AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0862790

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0862790 MtrunA17_Chr5g0444551 96.622 148 5 0 1 148 1 148 1.74e-102 290
Msa0862790 MtrunA17_Chr5g0444571 95.745 94 4 0 1 94 1 94 2.33e-59 179
Msa0862790 MtrunA17_Chr4g0024941 48.936 141 72 0 1 141 1 141 5.42e-45 146
Msa0862790 MtrunA17_Chr2g0288831 50.694 144 70 1 1 143 1 144 1.14e-43 143
Msa0862790 MtrunA17_Chr2g0322421 47.287 129 67 1 1 128 1 129 6.50e-32 113
Msa0862790 MtrunA17_Chr7g0235621 41.221 131 76 1 1 130 1 131 1.30e-30 109
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0862790 AT5G42570.1 51.064 141 69 0 1 141 1 141 1.95e-45 148
Msa0862790 AT1G11905.1 50.355 141 70 0 1 141 1 141 1.40e-43 143
Msa0862790 AT3G20450.1 45.736 129 69 1 1 128 5 133 4.15e-37 124
Msa0862790 AT1G11905.2 43.972 141 78 1 1 141 1 140 1.21e-33 118
Msa0862790 AT3G07190.1 45.312 128 69 1 1 127 1 128 2.51e-30 109
Msa0862790 AT5G48660.1 42.969 128 72 1 1 127 1 128 7.33e-30 108
Msa0862790 AT5G48660.2 48.077 52 27 0 76 127 1 52 2.89e-11 58.2

Find 31 sgRNAs with CRISPR-Local

Find 101 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAACATCCATTGAACGTTTA+TGG 0.094726 5_4:+62535761 None:intergenic
ACCACTGTATTTGTTGTATT+TGG 0.123258 5_4:-62535811 Msa0862790:CDS
TCCTCTATCTCTCTTCTCTT+TGG 0.214919 5_4:+62535163 None:intergenic
ACAGGTTTCTCTCTATTCTT+TGG 0.261214 5_4:-62535283 Msa0862790:intron
TTCTCGATTTGGGAGTTTCT+TGG 0.274478 5_4:+62535012 None:intergenic
TTGATATGCAATTCTCGATT+TGG 0.291370 5_4:+62535001 None:intergenic
TCTCTTAGAAGCATCTCTTA+TGG 0.322946 5_4:-62535698 Msa0862790:CDS
AGAGGAAACTGAGAAGAAAA+AGG 0.332303 5_4:-62535146 Msa0862790:CDS
TACAAAATAAGAGTTTGATT+TGG 0.335189 5_4:-62536040 Msa0862790:five_prime_UTR
TGATATGCAATTCTCGATTT+GGG 0.354851 5_4:+62535002 None:intergenic
CTCTTAGAAGCATCTCTTAT+GGG 0.365951 5_4:-62535697 Msa0862790:intron
GTACACATACAGACATGTTT+AGG 0.407202 5_4:+62535085 None:intergenic
TCTATCTCTCTTCTCTTTGG+AGG 0.415834 5_4:+62535166 None:intergenic
TCCAACAGAGGAGGTTCTAA+TGG 0.420935 5_4:-62535728 Msa0862790:CDS
AAAATAAGAGTTTGATTTGG+AGG 0.430028 5_4:-62536037 Msa0862790:five_prime_UTR
CAAAATCCATAAACGTTCAA+TGG 0.441548 5_4:-62535767 Msa0862790:CDS
TCCAAAGAGAAGAGAGATAG+AGG 0.454256 5_4:-62535164 Msa0862790:CDS
GACCCCTTCCACGCTTCAAA+AGG 0.463134 5_4:+62535857 None:intergenic
GCCATTAGAACCTCCTCTGT+TGG 0.483298 5_4:+62535727 None:intergenic
TACTTGAATGTTGGTTTCGA+TGG 0.490667 5_4:+62535992 None:intergenic
AATACGAAAATTAATGATGA+AGG 0.502617 5_4:-62535887 Msa0862790:CDS
CATAAACGTTCAATGGATGT+TGG 0.531550 5_4:-62535760 Msa0862790:CDS
TTGTAGAACTACTTGAATGT+TGG 0.532246 5_4:+62535983 None:intergenic
TCTTTGGATTGATGATCGAT+AGG 0.543666 5_4:-62535267 Msa0862790:CDS
ACGTTCAATGGATGTTGGCA+TGG 0.548399 5_4:-62535755 Msa0862790:CDS
TTTGAGTATCGTATATATGG+TGG 0.571975 5_4:+62535786 None:intergenic
TTAAAGAGATCACTTCATTG+AGG 0.591642 5_4:-62535231 Msa0862790:CDS
CACTTCATTGAGGAAGAATG+TGG 0.608657 5_4:-62535221 Msa0862790:CDS
CATGGTTAATCCAACAGAGG+AGG 0.638279 5_4:-62535737 Msa0862790:CDS
GCCAAATACAACAAATACAG+TGG 0.645246 5_4:+62535810 None:intergenic
TGGCATGGTTAATCCAACAG+AGG 0.731698 5_4:-62535740 Msa0862790:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAAATATTATATTATCTAC+TGG - chr5_4:62536044-62536063 Msa0862790:five_prime_UTR 10.0%
!!! TAATTTAGATTGTTTTTCAA+AGG - chr5_4:62535382-62535401 Msa0862790:intron 15.0%
!!! TAAAAAAACGTTTGATAATA+TGG + chr5_4:62535975-62535994 None:intergenic 15.0%
!!! TAATTTAGATTGTTTTTCAA+AGG - chr5_4:62535382-62535401 Msa0862790:intron 15.0%
!!! TAAAAAAACGTTTGATAATA+TGG + chr5_4:62535975-62535994 None:intergenic 15.0%
!! TACAAAATAAGAGTTTGATT+TGG - chr5_4:62534900-62534919 Msa0862790:three_prime_UTR 20.0%
!!! TTCATCATTAATTTTCGTAT+TGG + chr5_4:62535054-62535073 None:intergenic 20.0%
!! AATACGAAAATTAATGATGA+AGG - chr5_4:62535053-62535072 Msa0862790:three_prime_UTR 20.0%
!!! GCTATTGTTTTTATGATTAA+TGG + chr5_4:62535108-62535127 None:intergenic 20.0%
!!! CTAGTATTGAAAGAAAAATA+AGG + chr5_4:62535289-62535308 None:intergenic 20.0%
!! ATTAAAACTAAGACATCAAA+TGG - chr5_4:62535535-62535554 Msa0862790:intron 20.0%
!! TTTCCATATCCTATAAAATA+TGG - chr5_4:62535625-62535644 Msa0862790:intron 20.0%
!! TTCCATATCCTATAAAATAT+GGG - chr5_4:62535626-62535645 Msa0862790:intron 20.0%
!! GAAGAAAAAGGATAATTAAA+TGG - chr5_4:62535806-62535825 Msa0862790:CDS 20.0%
!! TACAAAATAAGAGTTTGATT+TGG - chr5_4:62534900-62534919 Msa0862790:three_prime_UTR 20.0%
!!! TTCATCATTAATTTTCGTAT+TGG + chr5_4:62535054-62535073 None:intergenic 20.0%
!! AATACGAAAATTAATGATGA+AGG - chr5_4:62535053-62535072 Msa0862790:three_prime_UTR 20.0%
!!! GCTATTGTTTTTATGATTAA+TGG + chr5_4:62535108-62535127 None:intergenic 20.0%
!!! CTAGTATTGAAAGAAAAATA+AGG + chr5_4:62535289-62535308 None:intergenic 20.0%
!! ATTAAAACTAAGACATCAAA+TGG - chr5_4:62535535-62535554 Msa0862790:intron 20.0%
!! TTTCCATATCCTATAAAATA+TGG - chr5_4:62535625-62535644 Msa0862790:intron 20.0%
!! TTCCATATCCTATAAAATAT+GGG - chr5_4:62535626-62535645 Msa0862790:intron 20.0%
!! GAAGAAAAAGGATAATTAAA+TGG - chr5_4:62535806-62535825 Msa0862790:CDS 20.0%
!!! AAAATAAGAGTTTGATTTGG+AGG - chr5_4:62534903-62534922 Msa0862790:three_prime_UTR 25.0%
!!! GATTTTGAGTATCGTATATA+TGG + chr5_4:62535160-62535179 None:intergenic 25.0%
! ACATAAAGATGCATTTATCA+TGG - chr5_4:62535329-62535348 Msa0862790:intron 25.0%
!!! TTGCATGAATATGTCATTTT+AGG + chr5_4:62535506-62535525 None:intergenic 25.0%
!! TTCCCATATTTTATAGGATA+TGG + chr5_4:62535631-62535650 None:intergenic 25.0%
!! GCAATATTCCCATATTTTAT+AGG + chr5_4:62535637-62535656 None:intergenic 25.0%
!!! AAAATAAGAGTTTGATTTGG+AGG - chr5_4:62534903-62534922 Msa0862790:three_prime_UTR 25.0%
!!! GATTTTGAGTATCGTATATA+TGG + chr5_4:62535160-62535179 None:intergenic 25.0%
! ACATAAAGATGCATTTATCA+TGG - chr5_4:62535329-62535348 Msa0862790:intron 25.0%
!!! TTGCATGAATATGTCATTTT+AGG + chr5_4:62535506-62535525 None:intergenic 25.0%
!! TTCCCATATTTTATAGGATA+TGG + chr5_4:62535631-62535650 None:intergenic 25.0%
!! GCAATATTCCCATATTTTAT+AGG + chr5_4:62535637-62535656 None:intergenic 25.0%
TTGTAGAACTACTTGAATGT+TGG + chr5_4:62534960-62534979 None:intergenic 30.0%
!! ACCACTGTATTTGTTGTATT+TGG - chr5_4:62535129-62535148 Msa0862790:exon 30.0%
! TTTGAGTATCGTATATATGG+TGG + chr5_4:62535157-62535176 None:intergenic 30.0%
CAAAATCCATAAACGTTCAA+TGG - chr5_4:62535173-62535192 Msa0862790:CDS 30.0%
AAAATATGGGAATATTGCAC+AGG - chr5_4:62535639-62535658 Msa0862790:intron 30.0%
TTAAAGAGATCACTTCATTG+AGG - chr5_4:62535709-62535728 Msa0862790:CDS 30.0%
TGATATGCAATTCTCGATTT+GGG + chr5_4:62535941-62535960 None:intergenic 30.0%
TTGATATGCAATTCTCGATT+TGG + chr5_4:62535942-62535961 None:intergenic 30.0%
TTGTAGAACTACTTGAATGT+TGG + chr5_4:62534960-62534979 None:intergenic 30.0%
!! ACCACTGTATTTGTTGTATT+TGG - chr5_4:62535129-62535148 Msa0862790:exon 30.0%
! TTTGAGTATCGTATATATGG+TGG + chr5_4:62535157-62535176 None:intergenic 30.0%
CAAAATCCATAAACGTTCAA+TGG - chr5_4:62535173-62535192 Msa0862790:CDS 30.0%
AAAATATGGGAATATTGCAC+AGG - chr5_4:62535639-62535658 Msa0862790:intron 30.0%
TTAAAGAGATCACTTCATTG+AGG - chr5_4:62535709-62535728 Msa0862790:CDS 30.0%
TGATATGCAATTCTCGATTT+GGG + chr5_4:62535941-62535960 None:intergenic 30.0%
TTGATATGCAATTCTCGATT+TGG + chr5_4:62535942-62535961 None:intergenic 30.0%
!! TACTTGAATGTTGGTTTCGA+TGG + chr5_4:62534951-62534970 None:intergenic 35.0%
GCCAAATACAACAAATACAG+TGG + chr5_4:62535133-62535152 None:intergenic 35.0%
CAACATCCATTGAACGTTTA+TGG + chr5_4:62535182-62535201 None:intergenic 35.0%
CATAAACGTTCAATGGATGT+TGG - chr5_4:62535180-62535199 Msa0862790:CDS 35.0%
!! TCTCTTAGAAGCATCTCTTA+TGG - chr5_4:62535242-62535261 Msa0862790:CDS 35.0%
!! CTCTTAGAAGCATCTCTTAT+GGG - chr5_4:62535243-62535262 Msa0862790:CDS 35.0%
ACAGGTTTCTCTCTATTCTT+TGG - chr5_4:62535657-62535676 Msa0862790:intron 35.0%
! TCTTTGGATTGATGATCGAT+AGG - chr5_4:62535673-62535692 Msa0862790:intron 35.0%
AGAGGAAACTGAGAAGAAAA+AGG - chr5_4:62535794-62535813 Msa0862790:CDS 35.0%
GTACACATACAGACATGTTT+AGG + chr5_4:62535858-62535877 None:intergenic 35.0%
!! TACTTGAATGTTGGTTTCGA+TGG + chr5_4:62534951-62534970 None:intergenic 35.0%
GCCAAATACAACAAATACAG+TGG + chr5_4:62535133-62535152 None:intergenic 35.0%
CAACATCCATTGAACGTTTA+TGG + chr5_4:62535182-62535201 None:intergenic 35.0%
CATAAACGTTCAATGGATGT+TGG - chr5_4:62535180-62535199 Msa0862790:CDS 35.0%
!! TCTCTTAGAAGCATCTCTTA+TGG - chr5_4:62535242-62535261 Msa0862790:CDS 35.0%
!! CTCTTAGAAGCATCTCTTAT+GGG - chr5_4:62535243-62535262 Msa0862790:CDS 35.0%
ACAGGTTTCTCTCTATTCTT+TGG - chr5_4:62535657-62535676 Msa0862790:intron 35.0%
! TCTTTGGATTGATGATCGAT+AGG - chr5_4:62535673-62535692 Msa0862790:intron 35.0%
AGAGGAAACTGAGAAGAAAA+AGG - chr5_4:62535794-62535813 Msa0862790:CDS 35.0%
GTACACATACAGACATGTTT+AGG + chr5_4:62535858-62535877 None:intergenic 35.0%
CACTTCATTGAGGAAGAATG+TGG - chr5_4:62535719-62535738 Msa0862790:CDS 40.0%
TCTATCTCTCTTCTCTTTGG+AGG + chr5_4:62535777-62535796 None:intergenic 40.0%
TCCAAAGAGAAGAGAGATAG+AGG - chr5_4:62535776-62535795 Msa0862790:CDS 40.0%
TCCTCTATCTCTCTTCTCTT+TGG + chr5_4:62535780-62535799 None:intergenic 40.0%
!! TTCTCGATTTGGGAGTTTCT+TGG + chr5_4:62535931-62535950 None:intergenic 40.0%
CACTTCATTGAGGAAGAATG+TGG - chr5_4:62535719-62535738 Msa0862790:CDS 40.0%
TCTATCTCTCTTCTCTTTGG+AGG + chr5_4:62535777-62535796 None:intergenic 40.0%
TCCAAAGAGAAGAGAGATAG+AGG - chr5_4:62535776-62535795 Msa0862790:CDS 40.0%
TCCTCTATCTCTCTTCTCTT+TGG + chr5_4:62535780-62535799 None:intergenic 40.0%
!! TTCTCGATTTGGGAGTTTCT+TGG + chr5_4:62535931-62535950 None:intergenic 40.0%
!!! GTGTTAGACCTTTTGAAGCG+TGG - chr5_4:62535075-62535094 Msa0862790:three_prime_UTR 45.0%
!!! TAGACCTTTTGAAGCGTGGA+AGG - chr5_4:62535079-62535098 Msa0862790:three_prime_UTR 45.0%
!!! AGACCTTTTGAAGCGTGGAA+GGG - chr5_4:62535080-62535099 Msa0862790:three_prime_UTR 45.0%
ACGTTCAATGGATGTTGGCA+TGG - chr5_4:62535185-62535204 Msa0862790:CDS 45.0%
TGGCATGGTTAATCCAACAG+AGG - chr5_4:62535200-62535219 Msa0862790:CDS 45.0%
CATGGTTAATCCAACAGAGG+AGG - chr5_4:62535203-62535222 Msa0862790:CDS 45.0%
! TCCAACAGAGGAGGTTCTAA+TGG - chr5_4:62535212-62535231 Msa0862790:CDS 45.0%
!!! GTGTTAGACCTTTTGAAGCG+TGG - chr5_4:62535075-62535094 Msa0862790:three_prime_UTR 45.0%
!!! TAGACCTTTTGAAGCGTGGA+AGG - chr5_4:62535079-62535098 Msa0862790:three_prime_UTR 45.0%
!!! AGACCTTTTGAAGCGTGGAA+GGG - chr5_4:62535080-62535099 Msa0862790:three_prime_UTR 45.0%
ACGTTCAATGGATGTTGGCA+TGG - chr5_4:62535185-62535204 Msa0862790:CDS 45.0%
TGGCATGGTTAATCCAACAG+AGG - chr5_4:62535200-62535219 Msa0862790:CDS 45.0%
CATGGTTAATCCAACAGAGG+AGG - chr5_4:62535203-62535222 Msa0862790:CDS 45.0%
! TCCAACAGAGGAGGTTCTAA+TGG - chr5_4:62535212-62535231 Msa0862790:CDS 45.0%
!!! GACCTTTTGAAGCGTGGAAG+GGG - chr5_4:62535081-62535100 Msa0862790:three_prime_UTR 50.0%
GCCATTAGAACCTCCTCTGT+TGG + chr5_4:62535216-62535235 None:intergenic 50.0%
!!! GACCTTTTGAAGCGTGGAAG+GGG - chr5_4:62535081-62535100 Msa0862790:three_prime_UTR 50.0%
GCCATTAGAACCTCCTCTGT+TGG + chr5_4:62535216-62535235 None:intergenic 50.0%
GACCCCTTCCACGCTTCAAA+AGG + chr5_4:62535086-62535105 None:intergenic 55.0%
GACCCCTTCCACGCTTCAAA+AGG + chr5_4:62535086-62535105 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr5_4 gene 62534898 62536064 62534898 ID=Msa0862790;Name=Msa0862790
chr5_4 mRNA 62534898 62536064 62534898 ID=Msa0862790-mRNA-1;Parent=Msa0862790;Name=Msa0862790-mRNA-1;_AED=0.03;_eAED=0.03;_QI=84|1|1|1|1|1|2|240|148
chr5_4 exon 62534898 62535301 62534898 ID=Msa0862790-mRNA-1:exon:19521;Parent=Msa0862790-mRNA-1
chr5_4 exon 62535698 62536064 62535698 ID=Msa0862790-mRNA-1:exon:19520;Parent=Msa0862790-mRNA-1
chr5_4 five_prime_UTR 62535981 62536064 62535981 ID=Msa0862790-mRNA-1:five_prime_utr;Parent=Msa0862790-mRNA-1
chr5_4 CDS 62535698 62535980 62535698 ID=Msa0862790-mRNA-1:cds;Parent=Msa0862790-mRNA-1
chr5_4 CDS 62535138 62535301 62535138 ID=Msa0862790-mRNA-1:cds;Parent=Msa0862790-mRNA-1
chr5_4 three_prime_UTR 62534898 62535137 62534898 ID=Msa0862790-mRNA-1:three_prime_utr;Parent=Msa0862790-mRNA-1
Gene Sequence

>Msa0862790

ATGTTACAACTTTTATTTGCACTTTTGTCAATAGAATTAACAGTAATTCTAATACTATCTTTTGCAAATCCAATACGAAAATTAATGATGAAGGTGTTAGACCTTTTGAAGCGTGGAAGGGGTCCATTAATCATAAAAACAATAGCAACCACTGTATTTGTTGTATTTGGCTCCACCATATATACGATACTCAAAATCCATAAACGTTCAATGGATGTTGGCATGGTTAATCCAACAGAGGAGGTTCTAATGGCACATCATCTCTTAGAAGCATCTCTTATGGGTTTCTCTCTATTCTTTGGATTGATGATCGATAGGCAACACTACTATATTAAAGAGATCACTTCATTGAGGAAGAATGTGGAAAAATCAAAGAAACAAAGCTACAATCATGAACCTCCAAAGAGAAGAGAGATAGAGGAAACTGAGAAGAAAAAGGATAATTAA
Protein sequence

>Msa0862790

MLQLLFALLSIELTVILILSFANPIRKLMMKVLDLLKRGRGPLIIKTIATTVFVVFGSTIYTILKIHKRSMDVGMVNPTEEVLMAHHLLEASLMGFSLFFGLMIDRQHYYIKEITSLRKNVEKSKKQSYNHEPPKRREIEETEKKKDN*