic
CCGCTGACCATATTCTATGA+TGG 0.457336 4.3:+280197 MS.gene047000:CDS
TCTACAGAAGAGAAAGAATA+GGG 0.468849 4.3:+280523 MS.gene047000:CDS
CTCATCAATTGTATAGCCCT+GGG 0.470700 4.3:+280465 MS.gene047000:CDS
TGAGGAGGCTGCACTATTGT+TGG 0.477785 4.3:-280446 None:intergenic
CAATTGTATAGCCCTGGGTC+TGG 0.482257 4.3:+280470 MS.gene047000:CDS
TTCTACAGAAGAGAAAGAAT+AGG 0.508590 4.3:+280522 MS.gene047000:CDS
CGCTGACCATATTCTATGAT+GGG 0.509614 4.3:+280198 MS.gene047000:CDS
GGCCAAATCCATCTTAATGC+TGG 0.519970 4.3:+280364 MS.gene047000:intron
GCAAAGATCTCTTCATTGAA+AGG 0.520559 4.3:-280493 None:intergenic
TTCATTGAAAGGCCAGACCC+AGG 0.532257 4.3:-280482 None:intergenic
GTTGTTCGCTCTGACCCTCT+CGG 0.542596 4.3:-280422 None:intergenic
CAATGAAGAGATCTTTGCAA+CGG 0.550495 4.3:+280498 MS.gene047000:CDS
GGGCTATACAATTGATGAGG+AGG 0.602793 4.3:-280461 None:intergenic
TCATTGAAAGGCCAGACCCA+GGG 0.615225 4.3:-280481 None:intergenic
CCAGGGCTATACAATTGATG+AGG 0.668057 4.3:-280464 None:intergenic
CCATCATAGAATATGGTCAG+CGG 0.671722 4.3:-280197 None:intergenic
TGATTGCCAGAATCATAGAG+AGG 0.688733 4.3:-280000 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATGATTTTCTTTTTATATTT+GGG + chr4.3:280103-280122 MS.gene047000:intron 10.0%
!!! TATGATTTTCTTTTTATATT+TGG + chr4.3:280102-280121 MS.gene047000:intron 10.0%
!!! TCATTTTTTCATTTAGTTAT+TGG - chr4.3:280291-280310 None:intergenic 15.0%
!! ACAAATTGAAAAAATGGAAA+TGG - chr4.3:280077-280096 None:intergenic 20.0%
!! AGTCTAACAAATTGAAAAAA+TGG - chr4.3:280083-280102 None:intergenic 20.0%
! TAATTTCTATCTCCATTGAA+GGG + chr4.3:280145-280164 MS.gene047000:intron 25.0%
! TTAATTTCTATCTCCATTGA+AGG + chr4.3:280144-280163 MS.gene047000:intron 25.0%
TCTACAGAAGAGAAAGAATA+GGG + chr4.3:280523-280542 MS.gene047000:CDS 30.0%
TTCTACAGAAGAGAAAGAAT+AGG + chr4.3:280522-280541 MS.gene047000:CDS 30.0%
TTTATTTGCCAGCATTAAGA+TGG - chr4.3:280375-280394 None:intergenic 30.0%
CAATGAAGAGATCTTTGCAA+CGG + chr4.3:280498-280517 MS.gene047000:CDS 35.0%
CAGAATCATAGAGAGGAAAA+AGG - chr4.3:279996-280015 None:intergenic 35.0%
CATCTTCCCATCATAGAATA+TGG - chr4.3:280207-280226 None:intergenic 35.0%
GCAAAGATCTCTTCATTGAA+AGG - chr4.3:280496-280515 None:intergenic 35.0%
GCATTCTCTTATCTTACATG+TGG - chr4.3:280041-280060 None:intergenic 35.0%
TTCTCTTATCTTACATGTGG+TGG - chr4.3:280038-280057 None:intergenic 35.0%
! CTTTTTCCTCTCTATGATTC+TGG + chr4.3:279994-280013 MS.gene047000:CDS 35.0%
AAAAAGTGAAGACACCGAGA+GGG + chr4.3:280408-280427 MS.gene047000:CDS 40.0%
CCATCATAGAATATGGTCAG+CGG - chr4.3:280200-280219 None:intergenic 40.0%
CGCTGACCATATTCTATGAT+GGG + chr4.3:280198-280217 MS.gene047000:CDS 40.0%
CTCATCAATTGTATAGCCCT+GGG + chr4.3:280465-280484 MS.gene047000:CDS 40.0%
GGTTAATGTGAATGTTGTGC+AGG + chr4.3:280343-280362 MS.gene047000:intron 40.0%
TGATTGCCAGAATCATAGAG+AGG - chr4.3:280003-280022 None:intergenic 40.0%
TTTCTATCTCCATTGAAGGG+AGG + chr4.3:280148-280167 MS.gene047000:intron 40.0%
! GCTGTTCCTGATTTTGCATT+GGG - chr4.3:280178-280197 None:intergenic 40.0%
! TGCCAGCATTAAGATGGATT+TGG - chr4.3:280369-280388 None:intergenic 40.0%
CCAGGGCTATACAATTGATG+AGG - chr4.3:280467-280486 None:intergenic 45.0%
CCGCTGACCATATTCTATGA+TGG + chr4.3:280197-280216 MS.gene047000:CDS 45.0%
CCTCATCAATTGTATAGCCC+TGG + chr4.3:280464-280483 MS.gene047000:CDS 45.0%
GAAAAAGTGAAGACACCGAG+AGG + chr4.3:280407-280426 MS.gene047000:CDS 45.0%
GACTGATGTCACAGAGTTTC+AGG + chr4.3:280232-280251 MS.gene047000:CDS 45.0%
GATGGTATGGAGATGCTTCT+TGG - chr4.3:280550-280569 None:intergenic 45.0%
GGAAAGCCCAATGCAAAATC+AGG + chr4.3:280169-280188 MS.gene047000:CDS 45.0%
GGCCAAATCCATCTTAATGC+TGG + chr4.3:280364-280383 MS.gene047000:intron 45.0%
GGGCTATACAATTGATGAGG+AGG - chr4.3:280464-280483 None:intergenic 45.0%
TTGGCCTAGTCAAGAACAGA+GGG - chr4.3:280272-280291 None:intergenic 45.0%
! ATTGGCCTAGTCAAGAACAG+AGG - chr4.3:280273-280292 None:intergenic 45.0%
! GGCTGTTCCTGATTTTGCAT+TGG - chr4.3:280179-280198 None:intergenic 45.0%
!! CTTTATAAAAATAAATAAAT+GGG + chr4.3:280322-280341 MS.gene047000:intron 5.0%
!! TCTTTATAAAAATAAATAAA+TGG + chr4.3:280321-280340 MS.gene047000:intron 5.0%
CAATTGTATAGCCCTGGGTC+TGG + chr4.3:280470-280489 MS.gene047000:CDS 50.0%
TCATTGAAAGGCCAGACCCA+GGG - chr4.3:280484-280503 None:intergenic 50.0%
TGAGGAGGCTGCACTATTGT+TGG - chr4.3:280449-280468 None:intergenic 50.0%
TTCATTGAAAGGCCAGACCC+AGG - chr4.3:280485-280504 None:intergenic 50.0%
TTGGGCTTTCCTCCCTTCAA+TGG - chr4.3:280160-280179 None:intergenic 50.0%
ACCGCCCTCTGTTCTTGACT+AGG + chr4.3:280265-280284 MS.gene047000:intron 55.0%
GCCTAGTCAAGAACAGAGGG+CGG - chr4.3:280269-280288 None:intergenic 55.0%
GTTGTTCGCTCTGACCCTCT+CGG - chr4.3:280425-280444 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 279964 280574 279964 ID=MS.gene047000
chr4.3 mRNA 279964 280574 279964 ID=MS.gene047000.t1;Parent=MS.gene047000
chr4.3 exon 279964 280043 279964 ID=MS.gene047000.t1.exon1;Parent=MS.gene047000.t1
chr4.3 CDS 279964 280043 279964 ID=cds.MS.gene047000.t1;Parent=MS.gene047000.t1
chr4.3 exon 280166 280253 280166 ID=MS.gene047000.t1.exon2;Parent=MS.gene047000.t1
chr4.3 CDS 280166 280253 280166 ID=cds.MS.gene047000.t1;Parent=MS.gene047000.t1
chr4.3 exon 280365 280574 280365 ID=MS.gene047000.t1.exon3;Parent=MS.gene047000.t1
chr4.3 CDS 280365 280574 280365 ID=cds.MS.gene047000.t1;Parent=MS.gene047000.t1
Gene Sequence

>MS.gene047000

ATGAGGAGGAATTGTAACTTAGAACTCTGCCTTTTTCCTCTCTATGATTCTGGCAATCACAACAACAGCAACCACCACATGTAAGATAAGAGAATGCTTTTCTTTGTATACCATTTCCATTTTTTCAATTTGTTAGACTATGATTTTCTTTTTATATTTGGGTATTAAAGTAATTCTTTGTTAATTTCTATCTCCATTGAAGGGAGGAAAGCCCAATGCAAAATCAGGAACAGCCGCTGACCATATTCTATGATGGGAAGATGTGTCTGACTGATGTCACAGAGTTTCAGGTATACTCATTACCGCCCTCTGTTCTTGACTAGGCCAATAACTAAATGAAAAAATGATTTTGCAATCTCTTTATAAAAATAAATAAATGGGTTAATGTGAATGTTGTGCAGGCCAAATCCATCTTAATGCTGGCAAATAAAATTAAGTTGCAAGAAAAAGTGAAGACACCGAGAGGGTCAGAGCGAACAACACCAACAATAGTGCAGCCTCCTCATCAATTGTATAGCCCTGGGTCTGGCCTTTCAATGAAGAGATCTTTGCAACGGTTTCTACAGAAGAGAAAGAATAGGGTCCAAGAAGCATCTCCATACCATCACTAG
Protein sequence

>MS.gene047000.t1

MRRNCNLELCLFPLYDSGNHNNSNHHMEESPMQNQEQPLTIFYDGKMCLTDVTEFQAKSILMLANKIKLQEKVKTPRGSERTTPTIVQPPHQLYSPGSGLSMKRSLQRFLQKRKNRVQEASPYHH