AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene42835

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene42835.t1 MTR_2g093770 100.000 107 0 0 1 107 1 107 1.25e-71 208
MS.gene42835.t1 MTR_1g082400 72.826 92 20 2 15 104 17 105 2.80e-36 119
MS.gene42835.t1 MTR_8g086330 60.976 82 26 1 21 102 4 79 7.47e-25 89.7
MS.gene42835.t1 MTR_4g028080 61.446 83 26 1 21 103 4 80 4.42e-24 87.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene42835.t1 AT5G60460 77.907 86 17 1 22 105 22 107 3.53e-37 122
MS.gene42835.t1 AT5G60460 77.907 86 17 1 22 105 22 107 3.53e-37 122
MS.gene42835.t1 AT2G45070 60.759 79 29 1 24 102 6 82 2.38e-23 85.9
MS.gene42835.t1 AT2G45070 60.759 79 29 1 24 102 6 82 2.38e-23 85.9
MS.gene42835.t1 AT2G45070 60.759 79 29 1 24 102 6 82 2.38e-23 85.9
MS.gene42835.t1 AT2G45070 60.759 79 29 1 24 102 6 82 2.38e-23 85.9
MS.gene42835.t1 AT3G60540 57.831 83 30 1 21 103 3 80 2.76e-23 85.9
MS.gene42835.t1 AT3G60540 57.831 83 30 1 21 103 3 80 2.76e-23 85.9
MS.gene42835.t1 AT3G60540 57.831 83 30 1 21 103 3 80 2.76e-23 85.9

Find 42 sgRNAs with CRISPR-Local

Find 41 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACGCTGGCGGTGCTGTTTC+CGG 0.263401 2.3:+7942374 None:intergenic
GATTTCACCGACGGTGGTTT+TGG 0.294926 2.3:-7942286 MS.gene42835:CDS
GTCACCGCGCTTCATGTGTT+CGG 0.324439 2.3:-7942237 MS.gene42835:CDS
GGCTCCGCTGCCGCCACTGC+CGG 0.376415 2.3:-7942420 MS.gene42835:CDS
TCACCGCGCTTCATGTGTTC+GGG 0.377638 2.3:-7942236 MS.gene42835:CDS
TCCTCCTGGACGGGAGGATG+TGG 0.389528 2.3:+7942464 None:intergenic
CATGCCGGCAGTGGCGGCAG+CGG 0.423583 2.3:+7942416 None:intergenic
GCGGCGAGTCCGCCTCCTCC+TGG 0.437060 2.3:+7942450 None:intergenic
GGCAGCGGAGCCGCGTGGTG+CGG 0.453027 2.3:+7942431 None:intergenic
TCCTCCCGTCCAGGAGGAGG+CGG 0.463865 2.3:-7942459 MS.gene42835:CDS
ACATCCTCCCGTCCAGGAGG+AGG 0.475747 2.3:-7942462 MS.gene42835:CDS
TATCGTTACAAAGCTGGTGC+TGG 0.477938 2.3:-7942207 MS.gene42835:CDS
ACCTCCACATCCTCCCGTCC+AGG 0.490070 2.3:-7942468 MS.gene42835:CDS
AACAGCACCGCCAGCGTTGG+AGG 0.491709 2.3:-7942369 MS.gene42835:CDS
AAGCTTTATCGTTACAAAGC+TGG 0.494177 2.3:-7942213 MS.gene42835:CDS
AGCACCGCCAGCGTTGGAGG+TGG 0.498786 2.3:-7942366 MS.gene42835:CDS
CGAGTCCGCCTCCTCCTGGA+CGG 0.500658 2.3:+7942454 None:intergenic
CTCCCACTCATCATGGCTAA+AGG 0.505690 2.3:-7942513 None:intergenic
GAGTCCGCCTCCTCCTGGAC+GGG 0.510389 2.3:+7942455 None:intergenic
ACGACGCATGCCGGCAGTGG+CGG 0.511102 2.3:+7942410 None:intergenic
GCTAGATCCACCTCCAACGC+TGG 0.511643 2.3:+7942359 None:intergenic
CGTCGTCGACGTCTCACCTC+CGG 0.514572 2.3:-7942393 MS.gene42835:CDS
ATTCTACACTGACGATGCAC+CGG 0.515056 2.3:-7942316 MS.gene42835:CDS
TTCTACACTGACGATGCACC+GGG 0.517664 2.3:-7942315 MS.gene42835:CDS
GGAAACAGCACCGCCAGCGT+TGG 0.527583 2.3:-7942372 MS.gene42835:CDS
TCCTGGACGGGAGGATGTGG+AGG 0.527989 2.3:+7942467 None:intergenic
TCGACGACGCATGCCGGCAG+TGG 0.528744 2.3:+7942407 None:intergenic
TCCGCCTCCTCCTGGACGGG+AGG 0.535956 2.3:+7942458 None:intergenic
GTTATGAGTCTCTGCTTCAT+CGG 0.539263 2.3:-7942264 MS.gene42835:CDS
GTGGCGGCAGCGGAGCCGCG+TGG 0.562105 2.3:+7942426 None:intergenic
TTTGAAGATTTCACCGACGG+TGG 0.598789 2.3:-7942292 MS.gene42835:CDS
GAGACGTCGACGACGCATGC+CGG 0.607455 2.3:+7942401 None:intergenic
GGCGGACTCGCCGCACCACG+CGG 0.608071 2.3:-7942441 MS.gene42835:CDS
CTCATAACCAAAACCACCGT+CGG 0.617981 2.3:+7942279 None:intergenic
GCTGGCGGTGCTGTTTCCGG+AGG 0.626090 2.3:+7942377 None:intergenic
AGATCCACCTCCAACGCTGG+CGG 0.627371 2.3:+7942362 None:intergenic
AGCGTTGGAGGTGGATCTAG+CGG 0.636568 2.3:-7942357 MS.gene42835:CDS
GTCGGTGAAATCTTCAAACC+CGG 0.639473 2.3:+7942297 None:intergenic
GGGTTTGAAGATTTCACCGA+CGG 0.641586 2.3:-7942295 MS.gene42835:CDS
TCCACATCCTCCCGTCCAGG+AGG 0.666674 2.3:-7942465 MS.gene42835:CDS
GTTGGAGGTGGATCTAGCGG+AGG 0.684640 2.3:-7942354 MS.gene42835:CDS
CTTCCCGAACACATGAAGCG+CGG 0.732527 2.3:+7942233 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAGCTTTATCGTTACAAAGC+TGG - chr2.3:7942488-7942507 MS.gene42835:CDS 35.0%
GTTATGAGTCTCTGCTTCAT+CGG - chr2.3:7942437-7942456 MS.gene42835:CDS 40.0%
ATTCTACACTGACGATGCAC+CGG - chr2.3:7942385-7942404 MS.gene42835:CDS 45.0%
CTCATAACCAAAACCACCGT+CGG + chr2.3:7942425-7942444 None:intergenic 45.0%
GGGTTTGAAGATTTCACCGA+CGG - chr2.3:7942406-7942425 MS.gene42835:CDS 45.0%
GTCGGTGAAATCTTCAAACC+CGG + chr2.3:7942407-7942426 None:intergenic 45.0%
TATCGTTACAAAGCTGGTGC+TGG - chr2.3:7942494-7942513 MS.gene42835:CDS 45.0%
TTTGAAGATTTCACCGACGG+TGG - chr2.3:7942409-7942428 MS.gene42835:CDS 45.0%
TTCTACACTGACGATGCACC+GGG - chr2.3:7942386-7942405 MS.gene42835:CDS 50.0%
! GATTTCACCGACGGTGGTTT+TGG - chr2.3:7942415-7942434 MS.gene42835:CDS 50.0%
CTTCCCGAACACATGAAGCG+CGG + chr2.3:7942471-7942490 None:intergenic 55.0%
GTCACCGCGCTTCATGTGTT+CGG - chr2.3:7942464-7942483 MS.gene42835:CDS 55.0%
TCACCGCGCTTCATGTGTTC+GGG - chr2.3:7942465-7942484 MS.gene42835:CDS 55.0%
! AGCGTTGGAGGTGGATCTAG+CGG - chr2.3:7942344-7942363 MS.gene42835:CDS 55.0%
AGATCCACCTCCAACGCTGG+CGG + chr2.3:7942342-7942361 None:intergenic 60.0%
GCTAGATCCACCTCCAACGC+TGG + chr2.3:7942345-7942364 None:intergenic 60.0%
GTTGGAGGTGGATCTAGCGG+AGG - chr2.3:7942347-7942366 MS.gene42835:CDS 60.0%
!! AACGCTGGCGGTGCTGTTTC+CGG + chr2.3:7942330-7942349 None:intergenic 60.0%
ACATCCTCCCGTCCAGGAGG+AGG - chr2.3:7942239-7942258 MS.gene42835:CDS 65.0%
ACCTCCACATCCTCCCGTCC+AGG - chr2.3:7942233-7942252 MS.gene42835:CDS 65.0%
CGTCGTCGACGTCTCACCTC+CGG - chr2.3:7942308-7942327 MS.gene42835:CDS 65.0%
GAGACGTCGACGACGCATGC+CGG + chr2.3:7942303-7942322 None:intergenic 65.0%
GGAAACAGCACCGCCAGCGT+TGG - chr2.3:7942329-7942348 MS.gene42835:CDS 65.0%
TCCACATCCTCCCGTCCAGG+AGG - chr2.3:7942236-7942255 MS.gene42835:CDS 65.0%
TCCTCCTGGACGGGAGGATG+TGG + chr2.3:7942240-7942259 None:intergenic 65.0%
TCCTGGACGGGAGGATGTGG+AGG + chr2.3:7942237-7942256 None:intergenic 65.0%
! AACAGCACCGCCAGCGTTGG+AGG - chr2.3:7942332-7942351 MS.gene42835:CDS 65.0%
ACGACGCATGCCGGCAGTGG+CGG + chr2.3:7942294-7942313 None:intergenic 70.0%
CGAGTCCGCCTCCTCCTGGA+CGG + chr2.3:7942250-7942269 None:intergenic 70.0%
GAGTCCGCCTCCTCCTGGAC+GGG + chr2.3:7942249-7942268 None:intergenic 70.0%
TCCTCCCGTCCAGGAGGAGG+CGG - chr2.3:7942242-7942261 MS.gene42835:CDS 70.0%
TCGACGACGCATGCCGGCAG+TGG + chr2.3:7942297-7942316 None:intergenic 70.0%
! AGCACCGCCAGCGTTGGAGG+TGG - chr2.3:7942335-7942354 MS.gene42835:CDS 70.0%
!! GCTGGCGGTGCTGTTTCCGG+AGG + chr2.3:7942327-7942346 None:intergenic 70.0%
CATGCCGGCAGTGGCGGCAG+CGG + chr2.3:7942288-7942307 None:intergenic 75.0%
TCCGCCTCCTCCTGGACGGG+AGG + chr2.3:7942246-7942265 None:intergenic 75.0%
! GCGGCGAGTCCGCCTCCTCC+TGG + chr2.3:7942254-7942273 None:intergenic 80.0%
! GGCAGCGGAGCCGCGTGGTG+CGG + chr2.3:7942273-7942292 None:intergenic 80.0%
! GGCTCCGCTGCCGCCACTGC+CGG - chr2.3:7942281-7942300 MS.gene42835:CDS 80.0%
!! GGCGGACTCGCCGCACCACG+CGG - chr2.3:7942260-7942279 MS.gene42835:CDS 80.0%
! GTGGCGGCAGCGGAGCCGCG+TGG + chr2.3:7942278-7942297 None:intergenic 85.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 7942200 7942523 7942200 ID=MS.gene42835
chr2.3 mRNA 7942200 7942523 7942200 ID=MS.gene42835.t1;Parent=MS.gene42835
chr2.3 exon 7942200 7942523 7942200 ID=MS.gene42835.t1.exon1;Parent=MS.gene42835.t1
chr2.3 CDS 7942200 7942523 7942200 ID=cds.MS.gene42835.t1;Parent=MS.gene42835.t1
Gene Sequence

>MS.gene42835

ATGGCTAAAGGCGCATCTCAATCTCAATCATCAACCTCCACATCCTCCCGTCCAGGAGGAGGCGGACTCGCCGCACCACGCGGCTCCGCTGCCGCCACTGCCGGCATGCGTCGTCGACGTCTCACCTCCGGAAACAGCACCGCCAGCGTTGGAGGTGGATCTAGCGGAGGAAGCAACATGCTGAGATTCTACACTGACGATGCACCGGGTTTGAAGATTTCACCGACGGTGGTTTTGGTTATGAGTCTCTGCTTCATCGGTTTCGTCACCGCGCTTCATGTGTTCGGGAAGCTTTATCGTTACAAAGCTGGTGCTGGTGTATAA
Protein sequence

>MS.gene42835.t1

MAKGASQSQSSTSTSSRPGGGGLAAPRGSAAATAGMRRRRLTSGNSTASVGGGSSGGSNMLRFYTDDAPGLKISPTVVLVMSLCFIGFVTALHVFGKLYRYKAGAGV