AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1019130


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1019130 MtrunA17_Chr7g0249081 83.333 78 8 1 62 139 185 257 1.20e-40 136
Msa1019130 MtrunA17_Chr1g0203361 76.000 75 15 1 1 72 718 792 3.24e-19 83.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1019130 AT1G79790.4 46.512 86 41 1 50 135 68 148 1.10e-20 82.8
Msa1019130 AT1G79790.1 35.556 135 78 2 5 135 113 242 4.60e-20 83.2
Msa1019130 AT1G79790.2 46.512 86 41 1 50 135 187 267 1.81e-19 82.0

Find 22 sgRNAs with CRISPR-Local

Find 126 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATATAGTTATTGTCTTGAT+AGG 0.293532 7_1:+40306216 Msa1019130:intron
CTCATTGTGTTTCAAGAAAG+AGG 0.321623 7_1:+40305903 Msa1019130:CDS
CGCGAAGAACTGTCATTGTT+GGG 0.354663 7_1:+40306308 Msa1019130:CDS
TCCTCATAGAATTCAGTATC+CGG 0.447494 7_1:-40305929 None:intergenic
GCGCGAAGAACTGTCATTGT+TGG 0.454550 7_1:+40306307 Msa1019130:CDS
GTGGAGGCAGCAGCTGAAGT+TGG 0.459723 7_1:+40306248 Msa1019130:CDS
AGCAGCTGAAGTTGGGATCA+AGG 0.467596 7_1:+40306256 Msa1019130:CDS
TGGAGGCAGCAGCTGAAGTT+GGG 0.474813 7_1:+40306249 Msa1019130:CDS
AGAAGCAGAATTAAATGCTA+TGG 0.479810 7_1:+40305154 Msa1019130:CDS
GTCAAAATCAGAAATGCATA+AGG 0.483727 7_1:+40305259 Msa1019130:CDS
AGCTGCCTCATTGTCTCTTG+AGG 0.501894 7_1:-40305219 None:intergenic
TGTTTCAAGAAAGAGGAAAC+CGG 0.511148 7_1:+40305910 Msa1019130:CDS
TATATCTCAATTAGAAGAAG+AGG 0.523544 7_1:+40305121 Msa1019130:CDS
TCTATGAAAATACAATATGT+TGG 0.531043 7_1:-40305977 None:intergenic
AAGAGACAATGAGGCAGCTA+AGG 0.534926 7_1:+40305223 Msa1019130:CDS
GCAGCTGAAGTTGGGATCAA+GGG 0.568479 7_1:+40306257 Msa1019130:CDS
ACCGGATACTGAATTCTATG+AGG 0.572307 7_1:+40305928 Msa1019130:CDS
CTCAAGAATAACAAAGGACG+AGG 0.579104 7_1:+40305185 Msa1019130:CDS
GCGAAGAACTGTCATTGTTG+GGG 0.610758 7_1:+40306309 Msa1019130:CDS
AAGAAGCTCAAGAATAACAA+AGG 0.616117 7_1:+40305179 Msa1019130:CDS
TATGACCTCAAGAGACAATG+AGG 0.680939 7_1:+40305214 Msa1019130:CDS
AATTCTATGAGGAAGTTGTG+AGG 0.684361 7_1:+40305939 Msa1019130:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAAATTATAAGTGATATCA+TGG - chr7_1:40306052-40306071 None:intergenic 15.0%
!! ATAAATTATAAGTGATATCA+TGG - chr7_1:40306052-40306071 None:intergenic 15.0%
!! TTGATATCTGATAATAAGTA+TGG - chr7_1:40305301-40305320 None:intergenic 20.0%
!!! CTCAAAGTTATTTTTCTTTA+AGG - chr7_1:40305540-40305559 None:intergenic 20.0%
!! TGATATTATCTACATTCTAA+TGG + chr7_1:40305798-40305817 Msa1019130:intron 20.0%
!! CAAAAAAACTTATCATTTGA+GGG + chr7_1:40305823-40305842 Msa1019130:intron 20.0%
!! GAATGTATCTACAATATATA+AGG - chr7_1:40305884-40305903 None:intergenic 20.0%
!! TCTATGAAAATACAATATGT+TGG - chr7_1:40305980-40305999 None:intergenic 20.0%
!! CTAATCAATTTATTTGGATT+TGG + chr7_1:40306142-40306161 Msa1019130:intron 20.0%
!! TATATAGTTATTGTCTTGAT+AGG + chr7_1:40306216-40306235 Msa1019130:intron 20.0%
!! TTGATATCTGATAATAAGTA+TGG - chr7_1:40305301-40305320 None:intergenic 20.0%
!!! CTCAAAGTTATTTTTCTTTA+AGG - chr7_1:40305540-40305559 None:intergenic 20.0%
!! TGATATTATCTACATTCTAA+TGG + chr7_1:40305798-40305817 Msa1019130:intron 20.0%
!! CAAAAAAACTTATCATTTGA+GGG + chr7_1:40305823-40305842 Msa1019130:intron 20.0%
!! GAATGTATCTACAATATATA+AGG - chr7_1:40305884-40305903 None:intergenic 20.0%
!! TCTATGAAAATACAATATGT+TGG - chr7_1:40305980-40305999 None:intergenic 20.0%
!! CTAATCAATTTATTTGGATT+TGG + chr7_1:40306142-40306161 Msa1019130:intron 20.0%
!! TATATAGTTATTGTCTTGAT+AGG + chr7_1:40306216-40306235 Msa1019130:intron 20.0%
! TATATCTCAATTAGAAGAAG+AGG + chr7_1:40305121-40305140 Msa1019130:CDS 25.0%
! GAACATACTTATTGCATATT+AGG + chr7_1:40305321-40305340 Msa1019130:intron 25.0%
! ACATTGATGAGTTTATTATG+TGG + chr7_1:40305364-40305383 Msa1019130:intron 25.0%
! TTAAAACTTGTATGAGACAT+GGG + chr7_1:40305477-40305496 Msa1019130:intron 25.0%
!! CTTTTACTAACTATCCTATA+TGG + chr7_1:40305567-40305586 Msa1019130:intron 25.0%
!!! CCTCAAATGATAAGTTTTTT+TGG - chr7_1:40305825-40305844 None:intergenic 25.0%
! CCAAAAAAACTTATCATTTG+AGG + chr7_1:40305822-40305841 Msa1019130:intron 25.0%
!! ATTGTATTTTCATAGATGAC+AGG + chr7_1:40305984-40306003 Msa1019130:CDS 25.0%
! AAATTTGTATGCAATACTGA+AGG + chr7_1:40306088-40306107 Msa1019130:intron 25.0%
! TCTCTGCTAATCAATTTATT+TGG + chr7_1:40306136-40306155 Msa1019130:intron 25.0%
! TATATCTCAATTAGAAGAAG+AGG + chr7_1:40305121-40305140 Msa1019130:CDS 25.0%
! GAACATACTTATTGCATATT+AGG + chr7_1:40305321-40305340 Msa1019130:intron 25.0%
! ACATTGATGAGTTTATTATG+TGG + chr7_1:40305364-40305383 Msa1019130:intron 25.0%
! TTAAAACTTGTATGAGACAT+GGG + chr7_1:40305477-40305496 Msa1019130:intron 25.0%
!! CTTTTACTAACTATCCTATA+TGG + chr7_1:40305567-40305586 Msa1019130:intron 25.0%
!!! CCTCAAATGATAAGTTTTTT+TGG - chr7_1:40305825-40305844 None:intergenic 25.0%
! CCAAAAAAACTTATCATTTG+AGG + chr7_1:40305822-40305841 Msa1019130:intron 25.0%
!! ATTGTATTTTCATAGATGAC+AGG + chr7_1:40305984-40306003 Msa1019130:CDS 25.0%
! AAATTTGTATGCAATACTGA+AGG + chr7_1:40306088-40306107 Msa1019130:intron 25.0%
! TCTCTGCTAATCAATTTATT+TGG + chr7_1:40306136-40306155 Msa1019130:intron 25.0%
AGAAGCAGAATTAAATGCTA+TGG + chr7_1:40305154-40305173 Msa1019130:CDS 30.0%
AAGAAGCTCAAGAATAACAA+AGG + chr7_1:40305179-40305198 Msa1019130:CDS 30.0%
GTCAAAATCAGAAATGCATA+AGG + chr7_1:40305259-40305278 Msa1019130:CDS 30.0%
TACTTATTGCATATTAGGAC+AGG + chr7_1:40305326-40305345 Msa1019130:intron 30.0%
ACATATGATCTTTAACTGTC+AGG + chr7_1:40305411-40305430 Msa1019130:intron 30.0%
! TGTTCTTCTTTTTCTTTGAC+AGG + chr7_1:40305452-40305471 Msa1019130:intron 30.0%
! CATGTCTCATACAAGTTTTA+AGG - chr7_1:40305478-40305497 None:intergenic 30.0%
CTTAAAACTTGTATGAGACA+TGG + chr7_1:40305476-40305495 Msa1019130:intron 30.0%
TATCCTATATGGTAAGACAA+TGG + chr7_1:40305578-40305597 Msa1019130:intron 30.0%
AATCCATTGTCTTACCATAT+AGG - chr7_1:40305584-40305603 None:intergenic 30.0%
TTGAAATTGTAAGTACCAGT+TGG + chr7_1:40305657-40305676 Msa1019130:intron 30.0%
AGAAGCAGAATTAAATGCTA+TGG + chr7_1:40305154-40305173 Msa1019130:CDS 30.0%
AAGAAGCTCAAGAATAACAA+AGG + chr7_1:40305179-40305198 Msa1019130:CDS 30.0%
GTCAAAATCAGAAATGCATA+AGG + chr7_1:40305259-40305278 Msa1019130:CDS 30.0%
TACTTATTGCATATTAGGAC+AGG + chr7_1:40305326-40305345 Msa1019130:intron 30.0%
ACATATGATCTTTAACTGTC+AGG + chr7_1:40305411-40305430 Msa1019130:intron 30.0%
! TGTTCTTCTTTTTCTTTGAC+AGG + chr7_1:40305452-40305471 Msa1019130:intron 30.0%
! CATGTCTCATACAAGTTTTA+AGG - chr7_1:40305478-40305497 None:intergenic 30.0%
CTTAAAACTTGTATGAGACA+TGG + chr7_1:40305476-40305495 Msa1019130:intron 30.0%
TATCCTATATGGTAAGACAA+TGG + chr7_1:40305578-40305597 Msa1019130:intron 30.0%
AATCCATTGTCTTACCATAT+AGG - chr7_1:40305584-40305603 None:intergenic 30.0%
TTGAAATTGTAAGTACCAGT+TGG + chr7_1:40305657-40305676 Msa1019130:intron 30.0%
AATGCATAAGGTAATTGCTC+AGG + chr7_1:40305271-40305290 Msa1019130:intron 35.0%
GCATATTAGGACAGGTTAAA+TGG + chr7_1:40305334-40305353 Msa1019130:intron 35.0%
CATGGGTATTCATACATAGA+AGG + chr7_1:40305494-40305513 Msa1019130:intron 35.0%
CAAAAAGATGATCGACACAA+AGG - chr7_1:40305770-40305789 None:intergenic 35.0%
!! TGTGTCGATCATCTTTTTGT+TGG + chr7_1:40305771-40305790 Msa1019130:intron 35.0%
CTCATTGTGTTTCAAGAAAG+AGG + chr7_1:40305903-40305922 Msa1019130:CDS 35.0%
TGTTTCAAGAAAGAGGAAAC+CGG + chr7_1:40305910-40305929 Msa1019130:CDS 35.0%
TCCTCATAGAATTCAGTATC+CGG - chr7_1:40305932-40305951 None:intergenic 35.0%
AATTCTATGAGGAAGTTGTG+AGG + chr7_1:40305939-40305958 Msa1019130:CDS 35.0%
!! GCAATACTGAAGGAGTATTA+AGG + chr7_1:40306098-40306117 Msa1019130:intron 35.0%
!! ATACTGAAGGAGTATTAAGG+AGG + chr7_1:40306101-40306120 Msa1019130:intron 35.0%
!! AAGGAGTATTAAGGAGGTTT+CGG + chr7_1:40306107-40306126 Msa1019130:intron 35.0%
CTACTTCAACTTCAACTGTT+TGG - chr7_1:40306174-40306193 None:intergenic 35.0%
TCTTGATAGGCCAAAAAATG+TGG + chr7_1:40306229-40306248 Msa1019130:CDS 35.0%
AATGCATAAGGTAATTGCTC+AGG + chr7_1:40305271-40305290 Msa1019130:intron 35.0%
GCATATTAGGACAGGTTAAA+TGG + chr7_1:40305334-40305353 Msa1019130:intron 35.0%
CATGGGTATTCATACATAGA+AGG + chr7_1:40305494-40305513 Msa1019130:intron 35.0%
CAAAAAGATGATCGACACAA+AGG - chr7_1:40305770-40305789 None:intergenic 35.0%
!! TGTGTCGATCATCTTTTTGT+TGG + chr7_1:40305771-40305790 Msa1019130:intron 35.0%
CTCATTGTGTTTCAAGAAAG+AGG + chr7_1:40305903-40305922 Msa1019130:CDS 35.0%
TGTTTCAAGAAAGAGGAAAC+CGG + chr7_1:40305910-40305929 Msa1019130:CDS 35.0%
TCCTCATAGAATTCAGTATC+CGG - chr7_1:40305932-40305951 None:intergenic 35.0%
AATTCTATGAGGAAGTTGTG+AGG + chr7_1:40305939-40305958 Msa1019130:CDS 35.0%
!! GCAATACTGAAGGAGTATTA+AGG + chr7_1:40306098-40306117 Msa1019130:intron 35.0%
!! ATACTGAAGGAGTATTAAGG+AGG + chr7_1:40306101-40306120 Msa1019130:intron 35.0%
!! AAGGAGTATTAAGGAGGTTT+CGG + chr7_1:40306107-40306126 Msa1019130:intron 35.0%
CTACTTCAACTTCAACTGTT+TGG - chr7_1:40306174-40306193 None:intergenic 35.0%
TCTTGATAGGCCAAAAAATG+TGG + chr7_1:40306229-40306248 Msa1019130:CDS 35.0%
CTCAAGAATAACAAAGGACG+AGG + chr7_1:40305185-40305204 Msa1019130:CDS 40.0%
TATGACCTCAAGAGACAATG+AGG + chr7_1:40305214-40305233 Msa1019130:CDS 40.0%
ACCGGATACTGAATTCTATG+AGG + chr7_1:40305928-40305947 Msa1019130:CDS 40.0%
!! AGGAGTATTAAGGAGGTTTC+GGG + chr7_1:40306108-40306127 Msa1019130:intron 40.0%
TGATAGGCCAAAAAATGTGG+AGG + chr7_1:40306232-40306251 Msa1019130:CDS 40.0%
CTCAAGAATAACAAAGGACG+AGG + chr7_1:40305185-40305204 Msa1019130:CDS 40.0%
TATGACCTCAAGAGACAATG+AGG + chr7_1:40305214-40305233 Msa1019130:CDS 40.0%
ACCGGATACTGAATTCTATG+AGG + chr7_1:40305928-40305947 Msa1019130:CDS 40.0%
!! AGGAGTATTAAGGAGGTTTC+GGG + chr7_1:40306108-40306127 Msa1019130:intron 40.0%
TGATAGGCCAAAAAATGTGG+AGG + chr7_1:40306232-40306251 Msa1019130:CDS 40.0%
AAGAGACAATGAGGCAGCTA+AGG + chr7_1:40305223-40305242 Msa1019130:CDS 45.0%
TTGTAAGTACCAGTTGGTCG+AGG + chr7_1:40305663-40305682 Msa1019130:intron 45.0%
!! TTAACTTGTCCTCGACCAAC+TGG - chr7_1:40305675-40305694 None:intergenic 45.0%
!! ACGTTTTGTTCGTGTGCACT+TGG + chr7_1:40305718-40305737 Msa1019130:intron 45.0%
CGCGAAGAACTGTCATTGTT+GGG + chr7_1:40306308-40306327 Msa1019130:CDS 45.0%
GCGAAGAACTGTCATTGTTG+GGG + chr7_1:40306309-40306328 Msa1019130:CDS 45.0%
AAGAGACAATGAGGCAGCTA+AGG + chr7_1:40305223-40305242 Msa1019130:CDS 45.0%
TTGTAAGTACCAGTTGGTCG+AGG + chr7_1:40305663-40305682 Msa1019130:intron 45.0%
!! TTAACTTGTCCTCGACCAAC+TGG - chr7_1:40305675-40305694 None:intergenic 45.0%
!! ACGTTTTGTTCGTGTGCACT+TGG + chr7_1:40305718-40305737 Msa1019130:intron 45.0%
CGCGAAGAACTGTCATTGTT+GGG + chr7_1:40306308-40306327 Msa1019130:CDS 45.0%
GCGAAGAACTGTCATTGTTG+GGG + chr7_1:40306309-40306328 Msa1019130:CDS 45.0%
AGCTGCCTCATTGTCTCTTG+AGG - chr7_1:40305222-40305241 None:intergenic 50.0%
! ACACAAAGGCGCAGAGAGAA+AGG - chr7_1:40305756-40305775 None:intergenic 50.0%
!!! GCTGCTGCCTCCACATTTTT+TGG - chr7_1:40306242-40306261 None:intergenic 50.0%
AGCAGCTGAAGTTGGGATCA+AGG + chr7_1:40306256-40306275 Msa1019130:CDS 50.0%
GCAGCTGAAGTTGGGATCAA+GGG + chr7_1:40306257-40306276 Msa1019130:CDS 50.0%
GCGCGAAGAACTGTCATTGT+TGG + chr7_1:40306307-40306326 Msa1019130:CDS 50.0%
AGCTGCCTCATTGTCTCTTG+AGG - chr7_1:40305222-40305241 None:intergenic 50.0%
! ACACAAAGGCGCAGAGAGAA+AGG - chr7_1:40305756-40305775 None:intergenic 50.0%
!!! GCTGCTGCCTCCACATTTTT+TGG - chr7_1:40306242-40306261 None:intergenic 50.0%
AGCAGCTGAAGTTGGGATCA+AGG + chr7_1:40306256-40306275 Msa1019130:CDS 50.0%
GCAGCTGAAGTTGGGATCAA+GGG + chr7_1:40306257-40306276 Msa1019130:CDS 50.0%
GCGCGAAGAACTGTCATTGT+TGG + chr7_1:40306307-40306326 Msa1019130:CDS 50.0%
TGGAGGCAGCAGCTGAAGTT+GGG + chr7_1:40306249-40306268 Msa1019130:CDS 55.0%
TGGAGGCAGCAGCTGAAGTT+GGG + chr7_1:40306249-40306268 Msa1019130:CDS 55.0%
GTGGAGGCAGCAGCTGAAGT+TGG + chr7_1:40306248-40306267 Msa1019130:CDS 60.0%
GTGGAGGCAGCAGCTGAAGT+TGG + chr7_1:40306248-40306267 Msa1019130:CDS 60.0%
Chromosome Type Strat End Strand Name
chr7_1 gene 40305110 40306385 40305110 ID=Msa1019130;Name=Msa1019130
chr7_1 mRNA 40305110 40306385 40305110 ID=Msa1019130-mRNA-1;Parent=Msa1019130;Name=Msa1019130-mRNA-1;_AED=0.47;_eAED=0.47;_QI=0|0|0|0.66|1|1|3|0|147
chr7_1 exon 40305110 40305280 40305110 ID=Msa1019130-mRNA-1:exon:7826;Parent=Msa1019130-mRNA-1
chr7_1 exon 40305896 40306005 40305896 ID=Msa1019130-mRNA-1:exon:7827;Parent=Msa1019130-mRNA-1
chr7_1 exon 40306223 40306385 40306223 ID=Msa1019130-mRNA-1:exon:7828;Parent=Msa1019130-mRNA-1
chr7_1 CDS 40305110 40305280 40305110 ID=Msa1019130-mRNA-1:cds;Parent=Msa1019130-mRNA-1
chr7_1 CDS 40305896 40306005 40305896 ID=Msa1019130-mRNA-1:cds;Parent=Msa1019130-mRNA-1
chr7_1 CDS 40306223 40306385 40306223 ID=Msa1019130-mRNA-1:cds;Parent=Msa1019130-mRNA-1
Gene Sequence

>Msa1019130

ATGAAGAAACATATATCTCAATTAGAAGAAGAGGTCAAGAAGAAAGAAGCAGAATTAAATGCTATGGAAAAGAAGCTCAAGAATAACAAAGGACGAGGTGCAGCTATGACCTCAAGAGACAATGAGGCAGCTAAGGCAAATGCGAAGAAGTCAAAATCAGAAATGCATAAGATACATTCTCATTGTGTTTCAAGAAAGAGGAAACCGGATACTGAATTCTATGAGGAAGTTGTGAGGCATCTTGAAGTTGATCCAACATATTGTATTTTCATAGATGACAGTTATTGTCTTGATAGGCCAAAAAATGTGGAGGCAGCAGCTGAAGTTGGGATCAAGGGTGTACATTTTAAGAATGTCGATTTAATGCGCGAAGAACTGTCATTGTTGGGGATTGACATTTCAACAGATGAAGATCAACAGCTTATTTTTTTTATATTTCTCTAA

Protein sequence

>Msa1019130

MKKHISQLEEEVKKKEAELNAMEKKLKNNKGRGAAMTSRDNEAAKANAKKSKSEMHKIHSHCVSRKRKPDTEFYEEVVRHLEVDPTYCIFIDDSYCLDRPKNVEAAAEVGIKGVHFKNVDLMREELSLLGIDISTDEDQQLIFFIFL*