AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene35379


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene35379.t1 MTR_2g085085 96.460 113 4 0 1 113 1 113 4.48e-70 205
MS.gene35379.t1 MTR_0227s0020 87.611 113 14 0 1 113 1 113 6.53e-38 124
MS.gene35379.t1 MTR_1g060600 73.451 113 29 1 1 113 1 112 1.06e-29 103
MS.gene35379.t1 MTR_2g085105 96.552 29 1 0 1 29 1 29 1.01e-12 58.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene35379.t1 AT2G27710 77.143 70 16 0 1 70 1 70 9.01e-32 108
MS.gene35379.t1 AT3G44590 67.257 113 35 2 1 113 1 111 8.06e-30 103
MS.gene35379.t1 AT3G44590 67.257 113 35 2 1 113 1 111 8.06e-30 103
MS.gene35379.t1 AT2G27720 66.087 115 37 1 1 113 1 115 1.86e-27 97.8
MS.gene35379.t1 AT2G27710 75.385 65 16 0 1 65 1 65 2.36e-25 92.4
MS.gene35379.t1 AT2G27710 75.385 65 16 0 1 65 1 65 2.36e-25 92.4
MS.gene35379.t1 AT2G27710 75.385 65 16 0 1 65 1 65 2.36e-25 92.4
MS.gene35379.t1 AT3G28500 55.652 115 49 2 1 113 1 115 3.03e-25 92.0
MS.gene35379.t1 AT2G27720 59.843 127 37 2 1 113 1 127 6.44e-24 89.0
MS.gene35379.t1 AT2G27720 57.692 130 38 2 1 113 1 130 1.39e-22 85.9
MS.gene35379.t1 AT5G40040 57.895 114 47 1 1 113 1 114 2.22e-16 69.3
MS.gene35379.t1 AT2G27720 66.667 87 27 1 29 113 5 91 5.49e-13 60.1

Find 34 sgRNAs with CRISPR-Local

Find 82 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGCTTACTTGTTGGCCGTTT+TGG 0.128749 2.1:+16351250 MS.gene35379:CDS
GCTGATCTTAAACAAATTCT+TGG 0.267351 2.1:+16351296 MS.gene35379:CDS
GTTGCTGTGTCTGCTGCAAC+TGG 0.362343 2.1:+16352413 MS.gene35379:CDS
TCTTCCTTTGCTGCTTCAGC+AGG 0.362525 2.1:-16352458 None:intergenic
CTTAAACAAATTCTTGGATC+AGG 0.372982 2.1:+16351302 MS.gene35379:CDS
GTTATCTTTGTGCAGGATAT+GGG 0.399106 2.1:+16352587 MS.gene35379:intron
AGAGAAGAAGGTGGAAGAGA+AGG 0.434796 2.1:+16352478 MS.gene35379:CDS
GATTATCGCAGCTTACTTGT+TGG 0.445399 2.1:+16351241 MS.gene35379:CDS
GTGTCTGCTGCAACTGGAGG+AGG 0.445905 2.1:+16352419 MS.gene35379:CDS
GATCAGCAGCTGAAGGGGAT+TGG 0.469713 2.1:-16351280 None:intergenic
CCTTGCCCTTGACTTCACTT+AGG 0.488662 2.1:-16352325 None:intergenic
TGCCAGTGGAAGAGAAAAGT+TGG 0.491656 2.1:+16352364 MS.gene35379:CDS
CACAGCAACAGCACCACCAC+CGG 0.500128 2.1:-16352399 None:intergenic
AGCAGCAAAGGAAGAGAAGA+AGG 0.518126 2.1:+16352466 MS.gene35379:CDS
GCTTCAGTTCCATCCGGTGG+TGG 0.522209 2.1:+16352386 MS.gene35379:CDS
TGCACCTGCTGAAGCAGCAA+AGG 0.528481 2.1:+16352454 MS.gene35379:CDS
GGATTGGTTGCCTCCCAAAA+CGG 0.534645 2.1:-16351264 None:intergenic
CAACTCAATGTTGCCATCCT+CGG 0.536919 2.1:-16352300 None:intergenic
GCAACAGCACCACCACCGGA+TGG 0.539099 2.1:-16352395 None:intergenic
TGTTTAAGATCAGCAGCTGA+AGG 0.541739 2.1:-16351287 None:intergenic
TCTTCCACTGGCAATAAGCT+CGG 0.547245 2.1:-16352354 None:intergenic
GTTTAAGATCAGCAGCTGAA+GGG 0.564265 2.1:-16351286 None:intergenic
TTTAAGATCAGCAGCTGAAG+GGG 0.564880 2.1:-16351285 None:intergenic
AAGTTGGCTTCAGTTCCATC+CGG 0.567453 2.1:+16352380 MS.gene35379:CDS
GTTGGAGTTGAGGCCGAGGA+TGG 0.573673 2.1:+16352287 MS.gene35379:intron
GTTGCTCCTAAGTGAAGTCA+AGG 0.590863 2.1:+16352319 MS.gene35379:CDS
GCTGTGTCTGCTGCAACTGG+AGG 0.592795 2.1:+16352416 MS.gene35379:CDS
TATGATTGTAGTTGGAGTTG+AGG 0.599920 2.1:+16352277 MS.gene35379:intron
TTTGCCGAGCTTATTGCCAG+TGG 0.606365 2.1:+16352350 MS.gene35379:CDS
TTGGCTTCAGTTCCATCCGG+TGG 0.607108 2.1:+16352383 MS.gene35379:CDS
CCTAAGTGAAGTCAAGGGCA+AGG 0.616488 2.1:+16352325 MS.gene35379:CDS
TGTAGTTGGAGTTGAGGCCG+AGG 0.617745 2.1:+16352283 MS.gene35379:intron
TTGCTCCTAAGTGAAGTCAA+GGG 0.680870 2.1:+16352320 MS.gene35379:CDS
AGCAAAGGAAGAGAAGAAGG+TGG 0.683753 2.1:+16352469 MS.gene35379:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTAGATTAAAGATTAAAT+TGG - chr2.1:16351340-16351359 None:intergenic 10.0%
!! ATTAGATTAAAGATTAAATT+GGG - chr2.1:16351339-16351358 None:intergenic 10.0%
!!! AAATAATTTTAATTCAAGTT+TGG + chr2.1:16351741-16351760 MS.gene35379:intron 10.0%
!!! AATAATTTTAATTCAAGTTT+GGG + chr2.1:16351742-16351761 MS.gene35379:intron 10.0%
!! ATGAAAATTGATCAAAATAT+TGG + chr2.1:16351823-16351842 MS.gene35379:intron 15.0%
!! ATTAAAATCAAACCAATATA+TGG - chr2.1:16352098-16352117 None:intergenic 15.0%
!! TTAAAATCAAACCAATATAT+GGG - chr2.1:16352097-16352116 None:intergenic 15.0%
!!! AAAAAAAGTGACTTTATTTT+TGG + chr2.1:16352251-16352270 MS.gene35379:intron 15.0%
!!! AAAAAAGTGACTTTATTTTT+GGG + chr2.1:16352252-16352271 MS.gene35379:intron 15.0%
!!! TTTAACTTTAATTCAAGTTT+GGG + chr2.1:16351775-16351794 MS.gene35379:intron 15.0%
!! ATGGATCTACTAAAATAATT+CGG - chr2.1:16351433-16351452 None:intergenic 20.0%
!! TAAAATCAAACCAATATATG+GGG - chr2.1:16352096-16352115 None:intergenic 20.0%
!! TATAGTTTATGCAAATTCAT+AGG + chr2.1:16352011-16352030 MS.gene35379:intron 20.0%
!!! AAATATTGGTTTATTTGGAT+TGG + chr2.1:16351837-16351856 MS.gene35379:intron 20.0%
!!! AATTTTGAAACTTACATCAT+CGG - chr2.1:16352510-16352529 None:intergenic 20.0%
!!! ATATTCTACACTTTTACTTA+TGG - chr2.1:16351452-16351471 None:intergenic 20.0%
!!! GATCAAAATATTGGTTTATT+TGG + chr2.1:16351832-16351851 MS.gene35379:intron 20.0%
!!! GGATTTGGTTAATTTATAAT+CGG + chr2.1:16351599-16351618 MS.gene35379:intron 20.0%
!!! GTTTAACTTTAATTCAAGTT+TGG + chr2.1:16351774-16351793 MS.gene35379:intron 20.0%
!!! TGCTAATTTAATTCAAGTTT+AGG + chr2.1:16351578-16351597 MS.gene35379:intron 20.0%
!!! TTTAATTCAAGTTTAGGATT+TGG + chr2.1:16351584-16351603 MS.gene35379:intron 20.0%
! AAATAATCAATCCTAGAATG+TGG + chr2.1:16351534-16351553 MS.gene35379:intron 25.0%
! AATAATCAATCCTAGAATGT+GGG + chr2.1:16351535-16351554 MS.gene35379:intron 25.0%
! TAAAATCGATGAATGAACAT+GGG + chr2.1:16351628-16351647 MS.gene35379:intron 25.0%
! TACTTTCAATTAGAGATTGT+GGG + chr2.1:16351477-16351496 MS.gene35379:intron 25.0%
! TTAAAATCGATGAATGAACA+TGG + chr2.1:16351627-16351646 MS.gene35379:intron 25.0%
! TTACTTTCAATTAGAGATTG+TGG + chr2.1:16351476-16351495 MS.gene35379:intron 25.0%
!! TAGTAGTATTGTTTGTTACT+TGG + chr2.1:16352532-16352551 MS.gene35379:intron 25.0%
!!! ATTTTAATTCAAGTTTGGGT+TGG + chr2.1:16351746-16351765 MS.gene35379:intron 25.0%
!!! GCTTAGTTTTATACATTGTT+TGG + chr2.1:16352118-16352137 MS.gene35379:intron 25.0%
!!! TTTTAATTCAAGTTTGGGTT+GGG + chr2.1:16351747-16351766 MS.gene35379:intron 25.0%
CTTAAACAAATTCTTGGATC+AGG + chr2.1:16351302-16351321 MS.gene35379:CDS 30.0%
GCTGATCTTAAACAAATTCT+TGG + chr2.1:16351296-16351315 MS.gene35379:CDS 30.0%
TATCTACTGTTAGACTGTTA+AGG + chr2.1:16351873-16351892 MS.gene35379:intron 30.0%
AATCAAACAGCCCCATATAT+TGG + chr2.1:16352083-16352102 MS.gene35379:intron 35.0%
ATTCGGATACTAATCGAAAC+CGG - chr2.1:16351416-16351435 None:intergenic 35.0%
CTTCATTATACCCACATTCT+AGG - chr2.1:16351548-16351567 None:intergenic 35.0%
GTTATCTTTGTGCAGGATAT+GGG + chr2.1:16352587-16352606 MS.gene35379:intron 35.0%
TATCTACTGTTGGACAGTTT+GGG + chr2.1:16351678-16351697 MS.gene35379:intron 35.0%
TATGATTGTAGTTGGAGTTG+AGG + chr2.1:16352277-16352296 MS.gene35379:intron 35.0%
TGTTATCTTTGTGCAGGATA+TGG + chr2.1:16352586-16352605 MS.gene35379:intron 35.0%
TTATCTACTGTTGGACAGTT+TGG + chr2.1:16351677-16351696 MS.gene35379:intron 35.0%
TTTGGGTCTATGATTGTAGT+TGG + chr2.1:16352269-16352288 MS.gene35379:intron 35.0%
!!! GCGTTTTTTGTTTGTTTTCC+CGG + chr2.1:16351394-16351413 MS.gene35379:intron 35.0%
CGTTTGAGCTTATCTACTGT+TGG + chr2.1:16351668-16351687 MS.gene35379:intron 40.0%
GATTATCGCAGCTTACTTGT+TGG + chr2.1:16351241-16351260 MS.gene35379:CDS 40.0%
GCGTAATGTTATCTTTGTGC+AGG + chr2.1:16352580-16352599 MS.gene35379:intron 40.0%
TGAATGAACATGGGTCTGTT+TGG + chr2.1:16351637-16351656 MS.gene35379:intron 40.0%
TTCGGATACTAATCGAAACC+GGG - chr2.1:16351415-16351434 None:intergenic 40.0%
TTGCTCCTAAGTGAAGTCAA+GGG + chr2.1:16352320-16352339 MS.gene35379:CDS 40.0%
! GTTTAAGATCAGCAGCTGAA+GGG - chr2.1:16351289-16351308 None:intergenic 40.0%
! TGTTTAAGATCAGCAGCTGA+AGG - chr2.1:16351290-16351309 None:intergenic 40.0%
! TTTAAGATCAGCAGCTGAAG+GGG - chr2.1:16351288-16351307 None:intergenic 40.0%
AGAGAAGAAGGTGGAAGAGA+AGG + chr2.1:16352478-16352497 MS.gene35379:CDS 45.0%
AGCAAAGGAAGAGAAGAAGG+TGG + chr2.1:16352469-16352488 MS.gene35379:CDS 45.0%
AGCAGCAAAGGAAGAGAAGA+AGG + chr2.1:16352466-16352485 MS.gene35379:CDS 45.0%
CAACTCAATGTTGCCATCCT+CGG - chr2.1:16352303-16352322 None:intergenic 45.0%
GAACATGGGTCTGTTTGGAT+TGG + chr2.1:16351642-16351661 MS.gene35379:intron 45.0%
GTTGCTCCTAAGTGAAGTCA+AGG + chr2.1:16352319-16352338 MS.gene35379:CDS 45.0%
TCTTCCACTGGCAATAAGCT+CGG - chr2.1:16352357-16352376 None:intergenic 45.0%
TGCCAGTGGAAGAGAAAAGT+TGG + chr2.1:16352364-16352383 MS.gene35379:CDS 45.0%
! AAGTTGGCTTCAGTTCCATC+CGG + chr2.1:16352380-16352399 MS.gene35379:CDS 45.0%
! AGCCAACTTTTCTCTTCCAC+TGG - chr2.1:16352369-16352388 None:intergenic 45.0%
!! AGCTTACTTGTTGGCCGTTT+TGG + chr2.1:16351250-16351269 MS.gene35379:CDS 45.0%
!! GCTTACTTGTTGGCCGTTTT+GGG + chr2.1:16351251-16351270 MS.gene35379:CDS 45.0%
CCTAAGTGAAGTCAAGGGCA+AGG + chr2.1:16352325-16352344 MS.gene35379:CDS 50.0%
CCTTGCCCTTGACTTCACTT+AGG - chr2.1:16352328-16352347 None:intergenic 50.0%
TTTGCCGAGCTTATTGCCAG+TGG + chr2.1:16352350-16352369 MS.gene35379:CDS 50.0%
! TCTTCCTTTGCTGCTTCAGC+AGG - chr2.1:16352461-16352480 None:intergenic 50.0%
!! GGATTGGTTGCCTCCCAAAA+CGG - chr2.1:16351267-16351286 None:intergenic 50.0%
!! TACTTGTTGGCCGTTTTGGG+AGG + chr2.1:16351254-16351273 MS.gene35379:CDS 50.0%
GATCAGCAGCTGAAGGGGAT+TGG - chr2.1:16351283-16351302 None:intergenic 55.0%
GTTGCTGTGTCTGCTGCAAC+TGG + chr2.1:16352413-16352432 MS.gene35379:CDS 55.0%
TGCACCTGCTGAAGCAGCAA+AGG + chr2.1:16352454-16352473 MS.gene35379:CDS 55.0%
TGTAGTTGGAGTTGAGGCCG+AGG + chr2.1:16352283-16352302 MS.gene35379:intron 55.0%
TTGGCTTCAGTTCCATCCGG+TGG + chr2.1:16352383-16352402 MS.gene35379:CDS 55.0%
CACAGCAACAGCACCACCAC+CGG - chr2.1:16352402-16352421 None:intergenic 60.0%
GCTGTGTCTGCTGCAACTGG+AGG + chr2.1:16352416-16352435 MS.gene35379:CDS 60.0%
GCTTCAGTTCCATCCGGTGG+TGG + chr2.1:16352386-16352405 MS.gene35379:CDS 60.0%
GTGTCTGCTGCAACTGGAGG+AGG + chr2.1:16352419-16352438 MS.gene35379:CDS 60.0%
GTTGGAGTTGAGGCCGAGGA+TGG + chr2.1:16352287-16352306 MS.gene35379:intron 60.0%
GCAACAGCACCACCACCGGA+TGG - chr2.1:16352398-16352417 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 16351236 16352628 16351236 ID=MS.gene35379
chr2.1 mRNA 16351236 16352628 16351236 ID=MS.gene35379.t1;Parent=MS.gene35379
chr2.1 exon 16351236 16351323 16351236 ID=MS.gene35379.t1.exon1;Parent=MS.gene35379.t1
chr2.1 CDS 16351236 16351323 16351236 ID=cds.MS.gene35379.t1;Parent=MS.gene35379.t1
chr2.1 exon 16352288 16352514 16352288 ID=MS.gene35379.t1.exon2;Parent=MS.gene35379.t1
chr2.1 CDS 16352288 16352514 16352288 ID=cds.MS.gene35379.t1;Parent=MS.gene35379.t1
chr2.1 exon 16352602 16352628 16352602 ID=MS.gene35379.t1.exon3;Parent=MS.gene35379.t1
chr2.1 CDS 16352602 16352628 16352602 ID=cds.MS.gene35379.t1;Parent=MS.gene35379.t1
Gene Sequence

>MS.gene35379

ATGAAGATTATCGCAGCTTACTTGTTGGCCGTTTTGGGAGGCAACCAATCCCCTTCAGCTGCTGATCTTAAACAAATTCTTGGATCAGGTTCGTATAAATCCCAATTTAATCTTTAATCTAATTCATTCTGTGTTTTTTTATTTTATTTTATTATTATGCGTTTTTTGTTTGTTTTCCCGGTTTCGATTAGTATCCGAATTATTTTAGTAGATCCATAAGTAAAAGTGTAGAATATGAATTTACTTTCAATTAGAGATTGTGGGTATAATAAAGTTTAGTTTTTTCTTTTTTTGCACAAAATAATCAATCCTAGAATGTGGGTATAATGAAGTGAATTTTTTTGCTAATTTAATTCAAGTTTAGGATTTGGTTAATTTATAATCGGCTCAATTAAAATCGATGAATGAACATGGGTCTGTTTGGATTGGACTCGTTTGAGCTTATCTACTGTTGGACAGTTTGGGAGAATTTATATGAAAACATCTTATAACAATTTTTTTGCAAAAATAATTTTAATTCAAGTTTGGGTTGGGATTTGTTTAACTTTAATTCAAGTTTGGGATTTGTTTCACTGATATTCATTTCAATGAAAATTGATCAAAATATTGGTTTATTTGGATTGGACTTATTTGAGCTTATCTACTGTTAGACTGTTAAGGAGAATTTATGAAAACATACAATTTTTCATAAGTTTTTTTCAAATACAGCTTATATTAAAACAACTTATAGCACATACAAAAACAAGTTAACATTTTTTTAATCTTTTGCTATTCATATAGTTTATGCAAATTCATAGGCTCATATCATGATATAAGTGCTTGTGCTATAAGCTGTAATAAGCTGTTTAATCAAACAGCCCCATATATTGGTTTGATTTTAATGCTTAGTTTTATACATTGTTTGGTAATATTTACAAAGTTTTCATTTTTACAGATGTATTATGTTTTTGTTGAATTTTCAATCAGTAAATCGTGCATACGTTTGTCTGCTTTTTCTGTATATTTTTTTACGTGTAAAAAAAGTGACTTTATTTTTGGGTCTATGATTGTAGTTGGAGTTGAGGCCGAGGATGGCAACATTGAGTTGCTCCTAAGTGAAGTCAAGGGCAAGGACTTTGCCGAGCTTATTGCCAGTGGAAGAGAAAAGTTGGCTTCAGTTCCATCCGGTGGTGGTGCTGTTGCTGTGTCTGCTGCAACTGGAGGAGGTGCTGCAGCTGCTGCACCTGCTGAAGCAGCAAAGGAAGAGAAGAAGGTGGAAGAGAAGGAAGAATCCGATGATGTAAGTTTCAAAATTTATAGTAGTATTGTTTGTTACTTGGTAAATTCATGACTATGCTAATGTTTGCGTAATGTTATCTTTGTGCAGGATATGGGATTCAGCTTATTTGATTAA

Protein sequence

>MS.gene35379.t1

MKIIAAYLLAVLGGNQSPSAADLKQILGSVGVEAEDGNIELLLSEVKGKDFAELIASGREKLASVPSGGGAVAVSAATGGGAAAAAPAEAAKEEKKVEEKEESDDDMGFSLFD