AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0990580


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0990580 MtrunA17_Chr6g0471211 100.000 109 0 0 1 109 1 109 2.28e-63 187
Msa0990580 MtrunA17_Chr1g0203261 87.500 72 9 0 3 74 4 75 2.14e-26 94.0
Msa0990580 MtrunA17_Chr8g0387471 50.704 71 34 1 4 74 3 72 2.94e-17 71.6
Msa0990580 MtrunA17_Chr6g0469651 50.000 70 34 1 3 72 2 70 6.95e-16 68.2
Msa0990580 MtrunA17_Chr7g0233191 48.684 76 38 1 4 79 3 77 8.05e-16 67.4
Msa0990580 MtrunA17_Chr7g0248671 53.731 67 30 1 4 70 3 68 1.35e-15 68.6
Msa0990580 MtrunA17_Chr7g0233201 47.368 76 39 1 4 79 3 77 2.40e-15 66.2
Msa0990580 MtrunA17_Chr7g0233251 50.000 74 36 1 4 77 3 75 2.67e-15 66.2
Msa0990580 MtrunA17_Chr7g0233181 47.368 76 39 1 4 79 3 77 1.31e-14 64.3
Msa0990580 MtrunA17_Chr6g0469541 45.333 75 40 1 4 78 3 76 2.92e-14 63.5
Msa0990580 MtrunA17_Chr7g0233211 46.053 76 40 1 4 79 3 77 3.47e-14 63.2
Msa0990580 MtrunA17_Chr7g0233231 46.053 76 40 1 4 79 3 77 3.62e-14 63.2
Msa0990580 MtrunA17_Chr1g0202561 49.296 71 35 1 4 74 3 72 6.30e-14 63.2
Msa0990580 MtrunA17_Chr6g0469591 49.275 69 34 1 4 72 3 70 8.12e-14 62.8
Msa0990580 MtrunA17_Chr1g0202541 49.296 71 35 1 4 74 3 72 8.43e-14 62.8
Msa0990580 MtrunA17_Chr6g0469571 49.275 69 34 1 4 72 3 70 9.05e-14 62.4
Msa0990580 MtrunA17_Chr6g0469671 46.575 73 38 1 3 75 2 73 1.03e-13 62.0
Msa0990580 MtrunA17_Chr6g0469551 47.826 69 35 1 4 72 3 70 2.03e-13 61.6
Msa0990580 MtrunA17_Chr6g0469681 43.836 73 40 1 3 75 2 73 9.22e-13 60.1
Msa0990580 MtrunA17_Chr1g0202501 49.315 73 36 1 3 75 2 73 2.19e-11 56.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0990580 AT5G23760.1 86.667 75 10 0 1 75 1 75 4.91e-28 98.6
Msa0990580 AT5G23760.2 84.375 64 10 0 12 75 1 64 1.83e-20 79.0
Msa0990580 AT1G01490.1 52.857 70 31 2 4 72 3 71 1.49e-15 68.6
Msa0990580 AT1G01490.2 52.857 70 31 2 4 72 3 71 1.49e-15 68.6
Msa0990580 AT1G01490.4 50.685 73 34 2 1 72 27 98 1.63e-15 69.3
Msa0990580 AT5G52740.1 48.571 70 33 2 3 72 2 68 8.89e-11 55.1

Find 16 sgRNAs with CRISPR-Local

Find 72 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAGCAGAAGGTTGTGTTAA+AGG 0.208879 6_4:+52550335 Msa0990580:intron
GAAAGAAGAGAAGAAATAAA+AGG 0.242019 6_4:+52550760 Msa0990580:exon
TACAGAAAGTAAATACTAAA+AGG 0.321970 6_4:-52550931 None:intergenic
GAGCCATTTGAAGAGTTATA+AGG 0.337013 6_4:-52550101 None:intergenic
AGAAAAGAAAGAAGAGAAGA+AGG 0.371134 6_4:+52550682 Msa0990580:CDS
GAGCAAAAGTTGACGGTGAT+TGG 0.372704 6_4:+52550566 Msa0990580:CDS
TTACCTACTCACTACTATAT+AGG 0.395939 6_4:+52550020 None:intergenic
AGAGAAGAAAGAAGAGAAGA+AGG 0.411074 6_4:+52550730 Msa0990580:CDS
GTTGACGGTGATTGGTTCAA+TGG 0.416041 6_4:+52550574 Msa0990580:CDS
GAAGCAGCTGCAGATATCTA+TGG 0.439199 6_4:+52550399 Msa0990580:CDS
ACTCCTTATAACTCTTCAAA+TGG 0.490526 6_4:+52550098 Msa0990580:exon
TGTAAAAGAGCAAAAGTTGA+CGG 0.513319 6_4:+52550559 Msa0990580:CDS
GAAGAAAGAAGAGAAGAAGG+AGG 0.516884 6_4:+52550733 Msa0990580:CDS
TATAACTCTTCAAATGGCTC+AGG 0.518462 6_4:+52550104 Msa0990580:exon
AAAGTTGATATTGTATCTGT+TGG 0.520457 6_4:+52550635 Msa0990580:CDS
GAAAACAAGAAATAAAATGA+AGG 0.568256 6_4:-52550073 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAATTAAATTAAATAGGAT+AGG - chr6_4:52550147-52550166 None:intergenic 10.0%
!! TGAACAAAATTAAATTAAAT+AGG - chr6_4:52550152-52550171 None:intergenic 10.0%
!!! ATTTAATTTAATTTTGTTCA+TGG + chr6_4:52550152-52550171 Msa0990580:intron 10.0%
!!! AATGTTATTTAATAAATCAA+AGG + chr6_4:52550478-52550497 Msa0990580:intron 10.0%
!! ATAATCAATATAGAAAAATA+TGG - chr6_4:52550862-52550881 None:intergenic 10.0%
!!! AAATTGTCTATAATTTTTTT+TGG + chr6_4:52550905-52550924 Msa0990580:three_prime_UTR 10.0%
!! AAAATTAAATTAAATAGGAT+AGG - chr6_4:52550147-52550166 None:intergenic 10.0%
!! TGAACAAAATTAAATTAAAT+AGG - chr6_4:52550152-52550171 None:intergenic 10.0%
!!! ATTTAATTTAATTTTGTTCA+TGG + chr6_4:52550152-52550171 Msa0990580:intron 10.0%
!!! AATGTTATTTAATAAATCAA+AGG + chr6_4:52550478-52550497 Msa0990580:intron 10.0%
!! ATAATCAATATAGAAAAATA+TGG - chr6_4:52550862-52550881 None:intergenic 10.0%
!!! AAATTGTCTATAATTTTTTT+TGG + chr6_4:52550905-52550924 Msa0990580:three_prime_UTR 10.0%
!! GAAAACAAGAAATAAAATGA+AGG - chr6_4:52550076-52550095 None:intergenic 20.0%
!! AAGAGAATGGAAAAAAAATA+TGG - chr6_4:52550294-52550313 None:intergenic 20.0%
!! TACAGAAAGTAAATACTAAA+AGG - chr6_4:52550934-52550953 None:intergenic 20.0%
!! GAAAACAAGAAATAAAATGA+AGG - chr6_4:52550076-52550095 None:intergenic 20.0%
!! AAGAGAATGGAAAAAAAATA+TGG - chr6_4:52550294-52550313 None:intergenic 20.0%
!! TACAGAAAGTAAATACTAAA+AGG - chr6_4:52550934-52550953 None:intergenic 20.0%
! ACATATATAGCTAAATCATG+AGG - chr6_4:52550218-52550237 None:intergenic 25.0%
!!! AAAGTTGATATTGTATCTGT+TGG + chr6_4:52550635-52550654 Msa0990580:CDS 25.0%
! AGAGAAAAAAGAAGAGAAAA+AGG + chr6_4:52550706-52550725 Msa0990580:CDS 25.0%
! GAAAGAAGAGAAGAAATAAA+AGG + chr6_4:52550760-52550779 Msa0990580:exon 25.0%
! ACATATATAGCTAAATCATG+AGG - chr6_4:52550218-52550237 None:intergenic 25.0%
!!! AAAGTTGATATTGTATCTGT+TGG + chr6_4:52550635-52550654 Msa0990580:CDS 25.0%
! AGAGAAAAAAGAAGAGAAAA+AGG + chr6_4:52550706-52550725 Msa0990580:CDS 25.0%
! GAAAGAAGAGAAGAAATAAA+AGG + chr6_4:52550760-52550779 Msa0990580:exon 25.0%
ACTCCTTATAACTCTTCAAA+TGG + chr6_4:52550098-52550117 Msa0990580:exon 30.0%
AATAGGATAGGATAAGAAAG+AGG - chr6_4:52550135-52550154 None:intergenic 30.0%
ACACAGGAAATCTAATAGAT+TGG - chr6_4:52550191-52550210 None:intergenic 30.0%
TAAATCATGAGGATTTACAC+AGG - chr6_4:52550207-52550226 None:intergenic 30.0%
CCAATGAAAGAATAAGAGAA+TGG - chr6_4:52550307-52550326 None:intergenic 30.0%
CCATTCTCTTATTCTTTCAT+TGG + chr6_4:52550304-52550323 Msa0990580:intron 30.0%
!! TGTTGTGGATTTTGATGTAT+AGG + chr6_4:52550515-52550534 Msa0990580:intron 30.0%
TGTAAAAGAGCAAAAGTTGA+CGG + chr6_4:52550559-52550578 Msa0990580:CDS 30.0%
AGAAAAGAAAGAAGAGAAGA+AGG + chr6_4:52550682-52550701 Msa0990580:CDS 30.0%
ACTCCTTATAACTCTTCAAA+TGG + chr6_4:52550098-52550117 Msa0990580:exon 30.0%
AATAGGATAGGATAAGAAAG+AGG - chr6_4:52550135-52550154 None:intergenic 30.0%
ACACAGGAAATCTAATAGAT+TGG - chr6_4:52550191-52550210 None:intergenic 30.0%
TAAATCATGAGGATTTACAC+AGG - chr6_4:52550207-52550226 None:intergenic 30.0%
CCAATGAAAGAATAAGAGAA+TGG - chr6_4:52550307-52550326 None:intergenic 30.0%
CCATTCTCTTATTCTTTCAT+TGG + chr6_4:52550304-52550323 Msa0990580:intron 30.0%
!! TGTTGTGGATTTTGATGTAT+AGG + chr6_4:52550515-52550534 Msa0990580:intron 30.0%
TGTAAAAGAGCAAAAGTTGA+CGG + chr6_4:52550559-52550578 Msa0990580:CDS 30.0%
AGAAAAGAAAGAAGAGAAGA+AGG + chr6_4:52550682-52550701 Msa0990580:CDS 30.0%
!! AAGGCTAGAGAATTTTGATG+AGG - chr6_4:52550057-52550076 None:intergenic 35.0%
GAGCCATTTGAAGAGTTATA+AGG - chr6_4:52550104-52550123 None:intergenic 35.0%
TATAACTCTTCAAATGGCTC+AGG + chr6_4:52550104-52550123 Msa0990580:exon 35.0%
TTGGATTGATTGAAAGCAGA+AGG + chr6_4:52550323-52550342 Msa0990580:intron 35.0%
AAAGCAGAAGGTTGTGTTAA+AGG + chr6_4:52550335-52550354 Msa0990580:intron 35.0%
GCTGATCTATTGAATTGTTG+TGG + chr6_4:52550500-52550519 Msa0990580:intron 35.0%
GTGAAGAAGCTGAAAAAAGT+AGG + chr6_4:52550611-52550630 Msa0990580:CDS 35.0%
! TCTTTCTTCTCTTCTTTTGC+AGG - chr6_4:52550662-52550681 None:intergenic 35.0%
AGAGAAGAAAGAAGAGAAGA+AGG + chr6_4:52550730-52550749 Msa0990580:CDS 35.0%
! ACAATTTTTGCAGCTTACAC+TGG - chr6_4:52550892-52550911 None:intergenic 35.0%
!! AAGGCTAGAGAATTTTGATG+AGG - chr6_4:52550057-52550076 None:intergenic 35.0%
GAGCCATTTGAAGAGTTATA+AGG - chr6_4:52550104-52550123 None:intergenic 35.0%
TATAACTCTTCAAATGGCTC+AGG + chr6_4:52550104-52550123 Msa0990580:exon 35.0%
TTGGATTGATTGAAAGCAGA+AGG + chr6_4:52550323-52550342 Msa0990580:intron 35.0%
AAAGCAGAAGGTTGTGTTAA+AGG + chr6_4:52550335-52550354 Msa0990580:intron 35.0%
GCTGATCTATTGAATTGTTG+TGG + chr6_4:52550500-52550519 Msa0990580:intron 35.0%
GTGAAGAAGCTGAAAAAAGT+AGG + chr6_4:52550611-52550630 Msa0990580:CDS 35.0%
! TCTTTCTTCTCTTCTTTTGC+AGG - chr6_4:52550662-52550681 None:intergenic 35.0%
AGAGAAGAAAGAAGAGAAGA+AGG + chr6_4:52550730-52550749 Msa0990580:CDS 35.0%
! ACAATTTTTGCAGCTTACAC+TGG - chr6_4:52550892-52550911 None:intergenic 35.0%
GAAGAAAGAAGAGAAGAAGG+AGG + chr6_4:52550733-52550752 Msa0990580:CDS 40.0%
GAAGAAAGAAGAGAAGAAGG+AGG + chr6_4:52550733-52550752 Msa0990580:CDS 40.0%
GAAGCAGCTGCAGATATCTA+TGG + chr6_4:52550399-52550418 Msa0990580:CDS 45.0%
GAGCAAAAGTTGACGGTGAT+TGG + chr6_4:52550566-52550585 Msa0990580:CDS 45.0%
! GTTGACGGTGATTGGTTCAA+TGG + chr6_4:52550574-52550593 Msa0990580:CDS 45.0%
GAAGCAGCTGCAGATATCTA+TGG + chr6_4:52550399-52550418 Msa0990580:CDS 45.0%
GAGCAAAAGTTGACGGTGAT+TGG + chr6_4:52550566-52550585 Msa0990580:CDS 45.0%
! GTTGACGGTGATTGGTTCAA+TGG + chr6_4:52550574-52550593 Msa0990580:CDS 45.0%
Chromosome Type Strat End Strand Name
chr6_4 gene 52550035 52550979 52550035 ID=Msa0990580;Name=Msa0990580
chr6_4 mRNA 52550035 52550979 52550035 ID=Msa0990580-mRNA-1;Parent=Msa0990580;Name=Msa0990580-mRNA-1;_AED=0.15;_eAED=0.15;_QI=82|1|1|1|1|1|3|201|109
chr6_4 exon 52550035 52550125 52550035 ID=Msa0990580-mRNA-1:exon:11000;Parent=Msa0990580-mRNA-1
chr6_4 exon 52550342 52550420 52550342 ID=Msa0990580-mRNA-1:exon:11001;Parent=Msa0990580-mRNA-1
chr6_4 exon 52550537 52550979 52550537 ID=Msa0990580-mRNA-1:exon:11002;Parent=Msa0990580-mRNA-1
chr6_4 five_prime_UTR 52550035 52550116 52550035 ID=Msa0990580-mRNA-1:five_prime_utr;Parent=Msa0990580-mRNA-1
chr6_4 CDS 52550117 52550125 52550117 ID=Msa0990580-mRNA-1:cds;Parent=Msa0990580-mRNA-1
chr6_4 CDS 52550342 52550420 52550342 ID=Msa0990580-mRNA-1:cds;Parent=Msa0990580-mRNA-1
chr6_4 CDS 52550537 52550778 52550537 ID=Msa0990580-mRNA-1:cds;Parent=Msa0990580-mRNA-1
chr6_4 three_prime_UTR 52550779 52550979 52550779 ID=Msa0990580-mRNA-1:three_prime_utr;Parent=Msa0990580-mRNA-1
Gene Sequence

>Msa0990580

ATGGCTCAGAAGGTTGTGTTAAAGGTGTTAACTATGACTGATGACAAAACAAAGCAAAAAGCTATAGAAGCAGCTGCAGATATCTATGGTGTTGATTCAATTGTAGCAGATGTAAAAGAGCAAAAGTTGACGGTGATTGGTTCAATGGATACAGTGAAAATTGTGAAGAAGCTGAAAAAAGTAGGAAAAGTTGATATTGTATCTGTTGGTCCTGCAAAAGAAGAGAAGAAAGAAGAAAAGAAAGAAGAGAAGAAGGAAGAGAAAAAAGAAGAGAAAAAGGAAGAGAAGAAAGAAGAGAAGAAGGAGGAAAAGAAAGAAGAGAAGAAATAA

Protein sequence

>Msa0990580

MAQKVVLKVLTMTDDKTKQKAIEAAADIYGVDSIVADVKEQKLTVIGSMDTVKIVKKLKKVGKVDIVSVGPAKEEKKEEKKEEKKEEKKEEKKEEKKEEKKEEKKEEKK*