AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1460510


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1460510 MtrunA17_Chr2g0322351 97.895 190 4 0 1 190 548 737 1.33e-127 375
Msa1460510 MtrunA17_Chr2g0322331 62.626 198 64 3 1 188 182 379 1.09e-75 231
Msa1460510 MtrunA17_Chr2g0322361 53.807 197 82 2 1 188 552 748 1.00e-63 209
Msa1460510 MtrunA17_Chr2g0322371 51.531 196 86 2 1 187 542 737 4.56e-60 199
Msa1460510 MtrunA17_Chr4g0025201 49.749 199 90 3 1 189 544 742 2.05e-52 178
Msa1460510 MtrunA17_Chr3g0137951 31.053 190 112 8 3 180 878 1060 2.05e-17 79.3
Msa1460510 MtrunA17_Chr3g0088821 29.255 188 118 8 3 180 870 1052 4.03e-16 75.9
Msa1460510 MtrunA17_Chr4g0073711 29.412 187 118 7 3 180 831 1012 6.29e-16 75.1
Msa1460510 MtrunA17_Chr2g0296991 27.273 187 122 7 3 180 837 1018 9.68e-16 74.7
Msa1460510 MtrunA17_Chr8g0352231 28.191 188 120 8 3 180 870 1052 2.81e-15 73.2
Msa1460510 MtrunA17_Chr8g0383701 27.419 186 117 7 3 177 889 1067 1.77e-13 68.2
Msa1460510 MtrunA17_Chr8g0364641 26.596 188 124 6 3 180 772 955 3.19e-12 64.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1460510 AT2G32540.1 37.688 199 102 4 3 181 553 749 7.83e-29 112
Msa1460510 AT2G32530.1 36.683 199 104 5 3 181 553 749 5.25e-26 104
Msa1460510 AT2G32610.1 35.821 201 107 4 3 181 553 753 7.07e-24 98.6
Msa1460510 AT2G32620.1 35.500 200 108 3 3 181 552 751 6.22e-23 95.9
Msa1460510 AT2G32620.4 35.500 200 108 3 3 181 456 655 6.57e-23 95.5
Msa1460510 AT4G15290.1 32.212 208 111 4 3 184 551 754 5.87e-21 90.1
Msa1460510 AT4G15320.4 33.173 208 106 5 3 181 565 768 1.04e-20 89.4
Msa1460510 AT4G15320.5 33.173 208 106 5 3 181 550 753 1.19e-20 89.4
Msa1460510 AT4G15320.3 33.173 208 106 5 3 181 550 753 1.25e-20 89.0
Msa1460510 AT4G32410.1 31.579 190 111 8 3 180 872 1054 2.90e-18 82.4
Msa1460510 AT5G17420.1 28.495 186 121 6 3 180 819 1000 1.46e-16 77.4
Msa1460510 AT5G05170.1 29.474 190 115 8 3 180 857 1039 3.08e-15 73.6
Msa1460510 AT2G25540.1 30.159 189 115 7 3 180 852 1034 6.86e-15 72.8
Msa1460510 AT4G24010.1 31.579 133 80 3 3 124 538 670 2.30e-14 70.9
Msa1460510 AT5G09870.1 28.342 187 116 7 2 177 861 1040 2.35e-13 68.2
Msa1460510 AT5G64740.1 27.807 187 117 7 2 177 876 1055 4.45e-13 67.4
Msa1460510 AT2G21770.1 26.203 187 120 7 2 177 879 1058 2.52e-12 65.1
Msa1460510 AT4G24000.2 26.289 194 125 6 3 183 336 524 2.86e-11 62.0
Msa1460510 AT4G24000.1 27.746 173 111 5 20 183 549 716 4.81e-11 61.2

Find 29 sgRNAs with CRISPR-Local

Find 106 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCATTGGCTACTAGCTTATT+TGG 0.148601 tig0040952:+831 Msa1460510:CDS
CTTACTTAGTTGCATGTTAT+TGG 0.184423 tig0040952:+913 Msa1460510:CDS
GTTAGAAGTGGGCTTGGATA+TGG 0.254382 tig0040952:+867 Msa1460510:CDS
TGGCTACTAGCTTATTTGGA+TGG 0.409969 tig0040952:+835 Msa1460510:CDS
GATGACTTATACAGAAACTT+TGG 0.421933 tig0040952:+520 Msa1460510:intron
TTCTGTGTTATTTCAAAGAC+AGG 0.422723 tig0040952:-717 None:intergenic
ATAGACCAATCATCTAATAC+TGG 0.425067 tig0040952:+741 Msa1460510:CDS
GACTTGAATATTGTAGATAA+AGG 0.436590 tig0040952:-978 None:intergenic
TTTAAAGGCTTGTTTGGGAC+TGG 0.447219 tig0040952:+942 Msa1460510:CDS
ACAAACAATATTGTTGTACT+AGG 0.447324 tig0040952:-798 None:intergenic
ACCTACCAGTATTAGATGAT+TGG 0.451041 tig0040952:-746 None:intergenic
TTAGAAGTGGGCTTGGATAT+GGG 0.462144 tig0040952:+868 Msa1460510:CDS
GGCTACTAGCTTATTTGGAT+GGG 0.463515 tig0040952:+836 Msa1460510:CDS
GAATTACAACCATGAGTGCT+TGG 0.486763 tig0040952:+646 Msa1460510:CDS
ACACGTGTTAGAAGTGGGCT+TGG 0.491184 tig0040952:+861 Msa1460510:CDS
AATATTCAAGTCAGTGATGT+TGG 0.493755 tig0040952:+989 Msa1460510:CDS
TCGTAATAACTTAAGTAAGA+TGG 0.506571 tig0040952:-685 None:intergenic
GTTTGTTCAACTCACAGCAT+TGG 0.507668 tig0040952:+815 Msa1460510:CDS
TGAATATGATCAATATGTAA+TGG 0.509211 tig0040952:-1042 None:intergenic
AGTGGGCTTGGATATGGGCC+TGG 0.524051 tig0040952:+873 Msa1460510:CDS
GCACTACAAAACACTTCTCC+AGG 0.542423 tig0040952:-891 None:intergenic
TTGTTTGGGACTGGAAAGCA+TGG 0.546457 tig0040952:+951 Msa1460510:CDS
CAGGGTTGTCAATTAGAACA+TGG 0.583196 tig0040952:+601 Msa1460510:CDS
TGGGCCACACGTGTTAGAAG+TGG 0.584751 tig0040952:+855 Msa1460510:CDS
TGTTTGGGACTGGAAAGCAT+GGG 0.620831 tig0040952:+952 Msa1460510:CDS
GGGCCACACGTGTTAGAAGT+GGG 0.636446 tig0040952:+856 Msa1460510:CDS
ACCAATCATCTAATACTGGT+AGG 0.667119 tig0040952:+745 Msa1460510:CDS
AAGCCCACTTCTAACACGTG+TGG 0.685603 tig0040952:-859 None:intergenic
GGTTGTCAATTAGAACATGG+TGG 0.736743 tig0040952:+604 Msa1460510:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAGTATGTAATTATAATCTT+GGG - tig0040952:196-215 None:intergenic 15.0%
!!! AAGAAAATATACATAGTTTT+TGG - tig0040952:452-471 None:intergenic 15.0%
!! TAGTATGTAATTATAATCTT+GGG - tig0040952:196-215 None:intergenic 15.0%
!!! AAGAAAATATACATAGTTTT+TGG - tig0040952:452-471 None:intergenic 15.0%
!! GTAGTATGTAATTATAATCT+TGG - tig0040952:197-216 None:intergenic 20.0%
!! TAACAAAAAAGATCAAGTAA+GGG - tig0040952:424-443 None:intergenic 20.0%
!! ATAACAAAAAAGATCAAGTA+AGG - tig0040952:425-444 None:intergenic 20.0%
!! TGAATATGATCAATATGTAA+TGG - tig0040952:1045-1064 None:intergenic 20.0%
!! GTAGTATGTAATTATAATCT+TGG - tig0040952:197-216 None:intergenic 20.0%
!! TAACAAAAAAGATCAAGTAA+GGG - tig0040952:424-443 None:intergenic 20.0%
!! ATAACAAAAAAGATCAAGTA+AGG - tig0040952:425-444 None:intergenic 20.0%
!! TGAATATGATCAATATGTAA+TGG - tig0040952:1045-1064 None:intergenic 20.0%
! TGTGATGTTATCAAATATCA+AGG - tig0040952:86-105 None:intergenic 25.0%
! TTATGAGTTCAAAATAGAGT+TGG - tig0040952:120-139 None:intergenic 25.0%
! TCGTAATAACTTAAGTAAGA+TGG - tig0040952:688-707 None:intergenic 25.0%
! GTTGTACTAGGTAAAAATAT+TGG - tig0040952:789-808 None:intergenic 25.0%
! ACAAACAATATTGTTGTACT+AGG - tig0040952:801-820 None:intergenic 25.0%
!!! TGTTATTGGCCATTTTTTAA+AGG + tig0040952:927-946 Msa1460510:CDS 25.0%
!!! CATTTTTTAAAGGCTTGTTT+GGG + tig0040952:937-956 Msa1460510:CDS 25.0%
! GACTTGAATATTGTAGATAA+AGG - tig0040952:981-1000 None:intergenic 25.0%
! TGTGATGTTATCAAATATCA+AGG - tig0040952:86-105 None:intergenic 25.0%
! TTATGAGTTCAAAATAGAGT+TGG - tig0040952:120-139 None:intergenic 25.0%
! TCGTAATAACTTAAGTAAGA+TGG - tig0040952:688-707 None:intergenic 25.0%
! GTTGTACTAGGTAAAAATAT+TGG - tig0040952:789-808 None:intergenic 25.0%
! ACAAACAATATTGTTGTACT+AGG - tig0040952:801-820 None:intergenic 25.0%
!!! TGTTATTGGCCATTTTTTAA+AGG + tig0040952:927-946 Msa1460510:CDS 25.0%
!!! CATTTTTTAAAGGCTTGTTT+GGG + tig0040952:937-956 Msa1460510:CDS 25.0%
! GACTTGAATATTGTAGATAA+AGG - tig0040952:981-1000 None:intergenic 25.0%
GATGACTTATACAGAAACTT+TGG + tig0040952:520-539 Msa1460510:intron 30.0%
ATATCAGAGAGCTTAAAAAC+AGG + tig0040952:582-601 Msa1460510:CDS 30.0%
TATCAGAGAGCTTAAAAACA+GGG + tig0040952:583-602 Msa1460510:CDS 30.0%
!! TTCTGTGTTATTTCAAAGAC+AGG - tig0040952:720-739 None:intergenic 30.0%
ATAGACCAATCATCTAATAC+TGG + tig0040952:741-760 Msa1460510:CDS 30.0%
CTTACTTAGTTGCATGTTAT+TGG + tig0040952:913-932 Msa1460510:CDS 30.0%
! CCAAACAAGCCTTTAAAAAA+TGG - tig0040952:939-958 None:intergenic 30.0%
!!! CCATTTTTTAAAGGCTTGTT+TGG + tig0040952:936-955 Msa1460510:CDS 30.0%
AATATTCAAGTCAGTGATGT+TGG + tig0040952:989-1008 Msa1460510:CDS 30.0%
GATGACTTATACAGAAACTT+TGG + tig0040952:520-539 Msa1460510:intron 30.0%
ATATCAGAGAGCTTAAAAAC+AGG + tig0040952:582-601 Msa1460510:CDS 30.0%
TATCAGAGAGCTTAAAAACA+GGG + tig0040952:583-602 Msa1460510:CDS 30.0%
!! TTCTGTGTTATTTCAAAGAC+AGG - tig0040952:720-739 None:intergenic 30.0%
ATAGACCAATCATCTAATAC+TGG + tig0040952:741-760 Msa1460510:CDS 30.0%
CTTACTTAGTTGCATGTTAT+TGG + tig0040952:913-932 Msa1460510:CDS 30.0%
! CCAAACAAGCCTTTAAAAAA+TGG - tig0040952:939-958 None:intergenic 30.0%
!!! CCATTTTTTAAAGGCTTGTT+TGG + tig0040952:936-955 Msa1460510:CDS 30.0%
AATATTCAAGTCAGTGATGT+TGG + tig0040952:989-1008 Msa1460510:CDS 30.0%
! TTATGTTTTGTACTCACCTC+TGG - tig0040952:51-70 None:intergenic 35.0%
TGAACCAAAATGTGCTTGTA+TGG + tig0040952:319-338 Msa1460510:intron 35.0%
! TGTACCATACAAGCACATTT+TGG - tig0040952:326-345 None:intergenic 35.0%
ACCAATCATCTAATACTGGT+AGG + tig0040952:745-764 Msa1460510:CDS 35.0%
ACCTACCAGTATTAGATGAT+TGG - tig0040952:749-768 None:intergenic 35.0%
! TTATGTTTTGTACTCACCTC+TGG - tig0040952:51-70 None:intergenic 35.0%
TGAACCAAAATGTGCTTGTA+TGG + tig0040952:319-338 Msa1460510:intron 35.0%
! TGTACCATACAAGCACATTT+TGG - tig0040952:326-345 None:intergenic 35.0%
ACCAATCATCTAATACTGGT+AGG + tig0040952:745-764 Msa1460510:CDS 35.0%
ACCTACCAGTATTAGATGAT+TGG - tig0040952:749-768 None:intergenic 35.0%
TTAGTCAGGATGCAATATGC+CGG - tig0040952:15-34 None:intergenic 40.0%
GCAAAAAGTTGGAGTTAGTC+AGG - tig0040952:29-48 None:intergenic 40.0%
! TAACTCCAACTTTTTGCCAG+AGG + tig0040952:32-51 Msa1460510:CDS 40.0%
CAGGGTTGTCAATTAGAACA+TGG + tig0040952:601-620 Msa1460510:CDS 40.0%
GGTTGTCAATTAGAACATGG+TGG + tig0040952:604-623 Msa1460510:CDS 40.0%
GAATTACAACCATGAGTGCT+TGG + tig0040952:646-665 Msa1460510:CDS 40.0%
!!! ACCATGAGTGCTTGGTTTTT+TGG + tig0040952:654-673 Msa1460510:CDS 40.0%
TCCAAAAAACCAAGCACTCA+TGG - tig0040952:658-677 None:intergenic 40.0%
GTTTGTTCAACTCACAGCAT+TGG + tig0040952:815-834 Msa1460510:CDS 40.0%
!! GCATTGGCTACTAGCTTATT+TGG + tig0040952:831-850 Msa1460510:CDS 40.0%
! TGGCTACTAGCTTATTTGGA+TGG + tig0040952:835-854 Msa1460510:CDS 40.0%
! GGCTACTAGCTTATTTGGAT+GGG + tig0040952:836-855 Msa1460510:CDS 40.0%
! TTAGAAGTGGGCTTGGATAT+GGG + tig0040952:868-887 Msa1460510:CDS 40.0%
! TTTAAAGGCTTGTTTGGGAC+TGG + tig0040952:942-961 Msa1460510:CDS 40.0%
TTAGTCAGGATGCAATATGC+CGG - tig0040952:15-34 None:intergenic 40.0%
GCAAAAAGTTGGAGTTAGTC+AGG - tig0040952:29-48 None:intergenic 40.0%
! TAACTCCAACTTTTTGCCAG+AGG + tig0040952:32-51 Msa1460510:CDS 40.0%
CAGGGTTGTCAATTAGAACA+TGG + tig0040952:601-620 Msa1460510:CDS 40.0%
GGTTGTCAATTAGAACATGG+TGG + tig0040952:604-623 Msa1460510:CDS 40.0%
GAATTACAACCATGAGTGCT+TGG + tig0040952:646-665 Msa1460510:CDS 40.0%
!!! ACCATGAGTGCTTGGTTTTT+TGG + tig0040952:654-673 Msa1460510:CDS 40.0%
TCCAAAAAACCAAGCACTCA+TGG - tig0040952:658-677 None:intergenic 40.0%
GTTTGTTCAACTCACAGCAT+TGG + tig0040952:815-834 Msa1460510:CDS 40.0%
!! GCATTGGCTACTAGCTTATT+TGG + tig0040952:831-850 Msa1460510:CDS 40.0%
! TGGCTACTAGCTTATTTGGA+TGG + tig0040952:835-854 Msa1460510:CDS 40.0%
! GGCTACTAGCTTATTTGGAT+GGG + tig0040952:836-855 Msa1460510:CDS 40.0%
! TTAGAAGTGGGCTTGGATAT+GGG + tig0040952:868-887 Msa1460510:CDS 40.0%
! TTTAAAGGCTTGTTTGGGAC+TGG + tig0040952:942-961 Msa1460510:CDS 40.0%
ACTCACCTCTGGCAAAAAGT+TGG - tig0040952:40-59 None:intergenic 45.0%
! GTTAGAAGTGGGCTTGGATA+TGG + tig0040952:867-886 Msa1460510:CDS 45.0%
GCACTACAAAACACTTCTCC+AGG - tig0040952:894-913 None:intergenic 45.0%
! TTGTTTGGGACTGGAAAGCA+TGG + tig0040952:951-970 Msa1460510:CDS 45.0%
! TGTTTGGGACTGGAAAGCAT+GGG + tig0040952:952-971 Msa1460510:CDS 45.0%
ACTCACCTCTGGCAAAAAGT+TGG - tig0040952:40-59 None:intergenic 45.0%
! GTTAGAAGTGGGCTTGGATA+TGG + tig0040952:867-886 Msa1460510:CDS 45.0%
GCACTACAAAACACTTCTCC+AGG - tig0040952:894-913 None:intergenic 45.0%
! TTGTTTGGGACTGGAAAGCA+TGG + tig0040952:951-970 Msa1460510:CDS 45.0%
! TGTTTGGGACTGGAAAGCAT+GGG + tig0040952:952-971 Msa1460510:CDS 45.0%
!! AGTTATTTAAAAAAAAAAAA+CGG + tig0040952:1139-1158 Msa1460510:three_prime_UTR 5.0%
!! AGTTATTTAAAAAAAAAAAA+CGG + tig0040952:1139-1158 Msa1460510:three_prime_UTR 5.0%
AAGCCCACTTCTAACACGTG+TGG - tig0040952:862-881 None:intergenic 50.0%
! ACACGTGTTAGAAGTGGGCT+TGG + tig0040952:861-880 Msa1460510:CDS 50.0%
AAGCCCACTTCTAACACGTG+TGG - tig0040952:862-881 None:intergenic 50.0%
! ACACGTGTTAGAAGTGGGCT+TGG + tig0040952:861-880 Msa1460510:CDS 50.0%
TGGGCCACACGTGTTAGAAG+TGG + tig0040952:855-874 Msa1460510:CDS 55.0%
GGGCCACACGTGTTAGAAGT+GGG + tig0040952:856-875 Msa1460510:CDS 55.0%
TGGGCCACACGTGTTAGAAG+TGG + tig0040952:855-874 Msa1460510:CDS 55.0%
GGGCCACACGTGTTAGAAGT+GGG + tig0040952:856-875 Msa1460510:CDS 55.0%
! AGTGGGCTTGGATATGGGCC+TGG + tig0040952:873-892 Msa1460510:CDS 60.0%
! AGTGGGCTTGGATATGGGCC+TGG + tig0040952:873-892 Msa1460510:CDS 60.0%
Chromosome Type Strat End Strand Name
tig0040952 gene 3 1237 3 ID=Msa1460510;Name=Msa1460510
tig0040952 mRNA 3 1237 3 ID=Msa1460510-mRNA-1;Parent=Msa1460510;Name=Msa1460510-mRNA-1;_AED=0.40;_eAED=0.40;_QI=0|1|0.5|1|0|0.5|2|182|190
tig0040952 exon 3 53 3 ID=Msa1460510-mRNA-1:exon:22783;Parent=Msa1460510-mRNA-1
tig0040952 exon 534 1237 534 ID=Msa1460510-mRNA-1:exon:22784;Parent=Msa1460510-mRNA-1
tig0040952 CDS 3 53 3 ID=Msa1460510-mRNA-1:cds;Parent=Msa1460510-mRNA-1
tig0040952 CDS 534 1055 534 ID=Msa1460510-mRNA-1:cds;Parent=Msa1460510-mRNA-1
tig0040952 three_prime_UTR 1056 1237 1056 ID=Msa1460510-mRNA-1:three_prime_utr;Parent=Msa1460510-mRNA-1
Gene Sequence

>Msa1460510

GCTGCTCTACCGGCATATTGCATCCTGACTAACTCCAACTTTTTGCCAGAGAAACTTTGGATACATGCTGCATTGTTTGTGACTTACAATATATCTACTATATCAGAGAGCTTAAAAACAGGGTTGTCAATTAGAACATGGTGGAACAATCAGAAGATGATGAGAATTACAACCATGAGTGCTTGGTTTTTTGGATTTTTAGCCATCTTACTTAAGTTATTACGAATATCTGAACCTGTCTTTGAAATAACACAGAAAATAGACCAATCATCTAATACTGGTAGGTTTAGTTTCAATGAGTCTCCAATATTTTTACCTAGTACAACAATATTGTTTGTTCAACTCACAGCATTGGCTACTAGCTTATTTGGATGGGCCACACGTGTTAGAAGTGGGCTTGGATATGGGCCTGGAGAAGTGTTTTGTAGTGCTTACTTAGTTGCATGTTATTGGCCATTTTTTAAAGGCTTGTTTGGGACTGGAAAGCATGGGATTCCTTTATCTACAATATTCAAGTCAGTGATGTTGGCTTTTCTTTTTGTGTATTCATGCAAACTTACCATTACATATTGA

Protein sequence

>Msa1460510

AALPAYCILTNSNFLPEKLWIHAALFVTYNISTISESLKTGLSIRTWWNNQKMMRITTMSAWFFGFLAILLKLLRISEPVFEITQKIDQSSNTGRFSFNESPIFLPSTTILFVQLTALATSLFGWATRVRSGLGYGPGEVFCSAYLVACYWPFFKGLFGTGKHGIPLSTIFKSVMLAFLFVYSCKLTITY*