AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1090240

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1090240 MtrunA17_Chr1g0201251 69.231 52 15 1 1 52 86 136 1.28e-17 75.1
Msa1090240 MtrunA17_Chr6g0466891 63.462 52 18 1 1 52 86 136 2.04e-16 72.0
Msa1090240 MtrunA17_Chr3g0090241 72.340 47 12 1 1 47 86 131 1.01e-14 66.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1090240 AT1G07140.1 63.462 52 18 1 1 52 89 139 1.77e-14 67.4
Msa1090240 AT2G30060.1 65.957 47 15 1 1 47 91 136 3.49e-13 63.5
Msa1090240 AT5G58590.1 59.615 52 20 1 1 52 88 138 1.71e-12 62.0

Find 39 sgRNAs with CRISPR-Local

Find 120 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACAACCGAGCCGTACTAAAT+TGG 0.252478 7_3:+4049285 None:intergenic
GCTGCTTCAACTGTGTTTGC+AGG 0.266451 7_3:-4048399 Msa1090240:CDS
CCGAGAGAGTAGGGTGTATT+TGG 0.267050 7_3:-4048665 Msa1090240:intron
AGCGCAGATCTTGAGGGTTT+TGG 0.290367 7_3:+4049159 None:intergenic
CAGTTCTGTTCGAGGAAGTT+GGG 0.316931 7_3:-4048490 Msa1090240:CDS
GTATATGTTGGTGTGCTTCC+TGG 0.324348 7_3:-4048375 Msa1090240:CDS
ATAAGGTTACTTGAAAAGTT+AGG 0.336456 7_3:-4049198 Msa1090240:five_prime_UTR
GATTCGGTTGCTAGCAGTTT+GGG 0.375277 7_3:-4048421 Msa1090240:CDS
TGATTCGGTTGCTAGCAGTT+TGG 0.405660 7_3:-4048422 Msa1090240:CDS
CGATGGAGTTCTTAAGCATA+AGG 0.412330 7_3:-4049215 Msa1090240:five_prime_UTR
GCAGTTCTGTTCGAGGAAGT+TGG 0.425432 7_3:-4048491 Msa1090240:CDS
GAATTGAGAAATCGTGTGTT+TGG 0.437554 7_3:-4048993 Msa1090240:CDS
CTATCTTGTTAAAGTGGTGT+TGG 0.446382 7_3:-4048691 Msa1090240:CDS
GAAAAGTTAGGCTTCTTATG+AGG 0.446917 7_3:-4049186 Msa1090240:exon
TAACTTTATGAGTTCTTGAC+TGG 0.460076 7_3:-4049240 Msa1090240:five_prime_UTR
AATCGTGTGTTTGGCATGCT+AGG 0.466273 7_3:-4048984 Msa1090240:CDS
CTGCTTCAACTGTGTTTGCA+GGG 0.486018 7_3:-4048398 Msa1090240:CDS
CGAGGAAGTTGGGGTCTAGT+TGG 0.486820 7_3:-4048480 Msa1090240:CDS
ACGATTAGCGCAGATCTTGA+GGG 0.489998 7_3:+4049153 None:intergenic
TTCTCTTGCATACTCATCAT+AGG 0.492591 7_3:+4049021 None:intergenic
GACGATTAGCGCAGATCTTG+AGG 0.502484 7_3:+4049152 None:intergenic
TCTGCCATGAGATGGTGATT+CGG 0.523598 7_3:-4048437 Msa1090240:CDS
CATGCTAGGGATTCTGCTGA+TGG 0.533927 7_3:-4048970 Msa1090240:intron
TGATAACTATCTTGTTAAAG+TGG 0.534578 7_3:-4048697 Msa1090240:CDS
ATCGTGTGTTTGGCATGCTA+GGG 0.537370 7_3:-4048983 Msa1090240:CDS
TGTTGGAATCCGAGAGAGTA+GGG 0.545544 7_3:-4048674 Msa1090240:CDS
CCAAATACACCCTACTCTCT+CGG 0.552355 7_3:+4048665 None:intergenic
ATGAGTATGCAAGAGAATGT+TGG 0.553283 7_3:-4049015 Msa1090240:CDS
TGAGTTCTTGACTGGTACGA+TGG 0.554894 7_3:-4049232 Msa1090240:five_prime_UTR
TGCTTCAACTGTGTTTGCAG+GGG 0.555834 7_3:-4048397 Msa1090240:CDS
AGTTCTGTTCGAGGAAGTTG+GGG 0.577830 7_3:-4048489 Msa1090240:CDS
GTGTTGGAATCCGAGAGAGT+AGG 0.584549 7_3:-4048675 Msa1090240:CDS
AGCAAAGATATTAGCTGCGG+AGG 0.590198 7_3:-4049310 None:intergenic
GCGGAGGATCCAATTTAGTA+CGG 0.590877 7_3:-4049294 Msa1090240:five_prime_UTR
GGATCCAATTTAGTACGGCT+CGG 0.591535 7_3:-4049289 Msa1090240:five_prime_UTR
GTGTTTGCAGGGGTATATGT+TGG 0.608820 7_3:-4048387 Msa1090240:CDS
ACTGCAGCAGAAATCAAACC+AGG 0.630618 7_3:+4048357 None:intergenic
AGCAGCAAAGATATTAGCTG+CGG 0.638123 7_3:-4049313 None:intergenic
GCAACCGAATCACCATCTCA+TGG 0.649274 7_3:+4048433 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGTTAGATGATGTTTTATTT+TGG - chr7_3:4048834-4048853 Msa1090240:intron 20.0%
!!! GTTAGATGATGTTTTATTTT+GGG - chr7_3:4048835-4048854 Msa1090240:intron 20.0%
!!! TTAGATGATGTTTTATTTTG+GGG - chr7_3:4048836-4048855 Msa1090240:intron 20.0%
!!! TGTTAGATGATGTTTTATTT+TGG - chr7_3:4048834-4048853 Msa1090240:intron 20.0%
!!! GTTAGATGATGTTTTATTTT+GGG - chr7_3:4048835-4048854 Msa1090240:intron 20.0%
!!! TTAGATGATGTTTTATTTTG+GGG - chr7_3:4048836-4048855 Msa1090240:intron 20.0%
! ATAAGGTTACTTGAAAAGTT+AGG - chr7_3:4048459-4048478 Msa1090240:CDS 25.0%
!!! TTTTGTGATTTTGATTGTTG+TGG - chr7_3:4048590-4048609 Msa1090240:intron 25.0%
!!! CAGATTTTTTGTAGTTAGAT+TGG - chr7_3:4048788-4048807 Msa1090240:intron 25.0%
!! ATTGGTTTAGATGAATATTG+TGG - chr7_3:4048806-4048825 Msa1090240:intron 25.0%
! TTGGTTTAGATGAATATTGT+GGG - chr7_3:4048807-4048826 Msa1090240:intron 25.0%
!!! TAGATGATGTTTTATTTTGG+GGG - chr7_3:4048837-4048856 Msa1090240:intron 25.0%
! TGATAACTATCTTGTTAAAG+TGG - chr7_3:4048960-4048979 Msa1090240:intron 25.0%
! AAATGAGTAAAATTACAGAC+CGG + chr7_3:4049053-4049072 None:intergenic 25.0%
! GTTTACTTATCCAAAAAGAT+AGG - chr7_3:4049085-4049104 Msa1090240:intron 25.0%
!! AGGAAAAATTCCTATCTTTT+TGG + chr7_3:4049098-4049117 None:intergenic 25.0%
! ATAAGGTTACTTGAAAAGTT+AGG - chr7_3:4048459-4048478 Msa1090240:CDS 25.0%
!!! TTTTGTGATTTTGATTGTTG+TGG - chr7_3:4048590-4048609 Msa1090240:intron 25.0%
!!! CAGATTTTTTGTAGTTAGAT+TGG - chr7_3:4048788-4048807 Msa1090240:intron 25.0%
!! ATTGGTTTAGATGAATATTG+TGG - chr7_3:4048806-4048825 Msa1090240:intron 25.0%
! TTGGTTTAGATGAATATTGT+GGG - chr7_3:4048807-4048826 Msa1090240:intron 25.0%
!!! TAGATGATGTTTTATTTTGG+GGG - chr7_3:4048837-4048856 Msa1090240:intron 25.0%
! TGATAACTATCTTGTTAAAG+TGG - chr7_3:4048960-4048979 Msa1090240:intron 25.0%
! AAATGAGTAAAATTACAGAC+CGG + chr7_3:4049053-4049072 None:intergenic 25.0%
! GTTTACTTATCCAAAAAGAT+AGG - chr7_3:4049085-4049104 Msa1090240:intron 25.0%
!! AGGAAAAATTCCTATCTTTT+TGG + chr7_3:4049098-4049117 None:intergenic 25.0%
TAACTTTATGAGTTCTTGAC+TGG - chr7_3:4048417-4048436 Msa1090240:CDS 30.0%
! AAGATGCACTTTTCTGTTTT+CGG - chr7_3:4048719-4048738 Msa1090240:intron 30.0%
! AAGATAGGAATTTTTCCTTG+TGG - chr7_3:4049100-4049119 Msa1090240:intron 30.0%
AAAGGAAAATATGTACCACA+AGG + chr7_3:4049118-4049137 None:intergenic 30.0%
! TTGTGGTACATATTTTCCTT+TGG - chr7_3:4049117-4049136 Msa1090240:intron 30.0%
TAACTTTATGAGTTCTTGAC+TGG - chr7_3:4048417-4048436 Msa1090240:CDS 30.0%
! AAGATGCACTTTTCTGTTTT+CGG - chr7_3:4048719-4048738 Msa1090240:intron 30.0%
! AAGATAGGAATTTTTCCTTG+TGG - chr7_3:4049100-4049119 Msa1090240:intron 30.0%
AAAGGAAAATATGTACCACA+AGG + chr7_3:4049118-4049137 None:intergenic 30.0%
! TTGTGGTACATATTTTCCTT+TGG - chr7_3:4049117-4049136 Msa1090240:intron 30.0%
GAAAAGTTAGGCTTCTTATG+AGG - chr7_3:4048471-4048490 Msa1090240:CDS 35.0%
TTCTCTTGCATACTCATCAT+AGG + chr7_3:4048639-4048658 None:intergenic 35.0%
ATGAGTATGCAAGAGAATGT+TGG - chr7_3:4048642-4048661 Msa1090240:intron 35.0%
GAATTGAGAAATCGTGTGTT+TGG - chr7_3:4048664-4048683 Msa1090240:intron 35.0%
ACTCAACAACTATTGACATG+TGG - chr7_3:4048905-4048924 Msa1090240:intron 35.0%
CTATCTTGTTAAAGTGGTGT+TGG - chr7_3:4048966-4048985 Msa1090240:intron 35.0%
! TTTCCTTTGGTAATTGTAGC+AGG - chr7_3:4049130-4049149 Msa1090240:intron 35.0%
! TTCCTTTGGTAATTGTAGCA+GGG - chr7_3:4049131-4049150 Msa1090240:intron 35.0%
GAAAAGTTAGGCTTCTTATG+AGG - chr7_3:4048471-4048490 Msa1090240:CDS 35.0%
TTCTCTTGCATACTCATCAT+AGG + chr7_3:4048639-4048658 None:intergenic 35.0%
ATGAGTATGCAAGAGAATGT+TGG - chr7_3:4048642-4048661 Msa1090240:intron 35.0%
GAATTGAGAAATCGTGTGTT+TGG - chr7_3:4048664-4048683 Msa1090240:intron 35.0%
ACTCAACAACTATTGACATG+TGG - chr7_3:4048905-4048924 Msa1090240:intron 35.0%
CTATCTTGTTAAAGTGGTGT+TGG - chr7_3:4048966-4048985 Msa1090240:intron 35.0%
! TTTCCTTTGGTAATTGTAGC+AGG - chr7_3:4049130-4049149 Msa1090240:intron 35.0%
! TTCCTTTGGTAATTGTAGCA+GGG - chr7_3:4049131-4049150 Msa1090240:intron 35.0%
CGATGGAGTTCTTAAGCATA+AGG - chr7_3:4048442-4048461 Msa1090240:CDS 40.0%
AAATTACAGACCGGACAAGA+TGG + chr7_3:4049044-4049063 None:intergenic 40.0%
!!! CAGTTTTTTCTGCCATGAGA+TGG - chr7_3:4049212-4049231 Msa1090240:five_prime_UTR 40.0%
CGATGGAGTTCTTAAGCATA+AGG - chr7_3:4048442-4048461 Msa1090240:CDS 40.0%
AAATTACAGACCGGACAAGA+TGG + chr7_3:4049044-4049063 None:intergenic 40.0%
!!! CAGTTTTTTCTGCCATGAGA+TGG - chr7_3:4049212-4049231 Msa1090240:five_prime_UTR 40.0%
GCGGAGGATCCAATTTAGTA+CGG - chr7_3:4048363-4048382 Msa1090240:CDS 45.0%
GGATCCAATTTAGTACGGCT+CGG - chr7_3:4048368-4048387 Msa1090240:CDS 45.0%
ACAACCGAGCCGTACTAAAT+TGG + chr7_3:4048375-4048394 None:intergenic 45.0%
TGAGTTCTTGACTGGTACGA+TGG - chr7_3:4048425-4048444 Msa1090240:CDS 45.0%
ACGATTAGCGCAGATCTTGA+GGG + chr7_3:4048507-4048526 None:intergenic 45.0%
AATCGTGTGTTTGGCATGCT+AGG - chr7_3:4048673-4048692 Msa1090240:CDS 45.0%
ATCGTGTGTTTGGCATGCTA+GGG - chr7_3:4048674-4048693 Msa1090240:CDS 45.0%
TGTTGGAATCCGAGAGAGTA+GGG - chr7_3:4048983-4049002 Msa1090240:CDS 45.0%
CCAAATACACCCTACTCTCT+CGG + chr7_3:4048995-4049014 None:intergenic 45.0%
CACCCTGCTACAATTACCAA+AGG + chr7_3:4049136-4049155 None:intergenic 45.0%
! GTCTTTTGCAGTTCTGTTCG+AGG - chr7_3:4049159-4049178 Msa1090240:CDS 45.0%
CAGTTCTGTTCGAGGAAGTT+GGG - chr7_3:4049167-4049186 Msa1090240:CDS 45.0%
AGTTCTGTTCGAGGAAGTTG+GGG - chr7_3:4049168-4049187 Msa1090240:CDS 45.0%
TCTGCCATGAGATGGTGATT+CGG - chr7_3:4049220-4049239 Msa1090240:five_prime_UTR 45.0%
!! TGATTCGGTTGCTAGCAGTT+TGG - chr7_3:4049235-4049254 Msa1090240:five_prime_UTR 45.0%
! GATTCGGTTGCTAGCAGTTT+GGG - chr7_3:4049236-4049255 Msa1090240:five_prime_UTR 45.0%
CTGCTTCAACTGTGTTTGCA+GGG - chr7_3:4049259-4049278 Msa1090240:five_prime_UTR 45.0%
TGCTTCAACTGTGTTTGCAG+GGG - chr7_3:4049260-4049279 Msa1090240:five_prime_UTR 45.0%
! GTGTTTGCAGGGGTATATGT+TGG - chr7_3:4049270-4049289 Msa1090240:five_prime_UTR 45.0%
GTATATGTTGGTGTGCTTCC+TGG - chr7_3:4049282-4049301 Msa1090240:five_prime_UTR 45.0%
ACTGCAGCAGAAATCAAACC+AGG + chr7_3:4049303-4049322 None:intergenic 45.0%
GCGGAGGATCCAATTTAGTA+CGG - chr7_3:4048363-4048382 Msa1090240:CDS 45.0%
GGATCCAATTTAGTACGGCT+CGG - chr7_3:4048368-4048387 Msa1090240:CDS 45.0%
ACAACCGAGCCGTACTAAAT+TGG + chr7_3:4048375-4048394 None:intergenic 45.0%
TGAGTTCTTGACTGGTACGA+TGG - chr7_3:4048425-4048444 Msa1090240:CDS 45.0%
ACGATTAGCGCAGATCTTGA+GGG + chr7_3:4048507-4048526 None:intergenic 45.0%
AATCGTGTGTTTGGCATGCT+AGG - chr7_3:4048673-4048692 Msa1090240:CDS 45.0%
ATCGTGTGTTTGGCATGCTA+GGG - chr7_3:4048674-4048693 Msa1090240:CDS 45.0%
TGTTGGAATCCGAGAGAGTA+GGG - chr7_3:4048983-4049002 Msa1090240:CDS 45.0%
CCAAATACACCCTACTCTCT+CGG + chr7_3:4048995-4049014 None:intergenic 45.0%
CACCCTGCTACAATTACCAA+AGG + chr7_3:4049136-4049155 None:intergenic 45.0%
! GTCTTTTGCAGTTCTGTTCG+AGG - chr7_3:4049159-4049178 Msa1090240:CDS 45.0%
CAGTTCTGTTCGAGGAAGTT+GGG - chr7_3:4049167-4049186 Msa1090240:CDS 45.0%
AGTTCTGTTCGAGGAAGTTG+GGG - chr7_3:4049168-4049187 Msa1090240:CDS 45.0%
TCTGCCATGAGATGGTGATT+CGG - chr7_3:4049220-4049239 Msa1090240:five_prime_UTR 45.0%
!! TGATTCGGTTGCTAGCAGTT+TGG - chr7_3:4049235-4049254 Msa1090240:five_prime_UTR 45.0%
! GATTCGGTTGCTAGCAGTTT+GGG - chr7_3:4049236-4049255 Msa1090240:five_prime_UTR 45.0%
CTGCTTCAACTGTGTTTGCA+GGG - chr7_3:4049259-4049278 Msa1090240:five_prime_UTR 45.0%
TGCTTCAACTGTGTTTGCAG+GGG - chr7_3:4049260-4049279 Msa1090240:five_prime_UTR 45.0%
! GTGTTTGCAGGGGTATATGT+TGG - chr7_3:4049270-4049289 Msa1090240:five_prime_UTR 45.0%
GTATATGTTGGTGTGCTTCC+TGG - chr7_3:4049282-4049301 Msa1090240:five_prime_UTR 45.0%
ACTGCAGCAGAAATCAAACC+AGG + chr7_3:4049303-4049322 None:intergenic 45.0%
! AGCGCAGATCTTGAGGGTTT+TGG + chr7_3:4048501-4048520 None:intergenic 50.0%
GACGATTAGCGCAGATCTTG+AGG + chr7_3:4048508-4048527 None:intergenic 50.0%
CATGCTAGGGATTCTGCTGA+TGG - chr7_3:4048687-4048706 Msa1090240:CDS 50.0%
GTGTTGGAATCCGAGAGAGT+AGG - chr7_3:4048982-4049001 Msa1090240:CDS 50.0%
CCGAGAGAGTAGGGTGTATT+TGG - chr7_3:4048992-4049011 Msa1090240:CDS 50.0%
GTTGCACATGCCATCTTGTC+CGG - chr7_3:4049031-4049050 Msa1090240:intron 50.0%
GCAGTTCTGTTCGAGGAAGT+TGG - chr7_3:4049166-4049185 Msa1090240:CDS 50.0%
GCAACCGAATCACCATCTCA+TGG + chr7_3:4049227-4049246 None:intergenic 50.0%
GCTGCTTCAACTGTGTTTGC+AGG - chr7_3:4049258-4049277 Msa1090240:five_prime_UTR 50.0%
! AGCGCAGATCTTGAGGGTTT+TGG + chr7_3:4048501-4048520 None:intergenic 50.0%
GACGATTAGCGCAGATCTTG+AGG + chr7_3:4048508-4048527 None:intergenic 50.0%
CATGCTAGGGATTCTGCTGA+TGG - chr7_3:4048687-4048706 Msa1090240:CDS 50.0%
GTGTTGGAATCCGAGAGAGT+AGG - chr7_3:4048982-4049001 Msa1090240:CDS 50.0%
CCGAGAGAGTAGGGTGTATT+TGG - chr7_3:4048992-4049011 Msa1090240:CDS 50.0%
GTTGCACATGCCATCTTGTC+CGG - chr7_3:4049031-4049050 Msa1090240:intron 50.0%
GCAGTTCTGTTCGAGGAAGT+TGG - chr7_3:4049166-4049185 Msa1090240:CDS 50.0%
GCAACCGAATCACCATCTCA+TGG + chr7_3:4049227-4049246 None:intergenic 50.0%
GCTGCTTCAACTGTGTTTGC+AGG - chr7_3:4049258-4049277 Msa1090240:five_prime_UTR 50.0%
CGAGGAAGTTGGGGTCTAGT+TGG - chr7_3:4049177-4049196 Msa1090240:exon 55.0%
CGAGGAAGTTGGGGTCTAGT+TGG - chr7_3:4049177-4049196 Msa1090240:exon 55.0%
Chromosome Type Strat End Strand Name
chr7_3 gene 4048353 4049326 4048353 ID=Msa1090240;Name=Msa1090240
chr7_3 mRNA 4048353 4049326 4048353 ID=Msa1090240-mRNA-1;Parent=Msa1090240;Name=Msa1090240-mRNA-1;_AED=0.39;_eAED=0.39;_QI=135|0.33|0.25|0.75|1|0.75|4|0|122
chr7_3 exon 4048353 4048527 4048353 ID=Msa1090240-mRNA-1:exon:1556;Parent=Msa1090240-mRNA-1
chr7_3 exon 4048666 4048735 4048666 ID=Msa1090240-mRNA-1:exon:1555;Parent=Msa1090240-mRNA-1
chr7_3 exon 4048971 4049048 4048971 ID=Msa1090240-mRNA-1:exon:1554;Parent=Msa1090240-mRNA-1
chr7_3 exon 4049149 4049326 4049149 ID=Msa1090240-mRNA-1:exon:1553;Parent=Msa1090240-mRNA-1
chr7_3 five_prime_UTR 4049192 4049326 4049192 ID=Msa1090240-mRNA-1:five_prime_utr;Parent=Msa1090240-mRNA-1
chr7_3 CDS 4049149 4049191 4049149 ID=Msa1090240-mRNA-1:cds;Parent=Msa1090240-mRNA-1
chr7_3 CDS 4048971 4049048 4048971 ID=Msa1090240-mRNA-1:cds;Parent=Msa1090240-mRNA-1
chr7_3 CDS 4048666 4048735 4048666 ID=Msa1090240-mRNA-1:cds;Parent=Msa1090240-mRNA-1
chr7_3 CDS 4048353 4048527 4048353 ID=Msa1090240-mRNA-1:cds;Parent=Msa1090240-mRNA-1
Gene Sequence

>Msa1090240

ATGAGGCAATCCAAAACCCTCAAGATCTGCGCTAATCGTCTTATTATACCTATGATGAGTATGCAAGAGAATGTTGGAATTGAGAAATCGTGTGTTTGGCATGCTAGGGATTCTGCTGATGTGAATGAATTAATTGATGATAACTATCTTGTTAAAGTGGTGTTGGAATCCGAGAGAGTAGGGTGTATTTGGGTGTTTGTCTTTTGCAGTTCTGTTCGAGGAAGTTGGGGTCTAGTTGGCTATAGATCAATCAGTTTTTTCTGCCATGAGATGGTGATTCGGTTGCTAGCAGTTTGGGCTGCTTCAACTGTGTTTGCAGGGGTATATGTTGGTGTGCTTCCTGGTTTGATTTCTGCTGCAGTCCAT
Protein sequence

>Msa1090240

MRQSKTLKICANRLIIPMMSMQENVGIEKSCVWHARDSADVNELIDDNYLVKVVLESERVGCIWVFVFCSSVRGSWGLVGYRSISFFCHEMVIRLLAVWAASTVFAGVYVGVLPGLISAAVH