AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0823790

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0823790 MtrunA17_Chr5g0444551 96.667 120 4 0 1 120 29 148 4.01e-83 239
Msa0823790 MtrunA17_Chr5g0444571 96.970 66 2 0 1 66 29 94 4.99e-41 131
Msa0823790 MtrunA17_Chr4g0024941 50.459 109 54 0 5 113 33 141 1.07e-36 124
Msa0823790 MtrunA17_Chr2g0288831 51.304 115 55 1 1 114 29 143 5.27e-35 120
Msa0823790 MtrunA17_Chr7g0235621 42.574 101 58 0 2 102 31 131 6.67e-26 96.7
Msa0823790 MtrunA17_Chr2g0322421 50.515 97 47 1 5 100 33 129 1.36e-23 90.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0823790 AT5G42570.1 53.097 113 53 0 1 113 29 141 5.85e-37 125
Msa0823790 AT1G11905.1 47.788 113 59 0 1 113 29 141 2.98e-32 113
Msa0823790 AT3G20450.1 46.535 101 53 1 1 100 33 133 2.60e-27 98.2
Msa0823790 AT5G48660.1 43.434 99 56 0 1 99 30 128 1.71e-24 93.2
Msa0823790 AT3G07190.1 46.392 97 52 0 1 97 30 126 7.91e-24 91.7
Msa0823790 AT1G11905.2 41.284 109 63 1 5 113 33 140 3.93e-22 87.0
Msa0823790 AT5G48660.2 48.077 52 27 0 48 99 1 52 1.06e-11 58.5

Find 32 sgRNAs with CRISPR-Local

Find 103 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAACATCCATTGAACGTTTA+TGG 0.094726 5_3:+62620003 None:intergenic
ACCACTGTATTTGTTGTATT+TGG 0.123258 5_3:-62620053 Msa0823790:CDS
CAATCCAATACGAAAATTAA+TGG 0.192639 5_3:-62620135 Msa0823790:exon
TCCTCTATCTCTCTTCTCTT+TGG 0.214919 5_3:+62619402 None:intergenic
ACAGGTTTCTCTCTATTCTT+TGG 0.261214 5_3:-62619522 Msa0823790:intron
TTCTCGATTTGGGAGTTTCT+TGG 0.274478 5_3:+62619251 None:intergenic
TTGATATGCAATTCTCGATT+TGG 0.291370 5_3:+62619240 None:intergenic
TCTCTTAGAAGCATCTCTTA+TGG 0.322946 5_3:-62619940 Msa0823790:CDS
AGAGGAAACTGAGAAGAAAA+AGG 0.332303 5_3:-62619385 Msa0823790:CDS
TACAAAATAAGAGTTTGATT+TGG 0.335189 5_3:-62620281 Msa0823790:five_prime_UTR
TGATATGCAATTCTCGATTT+GGG 0.354851 5_3:+62619241 None:intergenic
CTCTTAGAAGCATCTCTTAT+GGG 0.365951 5_3:-62619939 Msa0823790:intron
GTACACATACAGACATGTTT+AGG 0.407202 5_3:+62619324 None:intergenic
TCTATCTCTCTTCTCTTTGG+AGG 0.415834 5_3:+62619405 None:intergenic
TCCAACAGAGGAGGTTCTAA+TGG 0.420935 5_3:-62619970 Msa0823790:CDS
AAAATAAGAGTTTGATTTGG+AGG 0.430028 5_3:-62620278 Msa0823790:five_prime_UTR
CAAAATCCATAAACGTTCAA+TGG 0.441548 5_3:-62620009 Msa0823790:CDS
TCCAAAGAGAAGAGAGATAG+AGG 0.454256 5_3:-62619403 Msa0823790:CDS
GACCCCTTCCACGCTTCAAA+AGG 0.463134 5_3:+62620099 None:intergenic
GCCATTAGAACCTCCTCTGT+TGG 0.483298 5_3:+62619969 None:intergenic
TACTTGAATGTTGGTTTCGA+TGG 0.490667 5_3:+62620233 None:intergenic
CATAAACGTTCAATGGATGT+TGG 0.531550 5_3:-62620002 Msa0823790:CDS
TTGTAGAACTACTTGAATGT+TGG 0.532246 5_3:+62620224 None:intergenic
TCTTTGGATTGATGATCGAT+AGG 0.543666 5_3:-62619506 Msa0823790:CDS
ACGTTCAATGGATGTTGGCA+TGG 0.548399 5_3:-62619997 Msa0823790:CDS
AATACGAAAATTAATGGTGA+AGG 0.560690 5_3:-62620129 Msa0823790:exon
TTTGAGTATCGTATATATGG+TGG 0.571975 5_3:+62620028 None:intergenic
TTAAAGAGATCACTTCATTG+AGG 0.591642 5_3:-62619470 Msa0823790:CDS
CACTTCATTGAGGAAGAATG+TGG 0.608657 5_3:-62619460 Msa0823790:CDS
CATGGTTAATCCAACAGAGG+AGG 0.638279 5_3:-62619979 Msa0823790:CDS
GCCAAATACAACAAATACAG+TGG 0.645246 5_3:+62620052 None:intergenic
TGGCATGGTTAATCCAACAG+AGG 0.731698 5_3:-62619982 Msa0823790:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAAATATTATATTATCTAC+TGG - chr5_3:62620285-62620304 Msa0823790:five_prime_UTR 10.0%
!!! TAATTTAGATTGTTTTTCAA+AGG - chr5_3:62619620-62619639 Msa0823790:intron 15.0%
!!! TAAAAAAACGTTTGATAATA+TGG + chr5_3:62620216-62620235 None:intergenic 15.0%
!!! TAATTTAGATTGTTTTTCAA+AGG - chr5_3:62619620-62619639 Msa0823790:intron 15.0%
!!! TAAAAAAACGTTTGATAATA+TGG + chr5_3:62620216-62620235 None:intergenic 15.0%
!! TACAAAATAAGAGTTTGATT+TGG - chr5_3:62619139-62619158 Msa0823790:three_prime_UTR 20.0%
!!! GCTATTGTTTTTATGATTAA+TGG + chr5_3:62619346-62619365 None:intergenic 20.0%
!!! CTAGTATTGAAAGAAAAATA+AGG + chr5_3:62619527-62619546 None:intergenic 20.0%
!! ATTAAAACTAAGACATCAAA+TGG - chr5_3:62619774-62619793 Msa0823790:intron 20.0%
!! TTTCCATATCCTATAAAATA+TGG - chr5_3:62619866-62619885 Msa0823790:intron 20.0%
!! TTCCATATCCTATAAAATAT+GGG - chr5_3:62619867-62619886 Msa0823790:intron 20.0%
!! GAAGAAAAAGGATAATTAAA+TGG - chr5_3:62620047-62620066 Msa0823790:CDS 20.0%
!! TACAAAATAAGAGTTTGATT+TGG - chr5_3:62619139-62619158 Msa0823790:three_prime_UTR 20.0%
!!! GCTATTGTTTTTATGATTAA+TGG + chr5_3:62619346-62619365 None:intergenic 20.0%
!!! CTAGTATTGAAAGAAAAATA+AGG + chr5_3:62619527-62619546 None:intergenic 20.0%
!! ATTAAAACTAAGACATCAAA+TGG - chr5_3:62619774-62619793 Msa0823790:intron 20.0%
!! TTTCCATATCCTATAAAATA+TGG - chr5_3:62619866-62619885 Msa0823790:intron 20.0%
!! TTCCATATCCTATAAAATAT+GGG - chr5_3:62619867-62619886 Msa0823790:intron 20.0%
!! GAAGAAAAAGGATAATTAAA+TGG - chr5_3:62620047-62620066 Msa0823790:CDS 20.0%
!!! AAAATAAGAGTTTGATTTGG+AGG - chr5_3:62619142-62619161 Msa0823790:three_prime_UTR 25.0%
! CAATCCAATACGAAAATTAA+TGG - chr5_3:62619285-62619304 Msa0823790:three_prime_UTR 25.0%
!! TTCACCATTAATTTTCGTAT+TGG + chr5_3:62619292-62619311 None:intergenic 25.0%
! AATACGAAAATTAATGGTGA+AGG - chr5_3:62619291-62619310 Msa0823790:three_prime_UTR 25.0%
!!! GATTTTGAGTATCGTATATA+TGG + chr5_3:62619398-62619417 None:intergenic 25.0%
! ACATAAAGATGCATTTATCA+TGG - chr5_3:62619567-62619586 Msa0823790:intron 25.0%
!!! TTGCATGAATATGTCATTTT+AGG + chr5_3:62619745-62619764 None:intergenic 25.0%
!! TTCCCATATTTTATAGGATA+TGG + chr5_3:62619872-62619891 None:intergenic 25.0%
!! GCAATATTCCCATATTTTAT+AGG + chr5_3:62619878-62619897 None:intergenic 25.0%
!!! AAAATAAGAGTTTGATTTGG+AGG - chr5_3:62619142-62619161 Msa0823790:three_prime_UTR 25.0%
! CAATCCAATACGAAAATTAA+TGG - chr5_3:62619285-62619304 Msa0823790:three_prime_UTR 25.0%
!! TTCACCATTAATTTTCGTAT+TGG + chr5_3:62619292-62619311 None:intergenic 25.0%
! AATACGAAAATTAATGGTGA+AGG - chr5_3:62619291-62619310 Msa0823790:three_prime_UTR 25.0%
!!! GATTTTGAGTATCGTATATA+TGG + chr5_3:62619398-62619417 None:intergenic 25.0%
! ACATAAAGATGCATTTATCA+TGG - chr5_3:62619567-62619586 Msa0823790:intron 25.0%
!!! TTGCATGAATATGTCATTTT+AGG + chr5_3:62619745-62619764 None:intergenic 25.0%
!! TTCCCATATTTTATAGGATA+TGG + chr5_3:62619872-62619891 None:intergenic 25.0%
!! GCAATATTCCCATATTTTAT+AGG + chr5_3:62619878-62619897 None:intergenic 25.0%
TTGTAGAACTACTTGAATGT+TGG + chr5_3:62619199-62619218 None:intergenic 30.0%
!! ACCACTGTATTTGTTGTATT+TGG - chr5_3:62619367-62619386 Msa0823790:exon 30.0%
! TTTGAGTATCGTATATATGG+TGG + chr5_3:62619395-62619414 None:intergenic 30.0%
CAAAATCCATAAACGTTCAA+TGG - chr5_3:62619411-62619430 Msa0823790:CDS 30.0%
AAAATATGGGAATATTGCAC+AGG - chr5_3:62619880-62619899 Msa0823790:intron 30.0%
TTAAAGAGATCACTTCATTG+AGG - chr5_3:62619950-62619969 Msa0823790:CDS 30.0%
TGATATGCAATTCTCGATTT+GGG + chr5_3:62620182-62620201 None:intergenic 30.0%
TTGATATGCAATTCTCGATT+TGG + chr5_3:62620183-62620202 None:intergenic 30.0%
TTGTAGAACTACTTGAATGT+TGG + chr5_3:62619199-62619218 None:intergenic 30.0%
!! ACCACTGTATTTGTTGTATT+TGG - chr5_3:62619367-62619386 Msa0823790:exon 30.0%
! TTTGAGTATCGTATATATGG+TGG + chr5_3:62619395-62619414 None:intergenic 30.0%
CAAAATCCATAAACGTTCAA+TGG - chr5_3:62619411-62619430 Msa0823790:CDS 30.0%
AAAATATGGGAATATTGCAC+AGG - chr5_3:62619880-62619899 Msa0823790:intron 30.0%
TTAAAGAGATCACTTCATTG+AGG - chr5_3:62619950-62619969 Msa0823790:CDS 30.0%
TGATATGCAATTCTCGATTT+GGG + chr5_3:62620182-62620201 None:intergenic 30.0%
TTGATATGCAATTCTCGATT+TGG + chr5_3:62620183-62620202 None:intergenic 30.0%
!! TACTTGAATGTTGGTTTCGA+TGG + chr5_3:62619190-62619209 None:intergenic 35.0%
GCCAAATACAACAAATACAG+TGG + chr5_3:62619371-62619390 None:intergenic 35.0%
CAACATCCATTGAACGTTTA+TGG + chr5_3:62619420-62619439 None:intergenic 35.0%
CATAAACGTTCAATGGATGT+TGG - chr5_3:62619418-62619437 Msa0823790:CDS 35.0%
!! TCTCTTAGAAGCATCTCTTA+TGG - chr5_3:62619480-62619499 Msa0823790:CDS 35.0%
!! CTCTTAGAAGCATCTCTTAT+GGG - chr5_3:62619481-62619500 Msa0823790:CDS 35.0%
ACAGGTTTCTCTCTATTCTT+TGG - chr5_3:62619898-62619917 Msa0823790:intron 35.0%
! TCTTTGGATTGATGATCGAT+AGG - chr5_3:62619914-62619933 Msa0823790:intron 35.0%
AGAGGAAACTGAGAAGAAAA+AGG - chr5_3:62620035-62620054 Msa0823790:CDS 35.0%
GTACACATACAGACATGTTT+AGG + chr5_3:62620099-62620118 None:intergenic 35.0%
!! TACTTGAATGTTGGTTTCGA+TGG + chr5_3:62619190-62619209 None:intergenic 35.0%
GCCAAATACAACAAATACAG+TGG + chr5_3:62619371-62619390 None:intergenic 35.0%
CAACATCCATTGAACGTTTA+TGG + chr5_3:62619420-62619439 None:intergenic 35.0%
CATAAACGTTCAATGGATGT+TGG - chr5_3:62619418-62619437 Msa0823790:CDS 35.0%
!! TCTCTTAGAAGCATCTCTTA+TGG - chr5_3:62619480-62619499 Msa0823790:CDS 35.0%
!! CTCTTAGAAGCATCTCTTAT+GGG - chr5_3:62619481-62619500 Msa0823790:CDS 35.0%
ACAGGTTTCTCTCTATTCTT+TGG - chr5_3:62619898-62619917 Msa0823790:intron 35.0%
! TCTTTGGATTGATGATCGAT+AGG - chr5_3:62619914-62619933 Msa0823790:intron 35.0%
AGAGGAAACTGAGAAGAAAA+AGG - chr5_3:62620035-62620054 Msa0823790:CDS 35.0%
GTACACATACAGACATGTTT+AGG + chr5_3:62620099-62620118 None:intergenic 35.0%
CACTTCATTGAGGAAGAATG+TGG - chr5_3:62619960-62619979 Msa0823790:CDS 40.0%
TCTATCTCTCTTCTCTTTGG+AGG + chr5_3:62620018-62620037 None:intergenic 40.0%
TCCAAAGAGAAGAGAGATAG+AGG - chr5_3:62620017-62620036 Msa0823790:CDS 40.0%
TCCTCTATCTCTCTTCTCTT+TGG + chr5_3:62620021-62620040 None:intergenic 40.0%
!! TTCTCGATTTGGGAGTTTCT+TGG + chr5_3:62620172-62620191 None:intergenic 40.0%
CACTTCATTGAGGAAGAATG+TGG - chr5_3:62619960-62619979 Msa0823790:CDS 40.0%
TCTATCTCTCTTCTCTTTGG+AGG + chr5_3:62620018-62620037 None:intergenic 40.0%
TCCAAAGAGAAGAGAGATAG+AGG - chr5_3:62620017-62620036 Msa0823790:CDS 40.0%
TCCTCTATCTCTCTTCTCTT+TGG + chr5_3:62620021-62620040 None:intergenic 40.0%
!! TTCTCGATTTGGGAGTTTCT+TGG + chr5_3:62620172-62620191 None:intergenic 40.0%
!!! GTGTTAGACCTTTTGAAGCG+TGG - chr5_3:62619313-62619332 Msa0823790:three_prime_UTR 45.0%
!!! TAGACCTTTTGAAGCGTGGA+AGG - chr5_3:62619317-62619336 Msa0823790:three_prime_UTR 45.0%
!!! AGACCTTTTGAAGCGTGGAA+GGG - chr5_3:62619318-62619337 Msa0823790:three_prime_UTR 45.0%
ACGTTCAATGGATGTTGGCA+TGG - chr5_3:62619423-62619442 Msa0823790:CDS 45.0%
TGGCATGGTTAATCCAACAG+AGG - chr5_3:62619438-62619457 Msa0823790:CDS 45.0%
CATGGTTAATCCAACAGAGG+AGG - chr5_3:62619441-62619460 Msa0823790:CDS 45.0%
! TCCAACAGAGGAGGTTCTAA+TGG - chr5_3:62619450-62619469 Msa0823790:CDS 45.0%
!!! GTGTTAGACCTTTTGAAGCG+TGG - chr5_3:62619313-62619332 Msa0823790:three_prime_UTR 45.0%
!!! TAGACCTTTTGAAGCGTGGA+AGG - chr5_3:62619317-62619336 Msa0823790:three_prime_UTR 45.0%
!!! AGACCTTTTGAAGCGTGGAA+GGG - chr5_3:62619318-62619337 Msa0823790:three_prime_UTR 45.0%
ACGTTCAATGGATGTTGGCA+TGG - chr5_3:62619423-62619442 Msa0823790:CDS 45.0%
TGGCATGGTTAATCCAACAG+AGG - chr5_3:62619438-62619457 Msa0823790:CDS 45.0%
CATGGTTAATCCAACAGAGG+AGG - chr5_3:62619441-62619460 Msa0823790:CDS 45.0%
! TCCAACAGAGGAGGTTCTAA+TGG - chr5_3:62619450-62619469 Msa0823790:CDS 45.0%
!!! GACCTTTTGAAGCGTGGAAG+GGG - chr5_3:62619319-62619338 Msa0823790:three_prime_UTR 50.0%
GCCATTAGAACCTCCTCTGT+TGG + chr5_3:62619454-62619473 None:intergenic 50.0%
!!! GACCTTTTGAAGCGTGGAAG+GGG - chr5_3:62619319-62619338 Msa0823790:three_prime_UTR 50.0%
GCCATTAGAACCTCCTCTGT+TGG + chr5_3:62619454-62619473 None:intergenic 50.0%
GACCCCTTCCACGCTTCAAA+AGG + chr5_3:62619324-62619343 None:intergenic 55.0%
GACCCCTTCCACGCTTCAAA+AGG + chr5_3:62619324-62619343 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr5_3 gene 62619137 62620305 62619137 ID=Msa0823790;Name=Msa0823790
chr5_3 mRNA 62619137 62620305 62619137 ID=Msa0823790-mRNA-1;Parent=Msa0823790;Name=Msa0823790-mRNA-1;_AED=0.03;_eAED=0.03;_QI=167|1|1|1|1|1|2|240|120
chr5_3 exon 62619137 62619540 62619137 ID=Msa0823790-mRNA-1:exon:19506;Parent=Msa0823790-mRNA-1
chr5_3 exon 62619940 62620305 62619940 ID=Msa0823790-mRNA-1:exon:19505;Parent=Msa0823790-mRNA-1
chr5_3 five_prime_UTR 62620139 62620305 62620139 ID=Msa0823790-mRNA-1:five_prime_utr;Parent=Msa0823790-mRNA-1
chr5_3 CDS 62619940 62620138 62619940 ID=Msa0823790-mRNA-1:cds;Parent=Msa0823790-mRNA-1
chr5_3 CDS 62619377 62619540 62619377 ID=Msa0823790-mRNA-1:cds;Parent=Msa0823790-mRNA-1
chr5_3 three_prime_UTR 62619137 62619376 62619137 ID=Msa0823790-mRNA-1:three_prime_utr;Parent=Msa0823790-mRNA-1
Gene Sequence

>Msa0823790

ATGGTGAAGGTGTTAGACCTTTTGAAGCGTGGAAGGGGTCCATTAATCATAAAAACAATAGCAACCACTGTATTTGTTGTATTTGGCTCCACCATATATACGATACTCAAAATCCATAAACGTTCAATGGATGTTGGCATGGTTAATCCAACAGAGGAGGTTCTAATGGCACATCATCTCTTAGAAGCATCTCTTATGGGTTTCTCTCTATTCTTTGGATTGATGATCGATAGGCAACACTACTATATTAAAGAGATCACTTCATTGAGGAAGAATGTGGAAAAATCAAAGAAACAAAGCTACAATCATGAACCTCCAAAGAGAAGAGAGATAGAGGAAACTGAGAAGAAAAAGGATAATTAA
Protein sequence

>Msa0823790

MVKVLDLLKRGRGPLIIKTIATTVFVVFGSTIYTILKIHKRSMDVGMVNPTEEVLMAHHLLEASLMGFSLFFGLMIDRQHYYIKEITSLRKNVEKSKKQSYNHEPPKRREIEETEKKKDN*