AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1280490

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1280490 MtrunA17_Chr1g0202341 64.122 131 45 1 4 132 12 142 2.56e-51 172
Msa1280490 MtrunA17_Chr3g0077241 70.652 92 21 2 6 94 1 89 2.12e-39 129
Msa1280490 MtrunA17_Chr4g0052331 57.895 95 38 1 1 93 1 95 3.75e-33 112
Msa1280490 MtrunA17_Chr2g0329361 38.947 95 57 1 39 132 59 153 4.75e-18 77.8
Msa1280490 MtrunA17_Chr2g0329421 33.333 117 66 4 23 132 5 116 1.66e-15 70.1
Msa1280490 MtrunA17_Chr4g0033611 32.000 125 70 4 19 133 47 166 1.81e-15 70.9
Msa1280490 MtrunA17_Chr5g0448761 45.918 98 48 3 39 132 58 154 1.33e-13 66.6
Msa1280490 MtrunA17_Chr2g0287061 31.068 103 55 2 31 132 173 260 6.22e-12 62.0
Msa1280490 MtrunA17_Chr3g0078041 35.789 95 57 3 40 132 49 141 7.79e-12 60.5
Msa1280490 MtrunA17_Chr6g0458391 36.111 108 51 3 36 140 86 178 1.46e-11 60.8
Msa1280490 MtrunA17_Chr7g0233911 36.458 96 55 3 40 132 33 125 2.65e-11 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1280490 AT3G59470.3 36.170 94 56 2 40 132 69 159 1.93e-15 70.9
Msa1280490 AT3G59470.1 36.170 94 56 2 40 132 69 159 1.93e-15 70.9
Msa1280490 AT3G59470.2 35.789 95 57 2 40 133 81 172 2.31e-15 70.9
Msa1280490 AT4G38180.1 36.242 149 74 6 2 132 21 166 4.58e-14 68.6
Msa1280490 AT3G06250.2 35.789 95 45 3 39 132 26 105 5.90e-13 65.5
Msa1280490 AT3G06250.1 35.789 95 45 3 39 132 26 105 5.90e-13 65.5
Msa1280490 AT3G06250.3 35.789 95 45 3 39 132 26 105 5.90e-13 65.5
Msa1280490 AT3G07500.1 38.947 95 55 2 39 132 31 123 1.32e-12 62.8
Msa1280490 AT5G18960.2 33.684 95 47 3 39 132 41 120 3.14e-12 63.2
Msa1280490 AT5G18960.1 33.684 95 47 3 39 132 41 120 3.14e-12 63.2

Find 39 sgRNAs with CRISPR-Local

Find 114 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATTCCTTCAAAGGGCTCTA+AGG 0.261818 8_3:-19138155 None:intergenic
GAAGAAGATTATGGAAGTTT+TGG 0.293650 8_3:+19137741 Msa1280490:five_prime_UTR
AGAACGGATGGTAGAGTAAT+TGG 0.359499 8_3:+19138271 Msa1280490:CDS
ACAAGGTACGCGAGGAATAA+AGG 0.387113 8_3:+19138214 Msa1280490:CDS
CTTCTTCGAAGACGGTTCTC+AGG 0.416570 8_3:-19137725 None:intergenic
CATGAACATACCAACATGAT+TGG 0.442395 8_3:+19138070 Msa1280490:CDS
CTTAAACTCCATTCCTTCAA+AGG 0.451269 8_3:-19138164 None:intergenic
ACCGTCTTCGAAGAAGATTA+TGG 0.460480 8_3:+19137732 Msa1280490:five_prime_UTR
CTTAGAGCCCTTTGAAGGAA+TGG 0.476103 8_3:+19138156 Msa1280490:CDS
ATTCCTTCAAAGGGCTCTAA+GGG 0.488264 8_3:-19138154 None:intergenic
CTCCCCTTAGAGCCCTTTGA+AGG 0.489876 8_3:+19138151 Msa1280490:CDS
TCAATACAACAAAACTCAAT+CGG 0.502319 8_3:+19137595 Msa1280490:five_prime_UTR
ATATCAAGAAAAGTGAAGAT+AGG 0.503755 8_3:+19138407 Msa1280490:CDS
TCAAGAGATTCTTTGTTCAA+AGG 0.507548 8_3:+19138294 Msa1280490:CDS
GGCTCTAAGGGGAGCTCCAA+TGG 0.508044 8_3:-19138142 None:intergenic
TTAAACTCCATTCCTTCAAA+GGG 0.512155 8_3:-19138163 None:intergenic
TCCATAATCTTCTTCGAAGA+CGG 0.517402 8_3:-19137733 None:intergenic
AGATTCTTTGTTCAAAGGAG+GGG 0.523644 8_3:+19138299 Msa1280490:CDS
TCTCAATGATAGACTACCAT+TGG 0.530176 8_3:+19138126 Msa1280490:CDS
TCAAACGAACAAAAGAAAGT+AGG 0.536997 8_3:-19137661 None:intergenic
GAGATTCTTTGTTCAAAGGA+GGG 0.539548 8_3:+19138298 Msa1280490:CDS
ACTGTTTGTGTTGAAGCTGC+AGG 0.548752 8_3:+19138433 Msa1280490:CDS
AGAGATTCTTTGTTCAAAGG+AGG 0.550163 8_3:+19138297 Msa1280490:CDS
TTTGTGTTGAAGCTGCAGGC+AGG 0.559406 8_3:+19138437 Msa1280490:CDS
TCAAACAAGGGTAGGATGCA+AGG 0.583329 8_3:+19138375 Msa1280490:CDS
AATGGTAGTCTTATTGTACA+TGG 0.595875 8_3:+19138352 Msa1280490:CDS
TCAAGAAAAGTGAAGATAGG+TGG 0.599813 8_3:+19138410 Msa1280490:CDS
TTATTGTACATGGTCAAACA+AGG 0.601311 8_3:+19138362 Msa1280490:CDS
ATCATCTGAGCCAATCATGT+TGG 0.609119 8_3:-19138080 None:intergenic
GTTACTAAATCAAGAACGGA+TGG 0.614185 8_3:+19138259 Msa1280490:CDS
AATGGTAGTCTATCATTGAG+AGG 0.621900 8_3:-19138124 None:intergenic
TGGTCTGAGACATTATAACC+AGG 0.630311 8_3:+19137761 Msa1280490:five_prime_UTR
AGACGGTTCTCAGGTCGTAA+CGG 0.630551 8_3:-19137716 None:intergenic
GTACATGGTCAAACAAGGGT+AGG 0.635603 8_3:+19138367 Msa1280490:CDS
TCGTGTTACTAAATCAAGAA+CGG 0.641576 8_3:+19138255 Msa1280490:CDS
AATACTACACAAGGTACGCG+AGG 0.651596 8_3:+19138206 Msa1280490:CDS
TTCCTTCAAAGGGCTCTAAG+GGG 0.687755 8_3:-19138153 None:intergenic
TATTGTACATGGTCAAACAA+GGG 0.709401 8_3:+19138363 Msa1280490:CDS
CGGTTCTCAGGTCGTAACGG+CGG 0.719840 8_3:-19137713 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTCTTTTTTCAAATTTTTTT+GGG - chr8_3:19138332-19138351 None:intergenic 10.0%
!!! TTTCTTTTTTCAAATTTTTT+TGG - chr8_3:19138333-19138352 None:intergenic 10.0%
!! AAAAATTTGAAAAAAGAAAA+TGG + chr8_3:19138334-19138353 Msa1280490:CDS 10.0%
!!! TTCTTTTTTCAAATTTTTTT+GGG - chr8_3:19138332-19138351 None:intergenic 10.0%
!!! TTTCTTTTTTCAAATTTTTT+TGG - chr8_3:19138333-19138352 None:intergenic 10.0%
!! AAAAATTTGAAAAAAGAAAA+TGG + chr8_3:19138334-19138353 Msa1280490:CDS 10.0%
!! TTCATATTTAAACATGTTTG+TGG + chr8_3:19137899-19137918 Msa1280490:intron 20.0%
!!! TTAACTTGCTTTTCTAAATA+TGG + chr8_3:19137972-19137991 Msa1280490:intron 20.0%
!! ATGTAAAAAAATACTACACA+AGG + chr8_3:19138197-19138216 Msa1280490:CDS 20.0%
!! TTCATATTTAAACATGTTTG+TGG + chr8_3:19137899-19137918 Msa1280490:intron 20.0%
!!! TTAACTTGCTTTTCTAAATA+TGG + chr8_3:19137972-19137991 Msa1280490:intron 20.0%
!! ATGTAAAAAAATACTACACA+AGG + chr8_3:19138197-19138216 Msa1280490:CDS 20.0%
!!! ATTGAGTTTTGTTGTATTGA+CGG - chr8_3:19137595-19137614 None:intergenic 25.0%
! TCAATACAACAAAACTCAAT+CGG + chr8_3:19137595-19137614 Msa1280490:five_prime_UTR 25.0%
!! GAATTTTTATTCAGCATAAC+AGG + chr8_3:19138005-19138024 Msa1280490:intron 25.0%
! ATATCAAGAAAAGTGAAGAT+AGG + chr8_3:19138407-19138426 Msa1280490:CDS 25.0%
!!! ATTGAGTTTTGTTGTATTGA+CGG - chr8_3:19137595-19137614 None:intergenic 25.0%
! TCAATACAACAAAACTCAAT+CGG + chr8_3:19137595-19137614 Msa1280490:five_prime_UTR 25.0%
!! GAATTTTTATTCAGCATAAC+AGG + chr8_3:19138005-19138024 Msa1280490:intron 25.0%
! ATATCAAGAAAAGTGAAGAT+AGG + chr8_3:19138407-19138426 Msa1280490:CDS 25.0%
!!! TCTCTCTCTTTTTCAATTGA+AGG + chr8_3:19137619-19137638 Msa1280490:five_prime_UTR 30.0%
TCAAACGAACAAAAGAAAGT+AGG - chr8_3:19137664-19137683 None:intergenic 30.0%
! GAAGAAGATTATGGAAGTTT+TGG + chr8_3:19137741-19137760 Msa1280490:five_prime_UTR 30.0%
TTGTAGAACTAAAGAAACCA+AGG - chr8_3:19137810-19137829 None:intergenic 30.0%
! AGTCTCCAAAGATTTTTGTT+TGG + chr8_3:19137867-19137886 Msa1280490:intron 30.0%
CATTGCCAAACAAAAATCTT+TGG - chr8_3:19137875-19137894 None:intergenic 30.0%
TTAAACTCCATTCCTTCAAA+GGG - chr8_3:19138166-19138185 None:intergenic 30.0%
!!! TAAAGGTTTTAGCTTTCGTA+TGG + chr8_3:19138231-19138250 Msa1280490:CDS 30.0%
!!! AAAGGTTTTAGCTTTCGTAT+GGG + chr8_3:19138232-19138251 Msa1280490:CDS 30.0%
! TCGTGTTACTAAATCAAGAA+CGG + chr8_3:19138255-19138274 Msa1280490:CDS 30.0%
TCAAGAGATTCTTTGTTCAA+AGG + chr8_3:19138294-19138313 Msa1280490:CDS 30.0%
!! AATGGTAGTCTTATTGTACA+TGG + chr8_3:19138352-19138371 Msa1280490:CDS 30.0%
TTATTGTACATGGTCAAACA+AGG + chr8_3:19138362-19138381 Msa1280490:CDS 30.0%
TATTGTACATGGTCAAACAA+GGG + chr8_3:19138363-19138382 Msa1280490:CDS 30.0%
!!! TCTCTCTCTTTTTCAATTGA+AGG + chr8_3:19137619-19137638 Msa1280490:five_prime_UTR 30.0%
TCAAACGAACAAAAGAAAGT+AGG - chr8_3:19137664-19137683 None:intergenic 30.0%
! GAAGAAGATTATGGAAGTTT+TGG + chr8_3:19137741-19137760 Msa1280490:five_prime_UTR 30.0%
TTGTAGAACTAAAGAAACCA+AGG - chr8_3:19137810-19137829 None:intergenic 30.0%
! AGTCTCCAAAGATTTTTGTT+TGG + chr8_3:19137867-19137886 Msa1280490:intron 30.0%
CATTGCCAAACAAAAATCTT+TGG - chr8_3:19137875-19137894 None:intergenic 30.0%
TTAAACTCCATTCCTTCAAA+GGG - chr8_3:19138166-19138185 None:intergenic 30.0%
!!! TAAAGGTTTTAGCTTTCGTA+TGG + chr8_3:19138231-19138250 Msa1280490:CDS 30.0%
!!! AAAGGTTTTAGCTTTCGTAT+GGG + chr8_3:19138232-19138251 Msa1280490:CDS 30.0%
! TCGTGTTACTAAATCAAGAA+CGG + chr8_3:19138255-19138274 Msa1280490:CDS 30.0%
TCAAGAGATTCTTTGTTCAA+AGG + chr8_3:19138294-19138313 Msa1280490:CDS 30.0%
!! AATGGTAGTCTTATTGTACA+TGG + chr8_3:19138352-19138371 Msa1280490:CDS 30.0%
TTATTGTACATGGTCAAACA+AGG + chr8_3:19138362-19138381 Msa1280490:CDS 30.0%
TATTGTACATGGTCAAACAA+GGG + chr8_3:19138363-19138382 Msa1280490:CDS 30.0%
! TTCTTTTGTTCGTTTGAACG+AGG + chr8_3:19137667-19137686 Msa1280490:five_prime_UTR 35.0%
TCCATAATCTTCTTCGAAGA+CGG - chr8_3:19137736-19137755 None:intergenic 35.0%
AACCACATCTTCAATTACCT+TGG + chr8_3:19137790-19137809 Msa1280490:intron 35.0%
AACCAAGGTAATTGAAGATG+TGG - chr8_3:19137795-19137814 None:intergenic 35.0%
CATGAACATACCAACATGAT+TGG + chr8_3:19138070-19138089 Msa1280490:CDS 35.0%
AATGGTAGTCTATCATTGAG+AGG - chr8_3:19138127-19138146 None:intergenic 35.0%
TCTCAATGATAGACTACCAT+TGG + chr8_3:19138126-19138145 Msa1280490:CDS 35.0%
CTTAAACTCCATTCCTTCAA+AGG - chr8_3:19138167-19138186 None:intergenic 35.0%
GTTACTAAATCAAGAACGGA+TGG + chr8_3:19138259-19138278 Msa1280490:CDS 35.0%
AGAGATTCTTTGTTCAAAGG+AGG + chr8_3:19138297-19138316 Msa1280490:CDS 35.0%
GAGATTCTTTGTTCAAAGGA+GGG + chr8_3:19138298-19138317 Msa1280490:CDS 35.0%
AGATTCTTTGTTCAAAGGAG+GGG + chr8_3:19138299-19138318 Msa1280490:CDS 35.0%
TCAAGAAAAGTGAAGATAGG+TGG + chr8_3:19138410-19138429 Msa1280490:CDS 35.0%
! TTCTTTTGTTCGTTTGAACG+AGG + chr8_3:19137667-19137686 Msa1280490:five_prime_UTR 35.0%
TCCATAATCTTCTTCGAAGA+CGG - chr8_3:19137736-19137755 None:intergenic 35.0%
AACCACATCTTCAATTACCT+TGG + chr8_3:19137790-19137809 Msa1280490:intron 35.0%
AACCAAGGTAATTGAAGATG+TGG - chr8_3:19137795-19137814 None:intergenic 35.0%
CATGAACATACCAACATGAT+TGG + chr8_3:19138070-19138089 Msa1280490:CDS 35.0%
AATGGTAGTCTATCATTGAG+AGG - chr8_3:19138127-19138146 None:intergenic 35.0%
TCTCAATGATAGACTACCAT+TGG + chr8_3:19138126-19138145 Msa1280490:CDS 35.0%
CTTAAACTCCATTCCTTCAA+AGG - chr8_3:19138167-19138186 None:intergenic 35.0%
GTTACTAAATCAAGAACGGA+TGG + chr8_3:19138259-19138278 Msa1280490:CDS 35.0%
AGAGATTCTTTGTTCAAAGG+AGG + chr8_3:19138297-19138316 Msa1280490:CDS 35.0%
GAGATTCTTTGTTCAAAGGA+GGG + chr8_3:19138298-19138317 Msa1280490:CDS 35.0%
AGATTCTTTGTTCAAAGGAG+GGG + chr8_3:19138299-19138318 Msa1280490:CDS 35.0%
TCAAGAAAAGTGAAGATAGG+TGG + chr8_3:19138410-19138429 Msa1280490:CDS 35.0%
ACCGTCTTCGAAGAAGATTA+TGG + chr8_3:19137732-19137751 Msa1280490:five_prime_UTR 40.0%
! TGGTCTGAGACATTATAACC+AGG + chr8_3:19137761-19137780 Msa1280490:five_prime_UTR 40.0%
GAAGATGTGGTTAATTCACC+TGG - chr8_3:19137782-19137801 None:intergenic 40.0%
ATCATCTGAGCCAATCATGT+TGG - chr8_3:19138083-19138102 None:intergenic 40.0%
! ATTCCTTCAAAGGGCTCTAA+GGG - chr8_3:19138157-19138176 None:intergenic 40.0%
AGAACGGATGGTAGAGTAAT+TGG + chr8_3:19138271-19138290 Msa1280490:CDS 40.0%
ACCGTCTTCGAAGAAGATTA+TGG + chr8_3:19137732-19137751 Msa1280490:five_prime_UTR 40.0%
! TGGTCTGAGACATTATAACC+AGG + chr8_3:19137761-19137780 Msa1280490:five_prime_UTR 40.0%
GAAGATGTGGTTAATTCACC+TGG - chr8_3:19137782-19137801 None:intergenic 40.0%
ATCATCTGAGCCAATCATGT+TGG - chr8_3:19138083-19138102 None:intergenic 40.0%
! ATTCCTTCAAAGGGCTCTAA+GGG - chr8_3:19138157-19138176 None:intergenic 40.0%
AGAACGGATGGTAGAGTAAT+TGG + chr8_3:19138271-19138290 Msa1280490:CDS 40.0%
!! TTCCTTCAAAGGGCTCTAAG+GGG - chr8_3:19138156-19138175 None:intergenic 45.0%
CATTCCTTCAAAGGGCTCTA+AGG - chr8_3:19138158-19138177 None:intergenic 45.0%
! CTTAGAGCCCTTTGAAGGAA+TGG + chr8_3:19138156-19138175 Msa1280490:CDS 45.0%
AATACTACACAAGGTACGCG+AGG + chr8_3:19138206-19138225 Msa1280490:CDS 45.0%
ACAAGGTACGCGAGGAATAA+AGG + chr8_3:19138214-19138233 Msa1280490:CDS 45.0%
GTACATGGTCAAACAAGGGT+AGG + chr8_3:19138367-19138386 Msa1280490:CDS 45.0%
TCAAACAAGGGTAGGATGCA+AGG + chr8_3:19138375-19138394 Msa1280490:CDS 45.0%
ACTGTTTGTGTTGAAGCTGC+AGG + chr8_3:19138433-19138452 Msa1280490:CDS 45.0%
!! TTCCTTCAAAGGGCTCTAAG+GGG - chr8_3:19138156-19138175 None:intergenic 45.0%
CATTCCTTCAAAGGGCTCTA+AGG - chr8_3:19138158-19138177 None:intergenic 45.0%
! CTTAGAGCCCTTTGAAGGAA+TGG + chr8_3:19138156-19138175 Msa1280490:CDS 45.0%
AATACTACACAAGGTACGCG+AGG + chr8_3:19138206-19138225 Msa1280490:CDS 45.0%
ACAAGGTACGCGAGGAATAA+AGG + chr8_3:19138214-19138233 Msa1280490:CDS 45.0%
GTACATGGTCAAACAAGGGT+AGG + chr8_3:19138367-19138386 Msa1280490:CDS 45.0%
TCAAACAAGGGTAGGATGCA+AGG + chr8_3:19138375-19138394 Msa1280490:CDS 45.0%
ACTGTTTGTGTTGAAGCTGC+AGG + chr8_3:19138433-19138452 Msa1280490:CDS 45.0%
AGACGGTTCTCAGGTCGTAA+CGG - chr8_3:19137719-19137738 None:intergenic 50.0%
CTTCTTCGAAGACGGTTCTC+AGG - chr8_3:19137728-19137747 None:intergenic 50.0%
TTTGTGTTGAAGCTGCAGGC+AGG + chr8_3:19138437-19138456 Msa1280490:CDS 50.0%
AGACGGTTCTCAGGTCGTAA+CGG - chr8_3:19137719-19137738 None:intergenic 50.0%
CTTCTTCGAAGACGGTTCTC+AGG - chr8_3:19137728-19137747 None:intergenic 50.0%
TTTGTGTTGAAGCTGCAGGC+AGG + chr8_3:19138437-19138456 Msa1280490:CDS 50.0%
CTCCCCTTAGAGCCCTTTGA+AGG + chr8_3:19138151-19138170 Msa1280490:CDS 55.0%
CTCCCCTTAGAGCCCTTTGA+AGG + chr8_3:19138151-19138170 Msa1280490:CDS 55.0%
CGGTTCTCAGGTCGTAACGG+CGG - chr8_3:19137716-19137735 None:intergenic 60.0%
!! GGCTCTAAGGGGAGCTCCAA+TGG - chr8_3:19138145-19138164 None:intergenic 60.0%
CGGTTCTCAGGTCGTAACGG+CGG - chr8_3:19137716-19137735 None:intergenic 60.0%
!! GGCTCTAAGGGGAGCTCCAA+TGG - chr8_3:19138145-19138164 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr8_3 gene 19137572 19138474 19137572 ID=Msa1280490;Name=Msa1280490
chr8_3 mRNA 19137572 19138474 19137572 ID=Msa1280490-mRNA-1;Parent=Msa1280490;Name=Msa1280490-mRNA-1;_AED=0.11;_eAED=0.13;_QI=235|1|0.5|1|1|1|2|0|143
chr8_3 exon 19137572 19137782 19137572 ID=Msa1280490-mRNA-1:exon:7123;Parent=Msa1280490-mRNA-1
chr8_3 exon 19138019 19138474 19138019 ID=Msa1280490-mRNA-1:exon:7124;Parent=Msa1280490-mRNA-1
chr8_3 five_prime_UTR 19137572 19137782 19137572 ID=Msa1280490-mRNA-1:five_prime_utr;Parent=Msa1280490-mRNA-1
chr8_3 five_prime_UTR 19138019 19138042 19138019 ID=Msa1280490-mRNA-1:five_prime_utr;Parent=Msa1280490-mRNA-1
chr8_3 CDS 19138043 19138474 19138043 ID=Msa1280490-mRNA-1:cds;Parent=Msa1280490-mRNA-1
Gene Sequence

>Msa1280490

ATGACAGATCAAGAAATGACAGATATGCATGAACATACCAACATGATTGGCTCAGATGATATGCTTGCAAGTGATGCAGATCCTCTCAATGATAGACTACCATTGGAGCTCCCCTTAGAGCCCTTTGAAGGAATGGAGTTTAAGTCAATTGAAGATGTAAAAAAATACTACACAAGGTACGCGAGGAATAAAGGTTTTAGCTTTCGTATGGGTCGTGTTACTAAATCAAGAACGGATGGTAGAGTAATTGGTCAAGAGATTCTTTGTTCAAAGGAGGGGTTTAGATCCCAAAAAAATTTGAAAAAAGAAAATGGTAGTCTTATTGTACATGGTCAAACAAGGGTAGGATGCAAGGCACTCTTGTATATCAAGAAAAGTGAAGATAGGTGGACTGTTTGTGTTGAAGCTGCAGGCAGGTTGTTTTTAATCTGA
Protein sequence

>Msa1280490

MTDQEMTDMHEHTNMIGSDDMLASDADPLNDRLPLELPLEPFEGMEFKSIEDVKKYYTRYARNKGFSFRMGRVTKSRTDGRVIGQEILCSKEGFRSQKNLKKENGSLIVHGQTRVGCKALLYIKKSEDRWTVCVEAAGRLFLI*