AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1387070

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1387070 MtrunA17_Chr2g0322621 95.935 123 5 0 1 123 1 123 4.08e-70 206
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1387070 AT5G54970.1 44.444 90 38 3 13 95 15 99 3.46e-12 59.3

Find 44 sgRNAs with CRISPR-Local

Find 55 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATCTTGGTGTTGAATCTTT+TGG 0.258147 tig0020882:-10786 Msa1387070:CDS
TGGAGGCGAGCTAGGGTTCC+TGG 0.304575 tig0020882:+11056 None:intergenic
ACCATCGGCGGCTGCGGCTG+TGG 0.342585 tig0020882:+10923 None:intergenic
TTGAGTCGTGGAGGCGAGCT+AGG 0.397090 tig0020882:+11048 None:intergenic
GGTTTCCCTTACTTCTTCTC+CGG 0.397638 tig0020882:-10903 Msa1387070:CDS
AGGTCTTGTTCTCTGCTTCA+TGG 0.408985 tig0020882:+11112 None:intergenic
GCTGCTGACTCAGCAGATCT+TGG 0.415584 tig0020882:-10801 Msa1387070:CDS
TGGAAGTGGTTTGGTAAAGT+AGG 0.419142 tig0020882:+11092 None:intergenic
GTGGTTTGAGGCTGATCGGA+GGG 0.427050 tig0020882:+10942 None:intergenic
GCGGCTGCGGCTGTGGTTTG+AGG 0.438802 tig0020882:+10930 None:intergenic
GGAGTTGAGACGGTGAGATC+TGG 0.440317 tig0020882:+11016 None:intergenic
GTTTCCCTTACTTCTTCTCC+GGG 0.445512 tig0020882:-10902 Msa1387070:CDS
GAGCTAGGGTTCCTGGTTTG+AGG 0.446447 tig0020882:+11063 None:intergenic
TACTTCTTCTCCGGGATCTA+CGG 0.446448 tig0020882:-10894 Msa1387070:CDS
TAGATCCCGGAGAAGAAGTA+AGG 0.461075 tig0020882:+10897 None:intergenic
TTCCTGGTTTGAGGAATTTG+TGG 0.469740 tig0020882:+11072 None:intergenic
AGGAATTTGTGGAAGTGGTT+TGG 0.473781 tig0020882:+11083 None:intergenic
GTTTGAGGAATTTGTGGAAG+TGG 0.474784 tig0020882:+11078 None:intergenic
TCTGCTGAGTCAGCAGCAGC+AGG 0.484937 tig0020882:+10807 None:intergenic
GGCTGTGGTTTGAGGCTGAT+CGG 0.485771 tig0020882:+10938 None:intergenic
AGGGAAACCATCGGCGGCTG+CGG 0.493143 tig0020882:+10917 None:intergenic
GGTTTGAGGCTGATCGGAGG+GGG 0.498039 tig0020882:+10944 None:intergenic
GTTTGAGGCTGATCGGAGGG+GGG 0.501210 tig0020882:+10945 None:intergenic
TCAGCAGCAGCAGGACTACC+AGG 0.510522 tig0020882:+10816 None:intergenic
GCGGTGGTGAGGCTGGTGGA+CGG 0.525099 tig0020882:+10973 None:intergenic
GCGACGAGTTTCTTCCGTTG+TGG 0.540155 tig0020882:+10861 None:intergenic
TGTGGTTTGAGGCTGATCGG+AGG 0.556183 tig0020882:+10941 None:intergenic
TGAGTCGTGGAGGCGAGCTA+GGG 0.557294 tig0020882:+11049 None:intergenic
ACCACAGCCGCAGCCGCCGA+TGG 0.569502 tig0020882:-10924 Msa1387070:CDS
TGGCGGTTATCTTTGAGTCG+TGG 0.584042 tig0020882:+11036 None:intergenic
TCTGAGAGAGGGAGTTGAGA+CGG 0.588321 tig0020882:+11006 None:intergenic
TGGTTTGAGGCTGATCGGAG+GGG 0.598596 tig0020882:+10943 None:intergenic
TTCCACAAATTCCTCAAACC+AGG 0.613859 tig0020882:-11074 Msa1387070:CDS
TTCTTCCGTTGTGGACATCG+AGG 0.627074 tig0020882:+10870 None:intergenic
GAAACTCGTCGCTGCCAAGT+CGG 0.634754 tig0020882:-10850 Msa1387070:CDS
AGATCCCGGAGAAGAAGTAA+GGG 0.636111 tig0020882:+10898 None:intergenic
GTAGATTGAGATCTGAGAGA+GGG 0.642846 tig0020882:+10995 None:intergenic
AGGAACAAAGAAAACCGACT+TGG 0.643603 tig0020882:+10836 None:intergenic
GGTAGATTGAGATCTGAGAG+AGG 0.644225 tig0020882:+10994 None:intergenic
GTTGAGACGGTGAGATCTGG+CGG 0.649621 tig0020882:+11019 None:intergenic
CGGTTATCTTTGAGTCGTGG+AGG 0.654415 tig0020882:+11039 None:intergenic
ACGGTCCTCGATGTCCACAA+CGG 0.679494 tig0020882:-10875 Msa1387070:CDS
GAAGAAGTAAGGGAAACCAT+CGG 0.694352 tig0020882:+10908 None:intergenic
GAAGTAAGGGAAACCATCGG+CGG 0.750302 tig0020882:+10911 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GATCTTGGTGTTGAATCTTT+TGG - tig0020882:11085-11104 Msa1387070:CDS 35.0%
!! TGGAAGTGGTTTGGTAAAGT+AGG + tig0020882:10782-10801 None:intergenic 40.0%
AGGAATTTGTGGAAGTGGTT+TGG + tig0020882:10791-10810 None:intergenic 40.0%
GTTTGAGGAATTTGTGGAAG+TGG + tig0020882:10796-10815 None:intergenic 40.0%
TTCCACAAATTCCTCAAACC+AGG - tig0020882:10797-10816 Msa1387070:CDS 40.0%
! TTCCTGGTTTGAGGAATTTG+TGG + tig0020882:10802-10821 None:intergenic 40.0%
GTAGATTGAGATCTGAGAGA+GGG + tig0020882:10879-10898 None:intergenic 40.0%
GAAGAAGTAAGGGAAACCAT+CGG + tig0020882:10966-10985 None:intergenic 40.0%
AGGAACAAAGAAAACCGACT+TGG + tig0020882:11038-11057 None:intergenic 40.0%
!! AAGTCGGTTTTCTTTGTTCC+TGG - tig0020882:11037-11056 Msa1387070:CDS 40.0%
!!! CTTGGTGTTGAATCTTTTGG+CGG - tig0020882:11088-11107 Msa1387070:CDS 40.0%
GGTAGATTGAGATCTGAGAG+AGG + tig0020882:10880-10899 None:intergenic 45.0%
GGTTTCCCTTACTTCTTCTC+CGG - tig0020882:10968-10987 Msa1387070:CDS 45.0%
GTTTCCCTTACTTCTTCTCC+GGG - tig0020882:10969-10988 Msa1387070:CDS 45.0%
AGATCCCGGAGAAGAAGTAA+GGG + tig0020882:10976-10995 None:intergenic 45.0%
TAGATCCCGGAGAAGAAGTA+AGG + tig0020882:10977-10996 None:intergenic 45.0%
TACTTCTTCTCCGGGATCTA+CGG - tig0020882:10977-10996 Msa1387070:CDS 45.0%
CGGTTATCTTTGAGTCGTGG+AGG + tig0020882:10835-10854 None:intergenic 50.0%
TGGCGGTTATCTTTGAGTCG+TGG + tig0020882:10838-10857 None:intergenic 50.0%
TCTGAGAGAGGGAGTTGAGA+CGG + tig0020882:10868-10887 None:intergenic 50.0%
GAAGTAAGGGAAACCATCGG+CGG + tig0020882:10963-10982 None:intergenic 50.0%
TTCTTCCGTTGTGGACATCG+AGG + tig0020882:11004-11023 None:intergenic 50.0%
! GAGCTAGGGTTCCTGGTTTG+AGG + tig0020882:10811-10830 None:intergenic 55.0%
GTTGAGACGGTGAGATCTGG+CGG + tig0020882:10855-10874 None:intergenic 55.0%
GGAGTTGAGACGGTGAGATC+TGG + tig0020882:10858-10877 None:intergenic 55.0%
! TGGTTTGAGGCTGATCGGAG+GGG + tig0020882:10931-10950 None:intergenic 55.0%
! GTGGTTTGAGGCTGATCGGA+GGG + tig0020882:10932-10951 None:intergenic 55.0%
! TGTGGTTTGAGGCTGATCGG+AGG + tig0020882:10933-10952 None:intergenic 55.0%
! GGCTGTGGTTTGAGGCTGAT+CGG + tig0020882:10936-10955 None:intergenic 55.0%
ACATCGAGGACCGTAGATCC+CGG + tig0020882:10990-11009 None:intergenic 55.0%
ACGGTCCTCGATGTCCACAA+CGG - tig0020882:10996-11015 Msa1387070:CDS 55.0%
GCGACGAGTTTCTTCCGTTG+TGG + tig0020882:11013-11032 None:intergenic 55.0%
GAAACTCGTCGCTGCCAAGT+CGG - tig0020882:11021-11040 Msa1387070:CDS 55.0%
!! GCTGCTGACTCAGCAGATCT+TGG - tig0020882:11070-11089 Msa1387070:CDS 55.0%
TGAGTCGTGGAGGCGAGCTA+GGG + tig0020882:10825-10844 None:intergenic 60.0%
TTGAGTCGTGGAGGCGAGCT+AGG + tig0020882:10826-10845 None:intergenic 60.0%
! GTTTGAGGCTGATCGGAGGG+GGG + tig0020882:10929-10948 None:intergenic 60.0%
! GGTTTGAGGCTGATCGGAGG+GGG + tig0020882:10930-10949 None:intergenic 60.0%
TCAGCAGCAGCAGGACTACC+AGG + tig0020882:11058-11077 None:intergenic 60.0%
TCTGCTGAGTCAGCAGCAGC+AGG + tig0020882:11067-11086 None:intergenic 60.0%
TGGAGGCGAGCTAGGGTTCC+TGG + tig0020882:10818-10837 None:intergenic 65.0%
AGGGAAACCATCGGCGGCTG+CGG + tig0020882:10957-10976 None:intergenic 65.0%
GCGGTGGTGAGGCTGGTGGA+CGG + tig0020882:10901-10920 None:intergenic 70.0%
AGGCTGATCGGAGGGGGGTG+GGG + tig0020882:10924-10943 None:intergenic 70.0%
GAGGCTGATCGGAGGGGGGT+GGG + tig0020882:10925-10944 None:intergenic 70.0%
TGAGGCTGATCGGAGGGGGG+TGG + tig0020882:10926-10945 None:intergenic 70.0%
GCGGCTGCGGCTGTGGTTTG+AGG + tig0020882:10944-10963 None:intergenic 70.0%
TGATCGGAGGGGGGTGGGGG+CGG + tig0020882:10920-10939 None:intergenic 75.0%
GGCTGATCGGAGGGGGGTGG+GGG + tig0020882:10923-10942 None:intergenic 75.0%
ACCACAGCCGCAGCCGCCGA+TGG - tig0020882:10947-10966 Msa1387070:CDS 75.0%
ACCATCGGCGGCTGCGGCTG+TGG + tig0020882:10951-10970 None:intergenic 75.0%
! GGGGGCGGTGGTGAGGCTGG+TGG + tig0020882:10905-10924 None:intergenic 80.0%
! GGTGGGGGCGGTGGTGAGGC+TGG + tig0020882:10908-10927 None:intergenic 80.0%
! GGGGGGTGGGGGCGGTGGTG+AGG + tig0020882:10912-10931 None:intergenic 85.0%
! TCGGAGGGGGGTGGGGGCGG+TGG + tig0020882:10917-10936 None:intergenic 85.0%
Chromosome Type Strat End Strand Name
tig0020882 gene 10761 11132 10761 ID=Msa1387070;Name=Msa1387070
tig0020882 mRNA 10761 11132 10761 ID=Msa1387070-mRNA-1;Parent=Msa1387070;Name=Msa1387070-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|123
tig0020882 exon 10761 11132 10761 ID=Msa1387070-mRNA-1:exon:10495;Parent=Msa1387070-mRNA-1
tig0020882 CDS 10761 11132 10761 ID=Msa1387070-mRNA-1:cds;Parent=Msa1387070-mRNA-1
Gene Sequence

>Msa1387070

ATGAAGCAGAGAACAAGACCTACTTTACCAAACCACTTCCACAAATTCCTCAAACCAGGAACCCTAGCTCGCCTCCACGACTCAAAGATAACCGCCAGATCTCACCGTCTCAACTCCCTCTCTCAGATCTCAATCTACCGTCCACCAGCCTCACCACCGCCCCCACCCCCCTCCGATCAGCCTCAAACCACAGCCGCAGCCGCCGATGGTTTCCCTTACTTCTTCTCCGGGATCTACGGTCCTCGATGTCCACAACGGAAGAAACTCGTCGCTGCCAAGTCGGTTTTCTTTGTTCCTGGTAGTCCTGCTGCTGCTGACTCAGCAGATCTTGGTGTTGAATCTTTTGGCGGCGATATTATCGCTGCTAATTGA
Protein sequence

>Msa1387070

MKQRTRPTLPNHFHKFLKPGTLARLHDSKITARSHRLNSLSQISIYRPPASPPPPPPSDQPQTTAAAADGFPYFFSGIYGPRCPQRKKLVAAKSVFFVPGSPAAADSADLGVESFGGDIIAAN*