AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene76142

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene76142.t1 MTR_2g100020 87.892 223 18 4 1 223 63 276 4.65e-126 357
MS.gene76142.t1 MTR_8g017090 59.016 61 25 0 1 61 56 116 1.79e-17 79.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene76142.t1 AT1G72980 47.222 72 37 1 1 71 57 128 2.79e-15 72.4
MS.gene76142.t1 AT3G13850 43.662 71 40 0 1 71 80 150 1.28e-11 62.8

Find 35 sgRNAs with CRISPR-Local

Find 37 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTTGTAAAGGAACATAATT+AGG 0.133443 2.3:+3735203 None:intergenic
AATCAATGAAATGAATTCTT+TGG 0.228002 2.3:-3735036 MS.gene76142:CDS
AAGAATTCATTTCATTGATT+AGG 0.332115 2.3:+3735039 None:intergenic
GCAACATGTTCATATTCAAT+TGG 0.430357 2.3:+3735291 None:intergenic
CTTGTAAAGGAACATAATTA+GGG 0.440777 2.3:+3735204 None:intergenic
TCAATCTGATATGCGTGCTA+TGG 0.454015 2.3:-3735585 MS.gene76142:CDS
CAGCAGAAGTAGTATTGATC+CGG 0.456820 2.3:-3735006 MS.gene76142:CDS
ACCGCTGTCGCCGTTGACAT+TGG 0.480229 2.3:-3735147 MS.gene76142:CDS
TAGTATTGATCCGGGGCACC+AGG 0.481958 2.3:-3734997 MS.gene76142:CDS
AATCTATAACAACCACCAAC+AGG 0.483322 2.3:+3735560 None:intergenic
CATAATAATAACGATGATGA+TGG 0.501827 2.3:-3735374 MS.gene76142:CDS
AGCAGAAGTAGTATTGATCC+GGG 0.521215 2.3:-3735005 MS.gene76142:CDS
AATTAACAAACCTGGTGCCC+CGG 0.523440 2.3:+3734987 None:intergenic
GTATTAAAATCCTCTTGTAA+AGG 0.525655 2.3:+3735191 None:intergenic
GAACGTGTTGGTGATGATCA+AGG 0.525830 2.3:-3735086 MS.gene76142:CDS
TGCAGCAGTTGCAGTTGTTG+AGG 0.538937 2.3:+3735260 None:intergenic
TCATCATTATAATGACATGC+AGG 0.554364 2.3:-3735405 MS.gene76142:CDS
ATCAATACTACTTCTGCTGT+TGG 0.557959 2.3:+3735010 None:intergenic
TAATTATGTTCCTTTACAAG+AGG 0.560978 2.3:-3735201 MS.gene76142:CDS
CACCAACTAATTAACAAACC+TGG 0.563620 2.3:+3734979 None:intergenic
TGCAGTTGTTGAGGTTGTTG+AGG 0.566132 2.3:+3735269 None:intergenic
GCTGTCGCCGTTGACATTGG+AGG 0.577848 2.3:-3735144 MS.gene76142:CDS
GACATTGGAGGGTAACAAGA+AGG 0.582425 2.3:-3735132 MS.gene76142:CDS
CTGTCGCCGTTGACATTGGA+GGG 0.585568 2.3:-3735143 MS.gene76142:CDS
CGTGCTATGGATCCTGTTGG+TGG 0.590598 2.3:-3735572 MS.gene76142:CDS
CAATATGTTGTTGATGATGT+CGG 0.594144 2.3:-3735233 MS.gene76142:CDS
TTGTTACCCTCCAATGTCAA+CGG 0.595962 2.3:+3735137 None:intergenic
GTATGATCTCTAAGATGAGG+TGG 0.598062 2.3:+3735626 None:intergenic
TCCAATGTCAACGGCGACAG+CGG 0.601203 2.3:+3735146 None:intergenic
ATAGTATGATCTCTAAGATG+AGG 0.624071 2.3:+3735623 None:intergenic
GGTAACAAGAAGGAGGAAGA+CGG 0.630879 2.3:-3735122 MS.gene76142:CDS
GAACAAGATCAAGAACGTGT+TGG 0.646768 2.3:-3735098 MS.gene76142:CDS
ATGCGTGCTATGGATCCTGT+TGG 0.652692 2.3:-3735575 MS.gene76142:CDS
ATTGGAGGGTAACAAGAAGG+AGG 0.688764 2.3:-3735129 MS.gene76142:CDS
GCAGAAGTAGTATTGATCCG+GGG 0.729367 2.3:-3735004 MS.gene76142:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATCAATGAAATGAATTCTT+TGG - chr2.3:3735594-3735613 MS.gene76142:CDS 20.0%
!!! AAGAATTCATTTCATTGATT+AGG + chr2.3:3735594-3735613 None:intergenic 20.0%
! CATAATAATAACGATGATGA+TGG - chr2.3:3735256-3735275 MS.gene76142:CDS 25.0%
! CTTGTAAAGGAACATAATTA+GGG + chr2.3:3735429-3735448 None:intergenic 25.0%
! GTATTAAAATCCTCTTGTAA+AGG + chr2.3:3735442-3735461 None:intergenic 25.0%
! TAATTATGTTCCTTTACAAG+AGG - chr2.3:3735429-3735448 MS.gene76142:CDS 25.0%
! TCTTGTAAAGGAACATAATT+AGG + chr2.3:3735430-3735449 None:intergenic 25.0%
!! TTCATTGATTAGGTCAAAAA+CGG + chr2.3:3735584-3735603 None:intergenic 25.0%
!!! ACAAGAGGATTTTAATACAT+GGG - chr2.3:3735444-3735463 MS.gene76142:CDS 25.0%
!!! TACAAGAGGATTTTAATACA+TGG - chr2.3:3735443-3735462 MS.gene76142:CDS 25.0%
GCAACATGTTCATATTCAAT+TGG + chr2.3:3735342-3735361 None:intergenic 30.0%
TCATCATTATAATGACATGC+AGG - chr2.3:3735225-3735244 MS.gene76142:CDS 30.0%
! TCATTGATTAGGTCAAAAAC+GGG + chr2.3:3735583-3735602 None:intergenic 30.0%
!! ATAGTATGATCTCTAAGATG+AGG + chr2.3:3735010-3735029 None:intergenic 30.0%
!! CAATATGTTGTTGATGATGT+CGG - chr2.3:3735397-3735416 MS.gene76142:CDS 30.0%
AATCTATAACAACCACCAAC+AGG + chr2.3:3735073-3735092 None:intergenic 35.0%
ATCAATACTACTTCTGCTGT+TGG + chr2.3:3735623-3735642 None:intergenic 35.0%
GAACAAGATCAAGAACGTGT+TGG - chr2.3:3735532-3735551 MS.gene76142:CDS 40.0%
TCAATCTGATATGCGTGCTA+TGG - chr2.3:3735045-3735064 MS.gene76142:CDS 40.0%
TTGTTACCCTCCAATGTCAA+CGG + chr2.3:3735496-3735515 None:intergenic 40.0%
!! AGCAGAAGTAGTATTGATCC+GGG - chr2.3:3735625-3735644 MS.gene76142:CDS 40.0%
!! CAGCAGAAGTAGTATTGATC+CGG - chr2.3:3735624-3735643 MS.gene76142:CDS 40.0%
!! GTATGATCTCTAAGATGAGG+TGG + chr2.3:3735007-3735026 None:intergenic 40.0%
ATTGGAGGGTAACAAGAAGG+AGG - chr2.3:3735501-3735520 MS.gene76142:CDS 45.0%
GACATTGGAGGGTAACAAGA+AGG - chr2.3:3735498-3735517 MS.gene76142:CDS 45.0%
GGTAACAAGAAGGAGGAAGA+CGG - chr2.3:3735508-3735527 MS.gene76142:CDS 45.0%
TGCAGTTGTTGAGGTTGTTG+AGG + chr2.3:3735364-3735383 None:intergenic 45.0%
!! GAACGTGTTGGTGATGATCA+AGG - chr2.3:3735544-3735563 MS.gene76142:CDS 45.0%
!! GCAGAAGTAGTATTGATCCG+GGG - chr2.3:3735626-3735645 MS.gene76142:CDS 45.0%
ATGCGTGCTATGGATCCTGT+TGG - chr2.3:3735055-3735074 MS.gene76142:CDS 50.0%
TGCAGCAGTTGCAGTTGTTG+AGG + chr2.3:3735373-3735392 None:intergenic 50.0%
CGTGCTATGGATCCTGTTGG+TGG - chr2.3:3735058-3735077 MS.gene76142:CDS 55.0%
CTGTCGCCGTTGACATTGGA+GGG - chr2.3:3735487-3735506 MS.gene76142:CDS 55.0%
TCCAATGTCAACGGCGACAG+CGG + chr2.3:3735487-3735506 None:intergenic 55.0%
!! TAGTATTGATCCGGGGCACC+AGG - chr2.3:3735633-3735652 MS.gene76142:CDS 55.0%
ACCGCTGTCGCCGTTGACAT+TGG - chr2.3:3735483-3735502 MS.gene76142:CDS 60.0%
GCTGTCGCCGTTGACATTGG+AGG - chr2.3:3735486-3735505 MS.gene76142:CDS 60.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 3734989 3735663 3734989 ID=MS.gene76142
chr2.3 mRNA 3734989 3735663 3734989 ID=MS.gene76142.t1;Parent=MS.gene76142
chr2.3 exon 3734989 3735663 3734989 ID=MS.gene76142.t1.exon1;Parent=MS.gene76142.t1
chr2.3 CDS 3734989 3735663 3734989 ID=cds.MS.gene76142.t1;Parent=MS.gene76142.t1
Gene Sequence

>MS.gene76142

ATGATCAAGAATGTTCCACCTCATCTTAGAGATCATACTATGAGTTCTATTATTTTTCAATCTGATATGCGTGCTATGGATCCTGTTGGTGGTTGTTATAGATTTATTCAACAGCTTCAATCTCAATATGAATTTTATCAAGCTGAGCTTCATCTTACACGTCAACAAATTGCTATTTGTAAAGCTTCACAATCACAACATCAACAACAACAACTTGCTGCTGCTGCTGTTAATCATCATCATTATAATGACATGCAGGTCATTAATCATAATAATAACGATGATGATGGTCATAACGATGCTGCTTTGAATATTATTAATCATTTTAATCAGCATCATTTTGTTGATGACCAATTGAATATGAACATGTTGCCTCAACAACCTCAACAACTGCAACTGCTGCAGCAGCAATATGTTGTTGATGATGTCGGTATTAACCCTAATTATGTTCCTTTACAAGAGGATTTTAATACATGGGCGAACAATATTAATATACCGCTGTCGCCGTTGACATTGGAGGGTAACAAGAAGGAGGAAGACGGTGAACAAGATCAAGAACGTGTTGGTGATGATCAAGGAAGTGATCAGAAACCCGTTTTTGACCTAATCAATGAAATGAATTCTTTGGATACCAACAGCAGAAGTAGTATTGATCCGGGGCACCAGGTTTGTTAA
Protein sequence

>MS.gene76142.t1

MIKNVPPHLRDHTMSSIIFQSDMRAMDPVGGCYRFIQQLQSQYEFYQAELHLTRQQIAICKASQSQHQQQQLAAAAVNHHHYNDMQVINHNNNDDDGHNDAALNIINHFNQHHFVDDQLNMNMLPQQPQQLQLLQQQYVVDDVGINPNYVPLQEDFNTWANNINIPLSPLTLEGNKKEEDGEQDQERVGDDQGSDQKPVFDLINEMNSLDTNSRSSIDPGHQVC