AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene24530

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24530.t1 MTR_1g017000 93.452 168 10 1 20 187 86 252 6.34e-111 317
MS.gene24530.t1 MTR_6g009430 50.725 69 30 3 20 85 85 152 1.71e-12 65.1
MS.gene24530.t1 MTR_3g103570 41.096 73 43 0 20 92 86 158 1.99e-12 64.7
MS.gene24530.t1 MTR_7g102110 56.452 62 20 2 20 74 86 147 2.80e-12 63.9
MS.gene24530.t1 MTR_4g057635 70.588 34 10 0 20 53 86 119 2.04e-11 61.6
MS.gene24530.t1 MTR_6g090405 62.500 40 15 0 15 54 81 120 2.06e-11 61.2
MS.gene24530.t1 MTR_1g017140 67.647 34 11 0 20 53 86 119 5.14e-11 60.8
MS.gene24530.t1 MTR_5g014990 67.647 34 11 0 20 53 86 119 5.26e-11 60.5
MS.gene24530.t1 MTR_4g091490 53.333 45 19 1 20 64 86 128 5.85e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24530.t1 AT5G16770 38.136 118 60 6 20 134 85 192 1.34e-12 65.1
MS.gene24530.t1 AT5G16770 38.136 118 60 6 20 134 85 192 1.34e-12 65.1
MS.gene24530.t1 AT5G16770 38.136 118 60 6 20 134 85 192 2.20e-12 64.7
MS.gene24530.t1 AT5G16770 38.136 118 60 6 20 134 85 192 2.20e-12 64.7
MS.gene24530.t1 AT5G57620 53.846 52 21 1 20 71 86 134 1.65e-11 62.0
MS.gene24530.t1 AT4G37780 70.588 34 10 0 20 53 86 119 2.21e-11 61.6
MS.gene24530.t1 AT3G23250 45.000 80 41 2 15 92 23 101 3.65e-11 60.5
MS.gene24530.t1 AT5G23000 63.158 38 14 0 15 52 81 118 8.09e-11 60.1
MS.gene24530.t1 AT3G23250 45.000 80 41 2 15 92 80 158 9.21e-11 59.7
MS.gene24530.t1 AT5G65790 69.697 33 10 0 20 52 86 118 9.63e-11 60.1

Find 29 sgRNAs with CRISPR-Local

Find 78 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGGAATCATTGATGGATTT+TGG 0.132955 1.2:+5824734 MS.gene24530:CDS
ACTTTATTGTCTAGCATAAT+TGG 0.238985 1.2:-5824584 None:intergenic
AAAACTGAAGAAGAAGATTT+TGG 0.243833 1.2:+5824418 MS.gene24530:CDS
CAGCAATATTATTAATCCTT+TGG 0.356887 1.2:+5824652 MS.gene24530:CDS
GATGCTGTAGTATCAGAAAT+TGG 0.363867 1.2:+5824620 MS.gene24530:CDS
TTTCACCCTCTATTCTCAAA+TGG 0.370485 1.2:+5823426 MS.gene24530:CDS
TCAAGCTGGTGATGAATCTA+TGG 0.374214 1.2:+5824715 MS.gene24530:CDS
TGAGTTAGTGATGGAGTTGA+AGG 0.446977 1.2:-5824488 None:intergenic
GCCAGGTAGTTTAGATGCTA+TGG 0.455877 1.2:-5824360 None:intergenic
TGCTACCCATTTGAGAATAG+AGG 0.456147 1.2:-5823432 None:intergenic
TGAATCTATGGAATCATTGA+TGG 0.458518 1.2:+5824727 MS.gene24530:CDS
TTCACCCTCTATTCTCAAAT+GGG 0.465064 1.2:+5823427 MS.gene24530:CDS
ACATCATTGTCTGTTCTGCC+AGG 0.476737 1.2:-5824377 None:intergenic
TCTATTCTCAAATGGGTAGC+AGG 0.500149 1.2:+5823434 MS.gene24530:CDS
TCTTAACTGCTTTCCTGAGT+GGG 0.511907 1.2:+5824790 MS.gene24530:CDS
AGCATAATTGGAAGTGGTGA+AGG 0.515734 1.2:-5824572 None:intergenic
TTGTCTAGCATAATTGGAAG+TGG 0.518920 1.2:-5824578 None:intergenic
AGAATAGAGGGTGAAAATGA+TGG 0.524462 1.2:-5823419 None:intergenic
TTGGAACTTTGAGTTAGTGA+TGG 0.526757 1.2:-5824497 None:intergenic
GAGTTAGTGATGGAGTTGAA+GGG 0.551144 1.2:-5824487 None:intergenic
ATCTTAACTGCTTTCCTGAG+TGG 0.564962 1.2:+5824789 MS.gene24530:CDS
TGGAGGCTTCACTGAAGAAG+AGG 0.582932 1.2:+5823393 MS.gene24530:CDS
ATAATTGGAAGTGGTGAAGG+TGG 0.597724 1.2:-5824569 None:intergenic
GCTACCCATTTGAGAATAGA+GGG 0.601575 1.2:-5823431 None:intergenic
TCTTGAGAAATTGACACCAA+AGG 0.604458 1.2:-5824668 None:intergenic
TAACTAAAATCAACCCACTC+AGG 0.606546 1.2:-5824803 None:intergenic
GCCATAGCATCTAAACTACC+TGG 0.606568 1.2:+5824359 MS.gene24530:CDS
ATTGCAATTCAAGATCAAGC+TGG 0.635582 1.2:+5824701 MS.gene24530:CDS
TCATTGACATGATCATCATG+AGG 0.679338 1.2:-5824767 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTTTAAAATCAAGTTAT+TGG - chr1.2:5824142-5824161 None:intergenic 10.0%
!! ACTAAAATTTAAATTTCAGT+TGG + chr1.2:5823819-5823838 MS.gene24530:intron 15.0%
!! CGTTTATAATAATAACAATT+TGG - chr1.2:5823516-5823535 None:intergenic 15.0%
!! CTAAAATTTAAATTTCAGTT+GGG + chr1.2:5823820-5823839 MS.gene24530:intron 15.0%
!! TACAACTTAATTAAATAAGT+TGG - chr1.2:5823472-5823491 None:intergenic 15.0%
!! TTAAAAAAAGTGAGAAATTA+TGG + chr1.2:5824153-5824172 MS.gene24530:intron 15.0%
!!! ATATTCTATAACCATTTTTT+GGG - chr1.2:5824107-5824126 None:intergenic 15.0%
!!! TATATTCTATAACCATTTTT+TGG - chr1.2:5824108-5824127 None:intergenic 15.0%
!!! TGAAATTTAAATTTTAGTCT+CGG - chr1.2:5823817-5823836 None:intergenic 15.0%
!!! AAATTGATTTCTGAATTTTG+AGG - chr1.2:5824524-5824543 None:intergenic 20.0%
!!! AATTGATTTCTGAATTTTGA+GGG - chr1.2:5824523-5824542 None:intergenic 20.0%
!!! ATTTTTTATAGTCAGTTGAA+TGG + chr1.2:5824245-5824264 MS.gene24530:intron 20.0%
! AAGAAATTATAACAACCAAC+TGG + chr1.2:5823733-5823752 MS.gene24530:intron 25.0%
! ACAATGATGTGAAAAACTAT+TGG + chr1.2:5824390-5824409 MS.gene24530:CDS 25.0%
! ACAGAAAAAATGTGATTAGA+AGG + chr1.2:5824002-5824021 MS.gene24530:intron 25.0%
! ACTTTATTGTCTAGCATAAT+TGG - chr1.2:5824587-5824606 None:intergenic 25.0%
! AGAAATTATAACAACCAACT+GGG + chr1.2:5823734-5823753 MS.gene24530:intron 25.0%
! CAGCAATATTATTAATCCTT+TGG + chr1.2:5824652-5824671 MS.gene24530:CDS 25.0%
!! AAAACTGAAGAAGAAGATTT+TGG + chr1.2:5824418-5824437 MS.gene24530:CDS 25.0%
!! AACTCTAGTTTATAACATCA+TGG - chr1.2:5823788-5823807 None:intergenic 25.0%
!! ACTCTAGTTTATAACATCAT+GGG - chr1.2:5823787-5823806 None:intergenic 25.0%
!! GATTTTTAATGTGTACAAGT+TGG + chr1.2:5823678-5823697 MS.gene24530:intron 25.0%
!!! ATTTTTTGGGTCTTAATCTT+GGG - chr1.2:5824094-5824113 None:intergenic 25.0%
CAAGATTAAGACCCAAAAAA+TGG + chr1.2:5824093-5824112 MS.gene24530:intron 30.0%
GAAATTATAACAACCAACTG+GGG + chr1.2:5823735-5823754 MS.gene24530:intron 30.0%
GTACTATGAAACTAACTTTG+AGG - chr1.2:5824272-5824291 None:intergenic 30.0%
TAATTTCTCACTTTGACTGA+AGG - chr1.2:5823893-5823912 None:intergenic 30.0%
TAGTTTCATAGTACTTCAAG+AGG + chr1.2:5824278-5824297 MS.gene24530:intron 30.0%
TGAATCTATGGAATCATTGA+TGG + chr1.2:5824727-5824746 MS.gene24530:CDS 30.0%
TGAGAACTATTCAAACTTTG+AGG - chr1.2:5824310-5824329 None:intergenic 30.0%
! AATTTGTGATTTTGTGCAGA+TGG + chr1.2:5824333-5824352 MS.gene24530:intron 30.0%
! ATGTCGTATTTAGAGTTTGA+GGG + chr1.2:5823847-5823866 MS.gene24530:intron 30.0%
!!! AATGTTGATTTTGTGAAGCA+GGG - chr1.2:5824547-5824566 None:intergenic 30.0%
!!! ATGGAATCATTGATGGATTT+TGG + chr1.2:5824734-5824753 MS.gene24530:CDS 30.0%
!!! CATTTTTTGGGTCTTAATCT+TGG - chr1.2:5824095-5824114 None:intergenic 30.0%
!!! GTATTGTCATTTTCAGTCAA+TGG - chr1.2:5824464-5824483 None:intergenic 30.0%
!!! TTTTTTGGGTCTTAATCTTG+GGG - chr1.2:5824093-5824112 None:intergenic 30.0%
AGAATAGAGGGTGAAAATGA+TGG - chr1.2:5823422-5823441 None:intergenic 35.0%
ATTGCAATTCAAGATCAAGC+TGG + chr1.2:5824701-5824720 MS.gene24530:CDS 35.0%
CACTTAGACCAACATTATGT+CGG - chr1.2:5823927-5823946 None:intergenic 35.0%
GATGCTGTAGTATCAGAAAT+TGG + chr1.2:5824620-5824639 MS.gene24530:CDS 35.0%
GGAGAGAAACTACTAAATGT+TGG + chr1.2:5824023-5824042 MS.gene24530:intron 35.0%
TAACTAAAATCAACCCACTC+AGG - chr1.2:5824806-5824825 None:intergenic 35.0%
TCATTGACATGATCATCATG+AGG - chr1.2:5824770-5824789 None:intergenic 35.0%
TCTTGAGAAATTGACACCAA+AGG - chr1.2:5824671-5824690 None:intergenic 35.0%
TTCACCCTCTATTCTCAAAT+GGG + chr1.2:5823427-5823446 MS.gene24530:CDS 35.0%
TTGTCTAGCATAATTGGAAG+TGG - chr1.2:5824581-5824600 None:intergenic 35.0%
TTTCACCCTCTATTCTCAAA+TGG + chr1.2:5823426-5823445 MS.gene24530:CDS 35.0%
! AATGTTGGTCTAAGTGTAAC+TGG + chr1.2:5823931-5823950 MS.gene24530:intron 35.0%
! GATGTCGTATTTAGAGTTTG+AGG + chr1.2:5823846-5823865 MS.gene24530:intron 35.0%
! TTGGAACTTTGAGTTAGTGA+TGG - chr1.2:5824500-5824519 None:intergenic 35.0%
!! GATTTCTGAATTTTGAGGGT+TGG - chr1.2:5824519-5824538 None:intergenic 35.0%
!!! GAATGTTGATTTTGTGAAGC+AGG - chr1.2:5824548-5824567 None:intergenic 35.0%
!!! TCATTGATGGATTTTGGCTT+TGG + chr1.2:5824740-5824759 MS.gene24530:CDS 35.0%
AGCATAATTGGAAGTGGTGA+AGG - chr1.2:5824575-5824594 None:intergenic 40.0%
ATAATTGGAAGTGGTGAAGG+TGG - chr1.2:5824572-5824591 None:intergenic 40.0%
ATCTTAACTGCTTTCCTGAG+TGG + chr1.2:5824789-5824808 MS.gene24530:CDS 40.0%
GCTACCCATTTGAGAATAGA+GGG - chr1.2:5823434-5823453 None:intergenic 40.0%
GGAAAGACCATAATCATCAC+AGG - chr1.2:5824072-5824091 None:intergenic 40.0%
TCTATTCTCAAATGGGTAGC+AGG + chr1.2:5823434-5823453 MS.gene24530:CDS 40.0%
TCTTAACTGCTTTCCTGAGT+GGG + chr1.2:5824790-5824809 MS.gene24530:CDS 40.0%
TGCTACCCATTTGAGAATAG+AGG - chr1.2:5823435-5823454 None:intergenic 40.0%
TGGTCTAAGTGTAACTGGAT+TGG + chr1.2:5823936-5823955 MS.gene24530:intron 40.0%
TGTCGAACCTGTGATGATTA+TGG + chr1.2:5824062-5824081 MS.gene24530:intron 40.0%
! GAGTTAGTGATGGAGTTGAA+GGG - chr1.2:5824490-5824509 None:intergenic 40.0%
! TCAAGCTGGTGATGAATCTA+TGG + chr1.2:5824715-5824734 MS.gene24530:CDS 40.0%
! TGAGTTAGTGATGGAGTTGA+AGG - chr1.2:5824491-5824510 None:intergenic 40.0%
!! CTGAAGAAGAAGATTTTGGC+AGG + chr1.2:5824422-5824441 MS.gene24530:CDS 40.0%
ACATCATTGTCTGTTCTGCC+AGG - chr1.2:5824380-5824399 None:intergenic 45.0%
CCAACATTATGTCGGACTGT+CGG - chr1.2:5823919-5823938 None:intergenic 45.0%
GCCAGGTAGTTTAGATGCTA+TGG - chr1.2:5824363-5824382 None:intergenic 45.0%
GCCATAGCATCTAAACTACC+TGG + chr1.2:5824359-5824378 MS.gene24530:CDS 45.0%
TGGGGTTGAGTCAACTTGAA+GGG + chr1.2:5823753-5823772 MS.gene24530:intron 45.0%
CCGACAGTCCGACATAATGT+TGG + chr1.2:5823916-5823935 MS.gene24530:intron 50.0%
CTGGGGTTGAGTCAACTTGA+AGG + chr1.2:5823752-5823771 MS.gene24530:intron 50.0%
GGGGTTGAGTCAACTTGAAG+GGG + chr1.2:5823754-5823773 MS.gene24530:intron 50.0%
TGGAGGCTTCACTGAAGAAG+AGG + chr1.2:5823393-5823412 MS.gene24530:CDS 50.0%
! CAAGTTGACTCAACCCCAGT+TGG - chr1.2:5823751-5823770 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 5823392 5824847 5823392 ID=MS.gene24530
chr1.2 mRNA 5823392 5824847 5823392 ID=MS.gene24530.t1;Parent=MS.gene24530
chr1.2 exon 5823392 5823459 5823392 ID=MS.gene24530.t1.exon1;Parent=MS.gene24530.t1
chr1.2 CDS 5823392 5823459 5823392 ID=cds.MS.gene24530.t1;Parent=MS.gene24530.t1
chr1.2 exon 5824352 5824847 5824352 ID=MS.gene24530.t1.exon2;Parent=MS.gene24530.t1
chr1.2 CDS 5824352 5824847 5824352 ID=cds.MS.gene24530.t1;Parent=MS.gene24530.t1
Gene Sequence

>MS.gene24530

ATGGAGGCTTCACTGAAGAAGAGGATGCCATCATTTTCACCCTCTATTCTCAAATGGGTAGCAGGCAAGTACTATTTCCAACTTATTTAATTAAGTTGTATCTATTTTCACTATATAATTTCCAAATTGTTATTATTATAAACGTTGATCATTGTTAACTGTTATAATCACTTTATTTAATTTAGTATTATATATAGTTTTTCATAAGAGTTGATCATTGTTAAGTGCTAACTATTACAACTTTATTTAATTTAGTACTATGTATTGTTTTTCTTTAAGAGTTGATGATTTTTAATGTGTACAAGTTGGAAAGATTTGTTTTTTCATATAGATAATAAATTAAGAAATTATAACAACCAACTGGGGTTGAGTCAACTTGAAGGGGATAACTTCCCATGATGTTATAAACTAGAGTTCGAATTCCGAGACTAAAATTTAAATTTCAGTTGGGAGAGATGTCGTATTTAGAGTTTGAGGGTGTTTTAAATAAAATTATAACCTTCAGTCAAAGTGAGAAATTATAACCGACAGTCCGACATAATGTTGGTCTAAGTGTAACTGGATTGGACTCAAATTTTTTTAAGCAATGTCTCATGTTCAAACTTTATCAACAGAAAAAATGTGATTAGAAGGAGAGAAACTACTAAATGTTGGATTTTATTTAATTATCTGTCGAACCTGTGATGATTATGGTCTTTCCCCAAGATTAAGACCCAAAAAATGGTTATAGAATATAGATGCTTGATACCAATAACTTGATTTTAAAAAAAGTGAGAAATTATGGATTGATATTCTATCATTTAATTATTCATATATACAAAATAAATGTACTATCTATCTATTAGTAGTATTGATTTTTTATAGTCAGTTGAATGGTCCTCAAAGTTAGTTTCATAGTACTTCAAGAGGAATATGCCTCAAAGTTTGAATAGTTCTCATGAAATTTGTGATTTTGTGCAGATGGTCTGCCATAGCATCTAAACTACCTGGCAGAACAGACAATGATGTGAAAAACTATTGGAACACAAAACTGAAGAAGAAGATTTTGGCAGGAATAGTTAAGCTCAAACCATTGACTGAAAATGACAATACTATCCCTTCAACTCCATCACTAACTCAAAGTTCCAACCCTCAAAATTCAGAAATCAATTTCCCTGCTTCACAAAATCAACATTCTCCACCTTCACCACTTCCAATTATGCTAGACAATAAAGTTGACAAAATTCATGATGCTGTAGTATCAGAAATTGGTACAAGTAACAGCAATATTATTAATCCTTTGGTGTCAATTTCTCAAGACTCTTCAAGCATTGCAATTCAAGATCAAGCTGGTGATGAATCTATGGAATCATTGATGGATTTTGGCTTTGGATTTCCTCATGATGATCATGTCAATGATCTTAACTGCTTTCCTGAGTGGGTTGATTTTAGTTATGCTGACATTAAGCCAAATTGA
Protein sequence

>MS.gene24530.t1

MEASLKKRMPSFSPSILKWVAGKWSAIASKLPGRTDNDVKNYWNTKLKKKILAGIVKLKPLTENDNTIPSTPSLTQSSNPQNSEINFPASQNQHSPPSPLPIMLDNKVDKIHDAVVSEIGTSNSNIINPLVSISQDSSSIAIQDQAGDESMESLMDFGFGFPHDDHVNDLNCFPEWVDFSYADIKPN