AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1385540

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1385540 MtrunA17_Chr7g0236851 66.667 141 17 1 1 111 379 519 4.76e-52 174
Msa1385540 MtrunA17_Chr6g0468561 42.138 159 53 6 1 123 381 536 8.16e-24 95.9
Msa1385540 MtrunA17_Chr3g0125811 49.383 81 41 0 37 117 356 436 1.10e-14 69.7
Msa1385540 MtrunA17_Chr1g0159461 36.667 150 57 3 1 117 314 458 7.45e-14 67.4
Msa1385540 MtrunA17_Chr4g0076091 42.857 91 44 1 29 111 313 403 9.21e-13 64.3
Msa1385540 MtrunA17_Chr4g0037781 65.217 46 15 1 1 46 141 185 1.48e-11 59.3
Msa1385540 MtrunA17_Chr4g0037771 87.097 31 4 0 1 31 84 114 7.97e-11 55.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1385540 AT5G52510.1 45.652 92 45 2 23 113 416 503 1.22e-17 78.6

Find 18 sgRNAs with CRISPR-Local

Find 33 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAATCTACGCGACTGATTT+TGG 0.109152 tig0020757:-57490 Msa1385540:CDS
GAAAATCATCGGAGAACTTT+TGG 0.188442 tig0020757:-57706 Msa1385540:CDS
AGCTTCAAGGATTGCAATAT+TGG 0.275399 tig0020757:+57899 None:intergenic
GGTCGAGAAGCTGAGAGTTT+AGG 0.349907 tig0020757:-57684 Msa1385540:CDS
AAGAACTCTCACTGTTGATT+GGG 0.374869 tig0020757:-57458 Msa1385540:CDS
GAAGAACTCTCACTGTTGAT+TGG 0.399753 tig0020757:-57459 Msa1385540:CDS
TATCTTCGAATGCAGCTTCA+AGG 0.404851 tig0020757:+57886 None:intergenic
GAAATCCACGTGACTGGCTT+TGG 0.427416 tig0020757:+57416 None:intergenic
CGTGACTGGCTTTGGTTGGA+TGG 0.435707 tig0020757:+57424 None:intergenic
TCAAGTGAAATCCACGTGAC+TGG 0.491312 tig0020757:+57410 None:intergenic
AATCAAGTTTGAATTCAAAC+CGG 0.494743 tig0020757:-57661 Msa1385540:CDS
GCGAAATGAGAGCGTGTCAA+CGG 0.529082 tig0020757:-57544 Msa1385540:CDS
TCCACGTGACTGGCTTTGGT+TGG 0.544114 tig0020757:+57420 None:intergenic
GTGACTGGCTTTGGTTGGAT+GGG 0.569100 tig0020757:+57425 None:intergenic
GACGAGAATCTGAAAATCAT+CGG 0.593271 tig0020757:-57717 Msa1385540:CDS
AGAACTCTCACTGTTGATTG+GGG 0.605295 tig0020757:-57457 Msa1385540:CDS
TCCAACCAAAGCCAGTCACG+TGG 0.641232 tig0020757:-57421 Msa1385540:CDS
GTCATTGAATTGTGACTCAG+AGG 0.645367 tig0020757:-57607 Msa1385540:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AATCAAGTTTGAATTCAAAC+CGG - tig0020757:57655-57674 Msa1385540:CDS 25.0%
!! TGTGTTGTGGATTTTGATAT+TGG - tig0020757:57476-57495 Msa1385540:CDS 30.0%
!! GTGGATTTTGATATTGGTAA+TGG - tig0020757:57482-57501 Msa1385540:CDS 30.0%
! AAAATCATCGGAGAACTTTT+GGG - tig0020757:57611-57630 Msa1385540:CDS 30.0%
! TCTCATTTCGCATTTTGTAT+AGG + tig0020757:57763-57782 None:intergenic 30.0%
AGCTTCAAGGATTGCAATAT+TGG + tig0020757:57420-57439 None:intergenic 35.0%
! CGTGAAGAATTTTTGTGTTG+TGG - tig0020757:57463-57482 Msa1385540:CDS 35.0%
GACGAGAATCTGAAAATCAT+CGG - tig0020757:57599-57618 Msa1385540:CDS 35.0%
! GAAAATCATCGGAGAACTTT+TGG - tig0020757:57610-57629 Msa1385540:CDS 35.0%
!! TCTGTGAGTTTTATGTTCAC+CGG + tig0020757:57677-57696 None:intergenic 35.0%
! AAGAACTCTCACTGTTGATT+GGG - tig0020757:57858-57877 Msa1385540:CDS 35.0%
TATCTTCGAATGCAGCTTCA+AGG + tig0020757:57433-57452 None:intergenic 40.0%
GTCATTGAATTGTGACTCAG+AGG - tig0020757:57709-57728 Msa1385540:CDS 40.0%
!! GAAATCTACGCGACTGATTT+TGG - tig0020757:57826-57845 Msa1385540:intron 40.0%
GAAGAACTCTCACTGTTGAT+TGG - tig0020757:57857-57876 Msa1385540:CDS 40.0%
! AGAACTCTCACTGTTGATTG+GGG - tig0020757:57859-57878 Msa1385540:CDS 40.0%
!! TCTACGCGACTGATTTTGGT+TGG - tig0020757:57830-57849 Msa1385540:intron 45.0%
!!! GCGACTGATTTTGGTTGGAT+GGG - tig0020757:57835-57854 Msa1385540:intron 45.0%
TCAAGTGAAATCCACGTGAC+TGG + tig0020757:57909-57928 None:intergenic 45.0%
!! GCGCATGGAGTTTTTGGAGA+AGG + tig0020757:57523-57542 None:intergenic 50.0%
! TGAGACGCGCATGGAGTTTT+TGG + tig0020757:57529-57548 None:intergenic 50.0%
AAACTCCATGCGCGTCTCAA+CGG - tig0020757:57530-57549 Msa1385540:CDS 50.0%
GGTCGAGAAGCTGAGAGTTT+AGG - tig0020757:57632-57651 Msa1385540:CDS 50.0%
! GCGAAATGAGAGCGTGTCAA+CGG - tig0020757:57772-57791 Msa1385540:intron 50.0%
!!! CGCGACTGATTTTGGTTGGA+TGG - tig0020757:57834-57853 Msa1385540:intron 50.0%
!! GTGACTGGCTTTGGTTGGAT+GGG + tig0020757:57894-57913 None:intergenic 50.0%
!! GAAATCCACGTGACTGGCTT+TGG + tig0020757:57903-57922 None:intergenic 50.0%
GTTAACCGTTGAGACGCGCA+TGG + tig0020757:57538-57557 None:intergenic 55.0%
AGCGTGTCAACGGAGAATCC+AGG - tig0020757:57782-57801 Msa1385540:intron 55.0%
!! CGTGACTGGCTTTGGTTGGA+TGG + tig0020757:57895-57914 None:intergenic 55.0%
TCCAACCAAAGCCAGTCACG+TGG - tig0020757:57895-57914 Msa1385540:CDS 55.0%
!! TCCACGTGACTGGCTTTGGT+TGG + tig0020757:57899-57918 None:intergenic 55.0%
! TGACGAAGAAGCGTGTCGCC+TGG + tig0020757:57803-57822 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
tig0020757 gene 57410 57928 57410 ID=Msa1385540;Name=Msa1385540
tig0020757 mRNA 57410 57928 57410 ID=Msa1385540-mRNA-1;Parent=Msa1385540;Name=Msa1385540-mRNA-1;_AED=0.31;_eAED=0.31;_QI=0|0|0|1|1|1|2|0|142
tig0020757 exon 57841 57928 57841 ID=Msa1385540-mRNA-1:exon:9651;Parent=Msa1385540-mRNA-1
tig0020757 exon 57410 57750 57410 ID=Msa1385540-mRNA-1:exon:9650;Parent=Msa1385540-mRNA-1
tig0020757 CDS 57841 57928 57841 ID=Msa1385540-mRNA-1:cds;Parent=Msa1385540-mRNA-1
tig0020757 CDS 57410 57750 57410 ID=Msa1385540-mRNA-1:cds;Parent=Msa1385540-mRNA-1
Gene Sequence

>Msa1385540

ATGGCTGCCAATATTGCAATCCTTGAAGCTGCATTCGAAGATACAACAAAGAGCGTGAAGAATTTTTGTGTTGTGGATTTTGATATTGTGAACGTCGACGACGAGAATCTGAAAATCATCGGAGAACTTTTGGGTCGAGAAGCTGAGAGTTTAGGAATCAAGTTTGAATTCAAACCGGTGAACATAAAACTCACAGAATTAACTCGCGAGTCATTGAATTGTGACTCAGAGGATATTCTCGCTATGAATTTCGCATTCAACCTATACAAAATGCGAAATGAGAGCGTGTCAACGGAGAATCCAGGCGACACGCTTCTTCGTCACGTGAAATCTACGCGACTGATTTTGGTTGGATGGGAAGAACTCTCACTGTTGATTGGGGAGAGTTCTTCCCATCCAACCAAAGCCAGTCACGTGGATTTCACTTGA
Protein sequence

>Msa1385540

MAANIAILEAAFEDTTKSVKNFCVVDFDIVNVDDENLKIIGELLGREAESLGIKFEFKPVNIKLTELTRESLNCDSEDILAMNFAFNLYKMRNESVSTENPGDTLLRHVKSTRLILVGWEELSLLIGESSSHPTKASHVDFT*