AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene054163

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene054163.t1 MTR_6g048050 90.099 101 10 0 1 101 1 101 6.87e-60 189
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 29 sgRNAs with CRISPR-Local

Find 30 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCTTCAGCATTGGTGCTTT+TGG 0.137500 6.1:+27946753 MS.gene054163:CDS
CTGATGATCATTGGGGTGTT+TGG 0.308984 6.1:+27946724 MS.gene054163:CDS
CATATCTCCTGATGATCATT+GGG 0.348308 6.1:+27946716 MS.gene054163:CDS
TCATATCTCCTGATGATCAT+TGG 0.399513 6.1:+27946715 MS.gene054163:CDS
CAGTGACAGGTGGGTGTTTG+AGG 0.407502 6.1:-27946488 None:intergenic
TGAGGTTGTAGTACGAGGTT+TGG 0.417019 6.1:-27946600 None:intergenic
GATACGTGGCGTGATGGGAT+TGG 0.468761 6.1:-27946528 None:intergenic
TGGACATGAATTGAGGATGT+TGG 0.479367 6.1:-27946580 None:intergenic
TGATCATCAGGAGATATGAT+AGG 0.483007 6.1:-27946711 None:intergenic
CAAACACCCCAATGATCATC+AGG 0.499006 6.1:-27946723 None:intergenic
CGAGGTTTGGACATGAATTG+AGG 0.507643 6.1:-27946587 None:intergenic
CGGAATGATACGTGGCGTGA+TGG 0.509564 6.1:-27946534 None:intergenic
ATACGTGGCGTGATGGGATT+GGG 0.510171 6.1:-27946527 None:intergenic
TGGTCTGCTATCTTCAGCAT+TGG 0.510382 6.1:+27946744 MS.gene054163:CDS
GGAATGATACGTGGCGTGAT+GGG 0.553809 6.1:-27946533 None:intergenic
GGGTGTTTGAGGAGAGACAT+TGG 0.585033 6.1:-27946477 None:intergenic
GGATGTTGGAGAATCTAGTA+CGG 0.588596 6.1:-27946566 None:intergenic
TGCGTTGAGGTTGTAGTACG+AGG 0.590610 6.1:-27946605 None:intergenic
AATTTCCTCGTATCTGTCAA+AGG 0.599963 6.1:+27946638 MS.gene054163:CDS
CAGATACGAGGAAATTGTTG+TGG 0.612848 6.1:-27946631 None:intergenic
ATCTAGTACGGAGAGAATGT+CGG 0.625160 6.1:-27946554 None:intergenic
TGTTGAGAGAGAACAGTGAC+AGG 0.651533 6.1:-27946501 None:intergenic
ATTGTTGTGGTCGTGCGTTG+AGG 0.657429 6.1:-27946618 None:intergenic
GAGAATGTCGGAATGATACG+TGG 0.677053 6.1:-27946542 None:intergenic
ATATCTCCTGATGATCATTG+GGG 0.680137 6.1:+27946717 MS.gene054163:CDS
GAGAGAGAACAGTGACAGGT+GGG 0.691404 6.1:-27946497 None:intergenic
TGAGAGAGAACAGTGACAGG+TGG 0.699668 6.1:-27946498 None:intergenic
ACAACACTTCTAGTTATACG+AGG 0.723260 6.1:-27946663 None:intergenic
AGGTTCCTTTGACAGATACG+AGG 0.733659 6.1:-27946643 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AATTTCCTCGTATCTGTCAA+AGG + chr6.1:27946638-27946657 MS.gene054163:CDS 35.0%
ATATCTCCTGATGATCATTG+GGG + chr6.1:27946717-27946736 MS.gene054163:CDS 35.0%
CATATCTCCTGATGATCATT+GGG + chr6.1:27946716-27946735 MS.gene054163:CDS 35.0%
TCATATCTCCTGATGATCAT+TGG + chr6.1:27946715-27946734 MS.gene054163:CDS 35.0%
TGATCATCAGGAGATATGAT+AGG - chr6.1:27946714-27946733 None:intergenic 35.0%
! ACAACACTTCTAGTTATACG+AGG - chr6.1:27946666-27946685 None:intergenic 35.0%
ATCTAGTACGGAGAGAATGT+CGG - chr6.1:27946557-27946576 None:intergenic 40.0%
CAGATACGAGGAAATTGTTG+TGG - chr6.1:27946634-27946653 None:intergenic 40.0%
GGATGTTGGAGAATCTAGTA+CGG - chr6.1:27946569-27946588 None:intergenic 40.0%
TGGACATGAATTGAGGATGT+TGG - chr6.1:27946583-27946602 None:intergenic 40.0%
!!! ATCTTCAGCATTGGTGCTTT+TGG + chr6.1:27946753-27946772 MS.gene054163:CDS 40.0%
!!! TCTTCAGCATTGGTGCTTTT+GGG + chr6.1:27946754-27946773 MS.gene054163:CDS 40.0%
AGGTTCCTTTGACAGATACG+AGG - chr6.1:27946646-27946665 None:intergenic 45.0%
CAAACACCCCAATGATCATC+AGG - chr6.1:27946726-27946745 None:intergenic 45.0%
CGAGGTTTGGACATGAATTG+AGG - chr6.1:27946590-27946609 None:intergenic 45.0%
GAGAATGTCGGAATGATACG+TGG - chr6.1:27946545-27946564 None:intergenic 45.0%
TGAGGTTGTAGTACGAGGTT+TGG - chr6.1:27946603-27946622 None:intergenic 45.0%
TGGTCTGCTATCTTCAGCAT+TGG + chr6.1:27946744-27946763 MS.gene054163:CDS 45.0%
TGTTGAGAGAGAACAGTGAC+AGG - chr6.1:27946504-27946523 None:intergenic 45.0%
! CTGATGATCATTGGGGTGTT+TGG + chr6.1:27946724-27946743 MS.gene054163:CDS 45.0%
!!! GCATTGGTGCTTTTGGGATT+TGG + chr6.1:27946760-27946779 MS.gene054163:CDS 45.0%
ATTGTTGTGGTCGTGCGTTG+AGG - chr6.1:27946621-27946640 None:intergenic 50.0%
GAGAGAGAACAGTGACAGGT+GGG - chr6.1:27946500-27946519 None:intergenic 50.0%
GGAATGATACGTGGCGTGAT+GGG - chr6.1:27946536-27946555 None:intergenic 50.0%
TGAGAGAGAACAGTGACAGG+TGG - chr6.1:27946501-27946520 None:intergenic 50.0%
TGCGTTGAGGTTGTAGTACG+AGG - chr6.1:27946608-27946627 None:intergenic 50.0%
! ATACGTGGCGTGATGGGATT+GGG - chr6.1:27946530-27946549 None:intergenic 50.0%
CAGTGACAGGTGGGTGTTTG+AGG - chr6.1:27946491-27946510 None:intergenic 55.0%
CGGAATGATACGTGGCGTGA+TGG - chr6.1:27946537-27946556 None:intergenic 55.0%
! GATACGTGGCGTGATGGGAT+TGG - chr6.1:27946531-27946550 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr6.1 gene 27946480 27946785 27946480 ID=MS.gene054163
chr6.1 mRNA 27946480 27946785 27946480 ID=MS.gene054163.t1;Parent=MS.gene054163
chr6.1 exon 27946480 27946785 27946480 ID=MS.gene054163.t1.exon1;Parent=MS.gene054163.t1
chr6.1 CDS 27946480 27946785 27946480 ID=cds.MS.gene054163.t1;Parent=MS.gene054163.t1
Gene Sequence

>MS.gene054163

ATGTCTCTCCTCAAACACCCACCTGTCACTGTTCTCTCTCAACAACACCCAATCCCATCACGCCACGTATCATTCCGACATTCTCTCCGTACTAGATTCTCCAACATCCTCAATTCATGTCCAAACCTCGTACTACAACCTCAACGCACGACCACAACAATTTCCTCGTATCTGTCAAAGGAACCTCGTATAACTAGAAGTGTTGTTGCAGTGAAGTCACAGCTGAGATATCCTATCATATCTCCTGATGATCATTGGGGTGTTTGGTCTGCTATCTTCAGCATTGGTGCTTTTGGGATTTGGTAA
Protein sequence

>MS.gene054163.t1

MSLLKHPPVTVLSQQHPIPSRHVSFRHSLRTRFSNILNSCPNLVLQPQRTTTTISSYLSKEPRITRSVVAVKSQLRYPIISPDDHWGVWSAIFSIGAFGIW