AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0547720


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0547720 MtrunA17_Chr5g0425951 100.000 70 0 0 1 70 1 70 4.54e-43 135
Msa0547720 MtrunA17_Chr4g0030431 100.000 70 0 0 1 70 1 70 4.54e-43 135
Msa0547720 MtrunA17_Chr3g0100121 100.000 70 0 0 1 70 1 70 4.54e-43 135
Msa0547720 MtrunA17_Chr3g0113681 100.000 70 0 0 1 70 1 70 4.54e-43 135
Msa0547720 MtrunA17_Chr2g0327641 100.000 70 0 0 1 70 1 70 4.54e-43 135
Msa0547720 MtrunA17_Chr3g0103351 100.000 70 0 0 1 70 1 70 4.54e-43 135
Msa0547720 MtrunA17_Chr8g0352791 100.000 70 0 0 1 70 1 70 4.54e-43 135
Msa0547720 MtrunA17_Chr3g0103821 100.000 70 0 0 1 70 1 70 4.54e-43 135
Msa0547720 MtrunA17_Chr3g0104031 100.000 70 0 0 1 70 1 70 4.54e-43 135
Msa0547720 MtrunA17_Chr7g0225731 100.000 70 0 0 1 70 1 70 4.54e-43 135
Msa0547720 MtrunA17_Chr3g0103801 100.000 70 0 0 1 70 1 70 4.54e-43 135
Msa0547720 MtrunA17_Chr3g0103881 100.000 70 0 0 1 70 1 70 4.54e-43 135
Msa0547720 MtrunA17_Chr7g0262791 100.000 70 0 0 1 70 1 70 4.54e-43 135
Msa0547720 MtrunA17_Chr4g0072411 100.000 70 0 0 1 70 59 128 1.67e-42 136
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0547720 AT3G53730.1 100.000 70 0 0 1 70 1 70 6.26e-43 135
Msa0547720 AT1G07820.2 100.000 70 0 0 1 70 1 70 6.26e-43 135
Msa0547720 AT1G07820.1 100.000 70 0 0 1 70 1 70 6.26e-43 135
Msa0547720 AT5G59690.1 100.000 70 0 0 1 70 1 70 6.26e-43 135
Msa0547720 AT3G46320.1 100.000 70 0 0 1 70 1 70 6.26e-43 135
Msa0547720 AT2G28740.1 100.000 70 0 0 1 70 1 70 6.26e-43 135
Msa0547720 AT1G07660.1 100.000 70 0 0 1 70 1 70 6.26e-43 135
Msa0547720 AT3G45930.1 100.000 70 0 0 1 70 1 70 6.26e-43 135
Msa0547720 AT5G59970.1 100.000 70 0 0 1 70 1 70 6.26e-43 135
Msa0547720 AT5G59970.2 100.000 70 0 0 1 70 1 70 6.26e-43 135
Msa0547720 AT1G07660.2 100.000 38 0 0 33 70 16 53 1.15e-19 76.6

Find 31 sgRNAs with CRISPR-Local

Find 108 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATAGGTTGTGGAACAAATT+TGG 0.221076 4_1:-41078545 None:intergenic
TGATTTCTGATCAAGATGTC+TGG 0.330252 4_1:+41077806 None:intergenic
CTTCTTGGAGAATGTGATTA+GGG 0.347463 4_1:+41078003 Msa0547720:CDS
TCTTCTTGGAGAATGTGATT+AGG 0.365922 4_1:+41078002 Msa0547720:CDS
GGAAAGGGTTTGGGAAAGGG+TGG 0.366216 4_1:+41077842 Msa0547720:CDS
TTTGCACTTAACTACAAGAT+AGG 0.368327 4_1:-41078562 None:intergenic
TGGCGTGTTGAAGATCTTCT+TGG 0.370355 4_1:+41077988 Msa0547720:CDS
GGAAAAGGAGGAAAGGGTTT+GGG 0.378357 4_1:+41077833 Msa0547720:CDS
TATCAGTGGTTTGATTTATG+AGG 0.387367 4_1:+41077958 Msa0547720:CDS
TGGAAAAGGAGGAAAGGGTT+TGG 0.387838 4_1:+41077832 Msa0547720:CDS
AAGATGTCTGGGCGTGGAAA+AGG 0.429435 4_1:+41077818 None:intergenic
TCGCTGGCTTTGTGATTCCC+TGG 0.442319 4_1:-41077901 None:intergenic
GGAGGAAAGGGTTTGGGAAA+GGG 0.445686 4_1:+41077839 Msa0547720:CDS
AGGAGGAAAGGGTTTGGGAA+AGG 0.475381 4_1:+41077838 Msa0547720:CDS
GGTGCTTCGTGACAACATCC+AGG 0.512203 4_1:+41077883 Msa0547720:CDS
GATTTCTGATCAAGATGTCT+GGG 0.513702 4_1:+41077807 None:intergenic
GCTATCTTGAAACATCTGAA+TGG 0.521986 4_1:-41078523 None:intergenic
CTTAACTACAAGATAGGTTG+TGG 0.525118 4_1:-41078556 None:intergenic
CGAGCAAGACGACGAATCGC+TGG 0.534933 4_1:-41077917 None:intergenic
TGTTGTCACGAAGCACCTTA+CGG 0.540622 4_1:-41077877 None:intergenic
CGTCGTCTTGCTCGTAGAGG+AGG 0.557881 4_1:+41077926 Msa0547720:CDS
CTGATCAAGATGTCTGGGCG+TGG 0.573727 4_1:+41077812 None:intergenic
TGGAGCAAAACGACACCGTA+AGG 0.575994 4_1:+41077862 Msa0547720:CDS
GGGCGTGGAAAAGGAGGAAA+GGG 0.587932 4_1:+41077827 Msa0547720:CDS
GGAGGAGTGAAGCGTATCAG+TGG 0.591400 4_1:+41077944 Msa0547720:CDS
ATGTCTGGGCGTGGAAAAGG+AGG 0.593086 4_1:+41077821 Msa0547720:CDS
TGGGCGTGGAAAAGGAGGAA+AGG 0.624585 4_1:+41077826 Msa0547720:CDS
TTGATTTATGAGGAGACACG+TGG 0.648281 4_1:+41077968 Msa0547720:CDS
TTGACAGTGAAGATGAATTG+TGG 0.650371 4_1:+41078493 Msa0547720:CDS
GTGCTTCGTGACAACATCCA+GGG 0.652644 4_1:+41077884 Msa0547720:CDS
ATTCGTCGTCTTGCTCGTAG+AGG 0.654201 4_1:+41077923 Msa0547720:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTGTAATTGATGTTTAATTT+GGG + chr4_1:41078267-41078286 Msa0547720:intron 15.0%
!! TATAATTCATTATAGTGATT+TGG - chr4_1:41078370-41078389 None:intergenic 15.0%
!!! TATATTTCTATTCGAAAATT+AGG - chr4_1:41078471-41078490 None:intergenic 15.0%
!!! TTGTAATTGATGTTTAATTT+GGG + chr4_1:41078267-41078286 Msa0547720:intron 15.0%
!! TATAATTCATTATAGTGATT+TGG - chr4_1:41078370-41078389 None:intergenic 15.0%
!!! TATATTTCTATTCGAAAATT+AGG - chr4_1:41078471-41078490 None:intergenic 15.0%
!! GTTGTAATTGATGTTTAATT+TGG + chr4_1:41078266-41078285 Msa0547720:intron 20.0%
!!! TGGATAATAATGTAGATTTT+AGG + chr4_1:41078307-41078326 Msa0547720:intron 20.0%
!!! GGATAATAATGTAGATTTTA+GGG + chr4_1:41078308-41078327 Msa0547720:intron 20.0%
!!! TTGATTTTAACTGTGAAATT+TGG + chr4_1:41078431-41078450 Msa0547720:intron 20.0%
!! GTTGTAATTGATGTTTAATT+TGG + chr4_1:41078266-41078285 Msa0547720:intron 20.0%
!!! TGGATAATAATGTAGATTTT+AGG + chr4_1:41078307-41078326 Msa0547720:intron 20.0%
!!! GGATAATAATGTAGATTTTA+GGG + chr4_1:41078308-41078327 Msa0547720:intron 20.0%
!!! TTGATTTTAACTGTGAAATT+TGG + chr4_1:41078431-41078450 Msa0547720:intron 20.0%
!!! GGGGATTAATTTTTTTGTTT+TGG + chr4_1:41078244-41078263 Msa0547720:intron 25.0%
!!! GGGGATTAATTTTTTTGTTT+TGG + chr4_1:41078244-41078263 Msa0547720:intron 25.0%
! TATCAGTGGTTTGATTTATG+AGG + chr4_1:41077958-41077977 Msa0547720:CDS 30.0%
ACAAAGAACACAATATGAGA+TGG - chr4_1:41078402-41078421 None:intergenic 30.0%
! TATCAGTGGTTTGATTTATG+AGG + chr4_1:41077958-41077977 Msa0547720:CDS 30.0%
ACAAAGAACACAATATGAGA+TGG - chr4_1:41078402-41078421 None:intergenic 30.0%
TCTTCTTGGAGAATGTGATT+AGG + chr4_1:41078002-41078021 Msa0547720:CDS 35.0%
CTTCTTGGAGAATGTGATTA+GGG + chr4_1:41078003-41078022 Msa0547720:CDS 35.0%
TTGACAGTGAAGATGAATTG+TGG + chr4_1:41078493-41078512 Msa0547720:CDS 35.0%
GCTATCTTGAAACATCTGAA+TGG - chr4_1:41078526-41078545 None:intergenic 35.0%
GATAGGTTGTGGAACAAATT+TGG - chr4_1:41078548-41078567 None:intergenic 35.0%
TCTTCTTGGAGAATGTGATT+AGG + chr4_1:41078002-41078021 Msa0547720:CDS 35.0%
CTTCTTGGAGAATGTGATTA+GGG + chr4_1:41078003-41078022 Msa0547720:CDS 35.0%
TTGACAGTGAAGATGAATTG+TGG + chr4_1:41078493-41078512 Msa0547720:CDS 35.0%
GCTATCTTGAAACATCTGAA+TGG - chr4_1:41078526-41078545 None:intergenic 35.0%
GATAGGTTGTGGAACAAATT+TGG - chr4_1:41078548-41078567 None:intergenic 35.0%
TTGATTTATGAGGAGACACG+TGG + chr4_1:41077968-41077987 Msa0547720:CDS 40.0%
GTTTATGCTCTCAAGAGACA+GGG + chr4_1:41078182-41078201 Msa0547720:intron 40.0%
GGGTACGAATTGTTGCAATA+TGG + chr4_1:41078287-41078306 Msa0547720:intron 40.0%
TTGATTTATGAGGAGACACG+TGG + chr4_1:41077968-41077987 Msa0547720:CDS 40.0%
GTTTATGCTCTCAAGAGACA+GGG + chr4_1:41078182-41078201 Msa0547720:intron 40.0%
GGGTACGAATTGTTGCAATA+TGG + chr4_1:41078287-41078306 Msa0547720:intron 40.0%
TGGAAAAGGAGGAAAGGGTT+TGG + chr4_1:41077832-41077851 Msa0547720:CDS 45.0%
GGAAAAGGAGGAAAGGGTTT+GGG + chr4_1:41077833-41077852 Msa0547720:CDS 45.0%
! TGTTGTCACGAAGCACCTTA+CGG - chr4_1:41077880-41077899 None:intergenic 45.0%
TGGCGTGTTGAAGATCTTCT+TGG + chr4_1:41077988-41078007 Msa0547720:CDS 45.0%
AGCATAAACCACATCCATGG+CGG - chr4_1:41078171-41078190 None:intergenic 45.0%
! GAGAGCATAAACCACATCCA+TGG - chr4_1:41078174-41078193 None:intergenic 45.0%
GGTTTATGCTCTCAAGAGAC+AGG + chr4_1:41078181-41078200 Msa0547720:intron 45.0%
GAAGAACCCTCTACGGATTT+GGG + chr4_1:41078204-41078223 Msa0547720:intron 45.0%
AAGAACCCTCTACGGATTTG+GGG + chr4_1:41078205-41078224 Msa0547720:intron 45.0%
TGGAAAAGGAGGAAAGGGTT+TGG + chr4_1:41077832-41077851 Msa0547720:CDS 45.0%
GGAAAAGGAGGAAAGGGTTT+GGG + chr4_1:41077833-41077852 Msa0547720:CDS 45.0%
! TGTTGTCACGAAGCACCTTA+CGG - chr4_1:41077880-41077899 None:intergenic 45.0%
TGGCGTGTTGAAGATCTTCT+TGG + chr4_1:41077988-41078007 Msa0547720:CDS 45.0%
AGCATAAACCACATCCATGG+CGG - chr4_1:41078171-41078190 None:intergenic 45.0%
! GAGAGCATAAACCACATCCA+TGG - chr4_1:41078174-41078193 None:intergenic 45.0%
GGTTTATGCTCTCAAGAGAC+AGG + chr4_1:41078181-41078200 Msa0547720:intron 45.0%
GAAGAACCCTCTACGGATTT+GGG + chr4_1:41078204-41078223 Msa0547720:intron 45.0%
AAGAACCCTCTACGGATTTG+GGG + chr4_1:41078205-41078224 Msa0547720:intron 45.0%
AGGAGGAAAGGGTTTGGGAA+AGG + chr4_1:41077838-41077857 Msa0547720:CDS 50.0%
GGAGGAAAGGGTTTGGGAAA+GGG + chr4_1:41077839-41077858 Msa0547720:CDS 50.0%
TGGAGCAAAACGACACCGTA+AGG + chr4_1:41077862-41077881 Msa0547720:CDS 50.0%
GTGCTTCGTGACAACATCCA+GGG + chr4_1:41077884-41077903 Msa0547720:CDS 50.0%
ATTCGTCGTCTTGCTCGTAG+AGG + chr4_1:41077923-41077942 Msa0547720:CDS 50.0%
CTTACACTGAGCACGCTAGA+AGG + chr4_1:41078035-41078054 Msa0547720:intron 50.0%
AGACAGGGAAGAACCCTCTA+CGG + chr4_1:41078197-41078216 Msa0547720:intron 50.0%
GGAAGAACCCTCTACGGATT+TGG + chr4_1:41078203-41078222 Msa0547720:intron 50.0%
AGAACCCTCTACGGATTTGG+GGG + chr4_1:41078206-41078225 Msa0547720:intron 50.0%
CTAACCCCCAAATCCGTAGA+GGG - chr4_1:41078213-41078232 None:intergenic 50.0%
CTCTACGGATTTGGGGGTTA+GGG + chr4_1:41078212-41078231 Msa0547720:intron 50.0%
! TGGGGGTTAGGGTTAGGTTT+TGG + chr4_1:41078223-41078242 Msa0547720:intron 50.0%
! GGGGGTTAGGGTTAGGTTTT+GGG + chr4_1:41078224-41078243 Msa0547720:intron 50.0%
! GGGGTTAGGGTTAGGTTTTG+GGG + chr4_1:41078225-41078244 Msa0547720:intron 50.0%
AGGAGGAAAGGGTTTGGGAA+AGG + chr4_1:41077838-41077857 Msa0547720:CDS 50.0%
GGAGGAAAGGGTTTGGGAAA+GGG + chr4_1:41077839-41077858 Msa0547720:CDS 50.0%
TGGAGCAAAACGACACCGTA+AGG + chr4_1:41077862-41077881 Msa0547720:CDS 50.0%
GTGCTTCGTGACAACATCCA+GGG + chr4_1:41077884-41077903 Msa0547720:CDS 50.0%
ATTCGTCGTCTTGCTCGTAG+AGG + chr4_1:41077923-41077942 Msa0547720:CDS 50.0%
CTTACACTGAGCACGCTAGA+AGG + chr4_1:41078035-41078054 Msa0547720:intron 50.0%
AGACAGGGAAGAACCCTCTA+CGG + chr4_1:41078197-41078216 Msa0547720:intron 50.0%
GGAAGAACCCTCTACGGATT+TGG + chr4_1:41078203-41078222 Msa0547720:intron 50.0%
AGAACCCTCTACGGATTTGG+GGG + chr4_1:41078206-41078225 Msa0547720:intron 50.0%
CTAACCCCCAAATCCGTAGA+GGG - chr4_1:41078213-41078232 None:intergenic 50.0%
CTCTACGGATTTGGGGGTTA+GGG + chr4_1:41078212-41078231 Msa0547720:intron 50.0%
! TGGGGGTTAGGGTTAGGTTT+TGG + chr4_1:41078223-41078242 Msa0547720:intron 50.0%
! GGGGGTTAGGGTTAGGTTTT+GGG + chr4_1:41078224-41078243 Msa0547720:intron 50.0%
! GGGGTTAGGGTTAGGTTTTG+GGG + chr4_1:41078225-41078244 Msa0547720:intron 50.0%
ATGTCTGGGCGTGGAAAAGG+AGG + chr4_1:41077821-41077840 Msa0547720:CDS 55.0%
TGGGCGTGGAAAAGGAGGAA+AGG + chr4_1:41077826-41077845 Msa0547720:CDS 55.0%
GGGCGTGGAAAAGGAGGAAA+GGG + chr4_1:41077827-41077846 Msa0547720:CDS 55.0%
GGAAAGGGTTTGGGAAAGGG+TGG + chr4_1:41077842-41077861 Msa0547720:CDS 55.0%
GGTGCTTCGTGACAACATCC+AGG + chr4_1:41077883-41077902 Msa0547720:CDS 55.0%
!! TCGCTGGCTTTGTGATTCCC+TGG - chr4_1:41077904-41077923 None:intergenic 55.0%
GGAGGAGTGAAGCGTATCAG+TGG + chr4_1:41077944-41077963 Msa0547720:CDS 55.0%
CCTAACCCCCAAATCCGTAG+AGG - chr4_1:41078214-41078233 None:intergenic 55.0%
CCTCTACGGATTTGGGGGTT+AGG + chr4_1:41078211-41078230 Msa0547720:intron 55.0%
CGGATTTGGGGGTTAGGGTT+AGG + chr4_1:41078217-41078236 Msa0547720:intron 55.0%
ATGTCTGGGCGTGGAAAAGG+AGG + chr4_1:41077821-41077840 Msa0547720:CDS 55.0%
TGGGCGTGGAAAAGGAGGAA+AGG + chr4_1:41077826-41077845 Msa0547720:CDS 55.0%
GGGCGTGGAAAAGGAGGAAA+GGG + chr4_1:41077827-41077846 Msa0547720:CDS 55.0%
GGAAAGGGTTTGGGAAAGGG+TGG + chr4_1:41077842-41077861 Msa0547720:CDS 55.0%
GGTGCTTCGTGACAACATCC+AGG + chr4_1:41077883-41077902 Msa0547720:CDS 55.0%
!! TCGCTGGCTTTGTGATTCCC+TGG - chr4_1:41077904-41077923 None:intergenic 55.0%
GGAGGAGTGAAGCGTATCAG+TGG + chr4_1:41077944-41077963 Msa0547720:CDS 55.0%
CCTAACCCCCAAATCCGTAG+AGG - chr4_1:41078214-41078233 None:intergenic 55.0%
CCTCTACGGATTTGGGGGTT+AGG + chr4_1:41078211-41078230 Msa0547720:intron 55.0%
CGGATTTGGGGGTTAGGGTT+AGG + chr4_1:41078217-41078236 Msa0547720:intron 55.0%
CGAGCAAGACGACGAATCGC+TGG - chr4_1:41077920-41077939 None:intergenic 60.0%
CGTCGTCTTGCTCGTAGAGG+AGG + chr4_1:41077926-41077945 Msa0547720:CDS 60.0%
GACGGTTACCGCCATGGATG+TGG + chr4_1:41078160-41078179 Msa0547720:intron 60.0%
CGAGCAAGACGACGAATCGC+TGG - chr4_1:41077920-41077939 None:intergenic 60.0%
CGTCGTCTTGCTCGTAGAGG+AGG + chr4_1:41077926-41077945 Msa0547720:CDS 60.0%
GACGGTTACCGCCATGGATG+TGG + chr4_1:41078160-41078179 Msa0547720:intron 60.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 41077821 41078573 41077821 ID=Msa0547720;Name=Msa0547720
chr4_1 mRNA 41077821 41078573 41077821 ID=Msa0547720-mRNA-1;Parent=Msa0547720;Name=Msa0547720-mRNA-1;_AED=0.31;_eAED=0.31;_QI=0|0|0|0.5|1|1|2|0|99
chr4_1 exon 41077821 41078030 41077821 ID=Msa0547720-mRNA-1:exon:10501;Parent=Msa0547720-mRNA-1
chr4_1 exon 41078484 41078573 41078484 ID=Msa0547720-mRNA-1:exon:10502;Parent=Msa0547720-mRNA-1
chr4_1 CDS 41077821 41078030 41077821 ID=Msa0547720-mRNA-1:cds;Parent=Msa0547720-mRNA-1
chr4_1 CDS 41078484 41078573 41078484 ID=Msa0547720-mRNA-1:cds;Parent=Msa0547720-mRNA-1
Gene Sequence

>Msa0547720

ATGTCTGGGCGTGGAAAAGGAGGAAAGGGTTTGGGAAAGGGTGGAGCAAAACGACACCGTAAGGTGCTTCGTGACAACATCCAGGGAATCACAAAGCCAGCGATTCGTCGTCTTGCTCGTAGAGGAGGAGTGAAGCGTATCAGTGGTTTGATTTATGAGGAGACACGTGGCGTGTTGAAGATCTTCTTGGAGAATGTGATTAGGGATGCTAAATATAACTTGACAGTGAAGATGAATTGTGGAGCAAGACCATTCAGATGTTTCAAGATAGCCAAATTTGTTCCACAACCTATCTTGTAG

Protein sequence

>Msa0547720

MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAKYNLTVKMNCGARPFRCFKIAKFVPQPIL*