AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1461280


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1461280 MtrunA17_Chr1g0211051 100.000 94 0 0 1 94 215 308 9.09e-63 192
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1461280 AT2G16860.2 85.106 94 14 0 1 94 205 298 6.47e-54 169
Msa1461280 AT2G16860.1 85.106 94 14 0 1 94 205 298 6.47e-54 169

Find 37 sgRNAs with CRISPR-Local

Find 106 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTAATGCTGGGAAGTTTAAA+TGG 0.249290 tig0041415:-14604 Msa1461280:three_prime_UTR
GTTGATGAAGAAGTGTTTAT+AGG 0.253668 tig0041415:-15267 Msa1461280:intron
TACATCGACCTCAATGTTCT+TGG 0.295867 tig0041415:+15053 Msa1461280:intergenic
GAAGCATCACGGTAGAATTC+TGG 0.315653 tig0041415:+15000 Msa1461280:intergenic
GATTCAAGTCATTTGCATCT+AGG 0.359899 tig0041415:+14392 Msa1461280:intergenic
GACAGTATACCTTTCCATAC+TGG 0.367957 tig0041415:+14971 Msa1461280:intergenic
CGAGCGAGGAACTGCATTGC+CGG 0.368519 tig0041415:-14673 Msa1461280:CDS
TCTCATTGTTATTCTAATGC+TGG 0.378311 tig0041415:-14617 Msa1461280:three_prime_UTR
AAGAAGATTGAACGGGCCTT+TGG 0.407954 tig0041415:-14726 Msa1461280:CDS
TCTTGTTGAAATGCTCATTA+CGG 0.414024 tig0041415:+14745 Msa1461280:intergenic
AAATGGTGGATTGCGTTCTC+TGG 0.417439 tig0041415:-14587 Msa1461280:three_prime_UTR
CATGTGTTTGCATGAATACT+TGG 0.428828 tig0041415:-15309 Msa1461280:five_prime_UTR
CTCATTGTTATTCTAATGCT+GGG 0.435726 tig0041415:-14616 Msa1461280:three_prime_UTR
CAGGATGGTACAAGAACTTA+AGG 0.443877 tig0041415:-14844 Msa1461280:CDS
GATGCTTCAAGTCTCCAGTA+TGG 0.454556 tig0041415:-14985 Msa1461280:CDS
TTGAGTTTGAAGCATTTCCT+TGG 0.508471 tig0041415:-14417 Msa1461280:three_prime_UTR
TTTCAACAAGAAGATTGAAC+GGG 0.513427 tig0041415:-14733 Msa1461280:CDS
CCTCAGAGGATAAGATTGAC+AGG 0.514772 tig0041415:-14863 Msa1461280:CDS
TGGTACAAGAACTTAAGGAT+AGG 0.540824 tig0041415:-14839 Msa1461280:CDS
AGAAACGTAGGGCATTTAGC+AGG 0.569318 tig0041415:-14812 Msa1461280:CDS
GGTACAAGAACTTAAGGATA+GGG 0.574451 tig0041415:-14838 Msa1461280:CDS
CCTGTCAATCTTATCCTCTG+AGG 0.574499 tig0041415:+14863 Msa1461280:intergenic
CTCCAATGTGTATTTACCAA+AGG 0.590665 tig0041415:+14710 Msa1461280:intergenic
AGAGGATAAGATTGACAGGA+TGG 0.594250 tig0041415:-14859 Msa1461280:CDS
ACTGCAGAAGCAAATCAGTC+CGG 0.596042 tig0041415:+14654 Msa1461280:intergenic
AGGATAGGGACGAGAAACGT+AGG 0.596930 tig0041415:-14824 Msa1461280:CDS
ATTTCAACAAGAAGATTGAA+CGG 0.602140 tig0041415:-14734 Msa1461280:CDS
GGCCTTTGGTAAATACACAT+TGG 0.602906 tig0041415:-14712 Msa1461280:CDS
ATGCTGGGAAGTTTAAATGG+TGG 0.609597 tig0041415:-14601 Msa1461280:three_prime_UTR
TTCAAGTCTCCAGTATGGAA+AGG 0.627917 tig0041415:-14980 Msa1461280:intron
GGACTGATTTGCTTCTGCAG+TGG 0.634288 tig0041415:-14652 Msa1461280:exon
GGATAGGGACGAGAAACGTA+GGG 0.635157 tig0041415:-14823 Msa1461280:CDS
ACTGGAGACTTGAAGCATCA+CGG 0.643816 tig0041415:+14989 Msa1461280:intergenic
TCATTTGCATCTAGGTACCA+AGG 0.644622 tig0041415:+14400 Msa1461280:intergenic
GTATTCATGCAAACACATGT+AGG 0.659448 tig0041415:+15313 Msa1461280:intergenic
AAAGCGAACCAAGAACATTG+AGG 0.660498 tig0041415:-15061 Msa1461280:five_prime_UTR
TATGCACATATGGAGCATTG+TGG 0.763355 tig0041415:-14522 Msa1461280:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTACCAGTTTTTAATCAA+AGG - tig0041415:14548-14567 Msa1461280:three_prime_UTR 20.0%
!! CGATTCAAATAAAAATATAC+AGG - tig0041415:15288-15307 Msa1461280:five_prime_UTR 20.0%
!!! TTTTACCAGTTTTTAATCAA+AGG - tig0041415:14548-14567 Msa1461280:three_prime_UTR 20.0%
!! CGATTCAAATAAAAATATAC+AGG - tig0041415:15288-15307 Msa1461280:five_prime_UTR 20.0%
! GAATAACACCATGAAATATT+CGG - tig0041415:14410-14429 Msa1461280:three_prime_UTR 25.0%
! AATGTCCTTTGATTAAAAAC+TGG + tig0041415:14556-14575 Msa1461280:intergenic 25.0%
! AATTGTCTTTCCTTCATTAT+AGG - tig0041415:14757-14776 Msa1461280:CDS 25.0%
! ATTTCAACAAGAAGATTGAA+CGG - tig0041415:14918-14937 Msa1461280:intron 25.0%
!!! TATATTTTGCTATGCACATA+TGG - tig0041415:15120-15139 Msa1461280:intron 25.0%
! GAATAACACCATGAAATATT+CGG - tig0041415:14410-14429 Msa1461280:three_prime_UTR 25.0%
! AATGTCCTTTGATTAAAAAC+TGG + tig0041415:14556-14575 Msa1461280:intergenic 25.0%
! AATTGTCTTTCCTTCATTAT+AGG - tig0041415:14757-14776 Msa1461280:CDS 25.0%
! ATTTCAACAAGAAGATTGAA+CGG - tig0041415:14918-14937 Msa1461280:intron 25.0%
!!! TATATTTTGCTATGCACATA+TGG - tig0041415:15120-15139 Msa1461280:intron 25.0%
!! GTTGATGAAGAAGTGTTTAT+AGG - tig0041415:14385-14404 Msa1461280:three_prime_UTR 30.0%
TCTTGTTGAAATGCTCATTA+CGG + tig0041415:14910-14929 Msa1461280:intergenic 30.0%
TTTCAACAAGAAGATTGAAC+GGG - tig0041415:14919-14938 Msa1461280:intron 30.0%
ATTAAAAATAATCTCGAGCG+AGG - tig0041415:14965-14984 Msa1461280:intron 30.0%
! TCTCATTGTTATTCTAATGC+TGG - tig0041415:15035-15054 Msa1461280:exon 30.0%
! CTCATTGTTATTCTAATGCT+GGG - tig0041415:15036-15055 Msa1461280:exon 30.0%
!! GTTGATGAAGAAGTGTTTAT+AGG - tig0041415:14385-14404 Msa1461280:three_prime_UTR 30.0%
TCTTGTTGAAATGCTCATTA+CGG + tig0041415:14910-14929 Msa1461280:intergenic 30.0%
TTTCAACAAGAAGATTGAAC+GGG - tig0041415:14919-14938 Msa1461280:intron 30.0%
ATTAAAAATAATCTCGAGCG+AGG - tig0041415:14965-14984 Msa1461280:intron 30.0%
! TCTCATTGTTATTCTAATGC+TGG - tig0041415:15035-15054 Msa1461280:exon 30.0%
! CTCATTGTTATTCTAATGCT+GGG - tig0041415:15036-15055 Msa1461280:exon 30.0%
GTATTCATGCAAACACATGT+AGG + tig0041415:14342-14361 Msa0471570:intergenic 35.0%
CATGTGTTTGCATGAATACT+TGG - tig0041415:14343-14362 Msa1461280:three_prime_UTR 35.0%
GATCTAGACCGAATATTTCA+TGG + tig0041415:14421-14440 Msa1461280:intergenic 35.0%
! TGTGCCTTTAGAAGTTCTTA+CGG - tig0041415:14501-14520 Msa1461280:three_prime_UTR 35.0%
AGTTCCGTAAGAACTTCTAA+AGG + tig0041415:14508-14527 Msa1461280:intergenic 35.0%
TTTGTACTTCTGCACATCAA+TGG - tig0041415:14720-14739 Msa1461280:CDS 35.0%
TTGTACTTCTGCACATCAAT+GGG - tig0041415:14721-14740 Msa1461280:CDS 35.0%
!! CATCAATGGGTTATTGTATG+AGG - tig0041415:14734-14753 Msa1461280:CDS 35.0%
!!! GTTTTTGGTGCCTATAATGA+AGG + tig0041415:14770-14789 Msa1461280:intergenic 35.0%
!!! ATCTTATCCTCTGAGGTTTT+TGG + tig0041415:14785-14804 Msa1461280:intergenic 35.0%
TGGTACAAGAACTTAAGGAT+AGG - tig0041415:14813-14832 Msa1461280:CDS 35.0%
GGTACAAGAACTTAAGGATA+GGG - tig0041415:14814-14833 Msa1461280:CDS 35.0%
CTCCAATGTGTATTTACCAA+AGG + tig0041415:14945-14964 Msa1461280:intergenic 35.0%
CTAATGCTGGGAAGTTTAAA+TGG - tig0041415:15048-15067 Msa1461280:five_prime_UTR 35.0%
! TTGAGTTTGAAGCATTTCCT+TGG - tig0041415:15235-15254 Msa1461280:intron 35.0%
GATTCAAGTCATTTGCATCT+AGG + tig0041415:15263-15282 Msa1461280:intergenic 35.0%
GTATTCATGCAAACACATGT+AGG + tig0041415:14342-14361 Msa1461280:intergenic 35.0%
CATGTGTTTGCATGAATACT+TGG - tig0041415:14343-14362 Msa1461280:three_prime_UTR 35.0%
GATCTAGACCGAATATTTCA+TGG + tig0041415:14421-14440 Msa1461280:intergenic 35.0%
! TGTGCCTTTAGAAGTTCTTA+CGG - tig0041415:14501-14520 Msa1461280:three_prime_UTR 35.0%
AGTTCCGTAAGAACTTCTAA+AGG + tig0041415:14508-14527 Msa1461280:intergenic 35.0%
TTTGTACTTCTGCACATCAA+TGG - tig0041415:14720-14739 Msa1461280:CDS 35.0%
TTGTACTTCTGCACATCAAT+GGG - tig0041415:14721-14740 Msa1461280:CDS 35.0%
!! CATCAATGGGTTATTGTATG+AGG - tig0041415:14734-14753 Msa1461280:CDS 35.0%
!!! GTTTTTGGTGCCTATAATGA+AGG + tig0041415:14770-14789 Msa1461280:intergenic 35.0%
!!! ATCTTATCCTCTGAGGTTTT+TGG + tig0041415:14785-14804 Msa1461280:intergenic 35.0%
TGGTACAAGAACTTAAGGAT+AGG - tig0041415:14813-14832 Msa1461280:CDS 35.0%
GGTACAAGAACTTAAGGATA+GGG - tig0041415:14814-14833 Msa1461280:CDS 35.0%
CTCCAATGTGTATTTACCAA+AGG + tig0041415:14945-14964 Msa1461280:intergenic 35.0%
CTAATGCTGGGAAGTTTAAA+TGG - tig0041415:15048-15067 Msa1461280:five_prime_UTR 35.0%
! TTGAGTTTGAAGCATTTCCT+TGG - tig0041415:15235-15254 Msa1461280:intron 35.0%
GATTCAAGTCATTTGCATCT+AGG + tig0041415:15263-15282 Msa1461280:intergenic 35.0%
AAAGCGAACCAAGAACATTG+AGG - tig0041415:14591-14610 Msa1461280:three_prime_UTR 40.0%
TACATCGACCTCAATGTTCT+TGG + tig0041415:14602-14621 Msa1461280:intergenic 40.0%
TTCAAGTCTCCAGTATGGAA+AGG - tig0041415:14672-14691 Msa1461280:CDS 40.0%
GACAGTATACCTTTCCATAC+TGG + tig0041415:14684-14703 Msa1461280:intergenic 40.0%
AGAGGATAAGATTGACAGGA+TGG - tig0041415:14793-14812 Msa1461280:CDS 40.0%
CAGGATGGTACAAGAACTTA+AGG - tig0041415:14808-14827 Msa1461280:CDS 40.0%
GGCCTTTGGTAAATACACAT+TGG - tig0041415:14940-14959 Msa1461280:intron 40.0%
ATGCTGGGAAGTTTAAATGG+TGG - tig0041415:15051-15070 Msa1461280:five_prime_UTR 40.0%
!! TATGCACATATGGAGCATTG+TGG - tig0041415:15130-15149 Msa1461280:intron 40.0%
TCATTTGCATCTAGGTACCA+AGG + tig0041415:15255-15274 Msa1461280:intergenic 40.0%
AAAGCGAACCAAGAACATTG+AGG - tig0041415:14591-14610 Msa1461280:three_prime_UTR 40.0%
TACATCGACCTCAATGTTCT+TGG + tig0041415:14602-14621 Msa1461280:intergenic 40.0%
TTCAAGTCTCCAGTATGGAA+AGG - tig0041415:14672-14691 Msa1461280:CDS 40.0%
GACAGTATACCTTTCCATAC+TGG + tig0041415:14684-14703 Msa1461280:intergenic 40.0%
AGAGGATAAGATTGACAGGA+TGG - tig0041415:14793-14812 Msa1461280:CDS 40.0%
CAGGATGGTACAAGAACTTA+AGG - tig0041415:14808-14827 Msa1461280:CDS 40.0%
GGCCTTTGGTAAATACACAT+TGG - tig0041415:14940-14959 Msa1461280:intron 40.0%
ATGCTGGGAAGTTTAAATGG+TGG - tig0041415:15051-15070 Msa1461280:five_prime_UTR 40.0%
!! TATGCACATATGGAGCATTG+TGG - tig0041415:15130-15149 Msa1461280:intron 40.0%
TCATTTGCATCTAGGTACCA+AGG + tig0041415:15255-15274 Msa1461280:intergenic 40.0%
! GAAGCATCACGGTAGAATTC+TGG + tig0041415:14655-14674 Msa1461280:intergenic 45.0%
! ACTGGAGACTTGAAGCATCA+CGG + tig0041415:14666-14685 Msa1461280:intergenic 45.0%
GATGCTTCAAGTCTCCAGTA+TGG - tig0041415:14667-14686 Msa1461280:exon 45.0%
ATAGGCACCAAAAACCTCAG+AGG - tig0041415:14775-14794 Msa1461280:CDS 45.0%
CCTGTCAATCTTATCCTCTG+AGG + tig0041415:14792-14811 Msa1461280:intergenic 45.0%
CCTCAGAGGATAAGATTGAC+AGG - tig0041415:14789-14808 Msa1461280:CDS 45.0%
! AGAAACGTAGGGCATTTAGC+AGG - tig0041415:14840-14859 Msa1461280:CDS 45.0%
AAGAAGATTGAACGGGCCTT+TGG - tig0041415:14926-14945 Msa1461280:intron 45.0%
ACTGCAGAAGCAAATCAGTC+CGG + tig0041415:15001-15020 Msa1461280:intergenic 45.0%
!! AAATGGTGGATTGCGTTCTC+TGG - tig0041415:15065-15084 Msa1461280:five_prime_UTR 45.0%
! GAAGCATCACGGTAGAATTC+TGG + tig0041415:14655-14674 Msa1461280:intergenic 45.0%
! ACTGGAGACTTGAAGCATCA+CGG + tig0041415:14666-14685 Msa1461280:intergenic 45.0%
GATGCTTCAAGTCTCCAGTA+TGG - tig0041415:14667-14686 Msa1461280:exon 45.0%
ATAGGCACCAAAAACCTCAG+AGG - tig0041415:14775-14794 Msa1461280:CDS 45.0%
CCTGTCAATCTTATCCTCTG+AGG + tig0041415:14792-14811 Msa1461280:intergenic 45.0%
CCTCAGAGGATAAGATTGAC+AGG - tig0041415:14789-14808 Msa1461280:CDS 45.0%
! AGAAACGTAGGGCATTTAGC+AGG - tig0041415:14840-14859 Msa1461280:CDS 45.0%
AAGAAGATTGAACGGGCCTT+TGG - tig0041415:14926-14945 Msa1461280:intron 45.0%
ACTGCAGAAGCAAATCAGTC+CGG + tig0041415:15001-15020 Msa1461280:intergenic 45.0%
!! AAATGGTGGATTGCGTTCTC+TGG - tig0041415:15065-15084 Msa1461280:five_prime_UTR 45.0%
AGGATAGGGACGAGAAACGT+AGG - tig0041415:14828-14847 Msa1461280:CDS 50.0%
GGATAGGGACGAGAAACGTA+GGG - tig0041415:14829-14848 Msa1461280:CDS 50.0%
!! GGACTGATTTGCTTCTGCAG+TGG - tig0041415:15000-15019 Msa1461280:CDS 50.0%
AGGATAGGGACGAGAAACGT+AGG - tig0041415:14828-14847 Msa1461280:CDS 50.0%
GGATAGGGACGAGAAACGTA+GGG - tig0041415:14829-14848 Msa1461280:CDS 50.0%
!! GGACTGATTTGCTTCTGCAG+TGG - tig0041415:15000-15019 Msa1461280:CDS 50.0%
CGAGCGAGGAACTGCATTGC+CGG - tig0041415:14979-14998 Msa1461280:intron 60.0%
CGAGCGAGGAACTGCATTGC+CGG - tig0041415:14979-14998 Msa1461280:intron 60.0%
Chromosome Type Strat End Strand Name
tig0041415 gene 14331 15343 14331 ID=Msa1461280;Name=Msa1461280
tig0041415 mRNA 14331 15343 14331 ID=Msa1461280-mRNA-1;Parent=Msa1461280;Name=Msa1461280-mRNA-1;_AED=0.01;_eAED=0.01;_QI=156|1|1|1|0.5|0.66|3|337|94
tig0041415 exon 14331 14895 14331 ID=Msa1461280-mRNA-1:exon:23098;Parent=Msa1461280-mRNA-1
tig0041415 exon 14981 15117 14981 ID=Msa1461280-mRNA-1:exon:23097;Parent=Msa1461280-mRNA-1
tig0041415 exon 15268 15343 15268 ID=Msa1461280-mRNA-1:exon:23096;Parent=Msa1461280-mRNA-1
tig0041415 five_prime_UTR 15268 15343 15268 ID=Msa1461280-mRNA-1:five_prime_utr;Parent=Msa1461280-mRNA-1
tig0041415 five_prime_UTR 15038 15117 15038 ID=Msa1461280-mRNA-1:five_prime_utr;Parent=Msa1461280-mRNA-1
tig0041415 CDS 14981 15037 14981 ID=Msa1461280-mRNA-1:cds;Parent=Msa1461280-mRNA-1
tig0041415 CDS 14668 14895 14668 ID=Msa1461280-mRNA-1:cds;Parent=Msa1461280-mRNA-1
tig0041415 three_prime_UTR 14331 14667 14331 ID=Msa1461280-mRNA-1:three_prime_utr;Parent=Msa1461280-mRNA-1
Gene Sequence

>Msa1461280

ATGAAAGAAGCTGATCCAGAATTCTACCGTGATGCTTCAAGTCTCCAGTATGGAAAGGCACCAAAAACCTCAGAGGATAAGATTGACAGGATGGTACAAGAACTTAAGGATAGGGACGAGAAACGTAGGGCATTTAGCAGGAGAAGAACATTTCGTGAAGAGAAAGATGTTGACTCAATCAATGACCGTAATGAGCATTTCAACAAGAAGATTGAACGGGCCTTTGGTAAATACACATTGGAGATTAAAAATAATCTCGAGCGAGGAACTGCATTGCCGGACTGA

Protein sequence

>Msa1461280

MKEADPEFYRDASSLQYGKAPKTSEDKIDRMVQELKDRDEKRRAFSRRRTFREEKDVDSINDRNEHFNKKIERAFGKYTLEIKNNLERGTALPD*