AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene040773

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene040773.t1 MTR_1g052185 66.803 244 44 2 1 207 32 275 1.77e-95 280
MS.gene040773.t1 MTR_4g073310 39.394 231 85 9 1 211 32 227 1.87e-30 112
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 33 sgRNAs with CRISPR-Local

Find 44 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTCCTCTTGCTACCTTTAT+TGG 0.117903 1.2:-36226426 None:intergenic
GAAACTTTCCTGCGGTGATA+TGG 0.327630 1.2:+36226524 MS.gene040773:CDS
ACACAATCATGCTGTCAATA+AGG 0.336852 1.2:+36226226 MS.gene040773:CDS
ATATCGCATCAGACCAATAA+AGG 0.381574 1.2:+36226413 MS.gene040773:CDS
TGCTAACTGCGAGTCATGTT+AGG 0.385892 1.2:+36226577 MS.gene040773:CDS
CTTCTCTTCAATGTCAATAG+AGG 0.428268 1.2:-36226730 None:intergenic
GGTATTATTATCCTTTACCT+TGG 0.495202 1.2:-36226709 None:intergenic
ATAATCATGGTGAGAGGAAG+AGG 0.500570 1.2:+36226499 MS.gene040773:CDS
GAGATACTTTGTATGAGTGT+TGG 0.504205 1.2:-36226470 None:intergenic
GAGAAGAAGATCAATAATGA+AGG 0.510676 1.2:+36226747 MS.gene040773:CDS
TTCAACTCTGGCAACGCACT+CGG 0.512404 1.2:+36226155 MS.gene040773:CDS
GCTAACTGCGAGTCATGTTA+GGG 0.531070 1.2:+36226578 MS.gene040773:CDS
GTATCTCATGATAATAATCA+TGG 0.533222 1.2:+36226486 MS.gene040773:CDS
CTCATTAACCATATCACCGC+AGG 0.561714 1.2:-36226532 None:intergenic
TAGGGTTAATGATGAAATAG+TGG 0.562125 1.2:+36226596 MS.gene040773:CDS
ATCACGAGAGACCAAGGTAA+AGG 0.568045 1.2:+36226698 MS.gene040773:CDS
AGTGTGAGTTGTGCGGCAAA+AGG 0.579769 1.2:+36226132 MS.gene040773:CDS
CGGTGATATGGTTAATGAGA+CGG 0.580945 1.2:+36226536 MS.gene040773:CDS
TGCGGCAAAAGGTTCAACTC+TGG 0.586813 1.2:+36226143 MS.gene040773:CDS
TGATTTGAATGAGCGTCCGA+TGG 0.602910 1.2:+36226830 MS.gene040773:CDS
TCATCTGCAACATCTTCCAT+CGG 0.606110 1.2:-36226846 None:intergenic
AACTCTGGCAACGCACTCGG+TGG 0.616672 1.2:+36226158 MS.gene040773:CDS
TAATGAAGGTGAAACTGAGA+GGG 0.616761 1.2:+36226761 MS.gene040773:CDS
AGACCAATAAAGGTAGCAAG+AGG 0.628089 1.2:+36226423 MS.gene040773:CDS
TATGGTTAATGAGACGGTCA+AGG 0.630287 1.2:+36226542 MS.gene040773:CDS
ATGATAATAATCATGGTGAG+AGG 0.635487 1.2:+36226493 MS.gene040773:CDS
TGATGAATCACGAGAGACCA+AGG 0.650584 1.2:+36226692 MS.gene040773:CDS
TTGTTGTGATGTTTGCAACA+AGG 0.651265 1.2:+36226277 MS.gene040773:CDS
ATAATGAAGGTGAAACTGAG+AGG 0.653304 1.2:+36226760 MS.gene040773:CDS
ATCATGGTGAGAGGAAGAGG+CGG 0.703073 1.2:+36226502 MS.gene040773:CDS
ATGTATGAGTGTGAGTTGTG+CGG 0.703631 1.2:+36226125 MS.gene040773:CDS
AAGAGGCGGAAACTTTCCTG+CGG 0.719801 1.2:+36226516 MS.gene040773:CDS
ATCAAAGTGAAAGATGACAG+CGG 0.730896 1.2:+36226621 MS.gene040773:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! GTATCTCATGATAATAATCA+TGG + chr1.2:36226486-36226505 MS.gene040773:CDS 25.0%
!!! TGTCTTTTTTTCTTGTTTTG+AGG - chr1.2:36226209-36226228 None:intergenic 25.0%
AAGTCAATAGAAGATGAAGT+TGG - chr1.2:36226374-36226393 None:intergenic 30.0%
ATGATAATAATCATGGTGAG+AGG + chr1.2:36226493-36226512 MS.gene040773:CDS 30.0%
GAGAAGAAGATCAATAATGA+AGG + chr1.2:36226747-36226766 MS.gene040773:CDS 30.0%
GGTATTATTATCCTTTACCT+TGG - chr1.2:36226712-36226731 None:intergenic 30.0%
TAGGGTTAATGATGAAATAG+TGG + chr1.2:36226596-36226615 MS.gene040773:CDS 30.0%
ACACAATCATGCTGTCAATA+AGG + chr1.2:36226226-36226245 MS.gene040773:CDS 35.0%
ATAATGAAGGTGAAACTGAG+AGG + chr1.2:36226760-36226779 MS.gene040773:CDS 35.0%
ATATCGCATCAGACCAATAA+AGG + chr1.2:36226413-36226432 MS.gene040773:CDS 35.0%
ATCAAAGTGAAAGATGACAG+CGG + chr1.2:36226621-36226640 MS.gene040773:CDS 35.0%
ATGAGATGTCACAAAAGAGA+CGG + chr1.2:36226332-36226351 MS.gene040773:intron 35.0%
ATTCCTCTTGCTACCTTTAT+TGG - chr1.2:36226429-36226448 None:intergenic 35.0%
CTTCTCTTCAATGTCAATAG+AGG - chr1.2:36226733-36226752 None:intergenic 35.0%
GAGATACTTTGTATGAGTGT+TGG - chr1.2:36226473-36226492 None:intergenic 35.0%
TAATGAAGGTGAAACTGAGA+GGG + chr1.2:36226761-36226780 MS.gene040773:CDS 35.0%
TCAATAGAAGATGAAGTTGG+CGG - chr1.2:36226371-36226390 None:intergenic 35.0%
TTGTTGTGATGTTTGCAACA+AGG + chr1.2:36226277-36226296 MS.gene040773:CDS 35.0%
AGACCAATAAAGGTAGCAAG+AGG + chr1.2:36226423-36226442 MS.gene040773:CDS 40.0%
ATAATCATGGTGAGAGGAAG+AGG + chr1.2:36226499-36226518 MS.gene040773:CDS 40.0%
ATGTATGAGTGTGAGTTGTG+CGG + chr1.2:36226125-36226144 MS.gene040773:CDS 40.0%
CAATAGAAGATGAAGTTGGC+GGG - chr1.2:36226370-36226389 None:intergenic 40.0%
CGGTGATATGGTTAATGAGA+CGG + chr1.2:36226536-36226555 MS.gene040773:CDS 40.0%
TATGGTTAATGAGACGGTCA+AGG + chr1.2:36226542-36226561 MS.gene040773:CDS 40.0%
TCATCTGCAACATCTTCCAT+CGG - chr1.2:36226849-36226868 None:intergenic 40.0%
TGAGATGTCACAAAAGAGAC+GGG + chr1.2:36226333-36226352 MS.gene040773:intron 40.0%
!!! CAAGGTTTTTTCATCCAAGC+AGG + chr1.2:36226295-36226314 MS.gene040773:intron 40.0%
!!! TCTTGTTTTGAGGTTGTGAG+CGG - chr1.2:36226199-36226218 None:intergenic 40.0%
ATCACGAGAGACCAAGGTAA+AGG + chr1.2:36226698-36226717 MS.gene040773:CDS 45.0%
CTCATTAACCATATCACCGC+AGG - chr1.2:36226535-36226554 None:intergenic 45.0%
GAAACTTTCCTGCGGTGATA+TGG + chr1.2:36226524-36226543 MS.gene040773:CDS 45.0%
GCTAACTGCGAGTCATGTTA+GGG + chr1.2:36226578-36226597 MS.gene040773:CDS 45.0%
TGATGAATCACGAGAGACCA+AGG + chr1.2:36226692-36226711 MS.gene040773:CDS 45.0%
TGATTTGAATGAGCGTCCGA+TGG + chr1.2:36226830-36226849 MS.gene040773:CDS 45.0%
TGCTAACTGCGAGTCATGTT+AGG + chr1.2:36226577-36226596 MS.gene040773:CDS 45.0%
AAGAGGCGGAAACTTTCCTG+CGG + chr1.2:36226516-36226535 MS.gene040773:CDS 50.0%
AGTGTGAGTTGTGCGGCAAA+AGG + chr1.2:36226132-36226151 MS.gene040773:CDS 50.0%
ATCATGGTGAGAGGAAGAGG+CGG + chr1.2:36226502-36226521 MS.gene040773:CDS 50.0%
TGCGGCAAAAGGTTCAACTC+TGG + chr1.2:36226143-36226162 MS.gene040773:CDS 50.0%
TTCAACTCTGGCAACGCACT+CGG + chr1.2:36226155-36226174 MS.gene040773:CDS 50.0%
! GTGAGCGGTGAGATGTTTTG+TGG - chr1.2:36226184-36226203 None:intergenic 50.0%
! TCATCCAAGCAGGCTTTGTG+TGG + chr1.2:36226305-36226324 MS.gene040773:intron 50.0%
GTGTCCACACAAAGCCTGCT+TGG - chr1.2:36226312-36226331 None:intergenic 55.0%
AACTCTGGCAACGCACTCGG+TGG + chr1.2:36226158-36226177 MS.gene040773:CDS 60.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 36226125 36226872 36226125 ID=MS.gene040773
chr1.2 mRNA 36226125 36226872 36226125 ID=MS.gene040773.t1;Parent=MS.gene040773
chr1.2 exon 36226125 36226298 36226125 ID=MS.gene040773.t1.exon1;Parent=MS.gene040773.t1
chr1.2 CDS 36226125 36226298 36226125 ID=cds.MS.gene040773.t1;Parent=MS.gene040773.t1
chr1.2 exon 36226411 36226872 36226411 ID=MS.gene040773.t1.exon2;Parent=MS.gene040773.t1
chr1.2 CDS 36226411 36226872 36226411 ID=cds.MS.gene040773.t1;Parent=MS.gene040773.t1
Gene Sequence

>MS.gene040773

ATGTATGAGTGTGAGTTGTGCGGCAAAAGGTTCAACTCTGGCAACGCACTCGGTGGCCACAAAACATCTCACCGCTCACAACCTCAAAACAAGAAAAAAAGACACAATCATGCTGTCAATAAGGATGATAAAGATGATGAGAAACAGAAACATTGTTGTGATGTTTGCAACAAGGTTTTTTCATCCAAGCAGGCTTTGTGTGGACACATGAGATGTCACAAAAGAGACGGGAAGAGTATTCACCCGCCAACTTCATCTTCTATTGACTTATCAAAATATATGCTAGCAATATCGCATCAGACCAATAAAGGTAGCAAGAGGAATATCATTGATGACGATGTTGCTCCAACACTCATACAAAGTATCTCATGATAATAATCATGGTGAGAGGAAGAGGCGGAAACTTTCCTGCGGTGATATGGTTAATGAGACGGTCAAGGAACAAACTGTGATGCTAACTGCGAGTCATGTTAGGGTTAATGATGAAATAGTGGTGATCAAAGTGAAAGATGACAGCGGAAATAAAAGACTCAAACTTTCAAGCAATTCTGAAGATATTGTTGACATTGATGAATCACGAGAGACCAAGGTAAAGGATAATAATACCTCTATTGACATTGAAGAGAAGAAGATCAATAATGAAGGTGAAACTGAGAGGGAACAAAGTCATAATGAATTGAAGTCAAATAGAGTTGTTATGAATTTTGATTTGAATGAGCGTCCGATGGAAGATGTTGCAGATGAGTGA
Protein sequence

>MS.gene040773.t1

MYECELCGKRFNSGNALGGHKTSHRSQPQNKKKRHNHAVNKDDKDDEKQKHCCDVCNKQYRIRPIKVARGISLMTMLLQHSYKVSHDNNHGERKRRKLSCGDMVNETVKEQTVMLTASHVRVNDEIVVIKVKDDSGNKRLKLSSNSEDIVDIDESRETKVKDNNTSIDIEEKKINNEGETEREQSHNELKSNRVVMNFDLNERPMEDVADE