AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1043050


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1043050 MtrunA17_Chr7g0240411 92.405 79 6 0 1 79 1 79 5.24e-49 149
Msa1043050 MtrunA17_Chr4g0008691 62.963 81 28 2 1 79 1 81 2.30e-32 107
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 38 sgRNAs with CRISPR-Local

Find 117 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTACCTTGGTTTGAAATTA+AGG 0.129246 7_2:-874414 None:intergenic
GAGTTCGATATTATGTTAAA+TGG 0.198013 7_2:-875224 None:intergenic
CACTTTGATTTACAAAATTA+TGG 0.210495 7_2:+875127 Msa1043050:three_prime_UTR
TTCTCTAAACTTTGATATAT+AGG 0.300426 7_2:-874707 None:intergenic
ATGAGAACATGAGGCTTGTT+TGG 0.314452 7_2:-874326 None:intergenic
ATGAATTGTTACACAATTCA+TGG 0.321299 7_2:+875157 Msa1043050:three_prime_UTR
CTAAAGAGTTTAGAAGGATA+AGG 0.353995 7_2:+874993 Msa1043050:three_prime_UTR
CTTGAACCTCTCTAACTTTG+AGG 0.354710 7_2:+874245 Msa1043050:five_prime_UTR
AGTTGACTAAAGAGTTTAGA+AGG 0.373568 7_2:+874987 Msa1043050:three_prime_UTR
GAGTTGGGAGATATATAAAA+AGG 0.385399 7_2:-874205 None:intergenic
TTTGTGTCTGCTAGTGCTAA+TGG 0.389664 7_2:+874759 Msa1043050:three_prime_UTR
GAGGTACTTGCACTAGTACT+TGG 0.403825 7_2:+874599 Msa1043050:CDS
CTTTAGTCAACTTTAGTTGA+AGG 0.419390 7_2:-874976 None:intergenic
TAAAGAGTTTAGAAGGATAA+GGG 0.425247 7_2:+874994 Msa1043050:three_prime_UTR
ATGAATTGTGTAACAATTCA+TGG 0.427262 7_2:-875155 None:intergenic
AAGGATAAGGGATGGATATC+CGG 0.440238 7_2:+875006 Msa1043050:three_prime_UTR
TTTGGTTTGAAACAAGTCAA+TGG 0.446404 7_2:+874826 Msa1043050:three_prime_UTR
TGCAAATGTTGTGATGGAAT+TGG 0.452852 7_2:+874577 Msa1043050:CDS
TTGGTTTGAAACAAGTCAAT+GGG 0.459688 7_2:+874827 Msa1043050:three_prime_UTR
TTAGAGAGGTTCAAGAGCTA+TGG 0.483018 7_2:-874237 None:intergenic
TTGTGTCTGCTAGTGCTAAT+GGG 0.495526 7_2:+874760 Msa1043050:three_prime_UTR
GCTATGGAGCACTGATGAGT+TGG 0.497002 7_2:-874221 None:intergenic
CTATGGAGCACTGATGAGTT+GGG 0.500776 7_2:-874220 None:intergenic
GTCCTTGCTTCTATAAGTGA+TGG 0.503145 7_2:-874386 None:intergenic
AGGATAGGAAACTTGTAGGA+TGG 0.515633 7_2:-874185 None:intergenic
GGATAGGAAACTTGTAGGAT+GGG 0.533450 7_2:-874184 None:intergenic
GTTGTTTGCAAATGTTGTGA+TGG 0.534057 7_2:+874571 Msa1043050:CDS
AATAACTAGTGTGATTTCCA+AGG 0.557652 7_2:-874652 None:intergenic
GAGTTTAGAAGGATAAGGGA+TGG 0.574430 7_2:+874998 Msa1043050:three_prime_UTR
CTTTCCTTAATTTCAAACCA+AGG 0.576150 7_2:+874410 Msa1043050:CDS
ATAGGAAACTTGTAGGATGG+GGG 0.578714 7_2:-874182 None:intergenic
AACCATCACTTATAGAAGCA+AGG 0.587548 7_2:+874384 Msa1043050:CDS
ATAACTTAAAGTGTTCACCT+TGG 0.595348 7_2:+874635 Msa1043050:CDS
ATGAAACCTCAAAGTTAGAG+AGG 0.596758 7_2:-874251 None:intergenic
AAATGTTGTGATGGAATTGG+AGG 0.597103 7_2:+874580 Msa1043050:CDS
ATTAGTAATATGAGAACATG+AGG 0.602881 7_2:-874335 None:intergenic
GATAGGAAACTTGTAGGATG+GGG 0.605112 7_2:-874183 None:intergenic
AACAAGTTGCAATAGACATG+TGG 0.663724 7_2:-874876 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTATTATAATTAATTACCT+TGG - chr7_2:874430-874449 None:intergenic 10.0%
!! ATTATTATAATTAATTACCT+TGG - chr7_2:874430-874449 None:intergenic 10.0%
!! AAATAAAAAATTAGATCTAG+TGG - chr7_2:874494-874513 None:intergenic 15.0%
!!! TTATTTTGTTATGTATTTTC+AGG + chr7_2:874520-874539 Msa1043050:intron 15.0%
!!! TATTTTGTTATGTATTTTCA+GGG + chr7_2:874521-874540 Msa1043050:intron 15.0%
!!! TGTGTAATTTTATTTTGTTT+TGG + chr7_2:875051-875070 Msa1043050:three_prime_UTR 15.0%
!!! GTGTAATTTTATTTTGTTTT+GGG + chr7_2:875052-875071 Msa1043050:three_prime_UTR 15.0%
!! AAATAAAAAATTAGATCTAG+TGG - chr7_2:874494-874513 None:intergenic 15.0%
!!! TTATTTTGTTATGTATTTTC+AGG + chr7_2:874520-874539 Msa1043050:intron 15.0%
!!! TATTTTGTTATGTATTTTCA+GGG + chr7_2:874521-874540 Msa1043050:intron 15.0%
!!! TGTGTAATTTTATTTTGTTT+TGG + chr7_2:875051-875070 Msa1043050:three_prime_UTR 15.0%
!!! GTGTAATTTTATTTTGTTTT+GGG + chr7_2:875052-875071 Msa1043050:three_prime_UTR 15.0%
!! ATATAAAAACATCAATCATG+TGG + chr7_2:874137-874156 Msa1043050:five_prime_UTR 20.0%
!!! AGTTATTTTTGTGATTTTTC+TGG + chr7_2:874668-874687 Msa1043050:exon 20.0%
!! TTCTCTAAACTTTGATATAT+AGG - chr7_2:874710-874729 None:intergenic 20.0%
!!! ATGATTTTTCATTGATGATA+AGG + chr7_2:874942-874961 Msa1043050:three_prime_UTR 20.0%
!!! TGATTTTTCATTGATGATAA+GGG + chr7_2:874943-874962 Msa1043050:three_prime_UTR 20.0%
!!! CACTTTGATTTACAAAATTA+TGG + chr7_2:875127-875146 Msa1043050:three_prime_UTR 20.0%
!!! ATGAAGCATATTTTAACTTT+TGG + chr7_2:875187-875206 Msa1043050:three_prime_UTR 20.0%
!!! TGAAGCATATTTTAACTTTT+GGG + chr7_2:875188-875207 Msa1043050:three_prime_UTR 20.0%
!! ATATAAAAACATCAATCATG+TGG + chr7_2:874137-874156 Msa1043050:five_prime_UTR 20.0%
!!! AGTTATTTTTGTGATTTTTC+TGG + chr7_2:874668-874687 Msa1043050:exon 20.0%
!! TTCTCTAAACTTTGATATAT+AGG - chr7_2:874710-874729 None:intergenic 20.0%
!!! ATGATTTTTCATTGATGATA+AGG + chr7_2:874942-874961 Msa1043050:three_prime_UTR 20.0%
!!! TGATTTTTCATTGATGATAA+GGG + chr7_2:874943-874962 Msa1043050:three_prime_UTR 20.0%
!!! CACTTTGATTTACAAAATTA+TGG + chr7_2:875127-875146 Msa1043050:three_prime_UTR 20.0%
!!! ATGAAGCATATTTTAACTTT+TGG + chr7_2:875187-875206 Msa1043050:three_prime_UTR 20.0%
!!! TGAAGCATATTTTAACTTTT+GGG + chr7_2:875188-875207 Msa1043050:three_prime_UTR 20.0%
! ATTAGTAATATGAGAACATG+AGG - chr7_2:874338-874357 None:intergenic 25.0%
!! ATTACCTTGGTTTGAAATTA+AGG - chr7_2:874417-874436 None:intergenic 25.0%
!!! TATATGTGTCCATAGTTTTT+TGG + chr7_2:874808-874827 Msa1043050:three_prime_UTR 25.0%
! TGTTTCAAACCAAAAAACTA+TGG - chr7_2:874820-874839 None:intergenic 25.0%
! TAAAGAGTTTAGAAGGATAA+GGG + chr7_2:874994-875013 Msa1043050:three_prime_UTR 25.0%
! ATGAATTGTGTAACAATTCA+TGG - chr7_2:875158-875177 None:intergenic 25.0%
! ATGAATTGTTACACAATTCA+TGG + chr7_2:875157-875176 Msa1043050:three_prime_UTR 25.0%
! GAGTTCGATATTATGTTAAA+TGG - chr7_2:875227-875246 None:intergenic 25.0%
! ATTAGTAATATGAGAACATG+AGG - chr7_2:874338-874357 None:intergenic 25.0%
!! ATTACCTTGGTTTGAAATTA+AGG - chr7_2:874417-874436 None:intergenic 25.0%
!!! TATATGTGTCCATAGTTTTT+TGG + chr7_2:874808-874827 Msa1043050:three_prime_UTR 25.0%
! TGTTTCAAACCAAAAAACTA+TGG - chr7_2:874820-874839 None:intergenic 25.0%
! TAAAGAGTTTAGAAGGATAA+GGG + chr7_2:874994-875013 Msa1043050:three_prime_UTR 25.0%
! ATGAATTGTGTAACAATTCA+TGG - chr7_2:875158-875177 None:intergenic 25.0%
! ATGAATTGTTACACAATTCA+TGG + chr7_2:875157-875176 Msa1043050:three_prime_UTR 25.0%
! GAGTTCGATATTATGTTAAA+TGG - chr7_2:875227-875246 None:intergenic 25.0%
AAAAAGGATAGGAAACTTGT+AGG - chr7_2:874192-874211 None:intergenic 30.0%
GGGAGATATATAAAAAGGAT+AGG - chr7_2:874203-874222 None:intergenic 30.0%
GAGTTGGGAGATATATAAAA+AGG - chr7_2:874208-874227 None:intergenic 30.0%
CTTTCCTTAATTTCAAACCA+AGG + chr7_2:874410-874429 Msa1043050:CDS 30.0%
! TCAAAGATTTTTGCAACACT+TGG + chr7_2:874547-874566 Msa1043050:CDS 30.0%
! ATAACTTAAAGTGTTCACCT+TGG + chr7_2:874635-874654 Msa1043050:CDS 30.0%
AATAACTAGTGTGATTTCCA+AGG - chr7_2:874655-874674 None:intergenic 30.0%
!! TTTGGTTTGAAACAAGTCAA+TGG + chr7_2:874826-874845 Msa1043050:three_prime_UTR 30.0%
! TTGGTTTGAAACAAGTCAAT+GGG + chr7_2:874827-874846 Msa1043050:three_prime_UTR 30.0%
CTTTAGTCAACTTTAGTTGA+AGG - chr7_2:874979-874998 None:intergenic 30.0%
AGTTGACTAAAGAGTTTAGA+AGG + chr7_2:874987-875006 Msa1043050:three_prime_UTR 30.0%
CTAAAGAGTTTAGAAGGATA+AGG + chr7_2:874993-875012 Msa1043050:three_prime_UTR 30.0%
AAAAAGGATAGGAAACTTGT+AGG - chr7_2:874192-874211 None:intergenic 30.0%
GGGAGATATATAAAAAGGAT+AGG - chr7_2:874203-874222 None:intergenic 30.0%
GAGTTGGGAGATATATAAAA+AGG - chr7_2:874208-874227 None:intergenic 30.0%
CTTTCCTTAATTTCAAACCA+AGG + chr7_2:874410-874429 Msa1043050:CDS 30.0%
! TCAAAGATTTTTGCAACACT+TGG + chr7_2:874547-874566 Msa1043050:CDS 30.0%
! ATAACTTAAAGTGTTCACCT+TGG + chr7_2:874635-874654 Msa1043050:CDS 30.0%
AATAACTAGTGTGATTTCCA+AGG - chr7_2:874655-874674 None:intergenic 30.0%
!! TTTGGTTTGAAACAAGTCAA+TGG + chr7_2:874826-874845 Msa1043050:three_prime_UTR 30.0%
! TTGGTTTGAAACAAGTCAAT+GGG + chr7_2:874827-874846 Msa1043050:three_prime_UTR 30.0%
CTTTAGTCAACTTTAGTTGA+AGG - chr7_2:874979-874998 None:intergenic 30.0%
AGTTGACTAAAGAGTTTAGA+AGG + chr7_2:874987-875006 Msa1043050:three_prime_UTR 30.0%
CTAAAGAGTTTAGAAGGATA+AGG + chr7_2:874993-875012 Msa1043050:three_prime_UTR 30.0%
ATGAAACCTCAAAGTTAGAG+AGG - chr7_2:874254-874273 None:intergenic 35.0%
AACCATCACTTATAGAAGCA+AGG + chr7_2:874384-874403 Msa1043050:CDS 35.0%
AATTAGATCTAGTGGAAGAG+AGG - chr7_2:874486-874505 None:intergenic 35.0%
GTTGTTTGCAAATGTTGTGA+TGG + chr7_2:874571-874590 Msa1043050:CDS 35.0%
! TGCAAATGTTGTGATGGAAT+TGG + chr7_2:874577-874596 Msa1043050:CDS 35.0%
! AAATGTTGTGATGGAATTGG+AGG + chr7_2:874580-874599 Msa1043050:CDS 35.0%
AACAAGTTGCAATAGACATG+TGG - chr7_2:874879-874898 None:intergenic 35.0%
! AGCATCTTTTGAGCTAAAAC+CGG - chr7_2:875028-875047 None:intergenic 35.0%
ATGAAACCTCAAAGTTAGAG+AGG - chr7_2:874254-874273 None:intergenic 35.0%
AACCATCACTTATAGAAGCA+AGG + chr7_2:874384-874403 Msa1043050:CDS 35.0%
AATTAGATCTAGTGGAAGAG+AGG - chr7_2:874486-874505 None:intergenic 35.0%
GTTGTTTGCAAATGTTGTGA+TGG + chr7_2:874571-874590 Msa1043050:CDS 35.0%
! TGCAAATGTTGTGATGGAAT+TGG + chr7_2:874577-874596 Msa1043050:CDS 35.0%
! AAATGTTGTGATGGAATTGG+AGG + chr7_2:874580-874599 Msa1043050:CDS 35.0%
AACAAGTTGCAATAGACATG+TGG - chr7_2:874879-874898 None:intergenic 35.0%
! AGCATCTTTTGAGCTAAAAC+CGG - chr7_2:875028-875047 None:intergenic 35.0%
ATAGGAAACTTGTAGGATGG+GGG - chr7_2:874185-874204 None:intergenic 40.0%
GATAGGAAACTTGTAGGATG+GGG - chr7_2:874186-874205 None:intergenic 40.0%
GGATAGGAAACTTGTAGGAT+GGG - chr7_2:874187-874206 None:intergenic 40.0%
AGGATAGGAAACTTGTAGGA+TGG - chr7_2:874188-874207 None:intergenic 40.0%
TTAGAGAGGTTCAAGAGCTA+TGG - chr7_2:874240-874259 None:intergenic 40.0%
CTTGAACCTCTCTAACTTTG+AGG + chr7_2:874245-874264 Msa1043050:five_prime_UTR 40.0%
! ATGAGAACATGAGGCTTGTT+TGG - chr7_2:874329-874348 None:intergenic 40.0%
GTCCTTGCTTCTATAAGTGA+TGG - chr7_2:874389-874408 None:intergenic 40.0%
TTTGTGTCTGCTAGTGCTAA+TGG + chr7_2:874759-874778 Msa1043050:three_prime_UTR 40.0%
TTGTGTCTGCTAGTGCTAAT+GGG + chr7_2:874760-874779 Msa1043050:three_prime_UTR 40.0%
GAGTTTAGAAGGATAAGGGA+TGG + chr7_2:874998-875017 Msa1043050:three_prime_UTR 40.0%
AAGGATAAGGGATGGATATC+CGG + chr7_2:875006-875025 Msa1043050:three_prime_UTR 40.0%
ATAGGAAACTTGTAGGATGG+GGG - chr7_2:874185-874204 None:intergenic 40.0%
GATAGGAAACTTGTAGGATG+GGG - chr7_2:874186-874205 None:intergenic 40.0%
GGATAGGAAACTTGTAGGAT+GGG - chr7_2:874187-874206 None:intergenic 40.0%
AGGATAGGAAACTTGTAGGA+TGG - chr7_2:874188-874207 None:intergenic 40.0%
TTAGAGAGGTTCAAGAGCTA+TGG - chr7_2:874240-874259 None:intergenic 40.0%
CTTGAACCTCTCTAACTTTG+AGG + chr7_2:874245-874264 Msa1043050:five_prime_UTR 40.0%
! ATGAGAACATGAGGCTTGTT+TGG - chr7_2:874329-874348 None:intergenic 40.0%
GTCCTTGCTTCTATAAGTGA+TGG - chr7_2:874389-874408 None:intergenic 40.0%
TTTGTGTCTGCTAGTGCTAA+TGG + chr7_2:874759-874778 Msa1043050:three_prime_UTR 40.0%
TTGTGTCTGCTAGTGCTAAT+GGG + chr7_2:874760-874779 Msa1043050:three_prime_UTR 40.0%
GAGTTTAGAAGGATAAGGGA+TGG + chr7_2:874998-875017 Msa1043050:three_prime_UTR 40.0%
AAGGATAAGGGATGGATATC+CGG + chr7_2:875006-875025 Msa1043050:three_prime_UTR 40.0%
!! CTATGGAGCACTGATGAGTT+GGG - chr7_2:874223-874242 None:intergenic 45.0%
! GAGGTACTTGCACTAGTACT+TGG + chr7_2:874599-874618 Msa1043050:CDS 45.0%
!! CTATGGAGCACTGATGAGTT+GGG - chr7_2:874223-874242 None:intergenic 45.0%
! GAGGTACTTGCACTAGTACT+TGG + chr7_2:874599-874618 Msa1043050:CDS 45.0%
!!! ATGTTTTTATATTATTAATT+AGG - chr7_2:874129-874148 None:intergenic 5.0%
!! GCTATGGAGCACTGATGAGT+TGG - chr7_2:874224-874243 None:intergenic 50.0%
!! GCTATGGAGCACTGATGAGT+TGG - chr7_2:874224-874243 None:intergenic 50.0%
GTAGGATGGGGGATGCTGCT+TGG - chr7_2:874174-874193 None:intergenic 60.0%
GTAGGATGGGGGATGCTGCT+TGG - chr7_2:874174-874193 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 874129 875278 874129 ID=Msa1043050;Name=Msa1043050
chr7_2 mRNA 874129 875278 874129 ID=Msa1043050-mRNA-1;Parent=Msa1043050;Name=Msa1043050-mRNA-1;_AED=0.04;_eAED=0.04;_QI=191|1|1|1|1|1|2|609|79
chr7_2 exon 874129 874431 874129 ID=Msa1043050-mRNA-1:exon:102;Parent=Msa1043050-mRNA-1
chr7_2 exon 874542 875278 874542 ID=Msa1043050-mRNA-1:exon:103;Parent=Msa1043050-mRNA-1
chr7_2 five_prime_UTR 874129 874319 874129 ID=Msa1043050-mRNA-1:five_prime_utr;Parent=Msa1043050-mRNA-1
chr7_2 CDS 874320 874431 874320 ID=Msa1043050-mRNA-1:cds;Parent=Msa1043050-mRNA-1
chr7_2 CDS 874542 874669 874542 ID=Msa1043050-mRNA-1:cds;Parent=Msa1043050-mRNA-1
chr7_2 three_prime_UTR 874670 875278 874670 ID=Msa1043050-mRNA-1:three_prime_utr;Parent=Msa1043050-mRNA-1
Gene Sequence

>Msa1043050

ATGAGTCCAAACAAGCCTCATGTTCTCATATTACTAATCATCATGCTTGTTTCAGTTTCTAATAAACCATCACTTATAGAAGCAAGGACACTTTCCTTAATTTCAAACCAAGGGTACTCAAAGATTTTTGCAACACTTGGAGTTGTTTGCAAATGTTGTGATGGAATTGGAGGTACTTGCACTAGTACTTGGACACAATCTTGTAATAACTTAAAGTGTTCACCTTGGAAATCACACTAG

Protein sequence

>Msa1043050

MSPNKPHVLILLIIMLVSVSNKPSLIEARTLSLISNQGYSKIFATLGVVCKCCDGIGGTCTSTWTQSCNNLKCSPWKSH*